| Commit message (Collapse) | Author | Age | Files | Lines |
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* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* HDFFV-11229 update autotools test script for two ref files
* HDFFV-11229 merge dev changes for long double display in tools
* Committing clang-format changes
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* close #195. (#196)
* Update HDF5PluginMacros.cmake
* Update HDF5PluginMacros.cmake
* Modify temporary rpath for testing in java example scripts. (#230)
* Fix undefined left shifting of negative numbers (#338)
Undefined Bahavior Sanitizer errored here about left shifting negative numbers.
* Update license url (#332)
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>
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merge_func_enter_vol
Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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Complete revamp of package initialization/shutdown mechanism in the library.
Each package now has a single init/term routine.
This new way should avoid packages being re-initialized during library
shutdown and is also be _much_ more proactive about giving feedback for
resource leaks internal to the library.
Introduces a new "module" header file for packages in the library
(e.g src/H5Fmodule.h) which sets up some necessary package configuration macros
for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly
modified version of this header, src/H5FDdrvr_module.h)
Also cleaned up a bunch of resources leaks all across the library and tests,
along with addressing many warnings, as I encountered them.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/64 3.10.x (kituo) w/serial & parallel
Linux/64 2.6.x (ostrich) w/serial
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* H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z)))
- Rename UNUSED attribute characterstic to H5_ATTR_UNUSED.
- Rename NORETURN attribute characterstic to H5_ATTR_NORETURN
tested with h5committest.
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Switch propert list/class iteration from internal to external form of
iteration, cleaning up and simplifying the code a bit.
Bring other general improvements from plist_encode_decode branch back to
trunk.
Clean up many warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN
(too minor to require h5committest)
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Description:
When jumping out from between H5_BEGIN_TAG and H5_END_TAG macros using
HGOTO_ERROR or HGOTO_DONE, the previous metadata tag is not reset on the dxpl.
This could cause problems when, for example, calling H5Ocopy within an
H5Literate callback.
Added new HGOTO_ERROR_TAG and HGOTO_DONE_TAG macros which must be used in place
of the above between H5_BEGIN_TAG and H5_END_TAG.
Tested:
jam, koala, ostrich (h5committest), durandal
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Bring "merge committed datatypes during H5Ocopy" feature from branch to
trunk. (Also has some minor bugfixes with it)
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug
(h5committest coming up)
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Add FUNC_ENTER macros for package-private routines and begin process of
switching package routines to use them. All H5G routines are currently
finished.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
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Refactor function name macros and simplify the FUNC_ENTER macros, to clear
away the cruft and prepare for further cleanups.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
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Commit metadata tagging framework.
Description:
This check-in contains a new framework whose goal is to apply
a tag value to each new entry in the metadata cache as it is created.
This tag value is such that it relates each piece of metadata to the
HDF5 object that it belongs to (dataset, group, et cetera).
This changeset includes the framework that applies the tags as
well as a suite of tests to verify correct tag application, though does
not yet make use of the tag values to flush/evict individual objects.
Please refer to the "flush/evict individual objects" RFC for further
discussion of these changes.
Tested:
jam, amani, linew (h5committest)
liberty, abe, blue print
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Clean up compiler warnings
Tested on:
Mac OS X/32 10.6.3 (amazon) w/debug
(too minor to require h5committest)
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Bring "compress group's fractal heap" feature from branch back to
trunk.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.1 (amazon) in debug mode
Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Description:
When an attribute was created with a datatype or dataspace that was shared in
the same object header that the attribute was in, the attribute could not be
deleted. Changes made to ensure that the attribute can be deleted both when the
attribute is in the object header and when it is shared in the heap. Object
header message decode routines now take an "open_oh" parameter to enable them to
avoid opening the same object header twice.
Tested: jam, smirom (h5committest)
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Clean up warnings & formatting
Tested on:
Mac OS X/32 10.5.4 (amazon)
More tests forthcoming
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files with incorrect
datatype versions are encountered.
Description: The library now recognizes some problems with datatype versions in
H5O_decode_helper(), and, if not performing strict format checks, automatically
corrects them. Framework added for other message decode routines to
automatically correct file errors. Datatype version information added to
h5debug.
Tested: kagiso, smirom, linew (h5committest)
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Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Check in "unique, but sharable" optimization to ISOHM code, which
allows object header messages that are only used in one object to remain in
the sole user's header, but migrates messages that are used in more than one
header into the ISOHM heap.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Eliminate storing # of links in "link info" message, regenerate it
when the object is opened instead.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Move "creation order tracked" flag from "group info" to "link info"
object header message and make the "max. creation order value" optional in the
"link info", if the creation order for links is not tracked.
Also, get rid of unused "index names" flag - names are always indexed
currently.
Tested on:
FreeBSD/32 6.2 (duty)
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Remove unused "min. creation order" field from link info object
header message.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Add new object header message to track attribute information (unused
currently).
Tested on:
Mac OS X/32 10.4.8 (amazon)
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Revise latest form of superblock format pretty drastically, to
eliminate unused fields and move rarely used fields into superblock extension.
Finished removing last vestiges of references to (never used) i"shared"
object header message ID.
Added object header messages for non-default v1 B-tree 'K' values
and for driver info.
Updated testfiles to reflect size changes, etc.
Various minor cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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More cleanups on the object header message handling code, to make it
easier to work with and move forward on the creation order coding.
Various other minor cleanups & warning fixes.
Tested on:
FreeBSD/32 6.2 (duty)
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Remove the "scaffolding" for shared message method invocation and
simplify the way shared messages are dealt with in general.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Push code further toward shared message method calling refactor.
Tested on:
FreeBSD/32 6.2 (duty)
Too minor to require h5committest
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Add "set_crt_index" and "get_crt_index" methods for the object header
message class.
Unify fractal heap definitions for shared messages and attributes, under
"object header" fractal heap definitions.
Initial code for adding creation order index to object header messages.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Added can_share callback for OH messages. This determines whether the
message is allowed to be shared in the heap (committed and immutable datatypes
can't be).
Fixed a bug in the dense attribute storage that tried to open the shared message
heap when it hadn't been created yet.
Made the test to extend shared dataspace messages a bit more robust.
Refactored the code the searches a shared message list index to be a little
more efficient.
A few other minor changes.
Tested on smirom, kagiso, Windows, and juniper.
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Switch from using H5L_index_t/H5L_INDEX_<foo> to H5_index_t/H5_INDEX_<foo>
in order to accommodate indices on aspects of attributes as well as links.
Add basic support for deleting attributes in dense storage (needs more
support/tests for shared attributes in dense storage still).
Misc. cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Add first pass of "dense" attribute storage to objects. Lots of parts of
this are stubbed out, but all the tests are passing and I'll work on the corner
cases soon.
Eliminated several unused parameters from object header message callback
routines.
Other, miscellaneous code cleanups, etc. (and probably some things I've
forgotten about... :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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Migrate more object header routines to use the H5O_msg_ prefix and put
them into the src/H5Omessage.c code module.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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Finish implementation of H5Literate() [still needs real tests]
Clean up datatype macro warnings a bit more.
Unify iterator callback macros and put up in public header file, with the
iterator directions.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
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Basic support for H5Literate() routine. Still needs to be fleshed out and
refactored to simplify. Also, needs tests. :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
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Update datasets and the layout, attributes and fill-value
object header messages to use the latest version
of the file format flag.
Tested on:
FreeBSD 4.11 (sleipnir)
Linux/64 2.4 (mir)
Linux/32 2.4 (heping)
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Further minor modifications to the file format for tracking links in groups.
This is tentatively the "final" file format for groups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
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Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
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New feature
Description:
Check in Peter's code to add support for "shallow copy", "create
intermediate groups", "no attributes" and "expand soft links" support.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (chicago) w/ & w/o group-revision enabled
h5committest
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"Hide" file format changes (for now)
Description:
Add ifdef's (controlled by the --enable-group-revision configure flag)
to disable group revision changes to the file format, in order to allow alpha
release to go ahead without releasing an unsupported version into the wild.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 32-bit (heping)
Linux 2.4 64-bit (mir)
Solaris 2.9 (shanti)
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New feature
Description:
Add in a combination of Peter's & my code to support copying
variable-length data from one file to another, although currently only
supported with contiguous data storage.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
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