| Commit message (Collapse) | Author | Age | Files | Lines |
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unresolved issues - r19441 and 19466.
Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with
the 1.8 library to compile.
Tested on jam - backing out, simple.
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tested on jam and amani, heiwa hasn't finished yet.
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replaced by WIN32_LEAN_AND_MEAN macro. This was the cause of a define conflict causing the use of grp1 and grp2 to be replaced with constants in the h5dumpgentest.c file.
This also affected the use of the #include <winsock.h> needed by gethostname. The new include: winsock2.h has been added to h5private.h and either removed or updated in the other files.
Tested: Windows
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Bring r18413:18420 from trunk to 1.8 branch:
- unify srcdir query, etc.
- Move libhdf5.settings string out of H5Tinit.c
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 (amani) 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 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Trim trailing whitespace from source code files, with following command:
find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//'
Tested on:
None - eyeballed only
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refactored tests that were discovered to copy data files to avoid writing to data files checked into svn to use the new function.
Tested on amani, jam, and linew with h5committest and on jam with a read only mount of source files on pegdub.
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TFLOPS machine has retired long ago. Removed all code specific for its
support.
Test:
h5committested.
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Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
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Bring r16560 back from trunk.
Tested on:
Mac OS X/32 10.5.6 (amazon) debug & production
(Following up with tests on more platforms)
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Purpose:
On Windows, we were getting compile errors because h5test.c includes a function with variable declarations in the middle of the call. The Microsoft C compiler demands that all variables be declared at the top of the function. This checkin simply moves the declaration to the top to satisfy Visual Studio.
Tested:
VS2005 on WinXP
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Bring revision 15825 from trunk:
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:
FreeBSD/32 6.3 (duty)
Already tested on other machine, in trunk.
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Description:
On Windows, the pthread_self function cannot be used to print the returned thread ID for debugging. Instead, we need a separate function, GetCurrentThreadId. To eliminate some Windows ifdef's in the code, we create two new function macros which can be used by all platforms. It is conditionally defined in H5win32defs.h, and globally in H5private.h.
Tested:
VS2005 w/ pthreads on WinXP
kagiso w/ pthreads
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Description:
On Linux-like systems, we can get the ID of the current thread through a pthread_self. However on Windows, the return cannot be cast as a threadID, so we simply couldn't get the ID. Previously we simply gave up and printed a message that we couldn't get an ID. Instead, though, we can use the Windows-specific call to GetCurrentThreadId(), which achieves the same goal. This way we can provide better debug output with threadsafe features.
Tested:
VS2005 on WinXP
VS.NET on WinXP
(other platforms not tested because change is within _WIN32 ifdef)
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Change H5P[gs]et_format_bounds() => H5P[gs]et_libver_bounds() and also
enumerated values H5F_FORMAT_{EARLIEST, LATEST} => H5F_LIBVER_{EARLIEST, LATEST}
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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Switched from "H5P[gs]et_latest_format" to "H5P[gs]et_format_bounds".
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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- Add hash value for skip list string types, to reduce # of string
comparisons.
- Fixed bug with metadata/small data block aggregator adding size == 0
block into file free space list.
- Refactored metadata/small data block aggregator code into single set of
common routines.
- Changed block aggregator code to be smarter about releasing space in the
'other' block when the 'other' block has aggregated enough data.
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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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)
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First real use of API versioning code, H5E routines switched to use
new API versioning scheme.
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)
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Add a bit more information to the log VFD settings.
Tested on:
FreeBSD/32 6.2 (duty) w/check-vfd
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Allow a ".h5" suffix to be added to core files also, which prevents
overwriting the test binary (and confusing the tests on copper, etc.)
Tested on:
AIX 5.3 (copper) w/check-vfd
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
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HDF5_DRIVER value to activate the use of latest_format for file access
property list.
Platform tested: h5committested.
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Fix problems with 'check-vfd' target, that were [mostly] introduced with
the recent "unique, but sharable" ISOHM optimization.
The problems were mostly with using the 'core' VFD, so the
H5Pset_fapl_core() API call was changed to re-open existing files (therefore
operating more list the sec2, stdio, etc. VFDs). This allows many more of
the tests to run using the 'core' VFD, so those were enabled also.
Tested on:
Linux/64 2.6 (chicago2) w/check-vfd
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WIN32, so I've standardized all #ifdef's to use _WIN32. This should not affect any other platform.
Tested:
Visual Studio (32- and 64-bit) on Win XP
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avoid compiler's
warning of comparing values with "==" or "!=".
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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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Take out separate memory type in the file for SOHM objects and create
aliases for existing memory types for SOHM use.
Tested on:
FreeBSD/32 4.11 (sleipnir)
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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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systems like copper and sleipnir
doesn't require alignment for Direct I/O. If this's true, write or read data just like sec2
does.
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made the test more complete by writing
two data sets. One is aligned, and the other isn't.
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size is set through
H5Pset_fapl_direct. It's been added to H5FD_direct_read in the previous checkin. Still, a test is
needed at later checkin.
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H5Pset_fapl_direct to control
memory boundary, file block size, and maximal copy buffer size; second in H5FD_direct_write and
H5FD_direct_read, the library checks whether data buffer is aligned. If it is, then write and
read the data directly instead of making a copy buffer.
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Bug fix (related to 544)
Description:
h5_get_file_size() was coded to return 0 if failed but
file size can be 0. Changed the failure return value to -1
which is allowed by the returned type of off_t which is a signed
type.
Also changed the checking code of the stat call to just == 0
since that is how it is defined.
Test:
Could test it in heping only. Both Sol and Copper failed to
compiled due to error in the Direct IO VFD code.
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Altix (cobalt). There's a configure
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
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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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Feature
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.
Added a new routine 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.
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Code maintenance
Description:
Remove flexible parallel code
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Solaris 2.9 (shanti)
Linux 2.4/64 (mir)
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Description:
The file size test in C++ library failed on Copper because the
value returned by h5_get_file_size was intepreted incorrectly
due to different interger sizes.
Solution:
H5private.h: Added check to use stat64 and off64_t where appropriate.
h5test.c and h5test.h: used h5_stat_size_t in place of off_t.
tattr.cpp: used h5_stat_size_t in place of off_t.
Platforms tested:
Linux 2.4 (heping)
AIX 5.1 (copper)
SunOS 5.8 64-bit (sol) - still on going
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Bug fix.
Description:
getenv_all would fail if one calls it without calling MPI_initialized first.
This may happen if one uses PHDF5 library to build a serial nature code
and does not make any MPI calls.
Solution:
Added code to detect if MPI has been initialized. If not, use the
original getenv.
Platforms tested:
heping (serial) and mir (parallel).
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Bug fix.
Description:
getenv_all, like some implementations of getenv, keeps an internal buffer
for the getenv values. Application must make a copy of the content of the
returned pointer before calling getenv_all again IF it wants to use the
first content later. The previous code violated this rule and caused
error.
Solution:
Did a small revamp of the h5_fixname to fix the above problem by moving
the getenv_all for HDF5_NOCLEANUP eariler to avoid it clashing the
call of getenv_all for HDF5_PARAPREFIX. No a good permenant fix. Need
to really recode this routine.
Platforms tested:
h5committested.
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Bug fix.
Description:
getenv_all will be called even when it is NOT an MPI application.
Solution:
Moved the use of getenv_all("HDF5_NOCLEANUP") to fix_name so that it will
be invoked only if a parallel driver is used.
Platforms tested:
hand tested in copper.
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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 $HDF5_NOCLEANUP if
it is in parallel mode.
Platforms tested:
h5committested, tested pp in heping too.
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Feature.
Description:
Added ALARM_ON, ALARM_OFF feature to terminate tests that run more than
the default time limit. So far, the feature is applied in the standard test
frame.
Platforms tested:
heping PP.
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Description: Brought back changes from SX-6.
Solution: Tests will not compile. Fixed.
Platforms tested: SX-6, heping and mir with new g95
Misc. update:
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Bug fix
Description:
Incorrectly terminated the received string in getenv_all
Solution:
Tasks would incorrectly terminat the environment string they received from the
root task in getenv_all.
They did the equivalent of:
env[strlen(str) + 1] = '\0'.
This resulted in a single "garbage" character inserted
at the end of the string. This wasn't noticed until now because it seems that on most
platforms this garbage character was a 0 anyway.
This has been corrected to;
env[strlen(str)] = '\0'.
Platforms tested:
Red Storm (where the bug was discovered)
heping (pp)
Misc. update:
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Improvement for Windows
Description:
thread number can not be printed out on windows. Add a special
macro for WIN32 to print out some helpful messages
Solution:
Platforms tested:
Heping and MSVS 6.0 on Windows XP
Misc. update:
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Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Cosmic changes when folding getenv_all to v1.6.
No code changes.
Platforms tested:
heping.
Misc. update:
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Use getenv_all for determining HDF5_PARAPREFIX instead of getenv
Description:
the environment variable HDF5_PARAPREFIX is now determined collectively, instead of
having each task call getenv.
Solution:
Environment variables set for task 0 often do not propogate to other tasks which
leads to obscure and hard to track down bugs. getenv_all was written to overcome
this by having all tasks query a single task for the value of its environment.
Eventually, all calls to getenv will be migrated to use getenv_all. For now,
only HDF5_PARAPREFIX will be determined this way.
Platforms tested:
heping pp, sol pp
Misc. update:
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Feature
Description:
Added new function, getenv_all (only for parallel builds)
Solution:
getenv_all is a collective version of getenv. It is used to the return the value of
an environment variable in another task and can be used to synchronize all of the
environment variables used by all of the tasks. This helps to fix problems that commonly crop up
(like with HDF5_PARAPREFIX) when an environment variable does not propogate to other tasks.
This commit only includes the function. Future commits will replace the various getenv calls with getenv_all calls.
Platforms tested:
heping, sol, copper
Misc. update:
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