Final merge of changes from sblock_mdc branch back to trunk. The superblock is now managed by the metadata cache.
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 (kagiso) w/PGI compilers, 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 production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Updating autotools
Description:
Installed new autotools and used them to reconfigure HDF5.
- Automake upgraded to 1.11
- Autoconf upgraded to 2.64
- bin/reconfigure script edited to use new versions (on jam), and
run to generate new configure script and Makefile.in's.
- configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings
(in order to comply with new autoconf standard).
Tested:
Tested on machines jam, smirom, liberty, linew.
Tested w/ features c++, fortran, parallel.
Tested w/ compilers gcc, pgcc, icc.
Further testing via Daily Tests should catch any other outliers. Upon
passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
t_file.c: replace the old variable, color, with a more meaningfule name of
is_old.
t_mpi.c: use the official mpi_file_delete, instead of remove, to delete a file
in MPI environment.
Tested:
Only jam in parallel as changes are trivial.
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Re-generated Makefile.in's by running bin/reconfigure.
- Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran
libraries.
Tested:
jam, liberty, smirom
Remove unnecessary 'udata' parameter from H5AC_set() and 'notify' callback
(introduced with checkin that added the 'notify' callback)
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/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 production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Add 'notify' callback to metadata cache clients, so that they can be
aware when the cache has taken/will take certain actions. Notifications are
urrently limited to when an entry has successfully entered the cache (via an
insertion or a load from the file) and when an entry is about to be evicted
from the cache.
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/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 production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Fix another set of missing parameters to updated H5C_get_entry_status()
call.
Tested on:
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Bug Fix
Description:
Fixing BZ #1381. The --includedir=DIR configure option, which is used
to specify the installation location of C header files, did not work
correctly as the path was hard-coded in config/commence.am. I'm presuming
this is because an older version of automake didn't know where to put
c header files. In any case, removing this line now defaults the includedir
to the same directory that it is currently hard-coded to, and also fixes
the configure flag to allow customization of this value.
Tested:
jam, liberty
Remove another call to H5E_clear_stack() from within the library.
Clean up lots of compiler warnings.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(followup on other platforms forthcoming)
the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other
tested: h5committest
The failure was caused by some over active sanity checking code in
unlock_entry(). In essence the code did not consider the possibility
that under certain, very unusual circumstances, an entry could be flushed
to disk during the H5AC_unprotect() call. Instead, it simply failed
if a dirty entry was marked clean after the call to H5AC_unprotect().
This bug in the test code was exposed by recent changes to the default
cache configuration made as part of the "metadata blizard" bug fix.
Fixed the bug by adding code to detect when an entry is flushed during
the call to H5AC_unprotect(), and not trigger a failure if a dirty entry
is marked clean after a call to H5AC_unprotect() if the entry has been
flushed.
In passing also found and fixed another test bug in which expunged
entries were erroneously marked as dirty in the test code's independant
register of entry status.
Tested parallel on Phoenix (AMD64 Linux) and Jam. Also ran t_cache
manually hundreds of times looking for intermittant failures.
Larry kindly tested (parallel) on Mercury.
Description:
- Remove need to set LD_LIBRARY_PATH when using shared szip library.
- Libtool 2.2.6a is now used to generate libraries.
- 'make check install' dependency bug is fixed, and should no longer
break the build.
- removed hard coding of shell in config/commence.am, as this causes
problems on Solaris with the new version of libtool.
- RELEASE.txt with appropriate changes.
Tested:
- kagiso, smirom, linew (merged from 1.8, pretty quick tests)
Fix various problems with a the core & sec2 VFDs.
Improve the h5_get_file_size() routine to handle files created with
VFDs that use multiple files.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (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/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 production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (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/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 production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
When enable-debug is turned on, a special macro block H5_HAVE_INSTRUMENTED_LIBRARY inside HDF5 will be executed to check if some collective chunk IO test cases are being run with the correct settings(one link, multiple chunk etc.). However,when complicated derived datatype in some mpi-io packages are not supported, the library has to switch one link IO with/without the optimization to multiple chunk IO with/without the optimization. The current testsuite doesn't know this and generates a false assertion failure message.
This check-in fix this problem by providing a second property to avoid the false faiure message.
Tested at abe(NCSA linux cluster) and kagiso.
Description:
As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific.
Tested:
VS2005 on WinXP
VS.NET on WinXP
h5committest (kagisopp, smirom, linew)
Description:
The fortran Makefile.am used HDF_FORTRAN to indicate it is part of the
Fortran API source so that conclude.am will give fortran api prefix in the
test output. The symbox HDF_FORTRAN is also used in configure for a different
purpose (indicated --enable-fortran). They conflicted.
Similar problem for the symbol HDF_CXX.
Solution:
Changed all the involved Makefile.am to use "FORTRAN_API" instead. It is
a more appropriate name. Same for CXX_API.
Along the way, discovered that the Makefile.am of hl/fortran/test and
hl/cxx/test did not have those symbols at all. Added them in.
Platform tested:
Kagiso only. It is a trivia change.
Improvement.
Description:
src/libhdf5.settings was the initial configure summary and is installed.
Then configure is changed to dump a summary of the configure settings to
the output and also append it to src/libhdf5.settings. That created
two different output formats and duplicated information. This is the
initial attempt to clean up this confusion and unify the output format.
It is decided to use the src/libhdf5.settings template as the unified means.
This requires more macros symbols be defined. The following symbols are
all related to generating the src/libhdf5.settings file.
AC_SUBST(EXTERNAL_FILTERS)
AC_SUBST(MPE) MPE=no
AC_SUBST(STATIC_EXEC) STATIC_EXEC=no
AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no
AC_SUBST(FC) HDF_FORTRAN=no
AC_SUBST(HDF_CXX) HDF_CXX=no
AC_SUBST(CXX) HDF_CXX=no
AC_SUBST(HDF5_HL) HDF5_HL=yes
AC_SUBST(GPFS) GPFS=no
AC_SUBST(LINUX_LFS) LINUX_LFS=no
AC_SUBST(INSTRUMENT) INSTRUMENT=no
AC_SUBST(CODESTACK) CODESTACK=no
AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no
AC_SUBST(DIRECT_VFD) DIRECT_VFD=no
AC_SUBST(THREADSAFE) THREADSAFE=no
AC_SUBST(STATIC_SHARED)
AC_SUBST(enable_shared)
AC_SUBST(enable_static)
AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a`
The src/libhdf5.settings.in has CONDITIONAL's added to it too. The
untrue conditions turned into a "#" and these lines are cleaned by the
post processing script.
Platform tested:
h5committest on kagiso, smirom and linew.
Description: Applying update to autotools that was applied to 1.8 a couple
of weeks ago to the trunk.
Updated bin/reconfigure script to reflect the new versions of
libtool and automake in the /home1/packages/ directory.
Rearranged configure.in script. When using libtool 2.2.2, the
libtool script doesn't generate until later in the configuration
process, so I had to move a test that parsed through the libtool
script to a point after where it was actually being generated.
Ran libtoolize on the project, and ran bin/reconfigure to
regenerate configure and Makefile.in's throughout.
Tested: kagiso, smirom, linew (h5committest)
large entry, or to a large increases in the size of an existing entry.
This required some additions to the cache configuration structure, and
thus will require changes in the metadata cache documentation.
The basic idea is to monitor the size of entries as they are loaded,
inserted, or increased in size. If the size of the entry (or increase)
exceeds some user selected fraction of the size of the cache, increase
the size of the cache.
Note that this fix was designed quickly -- while it deals with the
use case that exposed the problem, we may have to revisit the issue
later.
Tested serial and parallel on Phoenix, and h5committest.
Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for
the coordinates, instead of 'hsize_t **'.
Tested on:
Mac OS X/32 10.5.1 (amazon)
Add work-around to allow reading files that were produced with a buggy
earlier version of the library, which could create objects with the wrong
object header message count. There is now a configure flag
"--enable-strict-format-checks" which triggers a failure on reading a file
with this sort of corruption (when enabled) and allows the object to be read
(when disabled). The default value for the "strict-format-checks" flag is
yes when the "debug" flag is enabled and no when the "debug" flag is disabled.
Note that if strict format checks are disabled (allowing objects with
this particular kind of corruption to be read) and the file is opened with
write access, the library will re-write the object header for the corrupt
object with the correct # of object header messages.
This closes bugzilla bug #1010.
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
Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with
other new API routines.
Re-added simpler form of H5Acreate2, which creates attributes directly
on an object.
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
Change H5Aopen -> H5Aopen_by_name, in order to be more consistent with
other new API routines.
Re-add H5Aopen as a simpler routine, to open attributes on a particular
object. (Much like the old H5Aopen_name routine).
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
Move H5Pinsert() out of old "compat v1.6" section and into API
versioning, switching internal usage to H5Pinsert2().
Add regression test for H5Pinsert1()
Clean up some other minor warnings.
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
Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
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
Deprecate H5Dextend in favor of H5Dset_extent (without using API
versioning, due to changed behavior) and switch internal usage to H5Dset_extent
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
Put H5Acreate() under API versioning, with all internal usage shifted
to H5Acreate2().
Add regression tests for H5Acreate1().
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
Move H5Aopen_name() routine to deprecated symbol section and replace
internal usage with H5Aopen().
Add simple regression test for H5Aopen_name() to deprecated routine
test.
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
Remove all plain calls to H5Gopen() from source, replacing them with
either H5Gopen2().
Add test for H5Gopen1().
Reformatted several pieces of code, to clean them up.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
Pursue calls to H5Gcreate() relentlessly and ruthlessly exterminate
them, leaving only a few tame specimens in text files and comments. ;-)
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes
in an empty buffer. This is mainly for MPIO programs that some processes may not have any
data to write or read but still participate the I/O. This solution solves some MPI's problem
like the ChaMPIon on tungsten which doesn't support empty buffer.
2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective
I/O when some processes don't have any data to write or read correctly. Detect the compiler
"cmpicc" in the system-specific config file and set the variables for these two cases to false.
The PHDF5 library already has set up a way to switch collective chunked I/O to independent
under these two cases.
3. A bug fix - During the work of the optimization for compound data I/O, the case for switching
collective chunked I/O to independent I/O was leftout. Fixed it by adding I/O caching to it in
H5D_multi_chunk_collective_io in H5Dmpio.c.
Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
Add --enable-deprecated-symbols configure option, to allow users to
remove deprecated public API symbols at configure time.
Add bin/make_vers script to bin/reconfigure actions.
Run bin/reconfigure to regenerate autotool components.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (kagiso)
2) Removing configuration of c++/src/H5cxx_pubconf.h file.
Reasoning: the additional pubconf file caused compilation complications, this is cleaner.
Tested: kagiso, smirom
Description: added new configuration to generate a pubconf file
in the c++/src directory, H5cxx_pubconf.h. When C++
compiler recognizes 'offsetof', the macro
H5_CXX_HAVE_OFFSETOF is defined in the new
pubconf file.
tested: kagiso, smirom
Description: a new configure flag has been created that will now set a macro
in the test/Makefile. The flag is with-default-vfd=. When set to
a virtual file driver (e.g. "--with-default-vfd=sec2"), the macro
DEFAULT_VFD will hold this value.
Tested: kagiso, smirom, linew
file size from MPI_File_get_size. Bypass this problem by replacing it with
stat. Add an option --disable-mpi-size in configure to indicate this function
doesn't work properly. Add a test in testpar/t_mpi.c, too. If it returns wrong
file size, print out a warning.
Tested on kagiso (parallel) because already tested the same change to v1.6 on
several platforms (kagiso, cobalt, copper, and sol).
Added a header message showing the purpose and explanation that the test is
for inoformation and always exits 0.
Also added a summary at the end.
Some other cosmetic changes (moved couple function code up, added some more
printf, fflush statements.)
Tested platform:
kagiso.
Description: Multiple copies of Copyright appeared in Makefile.in. This was
due to automake copying the copyright right in the included files such as
config/commence.am.
Solution: Automake treats double hashes as comments and does not copy them
to Makefile.in. Changed all the copyright notices in config/*.am to use
double hashes for the Copyright right notice.
Tested: kagiso via bin/reconfigure.
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.
It seems that while Cygwin supports the time command, it has trouble with
the syntax
srcdir="../../hdf5/test" time ./testhdf5
and complains.
The solution is to test the above case in configure and not to use the time
command if it fails; Cygwin is fine with
srcdir="../../hdf5/test" ./testhdf5
Tested on Cygwin and kagiso. This feature shouldn't be a major compatibility
problem since every platform but Cygwin is already fine with the current
syntax.
The h5_mpi_get_file_size() is no longer used. The unused code caused some
compiling warning messages. Removed the whole routine.
Tested in heping pp mode.
The version of libtool used by HDF5 isn't directly affected by the reconfigure
script; instead, libtoolize --force must be used by hand. Libtool was the
source of the problem, so rolling its version back to 1.5.14 should solve the
issue (at least temporarily).
Reconfigure should still work on both heping and kagiso.
Tested on heping, kagiso, and tg-login3.
Should disable linking against shared libraries in Fortran for compilers that
don't support shared libraries.
Should also fix problem when the wrong Fortran file extension was specified.
If these changes don't solve the Daily Test issues, I'll look at backing out
the autotool version change until I have time to fix them.
Tested on heping, kagiso, juniper.
Bug fix.
Description:
AIX complained if some files are still open when MPI_Finalize is called,
so code called _exit without calling MPI_Finalize. But in Linux hosts
with MPICH, the MPI processes terminated but the launch processes got
stuck waiting for those processes to end properly and they would hang
on forever. As more tests ran, more processes got stuck.
Solution:
In order to please both AIX and MPICH, the MPI file handles are retrieved
and closed outside of the HDF5 library, then call MPI_Finalize and then
_exit.
Tested:
in heping and copper.
Bug Fix (Bug 544)
Description:
SGI Altix's MPI_File_get_size overflowed at 2GB and more.
Replaced h5_mpi_get_file_size calls by h5_get_file_size.
Tested:
Cobalt.
Bug Fix (Bug 544)
Description:
SGI Altix's MPI_File_get_size overflowed at 2GB and more.
Put in a temporary patch to use stat() instead to make Cobalt
passing on this test (bigdset). A better fix (like detect if
MPI_File_get_size does not work before using this is preferred.)
Tested:
Cobalt and Heping.
Description:
It seems that, on AIX, calling MPI_Finalize without closing all files results in an error.
This causes t_pflush1 to fail because the whole point of the test is to see what happens if you
don't close a file. Try getting rid of the call to MPI_Finalize to see if this will silence the error.
Tested:
AIX (copper)
and quote its arguments. Also checks for the 'socket' library on
Solaris.
If this patch passes the Daily Tests and makes the user happy, I'll
port it back to the 1.6 branch.
Tested on mir and sol.
Since these examples need to follow filesystem paths, the Makefiles need
to create directories in the examples directory; added this to the
Makefile.am.
Tested on Windows, mir, juniper
To activite this test,
add the command option -i.
For example, at IBM AIX, type "poe testphdf5 -i" will test the library with independent IO with file setview. It simply replaces all the collective IO tests with independent IO with file setview.
"make check-vfd" will now run all tests in the test directory with different
file drivers (at least, all of those tests that use the testing framework's
FAPL). Tests that fail will be skipped.
This is not a perfect fix, but is better than nothing.
Along with this change, check-vfd should be added to the Daily Tests.
1) Added trace file support to the metadata cache. This allows capture
of all metadata cache calls in trace files for purposes of optimization
and debuging.
2) Added an expunge entry function. This allows an entry to be deleteded
from the cache without writing it to disk even if it is dirty.
3) Added a function call to resize pinned entries.
4) Added code to deal with entries that are dirty on load. This is
needed in support of a bug fix which can alter object headers on
load to repair files.
5) Added progress reporting code to the "MDC API smoke check" test in
cache_api.c. To enable the progress reporting, set report_progress
to TRUE in mdc_api_call_smoke_check().
Tested with h5committest, and a parallel test on phoenix (dual athelon
linux box).
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
Configuration feature
Description:
'make install' now tests both static and shared libraries if both are installed.
Solution:
Previously, shared libraries were only tested when static libraries were not installed.
Also cleaned up line in commence.am that was including HL library in all Makefiles.
Platforms tested:
mir (Makefile change only)
Bug fix - bugzilla #552
Description:
On Cray X1, trying to use : as an argument confused the system.
Solution:
Added a test in configure to see if : as an argument is bad.
If so, skipped the test.
Platforms tested:
mir, Cray X1 (change to configure only)
Bug fix.
Description:
It failed when only 1 is used to test.
Solution:
Cleanup the code a little so that it works for any number
of processes to invoke it.
Platforms tested:
h5committested,
Some collective chunk IO macro names are confusing, change them to more meaningful
names.
Description:
H5Pset_dxpl_mpio_chunk_opt will set a flag so that the library can do one linked IO or mul
ti-chunk IO with collective in chunking storage directly. That is, the library won't do an
alyses to determine this.
The flags for the enum type we used before are:
H5FD_MPIO_OPT_ONE_IO
H5FD_MPIO_OPT_MULTI_IO
They are not good names because of the following two reasons:
1. It doesn't reflect chunking storage
2. OPT is kind of redundant and misleading,
Solution:
We change the names to
H5FD_MPIO_CHUNK_ONE_IO
H5FD_MPIO_CHUNK_MULTI_IO
Platforms tested:
Since only macro names are changed, no need to test with h5committest.
Misc. update:
Bug fix.
Description:
Sometimes the parallel prefix is given in the form of nfs:/mnt/pfs which
if given to a non-MPIO VFD like the default H5Fcreate, it would fail.
Called h5_rmprefix which would return the non-prefix component
part of the file name which would be okay for the default H5Fcreate and
such.
Platforms tested:
Tested in heping parallel.
Feature
(Code and tests are done by Christian. I just committed the code.)
Description:
Rewrote the purpose of this test. Now it tests these three cases,
/*
* Test following possible scenarios,
* Case 1:
* Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY and large
* size, no write, close, reopen in parallel, read to verify all return
* the fill value.
* Case 2:
* Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY but small
* size, no write, close, reopen in parallel, extend to large size, then close,
* then reopen in parallel and read to verify all return the fill value.
* Case 3:
* Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY and large
* size, write just a small part of the dataset (second to the last), close,
* then reopen in parallel, read to verify all return the fill value except
* those small portion that has been written. Without closing it, writes
* all parts of the dataset in a interleave pattern, close it, and reopen
* it, read to verify all data are as written.
*/
Platforms tested:
Tested in copper, tg-ncsa and heping, all in parallel mode.
1) Check in potential fix to unreproduceable bug in t_cache observed on
Cobalt
2) Check in code supporting added pinned entry features in the metadata
cache.
Description:
1) Elena encountered a bug in t_cache when running on Cobalt. On
investigation I found a potential race condition in t_cache that
could explain her observation.
2) Quincey requested additions to the metadata cache allowing renaming
of pinned entryies, and marking of pinned or protected entries as
dirty.
Solution:
1) Modified t_cache.c to prevent the potential race condition. Elena
was unable to reproduce the bug on Cobalt, so we don't know if my
fix actually addressed the problem.
2) Added code supporting the requested functions. The changes were
relatively trivial, but required substantial new test code.
Platforms tested:
h5committest, serial test on heping, parallel test on phoenix.
Misc. update:
Bug fix.
Description:
The ${TR}, though avoid the error, is inconvenient. It is needed
because configure.in use the char range in the style of 'a-z'.
The other style of '[a-z]' is more commonly accepted by all tr
but autoconf tends to strip away [], making the syntax rather
clumsy.
Solution:
Learned from autoconf that it avoids the use of character range
by just spell all the letters out. Changed our tr commands to
use those variables defined by autoconf. Also removed the
definition of ${TR} since it will cause inconsistancy when
autoconf also use plain 'tr' in its generated code.
The Makefile.in are changed because the elimination of ${TR} from
configure triggered its removal from all Makefil.in. That is okay
because ${TR} is not used at all in Makefile.
Platforms tested:
h5committested. (sol failed to connected). also tested in shanti
using both /usr/ucb/tr and /bin/tr (the bad one before.)
Misc. update:
Updated both INSTALL and RELEASE files.
Bug fix
Description:
Fix two test bugs:
1) Unitialized variable bug in test of H5C_get_entry_status()
(in test/cache.c)
2) Incorrect initialization of constant in t_cache when running
with MPE. (in testpar/t_cache.c)
Solution:
1) Don't test uninitialize variable.
2) Correct initialzation of constant in MPE case.
Platforms tested:
Tested on Heping and Copper.
Misc. update:
Code cleanup/feature twist
Description:
Adjust recent H5AC routines to take H5F_t pointers instead of H5C_t
pointers, to match the rest of the H5AC routines.
This change propagated into a few of the tests, which also had some
compiler warnings cleaned up...
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Linux 2.4/64 (mir) w/C++ & FORTRAN
Add pinned entry capability to cache.
Description:
For frequently accessed cache entries, the protect/unprotect overhead
is sometimes a bottleneck.
Solution:
Allow entries to be pinned in the cache. Pinned entries can't be
evicted, but can be flushed or modified.
Platforms tested:
h5committested -- minus one small typo in test/cache.c whose fix was
tested on copper and heping only.
Misc. update:
Several bug fixes
Description:
Added config file for Cray X1 (previous file was misnamed)
Simplified some code in hyperslab.c test that seemed to have been
confusing compiler on Cray X1.
Fixed typo in config/commence.am
Cleaned up hl/src/Makefile.am
Solution:
All four fixes should be straightforward. The failure on Cray was
very difficult to debug, but involved arithmetic errors.
This change seems to fix it.
Platforms tested:
heping, copper, sol, some Cray X1 (more testing when system comes back up)
new feature
Description:
1) separated the HL library into "public" and "private" header files, with the same caracteristics as the basic library
2) added the public headers to hdf5.h (with a conditional include macro, defined in configure.in)
3) added the path to HL in all Makefile.am 's , because of the inclusion in hdf5.h
Solution:
Platforms tested:
linux 32, 64
AIX
solaris
with fortran and c++
(one packet table example fails)
Misc. update:
bug fix.
Description:
The MPE_Stop_log did not work in copper. It spewed out MPE errors
and ended in infinite looping.
Solution:
Changed to a smaller test size to avoid generating huge MPE log files
when MPE is configured in.
Platforms tested:
Copper (mpe)
Misc. update:
Bug fix.
Description:
When MPE is used, the test generates huge Clog files in /tmp that
could fill up the disk (like in Copper.)
Solution:
Turned off MPE logging.
Platforms tested:
heping (pp) and copper(pp)
Misc. update:
Adding parallel tests for optional collective chunk APIs
Description:
Three new APIs
"H5Pset_dxpl_mpio_chunk_opt_ratio
H5Pset_dxpl_mpio_chunk_opt_num
H5Pset_dxpl_mpio_chunk_opt"
for optional optimization choices from users
have been added to the libraries.
This check-in adds six tests to verify the funcationality and correctedness
of these APIs.
These tests need to be verified with 3 or more processors and with MPI-IO driver only.
Solution:
Using H5Pinsert, H5Pget, H5Pset to verify that the library indeed goes into the branch we hope for.
Using H5_HAVE_INSTRUMENT macro to isolate these changes so that it won't affect or be misused by the application.
Platforms tested:
h5committest(shanti still refused to be connected)
Parallel tests on heping somehow are skipped. Manually testing at heping. Have checked
1,2,3,4,5 processes.
Misc. update:
Bug fix
Description:
Previous checkin did a bad thing; 'make clean' failed in example directories.
Solution:
Fixed commence.am so that examples no longer break, and fixed a mistake
in conclude.am.
Platforms tested:
heping (minor makefile change)
Misc. update:
Add tests for optional APIs to support collective chunk IO
Description:
In order to test whether library picks up the user's options,
The number of chunks need to be varied for different processes,
Selection of the number of processes selected in one chunk also
need to be varied.
Solution:
Create two cases,
1. Each chunk only selected by one unique process, this case
library should use independent for collective call.
2. One-third of the processes occupies the top half of the whole domain,
The rest of the processes occupies the lower half of the domain.
The total number of chunk is a fixed number 8.
Platforms tested:
Linux 2.4 with mpich 1.2.6(only)
Since I only checked in the code that handles the selection, haven't added any new tests yet. So it won't affect any platforms.
Misc. update:
Bug fix
Description:
make check-clean didn't clean results of example tests
Solution:
Fixed Makefiles so that check-clean recurses into example directories.
Also a little Makefile cleanup.
Platforms tested:
mir, modi4, heping, copper
change the array size of collective chunking features of parallel tests.
Description:
Previously array size for collective optimization tests
including
cchunk1,
cchunk2,
cchunk3,
cchunk4,
ccontw,
ccontr,
cschunkw,
cschunkr,
ccchunkw,
ccchunkr
are fixed,
They are only valid for some good number of processors(1,2,3,4,6,8,12,16,24,32,48 etc).
Recently there are more requests for parallel tests to be valid on some odd number of processes such as 5,7,11,13 etc.
Solution:
I change the array size to be dynamic rather than static. Now the fastest change array size is a function of mpi_size. dim2 = constant *mpi_size. After some tunings, theoretically the above tests should be valid for any number of processors. However, other parallel tests still need to be tuned.
To verify the correctness of these tests, using mpirun -np 5 ./testphdf5 -b cchunk1 at heping.
Platforms tested:
h5committest(shanti is refused to be connected)
at heping, 5 and 7 processes are used to verify the correctness.
Misc. update:
Add new tests
Description:
Collective IO doesn't work for some platforms/mpio packages when more than
one process has no contributions to IO.
Solution:
1. Add a collective IO test to verify the correctness of the library when
more than one process has no contributions to IO.
2. Add the similar MPI-IO test in t_mpi to help us maintain in more platforms.
Platforms tested:
heping, mir, copper
Misc. update:
Improvement.
Description:
The t_cache takes a long long time to run and it tests HDF5 calls.
Move it to the back and let more basic tests to run first so that
basic features are tested first.
Platforms tested:
Tested in heping with pp.
code cleanup
Description:
remove two printf lines accidently added for debugging at NCSA cobalt.
Solution:
Platforms tested:
No need to test.
Misc. update:
Enhance collective chunk IO supports
Description:
Add a new test to check the correctness of the HDF5 library behavior for collective IO mode when one process doesn't have any contribution for IO.
Solution:
Platforms tested:
IBM AIX 5.2(copper)
Linux (heping) mpich-1.2.6
Misc. update:
Attempt to ensure that the parallel cache test runs at a reasonable
speed with large numbers of processors.
Description:
In some cases, the number of random locks and unlocks was a multiple of
the MPI rank.
Solution:
Use rank % 4 instead of simply rank.
Platforms tested:
copper
Misc. update:
Add a file that I forgot in my last checkin.
Description:
t_cache.c is the source file for the new parallel metadata cache test.
Solution:
See above.
Platforms tested:
h5committested before the last checkin. Will run another
h5committest shortly, but it shouldn't be necessary as there
are no new changes.
Misc. update:
1) Add parallel test for metadata cache
2) Split serial test for metadata cache into two parts
3) Fix bug in which cache was flushed needlessly when the
cache wasn't full.
4) Performance improvements
5) Update API for parallel cache coherency bug fix.
Description:
See above.
Solution:
See above.
Platforms tested:
h5committest
Misc. update:
bug fix 504
Description:
testpar/t_mpi would hang if $HDF5_NOCLEANUP is set. E.g.,
% env HDF5_NOCLEANUP=yes mpirun -np 3 ./t_mpi
This happened because the environment variables are not exported to all
mpi processes by the mpirun command. So, some attempted to do cleanup
while others don't and some hang waiting for others to act.
Solution:
Instead individual program checking getenv, they all just called h5_cleanup
no matter. h5_cleanup now uses getenv_all to check the $HDF5_NOCLEANUP if
it is in parallel mode.
Platforms tested:
h5committested, tested pp in heping too.
Feature.
Description:
Modified it so that it can be compiled outside of HDF5 library as a standalone
program. e.g., mpicc -DSTANDALONE prog.c.
Platforms tested:
Tested in Red storm and heping.
Patch.
Description:
Copper would fail with a message of
0032-113 Out of memory in routine unknown, task 0
when run with 3 processes and size 1MB in MPI-IO tests.
It seems to be a copper MPIO error.
Solution:
Reduced the upper bound of default write size to 1/2MB (but
tests only go to 1/4MB) for now, pending permenant fix from
Copper.
Platforms tested:
Copper.
Minor bug fixes.
Description:
1. Changed free() calls to HDfree()
2. Corrected behavior of -m command-line parameter
3. Changed return value to always return 0.
Solution:
2. The -m flag tells the test to run only the MPI IO tests. However, it would incorrectly make
the test run both the MPI and POSIX tests (same as the default behavior).
3. This test is known to fail on many platforms, and, even on those platforms where it usually passes,
it is known to suffer transient failures (especially with small test file sizes). It's outcome is
also very dependent on the filesystem on which the testfile is created. Corrected
the program to always return success, so that it doesn't interfere with the daily tests.
The motivation for this is that
this test has nothing to do with the HDF library and is an auxiliary test. Failures in t_posix_complaint
do not necessarily mean that parallel HDF will fail, but simply indicate something to look into,
especially on new platforms. This is now an "output only" test, and any errors will be only be visible
in the output.
Platforms tested:
copper (all of these were minor changes)
Misc. update:
bug fix.
Description:
Fixed the segmentation fault errors in modi4, copper and tg-login.
It was due to the misuse of trying to realloc a pointer returned by
getenv_all. (not supposed to.)
Also rearranged the code so that option is checked first, then check
with environment variable, then use default setup. This saves the
need to do realloc at all.
Platforms tested:
Heping, modi4, shanti, copper (copper showed a different error now.)
Bug fix.
Description:
For some strange reason, getopt() does not appear to be defined in unistd.h
on colonelk when the source is compiled with -D_POSIX_SOURCE.
Solution:
Inserted some extern's for the missing variables to make the compiler happy.
Platforms tested:
colonelk, copper
Misc. update:
Feature
Description:
Added blurb about future todo's for this test.
Added support for HDF5_PARAPREFIX to determine the directory where the test file
is stored.
Solution:
Used getenv_all to get the value of HDF5_PARAPREFIX. Note that, if a command-line
parameter is passed to the program to specify a path, it will override the value of
HDF5_PARAPREFIX.
Platforms tested:
copper, colonelk
Misc. update:
Added t_posix_compliant to the rest of the build and patched up minor
compile bugs/warnings encountered on other platforms.
Description:
It seems that <getopt.h> needs to be included to get the file to build, even though the man page
seems to indicate that <unistd.h> should be sufficient.
Solution:
Platforms tested:
copper, colonelk, sol
Feature
Description:
Added posix compliance tests.
Solution:
These tests do increasingly complicated sets of writes followed by reads.
POSIX standards say that any read that can be proven to occur after a write
must include the data in that write. These tests attempt to verify whether the
underlying filesystem and i/o layer provide such guarantees.
Platforms tested:
copper, colonelk, red storm
Misc. update:
Bug fix
Description:
Fortran type generation was broken in two ways. Fixed both.
Solution:
Firstly, there were a couple of path problems. Fixed a typo and
specified the full path of a file.
Secondly, the dependencies weren't right when building with HDF5-specific
commands (make lib, make check-s, etc.). Tweaked dependencies
to fix the problem.
Platforms tested:
mir, modi4, sleipnir
Configure feature
Description:
Added 'make trace' target.
Solution:
Added tracing to 1.7. This was done automatically in 1.6, but left out
of 1.7 until now (oops!).
Tracing in 1.7 only happens manually, when the user types 'make trace.'
Tracing automatically requires more framework than it's worth.
I also fixed a couple of tracing bugs and ran trace.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
Bug fix
Description:
Before this checkin, 'gmake check-s' would fail if there was a file in
the current directory named 'check-s'.
This is fixed under gmake (not sure how to fix for other makes).
Solution:
check, progs, install, etc. are what gmake calls "phony" targets,
which means that no file should be created. These targets can be
specified by a line of the form
.PHONY: check progs install ...
Automake adds this line for targets it knows about, but HDF5 has a
lot of custom rules. This checkin adds a .PHONY line for those rules.
I believe that only gmake recognizes the .PHONY line (at least, pmake
doesn't seem to), but a partial solution is better than none.
This error should occur very rarely anyway (the user has to manually
create files with names like 'build-check-s' or '_test').
Platforms tested:
mir, sleipnir, modi4
Bug fix/feature
Description:
Added support for -shlib in h5fc and h5c++.
Made check-install use -shlib when only shared libraries have been installed.
Solution:
h5fc and h5c++ didn't recognize -shlib. Stole code from h5cc to link against
shared libraries.
When static libraries are disabled, the examples Makefiles will automatically
use the -shlib option to link against shared libraries. Thus,
--disable-static and make check-install should work together.
Platforms tested:
heping(disable-static, enable-static, fortran, c++), modi4 (disable-static, fortran, c++, parallel, enable-static)
Bug fix
Description:
Failed parallel tests now cause make to exit with an error.
Solution:
Edited config/conclude.am to throw an error if parallel test programs fail.
Platforms tested:
heping, modi4
Adding comments and code clean-up for code that tests collective irregular selection
Description:
For better maintenance in the future, Add comments to list the number for
(start,count,block,stride) for irregular selection for effective testing
collective chunk IO feature development in the future.
Solution:
Platforms tested:
Linux 2.4(heping), mostly comments, no need to test on other platforms.
Misc. update:
Bug fix
Description:
Changed configure.in to use an environment variable TR to set the path
to the tr utility.
Solution:
There are two kind of tr on Solaris with slightly different syntax.
HDF5's configure relies on the "standard" tr. Traditionally, HDF5ers
have needed to make sure that the "right" tr was found before the
wrong one in their path; now they can use an environment variable.
Platforms tested:
mir, shanti, sol
Misc. update:
Forgot to update release notes. Off to do that now.
Code clean-up for collective regular chunk IO tests.
Description:
Add descriptions for each tests for future maintenance.
Solution:
Platforms tested:
Mostly comments, No need to use h5committest.
heping(linux 2.4)
Misc. update:
Makefile bug fix
Description:
Previously, automake didn't output rules to build perform/mpi-perf or
the test/gen_* programs.
Now these can be built by typing 'make mpi-perf' (or 'make foo') or by
configuring with --enable-build-all.
Solution:
Automake doesn't like having rules for programs it doesn't build. Tricked
it by having these programs built "sometimes"--whenever the user enables
--build-all. This should be used mostly for testing and to ensure that
these helper programs compile.
***IMPORTANT***
These programs do *not* currently compile. When --enable-build-all is used
(not the default), gen_new_fill fails because it uses an old API. This is
an existing "bug" that has simply been exposed by this checkin.
Platforms tested:
sleipnir, modi4, sol
Misc. update:
bug fix.
Description:
The complex derived datatype test assumed that the fill value would be 0. This is not
the case on all systems.
Solution:
Modified the test to check against a known value in the outbuf array, instead of the fill value.
Platforms tested:
heping and MCR.
Misc. update:
bug fix.
Description:
Fixed typo in a comment. The word "file" was supposed to be "fill." The explanation of
how the complex derived datatype test works is much clearer now.
Solution:
Platforms tested:
minor change.
Misc. update:
bug fix.
Description:
When a parallel test script test fails, make would continue because the
way it was setup inside a for loop. Fixed it by issuing an exit 1 inside
the loop.
There was also a typo error in the newer command comparision that it
must be $${chkname} in order to be valid. Also, the test script itself
was not checked in the newer lists. All fixed.
Platforms tested:
h5committested and also hand tested in heping pp mode.
Repair synchronization bug in the metadata cache in PHDF5
Also repair numerous other bugs that surfaced in testing the
bug fix.
Description:
While operations modifying metadata must be collective, we allow
independant reads. This allows metadata caches on different processes
to adjust to different sizes, and to place the entries on their dirty
lists in different orders. Since only process 0 actually writes
metadata to disk (all other processes thought they did, but the writes
were discarded on the theory that they had to be collective), this made
it possible for another process to modify metadata, flush it, and then
read it back in in its original form (pre-modification) form. The
possibilities for file corruption should be obvious.
Solution:
Make the policy that only process 0 can write to file explicit, and
visible to the metadata caches. Thus only process 0 may flush dirty
entries -- all other caches must retain dirty entries until they are
informed by process 0 that the entries are clean.
Synchronization is handled by counting the bytes of dirty cache entries
created, and then synching up between the caches whenever the sum
exceeds an (eventually user specified) limit. Dirty metadata creation
is consistent across all processes because all operations modifying
metadata must be collective.
This change uncovered may bugs which are repaired in this checkin.
It also required modification of H5HL and H5O to allocate file space
on insertion rather than on flush from cache.
Platforms tested:
H5committest, heping(parallel & serial)
Misc. update:
A bug fix
Description:
MPI_Status_IGNORE is treated as a NULL pointer for mpich 1.2.4 or similar MPI packages.
It caused segmentation fault for MPI derived datatype test.
Solution:
Define MPI_STATUS status,
and pass &status into MPI_File_read and MPI_File_write.
Platforms tested:
too trivial to test.
Misc. update:
Improvement.
Description:
The test may hang if there are system failures that some processors
are not working.
Solution:
Added the ALARM calls to limit all tests be done with the default
alarm time. So, even if a process is hanging, the ALARM signal
would terminate the process.
Platforms tested:
tg-login2 of NCSA.
Misc. update:
bug fix
Description:
the MPI_File_get_size returns a different value in one of the tests in Windows
comment the code and not run the test in windows
a ULL suffix on the harcoded return VRY return number is needed on AIX
Solution:
Platforms tested:
Windows
AIX
Misc. update:
new features
Description:
add support for compiling the library and testphdf5 in Windows
Solution:
Platforms tested:
Linux
AIX
Solaris
Windows VC6
Misc. update:
