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* merged NAG changes from develop, (HDFFV-10037)M. Scot Breitenfeld2017-08-031-0/+58
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* Change copyright headers to replace url referring to file to belrknox2017-05-161-6/+4
| | | | removed and replace it with new url for COPYING file.
* [svn-r29692] Applied fix for HDFFV-9439 to mpicc config as well as mpif90 in ↵Larry Knox2016-04-131-0/+1
| | | | | | config/linux-gnulibc1. Tested with h5committest.new on kituo, ostrich, osx1010dev and platypus.
* [svn-r29688] Merge of r29090 from trunk.Dana Robinson2016-04-131-1/+1
| | | | | | | | | Changes smart quotes to ASCII quotes in autotools gnu config file. Additional fix for HDFFV-9439. Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial w/ Fortran autotools parallel (MPICH 3.1.4) w/ Fortran
* [svn-r29687] Fix for HDFFV-9439 (previously in trunk).Larry Knox2016-04-121-0/+1
| | | | Tested with h5committest.new on kituo, ostrich, osx1010dev and platypus.
* [svn-r26674] merged r26657 and r26642 from the trunk into the branch.Scot Breitenfeld2015-03-311-4/+20
| | | | tested: h5committest
* [svn-r25017] Merge r24997 changes from trunk.Larry Knox2014-04-111-1/+20
| | | | | | | | | | | | | Added compiler versions for mpich to settings file and configure summary. For make installcheck, compile and run installed examples using the installed scripts. They were being compiled but not run. Add Fortran2003 examples to the run-ex-fortran script when fortran2003 is enabled. Set flag to -O3 in production mode for Intel compilers other than those with specified other settings. Gentoo patches: Remove unnecessary setting of LD_LIBRARY_PATH from configure. Prevent potential array subscript out of bounds error in perform/pio_engine.c and sio_engine.c. Tested with h5committest on jam, koala, ostrich and platypus.
* [svn-r21479] Merge revision 21101 from trunk to 1.8 branch:Mike McGreevy2011-10-051-17/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-7639 Purpose: Remove H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS and H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS #defines from source. Description: Two advanced parallel functionalities, special collective IO and complex derived datatypes, are not supported by older implementations of mpi, and thus our code limits the use of these features with #ifdefs and has checks in configure to set them (or not). Unfortunately, configure can't actually run a parallel check to see if these features are working (nor not) so it resorts to looking in the config files where they are explicity enabled or disabled based on versions of mpi, sytems being built on, or for no documented reason at all (i.e. just set to on or off as some 'default'). Overriding these settings is easy if need be, provided it is known that it needs to be done to get improved performance, and oftentimes it is not. Most new MPI implementations successfully handle the functionality requested when these #defines are set, and many of the "turn these features off" cases in the config files are for old (> 5 years) versions of MPI and retired systems (such as NCSA's tungsten). Therefore, the decision has been made to remove the support for these old versions of MPI and systems that cannot handle these behaviors. The #ifdefs and supporting setup in the config/ files and configure script has been removed, and the code executed when these options were not set removed from the source. In passing, this commit also cleans up some whitespace issues in both t_mpi.c and H5Dmpio.c. Furthermore, in t_mpi.c, the special collective IO test was not getting regularly run due to it being written to work only with four processes (we regularly test with six, previously with three), and thus it failed when actually run due to an out of bounds data buffer assignment. It has been modified to run at any number of processes greater than four, and the memory problem has been fixed so the test passes. Tested: Jam, h5committest, Ember
* [svn-r20059] Changed Linux system to use mpicc as the default parallel C ↵Albert Cheng2011-02-071-2/+8
| | | | | | | | | compiler. mpif90 is already the default parallel Fortran if mpicc is the C compiler. Tested: Amani (serial and parallel). No need for committest since this change is limited to Linux system.
* [svn-r18836] Added code to config files, libhdf5.settings.in and ↵Larry Knox2010-05-171-1/+89
| | | | | | configure.in to add compiler version information for fortran and C++ in the settings file and the configure output for our common compilers on linux, solaris, and mac(gnu only). Tested: amani, jam, linew (h5committest) and with configure on these machines and tejeda.
* [svn-r17655] Purpose:Mike McGreevy2009-10-151-4/+4
| | | | | | | | | | | | Configure cache-val cleanup Description: Corrected some misnamed cache values in configure / config files. Tested: h5committest
* [svn-r17197] Changed default Gnu fortran compiler from g95 to gfortran sinceAlbert Cheng2009-07-191-2/+2
| | | | | | | | | gfortran is more likely installed with gcc now. Tested: jam and amani which covers both linux and linux64. No h5committest because this is gnu compiler specific, usually applicable to Linux.
* [svn-r15605] The MPI compiler(mvapich2-0.9.8p2patched-intel-ofed-1.2) at ↵MuQun Yang2008-09-081-1/+3
| | | | | | | | | NCSA's linux cluster(Abe) fails to handle collective IO calls with very complicate MPI derived datatype. All the values of input parameters from HDF5 are correct before passing to MPI-IO collective calls. Sometimes the following errors happen: rank 0 in job 77 honest1.ncsa.uiuc.edu_60945 caused collective abort of all ranks exit status of rank 0: killed by signal 9 Up to this point, we decide to turn off the use of advanced MPI derived datatype features inside HDF5 so that complicated selection tests are ensured to be handled by HDF5. This check-in reflects this.
* [svn-r14096] There're 3 changes in this checkin as below:Raymond Lu2007-08-201-0/+10
| | | | | | | | | | | | | | | | | | 1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes in an empty buffer. This is mainly for MPIO programs that some processes may not have any data to write or read but still participate the I/O. This solution solves some MPI's problem like the ChaMPIon on tungsten which doesn't support empty buffer. 2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective I/O when some processes don't have any data to write or read correctly. Detect the compiler "cmpicc" in the system-specific config file and set the variables for these two cases to false. The PHDF5 library already has set up a way to switch collective chunked I/O to independent under these two cases. 3. A bug fix - During the work of the optimization for compound data I/O, the case for switching collective chunked I/O to independent I/O was leftout. Fixed it by adding I/O caching to it in H5D_multi_chunk_collective_io in H5Dmpio.c. Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
* [svn-r13324] Changed the default Fortran compiler for gcc from pgf90 to g95.Albert Cheng2007-02-171-2/+6
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* [svn-r13312] Updated copyright notice.Albert Cheng2007-02-141-2/+3
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* [svn-r12765] Description:Elena Pourmal2006-10-161-2/+2
| | | | | | | | | | Daily tests failed for Absoft f95 compiler Solution: Failure was due to several typos in H5f90prpto.h file; fixed I also removed redundant flags from the configration files. Platforms tested: heping with f95, g95, pgf90; pommier with f95
* [svn-r12301] Purpose:James Laird2006-04-251-2/+2
| | | | | | | | | | | | | | H5_CFLAGS change Description: Converted a few platforms to use H5_CFLAGS to "test the waters" Solution: Modified a few config/* files to use H5_CFLAGS for non-essential flags. Platforms tested: mir, heping
* [svn-r11962] Purpose:MuQun Yang2006-02-211-1/+1
| | | | | | | | | | | | | The previous check-in seems fixing the non-selection failure at heping. Description: release the special_collective_io_works macro at this platform. Solution: Platforms tested: heping mpich 1.2.6 Misc. update:
* [svn-r11942] Purpose:MuQun Yang2006-02-161-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add collective chunk IO supports Description: Added a macro hdf5_mpi_special_collective_io_works to filter out some mpi-io packages that don't support collective IO for no IO contributions in some processes. Solution: 1. "hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works= 'no'}" has been added at the end of file ia64-linux-gnu and linux-gnulibc1 2. Some comments are added in ia64-linux-gnu and linux-gnulibc1. 3. Documents are added inside RELEASE.txt. Platforms tested: Parallel: IBM AIX 5.2(copper) Linux (heping) mpich-1.2.6 SDSC Teragrid mpich-1.2.5 Linux(Tungsten) mpich-1.2.6 Altix(NCSA cobalt) Seq: Linux(heping) Misc. update:
* [svn-r11614] Frank Baker2005-10-281-1/+1
| | | | | | | Description: Correct typo in copyright notice. Platforms tested: Ran hdf5/bin/chkcopyright without errors.
* [svn-r11610] Purpose:Albert Cheng2005-10-261-16/+2
| | | | | | | | | | | | | | | | | | | | | | | | Bug fix. Description: The previous way of detecting the MPICH version fails if the suspected $CC does not give the expected MPICH version information. Though no consequence, it generates error messages that alarm users. Also, mpich2 gives the version information as if it were mpich v1.0.2 which was incorrectly included as an earlier version of the origianl mpich. Solution: Implemented a more robust code to detect the version and narrow the recognition down to v1.2.0-v1.2.5. Also, the code were duplicated in two files (linux-gnulibc1 and ia64-linux-gnu). Combined them into a new file called mpich. Platforms tested: Tested in heping using mpicc and mpich2/mpicc and also in tg-ncsa. Misc. update: Updated MANIFEST.
* [svn-r11592] Frank Baker2005-10-211-0/+13
| | | | | | | | Description: Add source code copyright notice; comment symbols vary by type of file. Platforms tested: No changes that should cause any problems. Nonetheless, the tree will be checked out fresh and tests run immediately post-commit.
* [svn-r11461] Purpose:James Laird2005-09-221-17/+0
| | | | | | | | | | | | | | | Code cleanup Description: Removed Fortran type sizes from config/* files. Solution: These lines weren't doing anything anymore; they've been replaced by automatic type generation. This is just housekeeping to remove them from the config/* files. Platforms tested: mir, sol, modi4
* [svn-r11405] Purpose:Leon Arber2005-09-131-0/+92
| | | | | | | | | | | | | | | Bug fix Description: A whole chunk of this file somehow got deleted and the heavily reduced file was accidentally checked in. This is the complete version of the file, with the mpiicc fix. Solution: Platforms tested: Misc. update:
* [svn-r11397] Purpose:Leon Arber2005-09-131-1/+0
| | | | | | | | | | | | | | | | Bug fix Description: Forgot to remove a debug statement before committing. Solution: The script printined out what it thought CC_BASENAME was for debugging. Removed this print statement. Platforms tested: minor change, mcr Misc. update:
* [svn-r11394] Purpose:Leon Arber2005-09-121-93/+2
| | | | | | | | | | | | | | | Bug fix Description: Same bug as was just checked in for v16. Do the complicated derived datatype check for compilers named mpiicc in addition to mpicc. Solution: Platforms tested: Misc. update:
* [svn-r11065] Purpose:MuQun Yang2005-07-121-0/+17
| | | | | | | | | | | | | | | | Updating phase 2 work of collective IO Description: When the size is bigger than some value for MPI derived data type, mpich 1.2.5 and lower version won't work any more, so in the configuration file, we will check the version number and switch from collective IO to independent IO by turning off complex derived datatype. Solution: Platforms tested: linux 2.4, AIX 5.1, Linux 2.4 IA64 and IRIX 6.5 Misc. update:
* [svn-r10158] Purpose:James Laird2005-03-071-16/+16
| | | | | | | | | | | | | | | | | | | | | | Automake version upgrade Description: Upgraded automake version from 1.6.2 to 1.9.5. Changed bin/reconfigure script to use automake 1.9.5. Changed configure.in and Makefiles to use new FCFLAGS and FC variables instead of FFLAGS and F9X. Automake and configure should now do the lion's share of the work supporting Fortran 9X; macros in acsite.m4 are now mostly unused (will be cleaned later). Altered how configure handles pmake; now root-level Makefile.in is processed by bin/reconfigure to have a .MAKEFLAGS target, since automake no longer allows us to define unused variables. Configure now always checks for C++ compiler even if it is not used, since automake thinks this is the Right Thing To Do and will break otherwise. Platforms tested: Sol, copper, heping, mir, sleipnir, eirene, pommier, kelgia, modi4.
* [svn-r9801] Purpose:Quincey Koziol2005-01-101-0/+1
| | | | | | | | | | | | Bug fix Description: Belatedly chase change of hobj_ref_t in C APIs. Platforms tested: FreeBSD 4.10 (sleipnir) w/backward compatibility turned on IRIX64 6.5 (modi4) w/FORTRAN h5committest
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r9491] Purpose:Quincey Koziol2004-10-311-13/+21
| | | | | | | | | | | Bug fix Description: "Teach" the configure scripts about Intel 7.1 compilers, which don't have _quite_ the same compiler flags Platforms tested: Linux 2.4 (eirene)
* [svn-r9404] Purpose:Quincey Koziol2004-10-121-0/+4
| | | | | | | | | | | | Code cleanup Description: Default to using mpif90 if CC=mpicc and --enable-fortran flag is given, but no F9X compiler is set. Platforms tested: Linux 2.4 (verbena) Too minor to require h5committest
* [svn-r9385] *** empty log message ***Quincey Koziol2004-10-091-45/+49
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* [svn-r8966] Purpose: MaintenanceElena Pourmal2004-07-291-11/+49
| | | | | | | | | | | Description: Added support for Absoft Fortran compiler Solution: Modified configuration file to check which Fortran compiler is used and set appropriate flags. Platforms tested: verbena with pgf90 and Absoft f95 compilers Misc. update:
* [svn-r7854] Purpose:Bill Wendling2003-11-141-1/+1
| | | | | | | | | | | | | | | | | | Bug Fix Description: The FFLAGS, CXXFLAGS, and CPPFLAGS variables weren't carrying user-defined values into the Makefiles. Solution: Changed the flags from FOO="..." to FOO="$FOO ..." Platforms tested: Copper Verbena Arabica Misc. update:
* [svn-r7269] Purpose:Bill Wendling2003-07-281-0/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | Update Description: Revamped the configuration system. The configurations for the Fortran and C++ libraries are no longer separate from the "main" configuration system. This involved removing the "configure*" and "aclocal.m4" files from the fortran/ and c++/ subdirectories. Also merging settings in the config/ subdirectories into the main config/ subdirectory. Fortran header files had to be modified a little for Linux. It was checking if it was a Linux machine by some #defines, however with the -std=c99 switch, these defines weren't there. I added a check for some other ones which should be there whether the -std=c99 switch is used or not. Platforms tested: Verbena (Fortran & C++) Sol (Fortran & C++) Copper (Fortran & C++) Modi4 (Parallel, Fortran, & C++) Misc. update:
* [svn-r3452] Purpose:Bill Wendling2001-02-191-3/+3
| | | | | | | | | | | Fix Description: The "make *clean" options weren't recursing through the subdirectories (if they exist). Solution: Force it to recurse through the subdirectories listed in SUBDIRS Platforms tested: Linux
* [svn-r1204] Changes since 19990415Robb Matzke1999-04-231-3/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./config/depend.in Fixed automatic dependencies. We were storing dependencies for *.o files instead of *.lo files after shared libraries were added. ./config/gnu-flags ./config/linux-gnulibc1 Moved `-march=pentiumpro -mcpu=pentiumpro -malign-double' from the linux file to this file and caused it to depend on the CPU name. This fixes one of Elena's bugs. ./src/H5B.c ./src/H5Bprivate.h ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h ./src/H5F.c ./src/H5Farray.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fprivate.h ./src/H5Fpublic.h ./src/H5Gnode.c ./src/H5P.c ./src/H5RA.c ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Smpio.c ./src/H5Spoint.c ./src/H5Sprivate.h ./src/H5Tpublic.h ./test/istore.c Added an H5Dget_storage_size() function that reports the amount of storage allocated for raw data in a dataset. Changed H5D_xfer_* to H5F_xfer_* because these properties are more general than datasets. This also allows some of the lower-level I/O functions to get this information easier. ./src/H5S.c ./src/H5Sall.c Added two new functions H5S_all_read() and H5S_all_write() which are optimizations that copy data directly between file and memory without having to go through the scatter gather step. This knocks quite a bit of time off the I/O and reading/writing entire datasets is a fairly common operation. ./tools/h5ls.c Reports the logical size of data, the allocated size of data, and the percent utilization. ./MANIFEST Removed old pablo files, added new files. Snapshots should now start to work again. ./src/H5D.c ./src/H5Fmpio.c Removed two warnings signed vs. unsigned comparisons and check for overflow.
* [svn-r1151] Changes since 19990318Robb Matzke1999-03-191-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./Makefile.in ./configure.in ./configure [REGENERATED] ./src/H5config.h.in [REGENERATED] ./config/commence.in ./config/conclude.in ./config/dec-osf4.x ./config/depend.in ./config/freebsd ./config/linux-gnu ./config/linux-gnulibc1 ./config/linux-gnulibc2 ./config/solaris2.x ./examples/Makefile.in ./src/Makefile.in ./test/Makefile.in ./testpar/Makefile.in ./tools/Makefile.in ./tools/testh5dump.sh Changes that allow hdf5 to be configured and compiled in a directory other than the source directory. This is especially useful if you want to concurrently compile with different compilers and/or compile flags, or if the hdf5 source is on read-only media like a CDROM. The changes were surprisingly easy ;-) Here's what you can do now... $ mkdir /tmp/build1 # or something $ cd /tmp/build1 $ /cdrom/hdf5/configure # where ever the source is $ make Paul, you'll have to change the testh5toh4 script similar to the way I changed testh5dump.sh. I started working on it but then gave up because of a number of problems: (1) I had to comment out all the tests that let h5toh4 choose the output file name because it always tried to put the output file in the same directory as the input file, (2) if path names are used during the h4 dump then they interfere with the diff. The test works fine when run in the source directory, but try this instead: $ gunzip <hdf5-1.1.67.tar.gz |tar xf - $ chmod -R ugo-w hdf5-1.1.67 $ mkdir build $ cd build $ ../hdf5-1.1.67/configure $ make check Dan, I didn't modify the pablo/Makefile.in because I have no way to test it. I think all you need to do is add a couple lines before the @COMMENCE@ line and add a couple search directories for header files. Anyway, it seems like almost an exact duplicate of the src/Makefile.in, so it shouldn't be a problem... ./Makefile.in Removes a few more temporary files during make clean and distclean. ./configure.in I fixed the creation of the time-stamp files so that the initial make doesn't have to regenerated all the makefiles (only GNU make users will see any change). ./src/H5R.c Changed a return type from `intn' to `int' for an API function. ./src/H5detect.c Added the volatile qualifier to a couple more variables. ./tools/h5tools.c Fixed a compiler warning about an unused local. ./tools/h5toh4.c Initialized `optind' to 1 because it's zero on my system. It should always be one on a unix system. ./tools/testh5toh4 Redirected "broken pipe" messages to /dev/null so outut is formatted correctly.
* [svn-r1117] Changes since 19990303Robb Matzke1999-03-041-60/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------- ./configure.in ./configure [REGENERATED] The path for a command is calculated explicitly the hard way because `type -path' isn't portable. ./config/freebsd ./config/linux-gnu ./config/linux-gnulibc2 Changed the way files reference each other. ./config/gnu-flags [NEW] ./config/dec-flags [NEW] These files figure out what flags to pass to certain compilers so we can reuse code in more than one config/* file. They also have better warning messages when old compilers are used. ./config/linux-gnulibc1 ./config/dec-osf4.x These files use the new *-flags files. ./src/H5D.c ./src/H5Onull.c ./src/H5Tconv.c ./tools/h5ls.c Fixed a compiler warning. ./src/H5detect.c Added a better comment to the top of the generated file.
* [svn-r1112] Changes since 19990301Robb Matzke1999-03-021-0/+76
---------------------- ./INSTALL Reorganized and added some additional examples. ./MANIFEST ./aclocal.m4 [NEW] ./configure.in ./configure [REGENERATED] ./src/H5config.h.in [REGENERATED] ./bin/ltconfig [NEW] ./bin/ltmain.sh [NEW] Added tests to determine how to compile shared libraries and how to link programs with them before the libraries are installed. Also how to install and uninstall shared libraries. The configure step also prints the names of the config files it's trying to load for easier debugging. ./bin/config.guess ./bin/config.sub Replaced with a newer version from GNU. The changes we made to that file to report `irix6.x' and `FreeBSD' without version numbers have been incorporated into configure.in instead. In the future, do not change these two files (see the top of configure.in instead). By the way, this update was required to get shared libraries working. ./config/linux [REMOVED] ./config/linux-gnulibc1 [NEW] ./config/linux-gnu [NEW] ./config/alpha-dec [REMOVED] ./config/alpha-dec-osf4.0 [REMOVED] ./config/dec-osf4.x [NEW] ./config/irix5.3 [REMOVED] ./config/irix5.x [NEW] ./config/irix64 [REMOVED] ./config/freebsd Moved config files around to agree with output from the new config.guess. The linux file was split into gnu (RedHat), gnulibc1, and gnulibc2 versions. The alpha-dec file was removed (I think it was unused) and the alpha-dec-osf4.0 was changed to dec-osf4.x. The irix5.3 file renamed to irix5.x and the irix64 file was renamed to irix6.x. The freebsd file was changed to point to linux-gnulibc1. These changes were tested on: Linux 2.0 Linux 2.1 FreeBSD 3.2 Irix 5.3 Irix64 6.2 Irix64 6.4 HP/UX 10.20 OSF1 4.0 ./config/alphaev56-dec-osf4.x ./config/irix64 Added warnings similar to linux/freebsd about using compilers with known bugs. ./config/commence.in ./config/conclude.in ./src/Makefile.in ./test/Makefile.in ./testpar/Makefile.in ./tools/Makefile.in Added definitions for shared libraries. This has been tested on the following systems: Linux 2.0 Linux 2.1 FreeBSD 3.2 Irix 5.3 Irix64 6.2 Irix64 6.4 HP/UX 10.20 static only OSF1 4.0 If you want to disable use of shared libraries (you probably do for development purposes since it takes a lot longer to compile and because you have to run dynamically linked programs in a special way if the library hasn't been installed) then add `--disable-shared' to the configure command line. This is all documented in the INSTALL file. ./bin/release Temprarily commented out the MANIFEST checking when running under svf since svf is about to be replaced by a newer version. This change only affects error checking during the release process. ./Makefile.dist ./Makefile.in Added `make check' which does the same thing as `make _test' since the former is endorsed by the GNU coding style and people are used to it. The old `make _test' still works too (and so does `make test' if you use GNU make).