Also updated root CMakeLists.txt to output a message when unsopported options are configured with the PARALLEL option. CMake will still generate files.
Tested: windows and local linux
1) Move the test for H5D_EXT_PREFIX in links.c to a separate file: links_env.c
2) links_env.c will be used by testlinks_env.sh to test for the environmental
variable H5D_EXT_PREFIX in searching for the external linked file.
Add another test for shutting down open object IDs without using the
standard "close" routines.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
double to (unsigned) long and from (unsigned) long to long double. I added tests in configure.in
to detect these algorithms. Before I can figure out them, I disable the tests in dt_arith.c.
There are property changes to tools/misc, config, and Makefile.am when I brought the fix from 1.8.
Tested on jam, heiwa, amani, IBM Power6 Linux machine in Holland (huygens.sara.nl).
Do some extra range-checking on H5Pset_elink_acc_flags() calls.
Clean up some minor compiler warnings also.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
Bring Coverity revisions from branch back to trunk, and clean up some other
misc. compiler warnings also.
r19500:
Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in
ohdr.c so the test never tries to close uninitialized locations.
r19501:
Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c.
r19502:
Fixed coverity issue 579 and some additional warnings in the file as well.
r19503:
Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26
r19504:
minor mods to try to keep coverity from flagging false positives.
r19505:
Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel
(h5committested on trunk)
- Fix a bug in each of the metadata accumulator source and test code
Description:
- In accum.c test file, switch dxpl_id used in H5F_accum_*
function calls to H5P_DATASET_XFER_DEFAULT (instead of
H5AC_dxpl_id), to fix compilation on windows.
- Changed boundary checking from <= to < when checking
if a read from disk with overlapping dirty metadata in the
accumulator has the read ending such that it aligns exactly
with the dirty accumulator (line 234 of H5Faccum.c).
Tested:
- h5committested
Merge accum_tests branch back to the trunk.
Description:
Changes consist of addition of tests for H5Faccum.c source code,
as well as some fixes that address some discovered bugs in the
metadata accumulator on several corner cases.
Tested:
h5committested
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2
set through H5Eset_auto. I changed the structure H5E_auto_t. I added a IS_DEDAULT flag in
it. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function.
Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2.
Tested on heiwa, jam, and amani.
The property change in configure.in, config, and Makefile.am came from the merge of the 1.8
library change.
flag IS_DEDAULT in the H5E_auto_t structure. Both H5Eprint1/2 are the default now. If the user
sets his/her own printing function. Then a call to H5Eget_auto1/2 will have to match
H5Eset_auto1/2.
Tested on jam, heiwa, and amani.
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.
I created a branch off the trunk called set_auto to continue working on the problem.
Tested on jam - backing out, simple.
Create a new, more streamlined method of generating I/O sequences when
there is only a single block defined by a hyperslab. This improves the
performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%.
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
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Description:
The AIX platform does not install the lib*.so for some reason but libhdf5.a
acts like a shared library. Until we can find out how to fix this, patch
up tetlibinfo.sh to not look for an lib*.so in AIX. (Note the test results
look wierd as it says libhdf5.a passed and skipped.)
Tested: NCSA BP for both enable and disable-shared.
through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to
make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a
document for it.
Tested on heiwa, jam, and amani.
The property change in configure.in, config, and Makefile.am came from the merge of the 1.8
library change.
Correct Bz#1968 (Problem when opening new format file with
H5F_LIBVER_EARLIEST) by initializing symbol table leaf information in a
more universal way. Also cleaned up other superblock initialization a
little bit while I'm here.
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Clean up the internal usage H5I_dec_ref() to eliminate the sequence of
flags that has been creeping in.
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Bring back various modifications to the v2 B-trees that were introduced
in the revise_chunks branch but aren't dependent on any file format or API
changes.
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Description:
The fractal heap header structure keeps a pointer to the file associated with
it. However, it is possible for that file pointer to be closed while the
header is still in cache (through the shared file pointer). Previously, the
header's file pointer was not updated and subsequently pointed to an invalid
file structure. Modified fractal heap code to update the file pointer every
time the header is accessed.
Tested: jam, linew, amani (h5committest)
Add windows threads support to HDF5.
Description:
Added calls to the windows threads library to the H5TS layer, and wrapped
most calls to either pthreads or windows threads library with portable
H5TS-style defines. Modified tests to use portable function definitions
as well.
This can be configured via CMake with the HDF5_ENABLE_THREADSAFE
option, and should work on windows vista and later operating systems.
Tested:
h5committest, plus threadsafe with pthreads on jam and amani,
and tested on a Windows Vista VM with threadsafe using windows threads.
Add some extra range checking for invalid chunk sizes.
Tweak default chunk sizes to be zero, so that it's more likely that
application developers will be forced to set them correctly.
Add a few tests to verify these checks.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
Corrected use/name of source folder aliases.
Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work).
Tested: local linux with mpich
Clean up a few compiler warnings and style issues in/near recent changes.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
Bring revisions from Coverity branch back to trunk:
r19191:
Fix coverity items 104 and 105. Added calls to H5HF_sect_indirect_free to
H5HF_sect_indirect_reduce and H5HF_sect_indirect_reduce_row if there is an errorbefore "peer_sect" is linked into the main free space structure via its direct
sections. Also delayed call to H5HF_sect_indirect_first to prevent peer_sect
from being left in an inconsistent state.
r19268:
Added fix to disallow extendible compact dataset.
This was the same check as in H5D_contig_construct() in H5Dcontig.c.
Added test to verify the creation of extendible dataset with various layouts.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(h5committested on branch)
Whack a few more memory errors exposed by valgrind.
Make the debugging dump output a little bit prettier.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug
(h5committest forthcoming)
H5T_ORDER_MIXED specifically for compound types and its derived types. They report mixed
orders if they have members of different orders.
There is no change to configure.in, config, and Makefile.am in the top directory. They have
some property changes when I merged the code from 1.8.
Tested on jam. I tested the same change for 1.8 with h5committest.
More fixes to memory allocation, etc. exposed by valgrind.
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Close out various resource leaks and usages of uninitialized memory that
were flagged by valgrind. [There's still some more valgrind warnings, but
it's better now... :-/ ]
Also clean up warnings and code formatting.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & valgrind
(h5committest forthcoming)
1. For enum type, members shouldn't be defined yet.
2. H5T_ORDER_NONE only works for reference and fixed-length
string.
3. For opaque type, the order will be ignored.
4. For compound type, all restrictions above apply to the
members.
I'll change H5Tget_order and do another commit.
There is no change to configure.in, config, and Makefile.am. There is some property change for
these files when I did a merge from 1.8.
Tested on jam. But I tested the 1.8 on heiwa, and amani.
Add in override for testing timeout alarm to allow "HDF5_ALARM_SECONDS"
environment variable to change the timeout value from the default value.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
Clean up misc. compiler warnings.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Description:
honest3 v1.8 failed in parallel test. It got stuck in the same
testpar/testphdf5 subtest (cbhsssdrpio). This is an old problem.
Upon closer inspection, the testphdf5, when terminated, had clocked
up 1hr 9min 46 sec wall clock time. Honest1 system also sent a message
that an mpi process has used up 30+ CPU minutes which exceeded their login
node cpu time limit and they killed the process. I also did a hand-run
of testphdf5. All subtests before cbhsssdrpio completed in a few minutes.
Therefore, it is safe to say the majority of the 70 minutes of wall clock
time are spent in the sub-test cbhsssdrpio. It also used up lots of CPU
time. cbhsssdrpio is likely infinite looping.
Since MPI application is prone to infinite looping due to message deadlock,
the testphdf5 has a built-in protection to give each subtest at most 20 minutes
of wall-clock time to run. When the 20 minutes wall-clock time is exceeded,
the testphdf5 will attempt to terminate itself. This prevents unnecessary
CPU time consumption in infinite looping.
But that clock limit was changed to 30 and then 60 minutes. I should have
but failed to, noticed the change mentioned by Quincey. IMO, 20 wall clock
time is more than sufficient for each subtest of testphdf5 to complete.
If a subtest takes longer than 20 minutes, it is likely infinite looping.
Giving it more time will not help.
If a subtest of testphdf5 takes more than 20 minutes, it should be broken
down to small tests that will finish way under 20 minutes so that it is
much easier to see progress and identify any deadlock problems.
In view of this, I am changing the testphdf5 time limit back to 20 minutes.
This will at least stop the CPU TIME exceeding limits and annoying the
system administrators.
Maybe there could be a provision, such as environment variable like
$HDF5_ALARM_SECOND to modify the alarm duration on individual execution.
Even so, that should be used temporary to see if an execution just needs
a little more time.
Tested: just eyeballed as the change is trivia.
