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* Removes dead H5ST package from the library (#528)Dana Robinson2021-03-301-1/+0
| | | | | | | * Committing clang-format changes * Removes the unused H5ST package from the library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* HD prefix updates in src/ and test/Dana Robinson2020-10-241-1/+1
| | | | | | | Adds missing HD prefixes to API calls in src and test. Adds some extra processing to bin/checkposix to keep the noise levels down when running the script (not comprehensive).
* Clang-format of source filesAllen Byrne2020-09-301-23/+22
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
* Normalization with vol_integration (test code and H5Xtest.c)Dana Robinson2018-09-201-2/+2
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* [svn-r30201] Description:Quincey Koziol2016-07-181-0/+3
| | | | | | | | | Switch test framework to dynamically allocate the testing array, and expand the length of the description field. Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r24652] HDFFV-8572: test/testhdf5.c main() should not return number of ↵Albert Cheng2014-01-271-1/+6
| | | | | | | | | errors Solution: testhdf5 now exits EXIT_SUCCESS(0) if no errors, else EXIT_FAILURE(1). Tested: Jam only since it is a trivial fix.
* [svn-r17351] Description:Quincey Koziol2009-08-131-0/+1
| | | | | | | | | | | | | | | | | | | | | Clean up code (to align w/future sblock_mdc branch changes), tweak tests for [slightly] easier debugging, fix memory leak when copying chunked datasets with I/O filters, fix memory leak of free space section when it was exactly the right size to use for extending an existing block in the file. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15395] When an attribute was opened twice and data was written with ↵Raymond Lu2008-07-221-1/+1
| | | | | | | | | | | one of the handles, the file didn't have the data. It happened because each handle had its own object structure, and the empty one overwrote the data with fill value. This is fixed by making some attribute information like the data be shared in the attribute structure. Tested on smirom, kagiso, and linew.
* [svn-r14354] Bug fix for #956 where the element coordinates went wrong for ↵Raymond Lu2007-12-201-0/+1
| | | | | | | | dataspace selection. Added a test for it, too. This round of checkin isn't well tarnished yet. I'll come back to work on Jan. 8. I'll revise it then. Tested it on kagiso, smirom, linew.
* [svn-r13914] Description:Quincey Koziol2007-06-261-1/+1
| | | | | | | Clean up files generated during testing. Tested on: Linux/32 2.6 (chicago)
* [svn-r13340] Fixed a bug where shared messages with the same hash values ↵James Laird2007-02-201-1/+1
| | | | | | | | | | could be sorted in the wrong order. This also makes the "unique but shareable" checkin a little easier. Tested on smirom, kagiso, and juniper.
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r12935] Added list-to-btree conversion, changed SOHM apis, and pushed ↵James Laird2006-11-171-1/+1
| | | | | | | | | | | SOHM table version and size information into the superblock to eliminate a read when loading it. This is a file format change, and hopefully the last one (knock on wood). Tested on kagiso and Windows (mostly just a SOHM change).
* [svn-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-131-0/+1
| | | | | | | | | | | | This feature is still in progress; Shared Object Header Messages are not complete as a feature and are not thoroughly tested. There are still "TODO" comments in the code (comments with the word "JAMES" in them, so as not to be confused with other TODO comments). Hopefully this checkin will reduce the liklihood of conflicts as I finish implementing this feature. All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
* [svn-r12605] Description:Quincey Koziol2006-08-211-1/+2
| | | | | | | | | | | | | Break out a bunch of the misc. routines that were in src/H5.c into more specific modules. Add optimized fletcher32 checksum routine, for checksumming metadata as well as raw data. Tested On: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) Will test further after checkin...
* [svn-r12528] Added User-Defined links to the library.James Laird2006-08-021-0/+1
| | | | | | | | | | | | | | Users can create external links using H5L_create_external(). These links point to an object in another HDF5 file. Users can alter the behavior of external links or create new kinds of links by registering callbacks using the H5L interface. Added tests, tools support, etc. Also a number of other, minor changes have been made (some restructuring of the H5L interface, for instance). Additional documentation and examples are forthcoming.
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-1/+1
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10944] Purpose:James Laird2005-06-171-0/+1
| | | | | | | | | | | | | | | Bug fix Description: tid.c is a test for user-defined hid_t's. It should be part of the testhdf5 tests, but was not being run. It also had a couple of minor bugs. Solution: Added id test to testhdf5 and fixed bugs. Platforms tested: mir, sleipnir, modi4
* [svn-r10785] Purpose:James Laird2005-05-231-0/+1
| | | | | | | | | | | | | | | | | Feature Description: Added "support" for UTF-8 character encoding. Solution: Wrote tests to check that UTF-8 can be used in a number of places in HDF5 (object names, data, etc.). These tests live in test/tunicode.c. Added a new UTF-8 character encoding for datatypes. Platforms tested: mir, modi4, heping Misc. update:
* [svn-r9778] Purpose:Quincey Koziol2005-01-081-1/+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-r9580] Purpose:Quincey Koziol2004-11-271-0/+1
| | | | | | | | | | | | | | | | | | | | 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-r9420] Bug fix.Albert Cheng2004-10-141-1/+1
| | | | | | | | | | | | | | tconfig.c: Verified only the unsigned int types and did not detect inconsistencies on signed type such as int_fast16_t. Changed code to verify both signed and unsigned int types wherever applicable. It also depends on signed and unsigned forms of an int type must be of the same sizes. testhdf5.c: Shorten the configure test name to 'config'--easier to type. Tested on LLNL Frost and Snow. Will test in Copper after commit.
* [svn-r9115] Purpose:Albert Cheng2004-08-191-8/+4
| | | | | | | | | | | | | | | | | | | | | | | | | feature Description: Another revamp of the test interface. TestInit: is used to register Test Program name, test program specific Usage and option parsing routines. TestUsage: will invoke extra usage routine if provided. TestParseCmdLine: will invoke extra option parsing routine if provided. GetTestSummary() and GetTestCleanup() replaces the previous Summary and CleanUp arguments of TestParseCmdLine. test/testhdf5, test/ttsafe.c, testpar/t_mpi.c, testpar/testphdf5.c: All have been updated to use the new Test Routines. testpar/t_mpi.c: Also a fix of a compiler optimization bug when pgcc in Linux is used to compile it. Changed buf[] and expected to unsigned char type to avoid a bug that failed to do sign-extension. Platforms tested: "h5committested" Also tested thread-safe option in eirene.
* [svn-r9079] Purpose:Albert Cheng2004-08-131-1/+1
| | | | | | | | | | | | | | Feature Description: Changed TestParseCmdLine to accept an optional extra_parse() function provided by indidivual test application. Extra_parse() can handle extra options special to that test application. Updated testhdf5.c to use the new syntax of TestParseCmdLine(). Platforms tested: On eirene both serial and parallel.
* [svn-r8707] Changed the way HDF5 handles hid_t's and added API functions to ↵James Laird2004-06-181-0/+1
| | | | allow users to register IDs and ID types at runtime.
* [svn-r8289] Purpose:Albert Cheng2004-03-301-18/+18
| | | | | | | | | | | | | | Feature Description: Added to AddTest() a generic parameters pointer argument to allow some extra parameters for some tests. E.g., test file names can be customized during runtime and passed into the test routines. Platforms tested: "h5committested". Also run compat test in eirene.
* [svn-r8048] Purpose:Quincey Koziol2004-01-101-5/+1
| | | | | | | | | | | | | Code cleanup & reorganization Description: Move further in the testing framework cleanup, eliminating all the global variables (moving them into testframe.c as static variables) from the testing framework code and moving it into the libh5test.a. Platforms tested: FreeBSD 4.9 (sleipnir) w & w/o thread-safety, c++ & parallel h5committested
* [svn-r8022] Purpose:Quincey Koziol2004-01-061-223/+40
| | | | | | | | | | | | | Code cleanup Description: Refactor library testing framework (used for the testhdf5 & ttsafe tests) to remove almost all of the duplicated code, moving the common code into a new 'testframe.c' source file. Platforms tested: FreeBSD 4.9 (sleipnir) w & w/o thread-safety h5committest
* [svn-r8020] Purpose:Albert Cheng2004-01-061-1/+0
| | | | | | | | | | | Bug fix. Description: Cleaned up a duplicated definition of MAXNUMOFTEST that copper could not tolerate. Platforms tested: "h5committested"
* [svn-r8018] Purpose:Albert Cheng2004-01-051-3/+0
| | | | | | | | | | | | | | | Fixed a dumb mistake. Description: Other tests barked at the changes. Solution: Move the declaration of Index and Test[] into h5test.c. Platforms tested: Tested in eirene. Misc. update:
* [svn-r8017] Purpose:Albert Cheng2004-01-051-27/+3
| | | | | | | | | | | | Code reorg. Description: Move the InitTest() from individual tests (testhdf5 and ttsafe) to libh5test (h5test.c) so that it can be shared among all tests. Platforms tested: Only tested in Eirene via serial with thread-safe enabled. No other platforms test since this is pretty trivial.
* [svn-r7677] Purpose:Pedro Vicente Nunes2003-10-201-4/+0
| | | | | | | | | | | | | | | | | | | | | | bug fix, update documentation Description: version 8 of Code Warrior has a bug on the open file function that causes one of our tests to fail documented this in the install instructions removed a CW specific header file include , that was left from version 6 from the file testhdf5.c Platforms tested: Code Warrior linux Misc. update:
* [svn-r7507] *** empty log message ***Raymond Lu2003-09-241-0/+4
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* [svn-r7265] *** empty log message ***Raymond Lu2003-07-261-1/+1
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* [svn-r6538] Purpose:Bill Wendling2003-03-311-11/+13
| | | | | | | | | | | | | Update Description: Updated the Copyright statement Platforms tested: Linux (This change is only in the comments, so I just check that the modules still compile) Misc. update:
* [svn-r6436] Purpose:Quincey Koziol2003-02-241-0/+1
| | | | | | | | | | | | | New internal feature Description: Add internal API for building and working with heaps (H5HP). This will be used for the LRU algorithm in the new metadata cache code. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r6252] Purpose:Quincey Koziol2003-01-091-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Lots of performance improvements & a couple new internal API interfaces. Description: Performance Improvements: - Cached file offset & length sizes in shared file struct, to avoid constantly looking them up in the FCPL. - Generic property improvements: - Added "revision" number to generic property classes to speed up comparisons. - Changed method of storing properties from using a hash-table to the TBBT routines in the library. - Share the propery names between classes and the lists derived from them. - Removed redundant 'def_value' buffer from each property. - Switching code to use a "copy on write" strategy for properties in each list, where the properties in each list are shared with the properties in the class, until a property's value is changed in a list. - Fixed error in layout code which was allocating too many buffers. - Redefined public macros of the form (H5open()/H5check, <variable>) internally to only be (<variable>), avoiding innumerable useless calls to H5open() and H5check_version(). - Reuse already zeroed buffers in H5F_contig_fill instead of constantly re-zeroing them. - Don't write fill values if writing entire dataset. - Use gettimeofday() system call instead of time() system when checking the modification time of a dataset. - Added reference counted string API and use it for tracking the names of objects opening in a file (for the ID->name code). - Removed redundant H5P_get() calls in B-tree routines. - Redefine H5T datatype macros internally to the library, to avoid calling H5check redundantly. - Keep dataspace information for dataset locally instead of reading from disk each time. Added new module to track open objects in a file, to allow this (which will be useful eventually for some FPH5 metadata caching issues). - Remove H5AC_find macro which was inlining metadata cache lookups, and call function instead. - Remove redundant memset() calls from H5G_namei() routine. - Remove redundant checking of object type when locating objects in metadata cache and rely on the address only. - Create default dataset object to use when default dataset creation property list is used to create datasets, bypassing querying for all the property list values. - Use default I/O vector size when performing raw data with the default dataset transfer property list, instead of querying for I/O vector size. - Remove H5P_DEFAULT internally to the library, replacing it with more specific default property list based on the type of property list needed. - Remove redundant memset() calls in object header message (H5O*) routines. - Remove redunant memset() calls in data I/O routines. - Split free-list allocation routines into malloc() and calloc()- like routines, instead of one combined routine. - Remove lots of indirection in H5O*() routines. - Simplify metadata cache entry comparison routine (used when flushing entire cache out). - Only enable metadata cache statistics when H5AC_DEBUG is turned on, instead of always tracking them. - Simplify address comparison macro (H5F_addr_eq). - Remove redundant metadata cache entry protections during dataset creation by protecting the object header once and making all the modifications necessary for the dataset creation before unprotecting it. - Reduce # of "number of element in extent" computations performed by computing and storing the value during dataspace creation. - Simplify checking for group location's file information, when file has not been involving in file-mounting operations. - Use binary encoding for modification time, instead of ASCII. - Hoist H5HL_peek calls (to get information in a local heap) out of loops in many group routine. - Use static variable for iterators of selections, instead of dynamically allocation them each time. - Lookup & insert new entries in one step, avoiding traversing group's B-tree twice. - Fixed memory leak in H5Gget_objname_idx() routine (tangential to performance improvements, but fixed along the way). - Use free-list for reference counted strings. - Don't bother copying object names into cached group entries, since they are re-created when an object is opened. The benchmark I used to measure these results created several thousand small (2K) datasets in a file and wrote out the data for them. This is Elena's "regular.c" benchmark. These changes resulted in approximately ~4.3x speedup of the development branch when compared to the previous code in the development branch and ~1.4x speedup compared to the release branch. Additionally, these changes reduce the total memory used (code and data) by the development branch by ~800KB, bringing the development branch back into the same ballpark as the release branch. I'll send out a more detailed description of the benchmark results as a followup note. New internal API routines: Added "reference counted strings" API for tracking strings that get used by multiple owners without duplicating the strings. Added "ternary search tree" API for text->object mappings. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Other platforms/configurations tested? FreeBSD 4.7 (sleipnir) serial & parallel Solaris 2.6 (baldric) serial
* [svn-r4851] Purpose:Quincey Koziol2002-01-231-3/+2
| | | | | | | | | | | | | | | | | | Bug Fix Description: When file space was returned to the file space free-list for reuse, occasionally raw data allocations which used space from the free-list would overlap with the metadata accumulator and get over-written with the cached information in the accumulator, corrupting the data. Solution: Check if the space about to be recycled on the free-list is going to be used for raw data and also overlaps with the metadata accumulator cache, avoiding using space that fits those criteria. This fixes bug #701 Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r4474] Purpose:Albert Cheng2001-09-261-0/+1
| | | | | | | | | | | | New feature. Description: Added a test to verify the correctness of information provided by configure in H5config.h. Some information, such as SIZEOF some types can be hardcoded by config/<machine>. This test verified the information is indeed correct. Currenly, only size of C language types are verified. Platforms tested: Eirene, regular, arabica.
* [svn-r4355] Purpose:Quincey Koziol2001-08-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | Code cleanup (sorta) Description: When the first versions of the HDF5 library were designed, I remembered vividly the difficulties of porting code from a 32-bit platform to a 16-bit platform and asked that people use intn & uintn instead of int & unsigned int, respectively. However, in hindsight, this was overkill and unnecessary since we weren't going to be porting the HDF5 library to 16-bit architectures. Currently, the extra uintn & intn typedefs are causing problems for users who'd like to include both the HDF5 and HDF4 header files in one source module (like Kent's h4toh5 library). Solution: Changed the uintn & intn's to unsigned and int's respectively. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r3974] code warrior portPedro Vicente Nunes2001-06-071-3/+1
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* [svn-r3770] Purpose:Bill Wendling2001-04-031-1/+1
| | | | | | | | | | | | | | | | | Update Description: Changed includes of the form: #include <hdf5_file.h> to #include "hdf5_file.h" so that gcc can pick them up easier without including the system header files since we don't care about them. Platforms tested: Linux
* [svn-r3677] Purpose:Albert Cheng2001-03-201-4/+0
| | | | | | | | | | | | | Bug fix (sort of) Description: The RCSID string in H5public.h was causing the C++ code problem as it was included multiple times and C++ did not like multiple definitions of the same static variable. Solution: Since we don't really make use of the RCSID strings as we have not installed it in all source files, we decided to remove it. Platforms tested: eirene (linux), modi4 (IRIX64-64) both serial and parallel modes.
* [svn-r2872] Purpose:Quincey Koziol2000-11-121-0/+1
| | | | | | | | | Code update Description: Added stub for generic property testing, although it doesn't do anything yet. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2844] Purpose:Quincey Koziol2000-11-091-0/+1
| | | | | | | | | | | | | | | | | | | New Feature Description: Added array datatype tests to the regression tests. These datatype combinations are tested currently: 1-D array of atomic datatypes 3-D array of atomic datatypes array of array of atomic datatypes array of compound of atomic datatypes array of compound of array datatypes array of VL of atomic datatypes array of VL of array datatypes Also added a test to verify that the older style compound datatype with array fields works correctly. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2699] Purpose:Quincey Koziol2000-10-191-0/+1
| | | | | | | | | | | | | | | Bug fix Description: "Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved in the datatype object header message correctly. Solution: Store endian-ness and precision in the datatype object header message and added test to continue to track them working correctly. This fixes bug #512. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2533] Rolled back the changes I committed since Albert fixed the ↵Bill Wendling2000-09-111-4/+0
| | | | | | problem with FILENAME being extern global...
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