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* Incorporate patch from GE Healthcare (HDFFV-9934)Vailin Choi2017-04-251-49/+100
| | | | | This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
* 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-r30189] Description:Quincey Koziol2016-07-181-12/+25
| | | | | | | | | Clean up more warnings: drop the warning count from ~1310 down to ~940, with only 31 types of warnings in 148 files (down from 38 types in 167 files). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r29776] Description:Quincey Koziol2016-04-241-0/+4
| | | | | | | | 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-r29548] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-1/+1
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r29245] use HDONE_ERROR instead of HGOTO after done.Mohamad Chaarawi2016-03-011-2/+2
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* [svn-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-27/+99
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r27835] Description:Quincey Koziol2015-09-211-1/+1
|\ | | | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r27103] Merge revisions 26780 through 27102 from trunk to vds branch.Neil Fortner2015-05-211-10/+5
|\ \ | |/ | | | | Tested: ummon
| * [svn-r27045] Renamed H5_ASSIGN_OVERFLOW() to H5_CHECKED_ASSIGN() and re-orderedDana Robinson2015-05-101-2/+2
| | | | | | | | | | | | the arguments to be in a more logical order. Tested on: h5committest
| * [svn-r26842] Description:Quincey Koziol2015-04-181-8/+3
| | | | | | | | | | | | | | | | | | | | Cache the dataset's rank & dimension sizes, instead of querying them frequently, to speed up various checks & algorithms. Also, a few minor cleanups. Tested on: MacOSX/64 10.10.2 (amazon) w/serial & parallel Linux/32 2.6.18 (jam) w/serial & parallel
* | [svn-r26781] Merge revisions 26305 through 26780 from trunk to vds branch.Neil Fortner2015-04-101-2/+2
|\ \ | |/ | | | | Tested: ummon
| * [svn-r26757] Description:Quincey Koziol2015-04-071-2/+2
| | | | | | | | | | | | | | | | Minor typos & code cleanups Tested on: MacOSX/64 10.10.2 (amazon) w/serial & parallel (Too minor to require h5committest)
* | [svn-r26469] INCOMPLETE, UNWORKING CODENeil Fortner2015-03-171-1/+1
| | | | | | | | Commit progress through 3/17/15
* | [svn-r26411] Add support for I/O in very simple cases (virtual mapping and ↵Neil Fortner2015-03-091-4/+1
|/ | | | | | | | | file space are both H5S_ALL). Note make check fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26213] Description:Quincey Koziol2015-02-181-5/+5
| | | | | | | | Minor code cleanups, to align with revise_chunks branch. Tested on: Mac OSX/64 10.10.2 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial
* [svn-r25766] Description:Quincey Koziol2014-11-031-17/+17
| | | | | | | | | | Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They are buggy and it's taking me a long time to correct the problem. I'll check in a revised form of the changes when I've got them straightened out. Tested on: Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN Linux 2.6.x (jam) w/parallel
* [svn-r25468] some code refactoring to align trunk with VOL branch.Mohamad Chaarawi2014-07-221-53/+58
| | | | tested with h5committest.
* [svn-r25273] Description:Quincey Koziol2014-06-131-20/+20
| | | | | | | | | | | Bring in Chao/Neil/my changes to optimize hyperslab selection operations further, along with 3 new public API routines: H5Scombine_hyperslab(), H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to the code and fixing a few compiler warnings. Tested on: Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI (h5commttest forthcoming)
* [svn-r24995] Description:Quincey Koziol2014-04-091-36/+43
| | | | | | | Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls. Tested on: Linux/32 2.4.x (jam) w/gcc
* [svn-r24769] Description:Quincey Koziol2014-03-071-11/+20
| | | | | | | | | Check in Mohamad's changes to support collective I/O on point selections, along with some other minor cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (h5committest forthcoming)
* [svn-r23713] Description:Quincey Koziol2013-05-211-5/+2
| | | | | | | | | | Clean up warnings, switch library code to use Standard C/POSIX wrapper macros, remove internal calls to API routines, update checkapi and checkposix scripts. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN Big-Endian Linux/64 (ostrich)
* [svn-r23196] I changed the call to H5P_object_verify to H5I_object as the ↵Raymond Lu2013-01-231-3/+3
| | | | | | header file H5Iprivate.h is included but not H5Pprivate.h. Tested on jam.
* [svn-r23152] I took out the obsolete function H5PSIwrite_chunk and its ↵Raymond Lu2013-01-111-88/+0
| | | | | | related test and performance test. Tested on koala.
* [svn-r23075] I revised the code and test according to Quincey's review. I ↵Raymond Lu2012-12-041-13/+12
| | | | | | also added more test cases. Tested on koala.
* [svn-r23017] I added a prototype function H5DOwrite_chunk in HL library for ↵Raymond Lu2012-11-071-39/+145
| | | | | | | | | Dectris people to test performance. The library's API function H5PSIdirect_write is still in. I reorganized the internal library by adding H5D__pre_write function. Tested on koala.
* [svn-r22739] ported revisions 22615 to 22737 from the trunkRaymond Lu2012-09-051-1/+1
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| * [svn-r22735] Purpose:Jonathan Kim2012-09-041-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access Description: Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access. Reasons to break collective I/O: - SET_INDEPENDENT - DATATYPE_CONVERSION - DATA_TRANSFORMS - MPIPOSIX - NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space) - POINT_SELECTIONS - NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage) - FILTERS Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* | [svn-r22728] I forgot to include H5MMprivate.h header file for using ↵Raymond Lu2012-08-301-0/+1
| | | | | | | | | | | | H5MM_free function. Tested on koala.
* | [svn-r22655] Dectris project - I changed the rank of the offset for ↵Raymond Lu2012-08-091-5/+14
| | | | | | | | | | | | | | | | H5PSIdirect_write from RANK+1 to RANK. But internally, it expands to RANK+1 as the library requires it to terminate with a zero. Tested on koala.
* | [svn-r22653] Dectris project: I revised the code per Quincey's suggestion.Raymond Lu2012-08-091-4/+6
| | | | | | | | Tested on koala.
* | [svn-r22641] Dectris project: I revised the code per Quincey's and Neil's ↵Raymond Lu2012-08-081-3/+28
| | | | | | | | | | | | comments. I added a performance benchmark program dectris_perf.c in the test/ directory. Tested on koala and jam.
* | [svn-r22616] The code for H5PSIdirect_write and its test dectris_tst.c.Raymond Lu2012-07-301-0/+47
|/ | | | Tested on koala and jam.
* [svn-r22287] Description:Quincey Koziol2012-04-161-58/+58
| | | | | | | | Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r22134] Issue 7785 - follow-up checkin. I forgot to initialize a ↵Raymond Lu2012-03-231-0/+1
| | | | | | structure in H5D_read as I did in H5D_write. Tested on jam - simple change.
* [svn-r22122] Issue 7785 - Writing or reading many small chunks ran out of ↵Raymond Lu2012-03-221-0/+1
| | | | | | | | memory and caused seg fault. I added checks in two places to make sure the library returns error stack when it fails to allocate memory. I didn't add any test to the test suite since there is no good way to test it. But I tested and verified the error stack by hand. Tested on jam, koala, ostrich.
* [svn-r21919] Description:Quincey Koziol2012-02-091-9/+9
| | | | | | | | Refactor function name macros and simplify the FUNC_ENTER macros, to clear away the cruft and prepare for further cleanups. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r21442] Description:Quincey Koziol2011-10-011-8/+19
| | | | | | | | | | | | | | | | | | | | | | Check in "actual I/O mode" feature to trunk. Will merge back to 1.8 branch after it bakes over the weekend. 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 Linux/64-ia64 2.6 (ember) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, 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-r20588] Description:Quincey Koziol2011-04-211-3/+3
| | | | | | | | | Clean up code a bit, move new "terminate" VFD callback to new position in H5FD_class_t struct. Tested on: Mac OS X/32 10.6.7 (amazon) w/debug & production (h5committest not required on this branch)
* [svn-r20587] Description:Quincey Koziol2011-04-211-3/+4
| | | | | | | | Initial commit of John Biddescomb's VFD & MPI tweaks. Tested on: None (yet) (h5committest not required for this branch)
* [svn-r19092] Description:Quincey Koziol2010-07-191-0/+98
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring "shape same" changes from LBL branch to trunk. These changes allow shapes that are the same, but projected into dataspaces with different ranks to be detected correctly, and also contains code to project a dataspace into greater/lesser number of dimensions, so the I/O can proceed in a faster way. These changes also contain several bug fixes and _lots_ of code cleanups to the MPI datatype creation code. Many other misc. code cleanup are included as well... 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 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r19005] Purpose:Mike McGreevy2010-06-151-4/+4
| | | | | | | | | | | | | | | | | | | | | | | Commit metadata tagging framework. Description: This check-in contains a new framework whose goal is to apply a tag value to each new entry in the metadata cache as it is created. This tag value is such that it relates each piece of metadata to the HDF5 object that it belongs to (dataset, group, et cetera). This changeset includes the framework that applies the tags as well as a suite of tests to verify correct tag application, though does not yet make use of the tag values to flush/evict individual objects. Please refer to the "flush/evict individual objects" RFC for further discussion of these changes. Tested: jam, amani, linew (h5committest) liberty, abe, blue print
* [svn-r18445] Purpose: Fix bug 1637Neil Fortner2010-03-241-1/+1
| | | | | | | | | | Description: Modified algorithm for extending a dataset with early allocation so it only deals with the new chunks. Formerly, it would loop over all chunks, checking to see if each existed in cache and on disk, causing major performance issues with large numbers of chunks. Tested: jam, linew, amani (h5committest)
* [svn-r18031] Description:Quincey Koziol2009-12-171-6/+9
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r18030 from merge_metadata_journaling branch to trunk: Bring "brush clearing" changes (whitespace & style issues, mostly) from metadata_journaling branch to the "merging" branch, to converge the trunk and the metadata_journaling branch. Also, some other minor cleanups along the way. 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 (jam) w/PGI compilers, w/default API=1.8.x, 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 debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
| * [svn-r18030] Description:Quincey Koziol2009-12-171-6/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring "brush clearing" changes (whitespace & style issues, mostly) from metadata_journaling branch to the "merging" branch, to converge the trunk and the metadata_journaling branch. 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 (jam) w/PGI compilers, w/default API=1.8.x, 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 debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* | [svn-r17977] Bug fix for 1584. H5Tdetect_class said a VL string is a string ↵Raymond Lu2009-12-091-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | 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-r17813] Description:Quincey Koziol2009-11-031-1/+1
| | | | | | | | | | | | | | Correct 'src' to 'dst' in error message for H5D_read. (Bz#1683) Tested on: Eyeballed only - too minor to require h5committest
* | [svn-r17778] Description:Quincey Koziol2009-10-281-2/+2
| | | | | | | | | | | | | | | | Make check for NULL dataspace a bit safer. Tested on: FreeBSD/32 6.3 (duty) (too minor for h5committest)
* | [svn-r17281] Description:Quincey Koziol2009-07-311-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Further refactoring of the dataset layout information, to separate the storage information from the layout info. 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 (jam) 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 debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.5.7 (amazon) in debug mode Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
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