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* [svn-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-0941-163/+577
| | | | | | | couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. Tested with h5committest - jam, heiwa, amani.
* [svn-r19361] Move Windows specific compile and link flags to macrosAllen Byrne2010-09-0929-712/+172
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* [svn-r19360] Bug fix: ID 2026Albert Cheng2010-09-082-2/+2
| | | | | | | | | | | | | | | | Description: testhdf5/select runs very slow when in --disable-production mode using pgcc compiler. This was caused by the -Mchkfpstk compiler switch added to the DEBUG_FLAGS in config/pgi-flags file. Solution: Removed -Mchkfpstk from both pgi-flags and pgi-fflags. See Bug 2026 for dettails. Tested: (no h5committest test since they don't use PGI compilers.) Jam (linux32): using pgcc/pgf90/pgCC using default and --enable-production. Amani (linux64): using pgcc/pgf90/pgCC (32 bits mode by "-tp k8-32"), using default and --enable-production.
* [svn-r19357] Add POSIX warning to report ignore list.Allen Byrne2010-09-081-0/+1
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* [svn-r19354] Quincey and I made H5Eset_current_stack also close the stack to ↵Raymond Lu2010-09-073-1/+82
| | | | | | | | be set. This is to avoid H5Eclose_stack clearing the default stack. Please see bug 1799. Tested on jam - simple change.
* [svn-r19352] Description:Quincey Koziol2010-09-042-39/+14
| | | | | | | | Align w/changes on revise_chunks branch Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19348] Description:Quincey Koziol2010-09-031-25/+20
| | | | | | | | Clean up warnings, etc. Tested on: Linux/64 2.6 (abe) w/parallel (to specific to need h5committest)
* [svn-r19343] Corrected long long printf test.Allen Byrne2010-09-023-30/+102
| | | | | | | Added CMake commands to allow the install of the extlibs on windows. Updated ctest warning exception regex for VS2010 Tested: windows
* [svn-r19342] Added cmake tests for c++ examplesAllen Byrne2010-09-022-0/+8
| | | | Tetsed: local linux
* [svn-r19336] Change #ifndef _WIN32 to #ifdef H5_HAVE_UNISTD_HAllen Byrne2010-09-011-3/+3
| | | | Tested: windows and local linux
* [svn-r19334] Update CMake referenceAllen Byrne2010-09-011-6/+6
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* [svn-r19331] Correct list of h5 files needed for testsAllen Byrne2010-09-011-1/+3
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* [svn-r19328] Description:Quincey Koziol2010-08-313-13/+44
| | | | | | | | | | | | | 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)
* [svn-r19325] Added parallel build commands.Allen Byrne2010-08-3134-226/+838
| | | | | | | 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
* [svn-r19324] Description:Quincey Koziol2010-08-3110-100/+194
| | | | | | | | | | | | | | | | | | | | | | | Bring recent tweaks to extensible and fixed array file formats from revise_chunks branch back to trunk. 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
* [svn-r19320] Added correction to check for existence of H5PRINTF_LL in ↵Allen Byrne2010-08-271-37/+39
| | | | | | PRINTF_LL test. Tested: local linux
* [svn-r19318] Correct ENDIF text (non-executable) to match IF parameterAllen Byrne2010-08-271-1/+1
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* [svn-r19313] Description:Quincey Koziol2010-08-264-157/+191
| | | | | | | | 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)
* [svn-r19312] Description:Quincey Koziol2010-08-261-1/+1
| | | | | | | | | Bump optimization down for Intel 10.* compilers, due to apparent bad cod e generation. Tested on: Linux/64 2.6 (cobalt) w/debug & production & Intel 11.1 compilers (h5committest not appropriate)
* [svn-r19309] Description:Quincey Koziol2010-08-263-12/+174
| | | | | | | | | | | | | | | | | | | 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)
* [svn-r19307] Correct test for H5_LONE_COLON - added NOTAllen Byrne2010-08-261-1/+1
| | | | Tested: windows
* [svn-r19304] bug 1678: temporary fix.Albert Cheng2010-08-251-0/+5
| | | | | | | | | | | | | | | | Description: aix -q32 default to a memory limit that some HDF5 tests would fail in malloc. Solution: Temporary hardset RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA"} to bypass this problem until the test programs are fixed. Though -q64 binary has a higher default memory limit and does not need this patch, it is applied the same for the sake of simplicity since it is a temporary fix. Tested: in uP, both -q32 and -q64 modes. No h5committest since this applies to the AIX platform only.
* [svn-r19302] Correct typo in tools locationAllen Byrne2010-08-252-3/+2
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* [svn-r19300] BZ 1958: Add h5dump xml tests to CMake supportAllen Byrne2010-08-2512-106/+572
| | | | Tetsed: local linux
* [svn-r19297] Description:Quincey Koziol2010-08-257-13/+77
| | | | | | | | | | Whack a few more memory errors exposed by valgrind. Make the debugging dump output a little bit prettier. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug (h5committest forthcoming)
* [svn-r19293] bug 1678: temporary fix.Albert Cheng2010-08-251-0/+5
| | | | | | | | | | | | | | | | Description: aix -q32 default to a memory limit that some HDF5 tests would fail in malloc. Solution: Temporary hardset RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA"} to bypass this problem until the test programs are fixed. Though -q64 binary has a higher default memory limit and does not need this patch, it is applied the same for the sake of simplicity since it is a temporary fix. Tested: in BP, both -q32 and -q64 modes. No h5committest since this applies to the AIX platform only.
* [svn-r19292] Description:Quincey Koziol2010-08-246-71/+95
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Merge r19290 & r19291 from 1.8 branch to trunk: r19290: Correct another error in metadata accumulator dirty region calculations (this time with a corner case when freeing data in the file). r19291: Avoid getting object information for soft/external links if we aren't going to traverse across the link itself. 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
* [svn-r19288] Bug 1934 - I added support of all data types for H5Tget_order. ↵Raymond Lu2010-08-244-35/+105
| | | | | | | | | | | | I added a new byte order 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.
* [svn-r19286] Corrected name of file appearing in expected output.Allen Byrne2010-08-241-1/+1
| | | | (Missed edit from local test)
* [svn-r19282] Fix test scripts (Cmake needs to capture output yet)Allen Byrne2010-08-235-23/+44
| | | | | | linux script needed -R and double compare: Tested: local linux
* [svn-r19278] Description:Quincey Koziol2010-08-2310-184/+199
| | | | | | | | | | | | | | | | | | | | | | 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
* [svn-r19276] Description:Quincey Koziol2010-08-221-1/+1
| | | | | | | | | | | | | | | | | | | | | | Correct calculation of end of dirty information in metadata accumulator 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
* [svn-r19273] Description:Quincey Koziol2010-08-201-1/+1
| | | | | | | | | | | | | | | | | | Correct an off-by-one oversight with the valgrind changes in r19272. 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
* [svn-r19272] Description:Quincey Koziol2010-08-2030-494/+677
| | | | | | | | | | | | 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)
* [svn-r19269] Add warning exceptions.Allen Byrne2010-08-201-0/+16
| | | | Add memcheck ignore.
* [svn-r19265] Correct naming of SKIP testAllen Byrne2010-08-201-1/+4
| | | | Tested: local linux
* [svn-r19264] Remove configuration of cmake zlib config filed which has been ↵Allen Byrne2010-08-201-1/+0
| | | | | | deleted. Tested: local linux
* [svn-r19262] Undo r19261.Allen Byrne2010-08-201-0/+7
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* [svn-r19261] Remove unused variables and allocationAllen Byrne2010-08-201-7/+0
| | | | Tested: local linux
* [svn-r19260] Change Cmake to allow a local zlib header to be used in ↵Allen Byrne2010-08-209-118/+225
| | | | | | | | | | | H5Zdelate module. Corrected use of "SKIP" message in cmake. Corrections to cmake configuration files (for cmake external projects). Community suggested changes. Tested: local linux
* [svn-r19255] Description:Quincey Koziol2010-08-201-0/+1
| | | | | | | | | | | | | | | | | | | | | | Add missing include file from r19252. 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
* [svn-r19253] Description:Quincey Koziol2010-08-191-0/+5
| | | | Add missing files from r19252 checkin.
* [svn-r19252] Description:Quincey Koziol2010-08-1915-223/+267
| | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes from branch to trunk: r19161: Fixed the part for matching the subset info with dataset r19189: BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump. Changed all references to use new data structure. Added tests for each subset parameter. r19190: Added new h5dump ddl files Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (h5committested on branch)
* [svn-r19251] New feature(bug #1934): I made H5Tset_order support all data ↵Raymond Lu2010-08-195-39/+197
| | | | | | | | | | | | | | | | | | types with some restictions: 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.
* [svn-r19247] Description:Quincey Koziol2010-08-172-53/+234
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19246 from Coverity branch to trunk: Improve metadata "accumulator" for files to track the dirty region within the accumulator data. This allows the accumulator to drop clean data and reduces the number of I/O operations when it is dirtied. This is progress toward Bz#1142 - speeding up the fheap test (which it doesn't help much, actually, but it does help other aspects of file I/O). 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
* [svn-r19242] Description:Quincey Koziol2010-08-162-4/+22
| | | | | | | | | 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)
* [svn-r19237] Description:Quincey Koziol2010-08-1210-105/+84
| | | | | | | | | | 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
* [svn-r19236] Description:Quincey Koziol2010-08-121-131/+71
| | | | | | | | | | | | Clean up compiler warnings and misc. style issues with new internal tagged entry code. Tested on: FreeBSD/32 6.3 (duty) 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
* [svn-r19235] Description:Quincey Koziol2010-08-121-56/+62
| | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19234 from the 1.8 branch to the trunk: Initialize loop variable that caused failures in certain circumstances. Also clean up compiler warnings and release MPI datatype. 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
* [svn-r19230] Reset alarm_seconds back to 20 minutes.Albert Cheng2010-08-111-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
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