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* [svn-r20711] I added efc.c to the compile list.Raymond Lu2011-05-031-0/+6
| | | | Not tested yet.
* [svn-r20707] Added comments to the H5F_mem_t enumeration in H5Fpublic.h and ↵Dana Robinson2011-05-022-22/+35
| | | | the corresponding flavors[] array in the log VFD code.
* [svn-r20702] I added efc.c to the test list.Raymond Lu2011-05-021-0/+5
| | | | Not tested yet.
* [svn-r20700] I added H5Fefc.c to the compile list.Raymond Lu2011-05-021-2/+2
| | | | Not tested yet.
* [svn-r20694] Add description for new "external_open_twice" test.Neil Fortner2011-05-021-1/+2
| | | | Tested: jam
* [svn-r20691] Purpose: Fix problem exposed by external link cacheNeil Fortner2011-05-024-4/+262
| | | | | | | | | | | | | Description: When closing an object that had two open id's, the library would previously fail to account for the status of the "holding_file" field, potentially causing the file's "nopen_objs" field to become inconsistent. This caused problems when opening the same object twice through an external link using th external file cache. Modified the library to properly account for the status of the "holding_file" field when closing an object id, even when the underlying "shared" object isn't closed. Tested: jam, koala, heiwa (h5committest)
* [svn-r20689] Changed compiler name from xlf/mpxlf_r to xlf90/mpxlf90_r to avoidAlbert Cheng2011-04-291-2/+2
| | | | | misunderstanding. xlf/mpxlf_r are actually Fortran 77 compilers. HDF5 requires Fortran 90 or higher.
* [svn-r20686] Added "xlc_r" as a recognized XL compilers.Albert Cheng2011-04-291-1/+1
| | | | | | Tested: NCSA BP AIX system. No need of h5committest because the changes affect AIX systems only.
* [svn-r20677] Merge packed bits option from 1.8 branch to trunk. CMake only. ↵Allen Byrne2011-04-2965-15/+4814
| | | | | | Autotools merge to come. Tested: local Linux
* [svn-r20676] Purpose:Jonathan Kim2011-04-2914-57/+192
| | | | | | | | | | | | | | | | - HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Fixed: 1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications. 2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file. Test update: Updat prvious test cases (171, 172, 530) affected by this fix, so they still perfrom originally intended testing without bypassing. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [svn-r20673] Eliminate memory buffer errors, Allen Byrne2011-04-282-160/+164
| | | | | overhead - add free to successful path. zip_perf - filename handling needed inits to NULL and free
* [svn-r20670] Fixed file name handling with char pointer incorrectly causing ↵Jonathan Kim2011-04-281-4/+5
| | | | | | crash. (Reviewed by ADB)
* [svn-r20669] Add test_configuration settingAllen Byrne2011-04-281-0/+2
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* [svn-r20666] Bug fix: VMS has trouble to deal with absolute path. I changed ↵Raymond Lu2011-04-282-1/+5
| | | | | | | | dtypes.c to use the file name only. I also updated the current directory path in vms/test/H5srcdir_str.h. Tested on jam and OpenVMS.
* [svn-r20665] Remove extraneous memcheck parametersAllen Byrne2011-04-281-4/+0
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* [svn-r20658] Description:Quincey Koziol2011-04-2831-152/+119
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring code contribution from John Biddiscombe into trunk, according to IP assignment #002 (on file). Checkin message from John is: This patch includes the changes necessary to compile a Virtual File Driver outside of the main hdf5 build and still have it link against the hdf5 core and work correctly at run-time. Certain MPI-IO related VFD checks were hard-coded in the hdf5 source and so it was not possible to extend the functionality to new drivers. Removed IS_H5FD_MPI macros and replaced with H5F_HAS_FEATURE calls with new keys, H5FD_FEAT_HAS_MPI and H5FD_FEAT_ALLOCATE_EARLY. Change H5FD cleanup (term_interface) so that file drivers call terminate when their class types are deleted instead of explicitly being called from the finalization code. Move the terminate call out of H5I and put it into the FD class_free call. Remove the now obsolete check of handles after cleaning types at termination time. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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 (ember) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
| * [svn-r20650] Description:Quincey Koziol2011-04-261-1/+1
| | | | | | | | | | | | | | | | | | Fix spelling error: FUNC_ENTER_NOAPI_NOFUNC_NONIT -> FUNC_ENTER_NOAPI_NOINIT_NOFUNC Tested on: FreeBSD/32 8.2 (loyalty) FreeBSD/64 8.2 (loyalty)
| * [svn-r20648] Description:Quincey Koziol2011-04-261-1/+1
| | | | | | | | | | | | | | | | | | Correct spelling error in macro. (FUNC_ENTER_NOAPI_NOFUNC_NOINIT -> FUNC_ENTER_NOAPI_NOINIT_NOFUNC) Tested on: Eyeballed only. (h5committest not required for this branch)
| * [svn-r20588] Description:Quincey Koziol2011-04-2130-129/+98
| | | | | | | | | | | | | | | | | | Clean up code a bit, move new "terminate" VFD callback to new position in H5FD_class_t struct. Tested on: Mac OS X/32 10.6.7 (amazon) w/debug & production (h5committest not required on this branch)
| * [svn-r20587] Description:Quincey Koziol2011-04-2119-50/+48
| | | | | | | | | | | | | | | | Initial commit of John Biddescomb's VFD & MPI tweaks. Tested on: None (yet) (h5committest not required for this branch)
* | [svn-r20657] Description:Quincey Koziol2011-04-282-36/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Correct check for pthreads routine from pthread_join() to pthread_self() as intended. Tested on FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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 (ember) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* | [svn-r20652] Description:Quincey Koziol2011-04-263-1/+59
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Teach the tracing script & routines about the 'unsigned long' and 'unsigned long long' types, so that the H5Pset_fapl_log() API routine gets tracing information correct. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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 10.6.6 (amazon) in debug mode Mac OS X/32 10.6.6 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.6 (amazon) w/parallel, in debug mode
* | [svn-r20651] Description:Quincey Koziol2011-04-262-36/+36
| | | | | | | | | | | | | | | | | | | | Switch from using 'pthread_create' to 'pthread_self' when trying to detect the pthread library, so that the Intel C compiler is happier with the prototype. Tested on: Linux/64 2.6 (koala) w/Intel C (h5committested on duty, jam & linew)
* | [svn-r20646] Description:Quincey Koziol2011-04-262-15/+13
| | | | | | | | | | | | | | | | | | | | Small improvement to the core VFD's error reporting. Update FreeBSD information Tested on: FreeBSD/32 8.2 (loyalty) (too minor to require h5committest)
* | [svn-r20641] Add CPack overrides for NSIS install paths. Install for ↵Allen Byrne2011-04-264-40/+1990
| | | | | | | | | | | | products are: HDF Group/Product/Version Tested: windows , local linux
* | [svn-r20640] Remove export from "export LD_LIBRARY_PATH=${LL_PATH}" in ↵Larry Knox2011-04-266-19/+17
| | | | | | | | | | | | | | | | examples and hl/examples Makefiles. "export" breaks make install in Daily Tests on FreeBSD machines and isn't missed elsewhere. Tested on amani, freedom, jam, heiwa, and loyalty.
* | [svn-r20639] Add missing entry for "Bug HDFFV-4358"Jonathan Kim2011-04-261-0/+5
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* | [svn-r20635] Windows needs timeout at 3600Allen Byrne2011-04-251-2/+2
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* | [svn-r20627] Add dependency of t_pflush2 on t_pflush1Allen Byrne2011-04-251-0/+2
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* | [svn-r20626] Albert's test on bp reveals that the dumper had assertion ↵Raymond Lu2011-04-252-38/+46
| | | | | | | | | | | | | | | | failure when it tried to display empty attribute data. I added a check for empty attribute in h5dump.c. I also added a check for empty dataset in tools/lib/h5tools.c. Tested on jam. But I tested the same changes in 1.8 on jam, linew, and amani.
* | [svn-r20610] OpenVMS complainted about a test case in th5o.c which opened ↵Raymond Lu2011-04-222-0/+6
| | | | | | | | | | | | the same file twice. VMS doesn't allow it. I used the macro H5_CANNOT_OPEN_TWICE to skip the test case. In th5s.c, I created an attribute but fogot to close it in the test case for zero dimension size. Tested on jam. But I haven't tested on OpenVMS yet.
* | [svn-r20600] Purpose:Jonathan Kim2011-04-221-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases Description: Correct mistake in cmake script from previous commit r20595. Add three test cases for h5dump and h5ls. - h5ls: external link to soft link with follow symlink. - h5dump: external link to soft link with follow symlink. - h5ls: external link to soft link without follow symlink. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* | [svn-r20596] Add missing library suffix to ext lib install listAllen Byrne2011-04-221-1/+1
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* | [svn-r20595] Purpose:Jonathan Kim2011-04-2113-0/+62
| | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases Description: Add three test cases for h5dump and h5ls. - h5ls: external link to soft link with follow symlink. - h5dump: external link to soft link with follow symlink. - h5ls: external link to soft link without follow symlink. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* | [svn-r20590] On windows the ext libs did not work for cpack process. Changed ↵Allen Byrne2011-04-212-66/+26
|/ | | | ext lib handling to get the correct path. Needs more work to remove the the pre-install copying.
* [svn-r20584] I updated it for 2 new data files in h5diff/testfiles.Raymond Lu2011-04-201-1/+2
| | | | Tested with h5committest.
* [svn-r20581] Bug 1386 - allowing dimension size to be zero. I forgot to ↵Raymond Lu2011-04-202-0/+0
| | | | | | check in these 2 data files for the test. Now test is needed.
* [svn-r20577] Bug 1386 - allowing dimension size to be zero. I added test ↵Raymond Lu2011-04-2010-3/+164
| | | | | | | | cases in the tests for h5dump and h5diff. I also added the test cases in the CMAKE script. Tested on jam, linew, and amani. Tested CMAKE on jam.
* [svn-r20572] Bug #5929: On windows check for existence of ↵Allen Byrne2011-04-203-23/+93
| | | | | | InitOnceExecuteOnce for use by threads. merge from 1.8 r20568
* [svn-r20561] Description:Quincey Koziol2011-04-201-2/+2
| | | | | | | Remove C++ specific flag from C compilation flags, for gcc 4.5 & 4.6 Tested on: FreebSD/64 8.2 (freedom) w/gcc 4.6
* [svn-r20553] Description:Quincey Koziol2011-04-191-2/+3
| | | | | | | | | | | | | | | | | | Revert part of r20536 that was part of a Coverity merge. 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-r20551] Description:Quincey Koziol2011-04-191-2/+2
| | | | | | | | | Correct 'FILE **' back to 'FILE *' for H5Fget_vfd_handle call. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc 4.6 & debug FreeBSD/64 8.2 (freedom) w/gcc 4.6 & debug Solaris 2.6 (linew)
* [svn-r20548] Fixed bug in test/vfd.c (HDFFV-5936) that caused STDIO VFD test ↵Dana Robinson2011-04-181-11/+3
| | | | | | to fail on some platforms. The problem was that the test was a clone of the SEC2 test. The SEC2 test accepts a file descriptor (int) via a void pointer from H5Fget_vfd_handle() whereas the STDIO test needs to accept a FILE pointer. Storing the FILE pointer in an integer failed on some systems. The STDIO test now stores the file handle in FILE pointer and checks it for NULL instead of < 0.
* [svn-r20543] revert install command for External library builds - copy of ↵Allen Byrne2011-04-181-6/+6
| | | | lib fails if permission to install location is denied. Does not affect build otherwise.
* [svn-r20539] Description:Quincey Koziol2011-04-186-162/+214
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes back to trunk: r20276: Add recursive is vlen string function. Cleanup resource leaks for issues: 200,202,329,688,811,812 r20277: Check types and close by adding error section: issue 687 r20278: Replaced implicit pointer conversion with (ocrt_info.new_obj != NULL). r20280: Addressed coverity issues 927-929 & 583. The real issue is failure to check file name length -- at least at the H5FD interface level. This needs more work, but at least I have dealt with the issue in H5FDfamily.c r20337: H5O_type_t obj_type = H5O_TYPE_UNKNOWN; r20338: Added udata.name = NULL; to prevent potential uninitialized use after done: label. r20339: coverity issues: 686,828,1670-1673,1707-1711 Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode FreeBSD/32 8.2 (loyalty) w/gcc4.6, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* [svn-r20538] Description:Quincey Koziol2011-04-181-3/+67
| | | | | | | | Update with new warning flags for gcc 4.6.x Tested on: FreeBSD/32 8.2 (loyalty) w/gcc 4.6 FreeBSD/64 8.2 (freedom) w/gcc 4.6
* [svn-r20536] Description:Quincey Koziol2011-04-1720-108/+193
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up various warnings & code formatting issues. Bring changes from Coverity branch to trunk: r20085: Purpose: Fix coverity issue 793 Description: Modified H5S_hyper_project_simple_higher() to free the entire span list in new_space on failure. r20091: This is a fix for coverity bug #1683. Changed the two printfs to use %lu (unsigned long) for printing "dset_size". r20162: Purpose: Fix coverity issue 785 Description: Modified H5T_enum_nameof() to free "name" on failure if it was allocated. Also clarified some code in H5S_hyper_rebuild_helper(). r20189: Addressed coverity defect 783. H5SL_new_node() in H5SL.c was failing to free space allocated in its first alloc if the second alloc failed. Added a call to H5FL_FREE to address this issue. This is purely to keep coverity happy -- if this code is ever triggered, we have much larger problems. Note that this fix will trigger an unused return value complaint from coverity next week. r20190: Fixed Coverity issues 1561 1565 and 1678 (UNUSED_VALUES) by moving checks of return values to after the function call. r20191: Fixed coverity issues 643 644 and 1678 (CHECKED_RETURN). r20232: Addressed coverity issues 923-925. Replaced calls to sprintf with calls to HDsnprintf. r20233: Fix coverity issue 662. Don't try to sort 0 attributes in H5Aint.c. r20234: Fix coverity issue 664. Check for NULL before dereferencing in H5Gdeprec.c. r20271: Purpose: Fix coverity issue 784 Description: Modified H5_debug_mask() to keep a list of files opened for use as a debugging output stream, and modified H5_term_library to close these files on exit. r20272: addressed coverity issues 838 & 955. Issue was use of strcpy() -- existing code was safe, but modified to use strncpy() to keep coverity happy. r20273: Addresed coverity issues 1388 and 1389. Initialized sel_iter->type to NULL in H5S_select_iter_init. r20275: Purpose: Fix valgrind issue in mf.c Description: Fixed bug (incomplete if statement) in test_mf_fs_alloc_free() so the retrieved node gets freed. 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
* [svn-r20535] Description:Quincey Koziol2011-04-171-0/+106
| | | | | | | | | | | | | | | | | Add explicit test that checks that the 'fileno' field in H5O_info_t is the same for objects in the same file, whether the file was opened twice or not. 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
* [svn-r20529] Purpose: Add testing for bug 1864Neil Fortner2011-04-1531-0/+344
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r20520] Removed ibm-aix6.x file which just sourced ibm-aix file. ↵Albert Cheng2011-04-155-38/+6
| | | | | | | | | | Removed code in configure.in that tried to distinguish different versions of AIX. This is no longer needed. Tested: NCSA Blue-print. No h5committest since this affected AIX system only.
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