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* [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
* [svn-r19489] Correct dependency on extlib project when not using external ↵Allen Byrne2010-09-291-6/+8
| | | | projects.
* [svn-r19487] Add ExternalProject support for external libs - option added ↵Allen Byrne2010-09-281-18/+96
| | | | | | Defaults to NO. SVN allows downloading project from svn. Future option is to use a tar file. Tested: Windows, local Linux
* [svn-r19484] Description:Quincey Koziol2010-09-281-428/+424
| | | | | | | | Clean up formatting a bit. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug (Too minor to require h5committest)
* [svn-r19482] Description:Quincey Koziol2010-09-281-49/+85
| | | | | | | | | | | | | | | | | | | | | | | Speed up hyperslab sequence generation routine some more, giving about a 10% improvement in Ger Van Diepen's LOFAR benchmark. 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-r19481] I'm backing out my fix for bug 1707 because there're some ↵Raymond Lu2010-09-2723-342/+89
| | | | | | | | | | | unresolved issues - r19441 and 19467. Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with the 1.8 library to compile. I created a branch off the trunk called set_auto to continue working on the problem. Tested on jam - backing out, simple.
* [svn-r19476] Description:Quincey Koziol2010-09-234-141/+127
| | | | | | | | | | | | | | | | | | | | | | | Polish the vectorized memory <-> memory and memory <-> file I/O routines to speed them up a little bit (~10%) 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-r19472] Description:Quincey Koziol2010-09-234-400/+725
| | | | | | | | | | | | | | | | | | | | | | Create a new, more streamlined method of generating I/O sequences when there is only a single block defined by a hyperslab. This improves the performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%. 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 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-r19471] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Albert Cheng2010-09-221-0/+5
| | | | | | | | | | Description: The AIX platform does not install the lib*.so for some reason but libhdf5.a acts like a shared library. Until we can find out how to fix this, patch up tetlibinfo.sh to not look for an lib*.so in AIX. (Note the test results look wierd as it says libhdf5.a passed and skipped.) Tested: NCSA BP for both enable and disable-shared.
* [svn-r19470] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Albert Cheng2010-09-223-20/+81
| | | | | | | | | | | | | | | | | | 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-r19469] Bug fix for 1707 - My previous checkin wasn't complete. I left ↵Raymond Lu2010-09-222-2/+9
| | | | | | | | | out the case when the deprecated symbols were disabled. I made a different definition for H5E_auto_op_t when the deprecated symbols were disabled. Tested on jam - a simple change.
* [svn-r19461] Purpose: Fix bug 1864Neil Fortner2010-09-2120-75/+269
| | | | | | | | | | | Description: Library versions 1.6.3 and earlier contain a bug which causes them to be unable to perform certain operations on a group if that group's symbol table information is not cached in the parent group's symbol table. Versions 1.8.0 to 1.8.5 did not cache this information. Modified library to cache this information. Tested: jam, amani, heiwa (h5committest)
* [svn-r19460] Updated runTest.cmake to compare against the expected result ↵Allen Byrne2010-09-211-2/+2
| | | | code rather then just 0
* [svn-r19458] Add CMake tests for check-vfd; includes new vfdTest.cmake ↵Allen Byrne2010-09-213-0/+79
| | | | | | script and OPTION HDF5_TEST_VFD Tested: local linux
* [svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an ↵Raymond Lu2010-09-2123-89/+335
| | | | | | | | | | | | | 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 union in the structure H5E_auto_t. Another change is to make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a document for it. 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-r19447] Fix for Windows legacy test added for 1890 h5diff exclude-pathJonathan Kim2010-09-211-2/+2
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* [svn-r19445] Update for previous checkin r19443Jonathan Kim2010-09-201-0/+1
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* [svn-r19443] Purpose:Jonathan Kim2010-09-205-10/+35
| | | | | | | | | | Fix for group comparison with exclude-path case. Use relative path. Description: Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406) Tested: jam, amani and heiwa
* [svn-r19439] Description:Mike McGreevy2010-09-201-3/+3
| | | | | | | Update bin/chkconfigure to reflect version 2.67 of Autoconf Tested: ran bin/chkconfigure on jam
* [svn-r19437] add missing -C optionsAllen Byrne2010-09-201-1/+1
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* [svn-r19435] remove source package command - not neededAllen Byrne2010-09-201-1/+0
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* [svn-r19434] Correct use of lib, include, bin in INSTALL commands to use ↵Allen Byrne2010-09-2017-37/+50
| | | | | | proper variables. Tested: local linux
* [svn-r19431] Updated configuration section with optional command line usage. ↵Allen Byrne2010-09-201-24/+100
| | | | Also added section on CPack.
* [svn-r19430] Update to H5REPACK tests for layout info required a new ↵Allen Byrne2010-09-201-23/+161
| | | | | | function in batch file Tested: Windows
* [svn-r19427] Updates for cmake tests from the h5diff group recursive updates.Jonathan Kim2010-09-201-4/+4
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* [svn-r19425] Fix for legay Windows test for h5diff updates.Jonathan Kim2010-09-201-8/+10
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* [svn-r19418] On windows, an include bypassed the WIN32_LEAN_AND_MEAN define. ↵Allen Byrne2010-09-172-2/+2
| | | | | | Moved the define up. Moved the h5dif.h to after the h5private include Tested: Windows
* [svn-r19417] Error return value was FAIL. Should be NULL.Albert Cheng2010-09-171-1/+1
| | | | Tested: LLNL up which this was flagged.
* [svn-r19415] Fix for Cmake test.Jonathan Kim2010-09-171-22/+28
| | | | | Tested: jam
* [svn-r19412] Modified shape same tests to deal with the performance problem ↵John Mainzer2010-09-171-48/+570
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | on Abe. Problem appears to have been caused by file system contention. In the chunked dataset case, reshaping the chunks so that only one process would touch each chunk and setting the alignment equal to the default Lustre block size more or less dealt with the problem. For contiguous datasets, the problem was a bit more difficult, as re-working the test to avoid contention would have been very time consuming. Instead, I added code to time one execution of each type of shape same test, and skip additional tests of that type if the duration of the test exceeded some threshold In all cases, I set up code to turn off the above fixes if express test is 0. Tested on Abe and commit tested. On the commit test, the configure test failed -- probably because I was h5committest from heiwa due to some ssh wierdness. In any case a manual reconfigure run on jam seemed to work fine. Also, in h5committest, I ran into some data conversion warnings. I didn't worry about them as the only code I changed was in testpar.
* [svn-r19410] Purpose: Jonathan Kim2010-09-174-0/+0
| | | | | Add missing files from the previous checkin. (Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object)
* [svn-r19409] Purpose: Jonathan Kim2010-09-169-1/+503
| | | | | | | | | | | Add extra test cases for bug1975 h5diff - support recursive comparison on group when specified as an object. Description: Additional tests for combination of group recursive and --follow-symlinks with multi-linked external links with several files (same name/strucure). Tested: jam, amani, heiwa
* [svn-r19406] Purpose:Jonathan Kim2010-09-1617-18/+659
| | | | | | | | | | | Add --exclude-path option Description: Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded. Related to "1890: h5diff excluding object for file comparison via command line" Tested: jam, amani and heiwa
* [svn-r19403] Update to H5REPACK tests for layout info required a grep script ↵Allen Byrne2010-09-164-6/+139
| | | | | | | | like runTest.cmake. Update CMakeLists.txt for new h5repack layout tests. Tested: local linux
* [svn-r19402] Description:Quincey Koziol2010-09-164-12/+65
| | | | | | | | | | | | | | | | | | | | | | | | | Correct Bz#1968 (Problem when opening new format file with H5F_LIBVER_EARLIEST) by initializing symbol table leaf information in a more universal way. Also cleaned up other superblock initialization a little bit while I'm here. 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-r19400] Purpose:Jonathan Kim2010-09-1656-663/+2442
| | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani, heiwa
* [svn-r19398] Descriptino:Quincey Koziol2010-09-1635-439/+369
| | | | | | | | | | | | | | | | | | | | | | | Clean up the internal usage H5I_dec_ref() to eliminate the sequence of flags that has been creeping in. 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-r19396] Description:Quincey Koziol2010-09-1611-140/+61
| | | | | | | | | | | | | | | | | | | | | | | | Bring back various modifications to the v2 B-trees that were introduced in the revise_chunks branch but aren't dependent on any file format or API changes. 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-r19395] Purpose: Fixed bug 1903Binh-Minh Ribler2010-09-167-28/+14
| | | | | | | | | | | Description: After a C++ API object is closed, its id should be reset regardless of the reference count of the underlying HDF5 object. User reported the bug for Group, but it's applicable to all other objects. Fixed. Platforms tested: Linux/32 2.6 (jam) FreeBSD/64 6.3 (liberty) SunOS 5.10 (linew)
* [svn-r19392] Purpose:Jonathan Kim2010-09-151-3/+0
| | | | | | | | | | Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed to Description: Remove unnecessary lopping code, which only lowers performance. Tested: jam, amani, heiwa
* [svn-r19389] Purpose:Jonathan Kim2010-09-156-22/+264
| | | | | | | | | | Fix for Bug1896 h5repack - changing layout to COMPACT does not work Description: Make h5repack be able to convert a layout to COMPACT for small size dataset as default. Also add verifying layout changes in our test script. Tested: jam, amani, heiwa
* [svn-r19386] Purpose: Fix assertion failure caused by fractal heap header ↵Neil Fortner2010-09-154-7/+147
| | | | | | | | | | | | | | file pointer Description: The fractal heap header structure keeps a pointer to the file associated with it. However, it is possible for that file pointer to be closed while the header is still in cache (through the shared file pointer). Previously, the header's file pointer was not updated and subsequently pointed to an invalid file structure. Modified fractal heap code to update the file pointer every time the header is accessed. Tested: jam, linew, amani (h5committest)
* [svn-r19384] Description:Quincey Koziol2010-09-153-53/+50
| | | | | | | | | | Correct an error I convinced Mike to introduce with the phread_once() code, :-( along with another one that wasn't my fault. Also, clean up warnings and restructure code in the thread-safe code a bit. Tested on: Mac OS X/32 10.6.4 (amazon) w/production + thread-safe (not a configuration that h5committest tests)
* [svn-r19377] Added bug 1938 resolutionAllen Byrne2010-09-131-0/+3
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* [svn-r19374] [BZ1938] - VS2010 on windows requires stdint.h to compile C++ ↵Allen Byrne2010-09-131-2/+6
| | | | | | library. CMake will check if c++ compiler supports stdint.h and set the H5_HAVE_STDINT_H_CXX define. Tested: windows and local linux
* [svn-r19370] Removed entry for m4 directory.Larry Knox2010-09-101-1/+0
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* [svn-r19369] Update MANIFEST for new m4 directory and macros. Directory and ↵Larry Knox2010-09-101-0/+6
| | | | | | files are for reconfigure and therefore marked _DO_NOT_DISTRIBUTE_. Tested on jam.
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