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* [svn-r19654] Description:Quincey Koziol2010-10-2119-628/+570
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* [svn-r19650] Put back deleted library check in configure.Allen Byrne2010-10-202-5/+4
| | | | | | Remove shared library check around ws2_32.lib linking in test library. Issue on windows static builds. Tested: windows
* [svn-r19646] John Mainzer2010-10-191-6/+6
| | | | | | | | | | Replaced calls to H5Dcreate() and H5Acreate() with calls to H5Dcreate2() and H5Acreate2() respectively in t_mdset.c. This was done to repair a compile failure that occured on a build with the --with-default-api-version=v16 config option Cursory commit test
* [svn-r19643] Correct configuration library checks symbol namesAllen Byrne2010-10-191-4/+2
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* [svn-r19638] Description:Quincey Koziol2010-10-195-184/+221
| | | | | | | | | | | | | | | | | | | | | | | Bring some of Neil's changes to help support SWMR access in the v1 B-tree code from the revise_chunks branch back to the 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-r19637] Purpose:Jonathan Kim2010-10-191-291/+290
| | | | | | | | | | | | | | Fix nightly build error on non-linux platforms related to the Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. (r19633) Description: - Updated to use standard C functions instead of strndup() due to failure on non-linux platforms. - Changed to Use HDxxx macros for future reference. - Correct indentation. Tested: jam, amani, heiwa, linew
* [svn-r19633] Purpose:Jonathan Kim2010-10-185-26/+116
| | | | | | | | | | Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. Description: Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed. Tested: jam, amani, heiwa
* [svn-r19632] John Mainzer2010-10-181-1/+1
| | | | | | | Modified test code in t_mdset to use H5Dopen2() instead of H5Dopen1(). This should fix the compile failure when we used --disable-deprecated-symbols Cursory commit test
* [svn-r19628] Because h5diff fix (bug1975) which can compare groups ↵Jonathan Kim2010-10-181-6/+6
| | | | recursively, h5copy diff tests no longer should fail.
* [svn-r19623] Purpose:Mike McGreevy2010-10-182-7/+7
| | | | | | | | | | | | | | - 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
* [svn-r19622] Port of fix for the round robin parallel flush bug caused by ↵John Mainzer2010-10-178-0/+764
| | | | | | | | | | | | | | | | | | | | | | | | | | the failure of the H5Ocache.c code to update its image of the on disk representation of the object header on a call to the clear callback. This wasn't an issue as long as all flushes of the object header were made from the same process, but if an object header is modified, and then flushed on one process and cleared on the rest, the changes were not be reflected in the images of the on disk representation on all processes where the object header was cleared rather than flushed. If one of these processes did the next flush, the changes were lost in the on disk representation. Fixed this by causing all dirty messages and to be written to the copy of the on disk image maintained by the object header code on both flush and clear. Also added associated test code in t_mdset.c. Also checking in some cache debug code developed while chasing this bug. Commit tested and tested (parallel) on phoenix.
* [svn-r19617] Purpose:Mike McGreevy2010-10-1510-351/+2290
| | | | | | | | | | 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
* [svn-r19613] Add option command to set flags OFF for if not using ↵Allen Byrne2010-10-151-0/+2
| | | | ExternalProjects
* [svn-r19610] Add missing XXX_USE_EXTERNAL flags for ExternalProjectsAllen Byrne2010-10-151-2/+8
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* [svn-r19607] Add message when ExternalProject is builtAllen Byrne2010-10-151-0/+2
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* [svn-r19605] Purpose:Jonathan Kim2010-10-155-110/+21
| | | | | | | | | | | Backout the previous changes (r19598): (Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.) Description: Some failure occurred on talwit, so backout the changes and will put it back after the fix. (Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed. Merged from hdf5 trunk r19598.)
* [svn-r19600] Add ExternalProject noteAllen Byrne2010-10-141-3/+12
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* [svn-r19598] Purpose:Jonathan Kim2010-10-145-21/+110
| | | | | | | | | | Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. Description: Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. Expected to be failed. Tested: jam, amani, heiwa
* [svn-r19596] Added new file ./config/ibm-aix6.x.Albert Cheng2010-10-141-0/+1
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* [svn-r19594] Bug fix: H5D_create should return NULL on failure but one of ↵Albert Cheng2010-10-141-1/+1
| | | | | | | | | | return code was FAILED. Rejected by the xlc compiler. Solution: changed it to reutrn NULL. Tested: UP make passed. serial passed but some parallel tests failed. The parallel tests failed were not related to this fix.
* [svn-r19592] Bug fix: since the addition of Albert Cheng2010-10-134-156/+11
| | | | | | | | | | | | | | | | | | | | RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA"} kind of mess things up for the parallel HDF5 configure. Changed it to RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA MP_PROCS=1 MP_TASKS_PER_NODE=1 poe"} if --enable-parallel. Also merge powerpc-ibm-aix5.x with ibm-aix by making powerpc-ibm-aix5.x to source ibm-aix just like ibm-aix6.x. This is in preparation that all AIX platforms will eventually just use ibm-aix directly. Fixed a small problme in ibm-flags: some older xlc (e.g. v7.1) prints the version information with a leading blank. So, accommodate this pattern by removing the "^". Tested: LLNL uP, 32/64bits, serial/parallel. (parallel has tests failed but this change is mainily for configure issues.) Also tested BP, 32/64bits but serial only.
* [svn-r19590] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Albert Cheng2010-10-131-0/+21
| | | | | | | | | | | | | | | | | | | | (Forgot to commit this file when bin/config.guess was committed.) Description: In an AIX 6.1 system, configure --enable-shared could not build a shared HDF5 library. The problem was because the version of config.guess was too old to recongnize AIX 6.X and also configure.in had a local fix which did not recognize AIX 6.X. Solution: 1. Mike McGreevy updated bin/config.guess to handle AIX 6.X. 2 Albert fixed configure.in to recognize AIX 6.X. Note that though HDF5 can build shared lib for AIX 6.X systems but it still could not install the proper library as in AIX 5.X systems. Also, bin/config.sub should be updated too. Tested: BP which is the AIX 6.1 system that exposed this problem.
* [svn-r19587] Description:Quincey Koziol2010-10-1321-53/+404
| | | | | | | | | | | | | | | | | | | | | | | | | 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
* [svn-r19580] Correct target format in ADD_DEPENCIES commandAllen Byrne2010-10-121-2/+2
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* [svn-r19579] Description:Quincey Koziol2010-10-111-1/+0
| | | | | | | | | | | | | | | | | | Correct error reporting function when using 1.6 APIs as default API. 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-r19578] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-10-117-104/+446
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | application uses -DH5_USE_16_API 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.
| * [svn-r19539] Bug 1707 - I added some comments.Raymond Lu2010-10-073-8/+8
| | | | | | | | Tested on jam - simple change.
| * [svn-r19533] Bug 1707 - an update according to Neil's suggestion. I took ↵Raymond Lu2010-10-073-12/+24
| | | | | | | | | | | | | | | | out the VERS, IS_DEFAULT from H5E_auto_t structure in H5Epkg.h when the macro H5_NO_DEPRECATED_SYMBOLS is defined. Tested on jam, heiwa, amani.
| * [svn-r19507] Fix for bug 1707 - I changed the design from the previous fix ↵Raymond Lu2010-10-045-130/+297
| | | | | | | | | | | | | | | | | | | | as Quincey suggested. I added a 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.
* | [svn-r19573] Adjust external library names depending on build type for ↵Allen Byrne2010-10-111-12/+30
| | | | | | | | | | | | ExternalProject Command Tested: local linux, windows
* | [svn-r19570] Parameterize SVN URLs.Allen Byrne2010-10-111-2/+18
| | | | | | | | | | | | | | Add ExternalProject dependicies of external libs copy on project build. Force ExternalProject Libs to build release. Tested: local linux
* | [svn-r19569] Snapshot version 1.9 release 76HDF Tester2010-10-1014-28/+28
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* | [svn-r19566] Maintenance: Added -O3 to be used with the C Intel v 11 ↵Elena Pourmal2010-10-083-7/+29
| | | | | | | | | | | | | | | | | | compilers; set default to -O for all unknown versions of the C Intel compilers. Modified apple config file to display Intel compiler information. Updated RELEASE.txt notes accordingly. Platfroms tested: jam, amani and dubna (Mac 64-bit) with Intel C, Fortran and C++ compilers.
* | [svn-r19548] Remove reference files from clearall commandAllen Byrne2010-10-081-3/+0
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* | [svn-r19544] Purpose:Mike McGreevy2010-10-081-6/+9
| | | | | | | | | | | | | | | | | | | | | | | | Patch for metadata accumulator bug Description: Linew failed one of the randomly seeded fheap tests due to a corner case bug in the metadata accumulator code. This patch fixes the corner case. Tested: used same random seed in fheap tests to reproduce and verify on linew; plus full make check on jam. unit tests for accumulator code coming soon.
* | [svn-r19541] Description:Quincey Koziol2010-10-071-1/+1
| | | | | | | | | | | | | | | | Correct assert statement to acount for pinned entries. Tested: Linux/64 2.6 (chicago) (too peculiar to Chicago setup h5committest)
* | [svn-r19536] Cleanup formattingAllen Byrne2010-10-073-40/+38
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* | [svn-r19534] Add using-memchecker optionAllen Byrne2010-10-071-0/+8
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* | [svn-r19532] Added line to config/examples.am to remove execute permission ↵Larry Knox2010-10-078-8/+15
| | | | | | | | | | | | | | | | from example source files tha t are installed in .../share/hdf5_examples/. This will address bugzilla #2025. Tested with h5committest on amani, heiwa, and jam.
* | [svn-r19527] Add clear generated objects commands to test blocks.Allen Byrne2010-10-0616-69/+1107
| | | | | | | | | | | | Add configurefile command to copy CTestCustom to build folder. Tested: local linux
* | [svn-r19525] Updated tested Windows platformsAllen Byrne2010-10-061-7/+14
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* | [svn-r19523] I added another test case - disabling chunk cache. H5Dwrite ↵Raymond Lu2010-10-051-31/+58
| | | | | | | | | | | | | | | | will fail instead of H5Dclose when the chunk cache is disabled and the mandatory filter fails. Tested on jam - simple change.
* | [svn-r19520] Move 'int nerrors = 0' declaration out of '#ifdef' block to ↵Allen Byrne2010-10-051-1/+1
| | | | | | | | match return.
* | [svn-r19512] Snapshot version 1.9 release 75HDF Tester2010-10-0514-29/+29
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* | [svn-r19509] Improve CMake support for CYGWIN.Allen Byrne2010-10-0414-154/+164
| | | | | | | | | | | | Correct script comment in testh5diff.sh Tested: Windows Cygwin
* | [svn-r19506] Bring changes from revisions 19408, 19421, and 19442 from ↵Larry Knox2010-10-0460-263/+857
| | | | | | | | | | | | branches/hdf5_1_8 to trunk. These revisions reorganize the compile scripts using h5cc.in, h5fc.in, and h5c++.in, add checks for installed examples to the scripts that run them after installation, and add DESTDIR for install as needed for RPMs. Tested on amani, heiwa and jam by h5committest and with CYGWIN.
* | [svn-r19498] Description:Quincey Koziol2010-10-017-662/+1087
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Optimize the vector-vector memcpy() routine even further, for a total of ~2x speedup. :-) Make a generic vector-vector operation routine and convert other vector-vector read & write routines to use generic routine instead of multiple copies of the basic algorithm. 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-r19497] Change ExternalProject Dependicies guard to positive match ↵Allen Byrne2010-09-301-4/+4
| | | | | | | | | | | | (Windows configure error) Tested: Windows
* | [svn-r19495] Correct static external project library base names.Allen Byrne2010-09-291-2/+2
| | | | | | | | Tested: windows
* | [svn-r19491] Purpose:Jonathan Kim2010-09-2911-0/+264
| | | | | | | | | | | | | | | | | | | | Update help page for exclude-path feature. Description: Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406) Tested: jam, amani, heiwa
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