From 166ce5b02770b5f685d0a26688b17fa4c4bf0db1 Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Wed, 12 Jan 2022 16:58:45 -0600 Subject: Fix H5ACmpio dirty bytes creation debugging (#1357) --- src/H5ACmpio.c | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/H5ACmpio.c b/src/H5ACmpio.c index 500a05a..dc155f5 100644 --- a/src/H5ACmpio.c +++ b/src/H5ACmpio.c @@ -2093,11 +2093,11 @@ H5AC__run_sync_point(H5F_t *f, int sync_point_op) (sync_point_op == H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED)); #if H5AC_DEBUG_DIRTY_BYTES_CREATION - HDfprintf(stdout, "%d:H5AC_propagate...:%u: (u/uu/i/iu/r/ru) = %zu/%u/%zu/%u/%zu/%u\n", aux_ptr->mpi_rank, + HDfprintf(stdout, "%d:H5AC_propagate...:%u: (u/uu/i/iu/m/mu) = %zu/%u/%zu/%u/%zu/%u\n", aux_ptr->mpi_rank, aux_ptr->dirty_bytes_propagations, aux_ptr->unprotect_dirty_bytes, aux_ptr->unprotect_dirty_bytes_updates, aux_ptr->insert_dirty_bytes, - aux_ptr->insert_dirty_bytes_updates, aux_ptr->rename_dirty_bytes, - aux_ptr->rename_dirty_bytes_updates); + aux_ptr->insert_dirty_bytes_updates, aux_ptr->move_dirty_bytes, + aux_ptr->move_dirty_bytes_updates); #endif /* H5AC_DEBUG_DIRTY_BYTES_CREATION */ /* clear collective access flag on half of the entries in the @@ -2161,8 +2161,8 @@ H5AC__run_sync_point(H5F_t *f, int sync_point_op) aux_ptr->unprotect_dirty_bytes_updates = 0; aux_ptr->insert_dirty_bytes = 0; aux_ptr->insert_dirty_bytes_updates = 0; - aux_ptr->rename_dirty_bytes = 0; - aux_ptr->rename_dirty_bytes_updates = 0; + aux_ptr->move_dirty_bytes = 0; + aux_ptr->move_dirty_bytes_updates = 0; #endif /* H5AC_DEBUG_DIRTY_BYTES_CREATION */ done: -- cgit v0.12 From e56b0a3d508b73746c9676b56b275d0e7a486b7b Mon Sep 17 00:00:00 2001 From: Gerd Heber Date: Thu, 13 Jan 2022 22:11:39 -0600 Subject: Documentation fixes right in time for the holidays (#1321) * Sketch of the H5S life cycle. * Committing clang-format changes * Fix H5S_UNLIMITED snafu. * Updated RM template and RM page. * Added H5S life cycle. * Committing clang-format changes * Added H5T life cycle. * Committing clang-format changes * Cleaner layout (?) * Cleaned the H5F life cycle. Called out unfinished biz. * Committing clang-format changes * Remaining life cycle skeletons. * Committing clang-format changes * Committing clang-format changes * Added H5Z life cycle. * Committing clang-format changes * Added H5G life cycle. * Committing clang-format changes * H5 and H5I life cycle updates. * Committing clang-format changes * Added H5PL life cycle. * Committing clang-format changes * Added H5L life cycle. * Committing clang-format changes * Fix for Chris' comment. * Add a variable for Doxygen pre-processor definitions. * Forgot to add the H5M API. * Clarify the H5Z life cycle. * Committing clang-format changes * Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle. * Committing clang-format changes * Clarified introduction and fixed missing label declaration. * Added H5O life cycle. * Committing clang-format changes * H5O cleanup, part 1. * Committing clang-format changes * Cleaned up some of the endless repetition in H5O. * Committing clang-format changes * Cookbook & RFC draft layouts. * Updated manifest. * Updated the manifest, the example paths, and sketched the 1st recipe. * Committing clang-format changes * Outlined two more recipes. * Committing clang-format changes * More recipes and RFCs. * Committing clang-format changes * Draft of templatized RFC references. * Another batch of RFC changes. * Another batch of RFCs. * Fixed reference. * RFCs in reverse chronological order. * First cut of RFCs. * Fixed reference. * Updated recipes. * Updated recipes. * More RFCs. * Updated D*PL comments. * Added H5P descriptions. * Committing clang-format changes * H5R life-cycle snapshot. * Committing clang-format changes * H5R life-cycle. Added line numbers to life-cycle examples. * Committing clang-format changes * Fixed formatting for H5Dchunk_iter(). * Added comment on collective mode requirement w/ compression. * Simplified API compat. macro dox. * More API vers. updates. * Hide the async macro entrails. * Latest VFD SWMR RFC. * Create a tag file for permalinks. * Added TODOs for metadoc. * Removed duplication. * Revised RM landing page. * Trimmed more duplication. * Committing clang-format changes * Revised H5D. * Committing clang-format changes * Updated survey link. * Added Doxygen RM entry template link. * Added the "Multi-Thread HDF5" RFC. * Added DOXYGEN_TAG_FILE. * Added selection I/O RFC. * Added the VFD Sub-filing RFC. * Updated meta-documentation and added two old presentations. * Added a few more RFCs (4). * Fixed MANIFEST. * Updated meta-documentation. * Added Filters technical note. * Fixed MANIFEST. * Restore the path stripper. * Experimental full-text search via Google. * Better full-text search integration. * Whoops. Forgot this one. * Oh boy. * Make CMake happy. * Added "Debugging HDF5 Applications" technical note. * Another batch of RFCs. * Fixes for #1221. * Updated overview. * Fixed image dependencies. * CMake updates. * Fixed SET. * Better? * Update doxygen/dox/Overview.dox * Fixed documentation errors. Added missing version info. * Callback documentation updates. * Fixed indexing errors in the outline. * Doxygen-ized the HDF5 glossary. * Fix a few minor typos . Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox --- MANIFEST | 1 + doxygen/dox/About.dox | 2 - doxygen/dox/Glossary.dox | 565 ++++++++++++++++++++++++++++++++++++ doxygen/dox/Overview.dox | 9 +- doxygen/examples/H5.format.1.0.html | 14 +- doxygen/examples/H5.format.1.1.html | 14 +- doxygen/hdf5doxy_layout.xml | 2 +- src/H5Dpublic.h | 9 +- src/H5ESpublic.h | 13 +- src/H5FDmpio.h | 6 +- src/H5Fpublic.h | 4 +- src/H5Pmodule.h | 3 +- src/H5Ppublic.h | 281 +++++++++--------- 13 files changed, 759 insertions(+), 164 deletions(-) create mode 100644 doxygen/dox/Glossary.dox diff --git a/MANIFEST b/MANIFEST index 1fff5cc..c272a13 100644 --- a/MANIFEST +++ b/MANIFEST @@ -223,6 +223,7 @@ ./doxygen/dox/DDLBNF112.dox ./doxygen/dox/FTS.dox ./doxygen/dox/GettingStarted.dox +./doxygen/dox/Glossary.dox ./doxygen/dox/H5AC_cache_config_t.dox ./doxygen/dox/MetadataCachingInHDF5.dox ./doxygen/dox/Overview.dox diff --git a/doxygen/dox/About.dox b/doxygen/dox/About.dox index 0b21fcc..a8b31d7 100644 --- a/doxygen/dox/About.dox +++ b/doxygen/dox/About.dox @@ -124,6 +124,4 @@ version. Talk to your friendly IT-team if you need write access, or you need someone to push an updated version for you! -\todo Make the publication a GitHub action! - */ \ No newline at end of file diff --git a/doxygen/dox/Glossary.dox b/doxygen/dox/Glossary.dox new file mode 100644 index 0000000..9ccd27d --- /dev/null +++ b/doxygen/dox/Glossary.dox @@ -0,0 +1,565 @@ +/** \page GLS Glossary + +\section GLS_A A + +
+
Array datatype
+
A family of HDF5 datatypes whose elements are arrays of a fixed rank (≤ + 32) and fixed finite extent. All array elements must be of the same HDF5 + datatype.
+
+ +
+
Array variable
+

A variable that can store (logically) dense, rectilinear, multidimensional + arrays of elements of a given HDF5 datatype.

+

The combination of array rank (dimensionality) and extent is called an + array variable's shape. This includes the degenerate array shapes of a + singleton (scalar) and the empty array (null).

+

The array element datatype is sometimes referred to as the array + variable's type, which is not entirely accurate because the array variable's + type is 'array of element type' rather than 'element type'.

+

In HDF5, there are two kinds of array variables, attributes and datasets, + and the distinction is functional (i.e., how they can be used) rather than + conceptual. Attributes are commonly used for descriptive "light-weight" + HDF5 object metadata while datasets are HDF5 objects used to store + "heavy-weight" problem-sized data.

+
+
+ +
+
Attribute
+

A named array variable that is associated with an HDF5 object, its + owner or attributee, and used to represent application domain-specific + metadata of the object. Intuitively, the set of an object's attributes can + be thought of as its key-value pair collection. Attribute names (keys) can + be arbitrary Unicode strings, but must be unique per object, i.e., an + object can have at most one attribute with a given name.

+

A scalar attribute is an attribute backed by a singleton array + variable. A null attribute is attribute backed by an empty array + variable.

+
+
+ +\section GLS_B B + +
+
Bitfield datatype
+
A family of HDF5 datatypes whose elements are fixed-width bit fields.
+
+ +\section GLS_C C + +
+
Chunked layout
+
+

A dataset storage layout where the dataset elements are partitioned into + fixed-size multidimensional chunks or tiles. Chunked layout is mandatory + for datasets with one or more dimensions of indefinite (infinite) extent + or where compression or other filters are applied to the dataset elements.

+

Chunked layout may improve I/O performance for certain access patterns.

+
+
+ +
+
Committed datatype
+
An immutable kind of HDF5 object that is used to store an HDF5 datatype + definition, which can be referenced by multiple array variables. When linked + to an HDF5 group, a committed datatype can be located by an HDF5 path name, + and is sometimes called a named datatype.
+
+ +
+
Compact layout
+
+
+ +
+
Compound datatype
+
+

A family of HDF5 datatypes whose elements are records with named fields + of other HDF5 datatypes. Currently, on ASCII field names are supported.

+

Similar to a struct in C or a COMMON block in + Fortran.

+
+
+ +
+
Contiguous layout
+
A dataset storage layout where the dataset elements are physically stored + in an HDF5 file as a contiguous block of bytes.
+
+ +\section GLS_D D + +
+
Dataset
+
+

A kind of HDF5 object, a linked array variable. which can be located in + an HDF5 file through a path name. Datasets are commonly used to store + "heavy-weight" problem-sized data.

+

The HDF5 library offers a lot of features aimed at optimized dataset + access and storage, including compression and partial I/O.

+
+
+ +
+
Dataspace
+
The shape of an array variable. With the exception of degenerate cases + (empty set, singleton), this is a rectilinear lattice or grid of a certain + rank (dimensionality) and extent.
+
+ +
+
Datatype
+
+

An HDF5 datatype consists of an abstract data type (a set of elements) + and a bit-level representation of these elements in storage such as an HDF5 + file or memory.

+

The HDF5 library comes with a large set of predefined datatypes and + offers mechanisms for creating user-defined datatypes.

+

The ten major families or classes of HDF5 datatypes are:

+
    +
  • Integer datatypes
    • +
  • Floating-point number datatypes
    • +
  • String datatypes
    • +
  • Bitfield datatypes
    • +
  • Opaque datatypes
    • +
  • Compound datatypes
    • +
  • Reference datatypes
    • +
  • Enumerated datatypes
    • +
  • Variable-length sequence datatypes
    • +
  • Array datatypes
    • +
+
+
+ +\section GLS_E E + +
+
Enumeration datatype
+
A family of HDF5 datatypes whose elements represent named integer values + called members or enumerators. Currently, only ASCII names are supported.
+
+ +
+
External layout
+
A form of contiguous layout where a dataset's elements are physically + stored in unformatted binary files outside the HDF5 file.
+
+ +
+
External link
+
An HDF5 link whose destination is specified as a pair of an HDF5 file name +and an HDF5 path name in that file.
+
+ +\section GLS_F F + +
+
Field
+
See compound datatype.
+
+ +
+
File
+
+
    +
  1. A byte stream (in a storage context such as a file system or in + memory) formatted according to the HDF5 File Format Specification.
    2. +
  2. A (logical) container for HDF5 objects.
    3. +
+
+
+ +
+
File format
+
+
+ +
+
Fill value
+
+
+ +
+
Filter
+
+
+ +\section GLS_G G + +
+
Group
+
+

A kind of HDF5 object that stores a collection of HDF5 links. Each HDF5 + file contains at least one group, it's root group.

+

Among the destinations of an HDF5 group's links may be other HDF5 groups + (including the group itself!). This ability is sometimes referred to as the + closure property of groups. It is the basis for creating hierarchical or + more general graph-like structures.

+
+
+ +\section GLS_H H + +
+
Hard link
+
An HDF5 link whose destination is specified (internally) as the address of + an HDF5 object in the same HDF5 file.
+
+ +
+
Hierarchy
+
See group.
+
+ +
+
Hyperslab
+
+

A regular multidimensional pattern described by four vectors whose length + equals the rank of the pattern.

+
    +
  1. start - the offset where the first block of the hyperslab begins
    2. +
  2. stride - the offset between pattern blocks
    3. +
  3. count - the number of blocks
    4. +
  4. block - the extent of an individual pattern block
    5. +
+

For example, the black squares on a (two-dimensional) chessboard with + origin at (0,0) can be represented as the union of two + hyperslabs representing the even (0,2,4,6) and + odd (1,3,5,7) rows, respectively.

+ +

The hyperslab parameters for the even rows are: start (0,0), + stride (2,2), count (4,4), block + (1,1). Likewise the parameters for the odd rows are: start + (1,1), stride (2,2), count + (4,4), block (1,1).

+
+
+ +\section GLS_I I + +
+
Identifier
+
An opaque, transient handle used by the HDF5 library to manipulate + in-memory representations of HDF5 items.
+
+ +\section GLS_L L + +
+
Library
+
+
+ +
+
Link
+
+

A named, uni-directional association between a source and a + destination. In HDF5, the source is always the HDF5 group that hosts the + link in its link collection.

+

There are several ways to specify a link's destination:

+
    +
  • The address of an HDF5 object in the same HDF5 file; so-called hard + link.
    • +
  • A path name in the same or a different file; so-called soft or + external link.
    • +
  • User-defined
    • +
+

A link name can be any Unicode string that does not contain slashes + ("/") or consists of a single dot character + ("."). A link name must be unique in a group's link + collection.

+
+
+ +\section GLS_M M + +
+
Metadata
+
Data that in a given context has a descriptive or documentation function + for other data. Typically, the metadata is small compared to the data it + describes.
+
+ +
+
Member
+
+

A link destination is sometimes referred to as a member of the link's + source (group). This way of speaking invites confusion: A destination (e.g., + object) can be the destination of multiple links in the same (!) or + different groups. It would then be a "member" of a given group with + multiplicity greater than one and be a member of multiple groups.

+

It is the link that is a member of the group's link collection and not + the link destination.

+
+
+ +\section GLS_N N + +
+
Name
+
+

A Unicode string that depending on the item it names might be subject to + certain character restrictions, such as ASCII-encoded only. In HDF5, the + user might encounter the following names:

+
    +
  • A link name
    • +
  • A path name
    • +
  • An attribute name
    • +
  • A field name (compound datatypes)
    • +
  • A constant name (enumeration datatypes)
    • +
  • A tag name (opaque datatypes)
    • +
  • A file name
    • +
+
+
+ + +
+
Named datatype
+
See committed datatype.
+
+ +
+
Null dataspace
+
A shape which represents the empty set. Array variables with this shape + cannot store any values.
+
+ +\section GLS_O O + +
+
Object
+
An HDF5 group, dataset or named datatype; an HDF5 item that can be linked + to zero or more groups and decorated with zero or more HDF5 attributes.
+
+ +
+
Object reference
+
+
    +
  1. A datatype for representing references to objects in a file.
    2. +
  2. A value of the object reference datatype.
    3. +
+
+
+ +
+
Opaque datatype
+
A family of HDF5 datatypes whose elements are byte sequences of a given + fixed length. An opaque datatype can be tagged with a sequence of up to 256 + ASCII characters, e.g., MIME code.
+
+ +\section GLS_P P + +
+
Path name
+
A Unicode string that is the concatenation of link names separated by + slashes ('/'). In HDF5, path names are used to locate and refer + to HDF5 objects.
+
+ +
+
Plugin
+
An HDF5 library feature or capability that can be added dynamically at + application run time rather than library compilation time. Plugins are + usually implemented as shared libraries, and their discovery and loading + behavior can be controlled programmatically or through environment + variables. +
+
+ +
+
Point selection
+
A dataspace selection that consists of a set of points (coordinates) in + the same dataspace.
+
+ +
+
Property list
+
+

An HDF5 API construct, a means of customizing the behavior of the HDF5 + library when creating, accessing or modifying HDF5 items.

+

While the default property settings are sufficient in many cases, certain + HDF5 features, such as compression, can be reasonably controlled only by the + user who has to provide the desired settings via property lists.

+
+
+ +\section GLS_R R + +
+
Rank
+
The number of dimensions of a non-null dataspace.
+
+ +
+
Reference
+
+
    +
  1. An HDF5 object reference
    2. +
  2. An HDF5 dataset region reference
    3. +
+
+
+ +
+
Reference datatype
+
+
    +
  1. An HDF5 datatype whose elements represent references to HDF5 + objects.
    2. +
  2. An HDF5 datatype whose elements represent references to regions of an + HDF5 dataset.
    3. +
+
+
+ +
+
Region reference
+
See dataset region reference.
+
+ +
+
Root group
+
+

An HDF5 group that is present in all HDF5 files and that acts as the + entry or base point for all other data stored in an HDF5 file.

+

The root group is "the mother of all objects" in an HDF5 file in the + sense that all objects (and their attributes) can be discovered, + beginning at the root group, by combinations of the following + operations:

+
    +
  • Link traversal
    • +
  • De-referencing of object references
    • +
+

This discovery is portable and robust with respect to file-internal + storage reorganization.

+
+
+ +\section GLS_S S + +
+
Scalar dataspace
+
A kind of HDF5 dataspace that has the shape of a singleton, i.e., a set + containing a single element. Array variables with this shape store exactly one + element.
+
+ +
+
Selection
+
+
    +
  1. A subset of points of an HDF5 dataspace. The subset might be a point + selection or a combination (union, intersection, etc.) of hyperslabs.
    2. +
  2. A subset of dataset elements associated with a dataspace selection as + described under 1.
    3. +
+
+
+ +
+
Serialization
+
+
    +
  1. The flattening of an N-dimensional array into a 1-dimensional + array.
    2. +
  2. The encoding of a complex data item as a linear byte stream.
    3. +
+
+
+ +
+
Soft link
+
A kind of HDF5 link in which the link destination is specified as an HDF5 + path name. The path name may or may not refer to an actual object.
+
+ +
+
Storage layout
+
The storage arrangement for dataset elements, links in a group's link + collection, or attributes in an object's attribute collection.
+
+ +
+
String datatype
+
+
+ +
+
Super block
+
An HDF5 file format primitive; a block of data which contains information + required to access HDF5 files in a portable manner on multiple platforms. The + super block contains information such as version numbers, the size of offsets + and lengths, and the location of the root group.
+
+ +
+
SWMR
+
Single Writer Multiple Reader, a file access mode in which a single + process is permitted to write data to an HDF5 file while other processes are + permitted to read data from the same file without the need of inter-process + communication or synchronization.
+
+ +
+
Symbolic link
+
An external link or a soft link.
+
+ +\section GLS_U U + +
+
User block
+
An HDF5 file format primitive that allows one to set aside a fixed-size + (at least 512 bytes or any power of 2 thereafter) contiguous range of bytes at + the beginning of an HDF5 file for application purposes which will be + skipped/ignored by the HDF5 library.
+
+ +
+
UTF-8
+
+

A variable-length (1-4 bytes per code point) encoding of the Unicode set + of code points. This is the encoding supported by HDF5 to represent Unicode + strings.

+

The ASCII encoding is a proper subset of UTF-8.

+
+
+ +\section GLS_V V + +
+
Variable-length (sequence) datatype
+
A family of HDF5 datatypes whose elements are variable-length sequences of + a given datatype.
+
+ +
+
Virtual Dataset (VDS)
+
An HDF5 dataset with virtual storage layout. A dataset whose elements are + partially or entirely stored physically in other datasets.
+
+ +
+
Virtual File Driver (VFD)
+
+
+ + +
+
Virtual layout
+
+
+ + +
+
Virtual Object Layer (VOL)
+
+
+ +*/ diff --git a/doxygen/dox/Overview.dox b/doxygen/dox/Overview.dox index e9c52c2..040769c 100644 --- a/doxygen/dox/Overview.dox +++ b/doxygen/dox/Overview.dox @@ -1,9 +1,8 @@ /** \mainpage notitle -This is the documentation set for HDF5. You can -download it as a tgz archive for offline reading. -This documentation includes specifications and documentation +This is the documentation set for HDF5. +It includes specifications and documentation of software and tools developed and maintained by The HDF Group. It is impractical to document the entire HDF5 ecosystem in one place, and you should also consult the documentation @@ -38,8 +37,8 @@ documents cover a mix of tasks, concepts, and reference, to help a specific You can download it as a tgz archive for offline reading. \par History - A snapshot (April 2017) of the pre-Doxygen HDF5 documentation can be found - here. + A snapshot (~April 2017) of the pre-Doxygen HDF5 documentation can be found + here. \par ToDo List There is plenty of unfinished business. diff --git a/doxygen/examples/H5.format.1.0.html b/doxygen/examples/H5.format.1.0.html index cdc19ec7..d2b6610 100644 --- a/doxygen/examples/H5.format.1.0.html +++ b/doxygen/examples/H5.format.1.0.html @@ -10,12 +10,12 @@
-
    +
    1. Introduction
    2. Disk Format Level 0 - File Signature and Super Block
    3. Disk Format Level 1 - File Infrastructure -
        +
        1. Disk Format Level 1A - B-link Trees and B-tree Nodes
        2. Disk Format Level 1B - Group
        3. Disk Format Level 1C - Group Entry @@ -26,9 +26,9 @@
        4. Disk Format Level 2 - Data Objects -
            +
            1. Disk Format Level 2a - Data Object Headers -
                +
                1. Name: NIL
                2. Name: Simple Dataspace
                3. Name: Data Storage - External Data Files
                4. Name: Data Storage - Layout diff --git a/doxygen/examples/H5.format.1.1.html b/doxygen/examples/H5.format.1.1.html index 9894fad..b91ac90 100644 --- a/doxygen/examples/H5.format.1.1.html +++ b/doxygen/examples/H5.format.1.1.html @@ -36,18 +36,18 @@ TABLE.list TD { border:none; }
                  -
                    +
                    1. Introduction
                    2. Disk Format Level 0 - File Metadata -
                        +
                        1. Disk Format Level 0A - File Signature and Super Block
                        2. Disk Format Level 0B - File Driver Info
                      1. Disk Format Level 1 - File Infrastructure -
                          +
                          1. Disk Format Level 1A - B-link Trees and B-tree Nodes
                          2. Disk Format Level 1B - Group
                          3. Disk Format Level 1C - Group Entry @@ -58,9 +58,9 @@ TABLE.list TD { border:none; }
                          4. Disk Format Level 2 - Data Objects -
                              +
                              1. Disk Format Level 2a - Data Object Headers -
                                  +
                                  1. Name: NIL
                                  2. Name: Simple Dataspace @@ -73,13 +73,13 @@ TABLE.list TD { border:none; }
                  		   -
                    +
                    1. Disk Format Level 2 - Data Objects (Continued)
                      1. Disk Format Level 2a - Data Object Headers(Continued) -
                          +
                          1. Name: Reserved - not assigned yet
                          2. Name: Data Storage - External Data Files diff --git a/doxygen/hdf5doxy_layout.xml b/doxygen/hdf5doxy_layout.xml index 6efa690..24642b5 100644 --- a/doxygen/hdf5doxy_layout.xml +++ b/doxygen/hdf5doxy_layout.xml @@ -7,7 +7,7 @@ - + diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index 75f4b95..10e297f 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -77,7 +77,7 @@ typedef enum H5D_chunk_index_t { */ typedef enum H5D_alloc_time_t { H5D_ALLOC_TIME_ERROR = -1, /**< Error */ - H5D_ALLOC_TIME_DEFAULT = 0, /**< \todo Define this! */ + H5D_ALLOC_TIME_DEFAULT = 0, /**< Default (layout dependent) */ H5D_ALLOC_TIME_EARLY = 1, /**< Allocate on creation */ H5D_ALLOC_TIME_LATE = 2, /**< Allocate on first write */ H5D_ALLOC_TIME_INCR = 3 /**< Allocate incrementally (by chunk) */ @@ -127,8 +127,8 @@ typedef enum H5D_fill_value_t { */ typedef enum H5D_vds_view_t { H5D_VDS_ERROR = -1, /**< Error */ - H5D_VDS_FIRST_MISSING = 0, /**< \todo Define this! */ - H5D_VDS_LAST_AVAILABLE = 1 /**< \todo Define this! */ + H5D_VDS_FIRST_MISSING = 0, /**< Include all data before the first missing mapped data */ + H5D_VDS_LAST_AVAILABLE = 1 /**< Include all available mapped data */ } H5D_vds_view_t; //! @@ -682,8 +682,7 @@ H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, u * Iterate over all chunked datasets and chunks in a file. * \snippet H5D_examples.c H5Ovisit_cb * - * \version 1.?.? - * \todo When was this function introduced? + * \since 1.13.0 * */ H5_DLL herr_t H5Dchunk_iter(hid_t dset_id, hid_t dxpl_id, H5D_chunk_iter_op_t cb, void *op_data); diff --git a/src/H5ESpublic.h b/src/H5ESpublic.h index c8696b3..c8d1c7b 100644 --- a/src/H5ESpublic.h +++ b/src/H5ESpublic.h @@ -200,7 +200,18 @@ H5_DLL herr_t H5ESget_count(hid_t es_id, size_t *count); /** * \ingroup H5ES * - * \todo Fill in the blanks! + * \brief Retrieves the next operation counter to be assigned in an event set + * + * \es_id + * \param[out] counter The next counter value to be assigned to an event + * \returns \herr_t + * + * \details H5ESget_op_counter() retrieves the \p counter that will be assigned + * to the next operation inserted into the event set \p es_id. + * + * \note This is designed for wrapper libraries mainly, to use as a mechanism + * for matching operations inserted into the event set with possible + * errors that occur. * * \since 1.13.0 * diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h index 00dea1b..5ce98ca 100644 --- a/src/H5FDmpio.h +++ b/src/H5FDmpio.h @@ -223,7 +223,7 @@ H5_DLL herr_t H5Pset_dxpl_mpio_collective_opt(hid_t dxpl_id, H5FD_mpio_collectiv * * Use of this function is optional. * - * \todo Add missing version information + * \since 1.8.0 * */ H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt(hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode); @@ -247,7 +247,7 @@ H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt(hid_t dxpl_id, H5FD_mpio_chunk_opt_t op * otherwise, a separate I/O process will be invoked for each chunk * (multi-chunk I/O). * - * \todo Add missing version information + * \since 1.8.0 * */ H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt_num(hid_t dxpl_id, unsigned num_chunk_per_proc); @@ -272,7 +272,7 @@ H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt_num(hid_t dxpl_id, unsigned num_chunk_p * percent_proc_per_chunk, the library will do collective I/O for this * chunk; otherwise, independent I/O will be done for the chunk. * - * \todo Add missing version information + * \since 1.8.0 * */ H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt_ratio(hid_t dxpl_id, unsigned percent_num_proc_per_chunk); diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h index c3230e1..671eec3 100644 --- a/src/H5Fpublic.h +++ b/src/H5Fpublic.h @@ -1606,7 +1606,7 @@ H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], u * \brief Obtains information about a cache image if it exists * * \file_id - * \param[out] image_addr Offset of the cache image if it exists, or \c HADDR_UNDEF if it does not + * \param[out] image_addr Offset of the cache image if it exists, or #HADDR_UNDEF if it does not * \param[out] image_size Length of the cache image if it exists, or 0 if it does not * \returns \herr_t * @@ -1878,6 +1878,7 @@ H5_DLL herr_t H5Fget_info1(hid_t obj_id, H5F_info1_t *file_info); * * \deprecated When? * + * \todo In which version was this function introduced? * \todo In which version was this function deprecated? * */ @@ -1896,6 +1897,7 @@ H5_DLL herr_t H5Fset_latest_format(hid_t file_id, hbool_t latest_format); * \details H5Fis_hdf5() determines whether a file is in the HDF5 format. * * \todo In which version was this function deprecated? + * \todo In which version was this function introduced? * */ H5_DLL htri_t H5Fis_hdf5(const char *file_name); diff --git a/src/H5Pmodule.h b/src/H5Pmodule.h index 6e92e66..66a9574 100644 --- a/src/H5Pmodule.h +++ b/src/H5Pmodule.h @@ -111,7 +111,8 @@ * * \defgroup GAPL General Access Properties * \ingroup H5P - * \todo Should this be as standalone page? + * The functions in this section can be applied to different kinds of property + * lists. * * \defgroup GCPL Group Creation Properties * \ingroup H5P diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index 536407c..d0bc2b8 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -116,21 +116,70 @@ extern "C" { /* Define property list class callback function pointer types */ //! /** - * \todo Document me! + * \brief Callback function for H5Pcreate_class() + * + * \param[in] prop_id The identifier of the property list class being created + * \param[in] create_data User pointer to any class creation data required + * \return \herr_t + * + * \details This function is called when a new property list of the class + * with which this function was registered is being created. The + * function is called after any registered parent create function is + * called for each property value. + * + * If the create function returns a negative value, the new list is not + * returned to the user and the property list creation routine returns + * an error value. + * + * \since 1.4.0 + * */ typedef herr_t (*H5P_cls_create_func_t)(hid_t prop_id, void *create_data); //! //! /** - * \todo Document me! + * \brief Callback function for H5Pcreate_class() + * + * \param[in] new_prop_id The identifier of the property list copy + * \param[in] old_prop_id The identifier of the property list being copied + * \param[in] copy_data User pointer to any copy data required + * \return \herr_t + * + * \details This function is called when an existing property list of this + * class is copied. The copy callback function is called after any + * registered parent copy callback function is called for each property + * value. + * + * If the copy routine returns a negative value, the new list is not + * returned to the user and the property list copy function returns an + * error value. + * + * \since 1.4.0 + * */ typedef herr_t (*H5P_cls_copy_func_t)(hid_t new_prop_id, hid_t old_prop_id, void *copy_data); //! //! /** - * \todo Document me! + * \brief Callback function for H5Pcreate_class() + * + * \param[in] prop_id The identifier of the property list class being created + * \param[in] close_data User pointer to any close data required + * \return \herr_t + * + * \details This function is called when a property list of the class + * with which this function was registered is being closed. The + * function is called after any registered parent close function is + * called for each property value. + * + * If the close function returns a negative value, the new list is not + * returned to the user and the property list close routine returns + * an error value. + * + * \since 1.4.0 + * */ typedef herr_t (*H5P_cls_close_func_t)(hid_t prop_id, void *close_data); //! @@ -145,8 +194,8 @@ typedef herr_t (*H5P_cls_close_func_t)(hid_t prop_id, void *close_data); * \param[in,out] value The value for the property * \return \herr_t * - * \details The H5P_prp_cb1_t() describes the parameters used by the - * property create,copy and close callback functions. + * \details The H5P_prp_cb1_t() function describes the parameters used by the + * property create, copy and close callback functions. */ typedef herr_t (*H5P_prp_cb1_t)(const char *name, size_t size, void *value); //! @@ -161,8 +210,8 @@ typedef herr_t (*H5P_prp_cb1_t)(const char *name, size_t size, void *value); * \param[in] value The value for the property * \return \herr_t * - * \details The H5P_prp_cb2_t() describes the parameters used by the - * property set ,copy and delete callback functions. + * \details The H5P_prp_cb2_t() function describes the parameters used by the + * property set, copy and delete callback functions. */ typedef herr_t (*H5P_prp_cb2_t)(hid_t prop_id, const char *name, size_t size, void *value); //! @@ -172,13 +221,28 @@ typedef H5P_prp_cb2_t H5P_prp_set_func_t; typedef H5P_prp_cb2_t H5P_prp_get_func_t; //! /** - * \todo Document me! + * \brief Callback function for encoding property values + * + * \param[in] value The property value to be encoded + * \param[out] buf The encoded property value + * \param[out] size The size of \p buf + * \return \herr_t + * + * \note There is currently no public API which exposes a callback of this type. + * */ typedef herr_t (*H5P_prp_encode_func_t)(const void *value, void **buf, size_t *size); //! //! /** - * \todo Document me! + * \brief Callback function for decoding property values + * + * \param[in] buf A buffer containing an encoded property value + * \param[out] value The decoded property value + * \return \herr_t + * + * \note There is currently no public API which exposes a callback of this type. + * */ typedef herr_t (*H5P_prp_decode_func_t)(const void **buf, void *value); //! @@ -187,7 +251,16 @@ typedef H5P_prp_cb1_t H5P_prp_copy_func_t; //! /** - * \todo Document me! + * \brief Callback function for comparing property values + * + * \param[in] value1 A property value + * \param[in] value2 A property value + * \param[in] size The size of the \p value1 and \p value2 buffers + * \return Returns a positive value if \c value1 is greater than \c value2, a + * negative value if \c value2 is greater than \c value1 and zero if + * \c value1 and \c value2 are equal. + * + * \see H5Pregister(), H5Pinsert() */ typedef int (*H5P_prp_compare_func_t)(const void *value1, const void *value2, size_t size); //! @@ -197,7 +270,19 @@ typedef H5P_prp_cb1_t H5P_prp_close_func_t; /* Define property list iteration function type */ //! /** - * \todo Document me! + * \brief Callback function for H5Piterate() + * + * \param[in] id The identifier of a property list or property list class + * \param[in] name The name of the current property + * \param[in,out] iter_data The user context passed to H5Piterate() + * \return \herr_t_iter + * + * \details This function is called for each property encountered when + * iterating over a property list or property list class + * via H5Piterate(). + * + * \since 1.4.0 + * */ typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data); //! @@ -264,15 +349,15 @@ typedef enum H5D_mpio_no_collective_cause_t { H5D_MPIO_DATA_TRANSFORMS = 0x04, /**< Collective I/O was not performed because data transforms needed to be applied */ H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED = 0x08, - /**< \todo FIXME! */ + /**< Collective I/O was disabled by environment variable (\Code{HDF5_MPI_OPT_TYPES}) */ H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES = 0x10, /**< Collective I/O was not performed because one of the dataspaces was neither simple nor scalar */ H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET = 0x20, /**< Collective I/O was not performed because the dataset was neither contiguous nor chunked */ H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED = 0x40, - /**< \todo FIXME! */ + /**< Collective I/O was not performed because parallel filtered writes are disabled */ H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE = 0x80, - /**< \todo FIXME! */ + /**< Error */ H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE = 0x100 /**< Sentinel */ } H5D_mpio_no_collective_cause_t; @@ -577,77 +662,12 @@ H5_DLL hid_t H5Pcreate(hid_t cls_id); * those existing properties, only add or remove their own class * properties. Property list classes defined and supported in the * HDF5 library distribution are listed and briefly described in - * H5Pcreate(). The \p create routine is called when a new property - * list of this class is being created. The #H5P_cls_create_func_t - * callback function is defined as follows: - * - * \snippet this H5P_cls_create_func_t_snip + * H5Pcreate(). The \p create, \p copy, \p close functions are called + * when a property list of the new class is created, copied, or closed, + * respectively. * - * The parameters to this callback function are defined as follows: - * - * - * - * - * - * - * - * - * - *
                            \ref hid_t \c prop_idIN: The identifier of the property list being created
                            \Code{void * create_data}IN: User pointer to any class creation data required
                            - * - * The \p create routine is called after any registered - * \p create function is called for each property value. If the - * \p create routine returns a negative value, the new list is not - * returned to the user and the property list creation routine returns - * an error value. - * - * The \p copy routine is called when an existing property - * list of this class is copied. The #H5P_cls_copy_func_t callback - * function is defined as follows: - * \snippet this H5P_cls_copy_func_t_snip - * - * The parameters to this callback function are defined as follows: - * - * - * - * - * - * - * - * - * - *
                            \ref hid_t \c prop_idIN: The identifier of the property list created by copying
                            \Code{void * copy_data}IN: User pointer to any class copy data required
                            - * - * The \p copy routine is called after any registered \p copy function - * is called for each property value. If the \p copy routine returns a - * negative value, the new list is not returned to the user and the - * property list \p copy routine returns an error value. - * - * The \p close routine is called when a property list of this class - * is being closed. The #H5P_cls_close_func_t callback function is - * defined as follows: - * \snippet this H5P_cls_close_func_t_snip - * - * The parameters to this callback function are defined as follows: - * - * - * - * - * - * - * - * - * - *
                            \ref hid_t \c prop_idIN: The identifier of the property list being closed
                            \Code{void * close_data}IN: User pointer to any class close data required
                            - * - * The \p close routine is called before any registered \p close - * function is called for each property value. If the \p close routine - * returns a negative value, the property list close routine returns - * an error value but the property list is still closed. - * - * H5Pclose_class() can be used to release the property list class - * identifier returned by this function so that resources leaks will - * not develop. + * H5Pclose_class() must be used to release the property list class + * identifier returned by this function. * * \since 1.4.0 * @@ -1376,35 +1396,12 @@ H5_DLL htri_t H5Pisa_class(hid_t plist_id, hid_t pclass_id); * returned in this case, the iterator cannot be restarted if * one of the calls to its operator returns non-zero. * - * The prototype for the #H5P_iterate_t operator is as follows: - * \snippet this H5P_iterate_t_snip - * - * The operation receives the property list or class + * The operation \p iter_func receives the property list or class * identifier for the object being iterated over, \p id, the * name of the current property within the object, \p name, * and the pointer to the operator data passed in to H5Piterate(), - * \p iter_data. The valid return values from an operator are - * as follows: + * \p iter_data. * - * - * - * - * - * - * - * - * - * - * - * - * - * - *
                            ZeroCauses the iterator to continue, returning zero when all - * properties have been processed
                            PositiveCauses the iterator to immediately return that positive - * value, indicating short-circuit success. The iterator - * can be restarted at the index of the next property
                            NegativeCauses the iterator to immediately return that value, - * indicating failure. The iterator can be restarted at the - * index of the next property
                            * H5Piterate() assumes that the properties in the object * identified by \p id remain unchanged through the iteration. * If the membership changes during the iteration, the function's @@ -1877,9 +1874,6 @@ H5_DLL herr_t H5Pget_attr_phase_change(hid_t plist_id, unsigned *max_compact, un * * \brief Returns information about a filter in a pipeline * - * \todo Signature for H5Pget_filter2 is different in H5Pocpl.c than in - * H5Ppublic.h - * * \ocpl_id{plist_id} * \param[in] idx Sequence number within the filter pipeline of the filter * for which information is sought @@ -4205,17 +4199,14 @@ H5_DLL herr_t H5Pset_alignment(hid_t fapl_id, hsize_t threshold, hsize_t alignme * * \note Note: Raw dataset chunk caching is not currently * supported when using the MPI I/O and MPI POSIX file drivers - * in read/write mode; see H5Pset_fapl_mpio() and - * H5Pset_fapl_mpiposix(), respectively. When using one of these - * file drivers, all calls to H5Dread() and H5Dwrite() will access + * in read/write mode; see H5Pset_fapl_mpio(). When using this + * file driver, all calls to H5Dread() and H5Dwrite() will access * the disk directly, and H5Pset_cache() will have no effect on * performance. * * \note Raw dataset chunk caching is supported when these drivers are * used in read-only mode. * - * \todo Check on H5Pset_fapl_mpio() and H5Pset_fapl_mpiposix(). - * * \version 1.8.0 The use of the \p mdc_nelmts parameter was discontinued. * Metadata cache configuration is managed with * H5Pset_mdc_config() and H5Pget_mdc_config(). @@ -5483,12 +5474,38 @@ H5_DLL herr_t H5Pset_coll_metadata_write(hid_t plist_id, hbool_t is_collective); H5_DLL herr_t H5Pget_coll_metadata_write(hid_t plist_id, hbool_t *is_collective); /** - * \todo Add missing documentation + * \ingroup FAPL + * + * \brief Get the MPI communicator and info + * + * \fapl_id + * \param[out] comm MPI communicator + * \param[out] info MPI info object + * \return \herr_t + * + * \details H5Pget_mpi_params() gets the MPI communicator and info stored in + * the file access property list \p fapl_id. + * + * \todo When was this introduced? + * */ H5_DLL herr_t H5Pget_mpi_params(hid_t fapl_id, MPI_Comm *comm, MPI_Info *info); /** - * \todo Add missing documentation + * \ingroup FAPL + * + * \brief Set the MPI communicator and info + * + * \fapl_id + * \param[in] comm MPI communicator + * \param[in] info MPI info object + * \return \herr_t + * + * \details H5Pset_mpi_params() sets the MPI communicator and info stored in + * the file access property list \p fapl_id. + * + * \todo When was this introduced? + * */ H5_DLL herr_t H5Pset_mpi_params(hid_t fapl_id, MPI_Comm comm, MPI_Info info); #endif /* H5_HAVE_PARALLEL */ @@ -7100,9 +7117,6 @@ H5_DLL herr_t H5Pget_virtual_printf_gap(hid_t dapl_id, hsize_t *gap_size); * * \dapl_id * \param[out] view The flag specifying the view of the virtual dataset. - * Valid values are: - * \li #H5D_VDS_FIRST_MISSING - * \li #H5D_VDS_LAST_AVAILABLE * * \return \herr_t * @@ -7456,11 +7470,7 @@ H5_DLL herr_t H5Pset_virtual_printf_gap(hid_t dapl_id, hsize_t gap_size); * * \dapl_id * \param[in] view Flag specifying the extent of the data to be included - * in the view. Valid values are: - * \li #H5D_VDS_FIRST_MISSING: View includes all data - * before the first missing mapped data - * \li #H5D_VDS_LAST_AVAILABLE View includes all - * available mapped data + * in the view. * * \return \herr_t * @@ -7628,8 +7638,11 @@ H5_DLL herr_t H5Pget_hyper_vector_size(hid_t fapl_id, size_t *size /*out*/); * \details H5Pget_preserve() checks the status of the dataset transfer * property list. * + * \since 1.0.0 + * * \version 1.6.0 The flag parameter was changed from INTEGER to LOGICAL to * better match the C API. (Fortran 90) + * \version 1.8.2 Deprecated. * */ H5_DLL int H5Pget_preserve(hid_t plist_id); @@ -7657,6 +7670,8 @@ H5_DLL int H5Pget_preserve(hid_t plist_id); * * Please refer to the function H5Pset_type_conv_cb() for more details. * + * \since 1.8.0 + * */ H5_DLL herr_t H5Pget_type_conv_cb(hid_t dxpl_id, H5T_conv_except_func_t *op, void **operate_data); /** @@ -7680,6 +7695,8 @@ H5_DLL herr_t H5Pget_type_conv_cb(hid_t dxpl_id, H5T_conv_except_func_t *op, voi * H5Pset_vlen_mem_manager(), returning the parameters set by * that function. * + * \since 1.0.0 + * */ H5_DLL herr_t H5Pget_vlen_mem_manager(hid_t plist_id, H5MM_allocate_t *alloc_func, void **alloc_info, H5MM_free_t *free_func, void **free_info); @@ -7923,8 +7940,9 @@ H5_DLL herr_t H5Pset_hyper_vector_size(hid_t plist_id, size_t size); * I/O pipeline treats the destination datapoints as completely * uninitialized. * - * \todo Add missing version information: introduction, deprecation, etc. - * Why is the declaration not in the deprecated section? + * \since 1.0.0 + * + * \version 1.8.2 Deprecated. * */ H5_DLL herr_t H5Pset_preserve(hid_t plist_id, hbool_t status); @@ -7952,7 +7970,7 @@ H5_DLL herr_t H5Pset_preserve(hid_t plist_id, hbool_t status); * function prototype is as follows: * \snippet H5Tpublic.h H5T_conv_except_func_t_snip * - * \todo Add version information. + * \since 1.8.0 * */ H5_DLL herr_t H5Pset_type_conv_cb(hid_t dxpl_id, H5T_conv_except_func_t op, void *operate_data); @@ -8002,7 +8020,8 @@ H5_DLL herr_t H5Pset_type_conv_cb(hid_t dxpl_id, H5T_conv_except_func_t op, void * set to \c NULL and the \p alloc_info and \p free_info parameters are * ignored. * - * \todo Add version information. + * \since 1.0.0 + * */ H5_DLL herr_t H5Pset_vlen_mem_manager(hid_t plist_id, H5MM_allocate_t alloc_func, void *alloc_info, H5MM_free_t free_func, void *free_info); -- cgit v0.12 From 8b3c09f780e31ba96b9f5c370a0c19f8a0dcfe6c Mon Sep 17 00:00:00 2001 From: Scot Breitenfeld Date: Fri, 14 Jan 2022 17:28:04 -0600 Subject: Updated README.txt to README.md (#1375) * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * Converted README.txt to README.md and updated files referring to README.txt to README.md. * removed references to README.txt * updated MANIFEST --- CMakeInstallation.cmake | 2 +- MANIFEST | 5 ++- README.md | 85 +++++++++++++++++++++++++++++++++++ README.txt | 80 --------------------------------- bin/bbrelease | 4 +- bin/h5vers | 12 ++--- bin/release | 4 +- config/cmake/README.md.cmake.in | 80 +++++++++++++++++++++++++++++++++ config/cmake/README.txt.cmake.in | 80 --------------------------------- config/cmake_ext_mod/HDFMacros.cmake | 6 +-- configure.ac | 4 +- doxygen/img/HDF5.png | Bin 0 -> 10660 bytes 12 files changed, 184 insertions(+), 178 deletions(-) create mode 100644 README.md delete mode 100644 README.txt create mode 100644 config/cmake/README.md.cmake.in delete mode 100644 config/cmake/README.txt.cmake.in create mode 100644 doxygen/img/HDF5.png diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake index b506f05..609cd7e 100644 --- a/CMakeInstallation.cmake +++ b/CMakeInstallation.cmake @@ -182,7 +182,7 @@ if (HDF5_PACK_EXAMPLES) endif () #----------------------------------------------------------------------------- -# Configure the README.txt file for the binary package +# Configure the README.md file for the binary package #----------------------------------------------------------------------------- HDF_README_PROPERTIES(HDF5_BUILD_FORTRAN) diff --git a/MANIFEST b/MANIFEST index c272a13..72e969a 100644 --- a/MANIFEST +++ b/MANIFEST @@ -28,7 +28,7 @@ ./MANIFEST ./Makefile.dist ./Makefile.am -./README.txt +./README.md ./acsite.m4 ./autogen.sh ./configure.ac @@ -290,6 +290,7 @@ ./doxygen/img/FF-IH_FileGroup.gif ./doxygen/img/FF-IH_FileObject.gif ./doxygen/img/FileFormatSpecChunkDiagram.jpg +./doxygen/img/HDF5.png ./doxygen/img/HDFG-logo.png ./doxygen/img/IOFlow.gif ./doxygen/img/IOFlow2.gif @@ -3629,7 +3630,7 @@ ./config/cmake/mccacheinit.cmake ./config/cmake/patch.xml ./config/cmake/PkgInfo.in -./config/cmake/README.txt.cmake.in +./config/cmake/README.md.cmake.in ./config/cmake/UseJava.cmake ./config/cmake/UseJavaClassFilelist.cmake ./config/cmake/UseJavaSymlinks.cmake diff --git a/README.md b/README.md new file mode 100644 index 0000000..ce92342 --- /dev/null +++ b/README.md @@ -0,0 +1,85 @@ +HDF5 version 1.13.1-1 currently under development + +![HDF5 Logo](doxygen/img/HDF5.png) + +*Please refer to the release_docs/INSTALL file for installation instructions.* + +THE HDF GROUP +--------------- + +The HDF Group is the developer of HDF5®, a high-performance software library and +data format that has been adopted across multiple industries and has become a +de facto standard in scientific and research communities. + +More information about The HDF Group, the HDF5 Community and the HDF5 software +project, tools and services can be found at the Group's website. + + https://www.hdfgroup.org/ + + +DOCUMENTATION +------------- +This release is fully functional for the API described in the documentation. + + https://portal.hdfgroup.org/display/HDF5/The+HDF5+API + +Full Documentation and Programming Resources for this release can be found at + + https://portal.hdfgroup.org/display/HDF5 + +See the RELEASE.txt file in the release_docs/ directory for information specific +to the features and updates included in this release of the library. + +Several more files are located within the release_docs/ directory with specific +details for several common platforms and configurations. + + INSTALL - Start Here. General instructions for compiling and installing the library + INSTALL_CMAKE - instructions for building with CMake (Kitware.com) + INSTALL_parallel - instructions for building and configuring Parallel HDF5 + INSTALL_Windows and INSTALL_Cygwin - MS Windows installations. + + + +HELP AND SUPPORT +---------------- +Information regarding Help Desk and Support services is available at + + https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk + + + +FORUM and NEWS +-------------- +The following public forums are provided for public announcements and discussions +of interest to the general HDF5 Community. + + - Homepage of the Forum + https://forum.hdfgroup.org + + - News and Announcement + https://forum.hdfgroup.org/c/news-and-announcements-from-the-hdf-group + + - HDF5 and HDF4 Topics + https://forum.hdfgroup.org/c/hdf5 + +These forums are provided as an open and public service for searching and reading. +Posting requires completing a simple registration and allows one to join in the +conversation. Please read the following instructions pertaining to the Forum's +use and configuration + https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum + + +SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE +-------------------------------------------- +Periodically development code snapshots are provided at the following URL: + + https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/ + +Source packages for current and previous releases are located at: + + https://portal.hdfgroup.org/display/support/Downloads + +Development code is available at our Github location: + + https://github.com/HDFGroup/hdf5.git + diff --git a/README.txt b/README.txt deleted file mode 100644 index b9cfe8a..0000000 --- a/README.txt +++ /dev/null @@ -1,80 +0,0 @@ -HDF5 version 1.13.1-1 currently under development - ------------------------------------------------------------------------------- -Please refer to the release_docs/INSTALL file for installation instructions. ------------------------------------------------------------------------------- - -THE HDF GROUP ---------------- - -The HDF Group is the developer of HDF5®, a high-performance software library and -data format that has been adopted across multiple industries and has become a -de facto standard in scientific and research communities. - -More information about The HDF Group, the HDF5 Community and the HDF5 software -project, tools and services can be found at the Group's website. - - https://www.hdfgroup.org/ - - -DOCUMENTATION -------------- -This release is fully functional for the API described in the documentation. - https://portal.hdfgroup.org/display/HDF5/The+HDF5+API - -Full Documentation and Programming Resources for this release can be found at - https://portal.hdfgroup.org/display/HDF5 - -See the RELEASE.txt file in the release_docs/ directory for information specific -to the features and updates included in this release of the library. - -Several more files are located within the release_docs/ directory with specific -details for several common platforms and configurations. - - INSTALL - Start Here. General instructions for compiling and installing the library - INSTALL_CMAKE - instructions for building with CMake (Kitware.com) - INSTALL_parallel - instructions for building and configuring Parallel HDF5 - INSTALL_Windows and INSTALL_Cygwin - MS Windows installations. - - - -HELP AND SUPPORT ----------------- -Information regarding Help Desk and Support services is available at - - https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk - - - -FORUM and NEWS --------------- -The following public forums are provided for public announcements and discussions -of interest to the general HDF5 Community. - - Homepage of the Forum - https://forum.hdfgroup.org - - News and Announcement - https://forum.hdfgroup.org/c/news-and-announcements-from-the-hdf-group - - HDF5 and HDF4 Topics - https://forum.hdfgroup.org/c/hdf5 - -These forums are provided as an open and public service for searching and reading. -Posting requires completing a simple registration and allows one to join in the -conversation. Please read the following instructions pertaining to the Forum's -use and configuration - https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum - - -SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE --------------------------------------------- -Periodically development code snapshots are provided at the following URL: - https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/ - -Source packages for current and previous releases are located at: - https://portal.hdfgroup.org/display/support/Downloads - -Development code is available at our Github location: - https://github.com/HDFGroup/hdf5.git - diff --git a/bin/bbrelease b/bin/bbrelease index cdb8678..a45be2e 100755 --- a/bin/bbrelease +++ b/bin/bbrelease @@ -320,9 +320,9 @@ ln -s `pwd` $tmpdir/$HDF5_IN_VERS || exit 1 test -f Makefile && mv Makefile $tmpdir/Makefile.x cp -p Makefile.dist Makefile -# Update README.txt and release_docs/RELEASE.txt with release information in +# Update README.md and release_docs/RELEASE.txt with release information in # line 1. -for f in README.txt release_docs/RELEASE.txt; do +for f in README.md release_docs/RELEASE.txt; do echo "HDF5 version $VERS released on $release_date" >$f.x sed -e 1d $f >>$f.x mv $f.x $f diff --git a/bin/h5vers b/bin/h5vers index 8f75df1..04d5d03 100755 --- a/bin/h5vers +++ b/bin/h5vers @@ -66,7 +66,7 @@ use strict; # ./H5public.h or ./src/H5public.h. # # If the version number is changed (either `-s' or `-i' was used on -# the command line) then the first line of the README.txt and RELEASE.txt files +# the command line) then the version line of the README.md and RELEASE.txt files # one directory above the H5public.h file is also modified so it looks # something like: This is hdf5-1.2.3-pre1 currently under development. # The AC_INIT macro in configure.ac will also change in this case to be @@ -156,10 +156,10 @@ while ($_ = shift) { } die "mutually exclusive options given\n" if $set && $inc; -# Determine file to use as H5public.h, README.txt, +# Determine file to use as H5public.h, README.md, # release_docs/RELEASE.txt, configure.ac, windows/src/H5pubconf.h # config/lt_vers.am and config/cmake/scripts/HDF5config.cmake. -# The README.txt, release_docs/RELEASE.txt, configure.ac, +# The README.md, release_docs/RELEASE.txt, configure.ac, # windows/src/H5pubconf.h, config/lt_vers.am and # config/cmake/scripts/HDF5config.cmake # files are always in the directory above H5public.h @@ -178,9 +178,9 @@ die "unable to read file: $LT_VERS\n" unless -r $file; my $HDF5CONFIGCMAKE = $file; $HDF5CONFIGCMAKE =~ s/[^\/]*$/..\/config\/cmake\/scripts\/HDF5config.cmake/; die "unable to read file: $HDF5CONFIGCMAKE\n" unless -r $file; -# README.txt +# README.md my $README = $file; -$README =~ s/[^\/]*$/..\/README.txt/; +$README =~ s/[^\/]*$/..\/README.md/; die "unable to read file: $README\n" unless -r $file; # release_docs/RELEASE.txt my $RELEASE = $file; @@ -303,7 +303,7 @@ if ($LT_VERS && $version_increased) { # close FILE; } -# Update the README.txt file +# Update the README.md file if ($README) { open FILE, $README or die "$README: $!\n"; my @contents = ; diff --git a/bin/release b/bin/release index e40c3d3..e71a38e 100755 --- a/bin/release +++ b/bin/release @@ -572,9 +572,9 @@ ln -s `pwd` $tmpdir/$HDF5_VERS || exit 1 test -f Makefile && mv Makefile $tmpdir/Makefile.x cp -p Makefile.dist Makefile -# Update README.txt and release_docs/RELEASE.txt with release information in +# Update README.md and release_docs/RELEASE.txt with release information in # line 1. -for f in README.txt release_docs/RELEASE.txt; do +for f in README.md release_docs/RELEASE.txt; do echo "HDF5 version $VERS released on $release_date" >$f.x sed -e 1d $f >>$f.x mv $f.x $f diff --git a/config/cmake/README.md.cmake.in b/config/cmake/README.md.cmake.in new file mode 100644 index 0000000..b60e729 --- /dev/null +++ b/config/cmake/README.md.cmake.in @@ -0,0 +1,80 @@ +@HDF5_PACKAGE_NAME@ version @HDF5_PACKAGE_VERSION_STRING@ +------------------------------------------------------------------------------ + +This directory contains the binary (release) distribution of +@HDF5_PACKAGE_NAME@ @HDF5_PACKAGE_VERSION_MAJOR@ that was compiled on; + @BINARY_PLATFORM@. + +It was built with the following options: + -- @LIB_TYPE@ C/C++/Fortran libraries + -- SZIP (encoder enabled) and ZLIB + -- @LIB_TYPE@ HDF5 tools + -- Java @Java_VERSION@ + +The contents of this directory are: + + COPYING - Copyright notice + README.md - This file + @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_INSTALL_ENDING@ - HDF5 Install Package + +This binary was built with the ZLIB and SZIP/Libaec external libraries and are +included for convenience. Libaec is an unrestricted open-source replacement for SZIP +(version 1.0.4, Encoder ENABLED). + +The official ZLIB and SZIP/Libaec pages are at: + + ZLIB: https://git.savannah.gnu.org/cgit/gzip.git/ + https://git.savannah.gnu.org/cgit/gzip.git/tree/COPYING + SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec + https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt + + +Installation +=========================================================================== +1. Execute @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_INSTALL_ENDING@ +2. Follow prompts +=========================================================================== + +After Installation +=========================================================================== +The examples folder, HDF5Examples, located in the +HDF5 install folder, can be built and tested with CMake and the supplied +HDF5_Examples.cmake file. The HDF5_Examples.cmake expects HDF5 to have +been installed in the default location with above compilers (see the +libhdf5.settings file in the lib install folder). Also, the CMake +utility should be installed. + +To test the installation with the examples; + Create a directory to run the examples. + Copy HDF5Examples folder to this directory. + Copy CTestScript.cmake to this directory. + Copy HDF5_Examples.cmake to this directory. + Copy HDF5_Examples_options.cmake to this directory. + The default source folder is defined as "HDF5Examples". It can be changed + with the CTEST_SOURCE_NAME script option. + The default installation folder is defined as "@CMAKE_INSTALL_PREFIX@". + It can be changed with the INSTALLDIR script option. + The default ctest configuration is defined as "Release". It can be changed + with the CTEST_CONFIGURATION_TYPE script option. Note that this must + be the same as the value used with the -C command line option. + The default build configuration is defined to build and use static libraries. + Shared libraries can be used with the STATICONLYLIBRARIES script option set to "NO". + Other options can be changed by editing the HDF5_Examples_options.cmake file. + + If the defaults are okay, execute from this directory: + ctest -S HDF5_Examples.cmake -C Release -V -O test.log + If the defaults need change, execute from this directory: + ctest -S HDF5_Examples.cmake,CTEST_SOURCE_NAME=MyExamples,INSTALLDIR=MyLocation -C Release -V -O test.log + +When executed, the ctest script will save the results to the log file, test.log, as +indicated by the ctest command. If you wish the to see more build and test information, +add "-VV" to the ctest command. The output should show; + 100% tests passed, 0 tests failed out of 156. + +For more information see USING_CMake_Examples.txt in the install folder. +=========================================================================== + +Documentation for this release can be found at the following URL: + https://portal.hdfgroup.org/display/HDF5/HDF5 + +Bugs should be reported to help@hdfgroup.org. diff --git a/config/cmake/README.txt.cmake.in b/config/cmake/README.txt.cmake.in deleted file mode 100644 index 9289870..0000000 --- a/config/cmake/README.txt.cmake.in +++ /dev/null @@ -1,80 +0,0 @@ -@HDF5_PACKAGE_NAME@ version @HDF5_PACKAGE_VERSION_STRING@ ------------------------------------------------------------------------------- - -This directory contains the binary (release) distribution of -@HDF5_PACKAGE_NAME@ @HDF5_PACKAGE_VERSION_MAJOR@ that was compiled on; - @BINARY_PLATFORM@. - -It was built with the following options: - -- @LIB_TYPE@ C/C++/Fortran libraries - -- SZIP (encoder enabled) and ZLIB - -- @LIB_TYPE@ HDF5 tools - -- Java @Java_VERSION@ - -The contents of this directory are: - - COPYING - Copyright notice - README.txt - This file - @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_INSTALL_ENDING@ - HDF5 Install Package - -This binary was built with the ZLIB and SZIP/Libaec external libraries and are -included for convenience. Libaec is an unrestricted open-source replacement for SZIP -(version 1.0.4, Encoder ENABLED). - -The official ZLIB and SZIP/Libaec pages are at: - - ZLIB: https://git.savannah.gnu.org/cgit/gzip.git/ - https://git.savannah.gnu.org/cgit/gzip.git/tree/COPYING - SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec - https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt - - -Installation -=========================================================================== -1. Execute @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_INSTALL_ENDING@ -2. Follow prompts -=========================================================================== - -After Installation -=========================================================================== -The examples folder, HDF5Examples, located in the -HDF5 install folder, can be built and tested with CMake and the supplied -HDF5_Examples.cmake file. The HDF5_Examples.cmake expects HDF5 to have -been installed in the default location with above compilers (see the -libhdf5.settings file in the lib install folder). Also, the CMake -utility should be installed. - -To test the installation with the examples; - Create a directory to run the examples. - Copy HDF5Examples folder to this directory. - Copy CTestScript.cmake to this directory. - Copy HDF5_Examples.cmake to this directory. - Copy HDF5_Examples_options.cmake to this directory. - The default source folder is defined as "HDF5Examples". It can be changed - with the CTEST_SOURCE_NAME script option. - The default installation folder is defined as "@CMAKE_INSTALL_PREFIX@". - It can be changed with the INSTALLDIR script option. - The default ctest configuration is defined as "Release". It can be changed - with the CTEST_CONFIGURATION_TYPE script option. Note that this must - be the same as the value used with the -C command line option. - The default build configuration is defined to build and use static libraries. - Shared libraries can be used with the STATICONLYLIBRARIES script option set to "NO". - Other options can be changed by editing the HDF5_Examples_options.cmake file. - - If the defaults are okay, execute from this directory: - ctest -S HDF5_Examples.cmake -C Release -V -O test.log - If the defaults need change, execute from this directory: - ctest -S HDF5_Examples.cmake,CTEST_SOURCE_NAME=MyExamples,INSTALLDIR=MyLocation -C Release -V -O test.log - -When executed, the ctest script will save the results to the log file, test.log, as -indicated by the ctest command. If you wish the to see more build and test information, -add "-VV" to the ctest command. The output should show; - 100% tests passed, 0 tests failed out of 156. - -For more information see USING_CMake_Examples.txt in the install folder. -=========================================================================== - -Documentation for this release can be found at the following URL: - https://portal.hdfgroup.org/display/HDF5/HDF5 - -Bugs should be reported to help@hdfgroup.org. diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake index 6da2b74..a774130 100644 --- a/config/cmake_ext_mod/HDFMacros.cmake +++ b/config/cmake_ext_mod/HDFMacros.cmake @@ -223,7 +223,7 @@ macro (TARGET_C_PROPERTIES wintarget libtype) endmacro () #----------------------------------------------------------------------------- -# Configure the README.txt file for the binary package +# Configure the README.md file for the binary package #----------------------------------------------------------------------------- macro (HDF_README_PROPERTIES target_fortran) set (BINARY_SYSTEM_NAME ${CMAKE_SYSTEM_NAME}) @@ -301,8 +301,8 @@ macro (HDF_README_PROPERTIES target_fortran) endif () configure_file ( - ${HDF_RESOURCES_DIR}/README.txt.cmake.in - ${CMAKE_BINARY_DIR}/README.txt @ONLY + ${HDF_RESOURCES_DIR}/README.md.cmake.in + ${CMAKE_BINARY_DIR}/README.md @ONLY ) endmacro () diff --git a/configure.ac b/configure.ac index 2520249..8d7f359 100644 --- a/configure.ac +++ b/configure.ac @@ -3675,8 +3675,8 @@ fi ## and installed with the libraries (used to generate libhdf5.settings). ## -## HDF5 version from the first line of the README.txt file. -H5_VERSION="`cut -d' ' -f3 $srcdir/README.txt | head -1`" +## HDF5 version from the first line of the README.md file. +H5_VERSION="`cut -d' ' -f3 $srcdir/README.md | head -1`" AC_SUBST([H5_VERSION]) ## Configuration date diff --git a/doxygen/img/HDF5.png b/doxygen/img/HDF5.png new file mode 100644 index 0000000..0458fa8 Binary files /dev/null and b/doxygen/img/HDF5.png differ -- cgit v0.12 From 2f34c433dc26811909673922838e4a97d7c98b9c Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue, 18 Jan 2022 07:44:11 -0600 Subject: Update the java slf4j logging jars to latest 1.7.33 (#1369) --- .gitattributes | 6 +++--- CMakeLists.txt | 6 +++--- MANIFEST | 6 +++--- config/cmake/hdf5-config.cmake.in | 4 ++-- java/examples/datasets/JavaDatasetExample.sh.in | 6 +++--- java/examples/datasets/Makefile.am | 2 +- java/examples/datatypes/JavaDatatypeExample.sh.in | 6 +++--- java/examples/datatypes/Makefile.am | 2 +- java/examples/groups/JavaGroupExample.sh.in | 6 +++--- java/examples/groups/Makefile.am | 2 +- java/examples/intro/JavaIntroExample.sh.in | 6 +++--- java/examples/intro/Makefile.am | 2 +- java/lib/ext/slf4j-nop-1.7.25.jar | Bin 4007 -> 0 bytes java/lib/ext/slf4j-nop-1.7.33.jar | Bin 0 -> 4020 bytes java/lib/ext/slf4j-simple-1.7.25.jar | Bin 15257 -> 0 bytes java/lib/ext/slf4j-simple-1.7.33.jar | Bin 0 -> 15400 bytes java/lib/slf4j-api-1.7.25.jar | Bin 41203 -> 0 bytes java/lib/slf4j-api-1.7.33.jar | Bin 0 -> 41473 bytes java/src/Makefile.am | 2 +- java/test/Makefile.am | 2 +- java/test/junit.sh.in | 6 +++--- 21 files changed, 32 insertions(+), 32 deletions(-) delete mode 100644 java/lib/ext/slf4j-nop-1.7.25.jar create mode 100644 java/lib/ext/slf4j-nop-1.7.33.jar delete mode 100644 java/lib/ext/slf4j-simple-1.7.25.jar create mode 100644 java/lib/ext/slf4j-simple-1.7.33.jar delete mode 100644 java/lib/slf4j-api-1.7.25.jar create mode 100644 java/lib/slf4j-api-1.7.33.jar diff --git a/.gitattributes b/.gitattributes index 385f805..2ff0dab 100644 --- a/.gitattributes +++ b/.gitattributes @@ -192,12 +192,12 @@ java/examples/testfiles/examples.intro.H5_CreateGroup.txt -text java/examples/testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt -text java/examples/testfiles/examples.intro.H5_CreateGroupDataset.txt -text java/examples/testfiles/examples.intro.H5_ReadWrite.txt -text -java/lib/ext/slf4j-nop-1.7.25.jar -text svneol=unset#application/zip -java/lib/ext/slf4j-simple-1.7.25.jar -text svneol=unset#application/zip +java/lib/ext/slf4j-nop-1.7.33.jar -text svneol=unset#application/zip +java/lib/ext/slf4j-simple-1.7.33.jar -text svneol=unset#application/zip java/lib/hamcrest-core.jar -text svneol=unset#application/java-archive java/lib/junit.jar -text svneol=unset#application/java-archive java/lib/simplelogger.properties -text -java/lib/slf4j-api-1.7.25.jar -text svneol=unset#application/zip +java/lib/slf4j-api-1.7.33.jar -text svneol=unset#application/zip java/src/CMakeLists.txt -text java/src/Makefile.am -text java/src/hdf/CMakeLists.txt -text diff --git a/CMakeLists.txt b/CMakeLists.txt index dcee4f9..59595b6 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -229,9 +229,9 @@ set (HDF5_JAVA_JNI_SRC_DIR ${HDF5_SOURCE_DIR}/java/src/jni) set (HDF5_JAVA_HDF5_SRC_DIR ${HDF5_SOURCE_DIR}/java/src/hdf) set (HDF5_JAVA_TEST_SRC_DIR ${HDF5_SOURCE_DIR}/java/test) set (HDF5_JAVA_LIB_DIR ${HDF5_SOURCE_DIR}/java/lib) -set (HDF5_JAVA_LOGGING_JAR ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-1.7.25.jar) -set (HDF5_JAVA_LOGGING_NOP_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7.25.jar) -set (HDF5_JAVA_LOGGING_SIMPLE_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.25.jar) +set (HDF5_JAVA_LOGGING_JAR ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-1.7.33.jar) +set (HDF5_JAVA_LOGGING_NOP_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7.33.jar) +set (HDF5_JAVA_LOGGING_SIMPLE_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.33.jar) set (HDF5_DOXYGEN_DIR ${HDF5_SOURCE_DIR}/doxygen) #----------------------------------------------------------------------------- diff --git a/MANIFEST b/MANIFEST index 72e969a..3442ae8 100644 --- a/MANIFEST +++ b/MANIFEST @@ -3592,9 +3592,9 @@ ./java/lib/hamcrest-core.jar ./java/lib/junit.jar ./java/lib/simplelogger.properties -./java/lib/slf4j-api-1.7.25.jar -./java/lib/ext/slf4j-nop-1.7.25.jar -./java/lib/ext/slf4j-simple-1.7.25.jar +./java/lib/slf4j-api-1.7.33.jar +./java/lib/ext/slf4j-nop-1.7.33.jar +./java/lib/ext/slf4j-simple-1.7.33.jar # CMake-specific Files ./config/toolchain/build32.cmake diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in index eab09ba..589fa5f 100644 --- a/config/cmake/hdf5-config.cmake.in +++ b/config/cmake/hdf5-config.cmake.in @@ -68,8 +68,8 @@ endif () if (${HDF5_PACKAGE_NAME}_BUILD_JAVA) set (${HDF5_PACKAGE_NAME}_JAVA_INCLUDE_DIRS @PACKAGE_CURRENT_BUILD_DIR@/lib/jarhdf5-@HDF5_VERSION_STRING@.jar - @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-1.7.25.jar - @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-1.7.25.jar + @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-1.7.33.jar + @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-1.7.33.jar ) set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARY "@PACKAGE_CURRENT_BUILD_DIR@/lib") set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARIES "${${HDF5_PACKAGE_NAME}_JAVA_LIBRARY}") diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in index f29739a..9a5ddd8 100644 --- a/java/examples/datasets/JavaDatasetExample.sh.in +++ b/java/examples/datasets/JavaDatasetExample.sh.in @@ -57,8 +57,8 @@ $top_builddir/java/src/jni/.libs/libhdf5_java.* $top_builddir/java/src/$JARFILE " LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-1.7.25.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar +$HDFLIB_HOME/slf4j-api-1.7.33.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.33.jar " LIST_DATA_FILES=" $HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Alloc.txt @@ -220,7 +220,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.33.jar:"$BLDLIBDIR"/slf4j-simple-1.7.33.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am index 41a914b..8b71ced 100644 --- a/java/examples/datasets/Makefile.am +++ b/java/examples/datasets/Makefile.am @@ -27,7 +27,7 @@ classes: pkgpath = examples/datasets hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.33.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datasets.jar diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in index e26d8c0..c6f5dbc 100644 --- a/java/examples/datatypes/JavaDatatypeExample.sh.in +++ b/java/examples/datatypes/JavaDatatypeExample.sh.in @@ -54,8 +54,8 @@ $top_builddir/java/src/jni/.libs/libhdf5_java.* $top_builddir/java/src/$JARFILE " LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-1.7.25.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar +$HDFLIB_HOME/slf4j-api-1.7.33.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.33.jar " LIST_DATA_FILES=" $HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Array.txt @@ -216,7 +216,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.33.jar:"$BLDLIBDIR"/slf4j-simple-1.7.33.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am index 90790f7..55ff91f 100644 --- a/java/examples/datatypes/Makefile.am +++ b/java/examples/datatypes/Makefile.am @@ -27,7 +27,7 @@ classes: pkgpath = examples/datatypes hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.33.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datatypes.jar diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in index 3b0e9d1..86f90bf 100644 --- a/java/examples/groups/JavaGroupExample.sh.in +++ b/java/examples/groups/JavaGroupExample.sh.in @@ -56,8 +56,8 @@ $top_builddir/java/src/jni/.libs/libhdf5_java.* $top_builddir/java/src/$JARFILE " LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-1.7.25.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar +$HDFLIB_HOME/slf4j-api-1.7.33.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.33.jar " LIST_ITER_FILES=" $HDFTEST_HOME/h5ex_g_iterate.h5 @@ -255,7 +255,7 @@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR COPY_ITERFILES_TO_BLDITERDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.33.jar:"$BLDLIBDIR"/slf4j-simple-1.7.33.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am index bfde9ae..c520860 100644 --- a/java/examples/groups/Makefile.am +++ b/java/examples/groups/Makefile.am @@ -27,7 +27,7 @@ classes: pkgpath = examples/groups hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.33.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)groups.jar diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in index db741e5..a095f27 100644 --- a/java/examples/intro/JavaIntroExample.sh.in +++ b/java/examples/intro/JavaIntroExample.sh.in @@ -54,8 +54,8 @@ $top_builddir/java/src/jni/.libs/libhdf5_java.* $top_builddir/java/src/$JARFILE " LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-1.7.25.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar +$HDFLIB_HOME/slf4j-api-1.7.33.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.33.jar " LIST_DATA_FILES=" $HDFTEST_HOME/../testfiles/examples.intro.H5_CreateDataset.txt @@ -205,7 +205,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.33.jar:"$BLDLIBDIR"/slf4j-simple-1.7.33.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am index 7d1aeab..741f122 100644 --- a/java/examples/intro/Makefile.am +++ b/java/examples/intro/Makefile.am @@ -27,7 +27,7 @@ classes: pkgpath = examples/intro hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.33.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)intro.jar diff --git a/java/lib/ext/slf4j-nop-1.7.25.jar b/java/lib/ext/slf4j-nop-1.7.25.jar deleted file mode 100644 index 78c7295..0000000 Binary files a/java/lib/ext/slf4j-nop-1.7.25.jar and /dev/null differ diff --git a/java/lib/ext/slf4j-nop-1.7.33.jar b/java/lib/ext/slf4j-nop-1.7.33.jar new file mode 100644 index 0000000..aa8fc09 Binary files /dev/null and b/java/lib/ext/slf4j-nop-1.7.33.jar differ diff --git a/java/lib/ext/slf4j-simple-1.7.25.jar b/java/lib/ext/slf4j-simple-1.7.25.jar deleted file mode 100644 index b29ca12..0000000 Binary files a/java/lib/ext/slf4j-simple-1.7.25.jar and /dev/null differ diff --git a/java/lib/ext/slf4j-simple-1.7.33.jar b/java/lib/ext/slf4j-simple-1.7.33.jar new file mode 100644 index 0000000..ebf4846 Binary files /dev/null and b/java/lib/ext/slf4j-simple-1.7.33.jar differ diff --git a/java/lib/slf4j-api-1.7.25.jar b/java/lib/slf4j-api-1.7.25.jar deleted file mode 100644 index 7e62f13..0000000 Binary files a/java/lib/slf4j-api-1.7.25.jar and /dev/null differ diff --git a/java/lib/slf4j-api-1.7.33.jar b/java/lib/slf4j-api-1.7.33.jar new file mode 100644 index 0000000..db3730d Binary files /dev/null and b/java/lib/slf4j-api-1.7.33.jar differ diff --git a/java/src/Makefile.am b/java/src/Makefile.am index a0abb32..5bb72ad 100644 --- a/java/src/Makefile.am +++ b/java/src/Makefile.am @@ -36,7 +36,7 @@ jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar hdf5_javadir = $(libdir) pkgpath = hdf/hdf5lib -CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$$CLASSPATH AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation diff --git a/java/test/Makefile.am b/java/test/Makefile.am index 6dd309c..4a6785d 100644 --- a/java/test/Makefile.am +++ b/java/test/Makefile.am @@ -27,7 +27,7 @@ classes: pkgpath = test hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.33.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)test.jar diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in index e096302..ca2b3a9 100644 --- a/java/test/junit.sh.in +++ b/java/test/junit.sh.in @@ -66,8 +66,8 @@ $top_builddir/java/src/jni/.libs/libhdf5_java.* LIST_JAR_TESTFILES=" $HDFLIB_HOME/hamcrest-core.jar $HDFLIB_HOME/junit.jar -$HDFLIB_HOME/slf4j-api-1.7.25.jar -$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar +$HDFLIB_HOME/slf4j-api-1.7.33.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.33.jar " LIST_JAR_FILES=" $top_builddir/java/src/$JARFILE @@ -299,7 +299,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@ COPY_LIBFILES_TO_BLDLIBDIR COPY_DATAFILES_TO_BLDDIR -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/junit.jar:"$BLDLIBDIR"/hamcrest-core.jar:"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE"" +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/junit.jar:"$BLDLIBDIR"/hamcrest-core.jar:"$BLDLIBDIR"/slf4j-api-1.7.33.jar:"$BLDLIBDIR"/slf4j-simple-1.7.33.jar:"$TESTJARFILE"" TEST=/usr/bin/test if [ ! -x /usr/bin/test ] -- cgit v0.12 From 8dc72928b8c2f0390659d14011b34983cf9b1171 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue, 18 Jan 2022 14:02:53 -0600 Subject: Develop java newrefs fixes for obj ref datasets (#1354) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> --- .../examples/datatypes/H5Ex_T_ObjectReference.java | 165 ++++++++---------- .../datatypes/H5Ex_T_ObjectReferenceAttribute.java | 194 +++++++++------------ java/test/TestH5Ocopy.java | 97 ++++++----- 3 files changed, 207 insertions(+), 249 deletions(-) diff --git a/java/examples/datatypes/H5Ex_T_ObjectReference.java b/java/examples/datatypes/H5Ex_T_ObjectReference.java index 98a11df..b0f98de 100644 --- a/java/examples/datatypes/H5Ex_T_ObjectReference.java +++ b/java/examples/datatypes/H5Ex_T_ObjectReference.java @@ -205,113 +205,86 @@ public class H5Ex_T_ObjectReference { // Open an existing file. try { file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read data. - try { - if (dataset_id >= 0) { - H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(DATASETNAME + "[" + indx + "]:"); - System.out.print(" ->"); - // Open the referenced object, get its name and type. + // Open an existing dataset. try { - if (dataset_id >= 0) { - object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]); + dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); + + try { + // Get dataspace and allocate memory for read buffer. + dataspace_id = H5.H5Dget_space(dataset_id); + H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); + + // Read data. + H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + + // Output the data to the screen. + for (int indx = 0; indx < dims[0]; indx++) { + System.out.println(DATASETNAME + "[" + indx + "]:"); + System.out.print(" ->"); + // Open the referenced object, get its name and type. + try { + object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + try { + object_type = H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT); + String obj_name = null; + if (object_type >= 0) { + // Get the name. + obj_name = H5.H5Iget_name(object_id); + } + if ((object_id >= 0) && (object_type >= -1)) { + switch (H5G_obj.get(object_type)) { + case H5G_GROUP: + System.out.print("H5G_GROUP"); + break; + case H5G_DATASET: + System.out.print("H5G_DATASET"); + break; + case H5G_TYPE: + System.out.print("H5G_TYPE"); + break; + default: + System.out.print("UNHANDLED"); + } + } + // Print the name. + System.out.println(": " + obj_name); + } + catch (Exception e) { + e.printStackTrace(); + } + finally { + try {H5.H5Oclose(object_id);} catch (Exception e) {} + } + } + catch (Exception e4) { + e4.printStackTrace(); + } + finally { + try {H5.H5Rdestroy(dset_data[indx]);} catch (Exception e4) {} + } + } // end for } - String obj_name = null; - if (object_type >= 0) { - // Get the name. - obj_name = H5.H5Iget_name(object_id); + catch (Exception e3) { + e3.printStackTrace(); } - if ((object_id >= 0) && (object_type >= -1)) { - switch (H5G_obj.get(object_type)) { - case H5G_GROUP: - System.out.print("H5G_GROUP"); - break; - case H5G_DATASET: - System.out.print("H5G_DATASET"); - break; - case H5G_TYPE: - System.out.print("H5G_TYPE"); - break; - default: - System.out.print("UNHANDLED"); - } + finally { + try {H5.H5Sclose(dataspace_id);} catch (Exception e3) {} } - // Print the name. - System.out.println(": " + obj_name); } - catch (Exception e) { - e.printStackTrace(); + catch (Exception e2) { + e2.printStackTrace(); } finally { - try {H5.H5Oclose(object_id);} catch (Exception ex) {} + try {H5.H5Dclose(dataset_id);} catch (Exception e2) {} } } - - // End access to the dataset and release resources used by it. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); + catch (Exception e1) { + e1.printStackTrace(); } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); + finally { + try {H5.H5Fclose(file_id);} catch (Exception e1) {} } } diff --git a/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java b/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java index 885b1da..f61ae0d 100644 --- a/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java +++ b/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java @@ -85,7 +85,7 @@ public class H5Ex_T_ObjectReferenceAttribute { // Create dataset with a scalar dataspace. try { dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { + if ((file_id >= 0) && (dataspace_id >= 0)) { dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); if (dataset_id >= 0) @@ -197,7 +197,6 @@ public class H5Ex_T_ObjectReferenceAttribute { e.printStackTrace(); } - // Terminate access to the data space. try { if (dataspace_id >= 0) H5.H5Sclose(dataspace_id); @@ -229,129 +228,96 @@ public class H5Ex_T_ObjectReferenceAttribute { // Open an existing file. try { file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read data. - try { - if (attribute_id >= 0) - H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(ATTRIBUTENAME + "[" + indx + "]:"); - System.out.print(" ->"); - // Open the referenced object, get its name and type. + // Open an existing dataset. try { - if (dataset_id >= 0) { - object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]); + dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); + + try { + attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + + // Get dataspace and allocate memory for read buffer. + try { + dataspace_id = H5.H5Aget_space(attribute_id); + H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); + + // Read data. + H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF, dset_data); + + // Output the data to the screen. + for (int indx = 0; indx < dims[0]; indx++) { + System.out.println(ATTRIBUTENAME + "[" + indx + "]:"); + System.out.print(" ->"); + // Open the referenced object, get its name and type. + try { + object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + try { + object_type = H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT); + String obj_name = null; + if (object_type >= 0) { + // Get the name. + obj_name = H5.H5Iget_name(object_id); + } + if ((object_id >= 0) && (object_type >= -1)) { + switch (H5G_obj.get(object_type)) { + case H5G_GROUP: + System.out.print("H5G_GROUP"); + break; + case H5G_DATASET: + System.out.print("H5G_DATASET"); + break; + case H5G_TYPE: + System.out.print("H5G_TYPE"); + break; + default: + System.out.print("UNHANDLED"); + } + } + // Print the name. + System.out.println(": " + obj_name); + } + catch (Exception e) { + e.printStackTrace(); + } + finally { + try {H5.H5Oclose(object_id);} catch (Exception e) {} + } + } + catch (Exception e5) { + e5.printStackTrace(); + } + finally { + try {H5.H5Rdestroy(dset_data[indx]);} catch (Exception e5) {} + } + } // end for + } + catch (Exception e4) { + e4.printStackTrace(); + } + finally { + try {H5.H5Sclose(dataspace_id);} catch (Exception e3) {} + } } - String obj_name = null; - if (object_type >= 0) { - // Get the name. - obj_name = H5.H5Iget_name(object_id); + catch (Exception e3) { + e3.printStackTrace(); } - if ((object_id >= 0) && (object_type >= -1)) { - switch (H5G_obj.get(object_type)) { - case H5G_GROUP: - System.out.print("H5G_GROUP"); - break; - case H5G_DATASET: - System.out.print("H5G_DATASET"); - break; - case H5G_TYPE: - System.out.print("H5G_TYPE"); - break; - default: - System.out.print("UNHANDLED"); - } + finally { + try {H5.H5Aclose(attribute_id);} catch (Exception e4) {} } - // Print the name. - System.out.println(": " + obj_name); } - catch (Exception e) { - e.printStackTrace(); + catch (Exception e2) { + e2.printStackTrace(); } finally { - try {H5.H5Oclose(object_id);} catch (Exception ex) {} + try {H5.H5Dclose(dataset_id);} catch (Exception e2) {} } } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); + catch (Exception e1) { + e1.printStackTrace(); } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); + finally { + try {H5.H5Fclose(file_id);} catch (Exception e1) {} } } diff --git a/java/test/TestH5Ocopy.java b/java/test/TestH5Ocopy.java index 8ac73c6..821cad3 100644 --- a/java/test/TestH5Ocopy.java +++ b/java/test/TestH5Ocopy.java @@ -136,18 +136,16 @@ public class TestH5Ocopy { @Test public void testH5OcopyRefsAttr() { long ocp_plist_id = HDF5Constants.H5I_INVALID_HID; - byte[][] dset_data = null; - byte[][] read_data = null; + byte[][] dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; long attribute_id = HDF5Constants.H5I_INVALID_HID; try { - dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; try { dset_data[0] = H5.H5Rcreate_object(H5fid, "/G1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); - fail("testH5OcopyInvalidRef: H5Rcreate_object " + err); + fail("testH5OcopyRefsAttr: H5Rcreate_object " + err); } try { @@ -155,7 +153,7 @@ public class TestH5Ocopy { } catch (Throwable err) { err.printStackTrace(); - fail("testH5OcopyInvalidRef: H5Rcreate_object " + err); + fail("testH5OcopyRefsAttr: H5Rcreate_object " + err); } try { @@ -196,25 +194,30 @@ public class TestH5Ocopy { @Test public void testH5OcopyRefsDatasettodiffFile() { - byte[][] dset_data = null; - byte[][] read_data = null; + byte[][] dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; long ocp_plist_id = HDF5Constants.H5I_INVALID_HID; long dataset_id = HDF5Constants.H5I_INVALID_HID; long H5fid2 = HDF5Constants.H5I_INVALID_HID; try { - dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; + try { + dset_data[0] = H5.H5Rcreate_object(H5fid, "/G1", HDF5Constants.H5P_DEFAULT); + } + catch (Throwable err) { + err.printStackTrace(); + fail("testH5OcopyRefsDatasettodiffFile: H5Rcreate_object " + err); + } try { dset_data[1] = H5.H5Rcreate_object(H5fid, "DS2", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); - fail("testH5OcopyInvalidRef: H5Rcreate_object " + err); + fail("testH5OcopyRefsDatasettodiffFile: H5Rcreate_object " + err); } try { dataset_id = H5.H5Dcreate(H5fid, "DSREF", - HDF5Constants.H5T_STD_REF_OBJ, H5dsid, + HDF5Constants.H5T_STD_REF, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5OcopyRefsDatasettodiffFile.H5Dcreate: ", dataset_id >= 0); H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF, @@ -233,6 +236,7 @@ public class TestH5Ocopy { ex.printStackTrace(); } finally { + try {H5.H5Rdestroy(dset_data[0]);} catch (Exception ex) {} try {H5.H5Rdestroy(dset_data[1]);} catch (Exception ex) {} } @@ -270,21 +274,20 @@ public class TestH5Ocopy { @Test public void testH5OcopyRefsDatasettosameFile() { - byte[][] dset_data = null; - byte[][] read_data = null; + byte[][] dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; + byte[][] read_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; long ocp_plist_id = HDF5Constants.H5I_INVALID_HID; long dataset_id = HDF5Constants.H5I_INVALID_HID; long did = HDF5Constants.H5I_INVALID_HID; int obj_type = -1; try { - dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE]; try { dset_data[0] = H5.H5Rcreate_object(H5fid, "/G1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); - fail("testH5OcopyInvalidRef: H5Rcreate_object " + err); + fail("testH5OcopyRefsDatasettosameFile: H5Rcreate_object " + err); } try { @@ -292,7 +295,7 @@ public class TestH5Ocopy { } catch (Throwable err) { err.printStackTrace(); - fail("testH5OcopyInvalidRef: H5Rcreate_object " + err); + fail("testH5OcopyRefsDatasettosameFile: H5Rcreate_object " + err); } try { @@ -308,9 +311,11 @@ public class TestH5Ocopy { H5.H5Dclose(dataset_id); } catch (Exception ex) { - try {H5.H5Dclose(dataset_id);} catch (Exception exx) {} fail("testH5OcopyRefsDatasettosameFile: create dataset failed"); } + finally { + try {H5.H5Dclose(dataset_id);} catch (Exception exx) {} + } } catch (Exception ex) { ex.printStackTrace(); @@ -324,49 +329,63 @@ public class TestH5Ocopy { ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY); assertTrue("testH5OcopyRefsDatasettosameFile.H5Pcreate: ", ocp_plist_id >= 0); H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG); + //Perform copy function. + try { + H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT); + } + catch(Exception ex) { + fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed"); + } } catch (Exception ex) { - try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {} fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed"); } - - //Perform copy function. - try { - H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT); - } - catch(Exception ex) { + finally { try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {} - fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed"); } - //Open the dataset that has been copied try { - did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT); - assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0); + //Open the dataset that has been copied + try { + did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT); + assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0); + } + catch (Exception e) { + e.printStackTrace(); + fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed"); + } + + //Read the dataset object references in the read_data buffer. + try { + H5.H5Dread(did, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data); + } + catch (Exception e) { + e.printStackTrace(); + fail("testH5OcopyRefsDatasettosameFile: H5Dread failed"); + } } - catch (Exception e) { - try {H5.H5Dclose(did);} catch (Exception exx) {} - e.printStackTrace(); - fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed"); + catch (Exception ex) { + ex.printStackTrace(); + fail("testH5OcopyRefsDatasettosameFile: open and read dataset failed"); + } + finally { + try {H5.H5Dclose(did);} catch (Exception ex) {} } try { - //Read the dataset object references in the read_data buffer. - H5.H5Dread(did, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data); - //Get the type of object the reference points to. - obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, read_data[1]); + obj_type = H5.H5Rget_obj_type3(read_data[1], HDF5Constants.H5R_OBJECT); assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET); - - obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, read_data[0]); + + obj_type = H5.H5Rget_obj_type3(read_data[0], HDF5Constants.H5R_OBJECT); assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP); } catch (Exception ex) { ex.printStackTrace(); } finally { - try {H5.H5Dclose(did);} catch (Exception ex) {} - try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {} + try {H5.H5Rdestroy(read_data[1]);} catch (Exception ex) {} + try {H5.H5Rdestroy(read_data[0]);} catch (Exception ex) {} } } -- cgit v0.12 From bd37363332c0016262a05e4515b9f0e30e9b3d89 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue, 18 Jan 2022 15:52:01 -0600 Subject: various cleanup java test, test files, comments (#1363) --- examples/h5_extlink.c | 4 ++-- hl/test/test_packet.c | 2 +- java/examples/datasets/H5Ex_D_Sofloat.java | 13 +++++++++---- .../examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt | 8 ++++---- src/H5private.h | 2 +- 5 files changed, 17 insertions(+), 12 deletions(-) diff --git a/examples/h5_extlink.c b/examples/h5_extlink.c index f9d4046..61fd589 100644 --- a/examples/h5_extlink.c +++ b/examples/h5_extlink.c @@ -414,14 +414,14 @@ UD_hard_create(const char *link_name, hid_t loc_group, const void *udata, size_t token = *((H5O_token_t *)udata); - //! [H5Open_by_token_snip] + //! [H5Oopen_by_token_snip] /* Open the object this link points to so that we can increment * its reference count. This also ensures that the token passed * in points to a real object (although this check is not perfect!) */ target_obj = H5Oopen_by_token(loc_group, token); - //! [H5Open_by_token_snip] + //! [H5Oopen_by_token_snip] if (target_obj < 0) { ret_value = -1; diff --git a/hl/test/test_packet.c b/hl/test/test_packet.c index 5f30d4b..e8b90f7 100644 --- a/hl/test/test_packet.c +++ b/hl/test/test_packet.c @@ -47,7 +47,7 @@ typedef struct particle_t { */ static particle_t testPart[NRECORDS] = {{"zero", 0, 0, 0.0F, 0.0}, {"one", 10, 10, 1.0F, 10.0}, {"two", 20, 20, 2.0F, 20.0}, {"three", 30, 30, 3.0F, 30.0}, - {"Four", 40, 40, 4.0F, 40.0}, {"Five", 50, 50, 5.0F, 50.0}, + {"four", 40, 40, 4.0F, 40.0}, {"five", 50, 50, 5.0F, 50.0}, {"six", 60, 60, 6.0F, 60.0}, {"seven", 70, 70, 7.0F, 70.0}}; /*------------------------------------------------------------------------- diff --git a/java/examples/datasets/H5Ex_D_Sofloat.java b/java/examples/datasets/H5Ex_D_Sofloat.java index a42aba4..8edde09 100644 --- a/java/examples/datasets/H5Ex_D_Sofloat.java +++ b/java/examples/datasets/H5Ex_D_Sofloat.java @@ -21,6 +21,9 @@ ************************************************************/ package examples.datasets; +import java.text.DecimalFormat; +import java.text.DecimalFormatSymbols; +import java.util.Locale; import java.util.EnumSet; import java.util.HashMap; import java.util.Map; @@ -123,8 +126,9 @@ public class H5Ex_D_Sofloat { } // Print the maximum value. - System.out.println("Maximum value in write buffer is: " + max); - System.out.println("Minimum value in write buffer is: " + min); + DecimalFormat df = new DecimalFormat("#,##0.000000", new DecimalFormatSymbols(Locale.US)); + System.out.println("Maximum value in write buffer is: " + df.format(max)); + System.out.println("Minimum value in write buffer is: " + df.format(min)); // Create a new file using the default properties. try { @@ -308,8 +312,9 @@ public class H5Ex_D_Sofloat { } // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - System.out.println("Minimum value in " + DATASETNAME + " is: " + min); + DecimalFormat df = new DecimalFormat("#,##0.000000", new DecimalFormatSymbols(Locale.US)); + System.out.println("Maximum value in " + DATASETNAME + " is: " + df.format(max)); + System.out.println("Minimum value in " + DATASETNAME + " is: " + df.format(min)); // End access to the dataset and release resources used by it. try { diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt index 4d4b5d6..9025ce2 100644 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt +++ b/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt @@ -1,6 +1,6 @@ -Maximum value in write buffer is: 106.66666666666667 -Minimum value in write buffer is: 1.7692307692307692 +Maximum value in write buffer is: 106.666667 +Minimum value in write buffer is: 1.769231 Filter type is: H5Z_FILTER_SCALEOFFSET -Maximum value in DS1 is: 106.66169811320755 -Minimum value in DS1 is: 1.7692307692307692 +Maximum value in DS1 is: 106.661698 +Minimum value in DS1 is: 1.769231 diff --git a/src/H5private.h b/src/H5private.h index 7838f46..5b0e33b 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -576,7 +576,7 @@ typedef off_t h5_stat_size_t; #define HDoff_t off_t #endif -#/* Redefine all the POSIX and C functions. We should never see an +/* Redefine all the POSIX and C functions. We should never see an * undecorated POSIX or C function (or any other non-HDF5 function) * in the source. */ -- cgit v0.12 From 1a9662e04c4e469be8c4f822c2dc83f19a7be4be Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 18 Jan 2022 23:28:27 -0500 Subject: Do not set CMAKE_INSTALL_PREFIX when built externally (#1380) --- config/cmake_ext_mod/HDFMacros.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake index a774130..09492e7 100644 --- a/config/cmake_ext_mod/HDFMacros.cmake +++ b/config/cmake_ext_mod/HDFMacros.cmake @@ -427,7 +427,7 @@ macro (HDF_DIR_PATHS package_prefix) endif () endif () - if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) if (CMAKE_HOST_UNIX) set (CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}" CACHE PATH "Install path prefix, prepended onto install directories." FORCE) -- cgit v0.12 From 6c184e28d80dff5ae1efb63ca28043c62f1b7670 Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Wed, 19 Jan 2022 14:29:37 -0600 Subject: Fix documentation for H5D_space_status_t enum values (#1372) --- src/H5Dpublic.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index 10e297f..02644ed 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -91,9 +91,9 @@ typedef enum H5D_alloc_time_t { typedef enum H5D_space_status_t { H5D_SPACE_STATUS_ERROR = -1, /**< Error */ H5D_SPACE_STATUS_NOT_ALLOCATED = 0, /**< Space has not been allocated for this dataset. */ - H5D_SPACE_STATUS_PART_ALLOCATED = 1, /**< Space has been allocated for this dataset. */ - H5D_SPACE_STATUS_ALLOCATED = 2 /**< Space has been partially allocated for this dataset. (Used only for - datasets with chunked storage.) */ + H5D_SPACE_STATUS_PART_ALLOCATED = 1, /**< Space has been partially allocated for this dataset. + (Used only for datasets with chunked storage.) */ + H5D_SPACE_STATUS_ALLOCATED = 2 /**< Space has been allocated for this dataset. */ } H5D_space_status_t; //! -- cgit v0.12 From dd6ad33c75bf084f08d4e84f92ab997c704b2096 Mon Sep 17 00:00:00 2001 From: Neil Fortner Date: Thu, 20 Jan 2022 07:34:43 -0600 Subject: Implement H5ESget requests function to retrieve requests from an event set (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- release_docs/RELEASE.txt | 7 + src/H5ES.c | 55 ++++++ src/H5ESdevelop.h | 2 + src/H5ESint.c | 108 ++++++++++- src/H5ESlist.c | 11 +- src/H5ESpkg.h | 5 +- test/event_set.c | 489 ++++++++++++++++++++++++++++++++++++++++++++++- 7 files changed, 659 insertions(+), 18 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index fc7d4dd..d059fb3 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -516,6 +516,13 @@ New Features Library: -------- + - Add a new public function, H5ESget_requests() + + This function allows the user to retrieve request pointers from an event + set. It is intended for use primarily by VOL plug in developers. + + (NAF - 2022/01/11) + - Adds new file driver-level memory copy operation for "ctl" callback and updates compact dataset I/O routines to utilize it diff --git a/src/H5ES.c b/src/H5ES.c index ccc0dd8..9abaa54 100644 --- a/src/H5ES.c +++ b/src/H5ES.c @@ -236,6 +236,61 @@ done: } /* end H5ESget_op_counter() */ /*------------------------------------------------------------------------- + * Function: H5ESget_requests + * + * Purpose: Retrieve the requests in an event set. Up to *count + * requests are stored in the provided requests array, and + * the connector ids corresponding to these requests are + * stored in the provided connector_ids array. Either or + * both of these arrays may be NULL, in which case this + * information is not returned. If these arrays are + * non-NULL, they must be large enough to contain *count + * entries. On exit, *count is set to the total number of + * events in the event set. + * + * Events are returned in the order they were added to the + * event set. If order is H5_ITER_INC or H5_ITER_NATIVE, + * events will be returned starting from the oldest. If order + * is H5_ITER_DEC, events will be returned starting with the + * newest/most recent. + * + * Return: SUCCEED / FAIL + * + * Programmer: Neil Fortner + * Tuesday, November 23, 2021 + * + *------------------------------------------------------------------------- + */ +herr_t +H5ESget_requests(hid_t es_id, H5_iter_order_t order, hid_t *connector_ids, void **requests, size_t array_len, + size_t *count /*out*/) +{ + H5ES_t *es; /* Event set */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE5("e", "iIo*i**xx", es_id, order, connector_ids, requests, count); + + /* Check arguments */ + if (NULL == (es = H5I_object_verify(es_id, H5I_EVENTSET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid event set identifier") + if (order <= H5_ITER_UNKNOWN || order >= H5_ITER_N) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid iteration order specified") + + /* Call internal routine */ + if (array_len > 0 && (requests || connector_ids)) + if (H5ES__get_requests(es, order, connector_ids, requests, array_len) < 0) + HGOTO_ERROR(H5E_EVENTSET, H5E_CANTGET, FAIL, "can't get requests") + + /* Retrieve the count, if non-NULL */ + if (count) + *count = H5ES__list_count(&es->active); + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5ESget_requests() */ + +/*------------------------------------------------------------------------- * Function: H5ESwait * * Purpose: Wait (with timeout) for operations in event set to complete diff --git a/src/H5ESdevelop.h b/src/H5ESdevelop.h index 5a0f2b4..2fb9aeb 100644 --- a/src/H5ESdevelop.h +++ b/src/H5ESdevelop.h @@ -42,6 +42,8 @@ extern "C" { #endif H5_DLL herr_t H5ESinsert_request(hid_t es_id, hid_t connector_id, void *request); +H5_DLL herr_t H5ESget_requests(hid_t es_id, H5_iter_order_t order, hid_t *connector_ids, void **requests, + size_t array_len, size_t *count); #ifdef __cplusplus } diff --git a/src/H5ESint.c b/src/H5ESint.c index c66be16..7eb5909 100644 --- a/src/H5ESint.c +++ b/src/H5ESint.c @@ -50,6 +50,14 @@ /* Local Typedefs */ /******************/ +/* Callback context for get events operations */ +typedef struct H5ES_get_requests_ctx_t { + hid_t *connector_ids; /* Output buffer for list of connector IDs that match the above requests */ + void **requests; /* Output buffer for list of requests in event set */ + size_t array_len; /* Length of the above output buffers */ + size_t i; /* Number of elements filled in output buffers */ +} H5ES_get_requests_ctx_t; + /* Callback context for wait operations */ typedef struct H5ES_wait_ctx_t { H5ES_t * es; /* Event set being operated on */ @@ -84,6 +92,7 @@ static herr_t H5ES__close(H5ES_t *es); static herr_t H5ES__close_cb(void *es, void **request_token); static herr_t H5ES__insert(H5ES_t *es, H5VL_t *connector, void *request_token, const char *app_file, const char *app_func, unsigned app_line, const char *caller, const char *api_args); +static int H5ES__get_requests_cb(H5ES_event_t *ev, void *_ctx); static herr_t H5ES__handle_fail(H5ES_t *es, H5ES_event_t *ev); static herr_t H5ES__op_complete(H5ES_t *es, H5ES_event_t *ev, H5VL_request_status_t ev_status); static int H5ES__wait_cb(H5ES_event_t *ev, void *_ctx); @@ -282,7 +291,8 @@ H5ES__insert(H5ES_t *es, H5VL_t *connector, void *request_token, const char *app * there's no need to duplicate it. */ ev->op_info.api_name = caller; - if (NULL == (ev->op_info.api_args = H5MM_xstrdup(api_args))) + HDassert(ev->op_info.api_args == NULL); + if (api_args && NULL == (ev->op_info.api_args = H5MM_xstrdup(api_args))) HGOTO_ERROR(H5E_EVENTSET, H5E_CANTALLOC, FAIL, "can't copy API routine arguments") /* Append fully initialized event onto the event set's 'active' list */ @@ -419,6 +429,86 @@ done: } /* end H5ES__insert_request() */ /*------------------------------------------------------------------------- + * Function: H5ES__get_requests_cb + * + * Purpose: Iterator callback for H5ES__get_events - adds the event to + * the list. + * + * Return: SUCCEED / FAIL + * + * Programmer: Neil Fortner + * Tuesday, November 23, 2021 + * + *------------------------------------------------------------------------- + */ +static int +H5ES__get_requests_cb(H5ES_event_t *ev, void *_ctx) +{ + H5ES_get_requests_ctx_t *ctx = (H5ES_get_requests_ctx_t *)_ctx; /* Callback context */ + int ret_value = H5_ITER_CONT; /* Return value */ + + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ev); + HDassert(ctx); + HDassert(ctx->i < ctx->array_len); + + /* Get the connector ID for the event */ + if (ctx->connector_ids) + ctx->connector_ids[ctx->i] = ev->request->connector->id; + + /* Get the request for the event */ + if (ctx->requests) + ctx->requests[ctx->i] = ev->request->data; + + /* Check if we've run out of room in the arrays */ + if (++ctx->i == ctx->array_len) + ret_value = H5_ITER_STOP; + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5ES__get_requests_cb() */ + +/*------------------------------------------------------------------------- + * Function: H5ES__get_requests + * + * Purpose: Get all requests in an event set. + * + * Return: SUCCEED / FAIL + * + * Programmer: Neil Fortner + * Tuesday, November 23, 2021 + * + *------------------------------------------------------------------------- + */ +herr_t +H5ES__get_requests(H5ES_t *es, H5_iter_order_t order, hid_t *connector_ids, void **requests, size_t array_len) +{ + H5ES_get_requests_ctx_t ctx; /* Callback context */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Sanity check */ + HDassert(es); + HDassert(array_len > 0); + HDassert(requests || connector_ids); + + /* Set up context for iterator callbacks */ + ctx.connector_ids = connector_ids; + ctx.requests = requests; + ctx.array_len = array_len; + ctx.i = 0; + + /* Iterate over the events in the set */ + if (H5ES__list_iterate(&es->active, order, H5ES__get_requests_cb, &ctx) < 0) + HGOTO_ERROR(H5E_EVENTSET, H5E_BADITER, FAIL, "iteration failed") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5ES__get_requests() */ + +/*------------------------------------------------------------------------- * Function: H5ES__handle_fail * * Purpose: Handle a failed event @@ -661,7 +751,7 @@ H5ES__wait(H5ES_t *es, uint64_t timeout, size_t *num_in_progress, hbool_t *op_fa ctx.op_failed = op_failed; /* Iterate over the events in the set, waiting for them to complete */ - if (H5ES__list_iterate(&es->active, H5ES__wait_cb, &ctx) < 0) + if (H5ES__list_iterate(&es->active, H5_ITER_NATIVE, H5ES__wait_cb, &ctx) < 0) HGOTO_ERROR(H5E_EVENTSET, H5E_BADITER, FAIL, "iteration failed") done: @@ -769,7 +859,7 @@ H5ES__cancel(H5ES_t *es, size_t *num_not_canceled, hbool_t *op_failed) ctx.op_failed = op_failed; /* Iterate over the events in the set, attempting to cancel them */ - if (H5ES__list_iterate(&es->active, H5ES__cancel_cb, &ctx) < 0) + if (H5ES__list_iterate(&es->active, H5_ITER_NATIVE, H5ES__cancel_cb, &ctx) < 0) HGOTO_ERROR(H5E_EVENTSET, H5E_BADITER, FAIL, "iteration failed") done: @@ -806,13 +896,13 @@ H5ES__get_err_info_cb(H5ES_event_t *ev, void *_ctx) * so there's no need to duplicate them internally, but they are duplicated * here, when they are given back to the user. */ - if (NULL == (ctx->curr_err_info->api_name = H5MM_strdup(ev->op_info.api_name))) + if (NULL == (ctx->curr_err_info->api_name = H5MM_xstrdup(ev->op_info.api_name))) HGOTO_ERROR(H5E_EVENTSET, H5E_CANTALLOC, H5_ITER_ERROR, "can't copy HDF5 API routine name") - if (NULL == (ctx->curr_err_info->api_args = H5MM_strdup(ev->op_info.api_args))) + if (NULL == (ctx->curr_err_info->api_args = H5MM_xstrdup(ev->op_info.api_args))) HGOTO_ERROR(H5E_EVENTSET, H5E_CANTALLOC, H5_ITER_ERROR, "can't copy HDF5 API routine arguments") - if (NULL == (ctx->curr_err_info->app_file_name = H5MM_strdup(ev->op_info.app_file_name))) + if (NULL == (ctx->curr_err_info->app_file_name = H5MM_xstrdup(ev->op_info.app_file_name))) HGOTO_ERROR(H5E_EVENTSET, H5E_CANTALLOC, H5_ITER_ERROR, "can't copy HDF5 application file name") - if (NULL == (ctx->curr_err_info->app_func_name = H5MM_strdup(ev->op_info.app_func_name))) + if (NULL == (ctx->curr_err_info->app_func_name = H5MM_xstrdup(ev->op_info.app_func_name))) HGOTO_ERROR(H5E_EVENTSET, H5E_CANTALLOC, H5_ITER_ERROR, "can't copy HDF5 application function name") ctx->curr_err_info->app_line_num = ev->op_info.app_line_num; ctx->curr_err_info->op_ins_count = ev->op_info.op_ins_count; @@ -883,7 +973,7 @@ H5ES__get_err_info(H5ES_t *es, size_t num_err_info, H5ES_err_info_t err_info[], ctx.curr_err_info = &err_info[0]; /* Iterate over the failed events in the set, copying their error info */ - if (H5ES__list_iterate(&es->failed, H5ES__get_err_info_cb, &ctx) < 0) + if (H5ES__list_iterate(&es->failed, H5_ITER_NATIVE, H5ES__get_err_info_cb, &ctx) < 0) HGOTO_ERROR(H5E_EVENTSET, H5E_BADITER, FAIL, "iteration failed") /* Set # of failed events cleared from event set's failed list */ @@ -957,7 +1047,7 @@ H5ES__close(H5ES_t *es) "can't close event set while unfinished operations are present (i.e. wait on event set first)") /* Iterate over the failed events in the set, releasing them */ - if (H5ES__list_iterate(&es->failed, H5ES__close_failed_cb, (void *)es) < 0) + if (H5ES__list_iterate(&es->failed, H5_ITER_NATIVE, H5ES__close_failed_cb, (void *)es) < 0) HGOTO_ERROR(H5E_EVENTSET, H5E_BADITER, FAIL, "iteration failed") /* Release the event set */ diff --git a/src/H5ESlist.c b/src/H5ESlist.c index 3180322..61a9dd1 100644 --- a/src/H5ESlist.c +++ b/src/H5ESlist.c @@ -135,7 +135,10 @@ H5ES__list_count(const H5ES_event_list_t *el) * each event. * * Note: Iteration is safe for deleting the current event. Modifying - * the list in other ways is likely unsafe. + * the list in other ways is likely unsafe. If order is + * H5_ITER_INC or H5_ITER_NATIVE events are visited starting + * with the oldest, otherwise they are visited starting with + * the newest. * * Return: SUCCEED / FAIL * @@ -145,7 +148,7 @@ H5ES__list_count(const H5ES_event_list_t *el) *------------------------------------------------------------------------- */ int -H5ES__list_iterate(H5ES_event_list_t *el, H5ES_list_iter_func_t cb, void *ctx) +H5ES__list_iterate(H5ES_event_list_t *el, H5_iter_order_t order, H5ES_list_iter_func_t cb, void *ctx) { H5ES_event_t *ev; /* Event in list */ int ret_value = H5_ITER_CONT; /* Return value */ @@ -157,12 +160,12 @@ H5ES__list_iterate(H5ES_event_list_t *el, H5ES_list_iter_func_t cb, void *ctx) HDassert(cb); /* Iterate over events in list */ - ev = el->head; + ev = (order == H5_ITER_DEC) ? el->tail : el->head; while (ev) { H5ES_event_t *tmp; /* Temporary event */ /* Get pointer to next node, so it's safe if this one is removed */ - tmp = ev->next; + tmp = (order == H5_ITER_DEC) ? ev->prev : ev->next; /* Perform iterator callback */ if ((ret_value = (*cb)(ev, ctx)) != H5_ITER_CONT) { diff --git a/src/H5ESpkg.h b/src/H5ESpkg.h index a7a8e20..6ee50fa 100644 --- a/src/H5ESpkg.h +++ b/src/H5ESpkg.h @@ -81,6 +81,8 @@ typedef int (*H5ES_list_iter_func_t)(H5ES_event_t *ev, void *ctx); H5_DLL H5ES_t *H5ES__create(void); H5_DLL herr_t H5ES__insert_request(H5ES_t *es, H5VL_t *connector, void *token); H5_DLL herr_t H5ES__wait(H5ES_t *es, uint64_t timeout, size_t *num_in_progress, hbool_t *op_failed); +H5_DLL herr_t H5ES__get_requests(H5ES_t *es, H5_iter_order_t order, hid_t *connector_ids, void **requests, + size_t array_len); H5_DLL herr_t H5ES__cancel(H5ES_t *es, size_t *num_not_canceled, hbool_t *op_failed); H5_DLL herr_t H5ES__get_err_info(H5ES_t *es, size_t num_err_info, H5ES_err_info_t err_info[], size_t *num_cleared); @@ -88,7 +90,8 @@ H5_DLL herr_t H5ES__get_err_info(H5ES_t *es, size_t num_err_info, H5ES_err_info /* Event list operations */ H5_DLL void H5ES__list_append(H5ES_event_list_t *el, H5ES_event_t *ev); H5_DLL size_t H5ES__list_count(const H5ES_event_list_t *el); -H5_DLL int H5ES__list_iterate(H5ES_event_list_t *el, H5ES_list_iter_func_t cb, void *ctx); +H5_DLL int H5ES__list_iterate(H5ES_event_list_t *el, H5_iter_order_t order, H5ES_list_iter_func_t cb, + void *ctx); H5_DLL void H5ES__list_remove(H5ES_event_list_t *el, const H5ES_event_t *ev); /* Event operations */ diff --git a/test/event_set.c b/test/event_set.c index 5df49e9..22df510 100644 --- a/test/event_set.c +++ b/test/event_set.c @@ -19,8 +19,157 @@ #include "h5test.h" #include "H5srcdir.h" +#define EVENT_SET_NUM_CONNECTOR_IDS 2 + const char *FILENAME[] = {"event_set_1", NULL}; +hid_t connector_ids_g[EVENT_SET_NUM_CONNECTOR_IDS]; + +herr_t fake_wait_request_wait(void *req, uint64_t timeout, H5VL_request_status_t *status); +herr_t fake_wait_request_free(void *req); + +/* A VOL class struct that describes a VOL class with no + * functionality, other than a wait that returns success. + */ +static const H5VL_class_t fake_wait_vol_g = { + H5VL_VERSION, /* VOL class struct version */ + ((H5VL_class_value_t)501), /* value */ + "fake_wait", /* name */ + 0, /* connector version */ + 0, /* capability flags */ + NULL, /* initialize */ + NULL, /* terminate */ + { + /* info_cls */ + (size_t)0, /* size */ + NULL, /* copy */ + NULL, /* compare */ + NULL, /* free */ + NULL, /* to_str */ + NULL, /* from_str */ + }, + { + /* wrap_cls */ + NULL, /* get_object */ + NULL, /* get_wrap_ctx */ + NULL, /* wrap_object */ + NULL, /* unwrap_object */ + NULL, /* free_wrap_ctx */ + }, + { + /* attribute_cls */ + NULL, /* create */ + NULL, /* open */ + NULL, /* read */ + NULL, /* write */ + NULL, /* get */ + NULL, /* specific */ + NULL, /* optional */ + NULL /* close */ + }, + { + /* dataset_cls */ + NULL, /* create */ + NULL, /* open */ + NULL, /* read */ + NULL, /* write */ + NULL, /* get */ + NULL, /* specific */ + NULL, /* optional */ + NULL /* close */ + }, + { + /* datatype_cls */ + NULL, /* commit */ + NULL, /* open */ + NULL, /* get */ + NULL, /* specific */ + NULL, /* optional */ + NULL /* close */ + }, + { + /* file_cls */ + NULL, /* create */ + NULL, /* open */ + NULL, /* get */ + NULL, /* specific */ + NULL, /* optional */ + NULL /* close */ + }, + { + /* group_cls */ + NULL, /* create */ + NULL, /* open */ + NULL, /* get */ + NULL, /* specific */ + NULL, /* optional */ + NULL /* close */ + }, + { + /* link_cls */ + NULL, /* create */ + NULL, /* copy */ + NULL, /* move */ + NULL, /* get */ + NULL, /* specific */ + NULL /* optional */ + }, + { + /* object_cls */ + NULL, /* open */ + NULL, /* copy */ + NULL, /* get */ + NULL, /* specific */ + NULL /* optional */ + }, + { + /* introspect_cls */ + NULL, /* get_conn_cls */ + NULL, /* get_cap_flags */ + NULL, /* opt_query */ + }, + { + /* request_cls */ + fake_wait_request_wait, /* wait */ + NULL, /* notify */ + NULL, /* cancel */ + NULL, /* specific */ + NULL, /* optional */ + fake_wait_request_free /* free */ + }, + { + /* blob_cls */ + NULL, /* put */ + NULL, /* get */ + NULL, /* specific */ + NULL /* optional */ + }, + { + /* token_cls */ + NULL, /* cmp */ + NULL, /* to_str */ + NULL /* from_str */ + }, + NULL /* optional */ +}; + +herr_t +fake_wait_request_wait(void H5_ATTR_UNUSED *req, uint64_t H5_ATTR_UNUSED timeout, + H5VL_request_status_t *status) +{ + /* Set status if requested */ + if (status) + *status = H5VL_REQUEST_STATUS_SUCCEED; + + return 0; +} /* end H5_daos_req_wait() */ + +herr_t +fake_wait_request_free(void H5_ATTR_UNUSED *req) +{ + return 0; +} /* end fake_wait_request_free() */ + /*------------------------------------------------------------------------- * Function: test_es_create * @@ -159,6 +308,324 @@ error: } /*------------------------------------------------------------------------- + * Function: test_es_get_requests + * + * Purpose: Tests getting requests from event set. + * + * Return: Success: 0 + * Failure: number of errors + * + * Programmer: Neil Fortner + * Wednesday, November 24, 2021 + * + *------------------------------------------------------------------------- + */ +static int +test_es_get_requests(void) +{ + hid_t es_id; /* Event set ID */ + hid_t connector_ids[2]; /* Connector IDs */ + void * requests[2]; /* Requests */ + int req_targets[2]; /* Dummy targets for void * requests */ + size_t count; /* # of events in set */ + hbool_t op_failed; /* Whether an operation failed (unused) */ + + TESTING("event set get requests"); + + /* Create an event set */ + if ((es_id = H5EScreate()) < 0) + TEST_ERROR + + /* Get number of requests in event set */ + count = 3; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, NULL, 0, &count) < 0) + TEST_ERROR + if (count != 0) + TEST_ERROR + + /* Get only connector IDs */ + count = 3; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, NULL, 2, &count) < 0) + TEST_ERROR + if (count != 0) + TEST_ERROR + + /* Get only requests */ + count = 3; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, requests, 2, &count) < 0) + TEST_ERROR + if (count != 0) + TEST_ERROR + + /* Get both */ + count = 3; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, requests, 2, &count) < 0) + TEST_ERROR + if (count != 0) + TEST_ERROR + + /* Insert event into event set */ + if (H5ESinsert_request(es_id, connector_ids_g[0], &req_targets[0]) < 0) + TEST_ERROR + + /* Get number of requests in event set */ + count = 0; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, NULL, 0, &count) < 0) + TEST_ERROR + if (count != 1) + TEST_ERROR + + /* Get only connector IDs */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, NULL, 2, &count) < 0) + TEST_ERROR + if (count != 1) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[0]) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + + /* Get only requests */ + count = 0; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, requests, 2, &count) < 0) + TEST_ERROR + if (count != 1) + TEST_ERROR + if (requests[0] != &req_targets[0]) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR + + /* Get both */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, requests, 2, &count) < 0) + TEST_ERROR + if (count != 1) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[0]) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + if (requests[0] != &req_targets[0]) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR + + /* Insert second event into event set */ + if (H5ESinsert_request(es_id, connector_ids_g[1], &req_targets[1]) < 0) + TEST_ERROR + + /* Get number of requests in event set */ + count = 0; + if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, NULL, 0, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + + /* Get only connector IDs */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + if (H5ESget_requests(es_id, H5_ITER_INC, connector_ids, NULL, 2, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[0]) + TEST_ERROR + if (connector_ids[1] != connector_ids_g[1]) + TEST_ERROR + + /* Try with H5_ITER_DEC */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + if (H5ESget_requests(es_id, H5_ITER_DEC, connector_ids, NULL, 2, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[1]) + TEST_ERROR + if (connector_ids[1] != connector_ids_g[0]) + TEST_ERROR + + /* Get only requests */ + count = 0; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_INC, NULL, requests, 2, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (requests[0] != &req_targets[0]) + TEST_ERROR + if (requests[1] != &req_targets[1]) + TEST_ERROR + + /* Try with H5_ITER_DEC */ + count = 0; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_DEC, NULL, requests, 2, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (requests[0] != &req_targets[1]) + TEST_ERROR + if (requests[1] != &req_targets[0]) + TEST_ERROR + + /* Get both */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_INC, connector_ids, requests, 2, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[0]) + TEST_ERROR + if (connector_ids[1] != connector_ids_g[1]) + TEST_ERROR + if (requests[0] != &req_targets[0]) + TEST_ERROR + if (requests[1] != &req_targets[1]) + TEST_ERROR + + /* Try with H5_ITER_DEC */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_DEC, connector_ids, requests, 2, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[1]) + TEST_ERROR + if (connector_ids[1] != connector_ids_g[0]) + TEST_ERROR + if (requests[0] != &req_targets[1]) + TEST_ERROR + if (requests[1] != &req_targets[0]) + TEST_ERROR + + /* Get only first connector ID */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + if (H5ESget_requests(es_id, H5_ITER_INC, connector_ids, NULL, 1, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[0]) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + + /* Try with H5_ITER_DEC */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + if (H5ESget_requests(es_id, H5_ITER_DEC, connector_ids, NULL, 1, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[1]) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + + /* Get only first request */ + count = 0; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_INC, NULL, requests, 1, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (requests[0] != &req_targets[0]) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR + + /* Try with H5_ITER_DEC */ + count = 0; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_DEC, NULL, requests, 1, &count) < 0) + TEST_ERROR + if (count != 2) + TEST_ERROR + if (requests[0] != &req_targets[1]) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR + + /* Get only first of both */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_INC, connector_ids, requests, 1, &count) < 0) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[0]) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + if (requests[0] != &req_targets[0]) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR + + /* Try with H5_ITER_DEC */ + count = 0; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; + if (H5ESget_requests(es_id, H5_ITER_DEC, connector_ids, requests, 1, &count) < 0) + TEST_ERROR + if (connector_ids[0] != connector_ids_g[1]) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + if (requests[0] != &req_targets[1]) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR + + /* Close the event set */ + if (H5ESwait(es_id, 10000000, &count, &op_failed) < 0) + TEST_ERROR + if (H5ESclose(es_id) < 0) + TEST_ERROR + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY + { + H5ESclose(es_id); + } + H5E_END_TRY; + return 1; +} + +/*------------------------------------------------------------------------- * Function: main * * Purpose: Tests event sets @@ -175,27 +642,41 @@ int main(void) { hid_t fapl_id = H5I_INVALID_HID; /* File access property list */ + int i; /* Local index variable */ int nerrors = 0; /* Error count */ /* Setup */ h5_reset(); fapl_id = h5_fileaccess(); + /* Register dummy connector IDs */ + for (i = 0; i < EVENT_SET_NUM_CONNECTOR_IDS; i++) + if ((connector_ids_g[i] = H5VLregister_connector(&fake_wait_vol_g, H5P_DEFAULT)) < 0) + TEST_ERROR + /* Tests */ nerrors += test_es_create(); nerrors += test_es_none(); + nerrors += test_es_get_requests(); + + /* Unregister dummy connectors */ + for (i = 0; i < EVENT_SET_NUM_CONNECTOR_IDS; i++) + if (H5VLunregister_connector(connector_ids_g[i]) < 0) + TEST_ERROR /* Cleanup */ h5_cleanup(FILENAME, fapl_id); /* Check for any errors */ - if (nerrors) { - HDputs("***** EVENT SET TESTS FAILED *****"); - HDexit(EXIT_FAILURE); - } /* end if */ + if (nerrors) + goto error; /* Report status */ HDputs("All event set tests passed."); HDexit(EXIT_SUCCESS); + +error: + HDputs("***** EVENT SET TESTS FAILED *****"); + HDexit(EXIT_FAILURE); } /* end main() */ -- cgit v0.12 From d45124d7085de2771c0157f5d48d71b21a10de1f Mon Sep 17 00:00:00 2001 From: Sean McBride Date: Thu, 20 Jan 2022 09:38:56 -0500 Subject: Open bsd fixes (#1195) --- config/cmake_ext_mod/ConfigureChecks.cmake | 116 ++++++++++++++--------------- src/H5detect.c | 32 +++----- test/app_ref.c | 4 +- 3 files changed, 70 insertions(+), 82 deletions(-) diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake index 6a9c274..b322948 100644 --- a/config/cmake_ext_mod/ConfigureChecks.cmake +++ b/config/cmake_ext_mod/ConfigureChecks.cmake @@ -223,65 +223,63 @@ set (LINUX_LFS 0) set (HDF_EXTRA_C_FLAGS) set (HDF_EXTRA_FLAGS) if (MINGW OR NOT WINDOWS) - # Might want to check explicitly for Linux and possibly Cygwin - # instead of checking for not Solaris or Darwin. - if (NOT ${HDF_PREFIX}_HAVE_SOLARIS AND NOT ${HDF_PREFIX}_HAVE_DARWIN) - # Linux Specific flags - # This was originally defined as _POSIX_SOURCE which was updated to - # _POSIX_C_SOURCE=199506L to expose a greater amount of POSIX - # functionality so clock_gettime and CLOCK_MONOTONIC are defined - # correctly. This was later updated to 200112L so that - # posix_memalign() is visible for the direct VFD code on Linux - # systems. - # POSIX feature information can be found in the gcc manual at: - # http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html - set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) - - # Need to add this so that O_DIRECT is visible for the direct - # VFD on Linux systems. - set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE) - - option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON) - if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN) - set (msg "Performing TEST_LFS_WORKS") - try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE - ${CMAKE_BINARY_DIR} - ${HDF_RESOURCES_EXT_DIR}/HDFTests.c - COMPILE_DEFINITIONS "-DTEST_LFS_WORKS" - ) - - # The LARGEFILE definitions were from the transition period - # and are probably no longer needed. The FILE_OFFSET_BITS - # check should be generalized for all POSIX systems as it - # is in the Autotools. - if (TEST_LFS_WORKS_COMPILE) - if (TEST_LFS_WORKS_RUN MATCHES 0) - set (TEST_LFS_WORKS 1 CACHE INTERNAL ${msg}) - set (LARGEFILE 1) - set (HDF_EXTRA_FLAGS ${HDF_EXTRA_FLAGS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... yes") - endif () - else () - set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... no") - endif () - file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log - "Test TEST_LFS_WORKS Run failed with the following exit code:\n ${TEST_LFS_WORKS_RUN}\n" - ) - endif () - else () - set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... no") - endif () - file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log - "Test TEST_LFS_WORKS Compile failed\n" - ) - endif () - endif () - set (CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} ${HDF_EXTRA_FLAGS}) + if (CMAKE_SYSTEM_NAME MATCHES "Linux") + # Linux Specific flags + # This was originally defined as _POSIX_SOURCE which was updated to + # _POSIX_C_SOURCE=199506L to expose a greater amount of POSIX + # functionality so clock_gettime and CLOCK_MONOTONIC are defined + # correctly. This was later updated to 200112L so that + # posix_memalign() is visible for the direct VFD code on Linux + # systems. + # POSIX feature information can be found in the gcc manual at: + # http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html + set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) + + # Need to add this so that O_DIRECT is visible for the direct + # VFD on Linux systems. + set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE) + + option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON) + if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN) + set (msg "Performing TEST_LFS_WORKS") + try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE + ${CMAKE_BINARY_DIR} + ${HDF_RESOURCES_EXT_DIR}/HDFTests.c + COMPILE_DEFINITIONS "-DTEST_LFS_WORKS" + ) + + # The LARGEFILE definitions were from the transition period + # and are probably no longer needed. The FILE_OFFSET_BITS + # check should be generalized for all POSIX systems as it + # is in the Autotools. + if (TEST_LFS_WORKS_COMPILE) + if (TEST_LFS_WORKS_RUN MATCHES 0) + set (TEST_LFS_WORKS 1 CACHE INTERNAL ${msg}) + set (LARGEFILE 1) + set (HDF_EXTRA_FLAGS ${HDF_EXTRA_FLAGS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... yes") + endif () + else () + set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... no") + endif () + file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log + "Test TEST_LFS_WORKS Run failed with the following exit code:\n ${TEST_LFS_WORKS_RUN}\n" + ) + endif () + else () + set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... no") + endif () + file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log + "Test TEST_LFS_WORKS Compile failed\n" + ) + endif () + endif () + set (CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} ${HDF_EXTRA_FLAGS}) endif () endif () diff --git a/src/H5detect.c b/src/H5detect.c index e72d7a0..2b3df90 100644 --- a/src/H5detect.c +++ b/src/H5detect.c @@ -205,15 +205,12 @@ precision(detected_t *d) } /*------------------------------------------------------------------------- - * Function: DETECT_I/DETECT_BYTE + * Function: DETECT_I * - * Purpose: These macro takes a type like `int' and a base name like + * Purpose: This macro takes a type like `int' and a base name like * `nati' and detects the byte order. The VAR is used to * construct the names of the C variables defined. * - * DETECT_I is used for types that are larger than one byte, - * DETECT_BYTE is used for types that are exactly one byte. - * * Return: void * *------------------------------------------------------------------------- @@ -247,17 +244,8 @@ precision(detected_t *d) } \ } -#define DETECT_BYTE(TYPE, VAR, INFO) \ - { \ - HDcompile_assert(sizeof(TYPE) == 1); \ - \ - DETECT_I_BYTE_CORE(TYPE, VAR, INFO, int) \ - } - #define DETECT_I(TYPE, VAR, INFO) \ { \ - HDcompile_assert(sizeof(TYPE) > 1); \ - \ DETECT_I_BYTE_CORE(TYPE, VAR, INFO, TYPE) \ } @@ -1232,9 +1220,9 @@ bit.\n"; static void HDF_NO_UBSAN detect_C89_integers(void) { - DETECT_BYTE(signed char, SCHAR, d_g[nd_g]); + DETECT_I(signed char, SCHAR, d_g[nd_g]); nd_g++; - DETECT_BYTE(unsigned char, UCHAR, d_g[nd_g]); + DETECT_I(unsigned char, UCHAR, d_g[nd_g]); nd_g++; DETECT_I(short, SHORT, d_g[nd_g]); nd_g++; @@ -1278,17 +1266,17 @@ detect_C89_floats(void) static void HDF_NO_UBSAN detect_C99_integers8(void) { - DETECT_BYTE(int8_t, INT8, d_g[nd_g]); + DETECT_I(int8_t, INT8, d_g[nd_g]); nd_g++; - DETECT_BYTE(uint8_t, UINT8, d_g[nd_g]); + DETECT_I(uint8_t, UINT8, d_g[nd_g]); nd_g++; - DETECT_BYTE(int_least8_t, INT_LEAST8, d_g[nd_g]); + DETECT_I(int_least8_t, INT_LEAST8, d_g[nd_g]); nd_g++; - DETECT_BYTE(uint_least8_t, UINT_LEAST8, d_g[nd_g]); + DETECT_I(uint_least8_t, UINT_LEAST8, d_g[nd_g]); nd_g++; - DETECT_BYTE(int_fast8_t, INT_FAST8, d_g[nd_g]); + DETECT_I(int_fast8_t, INT_FAST8, d_g[nd_g]); nd_g++; - DETECT_BYTE(uint_fast8_t, UINT_FAST8, d_g[nd_g]); + DETECT_I(uint_fast8_t, UINT_FAST8, d_g[nd_g]); nd_g++; } diff --git a/test/app_ref.c b/test/app_ref.c index 2777dc0..c4ac60c 100644 --- a/test/app_ref.c +++ b/test/app_ref.c @@ -69,8 +69,10 @@ Abrt_Handler(int H5_ATTR_UNUSED sig) { int i, n; + const char *string = " ID reference count: "; for (i = 0; i < T_NUMCLASSES; i++) { - HDfprintf(stderr, "%s ID reference count: %n", IDNAME[i], &n); + HDfprintf(stderr, "%s%s", IDNAME[i], string); + n = (int)(strlen(IDNAME[i]) + strlen(string)); HDfprintf(stderr, "%*d\n", (n < ERR_WIDTH) ? (ERR_WIDTH - n) : 0, rc[i]); } } -- cgit v0.12 From 99d3962a831167298ebc087f0b8e8b6209034d95 Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Sat, 22 Jan 2022 08:40:33 -0600 Subject: Parallel rank0 deadlock fixes (#1183) * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- release_docs/RELEASE.txt | 12 ++++++ src/H5AC.c | 11 ++++-- src/H5ACmpio.c | 97 ++++++++++++++++++++++++++++++------------------ src/H5C.c | 42 +++++++++++++++++---- src/H5CX.c | 8 +--- src/H5Cimage.c | 3 ++ src/H5Dcontig.c | 13 +++++-- src/H5Dmpio.c | 12 +++++- src/H5FDmpio.c | 53 +++++++++++++++++++------- 9 files changed, 180 insertions(+), 71 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index d059fb3..bba27c9 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1083,6 +1083,18 @@ Bug Fixes since HDF5-1.12.0 release (DER - 2021/11/23, HDFFV-11286) + - Fixed several potential MPI deadlocks in library failure conditions + + In the parallel library, there were several places where MPI rank 0 + could end up skipping past collective MPI operations when some failure + occurs in rank 0-specific processing. This would lead to deadlocks + where rank 0 completes an operation while other ranks wait in the + collective operation. These places have been rewritten to have rank 0 + push an error and try to cleanup after the failure, then continue to + participate in the collective operation to the best of its ability. + + (JTH - 2021/11/09) + - Fixed an issue with collective metadata reads being permanently disabled after a dataset chunk lookup operation. This would usually cause a mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for diff --git a/src/H5AC.c b/src/H5AC.c index 6fbc63e..e20be3b 100644 --- a/src/H5AC.c +++ b/src/H5AC.c @@ -1636,9 +1636,14 @@ H5AC_unprotect(H5F_t *f, const H5AC_class_t *type, haddr_t addr, void *thing, un if (H5AC__log_dirtied_entry((H5AC_info_t *)thing) < 0) HGOTO_ERROR(H5E_CACHE, H5E_CANTUNPROTECT, FAIL, "can't log dirtied entry") - if (deleted && aux_ptr->mpi_rank == 0) - if (H5AC__log_deleted_entry((H5AC_info_t *)thing) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTUNPROTECT, FAIL, "H5AC__log_deleted_entry() failed") + if (deleted && aux_ptr->mpi_rank == 0) { + if (H5AC__log_deleted_entry((H5AC_info_t *)thing) < 0) { + /* If we fail to log the deleted entry, push an error but still + * participate in a possible sync point ahead + */ + HDONE_ERROR(H5E_CACHE, H5E_CANTUNPROTECT, FAIL, "H5AC__log_deleted_entry() failed") + } + } } /* end if */ #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5ACmpio.c b/src/H5ACmpio.c index dc155f5..7eaf751 100644 --- a/src/H5ACmpio.c +++ b/src/H5ACmpio.c @@ -304,8 +304,10 @@ H5AC__broadcast_candidate_list(H5AC_t *cache_ptr, unsigned *num_entries_ptr, had * are used to receiving from process 0, and also load it * into a buffer for transmission. */ - if (H5AC__copy_candidate_list_to_buffer(cache_ptr, &chk_num_entries, &haddr_buf_ptr) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't construct candidate buffer.") + if (H5AC__copy_candidate_list_to_buffer(cache_ptr, &chk_num_entries, &haddr_buf_ptr) < 0) { + /* Push an error, but still participate in following MPI_Bcast */ + HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't construct candidate buffer.") + } HDassert(chk_num_entries == num_entries); HDassert(haddr_buf_ptr != NULL); @@ -428,18 +430,23 @@ H5AC__broadcast_clean_list(H5AC_t *cache_ptr) /* allocate a buffer to store the list of entry base addresses in */ buf_size = sizeof(haddr_t) * num_entries; - if (NULL == (addr_buf_ptr = (haddr_t *)H5MM_malloc(buf_size))) - HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for addr buffer") - - /* Set up user data for callback */ - udata.aux_ptr = aux_ptr; - udata.addr_buf_ptr = addr_buf_ptr; - udata.u = 0; - - /* Free all the clean list entries, building the address list in the callback */ - /* (Callback also removes the matching entries from the dirtied list) */ - if (H5SL_free(aux_ptr->c_slist_ptr, H5AC__broadcast_clean_list_cb, &udata) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFREE, FAIL, "Can't build address list for clean entries") + if (NULL == (addr_buf_ptr = (haddr_t *)H5MM_malloc(buf_size))) { + /* Push an error, but still participate in following MPI_Bcast */ + HDONE_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for addr buffer") + } + else { + /* Set up user data for callback */ + udata.aux_ptr = aux_ptr; + udata.addr_buf_ptr = addr_buf_ptr; + udata.u = 0; + + /* Free all the clean list entries, building the address list in the callback */ + /* (Callback also removes the matching entries from the dirtied list) */ + if (H5SL_free(aux_ptr->c_slist_ptr, H5AC__broadcast_clean_list_cb, &udata) < 0) { + /* Push an error, but still participate in following MPI_Bcast */ + HDONE_ERROR(H5E_CACHE, H5E_CANTFREE, FAIL, "Can't build address list for clean entries") + } + } /* Now broadcast the list of cleaned entries */ if (MPI_SUCCESS != @@ -1448,8 +1455,10 @@ H5AC__receive_haddr_list(MPI_Comm mpi_comm, unsigned *num_entries_ptr, haddr_t * /* allocate buffers to store the list of entry base addresses in */ buf_size = sizeof(haddr_t) * num_entries; - if (NULL == (haddr_buf_ptr = (haddr_t *)H5MM_malloc(buf_size))) - HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for haddr buffer") + if (NULL == (haddr_buf_ptr = (haddr_t *)H5MM_malloc(buf_size))) { + /* Push an error, but still participate in following MPI_Bcast */ + HDONE_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for haddr buffer") + } /* Now receive the list of candidate entries */ if (MPI_SUCCESS != @@ -1800,10 +1809,14 @@ H5AC__rsp__dist_md_write__flush_to_min_clean(H5F_t *f) if (evictions_enabled) { /* construct candidate list -- process 0 only */ - if (aux_ptr->mpi_rank == 0) + if (aux_ptr->mpi_rank == 0) { + /* If constructing candidate list fails, push an error but still participate + * in collective operations during following candidate list propagation + */ if (H5AC__construct_candidate_list(cache_ptr, aux_ptr, H5AC_SYNC_POINT_OP__FLUSH_TO_MIN_CLEAN) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't construct candidate list.") + HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't construct candidate list.") + } /* propagate and apply candidate list -- all processes */ if (H5AC__propagate_and_apply_candidate_list(f) < 0) @@ -1899,15 +1912,21 @@ H5AC__rsp__p0_only__flush(H5F_t *f) aux_ptr->write_permitted = FALSE; /* Check for error on the write operation */ - if (result < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't flush.") - - /* this code exists primarily for the test bed -- it allows us to - * enforce POSIX semantics on the server that pretends to be a - * file system in our parallel tests. - */ - if (aux_ptr->write_done) - (aux_ptr->write_done)(); + if (result < 0) { + /* If write operation fails, push an error but still participate + * in collective operations during following cache entry + * propagation + */ + HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't flush.") + } + else { + /* this code exists primarily for the test bed -- it allows us to + * enforce POSIX semantics on the server that pretends to be a + * file system in our parallel tests. + */ + if (aux_ptr->write_done) + (aux_ptr->write_done)(); + } } /* end if */ /* Propagate cleaned entries to other ranks. */ @@ -2019,15 +2038,21 @@ H5AC__rsp__p0_only__flush_to_min_clean(H5F_t *f) aux_ptr->write_permitted = FALSE; /* Check for error on the write operation */ - if (result < 0) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "H5C_flush_to_min_clean() failed.") - - /* this call exists primarily for the test code -- it is used - * to enforce POSIX semantics on the process used to simulate - * reads and writes in t_cache.c. - */ - if (aux_ptr->write_done) - (aux_ptr->write_done)(); + if (result < 0) { + /* If write operation fails, push an error but still participate + * in collective operations during following cache entry + * propagation + */ + HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "H5C_flush_to_min_clean() failed.") + } + else { + /* this call exists primarily for the test code -- it is used + * to enforce POSIX semantics on the process used to simulate + * reads and writes in t_cache.c. + */ + if (aux_ptr->write_done) + (aux_ptr->write_done)(); + } } /* end if */ if (H5AC__propagate_flushed_and_still_clean_entries_list(f) < 0) diff --git a/src/H5C.c b/src/H5C.c index d34c650..889351d 100644 --- a/src/H5C.c +++ b/src/H5C.c @@ -2307,9 +2307,14 @@ H5C_protect(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *udata, unsign H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ - if (0 == mpi_rank) - if (H5C__generate_image(f, cache_ptr, entry_ptr) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, NULL, "can't generate entry's image") + if (0 == mpi_rank) { + if (H5C__generate_image(f, cache_ptr, entry_ptr) < 0) { + /* If image generation fails, push an error but + * still participate in the following MPI_Bcast + */ + HDONE_ERROR(H5E_CACHE, H5E_CANTGET, NULL, "can't generate entry's image") + } + } } /* end if */ HDassert(entry_ptr->image_ptr); @@ -7182,8 +7187,20 @@ H5C__load_entry(H5F_t *f, #ifdef H5_HAVE_PARALLEL if (!coll_access || 0 == mpi_rank) { #endif /* H5_HAVE_PARALLEL */ - if (H5F_block_read(f, type->mem_type, addr, len, image) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_READERROR, NULL, "Can't read image*") + + if (H5F_block_read(f, type->mem_type, addr, len, image) < 0) { + +#ifdef H5_HAVE_PARALLEL + if (coll_access) { + /* Push an error, but still participate in following MPI_Bcast */ + HDmemset(image, 0, len); + HDONE_ERROR(H5E_CACHE, H5E_READERROR, NULL, "Can't read image*") + } + else +#endif + HGOTO_ERROR(H5E_CACHE, H5E_READERROR, NULL, "Can't read image*") + } + #ifdef H5_HAVE_PARALLEL } /* end if */ /* if the collective metadata read optimization is turned on, @@ -7230,8 +7247,19 @@ H5C__load_entry(H5F_t *f, * loaded thing, go get the on-disk image again (the extra portion). */ if (H5F_block_read(f, type->mem_type, addr + len, actual_len - len, image + len) < - 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTLOAD, NULL, "can't read image") + 0) { + +#ifdef H5_HAVE_PARALLEL + if (coll_access) { + /* Push an error, but still participate in following MPI_Bcast */ + HDmemset(image + len, 0, actual_len - len); + HDONE_ERROR(H5E_CACHE, H5E_CANTLOAD, NULL, "can't read image") + } + else +#endif + HGOTO_ERROR(H5E_CACHE, H5E_CANTLOAD, NULL, "can't read image") + } + #ifdef H5_HAVE_PARALLEL } /* If the collective metadata read optimization is turned on, diff --git a/src/H5CX.c b/src/H5CX.c index b9ce682..89e4c91 100644 --- a/src/H5CX.c +++ b/src/H5CX.c @@ -1397,9 +1397,7 @@ H5CX_set_apl(hid_t *acspl_id, const H5P_libclass_t *libclass, /* If parallel is enabled and the file driver used is the MPI-IO * VFD, issue an MPI barrier for easier debugging if the API function - * calling this is supposed to be called collectively. Note that this - * happens only when the environment variable H5_COLL_BARRIER is set - * to non 0. + * calling this is supposed to be called collectively. */ if (H5_coll_api_sanity_check_g) { MPI_Comm mpi_comm; /* File communicator */ @@ -1456,9 +1454,7 @@ H5CX_set_loc(hid_t /* If parallel is enabled and the file driver used is the MPI-IO * VFD, issue an MPI barrier for easier debugging if the API function - * calling this is supposed to be called collectively. Note that this - * happens only when the environment variable H5_COLL_BARRIER is set - * to non 0. + * calling this is supposed to be called collectively. */ if (H5_coll_api_sanity_check_g) { MPI_Comm mpi_comm; /* File communicator */ diff --git a/src/H5Cimage.c b/src/H5Cimage.c index 7421c90..98c1291 100644 --- a/src/H5Cimage.c +++ b/src/H5Cimage.c @@ -997,6 +997,9 @@ H5C__read_cache_image(H5F_t *f, H5C_t *cache_ptr) #endif /* H5_HAVE_PARALLEL */ /* Read the buffer (if serial access, or rank 0 of parallel access) */ + /* NOTE: if this block read is being performed on rank 0 only, throwing + * an error here will cause other ranks to hang in the following MPI_Bcast. + */ if (H5F_block_read(f, H5FD_MEM_SUPER, cache_ptr->image_addr, cache_ptr->image_len, cache_ptr->image_buffer) < 0) HGOTO_ERROR(H5E_CACHE, H5E_READERROR, FAIL, "Can't read metadata cache image block") diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 2ace14b..3828e8e 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -278,9 +278,16 @@ H5D__contig_fill(const H5D_io_info_t *io_info) if (using_mpi) { /* Write the chunks out from only one process */ /* !! Use the internal "independent" DXPL!! -QAK */ - if (H5_PAR_META_WRITE == mpi_rank) - if (H5D__contig_write_one(&ioinfo, offset, size) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset") + if (H5_PAR_META_WRITE == mpi_rank) { + if (H5D__contig_write_one(&ioinfo, offset, size) < 0) { + /* If writing fails, push an error and stop writing, but + * still participate in following MPI_Barrier. + */ + blocks_written = TRUE; + HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset") + break; + } + } /* Indicate that blocks are being written */ blocks_written = TRUE; diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index f8bce33..cf8a6ef 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -2360,8 +2360,16 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") if (mpi_rank == 0) { - if (H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") + if (H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) { + size_t u; + + /* Clear total chunk address array */ + for (u = 0; u < (size_t)fm->layout->u.chunk.nchunks; u++) + total_chunk_addr_array[u] = HADDR_UNDEF; + + /* Push error, but still participate in following MPI_Bcast */ + HDONE_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") + } } /* end if */ /* Broadcasting the MPI_IO option info. and chunk address info. */ diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index c72578d..1feff43 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -864,14 +864,19 @@ H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR file->mpi_size = mpi_size; /* Only processor p0 will get the filesize and broadcast it. */ - if (mpi_rank == 0) + if (mpi_rank == 0) { + /* If MPI_File_get_size fails, broadcast file size as -1 to signal error */ if (MPI_SUCCESS != (mpi_code = MPI_File_get_size(fh, &file_size))) - HMPI_GOTO_ERROR(NULL, "MPI_File_get_size failed", mpi_code) + file_size = (MPI_Offset)-1; + } /* Broadcast file size */ if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&file_size, (int)sizeof(MPI_Offset), MPI_BYTE, 0, comm))) HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code) + if (file_size < 0) + HMPI_GOTO_ERROR(NULL, "MPI_File_get_size failed", mpi_code) + /* Determine if the file should be truncated */ if (file_size && (flags & H5F_ACC_TRUNC)) { /* Truncate the file */ @@ -1262,10 +1267,14 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU rank0_bcast = TRUE; /* Read on rank 0 Bcast to other ranks */ - if (file->mpi_rank == 0) + if (file->mpi_rank == 0) { + /* If MPI_File_read_at fails, push an error, but continue + * to participate in following MPI_Bcast */ if (MPI_SUCCESS != (mpi_code = MPI_File_read_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) - HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code) + HMPI_DONE_ERROR(FAIL, "MPI_File_read_at failed", mpi_code) + } + if (MPI_SUCCESS != (mpi_code = MPI_Bcast(buf, size_i, buf_type, 0, file->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) } /* end if */ @@ -1309,11 +1318,21 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if (!rank0_bcast || (rank0_bcast && file->mpi_rank == 0)) { /* How many bytes were actually read? */ #if MPI_VERSION >= 3 - if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&mpi_stat, buf_type, &bytes_read))) + if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&mpi_stat, buf_type, &bytes_read))) { #else - if (MPI_SUCCESS != (mpi_code = MPI_Get_elements(&mpi_stat, MPI_BYTE, &bytes_read))) + if (MPI_SUCCESS != (mpi_code = MPI_Get_elements(&mpi_stat, MPI_BYTE, &bytes_read))) { #endif - HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code) + if (rank0_bcast && file->mpi_rank == 0) { + /* If MPI_Get_elements(_x) fails for a rank 0 bcast strategy, + * push an error, but continue to participate in the following + * MPI_Bcast. + */ + bytes_read = -1; + HMPI_DONE_ERROR(FAIL, "MPI_Get_elements failed", mpi_code) + } + else + HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code) + } } /* end if */ /* If the rank0-bcast feature was used, broadcast the # of bytes read to @@ -1703,17 +1722,19 @@ H5FD__mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) /* Only processor p0 will get the filesize and broadcast it. */ - /* (Note that throwing an error here will cause non-rank 0 processes - * to hang in following Bcast. -QAK, 3/17/2018) - */ - if (0 == file->mpi_rank) + if (0 == file->mpi_rank) { + /* If MPI_File_get_size fails, broadcast file size as -1 to signal error */ if (MPI_SUCCESS != (mpi_code = MPI_File_get_size(file->f, &size))) - HMPI_GOTO_ERROR(FAIL, "MPI_File_get_size failed", mpi_code) + size = (MPI_Offset)-1; + } /* Broadcast file size */ if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&size, (int)sizeof(MPI_Offset), MPI_BYTE, 0, file->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) + if (size < 0) + HMPI_GOTO_ERROR(FAIL, "MPI_File_get_size failed", mpi_code) + if (H5FD_mpi_haddr_to_MPIOff(file->eoa, &needed_eof) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "cannot convert from haddr_t to MPI_Offset") @@ -1796,9 +1817,13 @@ H5FD__mpio_delete(const char *filename, hid_t fapl_id) HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) /* Delete the file */ - if (mpi_rank == 0) + if (mpi_rank == 0) { + /* If MPI_File_delete fails, push an error but + * still participate in the following MPI_Barrier + */ if (MPI_SUCCESS != (mpi_code = MPI_File_delete(filename, info))) - HMPI_GOTO_ERROR(FAIL, "MPI_File_delete failed", mpi_code) + HMPI_DONE_ERROR(FAIL, "MPI_File_delete failed", mpi_code) + } /* Set up a barrier (don't want processes to run ahead of the delete) */ if (MPI_SUCCESS != (mpi_code = MPI_Barrier(comm))) -- cgit v0.12 From 4d45d05078fb1f67cc449fd5a6826c6dcfe55bfe Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Mon, 24 Jan 2022 07:46:17 -0600 Subject: Fix cmake dynamic analysis on windows (#1373) * Fix sanitizer flag form on windows * Add search paths to windows code-coverage --- config/sanitizer/code-coverage.cmake | 15 +++++++++++---- config/sanitizer/sanitizers.cmake | 11 ++++++++++- 2 files changed, 21 insertions(+), 5 deletions(-) diff --git a/config/sanitizer/code-coverage.cmake b/config/sanitizer/code-coverage.cmake index c79aeac..e71bfd7 100644 --- a/config/sanitizer/code-coverage.cmake +++ b/config/sanitizer/code-coverage.cmake @@ -80,10 +80,17 @@ option( OFF) # Programs -find_program(LLVM_COV_PATH llvm-cov) -find_program(LLVM_PROFDATA_PATH llvm-profdata) -find_program(LCOV_PATH lcov) -find_program(GENHTML_PATH genhtml) +if(WIN32) + find_program(LLVM_COV_PATH llvm-cov PATHS ENV VS2019INSTALLDIR PATH_SUFFIXES "VC/Tools/Llvm/x64/bin") + find_program(LLVM_PROFDATA_PATH llvm-profdata PATHS ENV VS2019INSTALLDIR PATH_SUFFIXES "VC/Tools/Llvm/x64/bin") + find_program(LCOV_PATH lcov PATHS ENV VS2019INSTALLDIR PATH_SUFFIXES "VC/Tools/Llvm/x64/bin") + find_program(GENHTML_PATH genhtml PATHS ENV VS2019INSTALLDIR PATH_SUFFIXES "VC/Tools/Llvm/x64/bin") +else() + find_program(LLVM_COV_PATH llvm-cov) + find_program(LLVM_PROFDATA_PATH llvm-profdata) + find_program(LCOV_PATH lcov) + find_program(GENHTML_PATH genhtml) +endif() # Variables set(CMAKE_COVERAGE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/ccov) diff --git a/config/sanitizer/sanitizers.cmake b/config/sanitizer/sanitizers.cmake index 8bf1d5b..b06992f 100644 --- a/config/sanitizer/sanitizers.cmake +++ b/config/sanitizer/sanitizers.cmake @@ -83,12 +83,21 @@ if(USE_SANITIZER) elseif(MSVC) if(USE_SANITIZER MATCHES "([Aa]ddress)") message(STATUS "Building with Address sanitizer") - append("/fsanitize=address" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS) + append("-fsanitize=address" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS) else() message(FATAL_ERROR "This sanitizer not yet supported in the MSVC environment: ${USE_SANITIZER}") endif() else() message(FATAL_ERROR "USE_SANITIZER is not supported on this platform.") endif() + elseif(MSVC) + if(USE_SANITIZER MATCHES "([Aa]ddress)") + message(STATUS "Building with Address sanitizer") + append("/fsanitize=address" CMAKE_C_SANITIZER_FLAGS CMAKE_CXX_SANITIZER_FLAGS) + else() + message(FATAL_ERROR "This sanitizer not yet supported in the MSVC environment: ${USE_SANITIZER}") + endif() + else() + message(FATAL_ERROR "USE_SANITIZER is not supported on this platform.") endif() endif() -- cgit v0.12 From 5222abdd19c6636aad659ab47c29a77c631ee4ba Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed, 26 Jan 2022 09:05:25 -0600 Subject: Update code owners file with more names (#1386) --- .github/CODEOWNERS | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 29e5866..99daf78 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -7,36 +7,36 @@ # Order is important. The last matching pattern has the most precedence. # So if a pull request only touches javascript files, only these owners # will be requested to review. -*.cmake @byrnHDF @derobins -CMakeLists.txt @byrnHDF @derobins -CMakeTests.* @byrnHDF @derobins +*.cmake @byrnHDF @ChristopherHogan @gnuoyd @derobins +CMakeLists.txt @byrnHDF @ChristopherHogan @gnuoyd @derobins +CMakeTests.* @byrnHDF @ChristopherHogan @gnuoyd @derobins -/bin/ @lrknox @derobins @qkoziol +/bin/ @lrknox @ChristopherHogan @gnuoyd @derobins @qkoziol -/c++/ @bmribler @byrnHDF @derobins +/c++/ @bmribler @byrnHDF @ChristopherHogan @gnuoyd @derobins -/config/ @lrknox @derobins @qkoziol @byrnHDF +/config/ @lrknox @byrnHDF @ChristopherHogan @gnuoyd @derobins @qkoziol -/doc/ @gnuoyd @jrmainzer +/doc/ @ChristopherHogan @gnuoyd @jrmainzer -/examples/ @lrknox @derobins @bmribler +/examples/ @lrknox @bmribler @ChristopherHogan @gnuoyd @derobins /fortran/ @brtnfld @epourmal -/hl/ @bmribler @byrnHDF @derobins +/hl/ @bmribler @byrnHDF @ChristopherHogan @gnuoyd @derobins /java/ @jhendersonHDF @byrnHDF -/m4/ @lrknox @derobins +/m4/ @lrknox @ChristopherHogan @gnuoyd @derobins /release_docs/ @lrknox @bmribler @byrnHDF -/src/ @jhendersonHDF @derobins @fortnern @qkoziol @soumagne @vchoi-hdfgroup @jrmainzer +/src/ @jhendersonHDF @fortnern @soumagne @vchoi-hdfgroup @ChristopherHogan @gnuoyd @derobins @jrmainzer @qkoziol -/test/ @jhendersonHDF @derobins @fortnern @qkoziol @soumagne @vchoi-hdfgroup @jrmainzer +/test/ @jhendersonHDF @fortnern @soumagne @vchoi-hdfgroup @ChristopherHogan @gnuoyd @derobins @jrmainzer @qkoziol -/testpar/ @jhendersonHDF @rawarren @jrmainzer @qkoziol +/testpar/ @jhendersonHDF @ChristopherHogan @gnuoyd @jrmainzer @qkoziol -/tools/ @byrnHDF @bmribler @derobins +/tools/ @byrnHDF @bmribler @ChristopherHogan @gnuoyd @derobins -/utils/ @lrknox @byrnHDF @derobins +/utils/ @lrknox @byrnHDF @ChristopherHogan @gnuoyd @derobins -- cgit v0.12 From 5fb634ca26ce165bb09c5c920f345e546251876c Mon Sep 17 00:00:00 2001 From: Larry Knox Date: Wed, 26 Jan 2022 16:58:49 -0600 Subject: Revert 61464d7e (#1396) Commit 61464d7e was a fix for a compiler error on OpenBSD where int_fast8_t is in fact larger than 1 byte. However, the changes broke H5detect.c generation of H5Tinit.c on Power8 big-endian, and probably on all big-endian machines. Switching DETECT_BYTE to DETECT_I for 8 byte types doesn't work on our big-endian Power8 machine because switching the last parameter of DETECT_I_BYTE_CORE from "int" to the 8 byte type incorrectly sets dt->shared->u.atomic.order = H5T_ORDER_LE on a big-endian machine. A different fix to accomodate both big-endian and OpenBSD is needed. See commit 61464d7e for OpenBSD info. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- src/H5detect.c | 32 ++++++++++++++++++++++---------- 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/src/H5detect.c b/src/H5detect.c index 2b3df90..e72d7a0 100644 --- a/src/H5detect.c +++ b/src/H5detect.c @@ -205,12 +205,15 @@ precision(detected_t *d) } /*------------------------------------------------------------------------- - * Function: DETECT_I + * Function: DETECT_I/DETECT_BYTE * - * Purpose: This macro takes a type like `int' and a base name like + * Purpose: These macro takes a type like `int' and a base name like * `nati' and detects the byte order. The VAR is used to * construct the names of the C variables defined. * + * DETECT_I is used for types that are larger than one byte, + * DETECT_BYTE is used for types that are exactly one byte. + * * Return: void * *------------------------------------------------------------------------- @@ -244,8 +247,17 @@ precision(detected_t *d) } \ } +#define DETECT_BYTE(TYPE, VAR, INFO) \ + { \ + HDcompile_assert(sizeof(TYPE) == 1); \ + \ + DETECT_I_BYTE_CORE(TYPE, VAR, INFO, int) \ + } + #define DETECT_I(TYPE, VAR, INFO) \ { \ + HDcompile_assert(sizeof(TYPE) > 1); \ + \ DETECT_I_BYTE_CORE(TYPE, VAR, INFO, TYPE) \ } @@ -1220,9 +1232,9 @@ bit.\n"; static void HDF_NO_UBSAN detect_C89_integers(void) { - DETECT_I(signed char, SCHAR, d_g[nd_g]); + DETECT_BYTE(signed char, SCHAR, d_g[nd_g]); nd_g++; - DETECT_I(unsigned char, UCHAR, d_g[nd_g]); + DETECT_BYTE(unsigned char, UCHAR, d_g[nd_g]); nd_g++; DETECT_I(short, SHORT, d_g[nd_g]); nd_g++; @@ -1266,17 +1278,17 @@ detect_C89_floats(void) static void HDF_NO_UBSAN detect_C99_integers8(void) { - DETECT_I(int8_t, INT8, d_g[nd_g]); + DETECT_BYTE(int8_t, INT8, d_g[nd_g]); nd_g++; - DETECT_I(uint8_t, UINT8, d_g[nd_g]); + DETECT_BYTE(uint8_t, UINT8, d_g[nd_g]); nd_g++; - DETECT_I(int_least8_t, INT_LEAST8, d_g[nd_g]); + DETECT_BYTE(int_least8_t, INT_LEAST8, d_g[nd_g]); nd_g++; - DETECT_I(uint_least8_t, UINT_LEAST8, d_g[nd_g]); + DETECT_BYTE(uint_least8_t, UINT_LEAST8, d_g[nd_g]); nd_g++; - DETECT_I(int_fast8_t, INT_FAST8, d_g[nd_g]); + DETECT_BYTE(int_fast8_t, INT_FAST8, d_g[nd_g]); nd_g++; - DETECT_I(uint_fast8_t, UINT_FAST8, d_g[nd_g]); + DETECT_BYTE(uint_fast8_t, UINT_FAST8, d_g[nd_g]); nd_g++; } -- cgit v0.12 From 44de59b642c4d5ccf505a1072d10b63dc9fe0628 Mon Sep 17 00:00:00 2001 From: Sean McBride Date: Fri, 28 Jan 2022 09:31:26 -0500 Subject: Used clang-tidy to change all floating point f suffixes to F (#1359) --- c++/test/tattr.cpp | 2 +- c++/test/th5s.cpp | 2 +- hl/test/test_image.c | 6 +++--- src/H5Tconv.c | 2 +- test/dtypes.c | 2 +- tools/test/h5repack/h5repackgentest.c | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/c++/test/tattr.cpp b/c++/test/tattr.cpp index 26699d2..5627341 100644 --- a/c++/test/tattr.cpp +++ b/c++/test/tattr.cpp @@ -95,7 +95,7 @@ struct attr4_struct { const H5std_string ATTR5_NAME("Attr5"); const int ATTR5_RANK = 0; -float attr_data5 = -5.123f; // Test data for 5th attribute +float attr_data5 = -5.123F; // Test data for 5th attribute /* Info for another attribute */ const H5std_string ATTR1A_NAME("Attr1_a"); diff --git a/c++/test/th5s.cpp b/c++/test/th5s.cpp index 5808136..461d258 100644 --- a/c++/test/th5s.cpp +++ b/c++/test/th5s.cpp @@ -73,7 +73,7 @@ struct space4_struct { unsigned u; float f; char c2; -} space4_data = {'v', 987123, -3.14f, 'g'}; /* Test data for 4th dataspace */ +} space4_data = {'v', 987123, -3.14F, 'g'}; /* Test data for 4th dataspace */ /* Null dataspace */ int space5_data = 7; diff --git a/hl/test/test_image.c b/hl/test/test_image.c index 2251a04..4997df6 100644 --- a/hl/test/test_image.c +++ b/hl/test/test_image.c @@ -650,7 +650,7 @@ test_generate(void) HL_TESTING2("make indexed image from land data"); for (i = 0; i < n_elements; i++) { - if (data[i] < 0.0f) + if (data[i] < 0.0F) image_data[i] = 0; else image_data[i] = (unsigned char)((255 * data[i]) / xmax); @@ -671,10 +671,10 @@ test_generate(void) HL_TESTING2("make indexed image from sea data"); for (i = 0; i < n_elements; i++) { - if (data[i] > 0.0f) + if (data[i] > 0.0F) image_data[i] = 0; else { - image_data[i] = (unsigned char)((255.0f * (data[i] - xmin)) / (xmax - xmin)); + image_data[i] = (unsigned char)((255.0F * (data[i] - xmin)) / (xmax - xmin)); } } diff --git a/src/H5Tconv.c b/src/H5Tconv.c index 94697af..5efff10 100644 --- a/src/H5Tconv.c +++ b/src/H5Tconv.c @@ -2753,7 +2753,7 @@ H5T__conv_enum_init(H5T_t *src, H5T_t *dst, H5T_cdata_t *cdata) HDassert(domain[1] >= domain[0]); length = (unsigned)(domain[1] - domain[0]) + 1; if (src->shared->u.enumer.nmembs < 2 || - (double)length / src->shared->u.enumer.nmembs < (double)(1.2f)) { + (double)length / src->shared->u.enumer.nmembs < (double)(1.2F)) { priv->base = domain[0]; priv->length = length; if (NULL == (map = (int *)H5MM_malloc(length * sizeof(int)))) diff --git a/test/dtypes.c b/test/dtypes.c index 5a4f2d6..a6b2beb 100644 --- a/test/dtypes.c +++ b/test/dtypes.c @@ -2635,7 +2635,7 @@ test_compound_13(void) HDmemset(&data_out, 0, sizeof(data_out)); for (u = 0; u < COMPOUND13_ARRAY_SIZE + 1; u++) data_out.x[u] = (unsigned char)u; - data_out.y = 99.99f; + data_out.y = 99.99F; /* Set latest_format in access property list to enable the latest * compound datatype format. diff --git a/tools/test/h5repack/h5repackgentest.c b/tools/test/h5repack/h5repackgentest.c index b026cc0..c025891 100644 --- a/tools/test/h5repack/h5repackgentest.c +++ b/tools/test/h5repack/h5repackgentest.c @@ -307,7 +307,7 @@ generate_f32le(hbool_t external) /* Generate values */ for (i = 0, k = 0, n = 0; (hsize_t)i < dims[0]; i++) { for (j = 0; (hsize_t)j < dims[1]; j++, k++, n++) { - wdata[k] = n * 801.1f * ((k % 5 == 1) ? (-1) : (1)); + wdata[k] = n * 801.1F * ((k % 5 == 1) ? (-1) : (1)); } } -- cgit v0.12 From b5eed1b56324fc07154c2e2d8251d2b87505ca23 Mon Sep 17 00:00:00 2001 From: Sean McBride Date: Fri, 28 Jan 2022 11:34:57 -0500 Subject: Replaced several uses of sprintf with safer snprintf (#1383) * Replaced several uses of sprintf with safer snprintf * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- c++/test/tattr.cpp | 6 +++--- c++/test/titerate.cpp | 2 +- c++/test/tvlstr.cpp | 10 +++++----- config/cmake_ext_mod/HDFTests.c | 4 ++-- configure.ac | 2 +- examples/ph5example.c | 2 +- hl/tools/gif2h5/writehdf.c | 2 +- hl/tools/h5watch/h5watch.c | 4 ++-- src/H5AC.c | 2 +- src/H5Dchunk.c | 4 ++-- src/H5Dearray.c | 4 ++-- src/H5Dfarray.c | 4 ++-- src/H5EAdbg.c | 6 +++--- src/H5EAtest.c | 2 +- src/H5FAtest.c | 2 +- src/H5FDmulti.c | 6 +++--- src/H5RS.c | 2 +- src/H5VLpassthru.c | 13 +++++-------- src/H5private.h | 2 +- test/chunk_info.c | 2 +- test/flush1.c | 2 +- test/flush2.c | 2 +- test/unregister.c | 2 +- tools/test/perform/direct_write_perf.c | 2 +- 24 files changed, 43 insertions(+), 46 deletions(-) diff --git a/c++/test/tattr.cpp b/c++/test/tattr.cpp index 5627341..dc968f9 100644 --- a/c++/test/tattr.cpp +++ b/c++/test/tattr.cpp @@ -1782,7 +1782,7 @@ test_attr_dense_create(FileCreatPropList &fcpl, FileAccPropList &fapl) unsigned attr_num; for (attr_num = 0; attr_num < max_compact; attr_num++) { // Create attribute - sprintf(attr_name, "attr %02u", attr_num); + snprintf(attr_name, sizeof(attr_name), "attr %02u", attr_num); Attribute attr = dataset.createAttribute(attr_name, PredType::NATIVE_UINT, ds_space); // Write data to the attribute @@ -1794,7 +1794,7 @@ test_attr_dense_create(FileCreatPropList &fcpl, FileAccPropList &fapl) { // Add one more attribute, to push into "dense" storage // Create another attribute - sprintf(attr_name, "attr %02u", attr_num); + snprintf(attr_name, sizeof(attr_name), "attr %02u", attr_num); Attribute attr = dataset.createAttribute(attr_name, PredType::NATIVE_UINT, ds_space); // Write data to the attribute @@ -1804,7 +1804,7 @@ test_attr_dense_create(FileCreatPropList &fcpl, FileAccPropList &fapl) // Attempt to add attribute again, which should fail try { // Create another attribute - sprintf(attr_name, "attr %02u", attr_num); + snprintf(attr_name, sizeof(attr_name), "attr %02u", attr_num); Attribute attr = dataset.createAttribute(attr_name, PredType::NATIVE_UINT, ds_space); // continuation here, that means no exception has been thrown diff --git a/c++/test/titerate.cpp b/c++/test/titerate.cpp index b6a9436..bc4d892 100644 --- a/c++/test/titerate.cpp +++ b/c++/test/titerate.cpp @@ -160,7 +160,7 @@ test_iter_group(FileAccPropList &fapl) DataSpace filespace; for (int i = 0; i < NDATASETS; i++) { - sprintf(name, "Dataset %d", i); + snprintf(name, sizeof(name), "Dataset %d", i); // Create a dataset in the file DataSet dataset = file.createDataSet(name, datatype, filespace); diff --git a/c++/test/tvlstr.cpp b/c++/test/tvlstr.cpp index c91b566..405ca07 100644 --- a/c++/test/tvlstr.cpp +++ b/c++/test/tvlstr.cpp @@ -917,32 +917,32 @@ test_vl_rewrite() int i; char name[256]; // Buffer for names & data for (i = 0; i < REWRITE_NDATASETS; i++) { - sprintf(name, "/set_%d", i); + snprintf(name, sizeof(name), "/set_%d", i); write_scalar_dset(file1, type, space, name, name); } // Effectively copy data from file 1 to 2. for (i = 0; i < REWRITE_NDATASETS; i++) { - sprintf(name, "/set_%d", i); + snprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file1, type, space, name, name); write_scalar_dset(file2, type, space, name, name); } // Read back from file 2. for (i = 0; i < REWRITE_NDATASETS; i++) { - sprintf(name, "/set_%d", i); + snprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file2, type, space, name, name); } // Remove from file 2. for (i = 0; i < REWRITE_NDATASETS; i++) { - sprintf(name, "/set_%d", i); + snprintf(name, sizeof(name), "/set_%d", i); file2.unlink(name); } // Effectively copy from file 1 to file 2. for (i = 0; i < REWRITE_NDATASETS; i++) { - sprintf(name, "/set_%d", i); + snprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file1, type, space, name, name); write_scalar_dset(file2, type, space, name, name); } diff --git a/config/cmake_ext_mod/HDFTests.c b/config/cmake_ext_mod/HDFTests.c index c434be5..2b2a202 100644 --- a/config/cmake_ext_mod/HDFTests.c +++ b/config/cmake_ext_mod/HDFTests.c @@ -115,8 +115,8 @@ int main(void) for (currentArg = llwidthArgs; *currentArg != NULL; currentArg++) { char formatString[64]; - sprintf(formatString, "%%%sd", *currentArg); - sprintf(s, formatString, x); + snprintf(formatString, sizeof(formatString), "%%%sd", *currentArg); + snprintf(s, 128, formatString, x); if (strcmp(s, "1099511627776") == 0) { printf("PRINTF_LL_WIDTH=[%s]\n", *currentArg); diff --git a/configure.ac b/configure.ac index 8d7f359..4cf329c 100644 --- a/configure.ac +++ b/configure.ac @@ -2154,7 +2154,7 @@ for hdf5_cv_printf_ll in ll l L q unknown; do ],[[ char *s = malloc(128); long long x = (long long)1048576 * (long long)1048576; - sprintf(s,"%${hdf5_cv_printf_ll}d",x); + snprintf(s,128,"%${hdf5_cv_printf_ll}d",x); exit(strcmp(s,"1099511627776")); ]])] , [break],,[continue]) diff --git a/examples/ph5example.c b/examples/ph5example.c index 87632e5..23af477 100644 --- a/examples/ph5example.c +++ b/examples/ph5example.c @@ -934,7 +934,7 @@ mkfilenames(char *prefix) "Need to adjust the code to accommodate the large size.\n"); } for (i = 0; i < n; i++) { - sprintf(testfiles[i], "%s/ParaEg%d.h5", prefix, i); + snprintf(testfiles[i], PATH_MAX, "%s/ParaEg%d.h5", prefix, i); } return (0); } diff --git a/hl/tools/gif2h5/writehdf.c b/hl/tools/gif2h5/writehdf.c index c321519..b49e2a6 100644 --- a/hl/tools/gif2h5/writehdf.c +++ b/hl/tools/gif2h5/writehdf.c @@ -100,7 +100,7 @@ WriteHDF(GIFTOMEM GifMemoryStruct, char *HDFName) dims[1] = gifImageDesc->ImageWidth; /* create the image name */ - sprintf(ImageName, "Image%d", i); + snprintf(ImageName, sizeof(ImageName), "Image%d", i); /* write image */ if (H5IMmake_image_8bit(file_id, ImageName, dims[1], dims[0], (gifImageDesc->Image)) < 0) diff --git a/hl/tools/h5watch/h5watch.c b/hl/tools/h5watch/h5watch.c index c897c91..94ca4f1 100644 --- a/hl/tools/h5watch/h5watch.c +++ b/hl/tools/h5watch/h5watch.c @@ -174,9 +174,9 @@ doprint(hid_t did, const hsize_t *start, const hsize_t *block, int rank) } /* end else */ /* Floating point types should display full precision */ - sprintf(fmt_float, "%%1.%dg", FLT_DIG); + snprintf(fmt_float, sizeof(fmt_float), "%%1.%dg", FLT_DIG); info.fmt_float = fmt_float; - sprintf(fmt_double, "%%1.%dg", DBL_DIG); + snprintf(fmt_double, sizeof(fmt_double), "%%1.%dg", DBL_DIG); info.fmt_double = fmt_double; info.dset_format = "DSET-%s "; diff --git a/src/H5AC.c b/src/H5AC.c index e20be3b..47d3a65 100644 --- a/src/H5AC.c +++ b/src/H5AC.c @@ -303,7 +303,7 @@ H5AC_create(const H5F_t *f, H5AC_cache_config_t *config_ptr, H5AC_cache_image_co aux_ptr->sync_point_done = NULL; aux_ptr->p0_image_len = 0; - HDsprintf(prefix, "%d:", mpi_rank); + HDsnprintf(prefix, sizeof(prefix), "%d:", mpi_rank); if (mpi_rank == 0) { if (NULL == (aux_ptr->d_slist_ptr = H5SL_create(H5SL_TYPE_HADDR, NULL))) diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index b85b194..5d7c1b2 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -6696,10 +6696,10 @@ H5D__chunk_stats(const H5D_t *dset, hbool_t headers) miss_rate = 0.0; } if (miss_rate > 100) { - HDsprintf(ascii, "%7d%%", (int)(miss_rate + 0.5)); + HDsnprintf(ascii, sizeof(ascii), "%7d%%", (int)(miss_rate + 0.5)); } else { - HDsprintf(ascii, "%7.2f%%", miss_rate); + HDsnprintf(ascii, sizeof(ascii), "%7.2f%%", miss_rate); } HDfprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", "raw data chunks", rdcc->stats.nhits, diff --git a/src/H5Dearray.c b/src/H5Dearray.c index abce233..cd52b66 100644 --- a/src/H5Dearray.c +++ b/src/H5Dearray.c @@ -417,7 +417,7 @@ H5D__earray_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void HDassert(elmt); /* Print element */ - HDsprintf(temp_str, "Element #%" PRIuHSIZE ":", idx); + HDsnprintf(temp_str, sizeof(temp_str), "Element #%" PRIuHSIZE ":", idx); HDfprintf(stream, "%*s%-*s %" PRIuHADDR "\n", indent, "", fwidth, temp_str, *(const haddr_t *)elmt); FUNC_LEAVE_NOAPI(SUCCEED) @@ -573,7 +573,7 @@ H5D__earray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const HDassert(elmt); /* Print element */ - HDsprintf(temp_str, "Element #%" PRIuHSIZE ":", idx); + HDsnprintf(temp_str, sizeof(temp_str), "Element #%" PRIuHSIZE ":", idx); HDfprintf(stream, "%*s%-*s {%" PRIuHADDR ", %u, %0x}\n", indent, "", fwidth, temp_str, elmt->addr, elmt->nbytes, elmt->filter_mask); diff --git a/src/H5Dfarray.c b/src/H5Dfarray.c index 0741e8f..ab0f0f8 100644 --- a/src/H5Dfarray.c +++ b/src/H5Dfarray.c @@ -415,7 +415,7 @@ H5D__farray_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void HDassert(elmt); /* Print element */ - HDsprintf(temp_str, "Element #%" PRIuHSIZE ":", idx); + HDsnprintf(temp_str, sizeof(temp_str), "Element #%" PRIuHSIZE ":", idx); HDfprintf(stream, "%*s%-*s %" PRIuHADDR "\n", indent, "", fwidth, temp_str, *(const haddr_t *)elmt); FUNC_LEAVE_NOAPI(SUCCEED) @@ -675,7 +675,7 @@ H5D__farray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const HDassert(elmt); /* Print element */ - HDsprintf(temp_str, "Element #%" PRIuHSIZE ":", idx); + HDsnprintf(temp_str, sizeof(temp_str), "Element #%" PRIuHSIZE ":", idx); HDfprintf(stream, "%*s%-*s {%" PRIuHADDR ", %u, %0x}\n", indent, "", fwidth, temp_str, elmt->addr, elmt->nbytes, elmt->filter_mask); diff --git a/src/H5EAdbg.c b/src/H5EAdbg.c index b0e564c..b377422 100644 --- a/src/H5EAdbg.c +++ b/src/H5EAdbg.c @@ -237,7 +237,7 @@ H5EA__iblock_debug(H5F_t *f, haddr_t H5_ATTR_UNUSED addr, FILE *stream, int inde HDfprintf(stream, "%*sData Block Addresses in Index Block:\n", indent, ""); for (u = 0; u < iblock->ndblk_addrs; u++) { /* Print address */ - HDsprintf(temp_str, "Address #%u:", u); + HDsnprintf(temp_str, sizeof(temp_str), "Address #%u:", u); HDfprintf(stream, "%*s%-*s %" PRIuHADDR "\n", (indent + 3), "", MAX(0, (fwidth - 3)), temp_str, iblock->dblk_addrs[u]); } /* end for */ @@ -252,7 +252,7 @@ H5EA__iblock_debug(H5F_t *f, haddr_t H5_ATTR_UNUSED addr, FILE *stream, int inde HDfprintf(stream, "%*sSuper Block Addresses in Index Block:\n", indent, ""); for (u = 0; u < iblock->nsblk_addrs; u++) { /* Print address */ - HDsprintf(temp_str, "Address #%u:", u); + HDsnprintf(temp_str, sizeof(temp_str), "Address #%u:", u); HDfprintf(stream, "%*s%-*s %" PRIuHADDR "\n", (indent + 3), "", MAX(0, (fwidth - 3)), temp_str, iblock->sblk_addrs[u]); } /* end for */ @@ -341,7 +341,7 @@ H5EA__sblock_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, int fwidth, HDfprintf(stream, "%*sData Block Addresses in Super Block:\n", indent, ""); for (u = 0; u < sblock->ndblks; u++) { /* Print address */ - HDsprintf(temp_str, "Address #%u:", u); + HDsnprintf(temp_str, sizeof(temp_str), "Address #%u:", u); HDfprintf(stream, "%*s%-*s %" PRIuHADDR "\n", (indent + 3), "", MAX(0, (fwidth - 3)), temp_str, sblock->dblk_addrs[u]); } /* end for */ diff --git a/src/H5EAtest.c b/src/H5EAtest.c index 7924eaa..24efbc2 100644 --- a/src/H5EAtest.c +++ b/src/H5EAtest.c @@ -322,7 +322,7 @@ H5EA__test_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void * HDassert(elmt); /* Print element */ - HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsnprintf(temp_str, sizeof(temp_str), "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %llu\n", indent, "", fwidth, temp_str, (unsigned long long)*(const uint64_t *)elmt); diff --git a/src/H5FAtest.c b/src/H5FAtest.c index 384a657..b57f562 100644 --- a/src/H5FAtest.c +++ b/src/H5FAtest.c @@ -303,7 +303,7 @@ H5FA__test_debug(FILE *stream, int indent, int fwidth, hsize_t idx, const void * HDassert(elmt); /* Print element */ - HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsnprintf(temp_str, sizeof(temp_str), "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %llu\n", indent, "", fwidth, temp_str, (unsigned long long)*(const uint64_t *)elmt); diff --git a/src/H5FDmulti.c b/src/H5FDmulti.c index 3dcfa37..d9a6ce9 100644 --- a/src/H5FDmulti.c +++ b/src/H5FDmulti.c @@ -517,7 +517,7 @@ H5FD_split_populate_config(const char *meta_ext, hid_t meta_plist_id, const char meta_name_g[sizeof(meta_name_g) - 1] = '\0'; } else - sprintf(meta_name_g, "%%s%s", meta_ext); + snprintf(meta_name_g, sizeof(meta_name_g), "%%s%s", meta_ext); } else { strncpy(meta_name_g, "%s.meta", sizeof(meta_name_g)); @@ -535,7 +535,7 @@ H5FD_split_populate_config(const char *meta_ext, hid_t meta_plist_id, const char raw_name_g[sizeof(raw_name_g) - 1] = '\0'; } else - sprintf(raw_name_g, "%%s%s", raw_ext); + snprintf(raw_name_g, sizeof(raw_name_g), "%%s%s", raw_ext); } else { strncpy(raw_name_g, "%s.raw", sizeof(raw_name_g)); @@ -634,7 +634,7 @@ H5FD_multi_populate_config(const H5FD_mem_t *memb_map, const hid_t *memb_fapl, c if (!memb_name) { assert(strlen(letters) == H5FD_MEM_NTYPES); for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt = (H5FD_mem_t)(mt + 1)) { - sprintf(_memb_name_g[mt], "%%s-%c.h5", letters[mt]); + snprintf(_memb_name_g[mt], 16, "%%s-%c.h5", letters[mt]); _memb_name_ptrs[mt] = _memb_name_g[mt]; } memb_name = _memb_name_ptrs; diff --git a/src/H5RS.c b/src/H5RS.c index 117c8ea..16c2356 100644 --- a/src/H5RS.c +++ b/src/H5RS.c @@ -350,7 +350,7 @@ done: */ /* Disable warning for "format not a string literal" here -QAK */ /* - * This pragma only needs to surround the sprintf() calls with + * This pragma only needs to surround the snprintf() calls with * format_templ in the code below, but early (4.4.7, at least) gcc only * allows diagnostic pragmas to be toggled outside of functions. */ diff --git a/src/H5VLpassthru.c b/src/H5VLpassthru.c index 6b4c59f..6eda875 100644 --- a/src/H5VLpassthru.c +++ b/src/H5VLpassthru.c @@ -641,16 +641,13 @@ H5VL_pass_through_info_to_str(const void *_info, char **str) under_vol_str_len = strlen(under_vol_string); /* Allocate space for our info */ - *str = (char *)H5allocate_memory(32 + under_vol_str_len, (hbool_t)0); + size_t strSize = 32 + under_vol_str_len; + *str = (char *)H5allocate_memory(strSize, (hbool_t)0); assert(*str); - /* Encode our info - * Normally we'd use snprintf() here for a little extra safety, but that - * call had problems on Windows until recently. So, to be as platform-independent - * as we can, we're using sprintf() instead. - */ - sprintf(*str, "under_vol=%u;under_info={%s}", (unsigned)under_value, - (under_vol_string ? under_vol_string : "")); + /* Encode our info */ + snprintf(*str, strSize, "under_vol=%u;under_info={%s}", (unsigned)under_value, + (under_vol_string ? under_vol_string : "")); return 0; } /* end H5VL_pass_through_info_to_str() */ diff --git a/src/H5private.h b/src/H5private.h index 5b0e33b..fa52e7f 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -172,7 +172,7 @@ */ #define BEGIN_MPE_LOG \ if (H5_MPEinit_g) { \ - sprintf(p_event_start, "start %s", __func__); \ + snprintf(p_event_start, sizeof(p_event_start), "start %s", __func__); \ if (eventa(__func__) == -1 && eventb(__func__) == -1) { \ const char *p_color = "red"; \ eventa(__func__) = MPE_Log_get_event_number(); \ diff --git a/test/chunk_info.c b/test/chunk_info.c index 148c577..2bec42d 100644 --- a/test/chunk_info.c +++ b/test/chunk_info.c @@ -421,7 +421,7 @@ verify_idx_nchunks(hid_t dset, hid_t dspace, H5D_chunk_index_t exp_idx_type, hsi /* Ensure the correct chunk indexing scheme is used */ if (idx_type != exp_idx_type) { char msg[256]; - HDsprintf(msg, "Should be using %s.\n", index_type_str(idx_type)); + HDsnprintf(msg, sizeof(msg), "Should be using %s.\n", index_type_str(idx_type)); FAIL_PUTS_ERROR(msg); } diff --git a/test/flush1.c b/test/flush1.c index f5c4e2b..0ddceb6 100644 --- a/test/flush1.c +++ b/test/flush1.c @@ -81,7 +81,7 @@ create_file(const char *filename, hid_t fapl_id, hbool_t swmr) if ((top_gid = H5Gcreate2(fid, "top_group", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) STACK_ERROR for (i = 0; i < NGROUPS; i++) { - HDsprintf(group_name, "group%02d", i); + HDsnprintf(group_name, sizeof(group_name), "group%02d", i); if ((gid = H5Gcreate2(top_gid, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) STACK_ERROR if (H5Gclose(gid) < 0) diff --git a/test/flush2.c b/test/flush2.c index bf1187b..b6c7761 100644 --- a/test/flush2.c +++ b/test/flush2.c @@ -144,7 +144,7 @@ file_ok(const char *filename, hid_t fapl_id, hbool_t check_second_dset) if ((top_gid = H5Gopen2(fid, "top_group", H5P_DEFAULT)) < 0) goto error; for (i = 0; i < NGROUPS; i++) { - HDsprintf(group_name, "group%02d", i); + HDsnprintf(group_name, sizeof(group_name), "group%02d", i); if ((gid = H5Gopen2(top_gid, group_name, H5P_DEFAULT)) < 0) goto error; if (H5Gclose(gid) < 0) diff --git a/test/unregister.c b/test/unregister.c index 803f8373..ebb51b1 100644 --- a/test/unregister.c +++ b/test/unregister.c @@ -136,7 +136,7 @@ test_unregister_filters(hid_t fapl_id) /* Create multiple groups under the main group */ for (i = 0; i < GROUP_ITERATION; i++) { - HDsprintf(group_name, "group_%d", i); + HDsnprintf(group_name, sizeof(group_name), "group_%d", i); if ((gid_loop = H5Gcreate2(gid, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; if (H5Gclose(gid_loop) < 0) diff --git a/tools/test/perform/direct_write_perf.c b/tools/test/perform/direct_write_perf.c index 2076cf4..1d7756b 100644 --- a/tools/test/perform/direct_write_perf.c +++ b/tools/test/perform/direct_write_perf.c @@ -655,7 +655,7 @@ main(void) hid_t fapl = H5P_DEFAULT; int i; - sprintf(filename, "%s.h5", FILENAME[0]); + snprintf(filename, sizeof(filename), "%s.h5", FILENAME[0]); create_file(fapl); test_direct_write_uncompressed_data(fapl); -- cgit v0.12 From ad71539d30c799c497953c18352df37d83a75310 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Fri, 28 Jan 2022 16:30:33 -0600 Subject: Remove const from the argv tools/tests main sig. (#1390) * Remove const from the argv tools/tests main sig. * also remove const from H5_get_option and parse_command_line. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- hl/tools/h5watch/extend_dset.c | 2 +- hl/tools/h5watch/h5watch.c | 8 ++++---- src/H5private.h | 3 ++- src/H5system.c | 2 +- test/flushrefresh.c | 4 ++-- test/swmr_addrem_writer.c | 2 +- test/swmr_generator.c | 2 +- test/swmr_reader.c | 2 +- test/swmr_remove_reader.c | 2 +- test/swmr_remove_writer.c | 2 +- test/swmr_sparse_reader.c | 2 +- test/swmr_sparse_writer.c | 2 +- test/swmr_start_write.c | 2 +- test/swmr_writer.c | 2 +- tools/src/h5copy/h5copy.c | 4 ++-- tools/src/h5diff/h5diff_common.c | 2 +- tools/src/h5diff/h5diff_common.h | 2 +- tools/src/h5diff/h5diff_main.c | 4 ++-- tools/src/h5diff/ph5diff_main.c | 7 ++++--- tools/src/h5dump/h5dump.c | 6 +++--- tools/src/h5format_convert/h5format_convert.c | 6 +++--- tools/src/h5jam/h5jam.c | 8 ++++---- tools/src/h5jam/h5unjam.c | 6 +++--- tools/src/h5ls/h5ls.c | 2 +- tools/src/h5perf/pio_perf.c | 8 ++++---- tools/src/h5perf/sio_perf.c | 8 ++++---- tools/src/h5repack/h5repack_main.c | 8 ++++---- tools/src/h5stat/h5stat.c | 6 +++--- tools/src/misc/h5clear.c | 6 +++--- tools/src/misc/h5delete.c | 2 +- tools/src/misc/h5mkgrp.c | 6 +++--- tools/test/h5dump/binread.c | 2 +- tools/test/h5jam/getub.c | 8 ++++---- tools/test/h5jam/tellub.c | 6 +++--- tools/test/perform/pio_standalone.h | 3 ++- tools/test/perform/sio_standalone.h | 3 ++- tools/test/perform/zip_perf.c | 4 ++-- utils/tools/h5dwalk/h5dwalk.c | 6 +++--- 38 files changed, 82 insertions(+), 78 deletions(-) diff --git a/hl/tools/h5watch/extend_dset.c b/hl/tools/h5watch/extend_dset.c index 624eebc..7756506 100644 --- a/hl/tools/h5watch/extend_dset.c +++ b/hl/tools/h5watch/extend_dset.c @@ -392,7 +392,7 @@ error: *********************************************************************** */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char *dname = NULL; char *fname = NULL; diff --git a/hl/tools/h5watch/h5watch.c b/hl/tools/h5watch/h5watch.c index 94ca4f1..5a6fe6f 100644 --- a/hl/tools/h5watch/h5watch.c +++ b/hl/tools/h5watch/h5watch.c @@ -51,7 +51,7 @@ static herr_t process_cmpd_fields(hid_t fid, char *dsetname); static herr_t check_dataset(hid_t fid, char *dsetname); static void leave(int ret); static void usage(const char *prog); -static void parse_command_line(int argc, const char *argv[]); +static void parse_command_line(int argc, const char *const *argv); /* * Command-line options: The user can only specify long-named parameters. @@ -665,7 +665,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; /* Command line option */ int tmp; @@ -790,7 +790,7 @@ catch_signal(int H5_ATTR_UNUSED signo) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char drivername[50]; /* VFD name */ char *fname = NULL; /* File name */ @@ -819,7 +819,7 @@ main(int argc, const char *argv[]) } /* parse command line options */ - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); if (argc <= H5_optind) { error_msg("missing dataset name\n"); diff --git a/src/H5private.h b/src/H5private.h index fa52e7f..68aabc2 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -2602,7 +2602,8 @@ struct h5_long_options { */ }; -H5_DLL int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt); +H5_DLL int H5_get_option(int argc, const char *const *argv, const char *opt, + const struct h5_long_options *l_opt); #ifdef H5_HAVE_PARALLEL /* Generic MPI functions */ diff --git a/src/H5system.c b/src/H5system.c index 9a966b0..ee9077e 100644 --- a/src/H5system.c +++ b/src/H5system.c @@ -956,7 +956,7 @@ const char *H5_optarg; /* Flag argument (or value) */ *------------------------------------------------------------------------- */ int -H5_get_option(int argc, const char **argv, const char *opts, const struct h5_long_options *l_opts) +H5_get_option(int argc, const char *const *argv, const char *opts, const struct h5_long_options *l_opts) { static int sp = 1; /* character index in current token */ int optchar = '?'; /* option character passed back to user */ diff --git a/test/flushrefresh.c b/test/flushrefresh.c index 2757bbf..0c10238 100644 --- a/test/flushrefresh.c +++ b/test/flushrefresh.c @@ -93,7 +93,7 @@ FILE *errorfile; /* ===================== */ /* Main */ -int main(int argc, const char *argv[]); +int main(int argc, char *argv[]); /* Flush Test Framework */ herr_t test_flush(void); @@ -137,7 +137,7 @@ herr_t end_verification(void); *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { /* Variables */ const char *envval = NULL; diff --git a/test/swmr_addrem_writer.c b/test/swmr_addrem_writer.c index d39a698..c705d6b 100644 --- a/test/swmr_addrem_writer.c +++ b/test/swmr_addrem_writer.c @@ -283,7 +283,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nops = 0; /* # of times to grow or shrink the dataset */ diff --git a/test/swmr_generator.c b/test/swmr_generator.c index e1423b6..93cfa0f 100644 --- a/test/swmr_generator.c +++ b/test/swmr_generator.c @@ -258,7 +258,7 @@ usage(void) } /* end usage() */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int comp_level = -1; /* Compression level (-1 is no compression) */ hbool_t verbose = TRUE; /* Whether to emit some informational messages */ diff --git a/test/swmr_reader.c b/test/swmr_reader.c index 836e1cc..e849f67 100644 --- a/test/swmr_reader.c +++ b/test/swmr_reader.c @@ -387,7 +387,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { long nseconds = 0; /* # of seconds to test */ int poll_time = 1; /* # of seconds between polling */ diff --git a/test/swmr_remove_reader.c b/test/swmr_remove_reader.c index 910bc74..94cb7f8 100644 --- a/test/swmr_remove_reader.c +++ b/test/swmr_remove_reader.c @@ -371,7 +371,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { long nseconds = 0; /* # of seconds to test */ int poll_time = 1; /* # of seconds between polling */ diff --git a/test/swmr_remove_writer.c b/test/swmr_remove_writer.c index e52f4e2..3604935 100644 --- a/test/swmr_remove_writer.c +++ b/test/swmr_remove_writer.c @@ -217,7 +217,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nshrinks = 0; /* # of times to shrink the dataset */ diff --git a/test/swmr_sparse_reader.c b/test/swmr_sparse_reader.c index 00eb2e0..15dcb67 100644 --- a/test/swmr_sparse_reader.c +++ b/test/swmr_sparse_reader.c @@ -342,7 +342,7 @@ usage(void) } /* end usage() */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { long nrecords = 0; /* # of records to read */ int poll_time = 1; /* # of seconds to sleep when waiting for writer */ diff --git a/test/swmr_sparse_writer.c b/test/swmr_sparse_writer.c index a4fc93e..96eff6c 100644 --- a/test/swmr_sparse_writer.c +++ b/test/swmr_sparse_writer.c @@ -318,7 +318,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nrecords = 0; /* # of records to append */ diff --git a/test/swmr_start_write.c b/test/swmr_start_write.c index 3ddd57a..d046b40 100644 --- a/test/swmr_start_write.c +++ b/test/swmr_start_write.c @@ -352,7 +352,7 @@ usage(void) *H5Fstart_swmr_write(), add_records(), H5Fclose(). */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nrecords = 0; /* # of records to append */ diff --git a/test/swmr_writer.c b/test/swmr_writer.c index de8b054..c4178f0 100644 --- a/test/swmr_writer.c +++ b/test/swmr_writer.c @@ -275,7 +275,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nrecords = 0; /* # of records to append */ diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c index 4e9a25e..6f10fee 100644 --- a/tools/src/h5copy/h5copy.c +++ b/tools/src/h5copy/h5copy.c @@ -212,7 +212,7 @@ parse_flag(const char *s_flag, unsigned *flag) */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid_src = H5I_INVALID_HID; hid_t fid_dst = H5I_INVALID_HID; @@ -242,7 +242,7 @@ main(int argc, const char *argv[]) } /* end if */ /* parse command line options */ - while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { case 'd': oname_dst = HDstrdup(H5_optarg); diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c index ec41d21..77a6785 100644 --- a/tools/src/h5diff/h5diff_common.c +++ b/tools/src/h5diff/h5diff_common.c @@ -206,7 +206,7 @@ parse_subset_params(const char *dset) */ void -parse_command_line(int argc, const char *argv[], const char **fname1, const char **fname2, +parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2, const char **objname1, const char **objname2, diff_opt_t *opts) { int i; diff --git a/tools/src/h5diff/h5diff_common.h b/tools/src/h5diff/h5diff_common.h index 83f4255..35e5dfb 100644 --- a/tools/src/h5diff/h5diff_common.h +++ b/tools/src/h5diff/h5diff_common.h @@ -23,7 +23,7 @@ extern "C" { #endif void usage(void); -void parse_command_line(int argc, const char *argv[], const char **fname1, const char **fname2, +void parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2, const char **objname1, const char **objname2, diff_opt_t *opts); void h5diff_exit(int status); void print_info(diff_opt_t *opts); diff --git a/tools/src/h5diff/h5diff_main.c b/tools/src/h5diff/h5diff_main.c index 37c215b..2a43b56 100644 --- a/tools/src/h5diff/h5diff_main.c +++ b/tools/src/h5diff/h5diff_main.c @@ -65,7 +65,7 @@ */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int ret; int i; @@ -86,7 +86,7 @@ main(int argc, const char *argv[]) * process the command-line *------------------------------------------------------------------------- */ - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts); /* enable error reporting if command line option */ h5tools_error_report(); diff --git a/tools/src/h5diff/ph5diff_main.c b/tools/src/h5diff/ph5diff_main.c index ec78e49..8e5c3e8 100644 --- a/tools/src/h5diff/ph5diff_main.c +++ b/tools/src/h5diff/ph5diff_main.c @@ -44,7 +44,7 @@ static void ph5diff_worker(int); */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int nID = 0; const char *fname1 = NULL; @@ -72,7 +72,7 @@ main(int argc, const char *argv[]) g_Parallel = 0; - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts); h5diff(fname1, fname2, objname1, objname2, &opts); @@ -83,7 +83,8 @@ main(int argc, const char *argv[]) /* Have the manager process the command-line */ if (nID == 0) { - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, + &opts); h5diff(fname1, fname2, objname1, objname2, &opts); diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c index a57b0e3..8c04bc7 100644 --- a/tools/src/h5dump/h5dump.c +++ b/tools/src/h5dump/h5dump.c @@ -828,7 +828,7 @@ free_handler(struct handler_t *hand, int len) *------------------------------------------------------------------------- */ static struct handler_t * -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { struct handler_t *hand = NULL; struct handler_t *last_dset = NULL; @@ -1329,7 +1329,7 @@ error: *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid = H5I_INVALID_HID; hid_t gid = H5I_INVALID_HID; @@ -1349,7 +1349,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - if ((hand = parse_command_line(argc, argv)) == NULL) { + if ((hand = parse_command_line(argc, (const char *const *)argv)) == NULL) { goto done; } diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c index ddf129c..b9572fe 100644 --- a/tools/src/h5format_convert/h5format_convert.c +++ b/tools/src/h5format_convert/h5format_convert.c @@ -94,7 +94,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -383,7 +383,7 @@ error: *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid = H5I_INVALID_HID; @@ -394,7 +394,7 @@ main(int argc, const char *argv[]) h5tools_init(); /* Parse command line options */ - if (parse_command_line(argc, argv) < 0) + if (parse_command_line(argc, (const char *const *)argv) < 0) goto done; else if (verbose_g) HDfprintf(stdout, "Process command line options\n"); diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c index 07140b5..45978bb 100644 --- a/tools/src/h5jam/h5jam.c +++ b/tools/src/h5jam/h5jam.c @@ -22,7 +22,7 @@ herr_t write_pad(int ofile, hsize_t old_where, hsize_t *new_where); hsize_t compute_user_block_size(hsize_t); hsize_t copy_some_to_file(int, int, hsize_t, hsize_t, ssize_t); -void parse_command_line(int, const char *[]); +void parse_command_line(int, const char *const *); int do_clobber = FALSE; char *output_file = NULL; @@ -104,7 +104,7 @@ leave(int ret) */ void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt = FALSE; @@ -149,7 +149,7 @@ parse_command_line(int argc, const char *argv[]) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int ufid = -1; int h5fid = -1; @@ -174,7 +174,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); /* enable error reporting if command line option */ h5tools_error_report(); diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c index fa23b06..8ff354e 100644 --- a/tools/src/h5jam/h5unjam.c +++ b/tools/src/h5jam/h5unjam.c @@ -92,7 +92,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt = FALSE; @@ -172,7 +172,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t ifile = H5I_INVALID_HID; hid_t plist = H5I_INVALID_HID; @@ -189,7 +189,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - if (EXIT_FAILURE == parse_command_line(argc, argv)) + if (EXIT_FAILURE == parse_command_line(argc, (const char *const *)argv)) goto done; /* enable error reporting if command line option */ diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c index 17abf43..0d34574 100644 --- a/tools/src/h5ls/h5ls.c +++ b/tools/src/h5ls/h5ls.c @@ -2646,7 +2646,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t file_id = H5I_INVALID_HID; char * fname = NULL, *oname = NULL, *x = NULL; diff --git a/tools/src/h5perf/pio_perf.c b/tools/src/h5perf/pio_perf.c index bf5f62f..c233684 100644 --- a/tools/src/h5perf/pio_perf.c +++ b/tools/src/h5perf/pio_perf.c @@ -188,7 +188,7 @@ typedef struct _minmax { /* local functions */ static off_t parse_size_directive(const char *size); -static struct options *parse_command_line(int argc, char *argv[]); +static struct options *parse_command_line(int argc, const char *const *argv); static void run_test_loop(struct options *options); static int run_test(iotype iot, parameters parms, struct options *opts); static void output_all_info(minmax *mm, int count, int indent_level); @@ -260,7 +260,7 @@ main(int argc, char *argv[]) pio_comm_g = MPI_COMM_WORLD; h5_set_info_object(); - opts = parse_command_line(argc, argv); + opts = parse_command_line(argc, (const char *const *)argv); if (!opts) { exit_value = EXIT_FAILURE; @@ -1276,7 +1276,7 @@ report_parameters(struct options *opts) * Added 2D testing (Christian Chilan, 10. August 2005) */ static struct options * -parse_command_line(int argc, char *argv[]) +parse_command_line(int argc, const char *const *argv) { register int opt; struct options *cl_opts; @@ -1305,7 +1305,7 @@ parse_command_line(int argc, char *argv[]) cl_opts->h5_write_only = FALSE; /* Do both read and write by default */ cl_opts->verify = FALSE; /* No Verify data correctness by default */ - while ((opt = H5_get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { case 'a': cl_opts->h5_alignment = parse_size_directive(H5_optarg); diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c index 0eb4508..f245b92 100644 --- a/tools/src/h5perf/sio_perf.c +++ b/tools/src/h5perf/sio_perf.c @@ -164,7 +164,7 @@ typedef struct { /* local functions */ static hsize_t parse_size_directive(const char *size); -static struct options *parse_command_line(int argc, const char *argv[]); +static struct options *parse_command_line(int argc, const char *const *argv); static void run_test_loop(struct options *options); static int run_test(iotype iot, parameters parms, struct options *opts); static void output_all_info(minmax *mm, int count, int indent_level); @@ -185,7 +185,7 @@ static void report_parameters(struct options *opts); * Modifications: */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int exit_value = EXIT_SUCCESS; struct options *opts = NULL; @@ -197,7 +197,7 @@ main(int argc, const char *argv[]) output = stdout; - opts = parse_command_line(argc, argv); + opts = parse_command_line(argc, (const char *const *)argv); if (!opts) { exit_value = EXIT_FAILURE; @@ -817,7 +817,7 @@ report_parameters(struct options *opts) * Added multidimensional testing (Christian Chilan, April, 2008) */ static struct options * -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; struct options *cl_opts; diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index 0a26500..68e37fd 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -18,7 +18,7 @@ /* Name of tool */ #define PROGRAMNAME "h5repack" -static int parse_command_line(int argc, const char **argv, pack_opt_t *options); +static int parse_command_line(int argc, const char *const *argv, pack_opt_t *options); static void leave(int ret) H5_ATTR_NORETURN; /* module-scoped variables */ @@ -507,7 +507,7 @@ set_sort_order(const char *form) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv, pack_opt_t *options) +parse_command_line(int argc, const char *const *argv, pack_opt_t *options) { h5tools_vol_info_t in_vol_info; h5tools_vol_info_t out_vol_info; @@ -928,7 +928,7 @@ done: *------------------------------------------------------------------------- */ int -main(int argc, const char **argv) +main(int argc, char **argv) { pack_opt_t options; /*the global options */ int parse_ret; @@ -958,7 +958,7 @@ main(int argc, const char **argv) /* Initialize default indexing options */ sort_by = H5_INDEX_CRT_ORDER; - parse_ret = parse_command_line(argc, argv, &options); + parse_ret = parse_command_line(argc, (const char *const *)argv, &options); if (parse_ret < 0) { HDprintf("Error occurred while parsing command-line options\n"); h5tools_setstatus(EXIT_FAILURE); diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c index 6b01e49..f1156f0 100644 --- a/tools/src/h5stat/h5stat.c +++ b/tools/src/h5stat/h5stat.c @@ -830,7 +830,7 @@ hand_free(struct handler_t *hand) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) +parse_command_line(int argc, const char *const *argv, struct handler_t **hand_ret) { int opt; unsigned u; @@ -1677,7 +1677,7 @@ print_statistics(const char *name, const iter_t *iter) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { iter_t iter; const char * fname = NULL; @@ -1693,7 +1693,7 @@ main(int argc, const char *argv[]) HDmemset(&iter, 0, sizeof(iter)); - if (parse_command_line(argc, argv, &hand) < 0) + if (parse_command_line(argc, (const char *const *)argv, &hand) < 0) goto done; /* enable error reporting if command line option */ diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c index face2f0..15c170d 100644 --- a/tools/src/misc/h5clear.c +++ b/tools/src/misc/h5clear.c @@ -109,7 +109,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -224,7 +224,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char * fname = NULL; /* File name */ hid_t fapl = H5I_INVALID_HID; /* File access property list */ @@ -240,7 +240,7 @@ main(int argc, const char *argv[]) h5tools_init(); /* Parse command line options */ - if (parse_command_line(argc, argv) < 0) + if (parse_command_line(argc, (const char *const *)argv) < 0) goto done; if (fname_g == NULL) diff --git a/tools/src/misc/h5delete.c b/tools/src/misc/h5delete.c index 3c4f8d5..20e81a1 100644 --- a/tools/src/misc/h5delete.c +++ b/tools/src/misc/h5delete.c @@ -29,7 +29,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hbool_t quiet = FALSE; const char *name = NULL; diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c index 1e66fce..1b8b23d 100644 --- a/tools/src/misc/h5mkgrp.c +++ b/tools/src/misc/h5mkgrp.c @@ -131,7 +131,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options) +parse_command_line(int argc, const char *const *argv, mkgrp_opt_t *options) { int opt; /* Option from command line */ size_t curr_group; /* Current group name to copy */ @@ -281,7 +281,7 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid = H5I_INVALID_HID; /* HDF5 file ID */ hid_t lcpl_id = H5I_INVALID_HID; /* Link creation property list ID */ @@ -303,7 +303,7 @@ main(int argc, const char *argv[]) } /* Parse command line */ - if (parse_command_line(argc, argv, ¶ms_g) < 0) { + if (parse_command_line(argc, (const char *const *)argv, ¶ms_g) < 0) { error_msg("unable to parse command line arguments\n"); leave(EXIT_FAILURE); } diff --git a/tools/test/h5dump/binread.c b/tools/test/h5dump/binread.c index d6206ca..341a085 100644 --- a/tools/test/h5dump/binread.c +++ b/tools/test/h5dump/binread.c @@ -59,7 +59,7 @@ usage(void) */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { FILE * stream; size_t numread; diff --git a/tools/test/h5jam/getub.c b/tools/test/h5jam/getub.c index fd21d6c..4e67e98 100644 --- a/tools/test/h5jam/getub.c +++ b/tools/test/h5jam/getub.c @@ -15,7 +15,7 @@ #include "h5tools.h" #include "h5tools_utils.h" -void parse_command_line(int argc, const char *argv[]); +void parse_command_line(int argc, const char *const *argv); /* Name of tool */ #define PROGRAM_NAME "getub" @@ -52,7 +52,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -77,7 +77,7 @@ parse_command_line(int argc, const char *argv[]) } /* end parse_command_line() */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int fd = H5I_INVALID_HID; unsigned size; @@ -91,7 +91,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); if (NULL == nbytes) { /* missing arg */ diff --git a/tools/test/h5jam/tellub.c b/tools/test/h5jam/tellub.c index e6769ec..f264d9b 100644 --- a/tools/test/h5jam/tellub.c +++ b/tools/test/h5jam/tellub.c @@ -56,7 +56,7 @@ usage(const char *prog) */ static void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -98,7 +98,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char * ifname; hid_t ifile = H5I_INVALID_HID; @@ -113,7 +113,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); /* enable error reporting if command line option */ h5tools_error_report(); diff --git a/tools/test/perform/pio_standalone.h b/tools/test/perform/pio_standalone.h index f1fb946..e64a765 100644 --- a/tools/test/perform/pio_standalone.h +++ b/tools/test/perform/pio_standalone.h @@ -461,7 +461,8 @@ struct h5_long_options { */ }; -extern int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt); +extern int H5_get_option(int argc, const char *const *argv, const char *opt, + const struct h5_long_options *l_opt); extern int nCols; /*max number of columns for outputting */ diff --git a/tools/test/perform/sio_standalone.h b/tools/test/perform/sio_standalone.h index 99cca75..57180e5 100644 --- a/tools/test/perform/sio_standalone.h +++ b/tools/test/perform/sio_standalone.h @@ -476,7 +476,8 @@ struct h5_long_options { */ }; -extern int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt); +extern int H5_get_option(int argc, const char *const *argv, const char *opt, + const struct h5_long_options *l_opt); extern int nCols; /*max number of columns for outputting */ diff --git a/tools/test/perform/zip_perf.c b/tools/test/perform/zip_perf.c index 37e69e2..74b1685 100644 --- a/tools/test/perform/zip_perf.c +++ b/tools/test/perform/zip_perf.c @@ -489,7 +489,7 @@ do_write_test(unsigned long file_size, unsigned long min_buf_size, unsigned long * Modifications: */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { unsigned long min_buf_size = 128 * ONE_KB, max_buf_size = ONE_MB; unsigned long file_size = 64 * ONE_MB; @@ -500,7 +500,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) > 0) { + while ((opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) > 0) { switch ((char)opt) { case '0': case '1': diff --git a/utils/tools/h5dwalk/h5dwalk.c b/utils/tools/h5dwalk/h5dwalk.c index a1e66e0..d7e22ba 100644 --- a/utils/tools/h5dwalk/h5dwalk.c +++ b/utils/tools/h5dwalk/h5dwalk.c @@ -1322,7 +1322,7 @@ process_input_file(char *inputname, int myrank, int size) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int i; int rc = 0; @@ -1352,7 +1352,7 @@ main(int argc, const char *argv[]) if (env_var) { int enable = HDatoi(env_var); if (enable) { - + } } #endif @@ -1392,7 +1392,7 @@ main(int argc, const char *argv[]) mfu_pred *pred_head = NULL; while (!tool_selected) { - opt = H5_get_option(argc, argv, s_opts, l_opts); + opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts); switch ((char)opt) { default: usage(); -- cgit v0.12 From 4ac6ccc0213767be935b2686524937ae93c46e3f Mon Sep 17 00:00:00 2001 From: Sean McBride Date: Fri, 28 Jan 2022 17:43:48 -0500 Subject: Snprintf2 (#1399) * Replaced many uses of sprintf with safer snprintf Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable. * Removed unnecessary use of static on small buffers This improves thread safety. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- hl/c++/test/ptableTest.cpp | 2 +- hl/test/test_file_image.c | 5 +- hl/test/test_packet_vlen.c | 16 ++-- java/src/jni/h5util.c | 151 ++++++++++++++++++++----------------- src/H5Odtype.c | 38 +++++----- src/H5PLpath.c | 4 +- src/H5trace.c | 2 +- test/cache_api.c | 2 +- test/cache_common.c | 148 +++++++++++++++++++----------------- test/cache_image.c | 16 ++-- test/cmpd_dset.c | 12 +-- test/del_many_dense_attrs.c | 4 +- test/dtypes.c | 6 +- test/earray.c | 9 ++- test/enc_dec_plist.c | 4 +- test/external.c | 4 +- test/external_common.c | 8 +- test/fheap.c | 5 +- test/genall5.c | 90 +++++++++++----------- test/page_buffer.c | 16 ++-- test/reserved.c | 6 +- test/tattr.c | 153 +++++++++++++++++++------------------- test/tmisc.c | 6 +- test/trefstr.c | 10 +-- test/tselect.c | 36 +++++---- test/tvlstr.c | 10 +-- test/vds_env.c | 5 +- testpar/t_cache.c | 2 +- testpar/t_cache_image.c | 14 ++-- testpar/t_dset.c | 12 ++- testpar/t_file.c | 16 ++-- testpar/t_pflush1.c | 8 +- testpar/t_pflush2.c | 8 +- testpar/t_prop.c | 2 +- tools/src/h5dump/h5dump_ddl.c | 4 +- tools/src/h5dump/h5dump_xml.c | 10 +-- tools/src/h5import/h5import.c | 2 +- tools/src/h5perf/pio_engine.c | 6 +- tools/test/misc/h5clear_gentest.c | 4 +- tools/test/perform/perf_meta.c | 14 ++-- utils/tools/h5dwalk/h5dwalk.c | 22 +++--- 41 files changed, 467 insertions(+), 425 deletions(-) diff --git a/hl/c++/test/ptableTest.cpp b/hl/c++/test/ptableTest.cpp index 9db56e0..33199f1 100644 --- a/hl/c++/test/ptableTest.cpp +++ b/hl/c++/test/ptableTest.cpp @@ -622,7 +622,7 @@ TestHDFFV_9758() s1[i].a = static_cast(i); s1[i].b = 1.0F * static_cast(i * i); s1[i].c = 1.0 / static_cast(i + 1); - HDsprintf(s1[i].d, "string%" PRIuHSIZE "", i); + HDsnprintf(s1[i].d, STRING_LENGTH, "string%" PRIuHSIZE "", i); s1[i].e = static_cast(100 + i); } diff --git a/hl/test/test_file_image.c b/hl/test/test_file_image.c index 6bb36e4..4448e41 100644 --- a/hl/test/test_file_image.c +++ b/hl/test/test_file_image.c @@ -109,12 +109,13 @@ test_file_image(size_t open_images, size_t nflags, const unsigned *flags) input_flags[i] = flags[(nflags + i) % nflags]; /* allocate name buffer for image i */ - filename[i] = (char *)HDmalloc(sizeof(char) * 32); + size_t filenamelength = sizeof(char) * 32; + filename[i] = (char *)HDmalloc(filenamelength); if (!filename[i]) FAIL_PUTS_ERROR("HDmalloc() failed"); /* create file name */ - HDsprintf(filename[i], "image_file%d.h5", (int)i); + HDsnprintf(filename[i], filenamelength, "image_file%d.h5", (int)i); /* create file */ if ((file_id[i] = H5Fcreate(filename[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) diff --git a/hl/test/test_packet_vlen.c b/hl/test/test_packet_vlen.c index e704944..aa88a6c 100644 --- a/hl/test/test_packet_vlen.c +++ b/hl/test/test_packet_vlen.c @@ -109,7 +109,7 @@ test_VLof_atomic(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -246,7 +246,7 @@ test_VLof_comptype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -418,7 +418,7 @@ test_compound_VL_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -582,7 +582,7 @@ test_VLof_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1144,7 +1144,7 @@ testfl_VLof_atomic(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1281,7 +1281,7 @@ testfl_VLof_comptype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1453,7 +1453,7 @@ testfl_compound_VL_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1617,7 +1617,7 @@ testfl_VLof_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index 02e99af..5a01dc9 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -182,7 +182,7 @@ size_t h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf, size_t out_buf_offset) { unsigned char *ucptr = NULL; - static char fmt_llong[8], fmt_ullong[8]; + char fmt_llong[8], fmt_ullong[8]; H5T_class_t tclass = H5T_NO_CLASS; const char delimiter[] = " ," H5_COMPOUND_BEGIN_INDICATOR H5_COMPOUND_END_INDICATOR H5_ARRAY_BEGIN_INDICATOR H5_ARRAY_END_INDICATOR H5_VLEN_BEGIN_INDICATOR H5_VLEN_END_INDICATOR; @@ -211,10 +211,10 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_ /* Build default formats for long long types */ if (!fmt_llong[0]) { - if (HDsprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure"); - if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure"); + if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure"); + if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure"); } /* end if */ switch (tclass) { @@ -759,7 +759,7 @@ size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, int expand_data) { unsigned char *ucptr = (unsigned char *)in_buf; - static char fmt_llong[8], fmt_ullong[8]; + char fmt_llong[8], fmt_ullong[8]; H5T_class_t tclass = H5T_NO_CLASS; size_t typeSize = 0; H5T_sign_t nsign = H5T_SGN_ERROR; @@ -794,11 +794,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i HDmemcpy(&tmp_float, cptr, sizeof(float)); - if (NULL == (this_str = (char *)HDmalloc(25))) + size_t this_len = 25; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%g", tmp_float) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%g", tmp_float) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); break; } @@ -808,11 +809,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i HDmemcpy(&tmp_double, cptr, sizeof(double)); - if (NULL == (this_str = (char *)HDmalloc(25))) + size_t this_len = 25; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%g", tmp_double) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, "%g", this_len, tmp_double) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); break; } @@ -822,11 +824,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i HDmemcpy(&tmp_ldouble, cptr, sizeof(long double)); - if (NULL == (this_str = (char *)HDmalloc(27))) + size_t this_len = 27; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%Lg", tmp_ldouble) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%Lg", tmp_ldouble) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); break; } @@ -888,25 +891,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned char tmp_uchar = 0; char tmp_char = 0; + size_t this_len = 7; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char)); - if (NULL == (this_str = (char *)HDmalloc(7))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hhu", tmp_uchar) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hhu", tmp_uchar) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_char, cptr, sizeof(char)); - if (NULL == (this_str = (char *)HDmalloc(7))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hhd", tmp_char) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hhd", tmp_char) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -916,25 +920,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned short tmp_ushort = 0; short tmp_short = 0; + size_t this_len = 9; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short)); - if (NULL == (this_str = (char *)HDmalloc(9))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hu", tmp_ushort) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hu", tmp_ushort) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_short, cptr, sizeof(short)); - if (NULL == (this_str = (char *)HDmalloc(9))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hd", tmp_short) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hd", tmp_short) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -944,25 +949,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned int tmp_uint = 0; int tmp_int = 0; + size_t this_len = 14; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int)); - if (NULL == (this_str = (char *)HDmalloc(14))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%u", tmp_uint) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%u", tmp_uint) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_int, cptr, sizeof(int)); - if (NULL == (this_str = (char *)HDmalloc(14))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%d", tmp_int) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%d", tmp_int) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -972,25 +978,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned long tmp_ulong = 0; long tmp_long = 0; + size_t this_len = 23; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long)); - if (NULL == (this_str = (char *)HDmalloc(23))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%lu", tmp_ulong) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%lu", tmp_ulong) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_long, cptr, sizeof(long)); - if (NULL == (this_str = (char *)HDmalloc(23))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%ld", tmp_long) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%ld", tmp_long) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -1001,25 +1008,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned long long tmp_ullong = 0; long long tmp_llong = 0; + size_t this_len = 25; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long)); - if (NULL == (this_str = (char *)HDmalloc(25))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, fmt_ullong, tmp_ullong) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, fmt_ullong, tmp_ullong) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_llong, cptr, sizeof(long long)); - if (NULL == (this_str = (char *)HDmalloc(25))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, fmt_llong, tmp_llong) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, fmt_llong, tmp_llong) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -1079,17 +1087,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i else { size_t i; - if (NULL == (this_str = (char *)HDmalloc(4 * (typeSize + 1)))) + size_t this_len = 4 * (typeSize + 1); + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (1 == typeSize) { - if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%#02x", ucptr[0]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { for (i = 0; i < typeSize; i++) - if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%s%02x", i ? ":" : "", ucptr[i]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } } @@ -1134,11 +1143,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i else H5_LIBRARY_ERROR(ENVONLY); - if (NULL == (this_str = (char *)HDmalloc(14))) + size_t this_len = 14; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR( ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%u-", (unsigned)oi.type) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%u-", (unsigned)oi.type) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); if (!h5str_append(out_str, this_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); HDfree(this_str); @@ -1150,11 +1160,13 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i H5Otoken_to_str(tid, &oi.token, &token_str); - if (NULL == (this_str = (char *)HDmalloc(64 + strlen(token_str) + 1))) + size_t this_len = 64 + strlen(token_str) + 1; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR( ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%lu:%s", oi.fileno, token_str) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%lu:%s", oi.fileno, token_str) < + 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); H5free_memory(token_str); } @@ -1307,17 +1319,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i /* All other types get printed as hexadecimal */ - if (NULL == (this_str = (char *)HDmalloc(4 * (typeSize + 1)))) + size_t this_len = 4 * (typeSize + 1); + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (1 == typeSize) { - if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%#02x", ucptr[0]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { for (i = 0; i < typeSize; i++) - if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%s%02x", i ? ":" : "", ucptr[i]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -1519,8 +1532,9 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; - if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)ptdata[i * 2 * ndims + j]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); + if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : "(", + (unsigned long)ptdata[i * 2 * ndims + j]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsnprintf failure"); if (!h5str_append(str, tmp_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); @@ -1529,9 +1543,9 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; - if (HDsprintf(tmp_str, "%s%lu", j ? "," : ")-(", - (unsigned long)ptdata[i * 2 * ndims + j + ndims]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); + if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : ")-(", + (unsigned long)ptdata[i * 2 * ndims + j + ndims]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsnprintf failure"); if (!h5str_append(str, tmp_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); @@ -1696,8 +1710,9 @@ h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; - if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)(ptdata[i * ndims + j])) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure"); + if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : "(", + (unsigned long)(ptdata[i * ndims + j])) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsnprintf failure"); if (!h5str_append(str, tmp_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); diff --git a/src/H5Odtype.c b/src/H5Odtype.c index fa49924..9af79f4 100644 --- a/src/H5Odtype.c +++ b/src/H5Odtype.c @@ -1731,7 +1731,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_NO_CLASS: case H5T_NCLASSES: default: - HDsprintf(buf, "H5T_CLASS_%d", (int)(dt->shared->type)); + HDsnprintf(buf, sizeof(buf), "H5T_CLASS_%d", (int)(dt->shared->type)); s = buf; break; } /* end switch */ @@ -1746,7 +1746,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth, "Number of members:", dt->shared->u.compnd.nmembs); for (i = 0; i < dt->shared->u.compnd.nmembs; i++) { - HDsprintf(buf, "Member %u:", i); + HDsnprintf(buf, sizeof(buf), "Member %u:", i); HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, buf, dt->shared->u.compnd.memb[i].name); HDfprintf(stream, "%*s%-*s %lu\n", indent + 3, "", MAX(0, fwidth - 3), "Byte offset:", (unsigned long)(dt->shared->u.compnd.memb[i].offset)); @@ -1759,7 +1759,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth, "Number of members:", dt->shared->u.enumer.nmembs); for (i = 0; i < dt->shared->u.enumer.nmembs; i++) { - HDsprintf(buf, "Member %u:", i); + HDsnprintf(buf, sizeof(buf), "Member %u:", i); HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, buf, dt->shared->u.enumer.name[i]); HDfprintf(stream, "%*s%-*s 0x", indent, "", fwidth, "Raw bytes of value:"); for (k = 0; k < dt->shared->parent->shared->size; k++) @@ -1799,13 +1799,14 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_CSET_RESERVED_13: case H5T_CSET_RESERVED_14: case H5T_CSET_RESERVED_15: - HDsprintf(buf, "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.cset)); + HDsnprintf(buf, sizeof(buf), "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.cset)); s = buf; break; case H5T_CSET_ERROR: default: - HDsprintf(buf, "Unknown character set: %d", (int)(dt->shared->u.atomic.u.s.cset)); + HDsnprintf(buf, sizeof(buf), "Unknown character set: %d", + (int)(dt->shared->u.atomic.u.s.cset)); s = buf; break; } /* end switch */ @@ -1837,13 +1838,14 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_STR_RESERVED_13: case H5T_STR_RESERVED_14: case H5T_STR_RESERVED_15: - HDsprintf(buf, "H5T_STR_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.pad)); + HDsnprintf(buf, sizeof(buf), "H5T_STR_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.pad)); s = buf; break; case H5T_STR_ERROR: default: - HDsprintf(buf, "Unknown string padding: %d", (int)(dt->shared->u.atomic.u.s.pad)); + HDsnprintf(buf, sizeof(buf), "Unknown string padding: %d", + (int)(dt->shared->u.atomic.u.s.pad)); s = buf; break; } /* end switch */ @@ -1862,7 +1864,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_VLEN_BADTYPE: case H5T_VLEN_MAXTYPE: default: - HDsprintf(buf, "H5T_VLEN_%d", dt->shared->u.vlen.type); + HDsnprintf(buf, sizeof(buf), "H5T_VLEN_%d", dt->shared->u.vlen.type); s = buf; break; } /* end switch */ @@ -1880,7 +1882,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_LOC_BADLOC: case H5T_LOC_MAXLOC: default: - HDsprintf(buf, "H5T_LOC_%d", (int)dt->shared->u.vlen.loc); + HDsnprintf(buf, sizeof(buf), "H5T_LOC_%d", (int)dt->shared->u.vlen.loc); s = buf; break; } /* end switch */ @@ -1911,13 +1913,13 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_CSET_RESERVED_13: case H5T_CSET_RESERVED_14: case H5T_CSET_RESERVED_15: - HDsprintf(buf, "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.vlen.cset)); + HDsnprintf(buf, sizeof(buf), "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.vlen.cset)); s = buf; break; case H5T_CSET_ERROR: default: - HDsprintf(buf, "Unknown character set: %d", (int)(dt->shared->u.vlen.cset)); + HDsnprintf(buf, sizeof(buf), "Unknown character set: %d", (int)(dt->shared->u.vlen.cset)); s = buf; break; } /* end switch */ @@ -1949,13 +1951,13 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_STR_RESERVED_13: case H5T_STR_RESERVED_14: case H5T_STR_RESERVED_15: - HDsprintf(buf, "H5T_STR_RESERVED_%d", (int)(dt->shared->u.vlen.pad)); + HDsnprintf(buf, sizeof(buf), "H5T_STR_RESERVED_%d", (int)(dt->shared->u.vlen.pad)); s = buf; break; case H5T_STR_ERROR: default: - HDsprintf(buf, "Unknown string padding: %d", (int)(dt->shared->u.vlen.pad)); + HDsnprintf(buf, sizeof(buf), "Unknown string padding: %d", (int)(dt->shared->u.vlen.pad)); s = buf; break; } /* end switch */ @@ -1995,7 +1997,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_ORDER_ERROR: default: - HDsprintf(buf, "H5T_ORDER_%d", dt->shared->u.atomic.order); + HDsnprintf(buf, sizeof(buf), "H5T_ORDER_%d", dt->shared->u.atomic.order); s = buf; break; } /* end switch */ @@ -2069,9 +2071,9 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_NPAD: default: if (dt->shared->u.atomic.u.f.pad < 0) - HDsprintf(buf, "H5T_PAD_%d", -(dt->shared->u.atomic.u.f.pad)); + HDsnprintf(buf, sizeof(buf), "H5T_PAD_%d", -(dt->shared->u.atomic.u.f.pad)); else - HDsprintf(buf, "bit-%d", dt->shared->u.atomic.u.f.pad); + HDsnprintf(buf, sizeof(buf), "bit-%d", dt->shared->u.atomic.u.f.pad); s = buf; break; } /* end switch */ @@ -2092,7 +2094,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_NORM_ERROR: default: - HDsprintf(buf, "H5T_NORM_%d", (int)(dt->shared->u.atomic.u.f.norm)); + HDsnprintf(buf, sizeof(buf), "H5T_NORM_%d", (int)(dt->shared->u.atomic.u.f.norm)); s = buf; } /* end switch */ HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, "Normalization:", s); @@ -2129,7 +2131,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_SGN_ERROR: case H5T_NSGN: default: - HDsprintf(buf, "H5T_SGN_%d", (int)(dt->shared->u.atomic.u.i.sign)); + HDsnprintf(buf, sizeof(buf), "H5T_SGN_%d", (int)(dt->shared->u.atomic.u.i.sign)); s = buf; break; } /* end switch */ diff --git a/src/H5PLpath.c b/src/H5PLpath.c index 87ff831..b86fd6e 100644 --- a/src/H5PLpath.c +++ b/src/H5PLpath.c @@ -709,7 +709,7 @@ H5PL__path_table_iterate_process_path(const char *plugin_path, H5PL_iterate_type /* Specify a file mask. *.* = We want everything! - * skip the path if the directory can't be opened */ - HDsprintf(service, "%s\\*.dll", plugin_path); + HDsnprintf(service, sizeof(service), "%s\\*.dll", plugin_path); if ((hFind = FindFirstFileA(service, &fdFile)) == INVALID_HANDLE_VALUE) HGOTO_DONE(H5_ITER_CONT) @@ -934,7 +934,7 @@ H5PL__find_plugin_in_path(const H5PL_search_params_t *search_params, hbool_t *fo *found = FALSE; /* Specify a file mask. *.* = We want everything! */ - HDsprintf(service, "%s\\*.dll", dir); + HDsnprintf(service, sizeof(service), "%s\\*.dll", dir); if ((hFind = FindFirstFileA(service, &fdFile)) == INVALID_HANDLE_VALUE) HGOTO_ERROR(H5E_PLUGIN, H5E_OPENERROR, FAIL, "can't open directory") diff --git a/src/H5trace.c b/src/H5trace.c index 5d15fee..8790a88 100644 --- a/src/H5trace.c +++ b/src/H5trace.c @@ -4023,7 +4023,7 @@ H5_trace(const double *returning, const char *func, const char *type, ...) H5_timer_get_times(function_timer, &function_times); H5_timer_get_times(running_timer, &running_times); - HDsprintf(tmp, "%.6f", (function_times.elapsed - running_times.elapsed)); + HDsnprintf(tmp, sizeof(tmp), "%.6f", (function_times.elapsed - running_times.elapsed)); H5RS_asprintf_cat(rs, " %*s ", (int)HDstrlen(tmp), ""); } for (i = 0; i < current_depth; i++) diff --git a/test/cache_api.c b/test/cache_api.c index 2d642a6..6e897ec 100644 --- a/test/cache_api.c +++ b/test/cache_api.c @@ -1082,7 +1082,7 @@ mdc_api_call_smoke_check(int express_test, unsigned paged, hid_t fcpl_id) /* create the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dcreate2(file_id, dset_name, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, properties, H5P_DEFAULT); diff --git a/test/cache_common.c b/test/cache_common.c index 207daa1..9becfa8 100644 --- a/test/cache_common.c +++ b/test/cache_common.c @@ -2317,8 +2317,8 @@ verify_clean(void) void verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_entry_status expected[]) { - static char msg[256]; - int i; + char msg[256]; + int i; i = 0; while ((pass) && (i < num_entries)) { @@ -2330,14 +2330,15 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if ((!expected[i].in_cache) && ((expected[i].is_protected) || (expected[i].is_pinned))) { pass = FALSE; - HDsprintf(msg, "%d: Contradictory data in expected[%d].\n", tag, i); + HDsnprintf(msg, sizeof(msg), "%d: Contradictory data in expected[%d].\n", tag, i); failure_mssg = msg; } if ((!expected[i].in_cache) && (expected[i].is_dirty) && (!entry_ptr->expunged)) { pass = FALSE; - HDsprintf(msg, "%d: expected[%d] specs non-expunged, dirty, non-resident.\n", tag, i); + HDsnprintf(msg, sizeof(msg), "%d: expected[%d] specs non-expunged, dirty, non-resident.\n", tag, + i); failure_mssg = msg; } @@ -2348,9 +2349,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (in_cache != expected[i].in_cache) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) in cache actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, (int)in_cache, - (int)expected[i].in_cache); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) in cache actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, (int)in_cache, + (int)expected[i].in_cache); failure_mssg = msg; } } @@ -2360,9 +2361,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->size != expected[i].size) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) size actual/expected = %ld/%ld.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, (long)(entry_ptr->size), - (long)expected[i].size); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) size actual/expected = %ld/%ld.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, (long)(entry_ptr->size), + (long)expected[i].size); failure_mssg = msg; } } @@ -2372,9 +2373,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.size != expected[i].size) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header size actual/expected = %ld/%ld.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (long)(entry_ptr->header.size), (long)expected[i].size); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) header size actual/expected = %ld/%ld.\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (long)(entry_ptr->header.size), (long)expected[i].size); failure_mssg = msg; } } @@ -2384,9 +2385,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->at_main_addr != expected[i].at_main_addr) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) at main addr actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->at_main_addr), (int)expected[i].at_main_addr); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) at main addr actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->at_main_addr), (int)expected[i].at_main_addr); failure_mssg = msg; } } @@ -2396,9 +2397,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_dirty != expected[i].is_dirty) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_dirty actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_dirty), (int)expected[i].is_dirty); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_dirty actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_dirty), (int)expected[i].is_dirty); failure_mssg = msg; } } @@ -2408,9 +2409,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.is_dirty != expected[i].is_dirty) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header is_dirty actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->header.is_dirty), (int)expected[i].is_dirty); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) header is_dirty actual/expected = %d/%d.\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->header.is_dirty), (int)expected[i].is_dirty); failure_mssg = msg; } } @@ -2420,9 +2421,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_protected != expected[i].is_protected) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_protected actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_protected), (int)expected[i].is_protected); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_protected actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_protected), (int)expected[i].is_protected); failure_mssg = msg; } } @@ -2432,9 +2433,10 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.is_protected != expected[i].is_protected) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header is_protected actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->header.is_protected), (int)expected[i].is_protected); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header is_protected actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->header.is_protected), (int)expected[i].is_protected); failure_mssg = msg; } } @@ -2444,9 +2446,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_pinned != expected[i].is_pinned) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_pinned actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_pinned), (int)expected[i].is_pinned); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_pinned actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_pinned), (int)expected[i].is_pinned); failure_mssg = msg; } } @@ -2456,9 +2458,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_corked != expected[i].is_corked) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_corked actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_corked), (int)expected[i].is_corked); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_corked actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_corked), (int)expected[i].is_corked); failure_mssg = msg; } } @@ -2468,9 +2470,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.is_pinned != expected[i].is_pinned) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header is_pinned actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->header.is_pinned), (int)expected[i].is_pinned); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) header is_pinned actual/expected = %d/%d.\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->header.is_pinned), (int)expected[i].is_pinned); failure_mssg = msg; } } @@ -2482,11 +2484,12 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ (entry_ptr->destroyed != expected[i].destroyed)) { pass = FALSE; - HDsprintf(msg, "%d entry (%d,%d) deserialized = %d(%d), serialized = %d(%d), dest = %d(%d)\n", - tag, (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->deserialized), (int)(expected[i].deserialized), - (int)(entry_ptr->serialized), (int)(expected[i].serialized), - (int)(entry_ptr->destroyed), (int)(expected[i].destroyed)); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d,%d) deserialized = %d(%d), serialized = %d(%d), dest = %d(%d)\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->deserialized), (int)(expected[i].deserialized), + (int)(entry_ptr->serialized), (int)(expected[i].serialized), + (int)(entry_ptr->destroyed), (int)(expected[i].destroyed)); failure_mssg = msg; } } @@ -2497,18 +2500,19 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (pass) { if (entry_ptr->flush_dep_npar != expected[i].flush_dep_npar) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_npar actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_npar, - expected[i].flush_dep_npar); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) flush_dep_npar actual/expected = %u/%u.\n", + tag, expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_npar, + expected[i].flush_dep_npar); failure_mssg = msg; } /* end if */ } /* end if */ if ((pass) && (in_cache)) { if (entry_ptr->header.flush_dep_nparents != expected[i].flush_dep_npar) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header flush_dep_nparents actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, - entry_ptr->header.flush_dep_nparents, expected[i].flush_dep_npar); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header flush_dep_nparents actual/expected = %u/%u.\n", tag, + expected[i].entry_type, expected[i].entry_index, + entry_ptr->header.flush_dep_nparents, expected[i].flush_dep_npar); failure_mssg = msg; } /* end if */ } /* end if */ @@ -2519,9 +2523,10 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ for (u = 0; u < entry_ptr->flush_dep_npar; u++) { if (entry_ptr->flush_dep_par_type[u] != expected[i].flush_dep_par_type[u]) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_par_type[%u] actual/expected = %d/%d.\n", tag, - expected[i].entry_type, expected[i].entry_index, u, - entry_ptr->flush_dep_par_type[u], expected[i].flush_dep_par_type[u]); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) flush_dep_par_type[%u] actual/expected = %d/%d.\n", tag, + expected[i].entry_type, expected[i].entry_index, u, + entry_ptr->flush_dep_par_type[u], expected[i].flush_dep_par_type[u]); failure_mssg = msg; } /* end if */ } /* end for */ @@ -2530,9 +2535,10 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ for (u = 0; u < entry_ptr->flush_dep_npar; u++) { if (entry_ptr->flush_dep_par_idx[u] != expected[i].flush_dep_par_idx[u]) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_par_idx[%u] actual/expected = %d/%d.\n", tag, - expected[i].entry_type, expected[i].entry_index, u, - entry_ptr->flush_dep_par_idx[u], expected[i].flush_dep_par_idx[u]); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) flush_dep_par_idx[%u] actual/expected = %d/%d.\n", tag, + expected[i].entry_type, expected[i].entry_index, u, + entry_ptr->flush_dep_par_idx[u], expected[i].flush_dep_par_idx[u]); failure_mssg = msg; } /* end if */ } /* end for */ @@ -2542,37 +2548,39 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (pass) { if (entry_ptr->flush_dep_nchd != expected[i].flush_dep_nchd) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_nchd actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_nchd, - expected[i].flush_dep_nchd); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) flush_dep_nchd actual/expected = %u/%u.\n", + tag, expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_nchd, + expected[i].flush_dep_nchd); failure_mssg = msg; } /* end if */ } /* end if */ if ((pass) && (in_cache)) { if (entry_ptr->header.flush_dep_nchildren != expected[i].flush_dep_nchd) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header flush_dep_nchildren actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, - entry_ptr->header.flush_dep_nchildren, expected[i].flush_dep_nchd); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header flush_dep_nchildren actual/expected = %u/%u.\n", tag, + expected[i].entry_type, expected[i].entry_index, + entry_ptr->header.flush_dep_nchildren, expected[i].flush_dep_nchd); failure_mssg = msg; } /* end if */ } /* end if */ if (pass) { if (entry_ptr->flush_dep_ndirty_chd != expected[i].flush_dep_ndirty_chd) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_ndirty_chd actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_ndirty_chd, - expected[i].flush_dep_ndirty_chd); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) flush_dep_ndirty_chd actual/expected = %u/%u.\n", tag, + expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_ndirty_chd, + expected[i].flush_dep_ndirty_chd); failure_mssg = msg; } /* end if */ } /* end if */ if ((pass) && (in_cache)) { if (entry_ptr->header.flush_dep_ndirty_children != expected[i].flush_dep_ndirty_chd) { pass = FALSE; - HDsprintf(msg, - "%d entry (%d, %d) header flush_dep_ndirty_children actual/expected = %u/%u.\n", - tag, expected[i].entry_type, expected[i].entry_index, - entry_ptr->header.flush_dep_ndirty_children, expected[i].flush_dep_ndirty_chd); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header flush_dep_ndirty_children actual/expected = %u/%u.\n", + tag, expected[i].entry_type, expected[i].entry_index, + entry_ptr->header.flush_dep_ndirty_children, expected[i].flush_dep_ndirty_chd); failure_mssg = msg; } /* end if */ } /* end if */ @@ -2581,9 +2589,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (pass) { if (expected[i].flush_order >= 0 && entry_ptr->flush_order != (unsigned)expected[i].flush_order) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_order actual/expected = %u/%d.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_order, - expected[i].flush_order); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) flush_order actual/expected = %u/%d.\n", tag, + expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_order, + expected[i].flush_order); failure_mssg = msg; } /* end if */ } /* end if */ diff --git a/test/cache_image.c b/test/cache_image.c index d3961a8..419eb58 100644 --- a/test/cache_image.c +++ b/test/cache_image.c @@ -164,7 +164,7 @@ create_datasets(hid_t file_id, int min_dset, int max_dset) /* create the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dcreate2(file_id, dset_name, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, properties, H5P_DEFAULT); @@ -443,7 +443,7 @@ delete_datasets(hid_t file_id, int min_dset, int max_dset) i = min_dset; while ((pass) && (i <= max_dset)) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); if (H5Ldelete(file_id, dset_name, H5P_DEFAULT) < 0) { @@ -1019,7 +1019,7 @@ verify_datasets(hid_t file_id, int min_dset, int max_dset) /* open the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dopen2(file_id, dset_name, H5P_DEFAULT); if (dataset_ids[i] < 0) { @@ -4624,7 +4624,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) /* 2) Create a process specific group. */ if (pass) { - HDsprintf(process_group_name, "/process_%d", min_group); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", min_group); proc_gid = H5Gcreate2(file_id, process_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); @@ -4728,7 +4728,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) if (pass) { max_group++; - HDsprintf(process_group_name, "/process_%d", max_group); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", max_group); proc_gid = H5Gcreate2(file_id, process_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); @@ -4802,7 +4802,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) /* 11) Validate all the zoos. */ i = min_group; while (pass && i <= max_group) { - HDsprintf(process_group_name, "/process_%d", i); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", i); validate_zoo(file_id, process_group_name, i++); } @@ -4854,7 +4854,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) i = min_group; while ((pass) && (i <= max_group)) { - HDsprintf(process_group_name, "/process_%d", i); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", i); validate_zoo(file_id, process_group_name, i++); } @@ -4914,7 +4914,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) */ i = min_group; while ((pass) && (i <= max_group)) { - HDsprintf(process_group_name, "/process_%d", i); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", i); validate_zoo(file_id, process_group_name, i++); } diff --git a/test/cmpd_dset.c b/test/cmpd_dset.c index 04a931c..024b6c0 100644 --- a/test/cmpd_dset.c +++ b/test/cmpd_dset.c @@ -1766,7 +1766,7 @@ test_pack_ooo(void) /* Insert the compound members in the random order previously generated */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == sub_cmpd_order) { if (H5Tinsert(cmpd, name, (size_t)(4 * order[i]), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1799,7 +1799,7 @@ test_pack_ooo(void) /* Insert the compound members in the random order previously generated */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == sub_cmpd_order) { if (H5Tinsert(cmpd, name, (size_t)(4 * order[i]), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1834,7 +1834,7 @@ test_pack_ooo(void) /* Insert the compound members in reverse order, with compound last */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == PACK_NMEMBS - 1) { if (H5Tinsert(cmpd, name, (size_t)(4 * (PACK_NMEMBS - i - 1)), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1867,7 +1867,7 @@ test_pack_ooo(void) /* Insert the compound members in reverse order, with compound last */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == PACK_NMEMBS - 1) { if (H5Tinsert(cmpd, name, (size_t)(4 * (PACK_NMEMBS - i - 1)), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1902,7 +1902,7 @@ test_pack_ooo(void) /* Insert the compound members in forward order, with compound first */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == 0) { if (H5Tinsert(cmpd, name, (size_t)(4 * i), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1935,7 +1935,7 @@ test_pack_ooo(void) /* Insert the compound members in forward order */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == 0) { if (H5Tinsert(cmpd, name, (size_t)(4 * i), sub_cmpd) < 0) PACK_OOO_ERROR diff --git a/test/del_many_dense_attrs.c b/test/del_many_dense_attrs.c index cf7f607..78aba3b 100644 --- a/test/del_many_dense_attrs.c +++ b/test/del_many_dense_attrs.c @@ -119,7 +119,7 @@ main(void) /* Create attributes in the group */ for (i = ATTR_COUNT; i >= 0; i--) { /* Set up the attribute name */ - HDsprintf(aname, "%s%d", basename, i); + HDsnprintf(aname, sizeof(aname), "%s%d", basename, i); /* Create the attribute */ if ((aid = H5Acreate2(gid, aname, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -165,7 +165,7 @@ main(void) /* Delete the attributes */ for (i = 0; i <= ATTR_COUNT; i++) { /* Set up the attribute name */ - HDsprintf(aname, "%s%d", basename, i); + HDsnprintf(aname, sizeof(aname), "%s%d", basename, i); /* Delete the attribute */ if (H5Adelete(gid, aname) < 0) diff --git a/test/dtypes.c b/test/dtypes.c index a6b2beb..d2064b7 100644 --- a/test/dtypes.c +++ b/test/dtypes.c @@ -4969,7 +4969,7 @@ test_conv_str_2(void) } /* end for */ /* Do the conversions */ - HDsprintf(s, "Testing random string conversion speed"); + HDsnprintf(s, sizeof(s), "Testing random string conversion speed"); HDprintf("%-70s", s); HDfflush(stdout); if (H5Tconvert(c_type, f_type, nelmts, buf, NULL, H5P_DEFAULT) < 0) @@ -5184,14 +5184,14 @@ test_conv_enum_1(void) buf[u] = HDrand() % 26; /* Conversions */ - HDsprintf(s, "Testing random enum conversion O(N)"); + HDsnprintf(s, sizeof(s), "Testing random enum conversion O(N)"); HDprintf("%-70s", s); HDfflush(stdout); if (H5Tconvert(t1, t2, nelmts, buf, NULL, H5P_DEFAULT) < 0) goto error; PASSED(); - HDsprintf(s, "Testing random enum conversion O(N log N)"); + HDsnprintf(s, sizeof(s), "Testing random enum conversion O(N log N)"); HDprintf("%-70s", s); HDfflush(stdout); if (H5Tconvert(t2, t1, nelmts, buf, NULL, H5P_DEFAULT) < 0) diff --git a/test/earray.c b/test/earray.c index 4763d51..7c8dd1f 100644 --- a/test/earray.c +++ b/test/earray.c @@ -2543,15 +2543,16 @@ main(void) /* Test first element in data block */ nelmts = (hsize_t)((hsize_t)1 + cparam.idx_blk_elmts + tparam.sblk_info[sblk].start_idx + (tparam.sblk_info[sblk].dblk_nelmts * dblk)); - HDsprintf(test_str, "setting first element of array's data block #%llu", - (unsigned long long)ndblks); + HDsnprintf(test_str, sizeof(test_str), + "setting first element of array's data block #%llu", + (unsigned long long)ndblks); nerrors += test_set_elmts(fapl, &cparam, &tparam, nelmts, test_str); /* Test all elements in data block */ nelmts = (hsize_t)(cparam.idx_blk_elmts + tparam.sblk_info[sblk].start_idx + (tparam.sblk_info[sblk].dblk_nelmts * (dblk + 1))); - HDsprintf(test_str, "setting all elements of array's data block #%llu", - (unsigned long long)ndblks); + HDsnprintf(test_str, sizeof(test_str), "setting all elements of array's data block #%llu", + (unsigned long long)ndblks); nerrors += test_set_elmts(fapl, &cparam, &tparam, nelmts, test_str); /* Increment data block being tested */ diff --git a/test/enc_dec_plist.c b/test/enc_dec_plist.c index 60b229a..0a73273 100644 --- a/test/enc_dec_plist.c +++ b/test/enc_dec_plist.c @@ -199,8 +199,8 @@ main(void) /* Display testing info */ low_string = h5_get_version_string(low); high_string = h5_get_version_string(high); - HDsprintf(msg, "Testing ENCODE/DECODE with file version bounds: (%s, %s):", low_string, - high_string); + HDsnprintf(msg, sizeof(msg), + "Testing ENCODE/DECODE with file version bounds: (%s, %s):", low_string, high_string); HDputs(msg); if (VERBOSE_MED) diff --git a/test/external.c b/test/external.c index 281593c..11185b3 100644 --- a/test/external.c +++ b/test/external.c @@ -890,8 +890,8 @@ test_write_file_set(hid_t fapl) for (i = 0; i < N_EXT_FILES; i++) { char name1[64], name2[64]; - HDsprintf(name1, "extern_%dr.raw", i + 1); - HDsprintf(name2, "extern_%dw.raw", i + 1); + HDsnprintf(name1, sizeof(name1), "extern_%dr.raw", i + 1); + HDsnprintf(name2, sizeof(name2), "extern_%dw.raw", i + 1); if (!files_have_same_contents(name1, name2)) FAIL_PUTS_ERROR(" Output differs from expected value.") } /* end for */ diff --git a/test/external_common.c b/test/external_common.c index c37fd16..3f04260 100644 --- a/test/external_common.c +++ b/test/external_common.c @@ -59,9 +59,9 @@ reset_raw_data_files(hbool_t is_env) /* Open file */ if (is_env) - HDsprintf(filename, "extern_env_%lur.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_env_%lur.raw", (unsigned long)i + 1); else - HDsprintf(filename, "extern_%lur.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_%lur.raw", (unsigned long)i + 1); if ((fd = HDopen(filename, O_RDWR | O_CREAT | O_TRUNC, H5_POSIX_CREATE_MODE_RW)) < 0) goto error; @@ -96,9 +96,9 @@ reset_raw_data_files(hbool_t is_env) /* Open file */ if (is_env) - HDsprintf(filename, "extern_env_%luw.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_env_%luw.raw", (unsigned long)i + 1); else - HDsprintf(filename, "extern_%luw.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_%luw.raw", (unsigned long)i + 1); if ((fd = HDopen(filename, O_RDWR | O_CREAT | O_TRUNC, H5_POSIX_CREATE_MODE_RW)) < 0) goto error; diff --git a/test/fheap.c b/test/fheap.c index 5ded20f..2fcbb45 100644 --- a/test/fheap.c +++ b/test/fheap.c @@ -565,8 +565,9 @@ begin_test(fheap_test_param_t *tparam, const char *base_desc, fheap_heap_ids_t * */ del_str = get_del_string(tparam); HDassert(del_str); - test_desc = (char *)H5MM_malloc(HDstrlen(del_str) + HDstrlen(base_desc)); - HDsprintf(test_desc, base_desc, del_str); + size_t test_desc_len = HDstrlen(del_str) + HDstrlen(base_desc); + test_desc = (char *)H5MM_malloc(test_desc_len); + HDsnprintf(test_desc, test_desc_len, base_desc, del_str); TESTING(test_desc); H5MM_xfree(del_str); H5MM_xfree(test_desc); diff --git a/test/genall5.c b/test/genall5.c index f3b0e6a..ca96eeb 100644 --- a/test/genall5.c +++ b/test/genall5.c @@ -306,7 +306,7 @@ ns_grp_c(hid_t fid, const char *group_name, unsigned nlinks) while ((pass) && (u < nlinks)) { char linkname[16]; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); if (0 == (u % 3)) { ret = H5Lcreate_soft(group_name, gid, linkname, H5P_DEFAULT, H5P_DEFAULT); @@ -474,7 +474,7 @@ vrfy_ns_grp_c(hid_t fid, const char *group_name, unsigned nlinks) char linkname[16]; htri_t link_exists; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); link_exists = H5Lexists(gid, linkname, H5P_DEFAULT); if (link_exists < 0) { @@ -715,7 +715,7 @@ ns_grp_d(hid_t fid, const char *group_name, unsigned nlinks) while ((pass) && (u < nlinks)) { char linkname[16]; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); if (0 == (u % 3)) { ret = H5Lcreate_soft(group_name, gid, linkname, H5P_DEFAULT, H5P_DEFAULT); @@ -883,7 +883,7 @@ vrfy_ns_grp_d(hid_t fid, const char *group_name, unsigned nlinks) char linkname[16]; htri_t link_exists; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); link_exists = H5Lexists(gid, linkname, H5P_DEFAULT); if (link_exists < 0) { @@ -1321,7 +1321,7 @@ os_grp_n(hid_t fid, const char *group_name, int proc_num, unsigned nlinks) while ((pass) && (u < nlinks)) { char linkname[32]; - HDsprintf(linkname, "ln%d_%u", proc_num, u); + HDsnprintf(linkname, sizeof(linkname), "ln%d_%u", proc_num, u); if (0 == (u % 2)) { ret = H5Lcreate_soft(group_name, gid, linkname, H5P_DEFAULT, H5P_DEFAULT); @@ -1479,7 +1479,7 @@ vrfy_os_grp_n(hid_t fid, const char *group_name, int proc_num, unsigned nlinks) char linkname[32]; htri_t link_exists; - HDsprintf(linkname, "ln%d_%u", proc_num, u); + HDsnprintf(linkname, sizeof(linkname), "ln%d_%u", proc_num, u); link_exists = H5Lexists(gid, linkname, H5P_DEFAULT); if (link_exists < 0) { @@ -3056,26 +3056,26 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) /* Add & verify an empty "new style" group */ if (pass) { - HDsprintf(full_path, "%s/A", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/A", base_path); HDassert(HDstrlen(full_path) < 1024); ns_grp_0(fid, full_path); } if (pass) { - HDsprintf(full_path, "%s/A", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/A", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_0(fid, full_path); } /* Add & verify a compact "new style" group (3 link messages) */ if (pass) { - HDsprintf(full_path, "%s/B", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/B", base_path); HDassert(HDstrlen(full_path) < 1024); ns_grp_c(fid, full_path, 3); } if (pass) { - HDsprintf(full_path, "%s/B", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/B", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_c(fid, full_path, 3); } @@ -3084,26 +3084,26 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * fractal heap) */ if (pass) { - HDsprintf(full_path, "%s/C", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/C", base_path); HDassert(HDstrlen(full_path) < 1024); ns_grp_d(fid, full_path, 300); } if (pass) { - HDsprintf(full_path, "%s/C", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/C", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_d(fid, full_path, 300); } /* Add & verify an empty "old style" group to file */ if (pass) { - HDsprintf(full_path, "%s/D", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/D", base_path); HDassert(HDstrlen(full_path) < 1024); os_grp_0(fid, full_path); } if (pass) { - HDsprintf(full_path, "%s/D", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/D", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_0(fid, full_path); } @@ -3112,13 +3112,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * local heap) to file */ if (pass) { - HDsprintf(full_path, "%s/E", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/E", base_path); HDassert(HDstrlen(full_path) < 1024); os_grp_n(fid, full_path, proc_num, 300); } if (pass) { - HDsprintf(full_path, "%s/E", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/E", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_n(fid, full_path, proc_num, 300); } @@ -3127,13 +3127,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/F", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/F", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_i(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/F", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/F", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, FALSE); } @@ -3142,13 +3142,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/G", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/G", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_i(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/G", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/G", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, TRUE); } @@ -3157,13 +3157,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/H", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/H", base_path); HDassert(HDstrlen(full_path) < 1024); ds_chk_i(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/H", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/H", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, FALSE); } @@ -3172,13 +3172,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/I", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/I", base_path); HDassert(HDstrlen(full_path) < 1024); ds_chk_i(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/I", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/I", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, TRUE); } @@ -3187,13 +3187,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/J", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/J", base_path); HDassert(HDstrlen(full_path) < 1024); ds_cpt_i(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/J", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/J", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, FALSE); } @@ -3202,13 +3202,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/K", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/K", base_path); HDassert(HDstrlen(full_path) < 1024); ds_cpt_i(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/K", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/K", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, TRUE); } @@ -3217,13 +3217,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * (but no data) to file */ if (pass) { - HDsprintf(full_path, "%s/L", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/L", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_v(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/L", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/L", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, FALSE); } @@ -3232,13 +3232,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * (and data) to file */ if (pass) { - HDsprintf(full_path, "%s/M", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/M", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_v(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/M", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/M", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, TRUE); } @@ -3281,14 +3281,14 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) /* validate an empty "new style" group */ if (pass) { - HDsprintf(full_path, "%s/A", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/A", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_0(fid, full_path); } /* validate a compact "new style" group (3 link messages) */ if (pass) { - HDsprintf(full_path, "%s/B", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/B", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_c(fid, full_path, 3); } @@ -3297,14 +3297,14 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * fractal heap) */ if (pass) { - HDsprintf(full_path, "%s/C", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/C", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_d(fid, full_path, 300); } /* validate an empty "old style" group in file */ if (pass) { - HDsprintf(full_path, "%s/D", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/D", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_0(fid, full_path); } @@ -3313,7 +3313,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * local heap) */ if (pass) { - HDsprintf(full_path, "%s/E", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/E", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_n(fid, full_path, proc_num, 300); } @@ -3322,7 +3322,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file. */ if (pass) { - HDsprintf(full_path, "%s/F", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/F", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, FALSE); } @@ -3331,7 +3331,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file. */ if (pass) { - HDsprintf(full_path, "%s/G", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/G", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, TRUE); } @@ -3340,7 +3340,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/H", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/H", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, FALSE); } @@ -3349,7 +3349,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/I", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/I", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, TRUE); } @@ -3358,7 +3358,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/J", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/J", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, FALSE); } @@ -3367,7 +3367,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/K", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/K", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, TRUE); } @@ -3376,7 +3376,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * (but no data) to file */ if (pass) { - HDsprintf(full_path, "%s/L", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/L", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, FALSE); } @@ -3385,7 +3385,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * (and data) to file */ if (pass) { - HDsprintf(full_path, "%s/M", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/M", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, TRUE); } diff --git a/test/page_buffer.c b/test/page_buffer.c index c078ce8..64e88fb 100644 --- a/test/page_buffer.c +++ b/test/page_buffer.c @@ -120,28 +120,28 @@ create_file(char *filename, hid_t fcpl, hid_t fapl) for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "D1dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; if (H5Dclose(dset_id) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D2dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; if (H5Dclose(dset_id) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D3dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; if (H5Dclose(dset_id) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; @@ -166,13 +166,13 @@ create_file(char *filename, hid_t fcpl, hid_t fapl) } } - HDsprintf(dset_name, "D1dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", i); if (H5Ldelete(grp_id, dset_name, H5P_DEFAULT) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D2dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", i); if (H5Ldelete(grp_id, dset_name, H5P_DEFAULT) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D3dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", i); if (H5Ldelete(grp_id, dset_name, H5P_DEFAULT) < 0) FAIL_STACK_ERROR; } @@ -259,7 +259,7 @@ open_file(char *filename, hid_t fapl, hsize_t page_size, size_t page_buffer_size for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", i); if ((dset_id = H5Dopen2(grp_id, dset_name, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; diff --git a/test/reserved.c b/test/reserved.c index f864329..08e747e 100644 --- a/test/reserved.c +++ b/test/reserved.c @@ -71,7 +71,7 @@ rsrv_heap(void) } H5E_END_TRY - HDsprintf(dset_name, "Dset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "Dset %d", i); H5E_BEGIN_TRY { @@ -115,7 +115,7 @@ rsrv_heap(void) if (H5open() < 0) TEST_ERROR; - HDsprintf(dset_name, "Dset %d", i - 2); + HDsnprintf(dset_name, sizeof(dset_name), "Dset %d", i - 2); file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT); if (file_id < 0) @@ -218,7 +218,7 @@ rsrv_ohdr(void) } /* end for */ for (i = 0; i < 2000; i++) { - HDsprintf(attrname, "attr %d", i); + HDsnprintf(attrname, sizeof(attrname), "attr %d", i); H5E_BEGIN_TRY { aid = H5Screate_simple(2, dims, NULL); diff --git a/test/tattr.c b/test/tattr.c index d66fcc3..2859f4c 100644 --- a/test/tattr.c +++ b/test/tattr.c @@ -2094,7 +2094,7 @@ test_attr_dense_verify(hid_t loc_id, unsigned max_attr) /* Re-open all the attributes by name and verify the data */ for (u = 0; u < max_attr; u++) { /* Open attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Aopen(loc_id, attrname, H5P_DEFAULT); CHECK(attr, FAIL, "H5Aopen"); @@ -2119,7 +2119,7 @@ test_attr_dense_verify(hid_t loc_id, unsigned max_attr) CHECK(attr, FAIL, "H5Aopen_by_idx"); /* Verify Name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); name_len = H5Aget_name(attr, (size_t)ATTR_NAME_LEN, check_name); VERIFY(name_len, HDstrlen(attrname), "H5Aget_name"); if (HDstrcmp(check_name, attrname) != 0) @@ -2219,7 +2219,7 @@ test_attr_dense_create(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2238,7 +2238,7 @@ test_attr_dense_create(hid_t fcpl, hid_t fapl) /* Add one more attribute, to push into "dense" storage */ /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2361,7 +2361,7 @@ test_attr_dense_open(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2384,7 +2384,7 @@ test_attr_dense_open(hid_t fcpl, hid_t fapl) /* Add one more attribute, to push into "dense" storage */ /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2523,7 +2523,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) /* Add attributes, until well into dense storage */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2568,7 +2568,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) /* Delete attributes until the attributes revert to compact storage again */ for (u--; u >= min_dense; u--) { /* Delete attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -2582,7 +2582,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) VERIFY(is_dense, TRUE, "H5O__is_attr_dense_test"); /* Delete one more attribute, which should cause reversion to compact storage */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -2595,7 +2595,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) CHECK(ret, FAIL, "test_attr_dense_verify"); /* Delete another attribute, to verify deletion in compact storage */ - HDsprintf(attrname, "attr %02u", (u - 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (u - 1)); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -2724,7 +2724,7 @@ test_attr_dense_rename(hid_t fcpl, hid_t fapl) /* Add attributes, until well into dense storage */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, H5I_INVALID_HID, "H5Acreate2"); @@ -2790,7 +2790,7 @@ test_attr_dense_rename(hid_t fcpl, hid_t fapl) unsigned value; /* Attribute value */ /* Open attribute */ - HDsprintf(attrname, "new attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "new attr %02u", u); attr = H5Aopen(dataset, attrname, H5P_DEFAULT); CHECK(attr, H5I_INVALID_HID, "H5Aopen"); @@ -2914,7 +2914,7 @@ test_attr_dense_unlink(hid_t fcpl, hid_t fapl) /* Add attributes, until well into dense storage */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3057,7 +3057,7 @@ test_attr_dense_limits(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3077,7 +3077,7 @@ test_attr_dense_limits(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 1; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3107,7 +3107,7 @@ test_attr_dense_limits(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3216,7 +3216,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3239,7 +3239,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) CHECK(sid2, FAIL, "H5Screate_simple"); /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_INT, sid2, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3522,7 +3522,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) /* Delete a few attributes until the storage switches to compact */ for (u = min_dense - 1; u <= max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); add_attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(add_attr, FAIL, "H5Acreate2"); @@ -3590,7 +3590,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(gid1, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3756,7 +3756,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3774,7 +3774,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 1; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3792,7 +3792,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 2; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, big_sid, H5P_DEFAULT, H5P_DEFAULT); if (low == H5F_LIBVER_LATEST) { CHECK(attr, FAIL, "H5Acreate2"); @@ -3815,7 +3815,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 3; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, big_sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3837,7 +3837,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 1; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3851,7 +3851,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 3; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3865,7 +3865,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 2; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3879,7 +3879,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -4278,7 +4278,7 @@ test_attr_many(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create many attributes */ for (u = 0; u < nattr; u++) { - HDsprintf(attrname, "a-%06u", u); + HDsnprintf(attrname, sizeof(attrname), "a-%06u", u); exists = H5Aexists(gid, attrname); VERIFY(exists, FALSE, "H5Aexists"); @@ -4330,7 +4330,7 @@ test_attr_many(hbool_t new_format, hid_t fcpl, hid_t fapl) for (u = 0; u < nattr; u++) { unsigned value; /* Attribute value */ - HDsprintf(attrname, "a-%06u", u); + HDsnprintf(attrname, sizeof(attrname), "a-%06u", u); exists = H5Aexists(gid, attrname); VERIFY(exists, TRUE, "H5Aexists"); @@ -4578,7 +4578,7 @@ test_attr_corder_create_compact(hid_t fcpl, hid_t fapl) /* Create several attributes, but keep storage in compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -4667,7 +4667,7 @@ test_attr_corder_create_compact(hid_t fcpl, hid_t fapl) H5A_info_t ainfo; /* Attribute information */ /* Retrieve information for attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Aget_info_by_name(my_dataset, ".", attrname, &ainfo, H5P_DEFAULT); CHECK(ret, FAIL, "H5Aget_info_by_name"); @@ -4782,7 +4782,7 @@ test_attr_corder_create_dense(hid_t fcpl, hid_t fapl) /* Create several attributes, but keep storage in compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -4805,7 +4805,7 @@ test_attr_corder_create_dense(hid_t fcpl, hid_t fapl) } /* end for */ /* Create another attribute, to push into dense storage */ - HDsprintf(attrname, "attr %02u", max_compact); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", max_compact); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -4898,7 +4898,7 @@ test_attr_corder_create_dense(hid_t fcpl, hid_t fapl) H5A_info_t ainfo; /* Attribute information */ /* Retrieve information for attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Aget_info_by_name(my_dataset, ".", attrname, &ainfo, H5P_DEFAULT); CHECK(ret, FAIL, "H5Aget_info_by_name"); @@ -5171,7 +5171,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Create several attributes, but keep storage in compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5194,7 +5194,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) } /* end for */ /* Create another attribute, to push into dense storage */ - HDsprintf(attrname, "attr %02u", max_compact); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", max_compact); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5222,7 +5222,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Delete several attributes from object, until attribute storage resumes compact form */ for (u = max_compact; u >= min_dense; u--) { - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5242,7 +5242,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) } /* end for */ /* Delete another attribute, to push attribute storage into compact form */ - HDsprintf(attrname, "attr %02u", (min_dense - 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (min_dense - 1)); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5258,7 +5258,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Re-add attributes to get back into dense form */ for (u = (min_dense - 1); u < (max_compact + 1); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5345,7 +5345,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Delete several attributes from object, until attribute storage resumes compact form */ for (u = max_compact; u >= min_dense; u--) { - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5365,7 +5365,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) } /* end for */ /* Delete another attribute, to push attribute storage into compact form */ - HDsprintf(attrname, "attr %02u", (min_dense - 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (min_dense - 1)); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5381,7 +5381,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Re-add attributes to get back into dense form */ for (u = (min_dense - 1); u < (max_compact + 1); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5410,11 +5410,11 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Delete all attributes */ for (u = max_compact; u > 0; u--) { - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); } /* end for */ - HDsprintf(attrname, "attr %02u", 0); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", 0); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); } /* end for */ @@ -5554,7 +5554,7 @@ test_attr_corder_delete(hid_t fcpl, hid_t fapl) /* Create attributes, until attribute storage is in dense form */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5897,7 +5897,7 @@ test_attr_info_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5937,7 +5937,7 @@ test_attr_info_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6381,7 +6381,7 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6456,9 +6456,9 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)0, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", (u + 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (u + 1)); else - HDsprintf(attrname, "attr %02u", (max_compact - (u + 2))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (max_compact - (u + 2))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6494,7 +6494,7 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6584,9 +6584,10 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)0, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", (u + 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (u + 1)); else - HDsprintf(attrname, "attr %02u", ((max_compact * 2) - (u + 2))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", + ((max_compact * 2) - (u + 2))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6628,7 +6629,7 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, to push into dense form */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6697,9 +6698,10 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)u, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", ((u * 2) + 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", ((u * 2) + 1)); else - HDsprintf(attrname, "attr %02u", ((max_compact * 2) - ((u * 2) + 2))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", + ((max_compact * 2) - ((u * 2) + 2))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6749,9 +6751,10 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)0, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", ((u * 2) + 3)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", ((u * 2) + 3)); else - HDsprintf(attrname, "attr %02u", ((max_compact * 2) - ((u * 2) + 4))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", + ((max_compact * 2) - ((u * 2) + 4))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6832,7 +6835,7 @@ attr_iterate2_cb(hid_t loc_id, const char *attr_name, const H5A_info_t *info, vo } /* end if */ /* Verify name of link */ - HDsprintf(attrname, "attr %02u", (unsigned)my_info.corder); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (unsigned)my_info.corder); if (HDstrcmp(attr_name, attrname) != 0) return (H5_ITER_ERROR); @@ -7342,7 +7345,7 @@ test_attr_iterate2(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7414,7 +7417,7 @@ test_attr_iterate2(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7706,7 +7709,7 @@ test_attr_open_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7765,7 +7768,7 @@ test_attr_open_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7870,7 +7873,7 @@ attr_open_check(hid_t fid, const char *dsetname, hid_t obj_id, unsigned max_attr /* Open each attribute on object by index and check that it's the correct one */ for (u = 0; u < max_attrs; u++) { /* Open the attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr_id = H5Aopen(obj_id, attrname, H5P_DEFAULT); CHECK(attr_id, FAIL, "H5Aopen"); @@ -8039,7 +8042,7 @@ test_attr_open_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -8105,7 +8108,7 @@ test_attr_open_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -8288,7 +8291,7 @@ test_attr_create_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate_by_name(fid, dsetname, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate_by_name"); @@ -8345,7 +8348,7 @@ test_attr_create_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate_by_name(fid, dsetname, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate_by_name"); @@ -8570,7 +8573,7 @@ test_attr_shared_write(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -8907,7 +8910,7 @@ test_attr_shared_rename(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -9354,7 +9357,7 @@ test_attr_shared_delete(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -9462,7 +9465,7 @@ test_attr_shared_delete(hid_t fcpl, hid_t fapl) /* Delete attributes from second dataset */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Delete second dataset's attribute */ ret = H5Adelete_by_name(fid, DSET2_NAME, attrname, H5P_DEFAULT); @@ -9726,7 +9729,7 @@ test_attr_shared_unlink(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -9850,7 +9853,7 @@ test_attr_shared_unlink(hid_t fcpl, hid_t fapl) /* Check ref count on attributes of first dataset */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Open attribute on first dataset */ attr = H5Aopen(dataset, attrname, H5P_DEFAULT); diff --git a/test/tmisc.c b/test/tmisc.c index a28e12e..f8bf602 100644 --- a/test/tmisc.c +++ b/test/tmisc.c @@ -1083,7 +1083,7 @@ test_misc6(void) /* Loop through adding attributes to each dataset */ for (u = 0; u < MISC6_NUMATTR; u++) { /* Create name for attribute */ - HDsprintf(attr_name, "Attr#%u", u); + HDsnprintf(attr_name, sizeof(attr_name), "Attr#%u", u); /* Open the file */ loc_id = H5Fopen(MISC6_FILE, H5F_ACC_RDWR, H5P_DEFAULT); @@ -3034,7 +3034,7 @@ test_misc18(void) /* Loop creating attributes on each dataset, flushing them to the file each time */ for (u = 0; u < 10; u++) { /* Set up attribute name */ - HDsprintf(attr_name, "Attr %u", u); + HDsnprintf(attr_name, sizeof(attr_name), "Attr %u", u); /* Create & close attribute on first dataset */ aid = H5Acreate2(did1, attr_name, H5T_STD_U32LE, sid, H5P_DEFAULT, H5P_DEFAULT); @@ -5504,7 +5504,7 @@ test_misc30(void) CHECK(ret, FAIL, "test_misc30_get_info"); } - HDsprintf(gname, "/g0/group%d", i); + HDsnprintf(gname, sizeof(gname), "/g0/group%d", i); gid = H5Gcreate2(fid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHECK(gid, FAIL, "H5Gcreate2"); diff --git a/test/trefstr.c b/test/trefstr.c index d0575ab..89e62db 100644 --- a/test/trefstr.c +++ b/test/trefstr.c @@ -309,7 +309,7 @@ test_refstr_asprintf_cat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%d-%s", (int)10, "foo"); + HDsnprintf(buf, sizeof(buf), "%d-%s", (int)10, "foo"); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -320,7 +320,7 @@ test_refstr_asprintf_cat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%d-%s-%f", (int)10, "foo", (double)20.0); + HDsnprintf(buf, sizeof(buf), "%d-%s-%f", (int)10, "foo", (double)20.0); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -360,7 +360,7 @@ test_refstr_acat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%s", "foo"); + HDsnprintf(buf, sizeof(buf), "%s", "foo"); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -371,7 +371,7 @@ test_refstr_acat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%s", "foobar"); + HDsnprintf(buf, sizeof(buf), "%s", "foobar"); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -386,7 +386,7 @@ test_refstr_acat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%s", "foobar"); + HDsnprintf(buf, sizeof(buf), "%s", "foobar"); large_str2 = HDmalloc(1024 + 6); CHECK_PTR(large_str2, "HDmalloc"); HDstrcpy(large_str2, "foobar"); diff --git a/test/tselect.c b/test/tselect.c index d9b625b..0d4176b 100644 --- a/test/tselect.c +++ b/test/tselect.c @@ -10862,13 +10862,15 @@ test_shape_same_dr__full_space_vs_slice(int test_num, int small_rank, int large_ HDassert(edge_size > 0); HDassert(edge_size <= 1000); - HDsprintf(test_desc_0, "\tn-cube slice through m-cube (n <= m) test %d.\n", test_num); + HDsnprintf(test_desc_0, sizeof(test_desc_0), "\tn-cube slice through m-cube (n <= m) test %d.\n", + test_num); MESSAGE(7, (test_desc_0)); /* This statement must be updated if SS_DR_MAX_RANK is changed */ - HDsprintf(test_desc_1, "\t\tranks: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d.\n", small_rank, - large_rank, offset, (int)dim_selected[0], (int)dim_selected[1], (int)dim_selected[2], - (int)dim_selected[3], (int)dim_selected[4]); + HDsnprintf(test_desc_1, sizeof(test_desc_1), + "\t\tranks: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d.\n", small_rank, large_rank, offset, + (int)dim_selected[0], (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], + (int)dim_selected[4]); MESSAGE(7, (test_desc_1)); /* copy the edge size into the dims array */ @@ -11120,15 +11122,16 @@ test_shape_same_dr__checkerboard(int test_num, int small_rank, int large_rank, i HDassert(dims_selected >= 0); HDassert(dims_selected <= large_rank); - HDsprintf(test_desc_0, "\tcheckerboard n-cube slice through m-cube (n <= m) test %d.\n", test_num); + HDsnprintf(test_desc_0, sizeof(test_desc_0), + "\tcheckerboard n-cube slice through m-cube (n <= m) test %d.\n", test_num); MESSAGE(7, (test_desc_0)); /* This statement must be updated if SS_DR_MAX_RANK is changed */ - HDsprintf(test_desc_1, - "\tranks: %d/%d edge/chkr size: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d:%d.\n", - small_rank, large_rank, (int)edge_size, (int)checker_size, offset, (int)dim_selected[0], - (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], - dims_selected); + HDsnprintf(test_desc_1, sizeof(test_desc_1), + "\tranks: %d/%d edge/chkr size: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d:%d.\n", + small_rank, large_rank, (int)edge_size, (int)checker_size, offset, (int)dim_selected[0], + (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], + dims_selected); MESSAGE(7, (test_desc_1)); /* copy the edge size into the dims array */ @@ -11664,15 +11667,16 @@ test_shape_same_dr__irregular(int test_num, int small_rank, int large_rank, int HDassert(dims_selected >= 0); HDassert(dims_selected <= large_rank); - HDsprintf(test_desc_0, "\tirregular sub set of n-cube slice through m-cube (n <= m) test %d.\n", - test_num); + HDsnprintf(test_desc_0, sizeof(test_desc_0), + "\tirregular sub set of n-cube slice through m-cube (n <= m) test %d.\n", test_num); MESSAGE(7, (test_desc_0)); /* This statement must be updated if SS_DR_MAX_RANK is changed */ - HDsprintf(test_desc_1, "\tranks: %d/%d edge: %d s/p offset: %d/%d dim_selected: %d/%d/%d/%d/%d:%d.\n", - small_rank, large_rank, edge_size, slice_offset, pattern_offset, (int)dim_selected[0], - (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], - dims_selected); + HDsnprintf(test_desc_1, sizeof(test_desc_1), + "\tranks: %d/%d edge: %d s/p offset: %d/%d dim_selected: %d/%d/%d/%d/%d:%d.\n", small_rank, + large_rank, edge_size, slice_offset, pattern_offset, (int)dim_selected[0], + (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], + dims_selected); MESSAGE(7, (test_desc_1)); /* copy the edge size into the dims array */ diff --git a/test/tvlstr.c b/test/tvlstr.c index 68f6124..5168d39 100644 --- a/test/tvlstr.c +++ b/test/tvlstr.c @@ -817,33 +817,33 @@ test_vl_rewrite(void) /* Create in file 1 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); write_scalar_dset(file1, type, space, name, name); } /* Effectively copy data from file 1 to 2 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file1, type, space, name, name); write_scalar_dset(file2, type, space, name, name); } /* Read back from file 2 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file2, type, space, name, name); } /* end for */ /* Remove from file 2. */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); ret = H5Ldelete(file2, name, H5P_DEFAULT); CHECK(ret, FAIL, "H5Ldelete"); } /* end for */ /* Effectively copy from file 1 to file 2 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file1, type, space, name, name); write_scalar_dset(file2, type, space, name, name); } /* end for */ diff --git a/test/vds_env.c b/test/vds_env.c index 17c3876..e01f2e0 100644 --- a/test/vds_env.c +++ b/test/vds_env.c @@ -346,8 +346,9 @@ main(void) /* Display testing info */ low_string = h5_get_version_string(low); high_string = h5_get_version_string(high); - HDsprintf(msg, "Testing virtual dataset with file version bounds: (%s, %s):", low_string, - high_string); + HDsnprintf(msg, sizeof(msg), + "Testing virtual dataset with file version bounds: (%s, %s):", low_string, + high_string); HDputs(msg); for (bit_config = 0; bit_config < TEST_IO_NTESTS; bit_config++) { diff --git a/testpar/t_cache.c b/testpar/t_cache.c index 8c96756..df34560 100644 --- a/testpar/t_cache.c +++ b/testpar/t_cache.c @@ -6488,7 +6488,7 @@ trace_file_check(int metadata_write_strategy) } /* end if */ if (nerrors == 0) { - HDsprintf(trace_file_name, "t_cache_trace.txt.%d", (int)file_mpi_rank); + HDsnprintf(trace_file_name, sizeof(trace_file_name), "t_cache_trace.txt.%d", (int)file_mpi_rank); if ((trace_file_ptr = HDfopen(trace_file_name, "r")) == NULL) { diff --git a/testpar/t_cache_image.c b/testpar/t_cache_image.c index feb4325..4229a77 100644 --- a/testpar/t_cache_image.c +++ b/testpar/t_cache_image.c @@ -477,7 +477,7 @@ create_data_sets(hid_t file_id, int min_dset, int max_dset) /* create the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dcreate2(file_id, dset_name, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, properties, H5P_DEFAULT); @@ -766,7 +766,7 @@ delete_data_sets(hid_t file_id, int min_dset, int max_dset) while ( ( pass ) && ( i <= max_dset ) ) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); if ( H5Ldelete(file_id, dset_name, H5P_DEFAULT) < 0) { @@ -1334,7 +1334,7 @@ par_create_dataset(int dset_num, hid_t file_id, int mpi_rank, int mpi_size) show_progress = (show_progress && (mpi_rank == 0)); verbose = (verbose && (mpi_rank == 0)); - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -1707,7 +1707,7 @@ par_delete_dataset(int dset_num, hid_t file_id, int mpi_rank) show_progress = (show_progress && (mpi_rank == 0)); - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -1840,7 +1840,7 @@ par_verify_dataset(int dset_num, hid_t file_id, int mpi_rank) show_progress = (show_progress && (mpi_rank == 0)); verbose = (verbose && (mpi_rank == 0)); - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -2208,7 +2208,7 @@ serial_verify_dataset(int dset_num, hid_t file_id, int mpi_size) hid_t dset_id = -1; hid_t filespace_id = -1; - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -2460,7 +2460,7 @@ verify_data_sets(hid_t file_id, int min_dset, int max_dset) /* open the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dopen2(file_id, dset_name, H5P_DEFAULT); if (dataset_ids[i] < 0) { diff --git a/testpar/t_dset.c b/testpar/t_dset.c index 9f922e3..2aade32 100644 --- a/testpar/t_dset.c +++ b/testpar/t_dset.c @@ -3699,10 +3699,12 @@ test_no_collective_cause_mode(int selection_mode) /* Test values */ HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); + HDsnprintf(message, sizeof(message), + "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_local_write == no_collective_cause_local_expected), message); HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); + HDsnprintf(message, sizeof(message), + "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_global_write == no_collective_cause_global_expected), message); /* Release some resources */ @@ -3939,10 +3941,12 @@ test_no_collective_cause_mode_filter(int selection_mode) /* Test values */ HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); + HDsnprintf(message, sizeof(message), + "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_local_read == (uint32_t)no_collective_cause_local_expected), message); HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); + HDsnprintf(message, sizeof(message), + "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_global_read == (uint32_t)no_collective_cause_global_expected), message); /* Release some resources */ diff --git a/testpar/t_file.c b/testpar/t_file.c index 6c6ac69..229fd6c 100644 --- a/testpar/t_file.c +++ b/testpar/t_file.c @@ -514,25 +514,25 @@ create_file(const char *filename, hid_t fcpl, hid_t fapl, int metadata_write_str VRFY((mem_dataspace >= 0), ""); for (k = 0; k < NUM_DSETS; k++) { - HDsprintf(dset_name, "D1dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); ret = H5Dclose(dset_id); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D2dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); ret = H5Dclose(dset_id); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D3dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); ret = H5Dclose(dset_id); VRFY((ret == 0), ""); - HDsprintf(dset_name, "dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); @@ -555,13 +555,13 @@ create_file(const char *filename, hid_t fcpl, hid_t fapl, int metadata_write_str for (i = 0; i < num_elements; i++) VRFY((data_array[i] == mpi_rank + 1), "Dataset Verify failed"); - HDsprintf(dset_name, "D1dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", k); ret = H5Ldelete(grp_id, dset_name, H5P_DEFAULT); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D2dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", k); ret = H5Ldelete(grp_id, dset_name, H5P_DEFAULT); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D3dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", k); ret = H5Ldelete(grp_id, dset_name, H5P_DEFAULT); VRFY((ret == 0), ""); } @@ -667,7 +667,7 @@ open_file(const char *filename, hid_t fapl, int metadata_write_strategy, hsize_t VRFY((mem_dataspace >= 0), ""); for (k = 0; k < NUM_DSETS; k++) { - HDsprintf(dset_name, "dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", k); dset_id = H5Dopen2(grp_id, dset_name, H5P_DEFAULT); VRFY((dset_id >= 0), ""); diff --git a/testpar/t_pflush1.c b/testpar/t_pflush1.c index cc569f6..0500a2d 100644 --- a/testpar/t_pflush1.c +++ b/testpar/t_pflush1.c @@ -43,7 +43,7 @@ static int data_g[100][100]; *------------------------------------------------------------------------- */ static hid_t -create_test_file(char *name, hid_t fapl_id) +create_test_file(char *name, size_t name_length, hid_t fapl_id) { hid_t fid = H5I_INVALID_HID; hid_t dcpl_id = H5I_INVALID_HID; @@ -86,7 +86,7 @@ create_test_file(char *name, hid_t fapl_id) if ((top_level_gid = H5Gcreate2(fid, "some_groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; for (i = 0; i < N_GROUPS; i++) { - HDsprintf(name, "grp%02u", (unsigned)i); + HDsnprintf(name, name_length, "grp%02u", (unsigned)i); if ((gid = H5Gcreate2(top_level_gid, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; if (H5Gclose(gid) < 0) @@ -153,7 +153,7 @@ main(int argc, char *argv[]) /* Create the file */ h5_fixname(FILENAME[0], fapl_id, name, sizeof(name)); - if ((fid1 = create_test_file(name, fapl_id)) < 0) + if ((fid1 = create_test_file(name, sizeof(name), fapl_id)) < 0) goto error; /* Flush and exit without closing the library */ if (H5Fflush(fid1, H5F_SCOPE_GLOBAL) < 0) @@ -161,7 +161,7 @@ main(int argc, char *argv[]) /* Create the other file which will not be flushed */ h5_fixname(FILENAME[1], fapl_id, name, sizeof(name)); - if ((fid2 = create_test_file(name, fapl_id)) < 0) + if ((fid2 = create_test_file(name, sizeof(name), fapl_id)) < 0) goto error; if (mpi_rank == 0) diff --git a/testpar/t_pflush2.c b/testpar/t_pflush2.c index e782f8a..8cf40d0 100644 --- a/testpar/t_pflush2.c +++ b/testpar/t_pflush2.c @@ -43,7 +43,7 @@ static int data_g[100][100]; *------------------------------------------------------------------------- */ static herr_t -check_test_file(char *name, hid_t fapl_id) +check_test_file(char *name, size_t name_length, hid_t fapl_id) { hid_t fid = H5I_INVALID_HID; hid_t sid = H5I_INVALID_HID; @@ -89,7 +89,7 @@ check_test_file(char *name, hid_t fapl_id) if ((top_level_gid = H5Gopen2(fid, "some_groups", H5P_DEFAULT)) < 0) goto error; for (i = 0; i < N_GROUPS; i++) { - HDsprintf(name, "grp%02u", (unsigned)i); + HDsnprintf(name, name_length, "grp%02u", (unsigned)i); if ((gid = H5Gopen2(top_level_gid, name, H5P_DEFAULT)) < 0) goto error; if (H5Gclose(gid) < 0) @@ -182,7 +182,7 @@ main(int argc, char *argv[]) /* Check the case where the file was flushed */ h5_fixname(FILENAME[0], fapl_id1, name, sizeof(name)); - if (check_test_file(name, fapl_id1)) { + if (check_test_file(name, sizeof(name), fapl_id1)) { H5_FAILED() goto error; } @@ -199,7 +199,7 @@ main(int argc, char *argv[]) H5Eset_auto2(H5E_DEFAULT, NULL, NULL); h5_fixname(FILENAME[1], fapl_id2, name, sizeof(name)); - if (check_test_file(name, fapl_id2)) { + if (check_test_file(name, sizeof(name), fapl_id2)) { if (mpi_rank == 0) PASSED(); } diff --git a/testpar/t_prop.c b/testpar/t_prop.c index 5979c5d..606e100 100644 --- a/testpar/t_prop.c +++ b/testpar/t_prop.c @@ -556,7 +556,7 @@ external_links(void) /* test opening a group that is to an external link, the external linked file should inherit the source file's access properties */ - HDsprintf(link_path, "%s%s%s", group_path, "/", link_name); + HDsnprintf(link_path, sizeof(link_path), "%s%s%s", group_path, "/", link_name); group = H5Gopen2(fid, link_path, H5P_DEFAULT); VRFY((group >= 0), "H5Gopen succeeded"); ret = H5Gclose(group); diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c index 8002ec2..37bb82d 100644 --- a/tools/src/h5dump/h5dump_ddl.c +++ b/tools/src/h5dump/h5dump_ddl.c @@ -838,7 +838,7 @@ dump_group(hid_t gid, const char *name) type = H5Dget_type(dset); H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); - HDsprintf(type_name, "#%s", obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); H5free_memory(obj_tok_str); dump_function_table->dump_named_datatype_function(type, type_name); @@ -1970,7 +1970,7 @@ handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED *data, int pe, /* unnamed datatype */ H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_tok_str); - HDsprintf(name, "/#%s", obj_tok_str); + HDsnprintf(name, sizeof(name), "/#%s", obj_tok_str); H5free_memory(obj_tok_str); if (!HDstrcmp(name, real_name)) diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c index 8fec49c..19efd6f 100644 --- a/tools/src/h5dump/h5dump_xml.c +++ b/tools/src/h5dump/h5dump_xml.c @@ -600,7 +600,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen ref_path_table_gen_fake(str, &obj_token); H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsprintf(outstr, "xid_%s", obj_tok_str); + HDsnprintf(outstr, outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -615,7 +615,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen ref_path_table_gen_fake(str, &obj_token); H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsprintf(outstr, "xid_%s", obj_tok_str); + HDsnprintf(outstr, outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -627,7 +627,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen } H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsprintf(outstr, "xid_%s", obj_tok_str); + HDsnprintf(outstr, outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -2802,7 +2802,7 @@ xml_dump_group(hid_t gid, const char *name) type = H5Dget_type(dset); H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); - HDsprintf(type_name, "#%s", obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); H5free_memory(obj_tok_str); dump_function_table->dump_named_datatype_function(type, type_name); @@ -2895,7 +2895,7 @@ xml_dump_group(hid_t gid, const char *name) type = H5Dget_type(dset); H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); - HDsprintf(type_name, "#%s", obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); H5free_memory(obj_tok_str); dump_function_table->dump_named_datatype_function(type, type_name); diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c index 31fa7cf..317db81 100644 --- a/tools/src/h5import/h5import.c +++ b/tools/src/h5import/h5import.c @@ -3784,7 +3784,7 @@ setDefaultValues(struct Input *in, int count) in->path.count = 1; HDstrcpy(temp, "dataset"); - HDsprintf(num, "%d", count); + HDsnprintf(num, sizeof(num), "%d", count); HDstrcat(temp, num); HDstrcpy(in->path.group[0], temp); diff --git a/tools/src/h5perf/pio_engine.c b/tools/src/h5perf/pio_engine.c index 3edc74a..e316245 100644 --- a/tools/src/h5perf/pio_engine.c +++ b/tools/src/h5perf/pio_engine.c @@ -282,7 +282,7 @@ do_pio(parameters param) /* Open file for write */ char base_name[256]; - HDsprintf(base_name, "#pio_tmp_%lu", nf); + HDsnprintf(base_name, sizeof(base_name), "#pio_tmp_%lu", nf); pio_create_filename(iot, base_name, fname, sizeof(fname)); if (pio_debug_level > 0) HDfprintf(output, "rank %d: data filename=%s\n", pio_mpi_rank_g, fname); @@ -898,7 +898,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nby } /* end if */ } /* end else */ - HDsprintf(dname, "Dataset_%ld", ndset); + HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset); h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, h5dcpl); if (h5ds_id < 0) { @@ -1879,7 +1879,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbyt break; case PHDF5: - HDsprintf(dname, "Dataset_%ld", ndset); + HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset); h5ds_id = H5DOPEN(fd->h5fd, dname); if (h5ds_id < 0) { HDfprintf(stderr, "HDF5 Dataset open failed\n"); diff --git a/tools/test/misc/h5clear_gentest.c b/tools/test/misc/h5clear_gentest.c index 225fe16..97feabd 100644 --- a/tools/test/misc/h5clear_gentest.c +++ b/tools/test/misc/h5clear_gentest.c @@ -428,7 +428,7 @@ main(void) if ((my_fapl = H5Pcopy(fapl2)) < 0) goto error; /* Create the file */ - HDsprintf(fname, "%s%s", new_format ? "latest_" : "", FILENAME[0]); + HDsnprintf(fname, sizeof(fname), "%s%s", new_format ? "latest_" : "", FILENAME[0]); if ((fid = H5Fcreate(fname, H5F_ACC_TRUNC | (new_format ? 0 : H5F_ACC_SWMR_WRITE), H5P_DEFAULT, my_fapl)) < 0) goto error; @@ -453,7 +453,7 @@ main(void) goto error; /* Create the file */ - HDsprintf(fname, "%s%s", new_format ? "latest_" : "", FILENAME[1]); + HDsnprintf(fname, sizeof(fname), "%s%s", new_format ? "latest_" : "", FILENAME[1]); if ((fid = H5Fcreate(fname, H5F_ACC_TRUNC | (new_format ? 0 : H5F_ACC_SWMR_WRITE), H5P_DEFAULT, my_fapl)) < 0) goto error; diff --git a/tools/test/perform/perf_meta.c b/tools/test/perform/perf_meta.c index d8ed9ec..ad76711 100644 --- a/tools/test/perform/perf_meta.c +++ b/tools/test/perform/perf_meta.c @@ -304,7 +304,7 @@ create_dsets(hid_t file) * Create a dataset using the default dataset creation properties. */ for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dataset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", i); if ((dataset = H5Dcreate2(file, dset_name, H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; @@ -366,14 +366,14 @@ create_attrs_1(void) * Create all(user specifies the number) attributes for each dataset */ for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dataset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", i); open_t.start = retrieve_time(); if ((dataset = H5Dopen2(file, dset_name, H5P_DEFAULT)) < 0) goto error; perf(&open_t, open_t.start, retrieve_time()); for (j = 0; j < NUM_ATTRS; j++) { - HDsprintf(attr_name, "all attrs for each dset %d", j); + HDsnprintf(attr_name, sizeof(attr_name), "all attrs for each dset %d", j); attr_t.start = retrieve_time(); if ((attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -468,7 +468,7 @@ create_attrs_2(void) * Create all(user specifies the number) attributes for each new dataset */ for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dataset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", i); create_t.start = retrieve_time(); if ((dataset = H5Dcreate2(file, dset_name, H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -476,7 +476,7 @@ create_attrs_2(void) perf(&create_t, create_t.start, retrieve_time()); for (j = 0; j < NUM_ATTRS; j++) { - HDsprintf(attr_name, "all attrs for each dset %d", j); + HDsnprintf(attr_name, sizeof(attr_name), "all attrs for each dset %d", j); attr_t.start = retrieve_time(); if ((attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -579,14 +579,14 @@ create_attrs_3(void) for (i = 0; i < loop_num; i++) { for (j = 0; j < NUM_DSETS; j++) { - HDsprintf(dset_name, "dataset %d", j); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", j); open_t.start = retrieve_time(); if ((dataset = H5Dopen2(file, dset_name, H5P_DEFAULT)) < 0) goto error; perf(&open_t, open_t.start, retrieve_time()); for (k = 0; k < BATCH_ATTRS; k++) { - HDsprintf(attr_name, "some attrs for each dset %d %d", i, k); + HDsnprintf(attr_name, sizeof(attr_name), "some attrs for each dset %d %d", i, k); attr_t.start = retrieve_time(); if ((attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, H5P_DEFAULT)) < 0) diff --git a/utils/tools/h5dwalk/h5dwalk.c b/utils/tools/h5dwalk/h5dwalk.c index d7e22ba..5a22d75 100644 --- a/utils/tools/h5dwalk/h5dwalk.c +++ b/utils/tools/h5dwalk/h5dwalk.c @@ -1071,12 +1071,12 @@ run_command(int argc __attribute__((unused)), char **argv, char *cmdline, const if ((log_instance > 0) || processing_inputfile) { if (processing_inputfile) log_instance = current_input_index; - HDsprintf(logpath, "%s/%s_%s.log_%d", HDgetcwd(current_dir, sizeof(current_dir)), logbase, - thisapp, log_instance); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log_%d", + HDgetcwd(current_dir, sizeof(current_dir)), logbase, thisapp, log_instance); } else { - HDsprintf(logpath, "%s/%s_%s.log", HDgetcwd(current_dir, sizeof(current_dir)), logbase, - thisapp); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log", + HDgetcwd(current_dir, sizeof(current_dir)), logbase, thisapp); } } else { @@ -1085,15 +1085,17 @@ run_command(int argc __attribute__((unused)), char **argv, char *cmdline, const if (processing_inputfile) log_instance = current_input_index; if (txtlog[log_len - 1] == '/') - HDsprintf(logpath, "%s%s_%s.log_%d", txtlog, logbase, thisapp, log_instance); + HDsnprintf(logpath, sizeof(logpath), "%s%s_%s.log_%d", txtlog, logbase, thisapp, + log_instance); else - HDsprintf(logpath, "%s/%s_%s.log_%d", txtlog, logbase, thisapp, log_instance); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log_%d", txtlog, logbase, thisapp, + log_instance); } else { if (txtlog[log_len - 1] == '/') - HDsprintf(logpath, "%s%s_%s.log", txtlog, logbase, thisapp); + HDsnprintf(logpath, sizeof(logpath), "%s%s_%s.log", txtlog, logbase, thisapp); else - HDsprintf(logpath, "%s/%s_%s.log", txtlog, logbase, thisapp); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log", txtlog, logbase, thisapp); } } @@ -1204,7 +1206,7 @@ MFU_PRED_EXEC(mfu_flist flist, uint64_t idx, void *arg) } } - HDsprintf(cmdline, "\n---------\nCommand:"); + HDsnprintf(cmdline, sizeof(cmdline), "\n---------\nCommand:"); b_offset = strlen(cmdline); for (k = 0; k < count; k++) { HDsprintf(&cmdline[b_offset], " %s", argv[k]); @@ -1242,7 +1244,7 @@ static void add_executable(int argc, char **argv, char *cmdstring, int *f_index, int f_count __attribute__((unused))) { char cmdline[2048]; - HDsprintf(cmdline, "\n---------\nCommand: %s\n", cmdstring); + HDsnprintf(cmdline, sizeof(cmdline), "\n---------\nCommand: %s\n", cmdstring); argv[argc] = NULL; run_command(argc, argv, cmdline, argv[f_index[0]]); return; -- cgit v0.12 From 2b3bb3659cc7dca125a6e91080452b71632968cb Mon Sep 17 00:00:00 2001 From: David Young Date: Fri, 28 Jan 2022 16:44:47 -0600 Subject: Fix some spelling. (#1402) --- src/H5Tnative.c | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/H5Tnative.c b/src/H5Tnative.c index 4529e57..e6fab51 100644 --- a/src/H5Tnative.c +++ b/src/H5Tnative.c @@ -43,7 +43,7 @@ static herr_t H5T__cmp_offset(size_t *comp_size, size_t *offset, size_t elem_siz * * Purpose: High-level API to return the native type of a datatype. * The native type is chosen by matching the size and class of - * querried datatype from the following native premitive + * queried datatype from the following native primitive * datatypes: * H5T_NATIVE_CHAR H5T_NATIVE_UCHAR * H5T_NATIVE_SHORT H5T_NATIVE_USHORT @@ -56,7 +56,7 @@ static herr_t H5T__cmp_offset(size_t *comp_size, size_t *offset, size_t elem_siz * H5T_NATIVE_LDOUBLE * * Compound, array, enum, and VL types all choose among these - * types for their members. Time, Bifield, Opaque, Reference + * types for their members. Time, Bitfield, Opaque, Reference * types are only copy out. * * Return: Success: Returns the native data type if successful. @@ -696,7 +696,7 @@ H5_GCC_DIAG_OFF("duplicated-branches") /*------------------------------------------------------------------------- * Function: H5T__get_native_float * - * Purpose: Returns the native floatt type of a datatype. + * Purpose: Returns the native float type of a datatype. * * Return: Success: Returns the native data type if successful. * -- cgit v0.12 From bcf95655354ab9c92f823656ee1722fd91694305 Mon Sep 17 00:00:00 2001 From: Sean McBride Date: Sat, 29 Jan 2022 15:21:30 -0500 Subject: Added another missing override keyword on a dtor (#1384) --- c++/src/H5Location.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/c++/src/H5Location.h b/c++/src/H5Location.h index e990ec8..0aec4d2 100644 --- a/c++/src/H5Location.h +++ b/c++/src/H5Location.h @@ -334,7 +334,7 @@ class H5_DLLCPP H5Location : public IdComponent { #endif // DOXYGEN_SHOULD_SKIP_THIS // Noop destructor. - virtual ~H5Location(); + virtual ~H5Location() override; }; // end of H5Location } // namespace H5 -- cgit v0.12 From 86ef00fd67d4f5007ff8e3390631009ad75891a5 Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Sat, 29 Jan 2022 14:22:30 -0600 Subject: Unify handling of collective metadata reads status (#1206) --- release_docs/RELEASE.txt | 21 ++++++++ src/H5C.c | 39 ++++++++++---- src/H5CX.c | 2 +- src/H5Dchunk.c | 17 +++--- src/H5Dmpio.c | 109 +++++++++++++++++++++++++++----------- src/H5Fmpi.c | 132 +++++++++++++++++++++++++++++++++++++++++++++-- src/H5Fprivate.h | 2 + src/H5Pfapl.c | 24 ++++----- src/H5Z.c | 14 +---- testpar/t_cache.c | 40 ++++++++++---- testpar/t_coll_md_read.c | 93 +++++++++++++++++---------------- 11 files changed, 357 insertions(+), 136 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index bba27c9..ece00cc 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1083,6 +1083,27 @@ Bug Fixes since HDF5-1.12.0 release (DER - 2021/11/23, HDFFV-11286) + - Unified handling of collective metadata reads to correctly fix old bugs + + Due to MPI-related issues occurring in HDF5 from mismanagement of the + status of collective metadata reads, they were forced to be disabled + during chunked dataset raw data I/O in the HDF5 1.10.5 release. This + wouldn't generally have affected application performance because HDF5 + already disables collective metadata reads during chunk lookup, since + it is generally unlikely that the same chunks will be read by all MPI + ranks in the I/O operation. However, this was only a partial solution + that wasn't granular enough. + + This change now unifies the handling of the file-global flag and the + API context-level flag for collective metadata reads in order to + simplify querying of the true status of collective metadata reads. Thus, + collective metadata reads are once again enabled for chunked dataset + raw data I/O, but manually controlled at places where some processing + occurs on MPI rank 0 only and would cause issues when collective + metadata reads are enabled. + + (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562) + - Fixed several potential MPI deadlocks in library failure conditions In the parallel library, there were several places where MPI rank 0 diff --git a/src/H5C.c b/src/H5C.c index 889351d..22df59c 100644 --- a/src/H5C.c +++ b/src/H5C.c @@ -1518,17 +1518,26 @@ H5C_insert_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *thing, u #ifdef H5_HAVE_PARALLEL if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) - coll_access = H5CX_get_coll_metadata_read(); + coll_access = H5F_get_coll_metadata_reads(f); entry_ptr->coll_access = coll_access; if (coll_access) { H5C__INSERT_IN_COLL_LIST(cache_ptr, entry_ptr, FAIL) /* Make sure the size of the collective entries in the cache remain in check */ - if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) - if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") - } /* end if */ + if (H5P_USER_TRUE == H5F_COLL_MD_READ(f)) { + if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) { + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") + } /* end if */ + } /* end if */ + else { + if (cache_ptr->max_cache_size * 40 < cache_ptr->coll_list_size * 100) { + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") + } /* end if */ + } /* end else */ + } /* end if */ #endif done: @@ -2248,7 +2257,7 @@ H5C_protect(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *udata, unsign #ifdef H5_HAVE_PARALLEL if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) - coll_access = H5CX_get_coll_metadata_read(); + coll_access = H5F_get_coll_metadata_reads(f); #endif /* H5_HAVE_PARALLEL */ /* first check to see if the target is in cache */ @@ -2600,11 +2609,19 @@ H5C_protect(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *udata, unsign #ifdef H5_HAVE_PARALLEL /* Make sure the size of the collective entries in the cache remain in check */ - if (coll_access) - if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) - if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") -#endif /* H5_HAVE_PARALLEL */ + if (coll_access) { + if (H5P_USER_TRUE == H5F_COLL_MD_READ(f)) { + if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") + } /* end if */ + else { + if (cache_ptr->max_cache_size * 40 < cache_ptr->coll_list_size * 100) + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") + } /* end else */ + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ done: #if H5C_DO_EXTREME_SANITY_CHECKS diff --git a/src/H5CX.c b/src/H5CX.c index 89e4c91..c5bb8e4 100644 --- a/src/H5CX.c +++ b/src/H5CX.c @@ -1423,7 +1423,7 @@ done: * Purpose: Sanity checks and sets up collective operations. * * Note: Should be called for all API routines that modify file - * file metadata but don't pass in an access property list. + * metadata but don't pass in an access property list. * * Return: Non-negative on success / Negative on failure * diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 5d7c1b2..1b0e579 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -3178,7 +3178,9 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udat unsigned idx = 0; /* Index of chunk in cache, if present */ hbool_t found = FALSE; /* In cache? */ #ifdef H5_HAVE_PARALLEL - hbool_t reenable_coll_md_reads = FALSE; + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t restore_md_reads_state = FALSE; #endif herr_t ret_value = SUCCEED; /* Return value */ @@ -3252,11 +3254,10 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udat * processes. */ if (H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) { - hbool_t do_coll_md_reads = H5CX_get_coll_metadata_read(); - if (do_coll_md_reads) { - H5CX_set_coll_metadata_read(FALSE); - reenable_coll_md_reads = TRUE; - } + md_reads_file_flag = H5P_FORCE_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(idx_info.f, &md_reads_file_flag, &md_reads_context_flag); + restore_md_reads_state = TRUE; } #endif /* H5_HAVE_PARALLEL */ @@ -3302,8 +3303,8 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udat done: #ifdef H5_HAVE_PARALLEL /* Re-enable collective metadata reads if we disabled them */ - if (reenable_coll_md_reads) - H5CX_set_coll_metadata_read(TRUE); + if (restore_md_reads_state) + H5F_set_coll_metadata_reads(dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); #endif /* H5_HAVE_PARALLEL */ FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index cf8a6ef..ce790c4 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -808,10 +808,6 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HDassert(type_info); HDassert(fm); - /* Disable collective metadata reads for chunked dataset I/O operations - * in order to prevent potential hangs */ - H5CX_set_coll_metadata_read(FALSE); - /* Check the optional property list for the collective chunk IO optimization option */ if (H5CX_get_mpio_chunk_opt_mode(&chunk_opt_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get chunk optimization option") @@ -2306,17 +2302,20 @@ static herr_t H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, H5D_chunk_addr_info_t chunk_addr_info_array[], int sum_chunk) { - H5SL_node_t * chunk_node; /* Current node in chunk skip list */ - H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */ - haddr_t chunk_addr; /* Current chunking address of this node */ - haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */ - hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */ - int bsearch_coll_chunk_threshold; - int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND; - int mpi_size; /* Number of MPI processes */ - int mpi_code; /* MPI return code */ - int i; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ + H5SL_node_t * chunk_node; /* Current node in chunk skip list */ + H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */ + haddr_t chunk_addr; /* Current chunking address of this node */ + haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */ + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t restore_md_reads_state = FALSE; + hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */ + int bsearch_coll_chunk_threshold; + int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND; + int mpi_size; /* Number of MPI processes */ + int mpi_code; /* MPI return code */ + int i; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -2360,7 +2359,32 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") if (mpi_rank == 0) { - if (H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) { + herr_t result; + + /* + * If enabled, disable collective metadata reads here. + * Since the chunk address mapping is done on rank 0 + * only here, it will cause problems if collective + * metadata reads are enabled. + */ + if (H5F_get_coll_metadata_reads(io_info->dset->oloc.file)) { + md_reads_file_flag = H5P_FORCE_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, + &md_reads_context_flag); + restore_md_reads_state = TRUE; + } + + result = H5D__chunk_addrmap(io_info, total_chunk_addr_array); + + /* Ensure that we restore the old collective metadata reads state */ + if (restore_md_reads_state) { + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, + &md_reads_context_flag); + restore_md_reads_state = FALSE; + } + + if (result < 0) { size_t u; /* Clear total chunk address array */ @@ -2424,6 +2448,10 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, } /* end if */ done: + /* Re-enable collective metadata reads if we disabled them */ + if (restore_md_reads_state) + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); + if (total_chunk_addr_array) H5MM_xfree(total_chunk_addr_array); @@ -2471,20 +2499,23 @@ static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assign_io_mode[], haddr_t chunk_addr[]) { - size_t total_chunks; - unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk; - uint8_t * io_mode_info = NULL; - uint8_t * recv_io_mode_info = NULL; - uint8_t * mergebuf = NULL; - uint8_t * tempbuf; - H5SL_node_t * chunk_node; - H5D_chunk_info_t *chunk_info; - int mpi_size, mpi_rank; - MPI_Comm comm; - int root; - size_t ic; - int mpi_code; - herr_t ret_value = SUCCEED; + size_t total_chunks; + unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk; + uint8_t * io_mode_info = NULL; + uint8_t * recv_io_mode_info = NULL; + uint8_t * mergebuf = NULL; + uint8_t * tempbuf; + H5SL_node_t * chunk_node; + H5D_chunk_info_t * chunk_info; + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t restore_md_reads_state = FALSE; + int mpi_size, mpi_rank; + MPI_Comm comm; + int root; + size_t ic; + int mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -2544,6 +2575,20 @@ H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assig size_t nproc; unsigned *nproc_per_chunk; + /* + * If enabled, disable collective metadata reads here. + * Since the chunk address mapping is done on rank 0 + * only here, it will cause problems if collective + * metadata reads are enabled. + */ + if (H5F_get_coll_metadata_reads(io_info->dset->oloc.file)) { + md_reads_file_flag = H5P_FORCE_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, + &md_reads_context_flag); + restore_md_reads_state = TRUE; + } + /* pre-computing: calculate number of processes and regularity of the selection occupied in each chunk */ if (NULL == (nproc_per_chunk = (unsigned *)H5MM_calloc(total_chunks * sizeof(unsigned)))) @@ -2610,6 +2655,10 @@ H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assig #endif done: + /* Re-enable collective metadata reads if we disabled them */ + if (restore_md_reads_state) + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); + if (io_mode_info) H5MM_free(io_mode_info); if (mergebuf) diff --git a/src/H5Fmpi.c b/src/H5Fmpi.c index 53d2d78..78290c6 100644 --- a/src/H5Fmpi.c +++ b/src/H5Fmpi.c @@ -31,11 +31,12 @@ /***********/ /* Headers */ /***********/ -#include "H5private.h" /* Generic Functions */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5Fpkg.h" /* File access */ -#include "H5FDprivate.h" /* File drivers */ -#include "H5Iprivate.h" /* IDs */ +#include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Fpkg.h" /* File access */ +#include "H5FDprivate.h" /* File drivers */ +#include "H5Iprivate.h" /* IDs */ #include "H5VLnative_private.h" /* Native VOL connector */ @@ -402,4 +403,125 @@ H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm) done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5F_mpi_retrieve_comm */ + +/*------------------------------------------------------------------------- + * Function: H5F_get_coll_metadata_reads + * + * Purpose: Determines whether collective metadata reads should be + * performed. This routine is meant to be the single source of + * truth for the collective metadata reads status, as it + * coordinates between the file-global flag and the flag set + * for the current operation in the current API context. + * + * Return: TRUE/FALSE (can't fail) + * + *------------------------------------------------------------------------- + */ +hbool_t +H5F_get_coll_metadata_reads(const H5F_t *file) +{ + H5P_coll_md_read_flag_t file_flag = H5P_USER_FALSE; + hbool_t ret_value = FALSE; + + FUNC_ENTER_NOAPI_NOERR + + HDassert(file && file->shared); + + /* Retrieve the file-global flag */ + file_flag = H5F_COLL_MD_READ(file); + + /* If file flag is set to H5P_FORCE_FALSE, exit early + * with FALSE, since collective metadata reads have + * been explicitly disabled somewhere in the library. + */ + if (H5P_FORCE_FALSE == file_flag) + ret_value = FALSE; + else { + /* If file flag is set to H5P_USER_TRUE, ignore + * any settings in the API context. A file-global + * setting of H5P_USER_TRUE for collective metadata + * reads should ignore any settings on an Access + * Property List for an individual operation. + */ + if (H5P_USER_TRUE == file_flag) + ret_value = TRUE; + else { + /* Get the collective metadata reads flag from + * the current API context. + */ + ret_value = H5CX_get_coll_metadata_read(); + } + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5F_get_coll_metadata_reads() */ + +/*------------------------------------------------------------------------- + * Function: H5F_set_coll_metadata_reads + * + * Purpose: Used to temporarily modify the collective metadata reads + * status. This is useful for cases where either: + * + * * Collective metadata reads are enabled, but need to be + * disabled for an operation about to occur that may trigger + * an independent metadata read (such as only rank 0 doing + * something) + * + * * Metadata reads are currently independent, but it is + * guaranteed that the application has maintained + * collectivity at the interface level (e.g., an operation + * that modifies metadata is being performed). In this case, + * it should be safe to enable collective metadata reads, + * barring any internal library issues that may occur + * + * After completion, the `file_flag` parameter will be set to + * the previous value of the file-global collective metadata + * reads flag. The `context_flag` parameter will be set to the + * previous value of the API context's collective metadata + * reads flag. Another call to this routine should be made to + * restore these values (see below warning). + * + * !! WARNING !! + * It is dangerous to modify the collective metadata reads + * status, as this can cause crashes, hangs and corruption in + * the HDF5 file when improperly done. Therefore, the + * `file_flag` and `context_flag` parameters are both + * mandatory, and it is assumed that the caller will guarantee + * these settings are restored with another call to this + * routine once the bracketed operation is complete. + * !! WARNING !! + * + * Return: Nothing + * + *------------------------------------------------------------------------- + */ +void +H5F_set_coll_metadata_reads(H5F_t *file, H5P_coll_md_read_flag_t *file_flag, hbool_t *context_flag) +{ + H5P_coll_md_read_flag_t prev_file_flag = H5P_USER_FALSE; + hbool_t prev_context_flag = FALSE; + + FUNC_ENTER_NOAPI_NOERR + + HDassert(file && file->shared); + HDassert(file_flag); + HDassert(context_flag); + + /* Save old state */ + prev_file_flag = H5F_COLL_MD_READ(file); + prev_context_flag = H5CX_get_coll_metadata_read(); + + /* Set new desired state */ + if (prev_file_flag != *file_flag) { + file->shared->coll_md_read = *file_flag; + *file_flag = prev_file_flag; + } + if (prev_context_flag != *context_flag) { + H5CX_set_coll_metadata_read(*context_flag); + *context_flag = prev_context_flag; + } + + FUNC_LEAVE_NOAPI_VOID +} /* end H5F_set_coll_metadata_reads() */ + #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index a5ccbab..af65c9d 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -962,6 +962,8 @@ H5_DLL MPI_Comm H5F_mpi_get_comm(const H5F_t *f); H5_DLL int H5F_shared_mpi_get_size(const H5F_shared_t *f_sh); H5_DLL int H5F_mpi_get_size(const H5F_t *f); H5_DLL herr_t H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm); +H5_DLL hbool_t H5F_get_coll_metadata_reads(const H5F_t *f); +H5_DLL void H5F_set_coll_metadata_reads(H5F_t *f, H5P_coll_md_read_flag_t *file_flag, hbool_t *context_flag); #endif /* H5_HAVE_PARALLEL */ /* External file cache routines */ diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c index 47c17db..2c3caa8 100644 --- a/src/H5Pfapl.c +++ b/src/H5Pfapl.c @@ -5284,15 +5284,14 @@ H5P__decode_coll_md_read_flag_t(const void **_pp, void *_value) * Function: H5Pset_all_coll_metadata_ops * * Purpose: Tell the library whether the metadata read operations will - * be done collectively (1) or not (0). Default is independent. - * With collective mode, the library will optimize access to - * metadata operations on the file. + * be done collectively (1) or not (0). Default is independent. + * With collective mode, the library will optimize access to + * metadata operations on the file. * * Note: This routine accepts file access property lists, link - * access property lists, attribute access property lists, - * dataset access property lists, group access property lists, - * named datatype access property lists, - * and dataset transfer property lists. + * access property lists, attribute access property lists, + * dataset access property lists, group access property lists + * and named datatype access property lists. * * Return: Non-negative on success/Negative on failure * @@ -5312,7 +5311,7 @@ H5Pset_all_coll_metadata_ops(hid_t plist_id, hbool_t is_collective) H5TRACE2("e", "ib", plist_id, is_collective); /* Compare the property list's class against the other class */ - /* (Dataset, group, attribute, and named datype access property lists + /* (Dataset, group, attribute, and named datatype access property lists * are sub-classes of link access property lists -QAK) */ if (TRUE != H5P_isa_class(plist_id, H5P_LINK_ACCESS) && TRUE != H5P_isa_class(plist_id, H5P_FILE_ACCESS)) @@ -5342,10 +5341,9 @@ done: * Purpose: Gets information about collective metadata read mode. * * Note: This routine accepts file access property lists, link - * access property lists, attribute access property lists, - * dataset access property lists, group access property lists, - * named datatype access property lists, - * and dataset transfer property lists. + * access property lists, attribute access property lists, + * dataset access property lists, group access property lists, + * and named datatype access property lists. * * Return: Non-negative on success/Negative on failure * @@ -5363,7 +5361,7 @@ H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective /*out*/) H5TRACE2("e", "ix", plist_id, is_collective); /* Compare the property list's class against the other class */ - /* (Dataset, group, attribute, and named datype access property lists + /* (Dataset, group, attribute, and named datatype access property lists * are sub-classes of link access property lists -QAK) */ if (TRUE != H5P_isa_class(plist_id, H5P_LINK_ACCESS) && TRUE != H5P_isa_class(plist_id, H5P_FILE_ACCESS)) diff --git a/src/H5Z.c b/src/H5Z.c index bcdd837..763eac2 100644 --- a/src/H5Z.c +++ b/src/H5Z.c @@ -594,14 +594,9 @@ H5Z__flush_file_cb(void *obj_ptr, hid_t H5_ATTR_UNUSED obj_id, void H5_ATTR_PARA /* Do a global flush if the file is opened for write */ if (H5F_ACC_RDWR & H5F_INTENT(f)) { -/* When parallel HDF5 is defined, check for collective metadata reads on this - * file and set the flag for metadata I/O in the API context. -QAK, 2018/02/14 - */ #ifdef H5_HAVE_PARALLEL /* Check if MPIO driver is used */ if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { - H5P_coll_md_read_flag_t coll_md_read; /* Do all metadata reads collectively */ - /* Sanity check for collectively calling H5Zunregister, if requested */ /* (Sanity check assumes that a barrier on one file's comm * is sufficient (i.e. that there aren't different comms for @@ -621,13 +616,8 @@ H5Z__flush_file_cb(void *obj_ptr, hid_t H5_ATTR_UNUSED obj_id, void H5_ATTR_PARA /* Set the "sanity checked" flag */ object->sanity_checked = TRUE; } /* end if */ - - /* Check whether to use the collective metadata read DXPL */ - coll_md_read = H5F_COLL_MD_READ(f); - if (H5P_USER_TRUE == coll_md_read) - H5CX_set_coll_metadata_read(TRUE); - } /* end if */ -#endif /* H5_HAVE_PARALLEL */ + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ /* Call the flush routine for mounted file hierarchies */ if (H5F_flush_mounts((H5F_t *)obj_ptr) < 0) diff --git a/testpar/t_cache.c b/testpar/t_cache.c index df34560..70ada01 100644 --- a/testpar/t_cache.c +++ b/testpar/t_cache.c @@ -6623,13 +6623,15 @@ trace_file_check(int metadata_write_strategy) static hbool_t smoke_check_6(int metadata_write_strategy) { - hbool_t success = TRUE; - int i; - int max_nerrors; - hid_t fid = -1; - H5F_t * file_ptr = NULL; - H5C_t * cache_ptr = NULL; - struct mssg_t mssg; + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t success = TRUE; + int i; + int max_nerrors; + hid_t fid = -1; + H5F_t * file_ptr = NULL; + H5C_t * cache_ptr = NULL; + struct mssg_t mssg; switch (metadata_write_strategy) { @@ -6685,7 +6687,9 @@ smoke_check_6(int metadata_write_strategy) virt_num_data_entries = NUM_DATA_ENTRIES; /* insert the first half collectively */ - H5CX_set_coll_metadata_read(TRUE); + md_reads_file_flag = H5P_USER_TRUE; + md_reads_context_flag = TRUE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = 0; i < virt_num_data_entries / 2; i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6704,9 +6708,13 @@ smoke_check_6(int metadata_write_strategy) H5_CHECK_OVERFLOW(cache_ptr->max_cache_size, size_t, double); HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); /* insert the other half independently */ - H5CX_set_coll_metadata_read(FALSE); + md_reads_file_flag = H5P_USER_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = virt_num_data_entries / 2; i < virt_num_data_entries; i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6724,6 +6732,8 @@ smoke_check_6(int metadata_write_strategy) /* Make sure coll entries do not cross the 80% threshold */ HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); /* flush the file */ if (H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0) { @@ -6734,7 +6744,9 @@ smoke_check_6(int metadata_write_strategy) } /* Protect the first half of the entries collectively */ - H5CX_set_coll_metadata_read(TRUE); + md_reads_file_flag = H5P_USER_TRUE; + md_reads_context_flag = TRUE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = 0; i < (virt_num_data_entries / 2); i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6752,9 +6764,13 @@ smoke_check_6(int metadata_write_strategy) /* Make sure coll entries do not cross the 80% threshold */ HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); /* protect the other half independently */ - H5CX_set_coll_metadata_read(FALSE); + md_reads_file_flag = H5P_USER_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = virt_num_data_entries / 2; i < virt_num_data_entries; i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6772,6 +6788,8 @@ smoke_check_6(int metadata_write_strategy) /* Make sure coll entries do not cross the 80% threshold */ HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = 0; i < (virt_num_data_entries); i++) { unlock_entry(file_ptr, i, H5AC__NO_FLAGS_SET); diff --git a/testpar/t_coll_md_read.c b/testpar/t_coll_md_read.c index 66f3151..cabdea0 100644 --- a/testpar/t_coll_md_read.c +++ b/testpar/t_coll_md_read.c @@ -34,10 +34,9 @@ #define MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS 2 -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue" -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE 20000 -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE 1 -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1 +#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM 10000 +#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue" +#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1 /* * A test for issue HDFFV-10501. A parallel hang was reported which occurred @@ -339,21 +338,34 @@ test_multi_chunk_io_addrmap_issue(void) * collective metadata reads being made only by process 0 in H5D__sort_chunk(). * * NOTE: Due to the way that the threshold value which pertains to this test - * is currently calculated within HDF5, there are several conditions that this - * test must maintain. Refer to the function H5D__sort_chunk in H5Dmpio.c for - * a better idea of why. + * is currently calculated within HDF5, the following two conditions must be + * true to trigger the issue: * - * Condition 1: We need to make sure that the test always selects every single - * chunk in the dataset. It is fine if the selection is split up among multiple - * ranks, but their combined selection must cover the whole dataset. + * Condition 1: A certain threshold ratio must be met in order to have HDF5 + * obtain all chunk addresses collectively inside H5D__sort_chunk(). This is + * given by the following: * - * Condition 2: The number of chunks in the dataset divided by the number of MPI - * ranks must exceed or equal 10000. In other words, each MPI rank must be - * responsible for 10000 or more unique chunks. + * (sum_chunk * 100) / (dataset_nchunks * mpi_size) >= 30% * - * Condition 3: This test will currently only be reliably reproducible for 2 or 3 - * MPI ranks. The threshold value calculated reduces to a constant 100 / mpi_size, - * and is compared against a default value of 30%. + * where: + * * `sum_chunk` is the combined sum of the number of chunks selected in + * the dataset by all ranks (chunks selected by more than one rank count + * individually toward the sum for each rank selecting that chunk) + * * `dataset_nchunks` is the number of chunks in the dataset (selected + * or not) + * * `mpi_size` is the size of the MPI Communicator + * + * Condition 2: `sum_chunk` divided by `mpi_size` must exceed or equal a certain + * threshold (as of this writing, 10000). + * + * To satisfy both these conditions, we #define a macro, + * LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM, which corresponds to the + * value of the H5D_ALL_CHUNK_ADDR_THRES_COL_NUM macro in H5Dmpio.c (the + * 10000 threshold from condition 2). We then create a dataset of that many + * chunks and have each MPI rank write to and read from a piece of every single + * chunk in the dataset. This ensures chunk utilization is the max possible + * and exceeds our 30% target ratio, while always exactly matching the numeric + * chunk threshold value of condition 2. * * Failure in this test may either cause a hang, or, due to how the MPI calls * pertaining to this issue might mistakenly match up, may cause an MPI error @@ -375,10 +387,9 @@ void test_link_chunk_io_sort_chunk_issue(void) { const char *filename; - hsize_t * dataset_dims = NULL; - hsize_t max_dataset_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; - hsize_t sel_dims[1]; - hsize_t chunk_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS] = {LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS}; + hsize_t dataset_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; + hsize_t sel_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; + hsize_t chunk_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; hsize_t start[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; hsize_t stride[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; hsize_t count[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; @@ -412,14 +423,13 @@ test_link_chunk_io_sort_chunk_issue(void) file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); VRFY((file_id >= 0), "H5Fcreate succeeded"); - dataset_dims = HDmalloc(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS * sizeof(*dataset_dims)); - VRFY((dataset_dims != NULL), "malloc succeeded"); - - dataset_dims[0] = (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE * (hsize_t)mpi_size * - (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE; - max_dataset_dims[0] = H5S_UNLIMITED; + /* + * Create a one-dimensional dataset of exactly LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM + * chunks, where every rank writes to a piece of every single chunk to keep utilization high. + */ + dataset_dims[0] = (hsize_t)mpi_size * (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM; - fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, max_dataset_dims); + fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, NULL); VRFY((fspace_id >= 0), "H5Screate_simple succeeded"); /* @@ -428,6 +438,9 @@ test_link_chunk_io_sort_chunk_issue(void) dcpl_id = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl_id >= 0), "H5Pcreate succeeded"); + /* Chunk size is equal to MPI size since each rank writes to a piece of every chunk */ + chunk_dims[0] = (hsize_t)mpi_size; + VRFY((H5Pset_chunk(dcpl_id, LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded"); @@ -437,23 +450,21 @@ test_link_chunk_io_sort_chunk_issue(void) /* * Setup hyperslab selection to split the dataset among the ranks. - * - * The ranks will write rows across the dataset. */ - stride[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE; - count[0] = (dataset_dims[0] / LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) / (hsize_t)mpi_size; - start[0] = count[0] * (hsize_t)mpi_rank; - block[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE; + start[0] = (hsize_t)mpi_rank; + stride[0] = (hsize_t)mpi_size; + count[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM; + block[0] = 1; VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded"); - sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE); + sel_dims[0] = count[0]; mspace_id = H5Screate_simple(1, sel_dims, NULL); VRFY((mspace_id >= 0), "H5Screate_simple succeeded"); - data = HDcalloc(1, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int)); + data = HDcalloc(1, count[0] * sizeof(int)); VRFY((data != NULL), "calloc succeeded"); dxpl_id = H5Pcreate(H5P_DATASET_XFER); @@ -476,33 +487,25 @@ test_link_chunk_io_sort_chunk_issue(void) VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_ONE_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded"); - read_buf = HDmalloc(count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int)); + read_buf = HDmalloc(count[0] * sizeof(int)); VRFY((read_buf != NULL), "malloc succeeded"); VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded"); - sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE); + sel_dims[0] = count[0]; VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded"); mspace_id = H5Screate_simple(1, sel_dims, NULL); VRFY((mspace_id >= 0), "H5Screate_simple succeeded"); - read_buf = HDrealloc(read_buf, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int)); - VRFY((read_buf != NULL), "realloc succeeded"); - /* * Finally have each rank read their section of data back from the dataset. */ VRFY((H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, read_buf) >= 0), "H5Dread succeeded"); - if (dataset_dims) { - HDfree(dataset_dims); - dataset_dims = NULL; - } - if (data) { HDfree(data); data = NULL; -- cgit v0.12 From 1d598182d6097052060f15a6b0d744c42a2fd80a Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed, 2 Feb 2022 13:45:59 -0600 Subject: Update doc with HDF5_ROOT usage. (#1414) --- config/cmake/HDF5_Examples.cmake.in | 4 ++-- release_docs/USING_CMake_Examples.txt | 7 +++---- release_docs/USING_HDF5_CMake.txt | 19 +++++++++++-------- 3 files changed, 16 insertions(+), 14 deletions(-) diff --git a/config/cmake/HDF5_Examples.cmake.in b/config/cmake/HDF5_Examples.cmake.in index db638fd..9ff9b6f 100644 --- a/config/cmake/HDF5_Examples.cmake.in +++ b/config/cmake/HDF5_Examples.cmake.in @@ -83,12 +83,12 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDN ############################################################################################################### if(WIN32) set(SITE_OS_NAME "Windows") - set(ENV{HDF5_DIR} "${INSTALLDIR}/share/cmake") + set(ENV{HDF5_ROOT} "${INSTALLDIR}") set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}\\build) set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}\\${CTEST_SOURCE_NAME}") set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}\\${CTEST_BINARY_NAME}") else() - set(ENV{HDF5_DIR} "${INSTALLDIR}/share/cmake") + set(ENV{HDF5_ROOT} "${INSTALLDIR}") set(ENV{LD_LIBRARY_PATH} "${INSTALLDIR}/lib") set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}/build) set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_SOURCE_NAME}") diff --git a/release_docs/USING_CMake_Examples.txt b/release_docs/USING_CMake_Examples.txt index a12a952..920705b 100644 --- a/release_docs/USING_CMake_Examples.txt +++ b/release_docs/USING_CMake_Examples.txt @@ -20,15 +20,14 @@ Notes: This short instruction is written for users who want to quickly I. Preconditions ======================================================================== - 1. We suggest you obtain the latest CMake for windows from the Kitware + 1. We suggest you obtain the latest CMake for your platform from the Kitware web site. The HDF5 1.13.x product requires a minimum CMake version of 3.12. If you are using VS2019, the minimum version is 3.15. 2. You have installed the HDF5 library built with CMake, by executing the HDF Install Utility (the *.msi file in the binary package for - Windows or the *.sh on Linux). If you are using a Windows platform, - you can obtain a pre-built Windows binary from The HDF Group's website - at www.hdfgroup.org. + Windows or the *.sh on Linux). You can obtain pre-built binaries + from The HDF Group's website at www.hdfgroup.org. diff --git a/release_docs/USING_HDF5_CMake.txt b/release_docs/USING_HDF5_CMake.txt index 792c719..abe1906 100644 --- a/release_docs/USING_HDF5_CMake.txt +++ b/release_docs/USING_HDF5_CMake.txt @@ -29,27 +29,30 @@ Notes: This short instruction is written for users who want to quickly of using a ctest script for building and testing. See INSTALL_CMake.txt for more information. + 4. See https://cmake.org/cmake/help/latest/command/find_package.html + for more information on the CMake "Config Mode Search Procedure". ======================================================================== I. Preconditions ======================================================================== - 1. We suggest you obtain the latest CMake for windows from the Kitware + 1. We suggest you obtain the latest CMake for your platform from the Kitware web site. The HDF5 1.13.x product requires a minimum CMake version - of 3.12. + of 3.12. If you are using VS2019, the minimum version is 3.15. 2. You have installed the HDF5 library built with CMake, by executing the HDF Install Utility (the *.msi file in the binary package for - Windows). You can obtain pre-built binaries from The HDF Group's website at - www.hdfgroup.org. + Windows or the *.sh on Linux). You can obtain pre-built binaries + from The HDF Group's website at www.hdfgroup.org. - 3. Set the environment variable HDF5_DIR to the installed location of - the config files for HDF5. + 3. Set the HDF5_ROOT CMake variable, -DHDF5_ROOT= + or environment variable, set(ENV{HDF5_ROOT} "") + to the installed location of HDF5. On Windows: - HDF5_DIR=C:/Program Files/HDF_Group/HDF5/1.13.x/cmake + HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/1.13.x/ On unix: - HDF5_DIR=/HDF_Group/HDF5/1.13.x/cmake + HDF5_ROOT=/HDF_Group/HDF5/1.13.x/ If you are using shared libraries, you may need to add to the path environment variable. Set the path environment variable to the -- cgit v0.12 From 856de93673f2bd097b90e2803475ef4fc3d689fa Mon Sep 17 00:00:00 2001 From: David Young Date: Thu, 3 Feb 2022 10:41:41 -0600 Subject: Don't use a nonliteral format string in test/fheap.c:begin_test(). (#1401) * Avoid using a non-literal formatting string with sprintf in begin_test. Use snprintf. Don't duplicate a string on the heap unnecessarily. * Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format string any more. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- test/fheap.c | 147 ++++++++++++++++++++++++----------------------------------- 1 file changed, 60 insertions(+), 87 deletions(-) diff --git a/test/fheap.c b/test/fheap.c index 2fcbb45..b897063 100644 --- a/test/fheap.c +++ b/test/fheap.c @@ -466,40 +466,24 @@ error: return (1); } /* add_obj() */ -/*------------------------------------------------------------------------- - * Function: get_del_string - * - * Purpose: Return string describing the kind of deletion to perform - * - * Return: Success: 0 - * - * Failure: 1 - * - * Programmer: Quincey Koziol - * Monday, June 6, 2006 - * - *------------------------------------------------------------------------- - */ -static char * +/* Return a string describing the kind of deletion to perform. */ +static const char * get_del_string(const fheap_test_param_t *tparam) { - char *str; - /* Remove half of total objects from heap */ if (tparam->del_dir == FHEAP_DEL_FORWARD) if (tparam->drain_half == FHEAP_DEL_DRAIN_ALL) - str = H5MM_strdup("(all - forward)"); + return "(all - forward)"; else - str = H5MM_strdup("(half, refill, all - forward)"); + return "(half, refill, all - forward)"; else if (tparam->del_dir == FHEAP_DEL_REVERSE) if (tparam->drain_half == FHEAP_DEL_DRAIN_ALL) - str = H5MM_strdup("(all - reverse)"); + return "(all - reverse)"; else - str = H5MM_strdup("(half, refill, all - reverse)"); + return "(half, refill, all - reverse)"; else - str = H5MM_strdup("(all - deleting heap)"); + return "(all - deleting heap)"; - return (str); } /* get_del_string() */ /*------------------------------------------------------------------------- @@ -547,29 +531,20 @@ get_fill_size(const fheap_test_param_t *tparam) * *------------------------------------------------------------------------- */ -/* Disable warning for "format not a string literal" here -QAK */ -/* - * This pragma only needs to surround the snprintf() calls with - * test_desc in the code below, but early (4.4.7, at least) gcc only - * allows diagnostic pragmas to be toggled outside of functions. - */ -H5_GCC_CLANG_DIAG_OFF("format-nonliteral") static int begin_test(fheap_test_param_t *tparam, const char *base_desc, fheap_heap_ids_t *keep_ids, size_t *fill_size) { - char *del_str = NULL; /* Deletion order description */ - char *test_desc = NULL; /* Test description */ + char * test_desc; /* Test description */ + const char *del_str = get_del_string(tparam); /* * Test filling & removing all (small) objects from root direct block of absolute heap */ - del_str = get_del_string(tparam); - HDassert(del_str); - size_t test_desc_len = HDstrlen(del_str) + HDstrlen(base_desc); - test_desc = (char *)H5MM_malloc(test_desc_len); - HDsnprintf(test_desc, test_desc_len, base_desc, del_str); + size_t test_desc_len = strlen(base_desc) + sizeof(" ") + strlen(del_str); + test_desc = H5MM_malloc(test_desc_len); + (void)HDsnprintf(test_desc, test_desc_len, "%s %s", base_desc, del_str); + TESTING(test_desc); - H5MM_xfree(del_str); H5MM_xfree(test_desc); /* Initialize the heap ID structure */ @@ -582,7 +557,6 @@ begin_test(fheap_test_param_t *tparam, const char *base_desc, fheap_heap_ids_t * /* Success */ return (0); } /* end begin_test() */ -H5_GCC_CLANG_DIAG_ON("format-nonliteral") /*------------------------------------------------------------------------- * Function: reopen_file @@ -7770,7 +7744,7 @@ test_man_remove_root_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_ size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from root direct block of absolute heap %s"; + const char *base_desc = "removing all objects from root direct block of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -7843,7 +7817,7 @@ test_man_remove_two_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from two direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from two direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -7931,7 +7905,7 @@ test_man_remove_first_row(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from first row of direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from first row of direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8001,7 +7975,7 @@ test_man_remove_first_two_rows(hid_t fapl, H5HF_create_t *cparam, fheap_test_par size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from first two rows of direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from first two rows of direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8073,7 +8047,7 @@ test_man_remove_first_four_rows(hid_t fapl, H5HF_create_t *cparam, fheap_test_pa size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from first four rows of direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from first four rows of direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8149,7 +8123,7 @@ test_man_remove_all_root_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_pa size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from all direct blocks of root group in absolute heap %s"; + const char *base_desc = "removing all objects from all direct blocks of root group in absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8219,7 +8193,7 @@ test_man_remove_2nd_indirect(hid_t fapl, H5HF_create_t *cparam, fheap_test_param size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from 2nd level indirect blocks of absolute heap %s"; + const char *base_desc = "removing all objects from 2nd level indirect blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8293,7 +8267,7 @@ test_man_remove_3rd_indirect(hid_t fapl, H5HF_create_t *cparam, fheap_test_param size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from 3rd level indirect blocks of absolute heap %s"; + const char *base_desc = "removing all objects from 3rd level indirect blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8374,8 +8348,7 @@ test_man_skip_start_block(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t size_t obj_size; /* Size of object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = - "inserting object that is too large for starting block, then remove all objects %s"; + const char *base_desc = "inserting object that is too large for starting block, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -8454,7 +8427,7 @@ test_man_skip_start_block_add_back(hid_t fapl, H5HF_create_t *cparam, fheap_test fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = - "skipping starting block, then adding object back to first block, then remove all objects %s"; + "skipping starting block, then adding object back to first block, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -8554,7 +8527,7 @@ test_man_skip_start_block_add_skipped(hid_t fapl, H5HF_create_t *cparam, fheap_t fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = - "skipping starting block, then adding objects to backfill and extend, then remove all objects %s"; + "skipping starting block, then adding objects to backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8663,7 +8636,7 @@ test_man_skip_2nd_block(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *t fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = "insert object to initial block, then add object too large for starting direct " - "blocks, then remove all objects %s"; + "blocks, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -8762,7 +8735,7 @@ test_man_skip_2nd_block_add_skipped(hid_t fapl, H5HF_create_t *cparam, fheap_tes unsigned v; /* Local index variables */ /* Test description */ const char *base_desc = "insert object to initial block, then add object too large for starting direct " - "blocks, then backfill and extend, then remove all objects %s"; + "blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8908,7 +8881,7 @@ test_man_fill_one_partial_skip_2nd_block_add_skipped(hid_t fapl, H5HF_create_t * unsigned u; /* Local index variable */ /* Test description */ const char *base_desc = - "skipping blocks with indirect root, then backfill and extend, then remove all objects %s"; + "skipping blocks with indirect root, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9073,7 +9046,7 @@ test_man_fill_row_skip_add_skipped(hid_t fapl, H5HF_create_t *cparam, fheap_test fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = - "filling first row, then skipping rows, then backfill and extend, then remove all objects %s"; + "filling first row, then skipping rows, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9203,7 +9176,7 @@ test_man_skip_direct_skip_indirect_two_rows_add_skipped(hid_t fapl, H5HF_create_ unsigned v; /* Local index variables */ /* Test description */ const char *base_desc = "skipping direct blocks to last row and skipping two rows of root indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -9329,7 +9302,7 @@ test_man_fill_direct_skip_indirect_start_block_add_skipped(hid_t fapl, H5HF_crea fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = "filling direct blocks and skipping blocks in non-root indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9458,7 +9431,7 @@ test_man_fill_direct_skip_2nd_indirect_start_block_add_skipped(hid_t fapl, H5HF_ unsigned u; /* Local index variable */ /* Test description */ const char *base_desc = "filling direct blocks and skipping row of non-root indirect blocks, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9590,7 +9563,7 @@ test_man_fill_2nd_direct_less_one_wrap_start_block_add_skipped(hid_t fapl, H5HF_ /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, except last one, and insert object too " - "large for 2nd level indirect blocks, then backfill and extend, then remove all objects %s"; + "large for 2nd level indirect blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9736,7 +9709,7 @@ test_man_fill_direct_skip_2nd_indirect_skip_2nd_block_add_skipped(hid_t fapl, H5 unsigned u; /* Local index variable */ /* Test description */ const char *base_desc = "filling direct blocks and skipping row of non-root indirect blocks, then skip " - "row of direct blocks, then backfill and extend, then remove all objects %s"; + "row of direct blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9899,7 +9872,7 @@ test_man_fill_direct_skip_indirect_two_rows_add_skipped(hid_t fapl, H5HF_create_ unsigned u, v; /* Local index variables */ /* Test description */ const char *base_desc = "filling direct blocks and skipping two rows of root indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10056,7 +10029,7 @@ test_man_fill_direct_skip_indirect_two_rows_skip_indirect_row_add_skipped(hid_t /* Test description */ const char *base_desc = "filling direct blocks and skipping two rows of root indirect block, skip one row of root indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10236,7 +10209,7 @@ test_man_fill_2nd_direct_skip_start_block_add_skipped(hid_t fapl, H5HF_create_t /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, and skip first rows of direct blocks of " - "3rd level indirect block, then backfill and extend, then remove all objects %s"; + "3rd level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10368,7 +10341,7 @@ test_man_fill_2nd_direct_skip_2nd_indirect_start_block_add_skipped(hid_t fapl, H const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect block's direct " "blocks, and skip first rows of direct blocks of 3rd level indirect block's 2nd level indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10512,7 +10485,7 @@ test_man_fill_2nd_direct_fill_direct_skip_3rd_indirect_start_block_add_skipped(h /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level " "indirect block's direct blocks, and skip first row of indirect blocks of 3rd " - "level indirect block, then backfill and extend, then remove all objects %s"; + "level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10665,7 +10638,7 @@ test_man_fill_2nd_direct_fill_direct_skip2_3rd_indirect_start_block_add_skipped( /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level " "indirect block's direct blocks, and skip first two rows of indirect blocks of " - "3rd level indirect block, then backfill and extend, then remove all objects %s"; + "3rd level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10823,7 +10796,7 @@ test_man_fill_3rd_direct_less_one_fill_direct_wrap_start_block_add_skipped(hid_t const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling first row of 3rd level indirect " "blocks, except last one, fill all direct blocks in last 3rd level indirect block, and insert object " - "too large for it's 2nd level indirect blocks, then backfill and extend, then remove all objects %s"; + "too large for it's 2nd level indirect blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10987,7 +10960,7 @@ test_man_fill_1st_row_3rd_direct_fill_2nd_direct_less_one_wrap_start_block_add_s "filling direct blocks, filling 2nd level indirect blocks, filling first row of 3rd level indirect " "blocks, fill all direct blocks in next 3rd level indirect block, fill all 1st row of 2nd level " "indirect blocks, except last one, and insert object too large for 2nd level indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11155,7 +11128,7 @@ test_man_fill_3rd_direct_fill_direct_skip_start_block_add_skipped(hid_t fapl, H5 const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect blocks, fill " "4th level indirect block's direct blocks, and skip first row of 2nd indirect blocks of 4th level " - "indirect block, then backfill and extend, then remove all objects %s"; + "indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11319,7 +11292,7 @@ test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_start_blo "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect blocks, fill " "4th level indirect block's direct, 2nd level indirect blocks and 3rd level direct block, and skip " "first row of 2nd indirect blocks of 4th level indirect block's 3rd level indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11503,7 +11476,7 @@ test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_two_rows_ "first row of 4th level indirect blocks, fill 2nd row 4th level indirect block's direct, 2nd level " "indirect blocks, first row of 3rd level indirect blocks, 3rd level direct block in 2nd row, and " "skip first row of 2nd indirect blocks of 4th level indirect block's 3rd level indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11722,7 +11695,7 @@ test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_wrap_star "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect blocks, fill " "first row of 3rd level indirect blocks in 4th level indirect block except last 3rd level block, " "fill direct blocks in 3rd level block, and skip row of 2nd indirect blocks of 4th level indirect " - "block's 3rd level indirect block, then backfill and extend, then remove all objects %s"; + "block's 3rd level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11923,7 +11896,7 @@ test_man_fill_4th_direct_less_one_fill_2nd_direct_fill_direct_skip_3rd_indirect_ "first row of 4th level indirect blocks, except last one, fill first row of 3rd level indirect " "blocks in last 4th level indirect block except last 3rd level block, fill direct blocks in 3rd " "level block, and skip row of 2nd indirect blocks of 4th level indirect block's 3rd level indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -12144,7 +12117,7 @@ test_man_frag_simple(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar fheap_heap_state_t state; /* State of fractal heap */ unsigned u; /* Local index variables */ /* Test description */ - const char *base_desc = "fragmenting small blocks, then backfill and extend, then remove all objects %s"; + const char *base_desc = "fragmenting small blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -12276,7 +12249,7 @@ test_man_frag_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar fheap_heap_state_t state; /* State of fractal heap */ unsigned u, v; /* Local index variables */ /* Test description */ - const char *base_desc = "fragmenting direct blocks, then backfill and extend, then remove all objects %s"; + const char *base_desc = "fragmenting direct blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -12450,7 +12423,7 @@ test_man_frag_2nd_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t * unsigned u, v; /* Local index variables */ /* Test description */ const char *base_desc = "fill root direct blocks, then fragment 2nd level indirect block's direct " - "blocks, then backfill and extend, then remove all objects %s"; + "blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -12562,7 +12535,7 @@ test_man_frag_3rd_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t * /* Test description */ const char *base_desc = "fill root direct blocks and 2nd level indirect blocks, then fragment 3rd level indirect block's " - "direct blocks, then backfill and extend, then remove all objects %s"; + "direct blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -12676,7 +12649,7 @@ test_huge_insert_one(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert one huge object, then remove %s"; + const char *base_desc = "insert one huge object, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -12827,7 +12800,7 @@ test_huge_insert_two(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert two huge objects, then remove %s"; + const char *base_desc = "insert two huge objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -13058,7 +13031,7 @@ test_huge_insert_three(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tp unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert three huge objects, then remove %s"; + const char *base_desc = "insert three huge objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -13365,7 +13338,7 @@ test_huge_insert_mix(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert mix of normal & huge objects, then remove %s"; + const char *base_desc = "insert mix of normal & huge objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -13789,7 +13762,7 @@ test_filtered_huge(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tparam hbool_t huge_ids_direct; /* Are 'huge' objects directly accessed? */ hbool_t pline_init = FALSE; /* Whether the I/O pipeline has been initialized */ /* Test description */ - const char *base_desc = "insert 'huge' object into heap with I/O filters, then remove %s"; + const char *base_desc = "insert 'huge' object into heap with I/O filters, then remove"; /* Copy heap creation properties */ HDmemcpy(&tmp_cparam, cparam, sizeof(H5HF_create_t)); @@ -13997,7 +13970,7 @@ test_tiny_insert_one(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert one tiny object, then remove %s"; + const char *base_desc = "insert one tiny object, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -14148,7 +14121,7 @@ test_tiny_insert_two(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert two tiny objects, then remove %s"; + const char *base_desc = "insert two tiny objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -14384,7 +14357,7 @@ test_tiny_insert_mix(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert mix of normal, huge & tiny objects, then remove %s"; + const char *base_desc = "insert mix of normal, huge & tiny objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -14985,7 +14958,7 @@ test_filtered_man_root_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_para fheap_heap_state_t state; /* State of fractal heap */ unsigned deflate_level; /* Deflation level */ /* Test description */ - const char *base_desc = "insert one 'managed' object into heap with I/O filters, then remove %s"; + const char *base_desc = "insert one 'managed' object into heap with I/O filters, then remove"; /* Copy heap creation properties */ HDmemcpy(&tmp_cparam, cparam, sizeof(H5HF_create_t)); @@ -15159,7 +15132,7 @@ test_filtered_man_root_indirect(hid_t fapl, H5HF_create_t *cparam, fheap_test_pa fheap_heap_state_t state; /* State of fractal heap */ unsigned deflate_level; /* Deflation level */ /* Test description */ - const char *base_desc = "insert two 'managed' objects into heap with I/O filters, then remove %s"; + const char *base_desc = "insert two 'managed' objects into heap with I/O filters, then remove"; /* Copy heap creation properties */ HDmemcpy(&tmp_cparam, cparam, sizeof(H5HF_create_t)); -- cgit v0.12 From 36d9a165e428eb883f9fd72b6707555536292845 Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Fri, 4 Feb 2022 10:53:55 -0600 Subject: Fix a few issues noted by LGTM (#1421) --- src/H5Dlayout.c | 2 +- src/H5Znbit.c | 29 +++++++++++++++-------------- src/H5Zscaleoffset.c | 6 +++--- tools/lib/h5diff_array.c | 6 +++--- tools/lib/h5diff_attr.c | 2 +- tools/lib/h5tools.c | 2 +- tools/lib/h5tools_dump.c | 4 ++-- tools/src/h5dump/h5dump_ddl.c | 4 ++-- tools/src/h5dump/h5dump_xml.c | 13 +++++++++---- tools/src/h5perf/sio_perf.c | 2 +- 10 files changed, 38 insertions(+), 32 deletions(-) diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c index 6c4fc12..6fdec05 100644 --- a/src/H5Dlayout.c +++ b/src/H5Dlayout.c @@ -213,7 +213,7 @@ H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t includ ret_value++; /* Dimension sizes */ - ret_value += layout->u.chunk.ndims * layout->u.chunk.enc_bytes_per_dim; + ret_value += layout->u.chunk.ndims * (size_t)layout->u.chunk.enc_bytes_per_dim; /* Type of chunk index */ ret_value++; diff --git a/src/H5Znbit.c b/src/H5Znbit.c index 21363bc..905d417 100644 --- a/src/H5Znbit.c +++ b/src/H5Znbit.c @@ -975,7 +975,7 @@ H5Z__filter_nbit(unsigned flags, size_t cd_nelmts, const unsigned cd_values[], s /* input; decompress */ if (flags & H5Z_FLAG_REVERSE) { - size_out = d_nelmts * cd_values[4]; /* cd_values[4] stores datatype size */ + size_out = d_nelmts * (size_t)cd_values[4]; /* cd_values[4] stores datatype size */ /* allocate memory space for decompressed buffer */ if (NULL == (outbuf = (unsigned char *)H5MM_malloc(size_out))) @@ -1170,7 +1170,8 @@ H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset, unsigned n = total_size / p.size; for (i = 0; i < n; i++) - H5Z__nbit_decompress_one_atomic(data, data_offset + i * p.size, buffer, j, buf_len, &p); + H5Z__nbit_decompress_one_atomic(data, data_offset + i * (size_t)p.size, buffer, j, buf_len, + &p); break; case H5Z_NBIT_ARRAY: @@ -1178,8 +1179,8 @@ H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset, unsigned n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - if (H5Z__nbit_decompress_one_array(data, data_offset + i * base_size, buffer, j, buf_len, - parms, parms_index) < 0) + if (H5Z__nbit_decompress_one_array(data, data_offset + i * (size_t)base_size, buffer, j, + buf_len, parms, parms_index) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array") *parms_index = begin_index; } @@ -1190,8 +1191,8 @@ H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset, unsigned n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - if (H5Z__nbit_decompress_one_compound(data, data_offset + i * base_size, buffer, j, buf_len, - parms, parms_index) < 0) + if (H5Z__nbit_decompress_one_compound(data, data_offset + i * (size_t)base_size, buffer, j, + buf_len, parms, parms_index) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound") *parms_index = begin_index; } @@ -1291,7 +1292,7 @@ H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buff FUNC_ENTER_STATIC /* may not have to initialize to zeros */ - HDmemset(data, 0, d_nelmts * parms[4]); + HDmemset(data, 0, d_nelmts * (size_t)parms[4]); /* initialization before the loop */ j = 0; @@ -1309,7 +1310,7 @@ H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buff HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset") for (i = 0; i < d_nelmts; i++) - H5Z__nbit_decompress_one_atomic(data, i * p.size, buffer, &j, &buf_len, &p); + H5Z__nbit_decompress_one_atomic(data, i * (size_t)p.size, buffer, &j, &buf_len, &p); break; case H5Z_NBIT_ARRAY: @@ -1468,7 +1469,7 @@ H5Z__nbit_compress_one_array(unsigned char *data, size_t data_offset, unsigned c p.offset = parms[(*parms_index)++]; n = total_size / p.size; for (i = 0; i < n; i++) - H5Z__nbit_compress_one_atomic(data, data_offset + i * p.size, buffer, j, buf_len, &p); + H5Z__nbit_compress_one_atomic(data, data_offset + i * (size_t)p.size, buffer, j, buf_len, &p); break; case H5Z_NBIT_ARRAY: @@ -1476,8 +1477,8 @@ H5Z__nbit_compress_one_array(unsigned char *data, size_t data_offset, unsigned c n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - H5Z__nbit_compress_one_array(data, data_offset + i * base_size, buffer, j, buf_len, parms, - parms_index); + H5Z__nbit_compress_one_array(data, data_offset + i * (size_t)base_size, buffer, j, buf_len, + parms, parms_index); *parms_index = begin_index; } break; @@ -1487,8 +1488,8 @@ H5Z__nbit_compress_one_array(unsigned char *data, size_t data_offset, unsigned c n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - H5Z__nbit_compress_one_compound(data, data_offset + i * base_size, buffer, j, buf_len, parms, - parms_index); + H5Z__nbit_compress_one_compound(data, data_offset + i * (size_t)base_size, buffer, j, buf_len, + parms, parms_index); *parms_index = begin_index; } break; @@ -1574,7 +1575,7 @@ H5Z__nbit_compress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer p.offset = parms[7]; for (i = 0; i < d_nelmts; i++) - H5Z__nbit_compress_one_atomic(data, i * p.size, buffer, &new_size, &buf_len, &p); + H5Z__nbit_compress_one_atomic(data, i * (size_t)p.size, buffer, &new_size, &buf_len, &p); break; case H5Z_NBIT_ARRAY: diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c index 5bdc51c..46c1a10 100644 --- a/src/H5Zscaleoffset.c +++ b/src/H5Zscaleoffset.c @@ -1240,7 +1240,7 @@ H5Z__filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_valu p.minbits = minbits; /* calculate size of output buffer after decompression */ - size_out = d_nelmts * p.size; + size_out = d_nelmts * (size_t)p.size; /* allocate memory space for decompressed buffer */ if (NULL == (outbuf = (unsigned char *)H5MM_malloc(size_out))) @@ -1403,7 +1403,7 @@ H5Z__scaleoffset_convert(void *buf, unsigned d_nelmts, unsigned dtype_size) unsigned char *buffer, temp; buffer = (unsigned char *)buf; - for (i = 0; i < d_nelmts * dtype_size; i += dtype_size) + for (i = 0; i < d_nelmts * (size_t)dtype_size; i += dtype_size) for (j = 0; j < dtype_size / 2; j++) { /* swap pair of bytes */ temp = buffer[i + j]; @@ -1681,7 +1681,7 @@ H5Z__scaleoffset_decompress(unsigned char *data, unsigned d_nelmts, unsigned cha unsigned buf_len; /* must initialize to zeros */ - for (i = 0; i < d_nelmts * p.size; i++) + for (i = 0; i < d_nelmts * (size_t)p.size; i++) data[i] = 0; /* initialization before the loop */ diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c index 1b0d36f..e8cfacb 100644 --- a/tools/lib/h5diff_array.c +++ b/tools/lib/h5diff_array.c @@ -2063,7 +2063,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, opts->print_percentage = 0; print_pos(opts, elem_idx, 0); if (print_data(opts)) { - parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); + parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); } nfound++; } @@ -2110,7 +2110,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, opts->print_percentage = 0; print_pos(opts, elem_idx, 0); if (print_data(opts)) { - parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); + parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); } nfound++; } @@ -2157,7 +2157,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, opts->print_percentage = 0; print_pos(opts, elem_idx, 0); if (print_data(opts)) { - parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); + parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); } nfound++; } diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c index 5c1777a..63b6d8f 100644 --- a/tools/lib/h5diff_attr.c +++ b/tools/lib/h5diff_attr.c @@ -292,7 +292,7 @@ build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t **table_out, } if (opts->mode_verbose_level >= 1) - parallel_print("Attributes status: %d common, %d only in obj1, %d only in obj2\n", + parallel_print("Attributes status: %zu common, %zu only in obj1, %zu only in obj2\n", table_lp->nattrs - table_lp->nattrs_only1 - table_lp->nattrs_only2, table_lp->nattrs_only1, table_lp->nattrs_only2); diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c index db8df16..da55136 100644 --- a/tools/lib/h5tools.c +++ b/tools/lib/h5tools.c @@ -945,7 +945,7 @@ h5tools_fopen(const char *fname, unsigned flags, hid_t fapl_id, hbool_t use_spec * as TRUE, we should return failure now since the file couldn't be opened with * the VFL driver/VOL connector that was set on the FAPL by the caller. */ - if (fid < 0 && use_specific_driver) + if (use_specific_driver) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to open file using specified FAPL"); /* diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c index 0fc5d2d..b8c9a19 100644 --- a/tools/lib/h5tools_dump.c +++ b/tools/lib/h5tools_dump.c @@ -2486,7 +2486,7 @@ found_string_type: ctx->need_prefix = TRUE; h5tools_str_reset(buffer); - h5tools_str_append(buffer, "OPAQUE_SIZE \"%s\";", size); + h5tools_str_append(buffer, "OPAQUE_SIZE \"%zu\";", size); h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); } @@ -2996,7 +2996,7 @@ h5tools_dump_oid(FILE *stream, const h5tool_format_t *info, h5tools_context_t *c ctx->need_prefix = TRUE; h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s %s %d %s", OBJID, BEGIN, oid, END); + h5tools_str_append(&buffer, "%s %s %" PRId64 " %s", OBJID, BEGIN, oid, END); h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c index 37bb82d..b0bce0c 100644 --- a/tools/src/h5dump/h5dump_ddl.c +++ b/tools/src/h5dump/h5dump_ddl.c @@ -1318,7 +1318,7 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a j = (int)HDstrlen(op_name) - 1; /* find the last / */ while (j >= 0) { - if (op_name[j] == '/' && (j == 0 || (j > 0 && op_name[j - 1] != '\\'))) + if (op_name[j] == '/' && (j == 0 || (op_name[j - 1] != '\\'))) break; j--; } @@ -1541,7 +1541,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED *data, int H5 /* find the last / */ while (j >= 0) { - if (attr[j] == '/' && (j == 0 || (j > 0 && attr[j - 1] != '\\'))) + if (attr[j] == '/' && (j == 0 || (attr[j - 1] != '\\'))) break; j--; } diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c index 19efd6f..5f64d6c 100644 --- a/tools/src/h5dump/h5dump_xml.c +++ b/tools/src/h5dump/h5dump_xml.c @@ -591,6 +591,8 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen if (outlen < 22) return 1; + H5_CHECK_OVERFLOW(outlen, int, size_t); + lookup_ret = ref_path_table_lookup(str, &obj_token); if (lookup_ret < 0) { if (HDstrlen(str) == 0) { @@ -600,7 +602,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen ref_path_table_gen_fake(str, &obj_token); H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsnprintf(outstr, outlen, "xid_%s", obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -615,7 +617,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen ref_path_table_gen_fake(str, &obj_token); H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsnprintf(outstr, outlen, "xid_%s", obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -627,7 +629,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen } H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsnprintf(outstr, outlen, "xid_%s", obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -3598,7 +3600,10 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\""); for (i = 0; i < sz; i++) { - h5tools_str_append(&buffer, "%x ", *(unsigned int *)buf + (i * sizeof(unsigned int))); + unsigned long val = *(unsigned int *)buf + (i * sizeof(unsigned int)); + + H5_CHECK_OVERFLOW(val, unsigned long, unsigned); + h5tools_str_append(&buffer, "%x ", (unsigned)val); } h5tools_str_append(&buffer, "\""); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c index f245b92..87b9d65 100644 --- a/tools/src/h5perf/sio_perf.c +++ b/tools/src/h5perf/sio_perf.c @@ -277,7 +277,7 @@ run_test_loop(struct options *opts) } /* print size information */ - output_report("Transfer Buffer Size (bytes): %d\n", buf_bytes); + output_report("Transfer Buffer Size (bytes): %zu\n", buf_bytes); output_report("File Size(MB): %.2f\n", ((double)parms.num_bytes) / ONE_MB); print_indent(0); -- cgit v0.12 From c9347450c11edc8d73542a6244333d04f3462045 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Fri, 4 Feb 2022 16:50:45 -0600 Subject: Implemented suggestion in #1381 for dtransform test (#1415) * Implemented suggestion in #1380 * fix typo * Use differently named files in tests * format fix * Revise comments * fic typos * Change test display and file name --- c++/test/titerate.cpp | 7 ++++++- test/dtransform.c | 17 +++++++---------- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/c++/test/titerate.cpp b/c++/test/titerate.cpp index bc4d892..57761ea 100644 --- a/c++/test/titerate.cpp +++ b/c++/test/titerate.cpp @@ -351,7 +351,7 @@ test_iter_group(FileAccPropList &fapl) * Purpose Open an attribute and verify that it has a the correct name *------------------------------------------------------------------------- */ -const H5std_string FILE_NAME("titerate.h5"); +const H5std_string FILE_NAME("test_member_access.h5"); const H5std_string GRP_NAME("/Group_A"); const H5std_string FDATASET_NAME("file dset"); const H5std_string GDATASET_NAME("group dset"); @@ -396,6 +396,9 @@ test_HDFFV_9920() int attr_data[2] = {100, 200}; hsize_t dims[1] = {DIM1}; + /* Output message about test being performed */ + SUBTEST("Member access"); + try { // Create a new file and a group in it H5File file(FILE_NAME, H5F_ACC_TRUNC); @@ -425,6 +428,7 @@ test_HDFFV_9920() printelems(file, FDATASET_NAME, FATTR_NAME); printelems(gr1, GDATASET_NAME, GATTR_NAME); + PASSED(); } // end of try block // Catch all failures for handling in the same way @@ -473,4 +477,5 @@ extern "C" void cleanup_iterate() { HDremove(FILE_ITERATE.c_str()); + HDremove(FILE_NAME.c_str()); } // cleanup_iterate diff --git a/test/dtransform.c b/test/dtransform.c index 9f7e659..1f6d48b 100644 --- a/test/dtransform.c +++ b/test/dtransform.c @@ -122,9 +122,8 @@ const int transformData[ROWS][COLS] = {{36, 31, 25, 19, 13, 7, 1, 5, 11, 16, 22, { \ TYPE array[ROWS][COLS]; \ const char *f_to_c = "(5/9.0)*(x-32)"; \ - /* utrans is a transform for unsigned types: no negative numbers involved and results are < 255 to \ - * fit into uchar */ \ - const char *utrans = "((x+100)/4)*3"; \ + /* utrans is a transform for char types: numbers are restricted from -128 to 127, fits into char */ \ + const char *utrans = "(x/4+25)*3"; \ \ hid_t dataspace, dxpl_id_f_to_c, dxpl_id_utrans, dset, dset_nn, dt_nn; \ H5T_order_t order; \ @@ -211,9 +210,8 @@ const int transformData[ROWS][COLS] = {{36, 31, 25, 19, 13, 7, 1, 5, 11, 16, 22, { \ TYPE array[ROWS][COLS]; \ const char *f_to_c = "(5/9.0)*(x-32)"; \ - /* utrans is a transform for unsigned types: no negative numbers involved and results are < 255 to \ - * fit into uchar */ \ - const char *utrans = "((x+100)/4)*3"; \ + /* utrans is a transform for char types: numbers are restricted from -128 to 127, fits into char */ \ + const char *utrans = "(x/4+25)*3"; \ \ hid_t dataspace, dxpl_id_f_to_c, dxpl_id_utrans, cparms, memspace, dset_chunk, filespace; \ hsize_t dim[2] = {ROWS, COLS}; \ @@ -314,7 +312,7 @@ main(void) const char *simple = "(4/2) * ( (2 + 4)/(5 - 2.5))"; /* this equals 4.8 */ const char *polynomial = "(2+x)* ((x-8)/2)"; /* inverses the utrans transform in init_test to get back original array */ - const char *utrans_inv = "(x/3)*4 - 100"; + const char *utrans_inv = "(x/3 - 25)*4"; if ((file_id = H5Fcreate("dtransform.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR; @@ -436,9 +434,8 @@ static int init_test(hid_t file_id) { const char *f_to_c = "(5/9.0)*(x-32)"; - /* utrans is a transform for unsigned types: no negative numbers involved and results are < 255 to fit - * into uchar */ - const char *utrans = "((x+100)/4)*3"; + /* utrans is a transform for char types: numbers are restricted from -128 to 127, fits into char */ + const char *utrans = "(x/4+25)*3"; hid_t dataspace = -1; hid_t dxpl_id_f_to_c = -1; -- cgit v0.12 From 01092658a3095c31d7dc1ed1beebbd965095c244 Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Mon, 7 Feb 2022 22:04:41 -0600 Subject: Fix metadata cache bug when resizing a pinned/protected entry (#1358) When resizing a pinned/protected cache entry, the metadata cache code previously would wait until after resizing the entry to attempt to log the newly-dirtied entry. This would cause H5C_resize_entry to mark the entry as dirty and make H5AC_resize_entry think that it doesn't need to add the newly-dirtied entry to the dirty entries skiplist. Thus, a subsequent H5AC__log_moved_entry would think it needs to allocate a new entry for insertion into the dirty entry skip list, since the entry doesn't exist on that list. This causes an assertion failure, as the code to allocate a new entry assumes that the entry is not dirty. --- release_docs/RELEASE.txt | 17 +++++++++++++++++ src/H5AC.c | 8 ++++---- 2 files changed, 21 insertions(+), 4 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index ece00cc..d5dde34 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1075,6 +1075,23 @@ Bug Fixes since HDF5-1.12.0 release =================================== Library ------- + - Fixed a metadata cache bug when resizing a pinned/protected cache entry + + When resizing a pinned/protected cache entry, the metadata + cache code previously would wait until after resizing the + entry to attempt to log the newly-dirtied entry. This would + cause H5C_resize_entry to mark the entry as dirty and make + H5AC_resize_entry think that it doesn't need to add the + newly-dirtied entry to the dirty entries skiplist. + + Thus, a subsequent H5AC__log_moved_entry would think it + needs to allocate a new entry for insertion into the dirty + entry skip list, since the entry doesn't exist on that list. + This causes an assertion failure, as the code to allocate a + new entry assumes that the entry is not dirty. + + (JTH - 2022/01/12) + - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which diff --git a/src/H5AC.c b/src/H5AC.c index 47d3a65..7272c01 100644 --- a/src/H5AC.c +++ b/src/H5AC.c @@ -1440,10 +1440,6 @@ H5AC_resize_entry(void *thing, size_t new_size) cache_ptr = entry_ptr->cache_ptr; HDassert(cache_ptr); - /* Resize the entry */ - if (H5C_resize_entry(thing, new_size) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTRESIZE, FAIL, "can't resize entry") - #ifdef H5_HAVE_PARALLEL { H5AC_aux_t *aux_ptr; @@ -1455,6 +1451,10 @@ H5AC_resize_entry(void *thing, size_t new_size) } #endif /* H5_HAVE_PARALLEL */ + /* Resize the entry */ + if (H5C_resize_entry(thing, new_size) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTRESIZE, FAIL, "can't resize entry") + done: /* If currently logging, generate a message */ if (cache_ptr != NULL && cache_ptr->log_info != NULL) -- cgit v0.12 From 0f847f30bc9e5ac8c272fc745aa7c69499455034 Mon Sep 17 00:00:00 2001 From: Neil Fortner Date: Thu, 10 Feb 2022 17:23:26 -0600 Subject: Fix issue with H5_now_usec() with 32 bit systems (#1416) * Implement H5ESget_requests() to retrieve request pointers and corresponding connector IDs from an event set. Add tests for this function. * Add "order" parameter to H5ESget_requests, to allow the user to specify the order in which requests are returned. * Fix bugs with H5ESinsert_request() * Change H5ESget_requests() API to have separate input and output parameters for the allocated array length(s) (in) and the number of events in the event set (out). * Fix issue with H5_now_usec() with 32 bit systems. Also improve event set test. * Committing clang-format changes * Add comments to H5_now_usec() explaining rationale for uint64_t casts. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- src/H5timer.c | 15 ++++++++++++--- test/event_set.c | 30 +++++++++++++++++++++++++++--- 2 files changed, 39 insertions(+), 6 deletions(-) diff --git a/src/H5timer.c b/src/H5timer.c index b2cc5f0..b5dba97 100644 --- a/src/H5timer.c +++ b/src/H5timer.c @@ -193,17 +193,26 @@ H5_now_usec(void) struct timespec ts; HDclock_gettime(CLOCK_MONOTONIC, &ts); - now = (uint64_t)(ts.tv_sec * (1000 * 1000)) + (uint64_t)(ts.tv_nsec / 1000); + + /* Cast all values in this expression to uint64_t to ensure that all intermediate + * calculations are done in 64 bit, to prevent overflow */ + now = ((uint64_t)ts.tv_sec * ((uint64_t)1000 * (uint64_t)1000)) + + ((uint64_t)ts.tv_nsec / (uint64_t)1000); } #elif defined(H5_HAVE_GETTIMEOFDAY) { struct timeval now_tv; HDgettimeofday(&now_tv, NULL); - now = (uint64_t)(now_tv.tv_sec * (1000 * 1000)) + (uint64_t)now_tv.tv_usec; + + /* Cast all values in this expression to uint64_t to ensure that all intermediate + * calculations are done in 64 bit, to prevent overflow */ + now = ((uint64_t)now_tv.tv_sec * ((uint64_t)1000 * (uint64_t)1000)) + (uint64_t)now_tv.tv_usec; } #else /* H5_HAVE_GETTIMEOFDAY */ - now = (uint64_t)(HDtime(NULL) * (1000 * 1000)); + /* Cast all values in this expression to uint64_t to ensure that all intermediate calculations + * are done in 64 bit, to prevent overflow */ + now = ((uint64_t)HDtime(NULL) * ((uint64_t)1000 * (uint64_t)1000)); #endif /* H5_HAVE_GETTIMEOFDAY */ return (now); diff --git a/test/event_set.c b/test/event_set.c index 22df510..c2a17b1 100644 --- a/test/event_set.c +++ b/test/event_set.c @@ -344,25 +344,49 @@ test_es_get_requests(void) TEST_ERROR /* Get only connector IDs */ - count = 3; + count = 3; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, NULL, 2, &count) < 0) TEST_ERROR if (count != 0) TEST_ERROR + if (connector_ids[0] != H5I_INVALID_HID) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR /* Get only requests */ - count = 3; + count = 3; + requests[0] = NULL; + requests[1] = NULL; if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, requests, 2, &count) < 0) TEST_ERROR if (count != 0) TEST_ERROR + if (requests[0] != NULL) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR /* Get both */ - count = 3; + count = 3; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, requests, 2, &count) < 0) TEST_ERROR if (count != 0) TEST_ERROR + if (connector_ids[0] != H5I_INVALID_HID) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + if (requests[0] != NULL) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR /* Insert event into event set */ if (H5ESinsert_request(es_id, connector_ids_g[0], &req_targets[0]) < 0) -- cgit v0.12 From 7bfa873983414f98aaa3489962681b9105ccb562 Mon Sep 17 00:00:00 2001 From: Scot Breitenfeld Date: Fri, 11 Feb 2022 06:56:33 -0600 Subject: Fixed H5Dget_storage_size_f for zero sized datasets (#1430) * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * fixed handling size 0 datasets * fixed handling size 0 datasets * format --- fortran/src/H5Df.c | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/fortran/src/H5Df.c b/fortran/src/H5Df.c index 5c46cb3..a780683 100644 --- a/fortran/src/H5Df.c +++ b/fortran/src/H5Df.c @@ -495,10 +495,10 @@ h5dget_storage_size_c(hid_t_f *dset_id, hsize_t_f *size) c_dset_id = (hid_t)*dset_id; c_size = H5Dget_storage_size(c_dset_id); - if (c_size == 0) - return ret_value; - *size = (hsize_t_f)c_size; - ret_value = 0; + if (c_size != 0) { + ret_value = 0; + } + *size = (hsize_t_f)c_size; return ret_value; } -- cgit v0.12 From 4ce6373a0ba10250b4eed293653e55e348812012 Mon Sep 17 00:00:00 2001 From: David Young Date: Fri, 11 Feb 2022 07:39:52 -0600 Subject: Make a buffer bigger: GCC 8.3.0 warned that a `snprintf` may be (#1403) truncated because the recipient buffer was too small, and the warning is one that we promote to an error. Now there is a warning that the buffer is too big (-Wlarger-than=), but we don't promote those to errors, yet. --- tools/src/h5perf/sio_engine.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c index 98cb920..95ec3ce 100644 --- a/tools/src/h5perf/sio_engine.c +++ b/tools/src/h5perf/sio_engine.c @@ -1267,7 +1267,7 @@ done: static void do_cleanupfile(iotype iot, char *filename) { - char temp[2048]; + char temp[4096 + sizeof("-?.h5")]; int j; hid_t driver; -- cgit v0.12 From 96cf19499b540d8fe5547690b85d18b45f4c4b85 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Fri, 11 Feb 2022 07:46:09 -0600 Subject: Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391) * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note --- config/cmake/libh5cc.in | 23 ++++++++++++++++++++++- release_docs/RELEASE.txt | 7 +++++++ 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/config/cmake/libh5cc.in b/config/cmake/libh5cc.in index ecdd13e..f5d8d4c 100644 --- a/config/cmake/libh5cc.in +++ b/config/cmake/libh5cc.in @@ -27,6 +27,27 @@ prg=$dir/$(basename -- "$prg") || exit printf '%s\n' "$prg" printf 'dir is %s\n' "$dir" + +# Show the configuration summary of the library recorded in the +# libhdf5.settings file reside in the lib directory. +showconfigure() +{ + cat $dir/lib/libhdf5.settings + status=$? +} + export PKG_CONFIG_PATH=$dir/lib/pkgconfig -@_PKG_CONFIG_COMPILER@ $@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@` +for arg in $@ ; do + case "$arg" in + -showconfig) + showconfigure + exit $status + ;; + *) + @_PKG_CONFIG_COMPILER@ $@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@` + status=$? + exit $status + ;; + esac +done diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index d5dde34..56b5e42 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -47,6 +47,13 @@ New Features Configuration: ------------- + - Added new option to the h5cc scripts produced by CMake. + + Add -showconfig option to h5cc scripts that cat the + libhdf5-settings to the standard output. + + (ADB - 2022/01/25) + - CMake will now run the PowerShell script tests in test/ by default on Windows. -- cgit v0.12 From 97b8fad8edbfa4c4c482a0b43f86885914c19fa5 Mon Sep 17 00:00:00 2001 From: Larry Knox Date: Fri, 11 Feb 2022 22:34:16 -0600 Subject: Revert "Fix metadata cache bug when resizing a pinned/protected entry (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244. --- release_docs/RELEASE.txt | 17 ----------------- src/H5AC.c | 8 ++++---- 2 files changed, 4 insertions(+), 21 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 56b5e42..f68a7fe 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1082,23 +1082,6 @@ Bug Fixes since HDF5-1.12.0 release =================================== Library ------- - - Fixed a metadata cache bug when resizing a pinned/protected cache entry - - When resizing a pinned/protected cache entry, the metadata - cache code previously would wait until after resizing the - entry to attempt to log the newly-dirtied entry. This would - cause H5C_resize_entry to mark the entry as dirty and make - H5AC_resize_entry think that it doesn't need to add the - newly-dirtied entry to the dirty entries skiplist. - - Thus, a subsequent H5AC__log_moved_entry would think it - needs to allocate a new entry for insertion into the dirty - entry skip list, since the entry doesn't exist on that list. - This causes an assertion failure, as the code to allocate a - new entry assumes that the entry is not dirty. - - (JTH - 2022/01/12) - - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which diff --git a/src/H5AC.c b/src/H5AC.c index 7272c01..47d3a65 100644 --- a/src/H5AC.c +++ b/src/H5AC.c @@ -1440,6 +1440,10 @@ H5AC_resize_entry(void *thing, size_t new_size) cache_ptr = entry_ptr->cache_ptr; HDassert(cache_ptr); + /* Resize the entry */ + if (H5C_resize_entry(thing, new_size) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTRESIZE, FAIL, "can't resize entry") + #ifdef H5_HAVE_PARALLEL { H5AC_aux_t *aux_ptr; @@ -1451,10 +1455,6 @@ H5AC_resize_entry(void *thing, size_t new_size) } #endif /* H5_HAVE_PARALLEL */ - /* Resize the entry */ - if (H5C_resize_entry(thing, new_size) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTRESIZE, FAIL, "can't resize entry") - done: /* If currently logging, generate a message */ if (cache_ptr != NULL && cache_ptr->log_info != NULL) -- cgit v0.12 From d25d05d7406375e848857185c569377ec7c6fd33 Mon Sep 17 00:00:00 2001 From: loricooperhdf Date: Wed, 16 Feb 2022 07:46:19 -0600 Subject: Creating FUNDING.yml (#1427) * Creating FUNDING.yml Will add sponsor this project widget to the repo's page. * Correct file name Add sponsor widget; filename typo fixed. * Update MANIFEST --- .github/FUNDING.yml | 3 +++ MANIFEST | 1 + 2 files changed, 4 insertions(+) create mode 100644 .github/FUNDING.yml diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml new file mode 100644 index 0000000..7c4daaf --- /dev/null +++ b/.github/FUNDING.yml @@ -0,0 +1,3 @@ +# These are supported funding model platforms + +custom: "https://hdfgroup.org/about-us/donate-to-the-hdf-group/" diff --git a/MANIFEST b/MANIFEST index 3442ae8..0aa9957 100644 --- a/MANIFEST +++ b/MANIFEST @@ -40,6 +40,7 @@ ./.github/workflows/main.yml _DO_NOT_DISTRIBUTE_ ./.github/workflows/pr-check.yml _DO_NOT_DISTRIBUTE_ ./.github/workflows/codespell.yml _DO_NOT_DISTRIBUTE_ +./.github/FUNDING.yml _DO_NOT_DISTRIBUTE_ ./m4/aclocal_fc.m4 ./m4/aclocal_fc.f90 -- cgit v0.12 From bbb0acf353920f8315ad59e80e9e8d0754cca655 Mon Sep 17 00:00:00 2001 From: myd7349 Date: Thu, 17 Feb 2022 04:58:35 +0800 Subject: Fixed AbstractDs::getVarLenType documentation (#1441) --- c++/src/H5AbstractDs.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/c++/src/H5AbstractDs.cpp b/c++/src/H5AbstractDs.cpp index eeb0155..70d8531 100644 --- a/c++/src/H5AbstractDs.cpp +++ b/c++/src/H5AbstractDs.cpp @@ -302,7 +302,7 @@ AbstractDs::getStrType() const //-------------------------------------------------------------------------- // Function: AbstractDs::getVarLenType -///\brief Returns the floating-point datatype of this abstract dataset, +///\brief Returns the variable length datatype of this abstract dataset, /// which can be a dataset or an attribute. ///\return VarLenType instance ///\exception H5::DataTypeIException -- cgit v0.12 From 08ec5b45a5c069077087351923afe780488421a3 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu, 17 Feb 2022 10:05:08 -0600 Subject: Add SZ filter and adjust compression file names to avoid conflicts (#1434) * Updated plugins project required adjustments * Updated plugins need to distinguish external libs * Fix missed rename * Use same name for windows as linux - avoid name clash --- CMakeFilters.cmake | 10 +-- CMakeInstallation.cmake | 8 +-- CMakeLists.txt | 4 +- config/cmake/CTestCustom.cmake | 2 + config/cmake/HDF5PluginMacros.cmake | 4 +- config/cmake/cacheinit.cmake | 22 +++--- config/cmake/hdf5-config.cmake.in | 2 +- config/cmake_ext_mod/ConfigureChecks.cmake | 110 ++++++++++++++--------------- config/cmake_ext_mod/HDFLibMacros.cmake | 20 +++--- 9 files changed, 90 insertions(+), 92 deletions(-) diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake index 51ac61c..725390b 100644 --- a/CMakeFilters.cmake +++ b/CMakeFilters.cmake @@ -19,7 +19,7 @@ include (FetchContent) set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)") set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") - option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 1) + option (ZLIB_USE_EXTERNAL "Use External Library Building for HDF5_ZLIB" 1) option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 1) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT") set (ZLIB_URL ${ZLIB_GIT_URL} CACHE STRING "Path to zlib git repository") @@ -82,7 +82,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT) set (H5_HAVE_ZLIB_H 1) set (H5_HAVE_LIBZ 1) if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "Filter ZLIB is built") + message (VERBOSE "Filter HDF5_ZLIB is built") endif () else () message (FATAL_ERROR " ZLib is Required for ZLib support in HDF5") @@ -100,7 +100,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT) set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY}) INCLUDE_DIRECTORIES (${ZLIB_INCLUDE_DIRS}) if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "Filter ZLIB is ON") + message (VERBOSE "Filter HDF5_ZLIB is ON") endif () endif () @@ -149,9 +149,9 @@ if (HDF5_ENABLE_SZIP_SUPPORT) if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") message (VERBOSE "... with library AEC") endif () - set (SZ_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME}) + set (SZIP_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME}) else () - set (SZ_PACKAGE_NAME ${SZIP_PACKAGE_NAME}) + set (SZIP_PACKAGE_NAME ${SZIP_PACKAGE_NAME}) endif () else () message (FATAL_ERROR "SZIP is Required for SZIP support in HDF5") diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake index 609cd7e..f5e0897 100644 --- a/CMakeInstallation.cmake +++ b/CMakeInstallation.cmake @@ -442,11 +442,11 @@ The HDF5 data model, file format, API, library, and tools are open and distribut if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") if (ZLIB_FOUND AND ZLIB_USE_EXTERNAL) if (WIN32) - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;ALL;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;ALL;/") else () - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;libraries;/") - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;headers;/") - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;configinstall;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;libraries;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;headers;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;configinstall;/") endif () endif () if (SZIP_FOUND AND SZIP_USE_EXTERNAL) diff --git a/CMakeLists.txt b/CMakeLists.txt index 59595b6..fedce44 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -895,10 +895,10 @@ add_subdirectory (src) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") if (ZLIB_FOUND AND ZLIB_USE_EXTERNAL) if (NOT ONLY_SHARED_LIBS) - add_dependencies (${HDF5_LIB_TARGET} ZLIB) + add_dependencies (${HDF5_LIB_TARGET} HDF5_ZLIB) endif () if (BUILD_SHARED_LIBS) - add_dependencies (${HDF5_LIBSH_TARGET} ZLIB) + add_dependencies (${HDF5_LIBSH_TARGET} HDF5_ZLIB) endif () endif () if (SZIP_FOUND AND SZIP_USE_EXTERNAL) diff --git a/config/cmake/CTestCustom.cmake b/config/cmake/CTestCustom.cmake index f958804..9517e4b 100644 --- a/config/cmake/CTestCustom.cmake +++ b/config/cmake/CTestCustom.cmake @@ -19,6 +19,8 @@ set (CTEST_CUSTOM_MAXIMUM_FAILED_TEST_OUTPUT_SIZE 50000) set (CTEST_CUSTOM_WARNING_EXCEPTION ${CTEST_CUSTOM_WARNING_EXCEPTION} "note.*expected.*void.*but argument is of type.*volatile" + "plugin-build.*:[ \t]*warning" + "CMake Warning*stamp" "src.ZLIB.*:[ \t]*warning" "warning LNK4197:.*ZLIB-prefix" "src.SZIP.*:[ \t]*warning" diff --git a/config/cmake/HDF5PluginMacros.cmake b/config/cmake/HDF5PluginMacros.cmake index 4e05399..dbed15c 100644 --- a/config/cmake/HDF5PluginMacros.cmake +++ b/config/cmake/HDF5PluginMacros.cmake @@ -57,8 +57,8 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type) add_dependencies (h5ex_d_mafisc ${HDF5_LIBSH_TARGET}) target_include_directories (h5ex_d_mafisc PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR}") endif () - if (ENABLE_SZF) - add_dependencies (h5szf ${HDF5_LIBSH_TARGET}) + if (ENABLE_SZ) + add_dependencies (h5sz ${HDF5_LIBSH_TARGET}) add_dependencies (h5ex_d_sz ${HDF5_LIBSH_TARGET}) target_include_directories (h5ex_d_sz PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR}") endif () diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake index e423deb..221c0c9 100644 --- a/config/cmake/cacheinit.cmake +++ b/config/cmake/cacheinit.cmake @@ -47,12 +47,12 @@ set (HDF5_MINGW_STATIC_GCC_LIBS ON CACHE BOOL "Statically link libgcc/libstdc++" set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE) set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) -set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) +set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use HDF5_ZLib from compressed file" FORCE) set (SZIP_TGZ_NAME "SZip.tar.gz" CACHE STRING "Use SZip from compressed file" FORCE) set (SZAEC_TGZ_NAME "LIBAEC.tar.gz" CACHE STRING "Use SZip AEC from compressed file" FORCE) set (USE_LIBAEC ON CACHE BOOL "Use libaec szip replacement" FORCE) -set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) +set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of HDF5_ZLIB package" FORCE) set (LIBAEC_PACKAGE_NAME "libaec" CACHE STRING "Name of AEC SZIP package" FORCE) set (SZIP_PACKAGE_NAME "szip" CACHE STRING "Name of SZIP package" FORCE) @@ -85,12 +85,12 @@ set (BLOSC_TGZ_NAME "c-blosc.tar.gz" CACHE STRING "Use BLOSC from compressed fil set (BLOSC_PACKAGE_NAME "blosc" CACHE STRING "Name of BLOSC package" FORCE) -set (ZLIB_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/zlib.git" CACHE STRING "Use ZLIB from HDF repo" FORCE) -set (ZLIB_GIT_BRANCH "master" CACHE STRING "" FORCE) +set (BLOSC_ZLIB_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/zlib.git" CACHE STRING "Use BLOSC_ZLIB from HDF repo" FORCE) +set (BLOSC_ZLIB_GIT_BRANCH "master" CACHE STRING "" FORCE) -set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) +set (BLOSC_ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use BLOSC_ZLib from compressed file" FORCE) -set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) +set (BLOSC_ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of BLOSC_ZLIB package" FORCE) ####### # bzip2 @@ -159,15 +159,15 @@ set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE) #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE) ###### -# szf +# sz ###### -set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE) -set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE) +set (SZ_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ filter from github repository" FORCE) +set (SZ_GIT_BRANCH "master" CACHE STRING "" FORCE) -set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE) +set (SZ_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ filter from compressed file" FORCE) -set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE) +set (SZ_PACKAGE_NAME "SZ" CACHE STRING "Name of SZ filter package" FORCE) ###### # zfp diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in index 589fa5f..35cee4f 100644 --- a/config/cmake/hdf5-config.cmake.in +++ b/config/cmake/hdf5-config.cmake.in @@ -116,7 +116,7 @@ if (NOT TARGET "@HDF5_PACKAGE@") include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) endif () if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS) - include (@PACKAGE_SHARE_INSTALL_DIR@/@SZ_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) + include (@PACKAGE_SHARE_INSTALL_DIR@/@SZIP_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) endif () include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@@HDF_PACKAGE_EXT@-targets.cmake) endif () diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake index b322948..6242b12 100644 --- a/config/cmake_ext_mod/ConfigureChecks.cmake +++ b/config/cmake_ext_mod/ConfigureChecks.cmake @@ -224,61 +224,61 @@ set (HDF_EXTRA_C_FLAGS) set (HDF_EXTRA_FLAGS) if (MINGW OR NOT WINDOWS) if (CMAKE_SYSTEM_NAME MATCHES "Linux") - # Linux Specific flags - # This was originally defined as _POSIX_SOURCE which was updated to - # _POSIX_C_SOURCE=199506L to expose a greater amount of POSIX - # functionality so clock_gettime and CLOCK_MONOTONIC are defined - # correctly. This was later updated to 200112L so that - # posix_memalign() is visible for the direct VFD code on Linux - # systems. - # POSIX feature information can be found in the gcc manual at: - # http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html - set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) - - # Need to add this so that O_DIRECT is visible for the direct - # VFD on Linux systems. - set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE) - - option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON) - if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN) - set (msg "Performing TEST_LFS_WORKS") - try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE - ${CMAKE_BINARY_DIR} - ${HDF_RESOURCES_EXT_DIR}/HDFTests.c - COMPILE_DEFINITIONS "-DTEST_LFS_WORKS" - ) - - # The LARGEFILE definitions were from the transition period - # and are probably no longer needed. The FILE_OFFSET_BITS - # check should be generalized for all POSIX systems as it - # is in the Autotools. - if (TEST_LFS_WORKS_COMPILE) - if (TEST_LFS_WORKS_RUN MATCHES 0) - set (TEST_LFS_WORKS 1 CACHE INTERNAL ${msg}) - set (LARGEFILE 1) - set (HDF_EXTRA_FLAGS ${HDF_EXTRA_FLAGS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... yes") - endif () - else () - set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... no") - endif () - file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log - "Test TEST_LFS_WORKS Run failed with the following exit code:\n ${TEST_LFS_WORKS_RUN}\n" - ) - endif () - else () - set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... no") - endif () - file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log - "Test TEST_LFS_WORKS Compile failed\n" - ) - endif () - endif () + # Linux Specific flags + # This was originally defined as _POSIX_SOURCE which was updated to + # _POSIX_C_SOURCE=199506L to expose a greater amount of POSIX + # functionality so clock_gettime and CLOCK_MONOTONIC are defined + # correctly. This was later updated to 200112L so that + # posix_memalign() is visible for the direct VFD code on Linux + # systems. + # POSIX feature information can be found in the gcc manual at: + # http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html + set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) + + # Need to add this so that O_DIRECT is visible for the direct + # VFD on Linux systems. + set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE) + + option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON) + if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN) + set (msg "Performing TEST_LFS_WORKS") + try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE + ${CMAKE_BINARY_DIR} + ${HDF_RESOURCES_EXT_DIR}/HDFTests.c + COMPILE_DEFINITIONS "-DTEST_LFS_WORKS" + ) + + # The LARGEFILE definitions were from the transition period + # and are probably no longer needed. The FILE_OFFSET_BITS + # check should be generalized for all POSIX systems as it + # is in the Autotools. + if (TEST_LFS_WORKS_COMPILE) + if (TEST_LFS_WORKS_RUN MATCHES 0) + set (TEST_LFS_WORKS 1 CACHE INTERNAL ${msg}) + set (LARGEFILE 1) + set (HDF_EXTRA_FLAGS ${HDF_EXTRA_FLAGS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... yes") + endif () + else () + set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... no") + endif () + file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log + "Test TEST_LFS_WORKS Run failed with the following exit code:\n ${TEST_LFS_WORKS_RUN}\n" + ) + endif () + else () + set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... no") + endif () + file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log + "Test TEST_LFS_WORKS Compile failed\n" + ) + endif () + endif () set (CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} ${HDF_EXTRA_FLAGS}) endif () endif () diff --git a/config/cmake_ext_mod/HDFLibMacros.cmake b/config/cmake_ext_mod/HDFLibMacros.cmake index 2af3229..40d06e7 100644 --- a/config/cmake_ext_mod/HDFLibMacros.cmake +++ b/config/cmake_ext_mod/HDFLibMacros.cmake @@ -139,11 +139,11 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding) # add_subdirectory(${szip_SOURCE_DIR} ${szip_BINARY_DIR}) # endif() # -##include (${BINARY_DIR}/${SZ_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake) +##include (${BINARY_DIR}/${SZIP_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake) # Create imported target szip-static if (USE_LIBAEC) add_library(${HDF_PACKAGE_NAMESPACE}sz-static STATIC IMPORTED) - HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}sz-static "sz" STATIC "") + HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}sz-static "szaec" STATIC "") add_dependencies (${HDF_PACKAGE_NAMESPACE}sz-static SZIP) add_library(${HDF_PACKAGE_NAMESPACE}aec-static STATIC IMPORTED) HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}aec-static "aec" STATIC "") @@ -188,7 +188,7 @@ endmacro () #------------------------------------------------------------------------------- macro (EXTERNAL_ZLIB_LIBRARY compress_type) if (${compress_type} MATCHES "GIT") - EXTERNALPROJECT_ADD (ZLIB + EXTERNALPROJECT_ADD (HDF5_ZLIB GIT_REPOSITORY ${ZLIB_URL} GIT_TAG ${ZLIB_BRANCH} INSTALL_COMMAND "" @@ -207,7 +207,7 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type) -DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE} ) elseif (${compress_type} MATCHES "TGZ") - EXTERNALPROJECT_ADD (ZLIB + EXTERNALPROJECT_ADD (HDF5_ZLIB URL ${ZLIB_URL} URL_MD5 "" INSTALL_COMMAND "" @@ -226,19 +226,15 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type) -DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE} ) endif () - externalproject_get_property (ZLIB BINARY_DIR SOURCE_DIR) + externalproject_get_property (HDF5_ZLIB BINARY_DIR SOURCE_DIR) - if (WIN32) - set (ZLIB_LIB_NAME "zlib") - else () - set (ZLIB_LIB_NAME "z") - endif () + set (ZLIB_LIB_NAME "z") ##include (${BINARY_DIR}/${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake) # Create imported target zlib-static add_library(${HDF_PACKAGE_NAMESPACE}zlib-static STATIC IMPORTED) # add_library(${HDF_PACKAGE_NAMESPACE}zlib-static ALIAS zlib-static) HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}zlib-static ${ZLIB_LIB_NAME} STATIC "") - add_dependencies (${HDF_PACKAGE_NAMESPACE}zlib-static ZLIB) + add_dependencies (${HDF_PACKAGE_NAMESPACE}zlib-static HDF5_ZLIB) set (ZLIB_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}zlib-static") set (ZLIB_LIBRARIES ${ZLIB_STATIC_LIBRARY}) @@ -256,6 +252,6 @@ macro (PACKAGE_ZLIB_LIBRARY compress_type) ) set (EXTERNAL_HEADER_LIST ${EXTERNAL_HEADER_LIST} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/zconf.h) if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "TGZ") - add_dependencies (ZLIB-GenHeader-Copy ZLIB) + add_dependencies (ZLIB-GenHeader-Copy HDF5_ZLIB) endif () endmacro () -- cgit v0.12 From cfe4198b6cb1e145e57bf8eed65c5f6ae68e896e Mon Sep 17 00:00:00 2001 From: Gerd Heber Date: Fri, 18 Feb 2022 08:02:10 -0600 Subject: Updated reference for Multi Dataset RFC. (#1442) --- doxygen/aliases | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doxygen/aliases b/doxygen/aliases index f83a875..11fa691 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -299,7 +299,7 @@ ALIASES += ref_rfc20130630="HDF5 Dynamically Loaded Filters" ALIASES += ref_rfc20121114="Direct Chunk Write" ALIASES += ref_rfc20121024="HDF5 File Space Management" -ALIASES += ref_rfc20120828="New HDF5 API Routines for HPC Applications" +ALIASES += ref_rfc20120828="New HDF5 API Routines for HPC Applications - Read/Write Multiple Datasets in an HDF5 file" ALIASES += ref_rfc20120523="HDF5 File Space Management: Paged Aggregation" ALIASES += ref_rfc20120501="HDF5 File Image Operations" ALIASES += ref_rfc20120305="Enabling a Strict Consistency Semantics Model in Parallel HDF5" -- cgit v0.12 From feda52b08488dbb3e5b2450f6cd63baa98b0e57e Mon Sep 17 00:00:00 2001 From: Neil Fortner Date: Fri, 18 Feb 2022 09:27:05 -0600 Subject: Implement support for big I/O for independent reads (#1446) * Implement big I/O support for independent reads. Add test for this. * Committing clang-format changes * Update big I/O code in H5FD__mpio_write() to match that in H5FD__mpio_read(). Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- src/H5FDmpio.c | 50 ++++++++++++++++++++++++++++++++++---------------- testpar/t_bigio.c | 37 ++++++++++++++++++++++++++++++------- 2 files changed, 64 insertions(+), 23 deletions(-) diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 1feff43..1969899 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -1172,6 +1172,7 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU int n; #endif hbool_t use_view_this_time = FALSE; + hbool_t derived_type = FALSE; hbool_t rank0_bcast = FALSE; /* If read-with-rank0-and-bcast flag was used */ #ifdef H5FDmpio_DEBUG hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); @@ -1199,8 +1200,6 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if (H5FD_mpi_haddr_to_MPIOff(addr, &mpi_off /*out*/) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr to MPI off") size_i = (int)size; - if ((hsize_t)size_i != size) - HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size to size_i") /* Only look for MPI views for raw data transfers */ if (type == H5FD_MEM_DRAW) { @@ -1304,6 +1303,21 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) } /* end if */ else { + if (size != (hsize_t)size_i) { + /* If HERE, then we need to work around the integer size limit + * of 2GB. The input size_t size variable cannot fit into an integer, + * but we can get around that limitation by creating a different datatype + * and then setting the integer size (or element count) to 1 when using + * the derived_type. + */ + + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + + derived_type = TRUE; + size_i = 1; + } + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_r_flag) HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank); @@ -1377,6 +1391,9 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU HDmemset((char *)buf + bytes_read, 0, (size_t)n); done: + if (derived_type) + MPI_Type_free(&buf_type); + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_t_flag) HDfprintf(stderr, "%s: (%d) Leaving\n", __func__, file->mpi_rank); @@ -1489,20 +1506,6 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h */ mpi_off = 0; } /* end if */ - else if (size != (hsize_t)size_i) { - /* If HERE, then we need to work around the integer size limit - * of 2GB. The input size_t size variable cannot fit into an integer, - * but we can get around that limitation by creating a different datatype - * and then setting the integer size (or element count) to 1 when using - * the derived_type. - */ - - if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) - HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") - - derived_type = TRUE; - size_i = 1; - } /* Write the data. */ if (use_view_this_time) { @@ -1548,6 +1551,21 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) } /* end if */ else { + if (size != (hsize_t)size_i) { + /* If HERE, then we need to work around the integer size limit + * of 2GB. The input size_t size variable cannot fit into an integer, + * but we can get around that limitation by creating a different datatype + * and then setting the integer size (or element count) to 1 when using + * the derived_type. + */ + + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + + derived_type = TRUE; + size_i = 1; + } + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_w_flag) HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank); diff --git a/testpar/t_bigio.c b/testpar/t_bigio.c index 4df624b..0a971c5 100644 --- a/testpar/t_bigio.c +++ b/testpar/t_bigio.c @@ -1107,13 +1107,15 @@ single_rank_independent_io(void) HDprintf("\nSingle Rank Independent I/O\n"); if (MAIN_PROCESS) { - hsize_t dims[] = {LARGE_DIM}; - hid_t file_id = -1; - hid_t fapl_id = -1; - hid_t dset_id = -1; - hid_t fspace_id = -1; - hid_t mspace_id = -1; - void * data = NULL; + hsize_t dims[] = {LARGE_DIM}; + hid_t file_id = -1; + hid_t fapl_id = -1; + hid_t dset_id = -1; + hid_t fspace_id = -1; + hid_t mspace_id = -1; + herr_t ret; + int * data = NULL; + uint64_t i; fapl_id = H5Pcreate(H5P_FILE_ACCESS); VRFY_G((fapl_id >= 0), "H5P_FILE_ACCESS"); @@ -1135,6 +1137,10 @@ single_rank_independent_io(void) data = malloc(LARGE_DIM * sizeof(int)); + /* Initialize data */ + for (i = 0; i < LARGE_DIM; i++) + data[i] = (int)(i % (uint64_t)DXFER_BIGCOUNT); + if (mpi_rank_g == 0) H5Sselect_all(fspace_id); else @@ -1143,7 +1149,24 @@ single_rank_independent_io(void) dims[0] = LARGE_DIM; mspace_id = H5Screate_simple(1, dims, NULL); VRFY_G((mspace_id >= 0), "H5Screate_simple mspace_id succeeded"); + + /* Write data */ H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data); + VRFY_G((ret >= 0), "H5Dwrite succeeded"); + + /* Wipe buffer */ + HDmemset(data, 0, LARGE_DIM * sizeof(int)); + + /* Read data back */ + H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data); + VRFY_G((ret >= 0), "H5Dread succeeded"); + + /* Verify data */ + for (i = 0; i < LARGE_DIM; i++) + if (data[i] != (int)(i % (uint64_t)DXFER_BIGCOUNT)) { + HDfprintf(stderr, "verify failed\n"); + exit(1); + } free(data); H5Sclose(mspace_id); -- cgit v0.12 From 42c419e2661f67a80cef445084d28ac25572244e Mon Sep 17 00:00:00 2001 From: Neil Fortner Date: Fri, 18 Feb 2022 09:28:21 -0600 Subject: Fix issue with copying null new references (#1440) * Fix issue with copying null new references. Fix assertion failure when reference copying fails. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- src/H5Ocache.c | 8 +++--- src/H5Ocopy.c | 2 +- src/H5Ocopy_ref.c | 82 +++++++++++++++++++++++++++++-------------------------- src/H5Oint.c | 12 ++++---- src/H5Opkg.h | 2 +- 5 files changed, 57 insertions(+), 49 deletions(-) diff --git a/src/H5Ocache.c b/src/H5Ocache.c index ba47da3..c7586cc 100644 --- a/src/H5Ocache.c +++ b/src/H5Ocache.c @@ -346,7 +346,7 @@ H5O__cache_deserialize(const void *image, size_t len, void *_udata, hbool_t *dir done: /* Release the [possibly partially initialized] object header on errors */ if (!ret_value && oh) - if (H5O__free(oh) < 0) + if (H5O__free(oh, FALSE) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTRELEASE, NULL, "unable to destroy object header data") FUNC_LEAVE_NOAPI(ret_value) @@ -639,7 +639,7 @@ H5O__cache_free_icr(void *_thing) HDassert(oh->cache_info.type == H5AC_OHDR); /* Destroy object header */ - if (H5O__free(oh) < 0) + if (H5O__free(oh, FALSE) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "can't destroy object header") done: @@ -1242,7 +1242,7 @@ H5O__prefix_deserialize(const uint8_t *_image, H5O_cache_ud_t *udata) /* Save the object header for later use in 'deserialize' callback */ udata->oh = oh; - if (H5O__free(saved_oh) < 0) + if (H5O__free(saved_oh, FALSE) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "can't destroy object header") udata->free_oh = FALSE; } @@ -1255,7 +1255,7 @@ H5O__prefix_deserialize(const uint8_t *_image, H5O_cache_ud_t *udata) done: /* Release the [possibly partially initialized] object header on errors */ if (ret_value < 0 && oh) - if (H5O__free(oh) < 0) + if (H5O__free(oh, FALSE) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "unable to destroy object header data") FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c index 05dfc72..52b1b5c 100644 --- a/src/H5Ocopy.c +++ b/src/H5Ocopy.c @@ -772,7 +772,7 @@ done: /* Free destination object header on failure */ if (ret_value < 0) { if (oh_dst && !inserted) { - if (H5O__free(oh_dst) < 0) + if (H5O__free(oh_dst, TRUE) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to destroy object header data") if (H5O_loc_reset(oloc_dst) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to destroy object header data") diff --git a/src/H5Ocopy_ref.c b/src/H5Ocopy_ref.c index f1f8aaf..1cda3ea 100644 --- a/src/H5Ocopy_ref.c +++ b/src/H5Ocopy_ref.c @@ -288,21 +288,22 @@ H5O__copy_expand_ref_object2(H5O_loc_t *src_oloc, hid_t tid_src, const H5T_t *dt size_t nbytes_src, H5O_loc_t *dst_oloc, H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count, H5O_copy_t *cpy_info) { - H5T_t * dt_mem = NULL; /* Memory datatype */ - H5T_t * dt_dst = NULL; /* Destination datatype */ - hid_t tid_mem = H5I_INVALID_HID; /* Datatype ID for memory datatype */ - hid_t tid_dst = H5I_INVALID_HID; /* Datatype ID for memory datatype */ - H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ - size_t i; /* Local index variable */ - hbool_t reg_tid_src = (tid_src == H5I_INVALID_HID); - hid_t dst_loc_id = H5I_INVALID_HID; - void * conv_buf = NULL; /* Buffer for converting data */ - size_t conv_buf_size = 0; /* Buffer size */ - void * reclaim_buf = NULL; /* Buffer for reclaiming data */ - H5S_t * buf_space = NULL; /* Dataspace describing buffer */ - hsize_t buf_dim[1] = {ref_count}; /* Dimension for buffer */ - size_t token_size = H5F_SIZEOF_ADDR(src_oloc->file); - herr_t ret_value = SUCCEED; + H5T_t * dt_mem = NULL; /* Memory datatype */ + H5T_t * dt_dst = NULL; /* Destination datatype */ + hid_t tid_mem = H5I_INVALID_HID; /* Datatype ID for memory datatype */ + hid_t tid_dst = H5I_INVALID_HID; /* Datatype ID for memory datatype */ + H5T_path_t * tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ + size_t i; /* Local index variable */ + hbool_t reg_tid_src = (tid_src == H5I_INVALID_HID); + hid_t dst_loc_id = H5I_INVALID_HID; + void * conv_buf = NULL; /* Buffer for converting data */ + size_t conv_buf_size = 0; /* Buffer size */ + void * reclaim_buf = NULL; /* Buffer for reclaiming data */ + H5S_t * buf_space = NULL; /* Dataspace describing buffer */ + hsize_t buf_dim[1] = {ref_count}; /* Dimension for buffer */ + size_t token_size = H5F_SIZEOF_ADDR(src_oloc->file); + const unsigned char zeros[H5R_REF_BUF_SIZE] = {0}; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -353,29 +354,34 @@ H5O__copy_expand_ref_object2(H5O_loc_t *src_oloc, hid_t tid_src, const H5T_t *dt /* Making equivalent references in the destination file */ for (i = 0; i < ref_count; i++) { - H5R_ref_t * ref_ptr = (H5R_ref_t *)conv_buf; - H5R_ref_priv_t *ref = (H5R_ref_priv_t *)&ref_ptr[i]; - H5O_token_t tmp_token = {0}; - - /* Get src object address */ - if (H5R__get_obj_token(ref, &tmp_token, &token_size) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to get object token") - if (H5VL_native_token_to_addr(src_oloc->file, H5I_FILE, tmp_token, &src_oloc->addr) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTUNSERIALIZE, FAIL, "can't deserialize object token into address") - - /* Attempt to copy object from source to destination file */ - if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object") - - /* Set dst object address */ - if (H5VL_native_addr_to_token(dst_oloc->file, H5I_FILE, dst_oloc->addr, &tmp_token) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL, "can't serialize address into object token") - if (H5R__set_obj_token(ref, (const H5O_token_t *)&tmp_token, token_size) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set object token") - /* Do not set app_ref since references are released once the copy is done */ - if (H5R__set_loc_id(ref, dst_loc_id, TRUE, FALSE) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set destination loc id") - } /* end for */ + H5R_ref_t * ref_ptr = (H5R_ref_t *)conv_buf; + H5R_ref_priv_t *ref = (H5R_ref_priv_t *)&ref_ptr[i]; + + /* Check for null reference - only expand reference if it is not null */ + if (HDmemcmp(ref, zeros, H5R_REF_BUF_SIZE)) { + H5O_token_t tmp_token = {0}; + + /* Get src object address */ + if (H5R__get_obj_token(ref, &tmp_token, &token_size) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to get object token") + if (H5VL_native_token_to_addr(src_oloc->file, H5I_FILE, tmp_token, &src_oloc->addr) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTUNSERIALIZE, FAIL, + "can't deserialize object token into address") + + /* Attempt to copy object from source to destination file */ + if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object") + + /* Set dst object address */ + if (H5VL_native_addr_to_token(dst_oloc->file, H5I_FILE, dst_oloc->addr, &tmp_token) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL, "can't serialize address into object token") + if (H5R__set_obj_token(ref, (const H5O_token_t *)&tmp_token, token_size) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set object token") + /* Do not set app_ref since references are released once the copy is done */ + if (H5R__set_loc_id(ref, dst_loc_id, TRUE, FALSE) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set destination loc id") + } /* end if */ + } /* end for */ /* Copy into another buffer, to reclaim memory later */ if (NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, conv_buf_size))) diff --git a/src/H5Oint.c b/src/H5Oint.c index ee79b0c..2348790 100644 --- a/src/H5Oint.c +++ b/src/H5Oint.c @@ -289,7 +289,7 @@ H5O_create(H5F_t *f, size_t size_hint, size_t initial_rc, hid_t ocpl_id, H5O_loc HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "Can't apply object header to file") done: - if ((FAIL == ret_value) && (NULL != oh) && (H5O__free(oh) < 0)) + if ((FAIL == ret_value) && (NULL != oh) && (H5O__free(oh, TRUE) < 0)) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "can't delete object header") FUNC_LEAVE_NOAPI(ret_value) @@ -353,7 +353,7 @@ H5O_create_ohdr(H5F_t *f, hid_t ocpl_id) ret_value = oh; done: - if ((NULL == ret_value) && (NULL != oh) && (H5O__free(oh) < 0)) + if ((NULL == ret_value) && (NULL != oh) && (H5O__free(oh, TRUE) < 0)) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, NULL, "can't delete object header") FUNC_LEAVE_NOAPI(ret_value) @@ -3014,7 +3014,7 @@ H5O_get_proxy(const H5O_t *oh) *------------------------------------------------------------------------- */ herr_t -H5O__free(H5O_t *oh) +H5O__free(H5O_t *oh, hbool_t force) { unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ @@ -3038,10 +3038,12 @@ H5O__free(H5O_t *oh) for (u = 0; u < oh->nmesgs; u++) { #ifndef NDEBUG /* Verify that message is clean, unless it could have been marked - * dirty by decoding */ + * dirty by decoding, or if this is a forced free (in case of + * failure during creation of the object some messages may be dirty) + */ if (oh->ndecode_dirtied && oh->mesg[u].dirty) oh->ndecode_dirtied--; - else + else if (!force) HDassert(oh->mesg[u].dirty == 0); #endif /* NDEBUG */ diff --git a/src/H5Opkg.h b/src/H5Opkg.h index ebfe636..1fe918d 100644 --- a/src/H5Opkg.h +++ b/src/H5Opkg.h @@ -551,7 +551,7 @@ H5_DLL herr_t H5O__visit(H5G_loc_t *loc, const char *obj_name, H5_index_t idx_ty H5O_iterate2_t op, void *op_data, unsigned fields); H5_DLL herr_t H5O__inc_rc(H5O_t *oh); H5_DLL herr_t H5O__dec_rc(H5O_t *oh); -H5_DLL herr_t H5O__free(H5O_t *oh); +H5_DLL herr_t H5O__free(H5O_t *oh, hbool_t force); /* Object header message routines */ H5_DLL herr_t H5O__msg_alloc(H5F_t *f, H5O_t *oh, const H5O_msg_class_t *type, unsigned *mesg_flags, -- cgit v0.12 From f8b1ea3f9973b690a60b63ebb431568ce0e19a29 Mon Sep 17 00:00:00 2001 From: Neil Fortner Date: Fri, 18 Feb 2022 14:03:52 -0600 Subject: Implement big I/O support for vector I/O requests in the MPIO file driver. --- src/H5FDmpio.c | 253 +++++++++++++++++++++++++++++++++++++++++++++--------- testpar/t_bigio.c | 2 - 2 files changed, 214 insertions(+), 41 deletions(-) diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index cfb8f110..14a2739 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -128,10 +128,10 @@ static const H5FD_class_t H5FD_mpio_g = { H5FD__mpio_get_handle, /* get_handle */ H5FD__mpio_read, /* read */ H5FD__mpio_write, /* write */ - H5FD__mpio_read_vector, /*read_vector */ - H5FD__mpio_write_vector, /*write_vector */ - NULL, /*read_selection */ - NULL, /*write_selection */ + H5FD__mpio_read_vector, /* read_vector */ + H5FD__mpio_write_vector, /* write_vector */ + NULL, /* read_selection */ + NULL, /* write_selection */ H5FD__mpio_flush, /* flush */ H5FD__mpio_truncate, /* truncate */ NULL, /* lock */ @@ -1700,6 +1700,8 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou hbool_t buf_type_created = FALSE; MPI_Datatype file_type = MPI_BYTE; /* MPI description of the selection in file */ hbool_t file_type_created = FALSE; + MPI_Datatype * sub_types = NULL; + uint8_t * sub_types_created = NULL; int i; int j; int mpi_code; /* MPI return code */ @@ -1759,6 +1761,10 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") if (xfer_mode == H5FD_MPIO_COLLECTIVE) { + hsize_t bigio_count; /* Transition point to create derived type */ + + /* Get bio I/O transition point (may be lower than 2G for testing) */ + bigio_count = H5_mpi_get_bigio_count(); if (count == 1) { /* Single block. Just use a series of MPI_BYTEs for the file view. @@ -1775,6 +1781,24 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou /* some numeric conversions */ if (H5FD_mpi_haddr_to_MPIOff(addrs[0], &mpi_off) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't set MPI offset") + + /* Check for size overflow */ + if (sizes[0] > bigio_count) { + /* We need to work around the integer size limit of 2GB. The input size_t size + * variable cannot fit into an integer, but we can get around that limitation by + * creating a different datatype and then setting the integer size (or element + * count) to 1 when using the derived_type. */ + + if (H5_mpio_create_large_type(sizes[0], 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + buf_type_created = TRUE; + + if (H5_mpio_create_large_type(sizes[0], 0, MPI_BYTE, &file_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + file_type_created = TRUE; + + size_i = 1; + } } else if (count > 0) { /* create MPI derived types describing the vector write */ @@ -1787,7 +1811,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou * are allocated, populated, and returned in s_types, s_addrs, s_sizes, and s_bufs respectively. * In this case, this function must free the memory allocated for the sorted vectors. */ - if (H5FD_sort_vector_io_req(&vector_was_sorted, count, types, addrs, sizes, bufs, &s_types, + if (H5FD_sort_vector_io_req(&vector_was_sorted, count, types, addrs, sizes, (const void **)bufs, &s_types, &s_addrs, &s_sizes, &s_bufs) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't sort vector I/O request") @@ -1842,12 +1866,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou } } - /* There is an obvious possibility of an overflow here, as size_t - * will typically be 64 bits, where as int will typically be 32 bits. - * This must be fixed, but it should be good enough for initial - * correctness testing. - * JRM -- 3/17/21 - */ + /* Add to block lengths and displacements arrays */ mpi_block_lengths[i] = (int)size; mpi_displacments[i] = (MPI_Aint)s_addrs[i]; @@ -1862,13 +1881,54 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou #else mpi_bufs[i] = mpi_bufs[i] - mpi_bufs_base_Aint; #endif + + /* Check for size overflow */ + if (size > bigio_count) { + /* We need to work around the integer size limit of 2GB. The input size_t size + * variable cannot fit into an integer, but we can get around that limitation by + * creating a different datatype and then setting the integer size (or element + * count) to 1 when using the derived_type. */ + + /* Allocate arrays to keep track of types and whether they were created, if + * necessary */ + if (!sub_types) { + HDassert(!sub_types_created); + + if (NULL == (sub_types = (int *)HDmalloc((size_t)count * sizeof(MPI_Datatype)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types array") + if (NULL == (sub_types_created = (uint8_t *)HDcalloc((size_t)count, 1))) { + sub_types = H5MM_free(sub_types); + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types created array") + } + + /* Initialize sub_types to all MPI_BYTE */ + for (j = 0; j < (int)count; j++) + sub_types[j] = MPI_BYTE; + } + HDassert(sub_types_created); + + /* Create type for large block */ + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &sub_types[i]) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + sub_types_created[i] = TRUE; + + /* Only one of these large types for this vector element */ + mpi_block_lengths[i] = 1; + } + else + HDassert(size == (size_t)mpi_block_lengths[i]); } /* create the memory MPI derived types */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_bufs, - MPI_BYTE, &buf_type))) - - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) + if (sub_types) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, mpi_bufs, + sub_types, &buf_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for buf_type failed", mpi_code) + } + else + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_bufs, + MPI_BYTE, &buf_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) buf_type_created = TRUE; @@ -1877,10 +1937,15 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit for buf_type failed", mpi_code) /* create the file MPI derived type */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, - mpi_displacments, MPI_BYTE, &file_type))) - - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) + if (sub_types) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, + mpi_displacments, sub_types, &file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for file_type failed", mpi_code) + } + else + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, + mpi_displacments, MPI_BYTE, &file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) file_type_created = TRUE; @@ -2090,7 +2155,22 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou } } - size_i = (int)size; /* todo: fix potential for overflow */ + size_i = (int)size; + + if (size != (size_t)size_i) { + /* If HERE, then we need to work around the integer size limit + * of 2GB. The input size_t size variable cannot fit into an integer, + * but we can get around that limitation by creating a different datatype + * and then setting the integer size (or element count) to 1 when using + * the derived_type. + */ + + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + + buf_type_created = TRUE; + size_i = 1; + } /* Check if we actually need to do I/O */ if (addrs[i] < max_addr) { @@ -2099,7 +2179,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou /* Issue read */ if (MPI_SUCCESS != - (mpi_code = MPI_File_read_at(file->f, mpi_off, bufs[i], size_i, MPI_BYTE, &mpi_stat))) + (mpi_code = MPI_File_read_at(file->f, mpi_off, bufs[i], size_i, buf_type, &mpi_stat))) HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code) @@ -2111,8 +2191,15 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou #endif HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code) + /* Compute the actual number of bytes requested */ +#if MPI_VERSION >= 3 + io_size = (MPI_Count)sizes[i]; +#else + io_size = (int)sizes[i]; +#endif + /* Check for read failure */ - if (bytes_read < 0 || bytes_read > size_i) + if (bytes_read < 0 || bytes_read > io_size) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed") /* @@ -2120,7 +2207,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou * the physical MPI file and don't issue any more reads at higher * addresses. */ - if ((n = (size_i - bytes_read)) > 0) { + if ((n = (io_size - bytes_read)) > 0) { HDmemset((char *)bufs[i] + bytes_read, 0, (size_t)n); max_addr = addrs[i] + (haddr_t)bytes_read; } @@ -2183,6 +2270,19 @@ done: MPI_Type_free(&buf_type); } + if (sub_types) { + HDassert(sub_types_created); + + for (i = 0; i < (int)count; i++) + if (sub_types_created[i]) + MPI_Type_free(&sub_types[i]); + + HDfree(sub_types); + sub_types = NULL; + HDfree(sub_types_created); + sub_types_created = NULL; + } + if (file_type_created) { MPI_Type_free(&file_type); } @@ -2259,6 +2359,8 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co hbool_t buf_type_created = FALSE; MPI_Datatype file_type = MPI_BYTE; /* MPI description of the selection in file */ hbool_t file_type_created = FALSE; + MPI_Datatype * sub_types = NULL; + uint8_t * sub_types_created = NULL; int i; int j; int mpi_code; /* MPI return code */ @@ -2325,6 +2427,7 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co if (xfer_mode == H5FD_MPIO_COLLECTIVE) { if (count > 0) { /* create MPI derived types describing the vector write */ + hsize_t bigio_count; /* Transition point to create derived type */ if ((NULL == (mpi_block_lengths = (int *)HDmalloc((size_t)count * sizeof(int)))) || (NULL == (mpi_displacments = (MPI_Aint *)HDmalloc((size_t)count * sizeof(MPI_Aint)))) || @@ -2361,6 +2464,9 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co fixed_size = FALSE; + /* Get bio I/O transition point (may be lower than 2G for testing) */ + bigio_count = H5_mpi_get_bigio_count(); + /* load the mpi_block_lengths and mpi_displacements arrays */ for (i = 0; i < (int)count; i++) { @@ -2377,12 +2483,7 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co } } - /* There is an obvious possibility of an overflow here, as size_t - * will typically be 64 bits, where as int will typically be 32 bits. - * This must be fixed, but it should be good enough for initial - * correctness testing. - * JRM -- 3/17/21 - */ + /* Add to block lengths and displacements arrays */ mpi_block_lengths[i] = (int)size; mpi_displacments[i] = (MPI_Aint)s_addrs[i]; @@ -2397,13 +2498,54 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co #else mpi_bufs[i] = mpi_bufs[i] - mpi_bufs_base_Aint; #endif + + /* Check for size overflow */ + if (size > bigio_count) { + /* We need to work around the integer size limit of 2GB. The input size_t size + * variable cannot fit into an integer, but we can get around that limitation by + * creating a different datatype and then setting the integer size (or element + * count) to 1 when using the derived_type. */ + + /* Allocate arrays to keep track of types and whether they were created, if + * necessary */ + if (!sub_types) { + HDassert(!sub_types_created); + + if (NULL == (sub_types = (int *)HDmalloc((size_t)count * sizeof(MPI_Datatype)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types array") + if (NULL == (sub_types_created = (uint8_t *)HDcalloc((size_t)count, 1))) { + sub_types = H5MM_free(sub_types); + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types created array") + } + + /* Initialize sub_types to all MPI_BYTE */ + for (j = 0; j < (int)count; j++) + sub_types[j] = MPI_BYTE; + } + HDassert(sub_types_created); + + /* Create type for large block */ + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &sub_types[i]) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + sub_types_created[i] = TRUE; + + /* Only one of these large types for this vector element */ + mpi_block_lengths[i] = 1; + } + else + HDassert(size == (size_t)mpi_block_lengths[i]); } /* create the memory MPI derived types */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_bufs, - MPI_BYTE, &buf_type))) - - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) + if (sub_types) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, mpi_bufs, + sub_types, &buf_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for buf_type failed", mpi_code) + } + else + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_bufs, + MPI_BYTE, &buf_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) buf_type_created = TRUE; @@ -2412,10 +2554,15 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit for buf_type failed", mpi_code) /* create the file MPI derived type */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, - mpi_displacments, MPI_BYTE, &file_type))) - - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) + if (sub_types) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, + mpi_displacments, sub_types, &file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for file_type failed", mpi_code) + } + else + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, + mpi_displacments, MPI_BYTE, &file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) file_type_created = TRUE; @@ -2530,10 +2677,25 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co } } - size_i = (int)size; /* todo: fix potential for overflow */ + size_i = (int)size; + + if (size != (size_t)size_i) { + /* If HERE, then we need to work around the integer size limit + * of 2GB. The input size_t size variable cannot fit into an integer, + * but we can get around that limitation by creating a different datatype + * and then setting the integer size (or element count) to 1 when using + * the derived_type. + */ + + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + + buf_type_created = TRUE; + size_i = 1; + } if (MPI_SUCCESS != - (mpi_code = MPI_File_write_at(file->f, mpi_off, s_bufs[i], size_i, MPI_BYTE, &mpi_stat))) + (mpi_code = MPI_File_write_at(file->f, mpi_off, s_bufs[i], size_i, buf_type, &mpi_stat))) HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at failed", mpi_code) } @@ -2612,6 +2774,19 @@ done: MPI_Type_free(&file_type); } + if (sub_types) { + HDassert(sub_types_created); + + for (i = 0; i < (int)count; i++) + if (sub_types_created[i]) + MPI_Type_free(&sub_types[i]); + + HDfree(sub_types); + sub_types = NULL; + HDfree(sub_types_created); + sub_types_created = NULL; + } + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_t_flag) HDfprintf(stdout, "%s: Leaving, proc %d: ret_value = %d\n", __func__, file->mpi_rank, ret_value); diff --git a/testpar/t_bigio.c b/testpar/t_bigio.c index dd2514b..0a971c5 100644 --- a/testpar/t_bigio.c +++ b/testpar/t_bigio.c @@ -1103,7 +1103,6 @@ dataset_big_read(void) static void single_rank_independent_io(void) { -#if HDF5_BIG_SELECTION_IO_WORKS if (mpi_rank_g == 0) HDprintf("\nSingle Rank Independent I/O\n"); @@ -1179,7 +1178,6 @@ single_rank_independent_io(void) HDremove(FILENAME[1]); } MPI_Barrier(MPI_COMM_WORLD); -#endif } /* -- cgit v0.12 From f2aeb04c20551bec8f61f1f36c3239c8820f7c57 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 18 Feb 2022 20:06:32 +0000 Subject: Committing clang-format changes --- src/H5FDmpio.c | 62 ++++++++++++++++++++++++++++++---------------------------- 1 file changed, 32 insertions(+), 30 deletions(-) diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 14a2739..4775948 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -1761,7 +1761,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") if (xfer_mode == H5FD_MPIO_COLLECTIVE) { - hsize_t bigio_count; /* Transition point to create derived type */ + hsize_t bigio_count; /* Transition point to create derived type */ /* Get bio I/O transition point (may be lower than 2G for testing) */ bigio_count = H5_mpi_get_bigio_count(); @@ -1797,7 +1797,7 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") file_type_created = TRUE; - size_i = 1; + size_i = 1; } } else if (count > 0) { /* create MPI derived types describing the vector write */ @@ -1811,8 +1811,8 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou * are allocated, populated, and returned in s_types, s_addrs, s_sizes, and s_bufs respectively. * In this case, this function must free the memory allocated for the sorted vectors. */ - if (H5FD_sort_vector_io_req(&vector_was_sorted, count, types, addrs, sizes, (const void **)bufs, &s_types, - &s_addrs, &s_sizes, &s_bufs) < 0) + if (H5FD_sort_vector_io_req(&vector_was_sorted, count, types, addrs, sizes, (const void **)bufs, + &s_types, &s_addrs, &s_sizes, &s_bufs) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't sort vector I/O request") if ((NULL == (mpi_block_lengths = (int *)HDmalloc((size_t)count * sizeof(int)))) || @@ -1898,7 +1898,8 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types array") if (NULL == (sub_types_created = (uint8_t *)HDcalloc((size_t)count, 1))) { sub_types = H5MM_free(sub_types); - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types created array") + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't alloc sub types created array") } /* Initialize sub_types to all MPI_BYTE */ @@ -1925,10 +1926,9 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou sub_types, &buf_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for buf_type failed", mpi_code) } - else - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_bufs, - MPI_BYTE, &buf_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) + else if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, + mpi_bufs, MPI_BYTE, &buf_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) buf_type_created = TRUE; @@ -1938,14 +1938,15 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou /* create the file MPI derived type */ if (sub_types) { - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, - mpi_displacments, sub_types, &file_type))) + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, mpi_displacments, + sub_types, &file_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for file_type failed", mpi_code) } - else - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, - mpi_displacments, MPI_BYTE, &file_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) + else if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_displacments, + MPI_BYTE, &file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) file_type_created = TRUE; @@ -2191,11 +2192,11 @@ H5FD__mpio_read_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t cou #endif HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code) - /* Compute the actual number of bytes requested */ + /* Compute the actual number of bytes requested */ #if MPI_VERSION >= 3 io_size = (MPI_Count)sizes[i]; #else - io_size = (int)sizes[i]; + io_size = (int)sizes[i]; #endif /* Check for read failure */ @@ -2426,8 +2427,8 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co if (xfer_mode == H5FD_MPIO_COLLECTIVE) { - if (count > 0) { /* create MPI derived types describing the vector write */ - hsize_t bigio_count; /* Transition point to create derived type */ + if (count > 0) { /* create MPI derived types describing the vector write */ + hsize_t bigio_count; /* Transition point to create derived type */ if ((NULL == (mpi_block_lengths = (int *)HDmalloc((size_t)count * sizeof(int)))) || (NULL == (mpi_displacments = (MPI_Aint *)HDmalloc((size_t)count * sizeof(MPI_Aint)))) || @@ -2515,7 +2516,8 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types array") if (NULL == (sub_types_created = (uint8_t *)HDcalloc((size_t)count, 1))) { sub_types = H5MM_free(sub_types); - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't alloc sub types created array") + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't alloc sub types created array") } /* Initialize sub_types to all MPI_BYTE */ @@ -2542,10 +2544,9 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co sub_types, &buf_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for buf_type failed", mpi_code) } - else - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_bufs, - MPI_BYTE, &buf_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) + else if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, + mpi_bufs, MPI_BYTE, &buf_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for buf_type failed", mpi_code) buf_type_created = TRUE; @@ -2555,14 +2556,15 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co /* create the file MPI derived type */ if (sub_types) { - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, - mpi_displacments, sub_types, &file_type))) + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct((int)count, mpi_block_lengths, mpi_displacments, + sub_types, &file_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct for file_type failed", mpi_code) } - else - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, - mpi_displacments, MPI_BYTE, &file_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) + else if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_hindexed((int)count, mpi_block_lengths, mpi_displacments, + MPI_BYTE, &file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed for file_type failed", mpi_code) file_type_created = TRUE; -- cgit v0.12 From db99157eb4c2f9911580f3d68bf23670fc700cfe Mon Sep 17 00:00:00 2001 From: Neil Fortner Date: Fri, 18 Feb 2022 14:31:13 -0600 Subject: Update dummy file driver in h5test.c to match new struct. --- test/h5test.c | 74 +++++++++++++++++++++++++++++++---------------------------- 1 file changed, 39 insertions(+), 35 deletions(-) diff --git a/test/h5test.c b/test/h5test.c index 0528623..1403649 100644 --- a/test/h5test.c +++ b/test/h5test.c @@ -1773,41 +1773,45 @@ dummy_vfd_write(H5FD_t H5_ATTR_UNUSED *_file, H5FD_mem_t H5_ATTR_UNUSED type, hi /* Dummy VFD with the minimum parameters to make a VFD that can be registered */ #define DUMMY_VFD_VALUE (H5FD_class_value_t)155 static const H5FD_class_t H5FD_dummy_g = { - DUMMY_VFD_VALUE, /* value */ - "dummy", /* name */ - 1, /* maxaddr */ - H5F_CLOSE_WEAK, /* fc_degree */ - NULL, /* terminate */ - NULL, /* sb_size */ - NULL, /* sb_encode */ - NULL, /* sb_decode */ - 0, /* fapl_size */ - NULL, /* fapl_get */ - NULL, /* fapl_copy */ - NULL, /* fapl_free */ - 0, /* dxpl_size */ - NULL, /* dxpl_copy */ - NULL, /* dxpl_free */ - dummy_vfd_open, /* open */ - dummy_vfd_close, /* close */ - NULL, /* cmp */ - NULL, /* query */ - NULL, /* get_type_map */ - NULL, /* alloc */ - NULL, /* free */ - dummy_vfd_get_eoa, /* get_eoa */ - dummy_vfd_set_eoa, /* set_eoa */ - dummy_vfd_get_eof, /* get_eof */ - NULL, /* get_handle */ - dummy_vfd_read, /* read */ - dummy_vfd_write, /* write */ - NULL, /* flush */ - NULL, /* truncate */ - NULL, /* lock */ - NULL, /* unlock */ - NULL, /* del */ - NULL, /* ctl */ - H5FD_FLMAP_DICHOTOMY /* fl_map */ + DUMMY_VFD_VALUE, /* value */ + "dummy", /* name */ + 1, /* maxaddr */ + H5F_CLOSE_WEAK, /* fc_degree */ + NULL, /* terminate */ + NULL, /* sb_size */ + NULL, /* sb_encode */ + NULL, /* sb_decode */ + 0, /* fapl_size */ + NULL, /* fapl_get */ + NULL, /* fapl_copy */ + NULL, /* fapl_free */ + 0, /* dxpl_size */ + NULL, /* dxpl_copy */ + NULL, /* dxpl_free */ + dummy_vfd_open, /* open */ + dummy_vfd_close, /* close */ + NULL, /* cmp */ + NULL, /* query */ + NULL, /* get_type_map */ + NULL, /* alloc */ + NULL, /* free */ + dummy_vfd_get_eoa, /* get_eoa */ + dummy_vfd_set_eoa, /* set_eoa */ + dummy_vfd_get_eof, /* get_eof */ + NULL, /* get_handle */ + dummy_vfd_read, /* read */ + dummy_vfd_write, /* write */ + NULL, /* read_vector */ + NULL, /* write_vector */ + NULL, /* read_selection */ + NULL, /* write_selection */ + NULL, /* flush */ + NULL, /* truncate */ + NULL, /* lock */ + NULL, /* unlock */ + NULL, /* del */ + NULL, /* ctl */ + H5FD_FLMAP_DICHOTOMY /* fl_map */ }; /*------------------------------------------------------------------------- -- cgit v0.12