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* Merge all of my changes from merge-back-to-feature-vfd_swmr-attempt-1,David Young2019-12-091-3/+17
| | | | | | | | including the merge of `hdffv/hdf5/develop`, back to the branch that Vailin and I share. Now I need to put this branch on a fork with a less confusing name than vchoi_fork!
* Convert several warnings about const to non-const conversion at H5Tcopy()David Young2019-09-121-1/+1
| | | | invocations to one warning in the H5Tcopy() implementation.
* Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-1/+0
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* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-1/+1
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-2/+2
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Fix for HDFFV-10355 (CVE-2017-17506).Dana Robinson2018-02-271-1/+1
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| * Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-12-081-3/+3
| |\ | | | | | | | | | Merge from develop.
| * \ (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-1/+3
| |\ \ | | | | | | | | | | | | | | | | | | | | (2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds. (3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check. (4) Add version bounds check for cache image feature.
| * | | Initial checkin for library version boundsVailin Choi2017-10-031-1/+1
| | | | | | | | | | | | | | | | Code changes to provide versioning support when adding to the enumerated defines for H5F_libver_t.
* | | | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-8/+6
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* | | Normalization with VOL integration branch.Dana Robinson2017-11-301-3/+3
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* | Split internal H5R functionality into H5Rint.c.Dana Robinson2017-11-081-1/+3
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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-r30143] Fix for HDFFV-9940.Vailin Choi2016-07-041-0/+1
| | | | Tested on jam, osx1010test, moohan, platypus, emu, kite, kituo, mayll, ostrich, quail.
* [svn-r29776] Description:Quincey Koziol2016-04-241-0/+1
| | | | | | | | Bring "file pointer patching" code & test from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r27768] Description:Quincey Koziol2015-09-141-4/+3
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r22807] Description:Quincey Koziol2012-09-251-0/+2
| | | | | | | | | | | | | | | | | | | | | Add encode/decode API routines for property lists: H5Pencode/H5Pdecode. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) 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, w/threadsafe, in production mode Linux/PPC 2.6 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (ember) w/Intel compilers, w/parallel, C++ & FORTRAN, in production mode Mac OS X/32 10.7.3 (amazon) in debug mode Mac OS X/32 10.7.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.7.3 (amazon) w/parallel, in debug mode
* [svn-r22608] Description:Quincey Koziol2012-07-261-1/+1
| | | | | | | | | | | | | | | Switch propert list/class iteration from internal to external form of iteration, cleaning up and simplifying the code a bit. Bring other general improvements from plist_encode_decode branch back to trunk. Clean up many warnings. Tested on: Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN (too minor to require h5committest)
* [svn-r21152] Description:Quincey Koziol2011-07-281-0/+1
| | | | | | | | | | | | | | | | | | | | Further patches for Jira 7638, to ensure that H5D/Aget_type will be attached to the correct top file. (This change to the library should reverted when Jira 7638 is finally finished) Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) 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, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Mac OS X/32 10.6.8 (amazon) in debug mode Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r19313] Description:Quincey Koziol2010-08-261-1/+0
| | | | | | | | Clean up a few compiler warnings and style issues in/near recent changes. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19251] New feature(bug #1934): I made H5Tset_order support all data ↵Raymond Lu2010-08-191-0/+1
| | | | | | | | | | | | | | | | | | types with some restictions: 1. For enum type, members shouldn't be defined yet. 2. H5T_ORDER_NONE only works for reference and fixed-length string. 3. For opaque type, the order will be ignored. 4. For compound type, all restrictions above apply to the members. I'll change H5Tget_order and do another commit. There is no change to configure.in, config, and Makefile.am. There is some property change for these files when I did a merge from 1.8. Tested on jam. But I tested the 1.8 on heiwa, and amani.
* [svn-r18804] Purpose:Mike McGreevy2010-05-141-0/+1
| | | | | | | | | | | | | Fix memory leaks Description Added a routine to free memory which addresses a memory leak when variable length strings are used as fill values. Tested: h5committest and valgrind (on jam/amani) to confirm freed memory.
* [svn-r17977] Bug fix for 1584. H5Tdetect_class said a VL string is a string ↵Raymond Lu2009-12-091-1/+1
| | | | | | | | | | | | type. But when it's in a compound type, it says it's a VL type. We want to tell user a VL string is a string. But internally we treat it as a VL type. I added a flag as a parameter of H5T_detect_class. It tells whether the caller is the public function H5Tdetect_class. I also added a detection for VL string in the private function for the compound case (or array or nested VL type). Tested on jam and amani - I tested the same change for 1.8 with h5committest.
* [svn-r15682] Purpose: fix bug 1298Neil Fortner2008-09-221-1/+6
| | | | | | | | | | | Description: The optimized "subset" compound conversion function would improperly copy the "blank" space at the end of compound types. Modified H5T_conv_struct_init to detect when the subset type has extra space at the end, and calculate the size of the data that should be copied into the conversion buffer for each element. Changes to the functions that implement these conversions. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15628] Description:Quincey Koziol2008-09-161-1/+1
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15609] Description:Quincey Koziol2008-09-101-4/+17
| | | | | | | | Omnibus compiler warning cleanup & some reformatting also. Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15227] Description:Quincey Koziol2008-06-171-1/+1
| | | | | | | | | | | | | | | | | | Small clean up of datatype copying. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.5.3 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-301-1/+1
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-301-1/+1
| | | | New fortran wrappers added.
* [svn-r14860] Description:Quincey Koziol2008-04-241-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Omnibus raw data I/O revisions, with wide-ranging changes and refactoring, in order to prepare for implementing "fast append" feature. These changes remove the majority of the code duplication for raw data I/O which has crept in over the last ten years and introduces a more object- oriented design for operating on different types of dataset storage. Chunked storage no longer has it's own I/O routines, it is now handled as either contiguous (if chunk is not pulled into the cache) or compact (if the chunk is cached in memory). No bug or feature changes, at least intentionally... :-) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14208] Description:Quincey Koziol2007-10-181-0/+15
| | | | | | | | | | | | | | | | | | | | Make H5Pget_filter_by_id() API versioned and switch internal usage to H5Pget_filter_by_id2(). Add simple regression test for H5Pget_filter_by_id1(). Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14004] Description:Quincey Koziol2007-07-241-0/+1
| | | | | | | | | | | | Fix problem with datatype messages where the version of the format for a datatype message could depend on the "use the latest format" flag from the file after it was initially created. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Mac OS X/32 10.4.10 (amazon)
* [svn-r13926] Description:Quincey Koziol2007-06-291-0/+3
| | | | | | | | | | | | Add small interface to "wrap" a static buffer (usually on the stack), but still allow for buffers larger than the static buffer to be allocated. This can eliminate _many_ short-lived buffer allocations in situations where the buffer is a predictable size (or at least a "very likely" size). Also, some minor code cleanups, particularly in the SOHM caching code. Tested on: Mac OS X/32 10.4.10 (amazon)
* [svn-r13917] Description:Quincey Koziol2007-06-261-0/+1
| | | | | | | | | Code & warning cleanups Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13884] The second step of optimization for compound data for the ChicagoRaymond Lu2007-06-191-0/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | company. The I/O is optimized when the source and destination members are a subset of each other one way or another, and the order is the same, and no conversion is needed. For example: struct source { struct destination { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; or struct destination { struct source { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; The optimization is simply moving data from the source to the appropriate places in the buffer and bypass the reading of the background data and data conversion. Tested on smirom, liberty, sol, and copper.
* [svn-r13753] Description:Quincey Koziol2007-05-141-1/+3
| | | | | | | | | | | | | Check in "unique, but sharable" optimization to ISOHM code, which allows object header messages that are only used in one object to remain in the sole user's header, but migrates messages that are used in more than one header into the ISOHM heap. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13353] Description:Quincey Koziol2007-02-201-1/+1
| | | | | | | | | | | | Checkpoint progress on H5Aiterate2(). Mark H5Aiterate() as deprecated. Various code cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [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-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-131-0/+4
| | | | | | | | | | | | 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-r11758] Purpose:Quincey Koziol2005-12-041-1/+3
| | | | | | | | | | | | | New feature Description: Add in a combination of Peter's & my code to support copying variable-length data from one file to another, although currently only supported with contiguous data storage. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-6/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11424] Purpose:Quincey Koziol2005-09-171-1/+0
| | | | | | | | | | | | | | | | | | | | | Code cleanup/bug fix Description: Hoist function call out of inner loop of type conversion by retrieving source & destination precisions once, outside the loop. There's still some overhead because this information is stored in variables set at run-time, when it's really constant for the particular machine. Further work to set compiler macros would allow this code to be optimized better by the compiler with dead code removal. We'll continue to work on this area... Also, made new internal H5T_compiler_conv routine static instead of of private, until we need to reference it from another source code module. Platforms tested: h5committest FreeBSD 4.11 (sleipnir)
* [svn-r11415] Purpose: Internal design change.Raymond Lu2005-09-141-1/+1
| | | | | | | | | | | | | | | | | Description: H5T_register() replaces any existing data conversion path with a new path. Solution: Added a parameter to H5T_register() and H5T_path_find() to signal the library whether the new conversion path is from API function H5Tregister() or from private function like H5T_init_interface(). If it is from H5Tregister(), replace existing path. If it's from H5T_init_interface() and the library is trying to register default hard conversion functions, don't replace existing path because the path is registered by the library. For example, the library registered H5T_conv_int_float() and is trying to register H5T_conv_long_float(). The size of long is equal to int. There's no need to replace the path H5T_conv_int_float(). Platforms tested: h5committest and fuss.
* [svn-r11414] Purpose: Rename a API functionRaymond Lu2005-09-141-1/+1
| | | | | | | | | | | Description: The API function H5Tis_hard() which was recently checked in has been renamed to H5Tcompiler_conv() to be more descriptive. No other changes. Platforms tested: fuss - simple change. Misc. update: config/lt_vers.am to update libtool version.
* [svn-r11355] Purpose: A new API function and its test.Raymond Lu2005-09-061-0/+1
| | | | | | | | | Description: Put in a new API funciton, H5Tis_hard. It checks whether the conversion function from a native type to another native type is a compiler (hard) conversion. Also checked a test in test/dt_arith.c. Platforms tested: h5committest and fuss.
* [svn-r10238] Purpose:Quincey Koziol2005-03-201-1/+1
| | | | | | | | | | | | | | | | Optimization Description: Speed up I/O on enumerated datatypes (including those nested in compound datatypes, arrays, etc.) if the destination datatype is a proper superset of the source datatype. Solution: Detect the situation and treat as no-op datatype conversion. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r9959] Purpose: Bug fixRaymond Lu2005-02-081-1/+1
| | | | | | | | | | | | Description: For variable-length string, H5Tget_class returned H5T_STRING as its class. But H5Tdetect_class and H5Tget_member_class considered it as H5T_VLEN. This is fixed to let all these 3 functions treat it as H5T_STRING. Some test cases have been added to dtypes.c Platforms tested: heping - already tested for v1.6 with h5committest Misc. update: RELEASE.txt
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r9329] James Laird2004-09-281-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r8981] Purpose:Quincey Koziol2004-08-021-2/+0
| | | | | | | | | | | | | Code cleanup Description: Various minor tweaks to clean code up and bring it into closer syncronization with the release branch. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel h5committested IRIX64 6.5 (modi4)
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