| Commit message (Collapse) | Author | Age | Files | Lines |
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Purpose:
New feature
Description:
Added Adler32 checksum as a filter in pipeline
Platforms tested:
arabica (fortran), eirene (, C++), modi4 (parallel, fortran)
Misc. update:
Update release_docs/RELEASE.
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Update
Description:
Converted the "FUNC_LEAVE" macros to "FUNC_LEAVE_NOAPI" to be
consistent with the rest of the library.
Note: This is probably completely useless as the file is going to go
away with the new model of the SAP as metadata cache...But it helps
me compile...
Platforms tested:
Linux (FPHDF5)
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Update
Description:
Added support for defining what the haddr type is in terms of MPI
types.
Solution:
Include some #defines when we typedef haddr...
Platforms tested:
Linux (For FPHDF5 stuff)...
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Buglet
Description:
The title of the function in FUNC_ENTER_* was wrong.
Solution:
Changed to correct title.
Platforms tested:
Linux (small change).
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Update
Description:
Changes:
- Added support for the server dumping metadata writes to a
client.
- Some of the code wasn't handling allocated buffers correctly
(freeing twice).
- Modified server so that it handles metadata only.
Platforms tested:
Linux
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Update
Description:
This is the first conversion of the FPHDF5 code to be a metadata
cache. There's an extra error message. I rewrote the sync/change code
to be read metadata/write metadata instead.
I still need to hook these changes into the HDF5 code so that it
looks at the SAP first before checking the file for metadata.
Platforms tested:
Linux
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Bug Fix
Description:
When calling H5Fopen with the core VFL driver, but without the
H5F_ACC_CREAT flag goes ahead and creates a memory file.
Solution:
Check for the H5F_ACC_CREAT flag before allowing the memory file to be
created.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Updated
Description:
Updated Copyright notice.
Replaced HGOTO_ERROR calls involving MPI calls with HMPI_GOTO_ERROR.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? Tested on Eirene (PP) only since
the code is in the MPIO module only.
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Bug fix
Description:
Currently, when the library encounters an object header message that isn't
know, it fails to open that object in the file.
Solution:
Allow the library to skip over the unknown object header message and
continue to process the remaining messages, in the hope that the skipped
message isn't important later. If it is important, it will be caught at
a higher level of the library.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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This is generated by autoheader.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? YES
Other platforms/configurations tested? eirene with --enable-mpe
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Code cleanup & bug fix
Description:
Cleanup another set of warnings on Windows and also fix mis-placed assertion
that caused the daily tests to fail.
Platforms tested:
IRIX64 6.5 (modi4) w/-n32
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Code cleanup
Description:
Reduce warnings on Windows
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Purpose:
Change some macros to make windows happy
Description:
Currently no srandom and random functions on windows,
Function gethostname cannot be resolved when DLL turned on
Solution:
use srand and rand to replace srandom and random
turn off the option to check gethostname
Platforms tested:
windows 2000, linux 2.2.18smp
Misc. update:
Update MANIFEST if you add or remove any file.
Update release_docs/RELEASE for bug fixes, new features, etc.
Update applicable document files too.
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Code cleanup
Description:
Add 'H5_DLL' macro to H5FL macros, in order to allow Windows builds to
work.
Platforms tested:
FreeBSD 4.7 (sleipnir)
Visual Studio 6.0
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Code cleanup
Description:
Added "UNUSED" flag to an inlinable function
Platforms tested:
FreeBSD 4.7 (sleipnir) w/gcc 3.2.1
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Code cleanup
Description:
Fix preprocessor macros to declare variables correctly.
Platforms tested:
MS Visual Studio
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Code cleanup
Description:
Various code cleanups to allow the development branch to be compiled with
a C++ compiler (i.e. CC=g++ )
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) C++
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Code improvement
Description:
Add extra pair of braces to API versions of FUNC_ENTER/FUNC_LEAVE macros,
to make API <-> non-API mismatches obvious.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Code cleanup
Description:
Clean up a few more warnings and update dependencies.
Platforms tested:
Linux 2.2.18smp (eirene) serial & parallel
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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new feature
Description:
Added MPICH/MPE instrumentation support.
All source code are bracketed by the macro H5_HAVE_MPE.
Use "--enable-mpe" to configure it in.
Currently only worked in Eirene because the MPE library is
not installed in all machines yet.
The added file, H5MPprivate.h, holds HDF5/MPE related defintions.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? Yep.
Other platforms/configurations tested?
--enable-mpe feature tested in Eirene.
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Minor fix
Description:
By mistake, the MPI_Error handling macros were inserted outside the
overall macro bracket. Moved them back inside the bracket.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? Yep.
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When I removed the option (--enable-parallel=mpich), which did not work,
I failed to run autoheader to update this file. I am checking in the
updated version now.
Platforms tested:
No need to test since it just removed a #undefine and comments.
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Bug fix - informed by Kent
Description:
Some identifiers were flagged as unresolved symbols when building
with c++ on Windows. The reason is the name of these identifiers
were changed by the c++ compiler, also called name mangling.
Solution:
Moved
#ifdef __cplusplus
extern "C" {
#endif
to include the offending identifiers so the c++ compiler will take
them as is.
Platforms:
SunOS 5.7 (arabica)
Linux 6.2 (eirene)
Windows 2000
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Update
Description:
A few generic changes to the FPHDF5 code. Some error messages
reworked a bit. Cleaning up in case of failure improved in some
cases. Added another field to the synchronization messages...
Platforms tested:
Linux
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Update
Description:
Removed the EFL field from the FPHDF5 structure as the property list
already has this info.
Platforms tested:
Linux
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Bug Fix
Description:
Was encoding a value as DTYPE instead of MTIME, which would cause a
couple of errors. Also, got rid of the EFL field as it's encoded in
the PLIST already...
Platforms tested:
Linux...Modest test, FPHDF5 not fully implemented just yet.
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Purpose:
Improve error handling
Description:
make error handling better for VL string null pointer.
Platform tested:
arabica
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Purpose:
Fix bugs for windows platform.
Description:
1. Update HDlseek for windows
2. Update H5Otime.c for normal time(non-daylight time)
3. Add H5_DLL in front of two functions so that windows DLL can work.
Solution:
Platforms tested:
windows 2000, eirene(since most updates have WIN32 around it, not need to test other platforms)
Misc. update:
Update MANIFEST if you add or remove any file.
Update release_docs/RELEASE for bug fixes, new features, etc.
Update applicable document files too.
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Purpose:
error-detection improvement
Description:
verify string parameter in function H5T_vlen_str_mem_getlen isn't nil.
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Purpose:
Cleanup H5Tget_native_type code
Description:
improve code cosmetics.
Solution:
Platforms tested:
modi4, eirene, arabica
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Purpose:
New Feature; Optimization; Clean-up
(Merged from 1.4 branch)
Description:
There is no symbolic constant to pass to functions that take an
optional object ID for when the caller wants to indicate no object
ID. In the past the caller always passed a negative integer.
GPFS performs poorly.
The h5ls tool decides whether to list the file name in the output
based on a compile-time choice, which isn't always optimal at run
time.
Solution:
Added a symbolic constant H5I_INVALID_HID.
Added code to tell the mmfsd of GPFS to forego byte range token
prefetching.
h5ls decides whether to print the file name at runtime based on
the number of objects being listed.
Platforms tested:
SuSE Linux (arborea), gcc and mpich-1.2.4
SunOS (baldric), gcc
2002-12-03 22:51:43 Robb Matzke <matzke@arborea.spizella.com>
*: Added H5E_FCNTL minor error number.
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Purpose:
New Feature; Optimization; Clean-up
(Merged from 1.4 branch)
Description:
There is no symbolic constant to pass to functions that take an
optional object ID for when the caller wants to indicate no object
ID. In the past the caller always passed a negative integer.
GPFS performs poorly.
The h5ls tool decides whether to list the file name in the output
based on a compile-time choice, which isn't always optimal at run
time.
Solution:
Added a symbolic constant H5I_INVALID_HID.
Added code to tell the mmfsd of GPFS to forego byte range token
prefetching.
h5ls decides whether to print the file name at runtime based on
the number of objects being listed.
Platforms tested:
SuSE Linux (arborea), gcc and mpich-1.2.4
SunOS (baldric), gcc
2002-12-03 22:50:23 Robb Matzke <matzke@arborea.spizella.com>
*: Added H5E_FCNTL minor error number.
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Purpose:
New Feature; Optimization; Clean-up
(Merged from 1.4 branch)
Description:
There is no symbolic constant to pass to functions that take an
optional object ID for when the caller wants to indicate no object
ID. In the past the caller always passed a negative integer.
GPFS performs poorly.
The h5ls tool decides whether to list the file name in the output
based on a compile-time choice, which isn't always optimal at run
time.
Solution:
Added a symbolic constant H5I_INVALID_HID.
Added code to tell the mmfsd of GPFS to forego byte range token
prefetching.
h5ls decides whether to print the file name at runtime based on
the number of objects being listed.
Platforms tested:
SuSE Linux (arborea), gcc and mpich-1.2.4
SunOS (baldric), gcc
2002-12-03 23:23:45 Robb Matzke <matzke@arborea.spizella.com>
* H5_trace: Added printing for H5S_sel_type, code "St".
2002-12-03 22:45:11 Robb Matzke <matzke@arborea.spizella.com>
*: Removed a little white space. Other changes are probably due to
additional API tracing statements inserted
automatically.
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Bug fix
Description:
Correct another missing field I overlooked earlier.
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Bug fix
Description:
Add missing 'naccess' field required for GPFS token management code.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Purpose:
Feature; Optimization
Description:
Clients pass `-1' or make their own #define for HDF5 functions
that take an optional object ID.
Blue's GPFS is slow for typical SAF restart dumps.
Solution:
Added a #define for H5I_INVALID_HID
Added GPFS-specific code to H5FDmpiposix.c that tells mmfsd to
forego byte range token prefetching. This code can be compiled
into the library by defining USE_GPFS_HINTS. The plan is to either
generalize this so it's detected during configure and turned
on/off at runtime, or to move it up into DSL/SAF with the new HDF5
functions to that return the low-level file handle.
Platforms tested:
SuSE Linux (arborea), gcc and mpich-1.2.4
SunOS (baldric), gcc
2002-09-05 12:24:28 Robb Matzke <matzke@arborea.spizella.com>
*: Added #define for H5I_INVALID_HID. An invalid object handle is
actually any integer that isn't currently in use as a
handle, and non-positive integers are never used as a
handle. The #define is -1, and is mostly so that HDF5
users can pass a symbolic name instead of a negative
number to functions that take optional object ID
arguments.
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Purpose:
Feature; Optimization
Description:
Clients pass `-1' or make their own #define for HDF5 functions
that take an optional object ID.
Blue's GPFS is slow for typical SAF restart dumps.
Solution:
Added a #define for H5I_INVALID_HID
Added GPFS-specific code to H5FDmpiposix.c that tells mmfsd to
forego byte range token prefetching. This code can be compiled
into the library by defining USE_GPFS_HINTS. The plan is to either
generalize this so it's detected during configure and turned
on/off at runtime, or to move it up into DSL/SAF with the new HDF5
functions to that return the low-level file handle.
Platforms tested:
SuSE Linux (arborea), gcc and mpich-1.2.4
SunOS (baldric), gcc
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corrected a typo--H5Fget_obj_counts should be H5Fget_obj_count.
Platforms tested:
Eirene only since it is just a string typo.
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Purpose:
New feature to H5Dget_offset
Description:
If user block is set, H5Dget_offset should be able to return the absolute
offset from the beginning of file.
Platforms tested:
eirene, arabica
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Code cleanup
Description:
Clean up warnings with gcc 3.2.1
Platforms tested:
FreeBSD 4.7 (sleipnir) w/C++, changes too small for triple check
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code warrior fix
CW does not recognize the _stati64 type, changed HDstat macro accordingly
Platforms tested:
windows 2000 (MSVC, Code warrior)
linux
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Purpose:
new functions
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx.
Platforms tested:
modi4, arabica, eirene
Misc. update:
RELEASE.txt updated.
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Update
Description:
Cleaned up the debug printing of the generic property list. It was
printout NULL property values for non-existant properties and putting
multiple properties into one group.
Platforms tested:
Eirene (too small change for full testing)
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