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* [svn-r17740] Description:Quincey Koziol2009-10-2418-253/+263
| | | | | | | | | | | | | | | | | | | | | | | Refactor v2 B-tree code to take creation parameters to H5B2_create() as a struct (instead of individual arguments), call the client's class "cls" instead of "type" internally, and add client class name to client class struct. 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17737] Description:Quincey Koziol2009-10-231-1/+7
| | | | | | | | | Fix error in dataset's chunk index v1 B-tree debugging code to correctly pass userdata down to B-tree cache load routine. Tested on: Linux 2.4/64 (chicago1) (too minor to require h5committest)
* [svn-r17736] mf.c test commented out. Assert hangs daily tests.Allen Byrne2009-10-231-1/+2
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* [svn-r17731] Correct batch file typoAllen Byrne2009-10-231-1/+1
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* [svn-r17726] Updated the errorlevel checking for better error handling in ↵Allen Byrne2009-10-2212-59/+164
| | | | the windows batch files.
* [svn-r17724] Merge change from 1.8 branch to trunk that removes ↵Larry Knox2009-10-222-3/+3
| | | | | | -D_POSIX_SOURCE from CPPFLAGS in h5cc. Tested: amani, jam, linew (h5committest).
* [svn-r17723] Bug fix:Albert Cheng2009-10-221-2/+3
| | | | | | | | | | The file failed to compiled in AIX which flags syntax error. Fixed by making the statements more explicitly compare with NULL and added a missing trailing semi-colon. Tested: Tested in AIX (Up at LLNL) only. The changes are trivial and should be portable to all platforms.
* [svn-r17722] Added tcheckversion windows project filesAllen Byrne2009-10-221-0/+2
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* [svn-r17721] Added new files:Allen Byrne2009-10-227-0/+860
| | | | | tlinks.cpp, tcheck_version.c and tcheckversion projects
* [svn-r17716] Cosmetic change to use exit(EXIT_FAILURE) instead of exit(1).Albert Cheng2009-10-212-4/+4
| | | | Tested: jam-pp.
* [svn-r17715] Fixed to exit failure if no command option is given.Albert Cheng2009-10-211-1/+1
| | | | Tested: Jam
* [svn-r17703] Bug fix: (1192)Albert Cheng2009-10-214-30/+32
| | | | | | | Changed exit(1) to exit(EXIT_FAILURE) and exit(0) to exit(EXIT_SUCCESS) for better coding. Tested: jam.
* [svn-r17700] Bug fix: (1192)Albert Cheng2009-10-211-19/+19
| | | | | | | | Comment says Error exit code is -1 but actual code use 1. Changed it to EXIT_FAILURE (1) and exit(0) to exit(EXIT_SUCCESS) for better coding. Tested: jam.
* [svn-r17697] Bug fix: (1192)Albert Cheng2009-10-202-3/+3
| | | | | | | | Error exit code of -1 is illegal (exit code is unsigned). Changed it to EXIT_FAILURE (1). Also changed exit(0) to exit(EXIT_SUCCESS) for better coding. Tested: jam.
* [svn-r17693] Removed the erroneous test of using v16 API.Albert Cheng2009-10-201-1/+0
| | | | | | | | | | | | | | | | | | | | | | | | The error started out as an erroneous test of using v16 API via source code. (See bug 1264). It was implemented as: #include "hdf5.h" #define H5_USE_16_API That was incorrect and generated warnings in Linux but error in AIX for redefining macro H5_USE_16_API. I corrected it yesterday to pass AIX by moving H5_USE_16_API up as: #define H5_USE_16_API #include "hdf5.h" This is the proper way to turn on v16API and it passes all normal tests. I knew it would not work if somehow v16API is disabled but hoping it can be fixed later. Well, it broke last night under --disable-deprecated-symbols. Removed the #define H5_USE_16_API and let Raymond fix it after the release.
* [svn-r17692] Description:Binh-Minh Ribler2009-10-201-0/+1
| | | | Added c++/test/tlinks.cpp
* [svn-r17690] Purpose: Code improvementBinh-Minh Ribler2009-10-207-85/+800
| | | | | | | | | | | | | | Description: Fixed CommonFG::getComment and CommonFG::getLinkval to provide default values for buffer size to improve usability. Added test file tlinks.cpp, which only contains test for getLinkval and will expand when C++ wrappers for H5L functions are implemented. Platforms tested: Linux/32 2.6 (jam) FreeBSD/64 6.3 (liberty) SunOS 5.10 (linew)
* [svn-r17688] Merge make local copy of svn test data files for write access ↵Larry Knox2009-10-206-140/+91
| | | | | | | from v1.8 to trunk. Tested: amani, jam, linew (h5committest).
* [svn-r17685] Bug fix:Albert Cheng2009-10-201-1/+1
| | | | | | | | | | | #define H5_USE_16_API was inserted AFTER #include <hdf5.>, too late was it to take effect. Instead, it caused a macro redefinition, flagged as an error by AIX. Fixed by moving it before the <hdf5.h>. Tested: Jam.
* [svn-r17680] Use absolute comparison for use-system-epsilon and default option.Peter Cao2009-10-191-2/+2
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* [svn-r17675] Purpose:Mike McGreevy2009-10-192-37/+67
| | | | | | | | | | | | | Configure Cleanup Description: Make all AM_CFLAGS visible in CFLAGS during configure so all checks have full visibility of any set flags. Tested: h5committest
* [svn-r17671] Removed these two options from the fortran flags:Albert Cheng2009-10-181-2/+2
| | | | | | | | | -qmoddir=. because -qmoddir defaults to current directory already. -static because it is not mentioned in "man xlf". Don't know it was a typo or just an obsoleted option. Removing both of them produced no ill or visible effects. Tested: Up of LLNL
* [svn-r17670] Snapshot version 1.9 release 49Larry Knox2009-10-1814-29/+29
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* [svn-r17667] Bug 1656 fix:Albert Cheng2009-10-181-3/+22
| | | | | | | | added a signal handler to the tcheck_version to intercept the abort signal from H5check_version. Some systems would prints extra messages and/or core dump if the abort signal is not handled. This eliminates those unwanted side effect. Tested: h5committested.
* [svn-r17663] Purpose:Mike McGreevy2009-10-163-469/+31
| | | | | | | | | | | | | | | | | | | | | | | | | | | configure cleanup Description 1. Removed check that disables shared libraries when pgcc is used. Apparently they previously did not work with libtool 1.5.14 and on mir, neither of which is in use anymore. Testing on jam and amani appear fine, so this check is unnecessary. 2. Removed check that disables shared C++ libraries when -xarch is used to enable 64 bit mode. We now use m64 flag to build 64 bit binaries, so we shouldn't explicitly disable shared C++ libraries if -xarch is discovered. 3. Removed old configure output summary section from configure.in, since we now use the libhdf5.settings file. 4. Updated powerpc-ibm-aix5.x config file to once again put c99 flag into H5_CFLAGS (and thus NOT get into h5cc), as decided in our dev meeting. Tested: h5committest full build with pgcc on jam / amani
* [svn-r17659] Changed the default fortran compilers from xlf and mpxlf_r toAlbert Cheng2009-10-161-4/+4
| | | | | | | | | | xlf90 and mpxlf90_r respectively. The fortran 90 compilers support free format source files. This allows the removal of -k so that the default compiler command is cleaner. Tested: AIX Up at LLNL. (Note: mpxlf90_r does not work but this could have been an undetected old problem.)
* [svn-r17658] Description:Quincey Koziol2009-10-158-721/+721
| | | | | | | | | | | | | | | | | | | | | | Rename 'H5B2_t' -> 'H5B2_hdr_t' and 'bt2' -> 'hdr' in preparation for make v2 B-tree open/close routines library private (instead of static). 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17657] Description:Quincey Koziol2009-10-157-211/+273
| | | | | | | | | | | | | | | | | | | | | | | Refactor the v2 B-tree code to use an open & close call internally, in preparation for making those part of the library private APIs for dealing with v2 B-trees. 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17654] Purpose:Mike McGreevy2009-10-1511-97/+97
| | | | | | | | | | | | Configure cache-val cleanup Description: Corrected some misnamed cache values in configure / config files. Tested: h5committest
* [svn-r17653] Add new H5B2hdr.c file to hdf5 project files.Allen Byrne2009-10-152-0/+8
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* [svn-r17649] Description:Quincey Koziol2009-10-1511-1251/+1245
| | | | | | | | | | | | | | | | | | | | | | Refactor v2 B-trees to pin the B-tree header in the cache instead of using separate reference counted data structure. 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17647] Maintenance: Configure didn't cleanup Fortran module file; fixed.Elena Pourmal2009-10-152-3/+3
| | | | | | | Platforms tested: jam (trivial change) Note: Most of the Fortran compilers create module files with "mod" extension. In the past, I believe, there were systems (Cray?) that used different extensions. We should add those to the current fix when we find them.
* [svn-r17646] 1. tools/h5repack/h5repack_main.c: accept string for strategy ↵Vailin Choi2009-10-158-202/+379
| | | | | | | | | | | | | | | | | | instead of a number 2. tools/h5stat/h5stat.c: clean up and activate options as stated in usage 3. tools/h5stat/testfiles/*.ddl: modified according to the latest output -This line, and those below, will be ignored-- M tools/h5repack/h5repack_main.c M tools/h5stat/testfiles/h5stat_newgrat.ddl M tools/h5stat/testfiles/h5stat_filters.ddl M tools/h5stat/testfiles/h5stat_help1.ddl M tools/h5stat/testfiles/h5stat_help2.ddl M tools/h5stat/testfiles/h5stat_tsohm.ddl M tools/h5stat/testfiles/h5stat_filters-F.ddl M tools/h5stat/h5stat.c
* [svn-r17644] Maintenance: Removed duplicated entry for socket library. It ↵Elena Pourmal2009-10-151-4/+3
| | | | | | | | | | was there for stream VFD. -lsocket is still used for linking, but it is added by libtool and not by us. Set up debug flags for Fortran. Platforms tested: linew 32 and 64-bit.
* [svn-r17643] Purpose:Mike McGreevy2009-10-144-76/+74
| | | | | | | | | | | | | | | | | | | Configure / Config File Fixes Description: 1. Made AM_CPPFLAGS assignments in configure a bit safer. (i.e., check to ensure include paths exist before adding them to AM_CPPFLAGS). 2. Change AIX config file to add -D_LARGE_FILES into AM_CXXFLAGS instead of H5_CXXFLAGS (same with *_CFLAGS). This will propagate it into h5c++, where it is needed to compile correctly. 3. Added missing line containing AM_CFLAGS to configure output summary. Tested: h5committest, and uP (AIX machine, via Albert).
* [svn-r17639] Purpose:Mike McGreevy2009-10-133-28/+46
| | | | | | | | | | | | | | | | | | | | | | | | | | Configure Fix Description: uP (AIX Machine) was failing because configure needs to see -k flag in FCFLAGS for some checks to behave as intended. Since the config files were switched to passing all flags into H5_FCCFLAGS, this broke this behavior. To allow configure to see this again, FCFLAGS and all other user flags are saved before doing anything, and restored at the end of configure, so if needed we can set these values in configure and/or the config/ files without (permanently) overriding or changing anything a user sets. Also modified the powerpc-ibm-aix5.x config file to once again put -k into FCFLAGS in addition to H5_FCFLAGS (the former of which will be restored after configure completes the checks). Tested: h5committest (jam and amani finished, linew still running, though I wanted to get this in for daily tests since it needs to be run on uP for final verification).
* [svn-r17636] Maintenance: Changed default fortran compiler for Mac Intel to ↵Elena Pourmal2009-10-131-46/+23
| | | | | | | | | | | gfortran Cleaned up the file to be inline with other config files that use multiple compilers. Platforms tested: My Mac pahra with gfortran, ifort and g95
* [svn-r17635] Bug 1192:Albert Cheng2009-10-131-0/+30
| | | | | | | Added EXIT_SUCEESS and EXIT_FAILURE macro values test. Tested: h5committested.
* [svn-r17631] Removed vnet assignments and allow default /vs8 and /ivf91 on ↵Allen Byrne2009-10-122-46/+41
| | | | | | command line. Tested: windows
* [svn-r17628] Snapshot version 1.9 release 48Larry Knox2009-10-1114-29/+29
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* [svn-r17627] Purpose:Mike McGreevy2009-10-094-21/+22
| | | | | | | | | | | | | | | | | | | Couple quick configure cleanups Description: - Made a few AM_LDFLAGS assignments a bit safer. - Regenerated a couple Makefile.in's via bin/reconfigure to address some typo-fixes that didn't propagate in my last check-in. Tested: - h5committest - Also, I suspect this fix will address a failure on Sandia's clogin2 machine, but Albert currently has no password to gain access, so I have only minimal logs of the failure and no way to test it there. I'll just let the automated tests there determine if indeed I'm right.
* [svn-r17626] Description:Quincey Koziol2009-10-091-2/+2
| | | | | | | | | | Correct error with initializing test file name in non-srcdir situation (like Windows) Tested on: Mac OS X/32 10.6.1 (amazon) FreeBSD/32 6.3 (duty) Windows
* [svn-r17625] Purpose:Mike McGreevy2009-10-091-12/+0
| | | | | | | | | | | | | MANIFEST Update Description: Updated MANIFEST to remove config/ files taken out of subversion in my last check-in. Tested: Ran bin/chkmanifest.
* [svn-r17624] Description:Quincey Koziol2009-10-097-67/+187
| | | | | | | | | | | | | | | | | | | | | | | Don't allow reads to change or add to the metadata accumulator, since they might be speculative and could bring raw data into the 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17623] Description:Quincey Koziol2009-10-0932-1224/+2086
| | | | | | | | | | | | | | | | | | | | | | Bring "compress group's fractal heap" feature from branch back to 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17619] Add comments about h5diff change made for epsilon.Peter Cao2009-10-081-0/+3
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* [svn-r17616] Purpose:Mike McGreevy2009-10-0899-2101/+991
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | CFLAGS overhaul Description: Modified the way configure handles CFLAGS. (note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS). 1. The configure process will now always preserve a user's CFLAGS environment variable setup. Any additional flags necessary for compilation added at configure time will be passed into the Makefiles as AM_CFLAGS, which is an automake construct to be used in addition to CFLAGS. This will allow a user to have the final say, as CFLAGS will always appear later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS during make will no longer completely erase all flags set by configure, since they're maintained in AM_CFLAGS. 2. Additionally, where possible, flags previously being assigned directly into CFLAGS (and thus propagating into h5cc) have now been redirected into H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into the h5cc wrapper script as well. *Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the Makefiles. Complete description of changes and build process will be included in a Configure Document that Elena and I are working on. 3. Removed unsupported config files. This includes: config/dec-osf* config/hpux11.00 config/irix5.x config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* 4. Modified configure summary to display additional values. Specifically, appropriate AM_* variables are being shown, as well as H5_FCFLAGS and H5_CXXFLAGS, which were for some reason not already present. Tested: - H5committest - Tested on all THG / NCSA machines, using several combinations of the more prominent configure options (c++, fortran, szip, threadsafe, parallel, et cetera). (Thanks to Quincey for rysnc testing setup!) - With regards to new automated testing, anything *necessary* for compilation will be caught by the daily tests as it stands now. (i.e., if LDFLAGS is not properly set when szip is used, linking will fail). Additionally, with regards to which flags get into h5cc, if any *necessary* flags have been improperly removed, then daily tests should fail during make installcheck. Additional machine-specific desired behaviors and/or checks may have to be set up separately within the daily tests, so this is something to work on.
* [svn-r17615] Updated with H5Pget_preserve fix information.Albert Cheng2009-10-081-0/+1
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* [svn-r17611] Bug fix (ID 1628):Albert Cheng2009-10-082-3/+15
| | | | | | | | | There was a typo in the H5Pget_preserve that it was returning the wrong value. Fixed. Also added a test in test/cmpd_dset.c to verify the correctness of H5Pset_preserve and H5Pget_preserve. Tested: h5committest plus jam serial.
* [svn-r17606] Code Cleanup:Albert Cheng2009-10-0710-276/+25
| | | | | | | | TFLOPS machine has retired long ago. Removed all code specific for its support. Test: h5committested.
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