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* [svn-r10632] Snapshot version 1.7 release 46HDF Admin2005-04-201-1/+1
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* [svn-r10627] Purpose:James Laird2005-04-181-2/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | Feature - libtool shared library versioning Description: Libtool provides a mechanism for different versions of the same shared library to be distinguished. Now this is applied to HDF5 when it is built as a shared library. Solution: The version number is stored in config/lt_vers.am, and included in src/Makefile.am. This number will be automatically updated by bin/h5vers; developers only need to update it when they change the API. *** IMPORTANT *** Any time the API changes, the version number in config/lt_vers.am must be updated! Platforms tested: mir, eirene, verbena, modi4 Misc. update:
* [svn-r10587] Purpose:James Laird2005-04-111-2/+17
| | | | | | | | | | | | | | | | | | | | | | | | | Minor feature Description: If a user configures without C++ or Fortran, 'make' will not recurse into c++ or fortran directories. However, if the user cd's into these directories and 'makes,' the Makefiles will attempt to build interfaces that have not been configured, usually failing. In an unrelated but minor change, src/H5detect should be compiled with the -g flag to disable compiler optimizations since it is only executed once. Solution: Make it harder for users to try to compile interfaces that have not been configured by making c++, fortran, and hl directories not recurse into their subdirectories unless they have been configured. Thus, 'make' in /fortran/src will break if Fortran has not been configured, but 'make' in /fortran will not break. Platforms tested: mir, modi4, copper Misc. update:
* [svn-r10570] Purpose: MaintenanceElena Pourmal2005-04-071-47/+6
| | | | | | | | | | | Description: Removed support for SRB driver Solution: Removed or modified appropriate files; ran reconfigure to regenerate Makefile.in and configure files. Platforms tested: heping and shanti Misc. update: ran bin/chkmanifest on heping
* [svn-r10534] Purpose:James Laird2005-04-041-0/+1
| | | | | | | | | | | | | | | | | | | | Configuration feature Description: Different Fortran compilers mangle function names in different ways (upper case, lower case, adding underscores). To link between Fortran and C functions, we need to know what a given function's name is under a given compiler. Solution: Use autoconf's FC_WRAPPERS check to determine the Fortran naming scheme and define the FC_FUNC_ macro to name our functions (in H5f90proto.h). Removed references to our old FNAME macro, as well as flags that indicated whether function names were upper or lower case. Platforms tested: mir, pommier, modi4, copper, more
* [svn-r10517] Purpose:James Laird2005-03-311-6/+15
| | | | | | | | | | | | | | | | Bug fix Description: On some machines, $RUNSERIAL variable needs to be used to run tests. Set $RUNTESTS (which is used for non-parallel tests) to be $RUNSERIAL in configure.am. Also, since I was updating all Makefiles.in anyway, I updated commence.am to point to autotools installs in AFS instead of those on heping. Platforms tested: mir, sleipnir, modi4, copper
* [svn-r10511] James Laird2005-03-301-1/+6
| | | | | | | | | | | | | Purpose: "Bug fix" Description: Hardcoded Makefiles to use /bin/sh instead of letting configure detect shell automatically. This is what v1.6 does, and avoids problems on janus. Platforms tested: sleipnir, copper, modi4, mir
* [svn-r10506] Purpose:Quincey Koziol2005-03-291-18/+26
| | | | | | | | | | | | New feature Description: Add first iteration of "segmented heap" code, which will be used to store links in groups in a more flexible way than the previous "local heap" mechanism. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Solaris 2.9 (shanti)
* [svn-r10475] Purpose:James Laird2005-03-291-6/+43
| | | | | | | | | | | | | | | | | Feature - conditional compilation Description: SRB file driver and tests are now compiled only when SRB is enabled (using --with-srb during configure). Solution: Added an automake conditional in configure.in, altered Makefiles.am in src and test directories to depend on that conditional. This should make a nice example for posterity to add conditionally compiled sources. Platforms tested: heping (only configure change)
* [svn-r10459] James Laird2005-03-281-0/+1
| | | | | | | | | | | | | | | | | Purpose: Added C++ wrapper for Packet Table API. Description: Added macro for high-level C++ library (LIBH5CPP_HL), which changes every Makefile.in. Added directories for high-level C++ library (though currently only Packet Table API is supported). Added both C++ source and tests. Platforms tested: sleipnir, mir, modi4 Misc. update:
* [svn-r10191] Purpose:Quincey Koziol2005-03-111-2/+3
| | | | | | | | | | | | New tests Description: Add some internal validation routines and make certain that the max & min block sizes get tracked accurately, at least for a simple series of insertions Platforms tested: FreeBSD 4.11 (sleipnir) Solaris 2.9 (shanti)
* [svn-r10184] Purpose:Quincey Koziol2005-03-111-3/+9
| | | | | | | | | | | | | | | | | | | | New feature Description: Add new "block tracker" data structure to library, for tracking blocks of bytes in a file. Block trackers will be used to keep track of the blocks belonging to the soon-to-be-implemented "segmented heap" which is designed to replace the current local & global heaps (starting with the local heap). Block trackers will also keep track of the free space in the segmented heap and someday could be used to track the free space in the entire HDF5 file. They are implemented as a small header of information to cache the state of the blocks (max & min sizes of blocks tracked, etc.) and the records of the blocks themselves are stored in a v2 B-tree. Platforms tested: FreeBSD 4.11 (sleipnir) Solaris 2.9 (shanti) h5committest
* [svn-r10158] Purpose:James Laird2005-03-071-264/+311
| | | | | | | | | | | | | | | | | | | | | | 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-r10130] Purpose:Albert Cheng2005-03-031-8/+6
| | | | | | | Retired GASS driver. Platforms tested: H5committested.
* [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-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-r10025] Purpose:Xiaowen Wu2005-02-171-5/+9
| | | | | | | | | | | | | | 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-r9993] Purpose:James Laird2005-02-111-3/+0
| | | | | | | | | | | | | | | | | | | | 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-r9955] Purpose:Quincey Koziol2005-02-081-8/+11
| | | | | | | | | | | | | | New feature & bug fix Description: Allow h5debug tool to dump "test" v2 B-trees correctly. Also, fix incorrect parameter passing that was causing failures on various platforms. Platforms tested: FreeBSD 4.11 (sleipnir) AIX 5.2 (copper)
* [svn-r9939] Purpose:Quincey Koziol2005-02-041-27/+29
| | | | | | | | | | | | | New feature Description: Expand v2 B-tree code to support splitting the root node when enough records are inserted and move metadata cache callbacks into their own source file. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Too minor for h5committest
* [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 Koziol2005-02-031-25/+32
| | | | | | | | | | | | | 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 Laird2005-02-021-3/+4
| | | | | | | | | | | | | | | | | | | 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 Laird2005-02-011-97/+1019
| | | | | | | | | | | | | | | 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-r9778] Purpose:Quincey Koziol2005-01-081-2/+2
| | | | | | | | | | | | | | | 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-r9758] Purpose:MuQun Yang2005-01-061-1/+1
| | | | | | | | | | | | | | | | | Adding framework of N-bit filter Description: N-bit filter is required for NetCDF project. To add N-bit filter, configure.in configure, Makefile.in under src and other filter-related source code needs to be updated. Currently, N-bit tests are turned off from the library. So the change will affect daily test. Solution: Platforms tested: sol 2.7, linux 2.4, aix 5.1 Misc. update:
* [svn-r9687] Purpose:John Mainzer2004-12-181-9/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modify the cache code (H5C) to support automatic cache resizing to adapt to the work load at run time. Description: Different applications require different sized caches to maintain an acceptable hit rate. This set of changes attempts to provide the ability to adjust to circumstances automatically. Solution: Added highly configurable code to allow the user to either set a fixed cache size, or allow the cache to grow and shrink according to conditions. If enabled, cache size increases are triggered when the hit rate drops below a user specified threshold in a user specified interval. Cache size reductions (if enabled) are triggered when either the hit rate exceeds some user specified threshold over a user specified interval, when the cache contains "enough" entries that haven't been accessed for a user specified interval, or some mix of the above. See the header comments on the H5C_auto_size_ctl_t structure in H5Cprivate.h for further details. At present, the cache resize configuration options are not accessible via the user API. Must add this. Platforms tested: h5committested, heping (serial), and copper (parallel) Misc. update:
* [svn-r9580] Purpose:Quincey Koziol2004-11-271-2/+4
| | | | | | | | | | | | | | | | | | | | Add new internal data structure Description: Add an implementation of skip lists to the library (see comment in src/H5SL.c for references to the papers describing them) as a potential replacement for our current threaded, balanced binary tree container. Skip lists are much simpler to implement and should be faster to use. Also, added new error codes to release branch, so bump the minor version number to indicate that the library is no longer perfectly compatible with the 1.6.3 release. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require further testing (the skip lists aren't actually used by any library code yet)
* [svn-r9354] Purpose:Quincey Koziol2004-10-011-2/+3
| | | | | | | | | | | | | | | | Bug fix & code cleanup Description: More dataset cleanups to get to a point where we can fix the chunked I/O bug. Also fix a couple of errors in the recent file object resurrection changes which should hopefully address the recent daily test failres (H5T.c) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r9342] Purpose:Quincey Koziol2004-09-301-1/+1
| | | | | | | | | | | | | | | | Bug fix/code cleanup Description: Clean up raw data I/O code to bundle the I/O parameters (dataset, DXPL ID, etc) into a single struct to pass around through the dataset I/O routines, since they are always passed together, until very near the bottom of the I/O stack. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) IRIX64 6.5 (modi4) h5committest
* [svn-r8932] Purpose:Quincey Koziol2004-07-221-1/+1
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up collective chunking code a bit. Also, add '--enable-instrument' configure flag to have a mechanism for determining that optimized operations happened correctly in the library (instead of just the "normal" way) by allowing 'flag' properties to be set outside the library and set when the "right" thing happens. This is mainly for debugging and regression checks, so we make certain we don't break optimized I/O by accident. It's enabled by default when --enable-debug is on (which is on by default in the development branch and off by default in the release branch), but can also be independently controlled with its own configure flag. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IBM p690 (copper) w/parallel
* [svn-r8844] Purpose:Quincey Koziol2004-07-091-4/+4
| | | | | | | | | | | | | | | | | | Bug fix Description: The "shared" raw B-tree node can get freed before all the B-tree nodes had been flushed out to disk and released by the cache. Solution: Implement a simple reference counting wrapper for objects in the library and use it to hold the shared raw B-tree nodes so they aren't freed before all references to them in memory are released. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) IRIX64 6.5 (modei4)
* [svn-r8791] Purpose: Rewrote metadata cache (H5AC.c, etc.) to improve ↵John Mainzer2004-07-021-15/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | performance. Description: Replaced the old metadata cache with a cache with a modified LRU replacement policy. This should improve the hit rate. Solution: Since we want to flush cache entries in increasing address order, I used the threaded binary B-tree code to store the cache entries. There is a fair bit of overhead here, so we may want to consider other options. While the code is designed to allow the support of other replacement algorithms, at present, only a modified version of LRU is supported. The modified LRU algorithm requires that a user selectable portion of the cache entries be clean. The clean entries are evicted first when writes are not permitted. If the pool of clean entries is used up, the cache grows beyond its user specified maximum size. The cache can also exceed its maximum size if the combined size of the protected (or locked) entries exceeds the maximum size of the cache. Platforms tested: eirene (serial, parallel, fp), h5committested Misc. update:
* [svn-r8618] Purpose:Quincey Koziol2004-06-051-2/+2
| | | | Fix makefiles, dependencies & manifest after source file rename.
* [svn-r8590] Purpose:Quincey Koziol2004-05-271-16/+17
| | | | | | | | | | | | | | | | | | | | | Code optimization & bug fix Description: When dimension information is being stored in the storage layout message on disk, it is stored as 32-bit quantities, possibly truncating the dimension information, if a dimension is greater than 32-bits in size. Solution: Fix the storage layout message problem by revising file format to not store dimension information, since it is already available in the dataspace. Also revise the storage layout data structures to be more compartmentalized for the information for contiguous, chunked and compact storage. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r8479] Purpose:Albert Cheng2004-05-031-1/+1
| | | | | | | | | | | | | New Feature Description: Add the data transform function, H5Pset_transform(). Platforms tested: "h5committested". Copper was down. Ran parallel tests in sol instead. Misc. update:
* [svn-r8212] Purpose:Albert Cheng2004-02-181-2/+2
| | | | | | | | | | | | | Bug fix. Description: The -g in H5detect somehow does not work with 64bit mpicc in arabica. Remove it for now for better solution. Platforms tested: no test as the change is trivia. Misc. update:
* [svn-r8207] Purpose:Albert Cheng2004-02-171-1/+5
| | | | | | | | | | | | | | | | | | | | Bug fix, sort of. Description: Some compilers, e.g., intel compiler, would take a long time to compiler H5detect.c if optimization is on. Solution: Setup special make rules for H5detect to be compiled always with optimization off by using -g. Since H5detect is run once to generate H5Tinit.c, it does not matter that much if it is optimized or not. Platforms tested: "h5committested". Tested in Titan too.
* [svn-r8126] Purpose:Quincey Koziol2004-01-311-2/+2
| | | | | | | | | | | | | | | | | Bug fix/optimization Description: Address slowdown in MPI-I/O file metadata operations that was introduced mid-stream. We now _require_ a POSIX compliant parallel file system for the MPI-I/O file driver (as well as for the MPI-POSIX file driver). Also optimized file open operation when the file is being created by reducing the number of collective & syncronizing calls. Additionally, refactor the MPI routines into a common place, eliminating duplicated code. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel h5committest
* [svn-r7355] Purpose:Quincey Koziol2003-08-131-13/+21
| | | | | | | | | | | | | | | | | | | | | | Code cleanup, etc. Description: Previously (in versions prior to 1.7), there were two locations to modify when an error was added to the library. Now, with the new error API, there were four. Solution: Created a single text file (src/H5err.txt) and a perl script (bin/make_err) which uses the text file to automatically create header files that are included in appropriate places in the library. This means that there is only one file (src/H5err.txt) which needs to be modified when a new error code is added to the library. The automatically generated headers depend on this file and the makefiles will take care of running the perl script to regenerate them when the text file changes, so no user action is required when a new error is added. Platforms tested: h5committested
* [svn-r7191] Purpose:Quincey Koziol2003-07-091-17/+17
| | | | | | | | | | Code cleanup Description: Track new "debug" modules for library. Platforms tested: h5committested
* [svn-r7009] Purpose:Albert Cheng2003-06-091-1/+3
| | | | | | | | | | | | | | Bug fix Description: libhdf5.settings should be removed in DISTCLEAN, not CLEAN. Solution: Platforms tested: COpper. Misc. update:
* [svn-r6952] Purpose:Quincey Koziol2003-06-041-6/+7
| | | | | | | | | | | | | Code cleanup Description: Move testing routines into their own module, to avoid linking them into user's applications needlessly. Platforms tested: FreeBSD 4.8 (sleipnir) w/C++ FreeBSD 4.8 (sleipnir) w/parallel h5committested
* [svn-r6825] Purpose:Quincey Koziol2003-05-071-16/+16
| | | | | | | | | | | | | | | | | | | | | | | | | New feature/enhancement Description: Chunked datasets are handled poorly in several circumstances involving certain selections and chunks that are too large for the chunk cache and/or chunks with filters, causing the chunk to be read from disk multiple times. Solution: Rearrange raw data I/O infrastructure to handle chunked datasets in a much more friendly way by creating a selection in memory and on disk for each chunk in a chunked dataset and performing all of the I/O on that chunk at one time. There are still some scalability (the current code attempts to create a selection for all the chunks in the dataset, instead of just the chunks that are accessed, requiring portions of the istore.c and fillval.c tests to be commented out) and performance issues, but checking this in will allow the changes to be tested by a much wider audience while I address the remaining issues. Platforms tested: h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
* [svn-r6711] Purpose:Albert Cheng2003-04-181-3/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: Sometimes when H5detect fails (incorrect code, incorrect mpi launch command, insufficient resources,...), it generates an incomplete or even empty H5Tinit.c file. If the empty file is not removed but the make is run again, make will just use the empty file to generate the library which will have lots of missing routines. Make won't fail until much later and the missing routines would be puzzling to inexperienced users. Solution: If H5detect fails, the generated H5Tinit.c will be removed unless $HDF5_Make_Ignore is set. This is similar to removing .o file if the compile fails. Platforms tested: Copper (parallel) which has a condition causing H5detect to fail. That verified the change works. Eirene (parallel) in which H5detect runs well. This verified the change works in normal conditions too. Did not do the h5committest because this is just a makefile change and the above two tests covered it well. Misc. update:
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