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* Small fixes (#285)Allen Byrne2021-01-271-21/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Small changes plus merge of tools arg parse from 1.12
* Clang-format of source filesAllen Byrne2020-09-301-228/+183
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* HDFFV-9984 Add options to merge/prune external links during repackAllen Byrne2020-08-141-1/+1
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* Misc changes for h5dump VOL changes.Dana Robinson2020-03-301-4/+4
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* Update Tools library to be better compatible with VOL connectorsJordan Henderson2020-03-171-56/+103
| | | | | | | | | | | | | | | | | | | | | Modify h5repack to integrate with VOL connectors Update tools library to accomodate VOL connectors Update logic in h5tools_fopen for VOL connectors Add command-line options to h5repack for specifying in/out VOL connectors Implement h5tools_set_vol_fapl Fix library shutdown issue Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme Avoid H5Ocopy in h5repack when using different VOL connectors Update h5tools_test_utils.c for ROS3 and HDFS integration
* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-31/+42
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* Update tools hid_t declarations with H5I_INVALID_HIDAllen Byrne2020-01-131-1/+1
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* Clean up tools warnings introduced by H5TOOLS_ERR_INIT macroJordan Henderson2019-12-311-2/+2
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* Refactor tools library error handling macrosJordan Henderson2019-12-281-16/+16
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* HDFFV-10980 - h5diff uses new ref APIsAllen Byrne2019-12-191-2/+2
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-12-021-1/+1
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0772b975d1d2bfa15aedeb4b6e2c2aac78c61a2f': Fix missing free in H5T__ref_mem_read() Fix bugs in H5VL file comparison code. Add short circuit success to H5VL_cmp_connector_cls(). Implement file comparison VOL callback. Other changes to allow references to work with non-native connectors. There is a bug somewhere. Add support for point selections to H5S_select_project_intersection. Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf3)" Revert "Oops, remove more C99 designated initializers for VS 2010 compatibility." H5R: fix H5Tconv to check for null references Trivial parameter renaming in VOL API calls. Move checking for zero offset in selection adjust calls to the selection callbacks. This makes the procedure for checking it consistent across selection types and between _s and _u, ensures it is always is performed even when called within the H5S package, and removes the redundant check that would occur when callins H5S_select_adjust_s() from outside the H5S package. Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() with H5Sselect_adjust. Implement "adjust_s" callback for all selection types. Add range checking to H5Sselect_adjust().
| * Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings ↵David Young2019-11-271-1/+1
| | | | | | | | level and fixing some code.' (commit 5c911d8baf3)"
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-261-1/+1
|\ \ | |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9': (45 commits) Oops, remove more C99 designated initializers for VS 2010 compatibility. Add an #include to get a function declaration. Don't use C99 designated initializers, they're not compatible with Visual Studio 2010. Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*. Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using. Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check. Only use -Werror=cast-function-type with GCC 8 and later. Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags. Add new source files to CMakeLists.txt. Mention the -Werror= flags in libhdf5.settings.in. free -> HDfree Promote decleration-after-statement warnings to errors. Quiet decleration-after-statement warnings. Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements. Document H5D__chunk_mem_xfree_wrapper(). Undo accidental test deletion. Oops, delete a debug printf that snuck in here. Undo my changes to the HD macros, hadn't really intended those to be on this branch.... Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options. Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *. ...
| * Mark an unused parameter H5_ATTR_UNUSED.David Young2019-11-131-1/+1
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* | HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-071-2/+2
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* Untangle #ifdef mess in ROS3 code.Dana Robinson2019-08-201-12/+6
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+1
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* Squashed commit of the following:Larry Knox2019-07-251-14/+503
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* Fixed typoBinh-Minh Ribler2019-01-081-1/+1
| | | | | Platforms tested: Darwin (osx1010test)
* Refixed HDFFV-10578Binh-Minh Ribler2019-01-081-1/+16
| | | | | | | | | | | | Description: Applied Neil's fix for this issue after removing previous attempt. The resources are now released in init_objs() when failure occurs there. Neil will fix HDFFV-10676 separately. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* Changes made based on feedback from pull request #1039.Vailin Choi2018-05-141-3/+3
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* Fix for HDFFV-10180 Performance issues with H5Oget_info.Vailin Choi2018-04-241-3/+3
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* HDFFV-10297 Cleanup, Initialize variablesAllen Byrne2017-10-231-3/+2
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* Windows had issues - revert code changes for get_optionAllen Byrne2017-10-191-4/+8
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* HDFFV-10296 Update tools lib to use the error handling macros.Allen Byrne2017-10-131-166/+65
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* HDFFV-10282 refactor out assert calls in toolsAllen Byrne2017-08-231-3/+5
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* Stripped C standard library headers (and a couple of macros)Dana Robinson2017-07-171-10/+0
| | | | | from the tools code. This is all handled in H5private.h, which should be included in all tools source files.
* 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-r30113] Description:Quincey Koziol2016-06-281-14/+16
| | | | | | | | Clean up warnings (from 2774 -> 1560, with my standard debug build) Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29222] HDFFV-9570: Fix segfault when optional args are last option on ↵Allen Byrne2016-02-281-23/+28
| | | | | | command line. Tested: java_merge DT
* [svn-r27626] Various minor warning fixes before major SWMR and VDS merges.Dana Robinson2015-08-311-0/+3
| | | | | | | | | | | gcc 4.9.2 was used to create the warning list - implicit casts - shadowed variables - various enum issues - other minor fixes (comments, unused macros, etc.) Tested on: h5committest
* [svn-r26635] Description:Quincey Koziol2015-03-281-18/+1
| | | | | | | | | | | Bring r26651 from autotools_rework branch to trunk: Remove the VSNPRINTF_WORKS macro, it's working around bugs in old SGI & HP compilers. Tested on: Linux/32 2.6.18 (jam) w/serial & parallel (Daily tested on branch for 2+ days)
* [svn-r23226] HDFFV-8285: suppress-ddl option: Changed file options to allow ↵Allen Byrne2013-02-041-0/+2
| | | | | | for filename F to be optional. Tested: local linux
* [svn-r23190] HDFFV-8285: Add suppress ddl option.Allen Byrne2013-01-221-8/+10
| | | | Tested: local linux
* [svn-r22625] HDFFV-8111: h5diff compare file to itself - removed path shortcutAllen Byrne2012-08-031-0/+2
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* [svn-r22012] Purpose:Jonathan Kim2012-03-011-2/+2
| | | | | | | | | | | | | | | | Task for HDFFV-7862 - Select data by chunk direction to improve performance in h5repack Description: h5repack sometimes became very slow when handling big chunked datasets in certain cases. (when chunk boundary doesn't match with a hyperslab boundary.) The main issue was from figuring out a hypeslab without considering chunk boundary to read from and write to such datasets. The update was made to figure out a better hyperslab unit with considering chunk boundary to improve performance for such cases prior to the update. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows
* [svn-r21985] Tools must call h5tools_init before command_line parsing or ↵Allen Byrne2012-02-241-18/+21
| | | | | | | | using tools_mesg functions. Tools library uses alais variables for stdout, stderr and tools library uses HDfprintf() functions. Tested: local linux
* [svn-r21982] Correct HD prefix in tools for exitAllen Byrne2012-02-241-1/+1
| | | | Checked for HD support.
* [svn-r21969] Added missing HD prefixAllen Byrne2012-02-221-66/+58
| | | | Correct indentation
* [svn-r21953] HDDFV-7560: h5dump refactoringAllen Byrne2012-02-171-3/+2
| | | | Tested: local linux
* [svn-r21586] Description:Jonathan Kim2011-10-141-0/+52
| | | | | | | | | Added a funtion to reset dataset & hyperslab buffer size for h5repack from an environment variable. This is performance debugging purpose for now. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE), cmake
* [svn-r21236] Purpose:Jonathan Kim2011-08-161-0/+18
| | | | | | | | | | | | | | | | | | | | Work for: HDFFV-7515 - GMQS: h5unjam - incorrect help page and should display when no file is given. and HDFFV-5941 - h5jam: specifying a user block file with a proper HDF5 magic number will result in a corrupted HDF5 file. Description: - Revised command help pages of h5jam and h5unjam. The descriptions were not up to date and some were missing. (HDFFV-7515) - Fixed h5jam not to allow specifying an HDF5 formatted file as input file for -u (user block file) option, because the original HDF5 file will not be accessible if allows. (HDFFV-5941) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Wondows)
* [svn-r20885] Description:Quincey Koziol2011-05-201-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes back to trunk: r20340: Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer. r20341: Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label. Do C-style initialization AFTER all variable definitions. r20342: Fix valgrind error in H5DUMP-XML-tall.h5 r20343: Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE. r20344: Added initialization udata.path = NULL; to prevent uninitialized used after done: label r20347: Purpose: Fix memory leak in overhead.c Description: Fixed leak in test() in overhead.c where array "had" was never freed. r20348: Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h. r20392: Purpose: Fix coverity issues 1677 and 1678 Description: Added return value checking for 4 funciton calls in H5tools_get_symlink_info(). r20394: Purpose: Fix coverity issues 1674 and 1675 Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether va_start() has been called, and to call va_end() at the end if so. r20395: Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh r20396: Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh Tested on: Mac OSX/32 10.6.7 (amazon) w/debug & production (h5committested on branch)
* [svn-r20536] Description:Quincey Koziol2011-04-171-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up various warnings & code formatting issues. Bring changes from Coverity branch to trunk: r20085: Purpose: Fix coverity issue 793 Description: Modified H5S_hyper_project_simple_higher() to free the entire span list in new_space on failure. r20091: This is a fix for coverity bug #1683. Changed the two printfs to use %lu (unsigned long) for printing "dset_size". r20162: Purpose: Fix coverity issue 785 Description: Modified H5T_enum_nameof() to free "name" on failure if it was allocated. Also clarified some code in H5S_hyper_rebuild_helper(). r20189: Addressed coverity defect 783. H5SL_new_node() in H5SL.c was failing to free space allocated in its first alloc if the second alloc failed. Added a call to H5FL_FREE to address this issue. This is purely to keep coverity happy -- if this code is ever triggered, we have much larger problems. Note that this fix will trigger an unused return value complaint from coverity next week. r20190: Fixed Coverity issues 1561 1565 and 1678 (UNUSED_VALUES) by moving checks of return values to after the function call. r20191: Fixed coverity issues 643 644 and 1678 (CHECKED_RETURN). r20232: Addressed coverity issues 923-925. Replaced calls to sprintf with calls to HDsnprintf. r20233: Fix coverity issue 662. Don't try to sort 0 attributes in H5Aint.c. r20234: Fix coverity issue 664. Check for NULL before dereferencing in H5Gdeprec.c. r20271: Purpose: Fix coverity issue 784 Description: Modified H5_debug_mask() to keep a list of files opened for use as a debugging output stream, and modified H5_term_library to close these files on exit. r20272: addressed coverity issues 838 & 955. Issue was use of strcpy() -- existing code was safe, but modified to use strncpy() to keep coverity happy. r20273: Addresed coverity issues 1388 and 1389. Initialized sel_iter->type to NULL in H5S_select_iter_init. r20275: Purpose: Fix valgrind issue in mf.c Description: Fixed bug (incomplete if statement) in test_mf_fs_alloc_free() so the retrieved node gets freed. 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, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
* [svn-r20294] Purpose:Jonathan Kim2011-03-221-2/+5
| | | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: Previously h5diff compared attributes correctly only when two objects have the same number of attributes and attribute names are identical. This fix covers all other cases. Also didn't display useful information about attribute difference. This fixes both issues. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r19400] Purpose:Jonathan Kim2010-09-161-4/+12
| | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani, heiwa
* [svn-r19292] Description:Quincey Koziol2010-08-241-31/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Merge r19290 & r19291 from 1.8 branch to trunk: r19290: Correct another error in metadata accumulator dirty region calculations (this time with a corner case when freeing data in the file). r19291: Avoid getting object information for soft/external links if we aren't going to traverse across the link itself. 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, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug 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 10.6.4 (amazon) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
* [svn-r19252] Description:Quincey Koziol2010-08-191-4/+76
| | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes from branch to trunk: r19161: Fixed the part for matching the subset info with dataset r19189: BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump. Changed all references to use new data structure. Added tests for each subset parameter. r19190: Added new h5dump ddl files Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (h5committested on branch)
* [svn-r19153] Description:Quincey Koziol2010-07-291-43/+34
| | | | | | | | | | | | | | | | | | | | | | | | Bring changes on Coverity branch back to trunk: r19040: Fixed coverity #440 - NULL check after dereference. We moved the NULL check up into the IF block and changed it to assertion. r19041: Maintenance: Addressed Coverity issues 441 and 449 by initializing proper variables r19042: In function H5O_chunk_protect (H5Ochunk.c): - Initialize H5O_chunk_proxy_t pointers chk_proxy and ret_value. - Free chk_proxy on error. r19043: Addressed coverity issues 442 - 448 by initializing pointers to NULL. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (Too minor to require h5committest)
* [svn-r19051] Purpose:Jonathan Kim2010-07-071-6/+5
| | | | | | | | | | | Add --no-dangling-links option to h5ls. Description: Related to "Bug 1830 - Following an dangling external link in h5ls should set non-zero return code." If --no-dangling-links option is specified and any dangling link is found, return exit code 1 (error). Tested: jam, amani and heiwa
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