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* [svn-r17616] Purpose:Mike McGreevy2009-10-082-11/+18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r17606] Code Cleanup:Albert Cheng2009-10-071-5/+0
| | | | | | | | TFLOPS machine has retired long ago. Removed all code specific for its support. Test: h5committested.
* [svn-r17345] Purpose:Mike McGreevy2009-08-121-49/+97
| | | | | | | | | | | | | | | | | | | | | | | | Updating autotools Description: Installed new autotools and used them to reconfigure HDF5. - Automake upgraded to 1.11 - Autoconf upgraded to 2.64 - bin/reconfigure script edited to use new versions (on jam), and run to generate new configure script and Makefile.in's. - configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings (in order to comply with new autoconf standard). Tested: Tested on machines jam, smirom, liberty, linew. Tested w/ features c++, fortran, parallel. Tested w/ compilers gcc, pgcc, icc. Further testing via Daily Tests should catch any other outliers. Upon passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
* [svn-r17268] Description:Quincey Koziol2009-07-301-1/+1
| | | | | | | | | | | Bring r17266 from 1.8 branch to trunk: Clean up various compiler warnings from IRIX64 build Tested on: Mac OS X/32 (amazon) debug & production (yes, I know it's not an IRIX64 system :-) Too minor to require h5committest
* [svn-r17228] Purpose:Mike McGreevy2009-07-232-2/+16
| | | | | | | | | | | | | | | | | | | | | | | Fix BZ #1583 Description: The --enable-static-exec flag was broken. Configure was adding the -all-static linker flag to an environment variable which was subsequently never used. (looks like it was used in 1.6 Makefile.ins, but never moved to 1.8's Makefile.ams when we added automake support). To fix, I've added this environment varibale to the link lines of all the tools. Now, when --enable-static-exec is invoked, it will correctly generate statically linked executables in the installed bin directory. Tested: I've tested manually to ensure that the generated execs are static when the flag is used and dynamic when not. I've also tested when szip is used, as this was a use case mentioned in the bug report. Also: ran full tests with make check on jam and smirom for good measure.
* [svn-r16969] Updated perf_serial test to work on windows.Allen Byrne2009-05-214-229/+235
| | | | | Tested: Windows and h5committest
* [svn-r16807] Purpose: Fix bug 1533Neil Fortner2009-04-201-1/+1
| | | | | | | | | | | Description: Previously, there was no versioning for H5Z_class_t. This prevented applications written for 1.6 using custom filters from being able to use the 1.8 library. There is now an H5Z_class1_t and H5Z_class2_t to enable compatibility. H5Zregister is *not* versioned, it determines which version of the struct has been passed in by the value of the first field (id or version, both are ints). Tested: jam, linew, smirom (h5committest), jam (--with-default-api-version=v16)
* [svn-r16792] Description:Mike McGreevy2009-04-201-4/+4
| | | | | | | | | | | | - Updated bin/reconfigure to use latest version of automake (1.10.2). Re-generated Makefile.in's by running bin/reconfigure. - Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran libraries. Tested: jam, liberty, smirom
* [svn-r16561] Purpose:Mike McGreevy2009-03-101-3/+3
| | | | | | | | | | | | | | | | | | Bug Fix Description: Fixing BZ #1381. The --includedir=DIR configure option, which is used to specify the installation location of C header files, did not work correctly as the path was hard-coded in config/commence.am. I'm presuming this is because an older version of automake didn't know where to put c header files. In any case, removing this line now defaults the includedir to the same directory that it is currently hard-coded to, and also fixes the configure flag to allow customization of this value. Tested: jam, liberty
* [svn-r16560] Description:Quincey Koziol2009-03-105-449/+404
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r16518] have 2 expected outputs for 2 h5ls runs depending if run on a ↵Pedro Vicente Nunes2009-02-261-0/+1
| | | | | | | big or little endian machine. Configure.in was modified to export a variable carrying endianess information to testh5ls.sh. This script then compares the current run with 2 expected outputs, one for a big-endian machine (linew was used to generate the output), other for little endian (jam was used to generate the output) the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other tested: h5committest
* [svn-r16489] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-186-93/+56
| | | | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 Vista 32, VS2005, IVF101 XP32, Cygwin
* [svn-r16340] Description:Frank Baker2009-01-221-1/+1
| | | | | | Changed 'THG' to 'The HDF Group' in various HDF5 source files, most of which are <subdirectory>/COPYING. -- Closes Bugzilla entry 1403.
* [svn-r16170] Code clean up.Albert Cheng2008-12-091-13/+12
| | | | | | | Function get_unique_name() had potential string overflow problem. Fixed. Also removed some unused macros. Tested by h5committest.
* [svn-r16167] Bug fix: 1089Albert Cheng2008-12-091-3/+3
| | | | | | | | | | | | Description: One open() call with O_CREAT flag did not have the third required argument. Solution: Added the right third argument. Also changed all open() calls to HDopen macros for more portable coding. Tested: h5committested.
* [svn-r15957] Revised the help page of h5perf.Christian Chilan2008-10-261-27/+49
| | | | Tested on kagiso.
* [svn-r15942] Purpose: Bug Fixes and Libtool UpgradeMike McGreevy2008-10-241-6/+6
| | | | | | | | | | | | | | | | | | Description: - Remove need to set LD_LIBRARY_PATH when using shared szip library. - Libtool 2.2.6a is now used to generate libraries. - 'make check install' dependency bug is fixed, and should no longer break the build. - removed hard coding of shell in config/commence.am, as this causes problems on Solaris with the new version of libtool. - RELEASE.txt with appropriate changes. Tested: - kagiso, smirom, linew (merged from 1.8, pretty quick tests)
* [svn-r15832] Modified the display of the accumulated times taken to open and ↵Christian Chilan2008-10-091-1/+1
| | | | | | close files. Tested on kagiso.
* [svn-r15808] Some test produced files were not cleaned by "make clean".Albert Cheng2008-10-082-2/+2
| | | | | | Added them to the clean list. Tested: kagiso, serial and parallel.
* [svn-r15772] Added feature to display file open and close times.Christian Chilan2008-10-031-4/+39
| | | | Tested on kagiso and cobalt.
* [svn-r15665] Bug fix: (ID 1157)Albert Cheng2008-09-191-2/+4
| | | | | | | | | | | | | | | | | | | Description: Program would crash, complaining MPI calls were invoked after MPI_Finalize() has occurred. Previously, H5close() before MPI_Finalize() would remove the crash. Solution: It turned out that two H5 property objects (mpio_pl and acc_tpl) were not closed before MPI_Finalize(). In the at_exit code, HDF5 library attempted to close them by releasing the MPI Communicators in them too. That was the error. Adding code to close them properly before MPI_Finalize() took care things. Tested: Only in kagiso parallel. Did not run h5committest since kagiso would have been the one running parallel test. This part of code would not be compiled at all in non-phdf5 mode.
* [svn-r15655] Changed the absolute path of the data file to a relative path.Christian Chilan2008-09-181-3/+7
| | | | Tested on kagiso, smirom, and linew.
* [svn-r15649] Included macros for portability of h5perf code among HDF5 versions.Christian Chilan2008-09-171-13/+35
| | | | Tested on kagiso, abe, and cobalt.
* [svn-r15628] Description:Quincey Koziol2008-09-163-68/+68
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15582] Added script to build h5perf_serial in standalone mode.Christian Chilan2008-09-021-0/+28
| | | | Tested on kagiso, smirom, and linew.
* [svn-r15563] Added support for serial prefix HDF5_PREFIX.Christian Chilan2008-08-292-20/+14
| | | | Tested on kagiso, smirom, and linew.
* [svn-r15397] Update to the h5perf files that includes bug fixes and extensions.Christian Chilan2008-07-233-2158/+2402
| | | | Tested on kagiso and abe.
* [svn-r15179] Change copyright notice to THG only.Christian Chilan2008-06-097-7/+0
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* [svn-r15150] Purpose: Separate Windows function macro definitions to win32defs.hScott Wegner2008-06-051-4/+4
| | | | | | | | | | | | | | Description: In library code, we try not to use system calls directly, but instead use the HD{function} macro instead. This way, we can map special versions of the call on particular systems. Previously, it was all done in H5private.h. However, in an effort to clean up platform-specific definitions, we move all of the Windows macros into a separate file, win32defs.h. This way, we can use the non-Posix versions that Visual Studio sends warnings about. Some macros are set specifically in the platform-specific header files. Then, any macros left unset will be set by the "default" implementation in H5private.h. This checkin also cleans up various source files to use the HD* macros when possible. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagiso, linew, smirom)
* [svn-r15149] Purpose: Bug FixMike McGreevy2008-06-052-2/+2
| | | | | | | | Description: Changing h5perf installation so only h5perf is installed when parallel is enabled, while only h5perf_serial is installed when parallel is disabled. Tested: kagiso
* [svn-r15090] Revise copyright notice.Christian Chilan2008-05-292-4/+6
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* [svn-r15043] Bug fix.Albert Cheng2008-05-201-2/+4
| | | | | | | | | | | | | | | | | | Description: perf would crash at the end as it complained it was doing MPI calls after MPI_Finalize() is called. I suspect the HDF5 library is making MPI calls in the at_exit area. This should not happened. Solution: Added the H5exit() right before MPI_Finalize() fixed the problem. But it needs to find out why HDF5 library is making MPI calls in the at_exit() area. It should not. Also, changed the temporay data file name from /tmp/test.out to perftest.out, both to avoid multiple instance of this may use the same /tmp/xxx name and also make the file name less generic. Tested: Kagiso PP.
* [svn-r15041] Purpose: Configure FixMike McGreevy2008-05-192-4/+0
| | | | | | | | Description: Removing make target "check-perform". The extra target is unneeded because the perform tests don't take as long to run as initially anticipated, and can be lumped in with 'make check'. Tested: kagiso
* [svn-r15036] Bug fix.Albert Cheng2008-05-191-4/+4
| | | | | | | | | | | | | | | | | | | Description: The fortran Makefile.am used HDF_FORTRAN to indicate it is part of the Fortran API source so that conclude.am will give fortran api prefix in the test output. The symbox HDF_FORTRAN is also used in configure for a different purpose (indicated --enable-fortran). They conflicted. Similar problem for the symbol HDF_CXX. Solution: Changed all the involved Makefile.am to use "FORTRAN_API" instead. It is a more appropriate name. Same for CXX_API. Along the way, discovered that the Makefile.am of hl/fortran/test and hl/cxx/test did not have those symbols at all. Added them in. Platform tested: Kagiso only. It is a trivia change.
* [svn-r15023] Revise man page of the serial benchmarking tool.Christian Chilan2008-05-161-3/+3
| | | | Tested on kagiso, smirom, and linew.
* [svn-r15009] Revise file of the serial benchmarking tool to include new man ↵Christian Chilan2008-05-151-83/+51
| | | | | | page. Tested on kagiso, smirom, and linew.
* [svn-r15007] Purpose: configure cleanupMike McGreevy2008-05-151-1/+0
| | | | | | | Description: cleaning up configure related to removal of --disable-hsizet flag, which we no longer support. Tested: kagiso
* [svn-r15003] Purpose:Albert Cheng2008-05-151-0/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Improvement. Description: src/libhdf5.settings was the initial configure summary and is installed. Then configure is changed to dump a summary of the configure settings to the output and also append it to src/libhdf5.settings. That created two different output formats and duplicated information. This is the initial attempt to clean up this confusion and unify the output format. It is decided to use the src/libhdf5.settings template as the unified means. This requires more macros symbols be defined. The following symbols are all related to generating the src/libhdf5.settings file. AC_SUBST(EXTERNAL_FILTERS) AC_SUBST(MPE) MPE=no AC_SUBST(STATIC_EXEC) STATIC_EXEC=no AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no AC_SUBST(FC) HDF_FORTRAN=no AC_SUBST(HDF_CXX) HDF_CXX=no AC_SUBST(CXX) HDF_CXX=no AC_SUBST(HDF5_HL) HDF5_HL=yes AC_SUBST(GPFS) GPFS=no AC_SUBST(LINUX_LFS) LINUX_LFS=no AC_SUBST(INSTRUMENT) INSTRUMENT=no AC_SUBST(CODESTACK) CODESTACK=no AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no AC_SUBST(DIRECT_VFD) DIRECT_VFD=no AC_SUBST(THREADSAFE) THREADSAFE=no AC_SUBST(STATIC_SHARED) AC_SUBST(enable_shared) AC_SUBST(enable_static) AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a` The src/libhdf5.settings.in has CONDITIONAL's added to it too. The untrue conditions turned into a "#" and these lines are cleaned by the post processing script. Platform tested: h5committest on kagiso, smirom and linew.
* [svn-r14969] Purpose: Bug Fix (Bug 1144)Mike McGreevy2008-05-122-17/+63
| | | | | | | | | | | | | Description: Tests in perform directory were never getting run, and h5perf* programs were not being installed. Solution: Added another build option, 'make check-perform', which runs the tests in the perform directory. Also modified the Makefiles in the perform directory to install (with 'make install') h5perf when parallel is enabled, and h5perf and h5perf_serial when parallel is disabled. Tested: kagiso, smirom, linew
* [svn-r14933] Purpose: Updating HDF5 to use automake 1.10.1 and libtool 2.2.2Mike McGreevy2008-05-051-14/+18
| | | | | | | | | | | | | | | | | | Description: Applying update to autotools that was applied to 1.8 a couple of weeks ago to the trunk. Updated bin/reconfigure script to reflect the new versions of libtool and automake in the /home1/packages/ directory. Rearranged configure.in script. When using libtool 2.2.2, the libtool script doesn't generate until later in the configuration process, so I had to move a test that parsed through the libtool script to a point after where it was actually being generated. Ran libtoolize on the project, and ran bin/reconfigure to regenerate configure and Makefile.in's throughout. Tested: kagiso, smirom, linew (h5committest)
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-309-7/+4424
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-309-4424/+7
| | | | New fortran wrappers added.
* [svn-r14831] Revise file of the serial benchmarking tool.Christian Chilan2008-04-121-9/+6
| | | | Tested on kagiso, smirom, linew, and tg-login.
* [svn-r14829] Revised files of the serial benchmarking tool.Christian Chilan2008-04-112-8/+6
| | | | Tested on kagiso, smirom, and linew.
* [svn-r14827] Makefiles configured to build and test the serial benchmarking ↵Christian Chilan2008-04-102-7/+24
| | | | | | tool. Tested on kagiso, smirom, and linew.
* [svn-r14826] Files for the serial benchmarking tool, h5perf_serial.Christian Chilan2008-04-105-0/+4132
| | | | Tested on kagiso, smirom, and linew.
* [svn-r14825] Files for the serial benchmarking tool, h5perf_serial.Christian Chilan2008-04-102-0/+273
| | | | Tested on kagiso, smirom, and linew.
* [svn-r14402] Description:Quincey Koziol2008-01-131-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add work-around to allow reading files that were produced with a buggy earlier version of the library, which could create objects with the wrong object header message count. There is now a configure flag "--enable-strict-format-checks" which triggers a failure on reading a file with this sort of corruption (when enabled) and allows the object to be read (when disabled). The default value for the "strict-format-checks" flag is yes when the "debug" flag is enabled and no when the "debug" flag is disabled. Note that if strict format checks are disabled (allowing objects with this particular kind of corruption to be read) and the file is opened with write access, the library will re-write the object header for the corrupt object with the correct # of object header messages. This closes bugzilla bug #1010. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14218] Description:Quincey Koziol2007-10-301-6/+6
| | | | | | | | | | | | | | | | | | | | | Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with other new API routines. Re-added simpler form of H5Acreate2, which creates attributes directly on an object. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14199] Description:Quincey Koziol2007-10-117-73/+69
| | | | | | | | | | | | | | | | | | | | | Add H5Dcreate to API versioned routines, replacing internal usage with H5Dcreate2 Fix thread-safe error stack initialization for API versioned error stack printing routines. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
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