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* [svn-r10158] Purpose:James Laird2005-03-071-186/+273
| | | | | | | | | | | | | | | | | | | | | | 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-r10144] Purpose:Quincey Koziol2005-03-041-0/+1
| | | | | | | | | | | | | | | | Bug fix Description: The GASS VFL driver header file was bringing in the <string.h> header file, which several other source code modules needed also, but weren't including explicitly themselves. Solution: Add includes for <string.h> to files which actually need them. Platforms tested: FreeBSD 4.11 (sleipnir) w/C++ as CC Configuration not tested by h5committest...
* [svn-r10123] Purpose:Albert Cheng2005-03-021-3/+0
| | | | | | | | | | | | | | | | | | | | | | | Removed GASS configuration and software packages associated with it. The following software are no longer configurable. checking for main in -lcrypto... yes checking for SSL_get_version in -lssl... yes checking globus_common.h usability... yes checking globus_common.h presence... yes checking for globus_common.h... yes checking for globus_module_activate in -lglobus_common... yes checking for main in -lglobus_gass_cache... yes checking for main in -lglobus_gaa... yes checking for main in -lglobus_gss... yes checking for main in -lglobus_gss_assist... yes checking for main in -lglobus_io... yes checking for main in -lglobus_gass_transfer_assist... yes checking for main in -lglobus_gass_transfer... yes checking for globus_gass_open in -lglobus_gass_file... yes Platforms tested: h5committested (but copper was down.) tested in modi4 too.
* [svn-r10067] Purpose:Robert E. McGrath2005-02-237-2/+233
| | | | | | | | | | | | | | | | | | | | | | | | | feature Description: h5repack support for scaleoffset compression Checking in early to help debug the filter. Solution: Added messages and command line to handle new scale offset filter. Note: TESTS ARE DISABLED FOR NOW. The filter is not complete, repack tests may fail due to know problems. PLEASE DO NOT MESS WITH THE SCALEOFFSET TESTS AT THIS TIME. They will be enabled when the filter is ready. Platforms tested: verbena,copper,shanti Misc. update: MANIFEST
* [svn-r10066] Purpose:James Laird2005-02-231-0/+4
| | | | | | | | | | Libtool upgrade Description: HDF5 was using libtool 1.4.2. Upgraded to libtool 1.5.14. Platforms tested: verbena, heping, pommier, copper, modi4, arabica
* [svn-r10027] Purpose:Xiaowen Wu2005-02-171-0/+1
| | | | | | | | | | | | | | New feature. Description: Add the scaleoffset internal library filter. Solution: Platforms tested: heping, copper, arabica Misc. update:
* [svn-r10016] James Laird2005-02-161-1/+0
| | | | | | | | | | | | | | | | | | | Purpose: Bug fix Description: modi4 dies during build with strange errors. The root cause of these is a two-year-old hack in HDF5's libtool script that only takes effect on IRIX. Solution: Edited the libtool hack (by editing ltmain.sh) to correct a bug in the hack. Also made sure that compiler-specific DEFAULT_LIBS are used when linking. Platforms tested: sleipnir, copper, modi4, sol
* [svn-r10009] Purpose:Robert E. McGrath2005-02-158-1/+257
| | | | | | | | | | | | | | | feature Description: support for nbit compression in h5repack Solution: Platforms tested: verbena,copper,shanti Misc. update: manifest
* [svn-r10000] Purpose:Pedro Vicente Nunes2005-02-141-0/+28
| | | | | | | | | | | | | | bug fix Description: in 1 case when there was not a requested layout, the original chunk was not preserved Solution: Platforms tested: linux (small change) Misc. update:
* [svn-r9993] Purpose:James Laird2005-02-112-2/+2
| | | | | | | | | | | | | | | | | | | | Bug fix Description: Arabica exhibited strange errors when linker found wrong versions of header files. This happened because include directories were given to linker in the wrong order. Solution: Move include directories from AM_CFLAGS variable to INCLUDES variable to put them before CPPFLAGS variable. Trust me, it works. This bug may also have contributed to strange errors on other platforms (kelgia?). Platforms tested: copper, sleipnir, arabica. (h5dump broke while building on arabica, but this happened in a clean checkout, too).
* [svn-r9988] Purpose:James Laird2005-02-111-15/+4
| | | | | | | | | | | | | | | | | | | | Bug fix Description: pmake (on modi4, for instance) complains about undefined variables if it is run without the -V flag, which turns those errors to warnings. Solution: Added test to configure.in to see if $MAKE will allow Makefiles with undefined variables. If not, sets -V flag in AM_MAKEFLAGS. Ensured that all custom make targets use AM_MAKEFLAGS. Also defined all variables that caused errors in top-level Makefile.am. This means that pmake can be used to build hdf5 *from the top level only*. To run make from a subdirectory, still need to use -V flag (or use make or gmake). Platforms tested: modi4, heping, copper, sleipnir
* [svn-r9951] Purpose: Minor bug fix.Raymond Lu2005-02-071-1/+1
| | | | | | | | | | | | | Description: The byte order for all 1-byte integer types was fixed as little-endian even on a big-endian machine. This's corrected in h5detect.c. When types are only 1 byte long, a native int is used substitute the type to detect byte order. Some tools like h5dump and h5repack are also corrected in this case. Platforms tested: fuss, copper, sol.(There're some failures from the recent configure change). Misc. update: Information in the RELEASE.txt.
* [svn-r9930] James Laird2005-02-031-1/+1
| | | | | | | | | | | | | | | | | | Purpose: Bug fix Description: Parallel builds were breaking in tools/lib Solution: talign didn't realize it depended on libh5tools.la because its dependencies listed the full path (../../tools/lib/libh5tools.la). Changed this, and made similar changes in a couple of other directories. This checkin should also add the --foreign flag to every Makefile.in Platforms tested: sleipnir (minor change)
* [svn-r9928] Purpose:Quincey Koziol2005-02-031-1/+1
| | | | | | | | | | | | | New feature Description: Add basic code for new B-tree implementation. They don't do much yet, aren't hooked up to anything yet and the format may change, but I'd like to start getting them into the daily tests. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r9920] Purpose:James Laird2005-02-021-2/+3
| | | | | | | | | | | | | | | | | | | Bug fix Description: Found the permanant fix to automake/CVS dependency problem Solution: Added AM_MAINTAINER_MODE macro to configure.in. Now automake will never try to regenerate Makefiles, Makefiles.in, configure, H5config.h, etc. when they are out of date, nor will it print any warnings. Developers should be very very careful to use reconfigure script, and can add --enable-maintainer-mode flag to configure on heping to regenerate these files correctly. Platforms tested: heping sleipnir copper
* [svn-r9915] Purpose:James Laird2005-02-021-6/+6
| | | | | | | | | | | | | | | Bug fix Description: Configuration files' timestamps were incorrect. Solution: Update Makefiles.in. Also added correct paths to autotools on heping, so heping build should be able to re-generate configuration files even if they are still broken. Platforms tested: sleipnir
* [svn-r9912] Purpose:James Laird2005-02-011-87/+8
| | | | | | | | | | | | | | | | | Bug fix Description: Dependencies between configure files (aclocal, configure.in, configure, Makefiles.am and .in) are still causing Makefiles to try to run autotools during build. Solution: Committed all Makefiles.in to update their timestamps. As a temporary measure, forcibly prevented automake from running autotools during build by redefining the variables it uses. Platforms tested: sleipnir (No changes to Makefile content)
* [svn-r9907] Purpose:James Laird2005-02-011-0/+1
| | | | | | | | | | | | | Bug fix Description: Different compilers use different flags to include Fortran module files Solution: Changed boilerplate to use configure variable rather than hardcoded -M flag. Platforms tested: sleipnir, sol, copper
* [svn-r9902] Purpose:James Laird2005-02-013-725/+843
| | | | | | | | | | | | | | | Configuration feature Description: HDF5 now uses automake to generate Makefiles Solution: Makefile.in files are now generated from Makefile.am files. To reconfigure (after chaning a Makefile.am or configure.in): /bin/sh bin/reconfigure.sh Platforms tested: Many
* [svn-r9885] Purpose:Pedro Vicente Nunes2005-01-291-1/+2
| | | | | | | | | | | | | | | bug fix Description: calling h5diff from the h5repack test script running mpicc , the path of one of the files was not found Solution: inserted the full path in the script Platforms tested: linux (with mpicc and gcc) Misc. update:
* [svn-r9778] Purpose:Quincey Koziol2005-01-081-47/+0
| | | | | | | | | | | | | | | Remove feature Description: Retire threaded, balanced binary tree code from HDF5 use. Requiescat in pace... Also, regenerate dependencies files. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require full h5committesting (the code is already disconnected from everything except its tests)
* [svn-r9727] Purpose:Quincey Koziol2004-12-2910-52/+66
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r9614] Purpose:Pedro Vicente Nunes2004-12-031-21/+34
| | | | | | | | | | | | | | | | | | new feature Description: when requesting a filter for all datasets and the filter cannot be applied for one dataset use the original dcpl withou filter and print a warning this check was done previously with buit in functions for szip that are now in the library Solution: Platforms tested: linux solaris aix Misc. update:
* [svn-r9572] Purpose:Pedro Vicente Nunes2004-11-241-112/+112
| | | | | | | | | | | | | | | | | bug fix Description: the routine for applying the layout for the new file of h5repack was not handling the logic correctly in cases where an input layout was not set Solution: changed the logic so that the original layout is preserved (this bug was introduced in the last change, October 19 04) Platforms tested: linux (small change) Misc. update:
* [svn-r9496] Purpose:Robert E. McGrath2004-11-025-18/+134
| | | | | | | | | | | | | | | | | | | | | | Fix SZIP filter to dynmically detect encoder. Description: Solution: See: http://hdf.ncsa.uiuc.edu/RFC/SZIP/Szip_dynamic_12_Oct.pdf Changes to h5repack tests, contingent on detecting SZIP encoder. Note new program: testh5repack_detect_szip Checks fo rencoder, prints out "yes" or "no". Used by hrepack.sh to detect encoder. Can also be used for windows tests. This is only used as part of the tests. Had to modify Makefile to build and clean this program.
* [svn-r9436] Purpose:Pedro Vicente Nunes2004-10-195-296/+209
| | | | | | | | | | | | | | | | | | | | | bug fix Description: Description: one case was not handled in the combination of input options (layout and filters) Solution: redo the algorythm that handles all cases Solution: Platforms tested: linux Misc. update:
* [svn-r9428] Purpose:Pedro Vicente Nunes2004-10-183-11/+24
| | | | | | | | | | | | | | | | | bug fix Description: when specifying both an input object e.g -f mydset:GZIP=1 and a defined chunk -l CHUNK=20x20 the filter used a defined default chunk instead Solution: add a check for the input chunk Platforms tested: linux (small change) Misc. update:
* [svn-r9370] Purpose:Quincey Koziol2004-10-062-46/+14
| | | | | | | | | | | | | | | Refactor code Description: Refactor common code for determining the native type for using in the tools into separate routine. Also, reduce diffs between the two branches and bring back some fixes from the development branch to the release branch. Platforms tested: FreeBSD 4.10 (sleipnir) too minor to require h5committest
* [svn-r9364] Raymond Lu2004-10-052-8/+48
| | | | | | | | | | | | Purpose: change feature Description: Back up support bitfield and time datatypes in H5Tget_native_type.Leave it to future support. Let it return "not supported" error message for now. Platforms tested: h5committest and fuss. Misc. update: RELEASE.txt
* [svn-r9329] James Laird2004-09-281-1/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Feature Description: Datatypes and groups now use H5FO "file object" code that was previously only used by datasets. These objects will hold a file open if the file is closed but they have not yet been closed. If these objects are unlinked then relinked, they will not be destroyed. If they are opened twice (even by two different names), both IDs will "see" changes made to the object using the other ID. When an object is opened using two different names (e.g., if a dataset was opened under one name, then mounted and opened under its new name), calling H5Iget_name() on a given hid_t will return the name used to open that hid_t, not the current name of the object (this is a feature, and a change from the previous behavior of datasets). Solution: Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's, and H5G_t's into a "shared" struct and a private struct. The shared structs (H5D_shared_t, etc.) hold the object's information and are used by all IDs that point to a given object in the file. The private structs are pointed to by the hid_t and contain the object's group entry information (including its name) and a pointer to the shared struct for that object. This changed the naming of structs throughout the library (e.g., datatype->size is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip. Platforms tested: Visual Studio 7, sleipnir, arabica, verbena Misc. update:
* [svn-r9204] Purpose:Pedro Vicente Nunes2004-09-031-118/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bug fix changed some datset names for h5repack etsts Description: Description: the dataset region reference data was not portable between the Cray T3E and other machines Solution: this was due to the fact that the buffer to store the heap ID and index was using a sizeof(int) for its size 4 is used instead of sizeof(int) to permit portability between the Crays and other machines (the heap ID is always encoded as an int32 anyway) Solution: Platforms tested: linux aix solaris Misc. update:
* [svn-r9146] Purpose:Pedro Vicente Nunes2004-08-243-38/+22
| | | | | | | | | | | | | | | | | | | h5repack test Description: modified a test file generation contents, for more easy debugging (generated just one reference dataset and one region reference ) Solution: Platforms tested: linux aix solaris Misc. update:
* [svn-r9137] Purpose:Pedro Vicente Nunes2004-08-234-30/+91
| | | | | | | | | | | | | | | | | | new test Description: added a test that generates and copies a file with a dataset with fill value (this is to test the property list function H5Pequal) Solution: Platforms tested: linux solaris aix Misc. update:
* [svn-r9121] Purpose:Pedro Vicente Nunes2004-08-194-360/+60
| | | | | | | | | | | | | | | | | | | | new feature Description: added a check that the chunk size must be smaller than pixels per block in SZIP request prints a message and exits, if not met Solution: Platforms tested: linux aix solaris Misc. update:
* [svn-r9106] Purpose:Pedro Vicente Nunes2004-08-175-21/+43
| | | | | | | | | | | | | | | | | bug fix Description: the option CHUNK:NONE (remove chunking ) was not setting the layout to contiguous Solution: Platforms tested: linux solaris AIX Misc. update:
* [svn-r9014] Elena Pourmal2004-08-041-2/+4
| | | | | | | | | | | | | | | | Purpose: Small bug fix Description: When SZIP filter is present but encoding is not enabled test_misc21 and h5repack tests failed. Solution: Those tests should not run in this situation at all. Used conditonal compilation to disable the tests. Platforms tested: sol (today I will enable the daily tests with the szip library that doesn't have encoder for few other platforms) Misc. update:
* [svn-r8983] Purpose:Quincey Koziol2004-08-021-776/+682
| | | | | | | | | | | | Update dependencies Description: Update dependencies after config/depend1.in bugfix Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IRIX64 6.5 (modi4) h5committested
* [svn-r8909] Purpose:Pedro Vicente Nunes2004-07-201-1/+2
| | | | | | | | | | | | | | | | update documentation and usage message Description: updated the html documentation for the new h5diff modes added a section for h5repack Solution: Platforms tested: linux Misc. update:
* [svn-r8904] Purpose:Pedro Vicente Nunes2004-07-2015-234/+424
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | h5diff and h5repack changes Description: h5diff introduced the following four modes of output: Normal mode: print the number of differences found and where they occured Report mode: print the above plus the differences Verbose mode: print the above plus a list of objects and warnings Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found) h5repack added an extra parameter for SZIP filter (coding method) the new syntax is -f SZIP=<pixels per block,coding> (pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN') Example of use: ./h5repack -i file1 -o file2 -f SZIP=8,NN -v updated usage messages, test scripts and files accordingly Solution: Platforms tested: linux AIX solaris Misc. update:
* [svn-r8882] Purpose:Pedro Vicente Nunes2004-07-158-64/+161
| | | | | | | | | | | | | | | | | | | | | | | | bug fix, new feature Description: fixed bug in the parse function: cases where we have an already inserted name but there is a new name also example: -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 dset1 is already inserted, but dset2 must also be (it was not) added a CHECK_SZIP symbol to enable/disable checking of library related szip parameters added the print of the filter name in verbose mode (confirms visually that the filter was applied ) Solution: Platforms tested: linux solaris AIX Misc. update:
* [svn-r8869] Purpose:Pedro Vicente Nunes2004-07-1316-707/+1071
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | h5repack changes Description: there were some requests to change some minor h5repack features h5repack only made a warning about a non available filter in verbose mode ( -v ) without -v it kept silent, and users sometimes missed this warning the request was that it should print this warning always. so, the new format, is e.g ./h5repack -i test_szip.h5 -o out.h5 Warning: dataset </dset_szip> cannot be read, SZIP filter is not available due to this, and to avoid a lot of these messages in the shell test script, I modified the script h5repack.sh so that it detects the presence of all filters in the environment (previously it only detected SZIP) the test files were also divided in more files , to make the script code easier to follow Solution: Platforms tested: linux AIX (no szip) solaris (no szip, no gzip ) Misc. update:
* [svn-r8781] James Laird2004-07-019-213/+366
| | | | | | | | | | | | | | | | Purpose: HDF5 now supports SZIP with no encoder. Description: SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled. Solution: Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC. Platforms tested: Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++) Misc. update:
* [svn-r8582] *** empty log message ***Raymond Lu2004-05-264-4/+56
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* [svn-r8495] Purpose:Quincey Koziol2004-05-081-657/+776
| | | | | | | | | | | | | | Bug fixes Description: Updated dependencies Fixed error with C++ compiler builds of main library Added H5Pset_data_transform to MPE info Platforms tested: FreeBSD 4.9 (sleipnir)
* [svn-r8383] Purpose:Quincey Koziol2004-04-189-79/+67
| | | | | | | | | | | | | Code cleanup Description: Clean up lots of warnings based on those reported from the SGI compilers as well as gcc. Platforms tested: SGI O3900, IRIX64 6.5 (Cheryl's SGI machine) FreeBSD 4.9 (sleipnir) w/ & w/o parallel h5committest
* [svn-r8352] Purpose:Pedro Vicente Nunes2004-04-142-7/+22
| | | | | | | | | | | | | | | | bug fix Description: the routine for reading the options from a file had the "old" parse syntax Solution: Platforms tested: linux solaris AIX Misc. update:
* [svn-r8345] Purpose:Albert Cheng2004-04-131-133/+76
| | | | | | | | | | | | | | | | | | | Bug fix. Description: Temporary output files were created in the source directory. If multiple build/tests using the same source directory occur at the same time, they would conflict because of the same file names. Solution: Changed it to create temporary output file in the current build directory. Platforms tested: sol. Misc. update:
* [svn-r8333] Purpose:Pedro Vicente Nunes2004-04-093-1/+133
| | | | | | | | | | | | | | | new test Description: add a test that generates a file with "holes" and then uses h5repack to clean the empty space. it works Solution: Platforms tested: linux Misc. update:
* [svn-r8323] Purpose:Pedro Vicente Nunes2004-04-082-119/+211
| | | | | | | | | | | | | | | | bug fix, new tests Description: added a couple of #ifdefs to check if a specific filter is available for read added more tests the h5tools check filters had a mismatched filter variable Solution: Platforms tested: linux, with several filter configurations (all, some , none ) Misc. update:
* [svn-r8320] Purpose:Pedro Vicente Nunes2004-04-084-12/+170
| | | | | | | | | | | | | | | | new tests for h5repack Description: added more tests both to the test program and shell script that test a variation of different filter converssions Solution: Platforms tested: linux Misc. update:
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