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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/qkoziol/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.
Quincey Koziol qkoziol Savoy, IL

hpc-io/h5bench 7

A benchmark suite for measuring HDF5 performance.

soumagne/hdf5_archive 6

Workspace clone of HDF5 bitbucket

hpc-io/pdc 2

Proactive Data Containers (PDC) software provides an object-centric API and a runtime system with a set of data object management services. These services allow placing data in the memory and storage hierarchy, performing data movement asynchronously, and providing scalable metadata operations to find data objects.

markcmiller86/hdf5stuff 1

Temporary place to collect various HDF5 test clients

NERSC/LibWrap 1

Function Tracer and Logging

qkoziol/hdf5 0

Official HDF5® Library Repository

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Allen Byrne

commit sha c88c0f2008a0a431ee64ae7a36ed29f927ba3e13

Correct number of args to Windows HDunsetenv macro (#939) * Correct number of args to Windows HDunsetenv macro * Correct format

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Allen Byrne

commit sha 2524b57a6f69e1a24212cba12d504748e13e9743

Develop windows compiler fixes (#912) * Fix windows compiler issues Restore MS C++ Default exception handling behavior #885 Remove clang toolchain as it skips compiler checks * Add check and header gaurd for pwd.h * Revert change * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Larry Knox

commit sha 564380d176ae71d9f4ece9df51957e3f817be45d

Fix issue #924 in develop branch: the ${HDF5_CXXLINKER} does not work in h5c++ (#925) * Committing clang-format changes * Fix issue #924, ${HDF5_CXXLINKER} does not work in h5c++. 2 instances of CLINKER corrected to CXXLINKER comment border aligned Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha 3600d33f10db1d520f360930c40bf99e282af101

CMake should use the output dir programs for shell scripts (#928)

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Jan-Willem Blokland

commit sha de60f08b0df0abdcac1c6959b393a6862dadd4ce

CMake: (fix) ph5example test (#935) Ensure that the used number of processes times an integer number is equal to SPACE1_DIM1 and SPACE_DIM2. These variables are equal to 24 and are defined in ph5example.c. If this is not the case the ph5example test will fail.

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Sean McBride

commit sha 09283ffbcb921efa89a7a1ca728f1d4b7064df8e

Get class name null str (#899) * Fixed MSVC compile error in C++23 mode Error message from MSVC with C++23 enabled: error C2440: 'return': cannot convert from 'int' to 'std::basic_string<char,std::char_traits,std::allocator>' * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha b38bc071e956bec607b180a7d3f8217197393f02

Remove incorrect compiler check for windows clang sanitizer (#942)

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Ben Boeckel

commit sha b5f5c59f297be19096051282068cdcc14275eb34

cmake: simplify try_run result comparisons (#950) Instead of looking at `MATCHES 0` which runs a regex and returns a false positive for any result such as `10`, check if they are equal to `0`. Also quote `0` to avoid looking it up as a variable (which was left behind prior to the fix to use `${RETURN_VAR}` in the `c_run` macro).

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Sean McBride

commit sha f6c49fe8911a39810b236f7babf09a70fcc76c7b

More clang tidy (#908) * Pacify clang-analyzer-unix.cstring.NullArg * Apply some bugprone-suspicious-string-compare * Apply some readability-simplify-boolean-expr * Apply some readability-make-member-function-const * Apple some bugprone-macro-parentheses * Changed an f suffix to L for `long double` * Applied some readability-uppercase-literal-suffix automatically * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Dana Robinson

commit sha e9765e6c09de2e278e2821faef656b6d61854196

Move pwd header check to alphabetical order (#954)

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Sean McBride

commit sha 131402a92de9bbd5df60d5859c37c4820c60d6b9

More various warnings (#958) * Committing clang-format changes * Fixed various -Wdouble-promotion warnings * Fixed -Wshadow warning for `optopt` conflict On macOS at least, there is a global various named `optopt` in unistd.h. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Scot Breitenfeld

commit sha 794acf489fa093a3a119723c7cea74cb2880624b

Fixed failure on BE with xlf (#968) * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Scot Breitenfeld

commit sha 01fe2549a36d7635b2cbe6f6a57cbcce29c1335b

Rework of PR #826 (#972) * H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c88c0f2008a0a431ee64ae7a36ed29f927ba3e13

Correct number of args to Windows HDunsetenv macro (#939) * Correct number of args to Windows HDunsetenv macro * Correct format

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Allen Byrne

commit sha 2524b57a6f69e1a24212cba12d504748e13e9743

Develop windows compiler fixes (#912) * Fix windows compiler issues Restore MS C++ Default exception handling behavior #885 Remove clang toolchain as it skips compiler checks * Add check and header gaurd for pwd.h * Revert change * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Larry Knox

commit sha 564380d176ae71d9f4ece9df51957e3f817be45d

Fix issue #924 in develop branch: the ${HDF5_CXXLINKER} does not work in h5c++ (#925) * Committing clang-format changes * Fix issue #924, ${HDF5_CXXLINKER} does not work in h5c++. 2 instances of CLINKER corrected to CXXLINKER comment border aligned Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha 3600d33f10db1d520f360930c40bf99e282af101

CMake should use the output dir programs for shell scripts (#928)

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Jan-Willem Blokland

commit sha de60f08b0df0abdcac1c6959b393a6862dadd4ce

CMake: (fix) ph5example test (#935) Ensure that the used number of processes times an integer number is equal to SPACE1_DIM1 and SPACE_DIM2. These variables are equal to 24 and are defined in ph5example.c. If this is not the case the ph5example test will fail.

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Sean McBride

commit sha 09283ffbcb921efa89a7a1ca728f1d4b7064df8e

Get class name null str (#899) * Fixed MSVC compile error in C++23 mode Error message from MSVC with C++23 enabled: error C2440: 'return': cannot convert from 'int' to 'std::basic_string<char,std::char_traits,std::allocator>' * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha b38bc071e956bec607b180a7d3f8217197393f02

Remove incorrect compiler check for windows clang sanitizer (#942)

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Ben Boeckel

commit sha b5f5c59f297be19096051282068cdcc14275eb34

cmake: simplify try_run result comparisons (#950) Instead of looking at `MATCHES 0` which runs a regex and returns a false positive for any result such as `10`, check if they are equal to `0`. Also quote `0` to avoid looking it up as a variable (which was left behind prior to the fix to use `${RETURN_VAR}` in the `c_run` macro).

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Sean McBride

commit sha f6c49fe8911a39810b236f7babf09a70fcc76c7b

More clang tidy (#908) * Pacify clang-analyzer-unix.cstring.NullArg * Apply some bugprone-suspicious-string-compare * Apply some readability-simplify-boolean-expr * Apply some readability-make-member-function-const * Apple some bugprone-macro-parentheses * Changed an f suffix to L for `long double` * Applied some readability-uppercase-literal-suffix automatically * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Dana Robinson

commit sha e9765e6c09de2e278e2821faef656b6d61854196

Move pwd header check to alphabetical order (#954)

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Sean McBride

commit sha 131402a92de9bbd5df60d5859c37c4820c60d6b9

More various warnings (#958) * Committing clang-format changes * Fixed various -Wdouble-promotion warnings * Fixed -Wshadow warning for `optopt` conflict On macOS at least, there is a global various named `optopt` in unistd.h. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Scot Breitenfeld

commit sha 794acf489fa093a3a119723c7cea74cb2880624b

Fixed failure on BE with xlf (#968) * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Scot Breitenfeld

commit sha 01fe2549a36d7635b2cbe6f6a57cbcce29c1335b

Rework of PR #826 (#972) * H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c88c0f2008a0a431ee64ae7a36ed29f927ba3e13

Correct number of args to Windows HDunsetenv macro (#939) * Correct number of args to Windows HDunsetenv macro * Correct format

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Allen Byrne

commit sha 2524b57a6f69e1a24212cba12d504748e13e9743

Develop windows compiler fixes (#912) * Fix windows compiler issues Restore MS C++ Default exception handling behavior #885 Remove clang toolchain as it skips compiler checks * Add check and header gaurd for pwd.h * Revert change * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Larry Knox

commit sha 564380d176ae71d9f4ece9df51957e3f817be45d

Fix issue #924 in develop branch: the ${HDF5_CXXLINKER} does not work in h5c++ (#925) * Committing clang-format changes * Fix issue #924, ${HDF5_CXXLINKER} does not work in h5c++. 2 instances of CLINKER corrected to CXXLINKER comment border aligned Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha 3600d33f10db1d520f360930c40bf99e282af101

CMake should use the output dir programs for shell scripts (#928)

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Jan-Willem Blokland

commit sha de60f08b0df0abdcac1c6959b393a6862dadd4ce

CMake: (fix) ph5example test (#935) Ensure that the used number of processes times an integer number is equal to SPACE1_DIM1 and SPACE_DIM2. These variables are equal to 24 and are defined in ph5example.c. If this is not the case the ph5example test will fail.

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Sean McBride

commit sha 09283ffbcb921efa89a7a1ca728f1d4b7064df8e

Get class name null str (#899) * Fixed MSVC compile error in C++23 mode Error message from MSVC with C++23 enabled: error C2440: 'return': cannot convert from 'int' to 'std::basic_string<char,std::char_traits,std::allocator>' * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha b38bc071e956bec607b180a7d3f8217197393f02

Remove incorrect compiler check for windows clang sanitizer (#942)

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Ben Boeckel

commit sha b5f5c59f297be19096051282068cdcc14275eb34

cmake: simplify try_run result comparisons (#950) Instead of looking at `MATCHES 0` which runs a regex and returns a false positive for any result such as `10`, check if they are equal to `0`. Also quote `0` to avoid looking it up as a variable (which was left behind prior to the fix to use `${RETURN_VAR}` in the `c_run` macro).

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Sean McBride

commit sha f6c49fe8911a39810b236f7babf09a70fcc76c7b

More clang tidy (#908) * Pacify clang-analyzer-unix.cstring.NullArg * Apply some bugprone-suspicious-string-compare * Apply some readability-simplify-boolean-expr * Apply some readability-make-member-function-const * Apple some bugprone-macro-parentheses * Changed an f suffix to L for `long double` * Applied some readability-uppercase-literal-suffix automatically * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Dana Robinson

commit sha e9765e6c09de2e278e2821faef656b6d61854196

Move pwd header check to alphabetical order (#954)

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Sean McBride

commit sha 131402a92de9bbd5df60d5859c37c4820c60d6b9

More various warnings (#958) * Committing clang-format changes * Fixed various -Wdouble-promotion warnings * Fixed -Wshadow warning for `optopt` conflict On macOS at least, there is a global various named `optopt` in unistd.h. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Scot Breitenfeld

commit sha 794acf489fa093a3a119723c7cea74cb2880624b

Fixed failure on BE with xlf (#968) * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Scot Breitenfeld

commit sha 01fe2549a36d7635b2cbe6f6a57cbcce29c1335b

Rework of PR #826 (#972) * H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Dana Robinson

commit sha 04f1bff6757892df07cd72520af276f7691ff43b

Updates the RELEASE.txt file with a note about the variable-length fill (#871) value issue. A fix is in progress, but it might be a while before we have time to finish it up.

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Dana Robinson

commit sha 5dabec4cf6b97793e3af6df3b6a3953394bbf27d

Removes partial long options from the tools (#872) Some of the command-line tools would allow partial long options (e.g., --datas instead of --dataset). These were inconsistently implemented, difficult to maintain, and occasionally blocked useful long options. They have been removed from all the tools. NOTE: This change should NOT be merged to 1.12 or earlier.

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Allen Byrne

commit sha acb186f6e5f0ac3e5bfb9501e3381c1968489a59

Add parallel version of h5pfc script (#881)

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Allen Byrne

commit sha 06a09a962acd30527aac7f8922ac7b6c6a571874

Reorg tools perform to provide h5perf for installation (#884) * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Reorg tools perform to provide h5perf for installation * Correct file paths * Correct path * Add new src folder to makefile list * Remove bin_PROGRAMS from TEST_PROG * Default h5perf executables to static build * Remove test lib dependency from h5perf * format adjustments * Remove test lib from autotools makefile * Add note * h5perf needs the math library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

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jhendersonHDF

commit sha baefe444942452a17f982081ca733f010557073c

Fix link issue with perf/h5perf in parallel library (#889)

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David Wells

commit sha 7c918e685fea4d58b632389999f092b1f4b33d17

Guard the SKIP_MPICXX macros against redefinition. (#892)

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Dana Robinson

commit sha b5c66529e9709839f336d2b6f0d453139a0744b5

Fixes a bad memory read and unfreed memory in fsinfo code (#893) * Fixes a bad memory read and unfreed memory in fsinfo code The segfaul from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c0f1db4b96d43cd2f7bcd0134e107061e866d6e3

Update examples version used by CMake (#882)

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Allen Byrne

commit sha 6968906418f9ecfc383ad960c975e65a504743b7

Fix clang/sanitizer for windows (#883) * Fix clang/sanitizer for windows * Restrict MSVC version for sanitize

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Allen Byrne

commit sha 451b472cdd63c8fef15c0866e0d3784e33a8b1c6

Fixed the CMake processing for C++ warnings and flags (#888)

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Allen Byrne

commit sha 04c504664b2cbb63b6a5cdf8c58a93dc65699f6d

Fix formatting (#923)

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Allen Byrne

commit sha af7989e858d383322ced07873c2e19b433e74988

Correct dataset close in java test (#919) * Correct dataset close * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c019db60eecc173e1d3b118c9aeb7885865fa50f

Remove non-published short arg names (#917) * Remove non-published short arg names * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Dana Robinson

commit sha 04f1bff6757892df07cd72520af276f7691ff43b

Updates the RELEASE.txt file with a note about the variable-length fill (#871) value issue. A fix is in progress, but it might be a while before we have time to finish it up.

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Dana Robinson

commit sha 5dabec4cf6b97793e3af6df3b6a3953394bbf27d

Removes partial long options from the tools (#872) Some of the command-line tools would allow partial long options (e.g., --datas instead of --dataset). These were inconsistently implemented, difficult to maintain, and occasionally blocked useful long options. They have been removed from all the tools. NOTE: This change should NOT be merged to 1.12 or earlier.

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Allen Byrne

commit sha acb186f6e5f0ac3e5bfb9501e3381c1968489a59

Add parallel version of h5pfc script (#881)

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Allen Byrne

commit sha 06a09a962acd30527aac7f8922ac7b6c6a571874

Reorg tools perform to provide h5perf for installation (#884) * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Reorg tools perform to provide h5perf for installation * Correct file paths * Correct path * Add new src folder to makefile list * Remove bin_PROGRAMS from TEST_PROG * Default h5perf executables to static build * Remove test lib dependency from h5perf * format adjustments * Remove test lib from autotools makefile * Add note * h5perf needs the math library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

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jhendersonHDF

commit sha baefe444942452a17f982081ca733f010557073c

Fix link issue with perf/h5perf in parallel library (#889)

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David Wells

commit sha 7c918e685fea4d58b632389999f092b1f4b33d17

Guard the SKIP_MPICXX macros against redefinition. (#892)

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Dana Robinson

commit sha b5c66529e9709839f336d2b6f0d453139a0744b5

Fixes a bad memory read and unfreed memory in fsinfo code (#893) * Fixes a bad memory read and unfreed memory in fsinfo code The segfaul from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c0f1db4b96d43cd2f7bcd0134e107061e866d6e3

Update examples version used by CMake (#882)

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Allen Byrne

commit sha 6968906418f9ecfc383ad960c975e65a504743b7

Fix clang/sanitizer for windows (#883) * Fix clang/sanitizer for windows * Restrict MSVC version for sanitize

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Allen Byrne

commit sha 451b472cdd63c8fef15c0866e0d3784e33a8b1c6

Fixed the CMake processing for C++ warnings and flags (#888)

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Allen Byrne

commit sha 04c504664b2cbb63b6a5cdf8c58a93dc65699f6d

Fix formatting (#923)

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Allen Byrne

commit sha af7989e858d383322ced07873c2e19b433e74988

Correct dataset close in java test (#919) * Correct dataset close * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c019db60eecc173e1d3b118c9aeb7885865fa50f

Remove non-published short arg names (#917) * Remove non-published short arg names * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Dana Robinson

commit sha 04f1bff6757892df07cd72520af276f7691ff43b

Updates the RELEASE.txt file with a note about the variable-length fill (#871) value issue. A fix is in progress, but it might be a while before we have time to finish it up.

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Dana Robinson

commit sha 5dabec4cf6b97793e3af6df3b6a3953394bbf27d

Removes partial long options from the tools (#872) Some of the command-line tools would allow partial long options (e.g., --datas instead of --dataset). These were inconsistently implemented, difficult to maintain, and occasionally blocked useful long options. They have been removed from all the tools. NOTE: This change should NOT be merged to 1.12 or earlier.

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Allen Byrne

commit sha acb186f6e5f0ac3e5bfb9501e3381c1968489a59

Add parallel version of h5pfc script (#881)

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Allen Byrne

commit sha 06a09a962acd30527aac7f8922ac7b6c6a571874

Reorg tools perform to provide h5perf for installation (#884) * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Reorg tools perform to provide h5perf for installation * Correct file paths * Correct path * Add new src folder to makefile list * Remove bin_PROGRAMS from TEST_PROG * Default h5perf executables to static build * Remove test lib dependency from h5perf * format adjustments * Remove test lib from autotools makefile * Add note * h5perf needs the math library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

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jhendersonHDF

commit sha baefe444942452a17f982081ca733f010557073c

Fix link issue with perf/h5perf in parallel library (#889)

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David Wells

commit sha 7c918e685fea4d58b632389999f092b1f4b33d17

Guard the SKIP_MPICXX macros against redefinition. (#892)

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Dana Robinson

commit sha b5c66529e9709839f336d2b6f0d453139a0744b5

Fixes a bad memory read and unfreed memory in fsinfo code (#893) * Fixes a bad memory read and unfreed memory in fsinfo code The segfaul from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c0f1db4b96d43cd2f7bcd0134e107061e866d6e3

Update examples version used by CMake (#882)

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Allen Byrne

commit sha 6968906418f9ecfc383ad960c975e65a504743b7

Fix clang/sanitizer for windows (#883) * Fix clang/sanitizer for windows * Restrict MSVC version for sanitize

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Allen Byrne

commit sha 451b472cdd63c8fef15c0866e0d3784e33a8b1c6

Fixed the CMake processing for C++ warnings and flags (#888)

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Allen Byrne

commit sha 04c504664b2cbb63b6a5cdf8c58a93dc65699f6d

Fix formatting (#923)

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Allen Byrne

commit sha af7989e858d383322ced07873c2e19b433e74988

Correct dataset close in java test (#919) * Correct dataset close * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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Allen Byrne

commit sha c019db60eecc173e1d3b118c9aeb7885865fa50f

Remove non-published short arg names (#917) * Remove non-published short arg names * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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pull request commentHDFGroup/hdf5

H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() …

This code looks fine, but it needs a test, to demonstrate that it actually works. Adding it to both the serial testing for data transforms (in the 'test' directory) and the parallel testing (in the 'testpar' directory) is probably necessary, since I believe that use in parallel HDF5 is desired.

Also, with a test, you'll guarantee that it stays working. :-)

jwsblokland

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pull request commentHDFGroup/hdf5

Improvement/data transform

The change to the src/H5Ztrans.c is fine, but it seems like the other pieces are out of date?

Or possibly, those are correct, but probably should be in a separate PR?

jwsblokland

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Larry Knox

commit sha 9fd356e2408b6f91bfbe6820cdb979b6fade3fb3

Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid (#866) warning that unsigned comparison < 0 is always false, which is known, but for later versions the comparison can possibly be true.

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Larry Knox

commit sha 48a05aa887ae7d18512756bf1eeb177e08d0feaf

Unsigned comparison to 0 warning avoidance (#869) * Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid warning that unsigned comparison < 0 is always false, which is known, but for later versions the comparison can possibly be true. * Better solution for avoiding warning that unsigned comparison < 0.

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Larry Knox

commit sha 9fd356e2408b6f91bfbe6820cdb979b6fade3fb3

Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid (#866) warning that unsigned comparison < 0 is always false, which is known, but for later versions the comparison can possibly be true.

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Larry Knox

commit sha 48a05aa887ae7d18512756bf1eeb177e08d0feaf

Unsigned comparison to 0 warning avoidance (#869) * Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid warning that unsigned comparison < 0 is always false, which is known, but for later versions the comparison can possibly be true. * Better solution for avoiding warning that unsigned comparison < 0.

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Larry Knox

commit sha 9fd356e2408b6f91bfbe6820cdb979b6fade3fb3

Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid (#866) warning that unsigned comparison < 0 is always false, which is known, but for later versions the comparison can possibly be true.

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Larry Knox

commit sha 48a05aa887ae7d18512756bf1eeb177e08d0feaf

Unsigned comparison to 0 warning avoidance (#869) * Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid warning that unsigned comparison < 0 is always false, which is known, but for later versions the comparison can possibly be true. * Better solution for avoiding warning that unsigned comparison < 0.

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Dana Robinson

commit sha 725da3768b6537d0cfae59f6b220396ea9fa042d

Removes unused commented-out code from h5jamgentest.c (#851)

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H. Joe Lee

commit sha f3441d54866d0736468b2697bbbee3ec81a83a5b

OESS-168:Remove clang warnings. (#835) * OESS-168:Remove implicit conversion increases floating-point precision warnings. * OESS-168:Remove clang warnings. * OESS-168:Remove clang warnings. * Committing clang-format changes * OESS-168:Remove clang warnings. * Committing clang-format changes * OESS-168:Remove clang warning. * OESS-168:Remove clang warnings. * OESS-168:Address @byrnHDF review. * Remove line added to generated hl/src/H5LTanalyze.c file. Issue #854 created for creating a fix. * Remove extra whitespace from H5LTanalyze.c. * Remove extra blank line. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

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Allen Byrne

commit sha 74f1590d47acd41cd9aea8d9f6be52a5947ee5af

Only test h5diff_830 in serial (#858)

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Allen Byrne

commit sha cfcdf215187653703a21f1f99cc18e207138c39b

Remove version-check for relnum in H5check. (#812) * Remove version-check for relnum in H5check. * Add in release exception code check * Fix typos * Fix more typos * Rework comments * format change * format whitespace * Library version must be less than or equal to headers * Need the NOT version of the compare * Enable release+1 check for PASS * Add release note * Update note

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Dana Robinson

commit sha 9bb1d6d78e305e73b5c882e8f5b3ef66a1acdf8d

Updates a comment in H5mpi.c (#863) MPI_Type_struct() is an MPI-1 call we no longer use.

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Dana Robinson

commit sha 725da3768b6537d0cfae59f6b220396ea9fa042d

Removes unused commented-out code from h5jamgentest.c (#851)

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H. Joe Lee

commit sha f3441d54866d0736468b2697bbbee3ec81a83a5b

OESS-168:Remove clang warnings. (#835) * OESS-168:Remove implicit conversion increases floating-point precision warnings. * OESS-168:Remove clang warnings. * OESS-168:Remove clang warnings. * Committing clang-format changes * OESS-168:Remove clang warnings. * Committing clang-format changes * OESS-168:Remove clang warning. * OESS-168:Remove clang warnings. * OESS-168:Address @byrnHDF review. * Remove line added to generated hl/src/H5LTanalyze.c file. Issue #854 created for creating a fix. * Remove extra whitespace from H5LTanalyze.c. * Remove extra blank line. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

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Allen Byrne

commit sha 74f1590d47acd41cd9aea8d9f6be52a5947ee5af

Only test h5diff_830 in serial (#858)

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Allen Byrne

commit sha cfcdf215187653703a21f1f99cc18e207138c39b

Remove version-check for relnum in H5check. (#812) * Remove version-check for relnum in H5check. * Add in release exception code check * Fix typos * Fix more typos * Rework comments * format change * format whitespace * Library version must be less than or equal to headers * Need the NOT version of the compare * Enable release+1 check for PASS * Add release note * Update note

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Dana Robinson

commit sha 9bb1d6d78e305e73b5c882e8f5b3ef66a1acdf8d

Updates a comment in H5mpi.c (#863) MPI_Type_struct() is an MPI-1 call we no longer use.

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Dana Robinson

commit sha 725da3768b6537d0cfae59f6b220396ea9fa042d

Removes unused commented-out code from h5jamgentest.c (#851)

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H. Joe Lee

commit sha f3441d54866d0736468b2697bbbee3ec81a83a5b

OESS-168:Remove clang warnings. (#835) * OESS-168:Remove implicit conversion increases floating-point precision warnings. * OESS-168:Remove clang warnings. * OESS-168:Remove clang warnings. * Committing clang-format changes * OESS-168:Remove clang warnings. * Committing clang-format changes * OESS-168:Remove clang warning. * OESS-168:Remove clang warnings. * OESS-168:Address @byrnHDF review. * Remove line added to generated hl/src/H5LTanalyze.c file. Issue #854 created for creating a fix. * Remove extra whitespace from H5LTanalyze.c. * Remove extra blank line. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

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Allen Byrne

commit sha 74f1590d47acd41cd9aea8d9f6be52a5947ee5af

Only test h5diff_830 in serial (#858)

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Allen Byrne

commit sha cfcdf215187653703a21f1f99cc18e207138c39b

Remove version-check for relnum in H5check. (#812) * Remove version-check for relnum in H5check. * Add in release exception code check * Fix typos * Fix more typos * Rework comments * format change * format whitespace * Library version must be less than or equal to headers * Need the NOT version of the compare * Enable release+1 check for PASS * Add release note * Update note

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Dana Robinson

commit sha 9bb1d6d78e305e73b5c882e8f5b3ef66a1acdf8d

Updates a comment in H5mpi.c (#863) MPI_Type_struct() is an MPI-1 call we no longer use.

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jhendersonHDF

commit sha 31027a997c3cc5de9140930560d5155bef26289b

Add support for parallel filters to h5repack (#832)

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Jan-Willem Blokland

commit sha 21c6bb38e6cf0776dbdc37841280dffd6ca79990

CMake: (feature) libaec (#703) * CMake: (feature) libaec Implemented better support for the compression library libaec. Especially, for the new version 1.0.5: - The CMake config files of this version 1.0.5 now set certain SZIP variables which can be used in the existing CMake structure. - Both static and shared SZIP compatible libaec library contains all required objects such it can be easily used when building HDF5 from scratch. - Introduced the USE_LIBAEC_STATIC option to make use of the static version of SZIP compatible libaec library. * CMake: (fix) libaec Implemented the fallback option for the case if version 1.0.5 of libaec could not be found. * Docs: Added description about libaec implementation. Added short description about the libaec improvement to the Bug Fixes section in the Configuration sub-section.

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Allen Byrne

commit sha 9ec773bb18b8e7ddce5e347577329fcc8f7a73a9

Changes to docs for using plugins (#814) * Changes to docs for using plugins * VS2019 corrections * Fix typo

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Allen Byrne

commit sha 436727dceab2df46ef688f31fa199254e64ec34a

Perform option arg variables (#834) * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Fix static perform tools compile for arg options Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

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jhendersonHDF

commit sha 50a37fde06457ee5e75ea65259c233cb6527bd91

Allow parallel filters feature for comm size of 1 (#840)

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Allen Byrne

commit sha 20dd1cedb35d95ecc21decb29352d7779d49a908

Issue #833 fix setting return result (#843)

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jhendersonHDF

commit sha 96b6872a1e7deac7673d31697dafa1f44763ede4

Avoid popping API context when one wasn't pushed (#848)

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Dana Robinson

commit sha 06de43332d80229dbe5f5a1ac4addf3fbc8325f5

Fixes a couple of warnings: (#849) - warn_unused_result warnings from h5jamgentest and j5stat_gentest that were triggered by write(2) calls where we didn't check the return value - A missing callback in the NULL VOL connector - A possibly uninitialized property list pointer

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jhendersonHDF

commit sha 31027a997c3cc5de9140930560d5155bef26289b

Add support for parallel filters to h5repack (#832)

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Jan-Willem Blokland

commit sha 21c6bb38e6cf0776dbdc37841280dffd6ca79990

CMake: (feature) libaec (#703) * CMake: (feature) libaec Implemented better support for the compression library libaec. Especially, for the new version 1.0.5: - The CMake config files of this version 1.0.5 now set certain SZIP variables which can be used in the existing CMake structure. - Both static and shared SZIP compatible libaec library contains all required objects such it can be easily used when building HDF5 from scratch. - Introduced the USE_LIBAEC_STATIC option to make use of the static version of SZIP compatible libaec library. * CMake: (fix) libaec Implemented the fallback option for the case if version 1.0.5 of libaec could not be found. * Docs: Added description about libaec implementation. Added short description about the libaec improvement to the Bug Fixes section in the Configuration sub-section.

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Allen Byrne

commit sha 9ec773bb18b8e7ddce5e347577329fcc8f7a73a9

Changes to docs for using plugins (#814) * Changes to docs for using plugins * VS2019 corrections * Fix typo

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Allen Byrne

commit sha 436727dceab2df46ef688f31fa199254e64ec34a

Perform option arg variables (#834) * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Fix static perform tools compile for arg options Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

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jhendersonHDF

commit sha 50a37fde06457ee5e75ea65259c233cb6527bd91

Allow parallel filters feature for comm size of 1 (#840)

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Allen Byrne

commit sha 20dd1cedb35d95ecc21decb29352d7779d49a908

Issue #833 fix setting return result (#843)

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jhendersonHDF

commit sha 96b6872a1e7deac7673d31697dafa1f44763ede4

Avoid popping API context when one wasn't pushed (#848)

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Dana Robinson

commit sha 06de43332d80229dbe5f5a1ac4addf3fbc8325f5

Fixes a couple of warnings: (#849) - warn_unused_result warnings from h5jamgentest and j5stat_gentest that were triggered by write(2) calls where we didn't check the return value - A missing callback in the NULL VOL connector - A possibly uninitialized property list pointer

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jhendersonHDF

commit sha 31027a997c3cc5de9140930560d5155bef26289b

Add support for parallel filters to h5repack (#832)

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Jan-Willem Blokland

commit sha 21c6bb38e6cf0776dbdc37841280dffd6ca79990

CMake: (feature) libaec (#703) * CMake: (feature) libaec Implemented better support for the compression library libaec. Especially, for the new version 1.0.5: - The CMake config files of this version 1.0.5 now set certain SZIP variables which can be used in the existing CMake structure. - Both static and shared SZIP compatible libaec library contains all required objects such it can be easily used when building HDF5 from scratch. - Introduced the USE_LIBAEC_STATIC option to make use of the static version of SZIP compatible libaec library. * CMake: (fix) libaec Implemented the fallback option for the case if version 1.0.5 of libaec could not be found. * Docs: Added description about libaec implementation. Added short description about the libaec improvement to the Bug Fixes section in the Configuration sub-section.

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Allen Byrne

commit sha 9ec773bb18b8e7ddce5e347577329fcc8f7a73a9

Changes to docs for using plugins (#814) * Changes to docs for using plugins * VS2019 corrections * Fix typo

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Allen Byrne

commit sha 436727dceab2df46ef688f31fa199254e64ec34a

Perform option arg variables (#834) * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly * Update missing release note info. * Update code owners * Correct JIRA note * add known problem. * Use only core library for testing dynamic plugins. * Fix static perform tools compile for arg options Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

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jhendersonHDF

commit sha 50a37fde06457ee5e75ea65259c233cb6527bd91

Allow parallel filters feature for comm size of 1 (#840)

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Allen Byrne

commit sha 20dd1cedb35d95ecc21decb29352d7779d49a908

Issue #833 fix setting return result (#843)

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jhendersonHDF

commit sha 96b6872a1e7deac7673d31697dafa1f44763ede4

Avoid popping API context when one wasn't pushed (#848)

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Dana Robinson

commit sha 06de43332d80229dbe5f5a1ac4addf3fbc8325f5

Fixes a couple of warnings: (#849) - warn_unused_result warnings from h5jamgentest and j5stat_gentest that were triggered by write(2) calls where we didn't check the return value - A missing callback in the NULL VOL connector - A possibly uninitialized property list pointer

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pull request commentHDFGroup/hdf5

VFD plugins

@jhendersonHDF - Some of these sound useful now, would you consider making some smaller PRs out of them?

I'm guessing you're referring to changes like the H5P package termination stuff? I can definitely make some small PRs out of changes like that.

Yes, super, thanks!

jhendersonHDF

comment created time in 2 months

pull request commentHDFGroup/hdf5

VFD plugins

@jhendersonHDF - Some of these sound useful now, would you consider making some smaller PRs out of them?

jhendersonHDF

comment created time in 2 months

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PullRequestReviewEvent
PullRequestReviewEvent

pull request commentHDFGroup/hdf5

Add support for parallel filters to h5repack

Is h5repack still being run from only one MPI process? (Or without using "mpirun ...")

In general, yes. This is mostly just to help with the fact that the parallel filters feature doesn't currently acknowledge a difference between running with one MPI rank and multiple. It just always requires collective I/O. However, this also might be useful if we start making more of HDF5's tools parallel-capable. I believe h5repack has been specifically called out as desirable for that.

OK, sounds reasonable. (And already merged :-) )

jhendersonHDF

comment created time in 2 months

pull request commentHDFGroup/hdf5

Add support for parallel filters to h5repack

Is h5repack still being run from only one MPI process? (Or without using "mpirun ...")

jhendersonHDF

comment created time in 2 months