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* [svn-r19257] Change Cmake to allow a local zlib header to be used in ↵Allen Byrne2010-08-209-96/+211
| | | | | | | | | | | 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-r19256] Description:Quincey Koziol2010-08-201-0/+1
| | | | | | | | | Bring r19255 from trunk to 1.8 branch: Add missing include file from r19252. Tested on: (Eyeballed only, too simple to require h5committest)
* [svn-r19254] Description:Quincey Koziol2010-08-1930-462/+510
| | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19252 & 19253 from trunk to 1.8 branch: 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 Coverity branch)
* [svn-r19250] New feature(bug #1934): I made H5Tset_order support all data ↵Raymond Lu2010-08-185-39/+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. Tested on jam, heiwa, and amani.
* [svn-r19248] Description:Quincey Koziol2010-08-172-53/+234
| | | | | | | | | | | | | | | | | Bring r19247 from trunk to 1.8 branch: 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 (h5committested on trunk)
* [svn-r19243] Description:Quincey Koziol2010-08-162-4/+22
| | | | | | | | | | | Bring r19242 from trunk to 1.8 branch: 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-r19238] Description:Quincey Koziol2010-08-1210-105/+84
| | | | | | | | | | | | Bring r19237 from trunk to 1.8 branch: 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-r19234] Description:Quincey Koziol2010-08-121-56/+62
| | | | | | | | | Initialize loop variable that caused failures in certain circumstances. Also clean up compiler warnings and release MPI datatype. Tested on: Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* [svn-r19229] 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-r19226] 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-r19224] 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-r19220] Move hl fortran ADD_SUBDIRECTORY to right after fortran ↵Allen Byrne2010-08-102-5/+6
| | | | | | ADD_SUBDIRECTORY. This fixes a problem with compiler generated files not including target module directory on some linux machines. Tested: local linux
* [svn-r19219] Corrected minor format/location of commands.Allen Byrne2010-08-102-5/+3
| | | | Tested: local linux
* [svn-r19216] 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-r19213] 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-r19212] 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-r19208] Description:Quincey Koziol2010-08-101-1/+1
| | | | | | | Switch from using "UINT16_MAX" to "64 * 1024" for assert macro. Tested on: None, just eyeballed.
* [svn-r19204] 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-r19200] Added tests that subdirectories exist before using ↵Allen Byrne2010-08-091-110/+130
| | | | | | | | ADD_SUBDIRECTORY CMake command Added cache set command for default install prefix Tested: local linux
* [svn-r19199] new expected output file for BZ1953 fixAllen Byrne2010-08-091-0/+1
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* [svn-r19198] [BZ1953]implementation for the proposed changes suggested by ↵Allen Byrne2010-08-095-15/+400
| | | | | | | 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-r19196] Defined the file format version H5F_LIBVER_18 to prepare for ↵Raymond Lu2010-08-091-0/+4
| | | | | | | | the 1.10 release. It isn't used anywhere yet. Tested on jam - very simple change and not used.
* [svn-r19194] 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-r19187] Bug fix: ID 1917Albert Cheng2010-08-061-31/+43
| | | | | | | | | | | 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-r19186] 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-r19184] Corrected h5repack verbose test for windowsAllen Byrne2010-08-063-28/+39
| | | | | | Updated tools/lib source dir variable for source list Tested: local linux
* [svn-r19182] Description:Quincey Koziol2010-08-068-12/+164
| | | | | | | | | | | | | | | | | | | | | | | | Bring r19179 from trunk to 1.8 branch: Bring changes from Coverity branch back to trunk: r19079 & 19080: [BZ1942] h5dump -u to generate XML, it does not respect the -m option xml version of dump_data function didn't check for use of fp_format variable. Added new test expected file for committed bug 1942 r19103, 19104 & 19105: [BZ1821] h5repack -v did not display correct output for a selected compression. Needed new test for comparing output of -v option. Added new test file for solution to BZ1821 BZ1821 - Bring test changes from the shell script actually used. Tested on: Mac OS X/32 10.6.4 (amazon) debug & production (h5committested on branch)
* [svn-r19177] Took out several redundant lines when object IDs are closed.Raymond Lu2010-08-051-9/+0
| | | | Tested on jam.
* [svn-r19172] Bug fix for #1239 - The filter's public function CAN_APPLY ↵Raymond Lu2010-08-058-30/+238
| | | | | | | | | | | | should return htri_t not herr_t. To minimize the change of the library's behavior, in the function H5Z_prelude_callback of H5Z.c, if the return value of can_apply is FALSE and the filter is MANDATE, this function returns a FAILURE. If the return value is FALSE but the filter is OPTIONAL, this function returns a SUCCEED. During the IO, the filter will fail and return a size of zero. But the pipeline will skip this filter. Tested on jam, linew, and amani. Tested on jam with szip.
* [svn-r19170] Bug fix: 1917.Albert Cheng2010-08-052-8/+11
| | | | | | | | The previous fix had the Windows code in H5private.h but they should have been in H5win32defs.h which holds all Windows-specific definitions. Moved the fix. Tested: BP (AIX) to confirm the fix is still valid. Windows tests will occur in daily tests tonight.
* [svn-r19169] Description:Quincey Koziol2010-08-042-3/+3
| | | | | | | | | Bring r19168 from trunk to 1.8 branch: Clean up compiler warning Tested on: None, eyeballed only (tested on trunk)
* [svn-r19166] Bug fix: 1917.Albert Cheng2010-08-033-29/+25
| | | | | | | | | | | | | | | | | Description: test/big incorrectly determined not able to write files larger than 2GB and skipped the SEC2 and STDIO driver tests. The reason was because it was using off_t while the SEC2 driver is using lseek64 which expects off64_t type. Solution: Created a new HDoff_t which is set to off_t or off64_t or other appropriate type depending on which of lseek or lseek64 is available. Changed SEC2 file driver and the big test to use this common definition. Tested: In BP (AIX), using --enable and --disable-largefile, for both 32 and 64 bits modes. Did not do h5committest because: 1. the error was exposed in the remote BP machine; 2. the change is trivial.
* [svn-r19164] Add configure changes from r19159 to CMake.Allen Byrne2010-08-022-0/+8
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* [svn-r19159] Added the tests for fseeko64 and ftello64 which will be used by ↵Albert Cheng2010-07-304-5/+11
| | | | | | | | | the STDIO VFD if they are available. Tested: jam only since it was tests for two new functions that are not used by the code yet.
* [svn-r19158] Description:Quincey Koziol2010-07-308-380/+423
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19156 from trunk to 1.8 branch: Bring revisions from Coverity branch back to trunk: r19044: Coverity #449 - Line 1560 called function H5O_chunk_protect for 2 pointers to allocate. But when there's failure on the second one, the first wasn't freed (H5O_chunk_unprotect). We fixed it by freeing the pointers when an error happens. r19045: Fixed coverity issue # 319. Free sec_node in done if it is not NULL. r19046: Add intended but missing assignments to initialize pointers to NULL (coverity issue fixes). r19049: Hdf5_1_8_coverity branch was recreated from hdf5_1_8 branch in revision 18839 without fix for Coverity issue #84 having been propagated to the hdf5_1_8 branch. This revision adds the fix again. r19060: added parentheses to see if they will keep subversion from getting confused r19061: Fix coverity item 139. Fixed incorrect condition for freeing buffer on error. Fix coverity items 20 and 21. Removed unused NTESTS facility from dtypes.c. Cleanup in H5Shyper.c. r19062: Fix coverity item 450. Check to see if chk_proxy has been allocated before attempting to free it. Fix coverity item 454. Check to see if allocation of buf failed in H5D_fill_refill_vl. Fix coverity items 455-457. Initilize hid_t's to -1, check their value before attempting to close them, and check if the close failed. r19063: New fix to address coverity issue #84. Check that pointers in H5Z_xform_find_type are not NULL before passing them to H5T_cmp. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r19157] Description:Quincey Koziol2010-07-301-14/+18
| | | | | | | | | | | | | | | | | Bring r19078 from Coverity branch to 1.8 branch (code doesn't exist on trunk): Purpose: Resolve Memory Leaks Description: Free saved ID structures in H5I interface when library shuts down. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (Too minor to require h5committest)
* [svn-r19155] Remove line in clean target that removes installed header files.Larry Knox2010-07-292-2/+0
| | | | Tested with h5 committest on amani, jam, heiwa and linew.
* [svn-r19154] Description:Quincey Koziol2010-07-298-343/+278
| | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19153 from trunk to 1.8 branch: Bring changes on Coverity branch back to trunk: r19040: Fixed coverity #440 - NULL check after dereference. We moved the NULL check up into the IF block and changed it to assertion. r19041: Maintenance: Addressed Coverity issues 441 and 449 by initializing proper variables r19042: In function H5O_chunk_protect (H5Ochunk.c): - Initialize H5O_chunk_proxy_t pointers chk_proxy and ret_value. - Free chk_proxy on error. r19043: Addressed coverity issues 442 - 448 by initializing pointers to NULL. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (Too minor to require h5committest)
* [svn-r19152] Correction from the previous checkin for H5Oattribute.c. ↵Raymond Lu2010-07-291-3/+8
| | | | | | | | | | Because the attribute structure it is shared now. The only situation that requires copying the data is when the metadata cache evicts and reloads this attribute. The attribute structure will be different in that situation. Tested on jam.
* [svn-r19149] Maintenance: Removed misleading information about the ↵Elena Pourmal2010-07-291-16/+6
| | | | | | | HDF4-to-HDF5 tools. The tools became a part of the h4h5tools distribution long time ago, but the INSTALL file was not updated in the development branch and slipped into 1.8 releases and current trunk.
* [svn-r19147] Purpose: Fix bug in direct IO driverNeil Fortner2010-07-282-80/+155
| | | | | | | | | | | Description: In certain circumstances, the direct I/O driver did not perform correctly when data was unaligned. The driver has been patched to fix this. Also added some potential performance improvements for the unaligned case, and strengthened the test for whether the data needs to be aligned. Tested: cobalt
* [svn-r19143] Update for the bug fix of #1956.Raymond Lu2010-07-281-0/+3
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* [svn-r19141] I added H5Itest.c. Raymond Lu2010-07-281-1/+1
| | | | Not tested yet.
* [svn-r19139] In line 861, there's no need to allocate data buffer or copy ↵Raymond Lu2010-07-281-10/+3
| | | | | | | | the data because the attribute structure is shared now. Only do an assertion check, instead. Tested the same change for 1.8.5 on jam - simple change.
* [svn-r19136] Added new file to windows project files.Allen Byrne2010-07-283-4/+13
| | | | Added new file to src/CMakeLists.txt
* [svn-r19134] Description:Quincey Koziol2010-07-2812-157/+339
| | | | | | | | | | | | | | | | | Bring r19133 from trunk to 1.8 branch: Correct traversal of user-defined links (including external links) to retain path information of object, allowing H5Iget_name() queries to work quickly (without searching entire destination file). This required some refactoring and addition of a mechanism to detect if a "fast" query was performed (for the tests). Minor code cleanups, etc. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode (h5committest performed on trunk)
* [svn-r19132] Description:Quincey Koziol2010-07-271-0/+4
| | | | | | | | Reduce compiler optimizations for v10.6, to work around bug with static constant char *'s. Tested on: Linux/32 2.4 (jam) w/PGI
* [svn-r19129] Description:Quincey Koziol2010-07-261-2/+2
| | | | | | | Correct another inadvertant use of macro instead of versioned API name. Tested on: Eyeballed only, too minor to require h5committest
* [svn-r19128] Description:Quincey Koziol2010-07-231-1/+1
| | | | | | | | Change use of API wrapper to using versioned API routine (i.e. H5Eprint -> H5Eprint2) Tested on: None, eyeballed only, too simple
* [svn-r19126] Description:Quincey Koziol2010-07-222-6/+21
| | | | | | | | | | Bring r19124 from trunk to 1.8 branch: Add some error checking to the process of creating superblock extension. Tested on: FreeBSD/32 6.3 (duty) in debug mode (h5committest performed on trunk)
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