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.
Purpose:
update the windows project file to catch up with new changes
Description:
various new files or modified file names need to be reflected
Solution:
Platforms tested:
windows 2000
Misc. update:
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
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++
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)
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
Update test
Description:
Some of the performance improvements changed the errors that are reported
for creating a duplicated dataset in a file, causing this test's hard-coded
errors to check for to fail.
Solution:
Updated error stack reported for dataset creation failure.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/threads
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
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.
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.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? Yep.
Other platforms/configurations tested?
--enable-mpe feature tested in Eirene.
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.
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.
Bug fix
Description:
SGI shell treats $0 as function name if used in a function.
Set the name here to avoid that ambiguity and better style too.
Platforms tested:
Just in modi4 and burrwhite since it is a shell script and the
change is machine independent.
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
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
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.
Purpose:
Bug fix
Description:
man pages for the following F90 functions were missing:
h5tget_super_f h5tarray_create_f h5tget_array_ndims_f
h5tget_array_dims_f
Solution:
Added missing man pages
Platforms tested:
IE
fortran/config/powerpc-ibm-aix5.x
To cover AIX 5.x.
Removed Files:
fortran/config/powerpc-ibm-aix4.2.1.0
fortran/config/powerpc-ibm-aix4.3.2.0
These files are outdated and have been replaced by powerpc-ibm-aix4.x.
Modified Files:
MANIFEST
Update it.
Platforms tested:
Only on LLNL blue. LLNL SP are the only machines that use
these files and that I have access.
Purpose:
bug fix
Description:
some arrays were too big, running out of memory limit for some machines.
Solution:
change to dynamic memory allocation.
Platforms tested:
arabica, sleipnir
Purpose:
Adding new H5Fget_obj_* functions. (Development branch only)
Description:
Added H5Fget_obj_count.
Stubbed in H5Fget_obj_ids, but the entry is not filled in.
Reordered entries to group similar functions.
Platforms tested:
IE 5
Purpose:
update windows project file
Description:
Solution:
Platforms tested:
windows 2000(not affect 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.
Purpose:
bug fix
Description:
Need to use HDopen, HDread for windows support.
off_t in windows is 32-bit; however, windows can support 64-bit file. So we
have to change off_t to int64 in order that >4G file can be supported.
Solution:
See above
Platforms tested:
linux2.2.18smp, windows 2000
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.
Purpose:
bug fixed for windows
Description:
windows fopen functions by default opens a text mode file. It will fail for HDF5 file.
So to use HDopen HDread HDclose for test.
Solution:
Change from fopen, fread, fclose to HDopen, HDread, HDclose.
Platforms tested:
linux2.2.18smp, windows 2000
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.
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.
Purpose:
Bug fix(kinda)
Description:
Windows handle "fopen, fseek, fread, fclose" C functions slightly different.
Solution:
change to HDopen, HDlseek, HDread, HDclose to cover both Unix and Windows.
Platforms tested:
arabica
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
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
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
