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* [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.
* [svn-r19228] File read/write happens at configure time, so moved windows ↵Allen Byrne2010-08-111-10/+11
| | | | | | specific copy from test macro to where the expected file is copied. Tested: windows
* [svn-r19225] Moved subfolder checked outside of OPTION command. If folder ↵Allen Byrne2010-08-111-37/+34
| | | | | | doesn't exists, there is no reason to have option enabled. Tested: local linux
* [svn-r19222] Move hl fortran ADD_SUBDIRECTORY to right after fortran ↵Allen Byrne2010-08-103-9/+8
| | | | | | | | ADD_SUBDIRECTORY. This fixes a problem with compiler generated files not including target module directory on some linux machines. Corrected minor format/location of commands. Tested: local linux
* [svn-r19217] Bug 1986, error1.Albert Cheng2010-08-101-1/+2
| | | | | | | | | It is an error to use the condition H5_HAVE_FSEEK64 to control the definition of HDlseek. It caused errors in AIX where lseek64 is available. Replaced it with H5_HAVE_LSEEK64. Also added the missing HDstrcasecmp macro. Tested: AIX using default and --disable-largefile.
* [svn-r19214] Test for compare of output text to expected needed to account ↵Allen Byrne2010-08-101-9/+17
| | | | | | | | for windows line endings. Moved ADD_TEST commands to macro. Tested: local linux, windows
* [svn-r19211] Updated cmake file with community suggested changes for cmake ↵Allen Byrne2010-08-106-37/+22
| | | | | | | | install files. Removed configure check for fseek Tested: local linux
* [svn-r19207] Description:Quincey Koziol2010-08-101-1/+1
| | | | | | | Switch from using "UINT16_MAX" to "64 * 1024" for assert macro. Tested on: None, just eyeballed.
* [svn-r19205] Bug 1917: post cleanup.Albert Cheng2010-08-093-9/+6
| | | | | | | | | | fseek64 was used to support large file access for the STDIO driver back in version 1.2.2 in year 2000. Some how it was not included in version 1.4.0. Now, fseeko64 is used to support large file. There is no more need for fseek64 which is not a standard call. Removed its presence from configure and related files. Tested: jam for configure only.
* [svn-r19203] new expected output file for BZ1953 fixAllen Byrne2010-08-091-0/+1
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* [svn-r19202] [BZ1953]implementation for the proposed changes suggested by ↵Allen Byrne2010-08-094-19/+404
| | | | | | | the "h5dump_output_option" RFC. This required that the region reference code be duplicated and reduced to allow the do_bin_output() function to understand region references. The container type-id also needed to be propagated into the do_bin_output() function and functions referenced (render_bin_output*). Existing tests tested the binary function, so only one test was added to test the region reference generated file. Tested: local linux
* [svn-r19201] Added tests that subdirectories exist before using ↵Allen Byrne2010-08-091-117/+139
| | | | | | | | ADD_SUBDIRECTORY CMake command Added cache set command for default install prefix Tested: local linux
* [svn-r19195] Bug fix: ID 1917Albert Cheng2010-08-091-1/+1
| | | | | | Fixed a typo in the Windows definitions. Had __ftelli64, should be _ftelli64. Tested by Allen in Windows platform.
* [svn-r19188] Bug fix: ID 1917Albert Cheng2010-08-061-32/+47
| | | | | | | | | | | The STDIO only checked for fseeko and incorrectly assumed it can support file sizes larger than 32bits. Fixed it by making to use fseeko64 if supported, else use fseeko. To simplify the code, assume fseeko which is a POSIX function must be supported. Therefore, fseek is not used at all. (Note: the above applies to Unix-like system. The Windows platform has hardcoding using Windows functions which are NOT POSIX compliant.) Tested: h5committested. Also tested in BP (AIX) 32/64 and enable/disable-largefile.
* [svn-r19185] Bug fix: ID 1917Albert Cheng2010-08-062-8/+8
| | | | | | | | In some machine (Linux), when --disable-largefile is used, it claims it has fseeko64 but off64_t is NOT supported. Moved the test of fseeko64 and ftello64 to where fseek64 is so that they are tested only if off64_t is supported. Tested: h5committested.
* [svn-r19183] Corrected h5repack verbose test for windowsAllen Byrne2010-08-062-21/+21
| | | | | | Updated tools/lib source dir variable for source list Tested: local linux
* [svn-r19181] Added new h5repack test for bug1797 to CMakeLists.txt. Added ↵Allen Byrne2010-08-062-8/+26
| | | | | | corrected changes to test script for verbose filters Tested: local linux
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