Merge 839 hdf5 1 10 (#879)

* Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. * Snapshot version 1.10 release 8-1. Update version to 1.10.8-2. Squashed commit of the following: commit 60734e63fe077238f10de3d6ca8f037f9a42af89 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 24 14:20:39 2021 -0500 Hdf5 1 10 Fix tools test (#796) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit bfb780a4441e4ef43dd23708d415e5e3b84800f4 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 23 14:11:46 2021 -0500 Hdf5 1 10 Release Note (#786) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 22 07:03:26 2021 -0500 Hdf5 1 10 Update missing release note info. (#778) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb Author: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri Jun 18 06:42:23 2021 -0700 Brings hash table IDs feature from develop/1.12 (#768) * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 17 11:21:43 2021 -0500 Hdf5 1 10 Fix cmake configure path (#762) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 16 15:45:58 2021 -0500 Hdf5 1 10 merge warnings changes (#756) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit e25980e7f35b8508db90648409ba80ee36d61c9e Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 8 14:37:13 2021 -0500 Hdf5 1 10 merges of CMake changes (#738) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jun 3 16:07:23 2021 -0500 Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> * (fix) Segmentation fault when using a compound type. (#143) * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * (fix) H5Z_xform_create function and scientific notation (#144) * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * Adds const to a few global variables (#623) * Committing clang-format changes * Adds consts to a few global variables Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Made private my_yyinput function static (#618) This prevents it being exported as a public symbol. * Reduces overly-pedantic casting in the public headers (#644) * Committing clang-format changes * Fixes overly pedantic casting in public headers Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Fixes for a couple of trivial warnings (#676) * Committing clang-format changes * Trivial warning fixes: * Removes an unused done target in H5Tbit.c * Add (void) to quiet "ignored return value" warnings in the generators (which generally ignore errors) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Various CMake changes (#679) * Committing clang-format changes * Several CMake updates: * Removes unused HDF5_ENABLE_HSIZET * Switches TEST_SHELL_SCRIPTS to ON * Sets SH_PROGRAM to bash instead of sh * Set default build type back to RelWithDebInfo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Removes alternative function enter/leave macro scheme (#678)" This reverts commit edddb11b791adbdcaafed3ba718c95dd349a4e9a. * err_compat test cleanup (#681) * Committing clang-format changes * Cleans up err_compat test and output * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Sets the memory alloc sanity check option to disabled in autotools (#686) * Revert "Sets the memory alloc sanity check option to disabled in autotools (#686)" This reverts commit 652ffca58699388fff960c6a92c8ecfd1fc5d19b. (Only for release branch). * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Squashed commit of the following: commit e2578640fedf671cf11535cf22313dd477da1165 Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jul 16 10:57:51 2021 -0500 Merge issue 839 changes to hdf5 1 10 (#841) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. * Snapshot version 1.10 release 8-1. Update version to 1.10.8-2. Squashed commit of the following: commit 60734e63fe077238f10de3d6ca8f037f9a42af89 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 24 14:20:39 2021 -0500 Hdf5 1 10 Fix tools test (#796) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit bfb780a4441e4ef43dd23708d415e5e3b84800f4 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 23 14:11:46 2021 -0500 Hdf5 1 10 Release Note (#786) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 22 07:03:26 2021 -0500 Hdf5 1 10 Update missing release note info. (#778) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb Author: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri Jun 18 06:42:23 2021 -0700 Brings hash table IDs feature from develop/1.12 (#768) * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 17 11:21:43 2021 -0500 Hdf5 1 10 Fix cmake configure path (#762) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 16 15:45:58 2021 -0500 Hdf5 1 10 merge warnings changes (#756) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit e25980e7f35b8508db90648409ba80ee36d61c9e Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 8 14:37:13 2021 -0500 Hdf5 1 10 merges of CMake changes (#738) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jun 3 16:07:23 2021 -0500 Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> * (fix) Segmentation fault when using a compound type. (#143) * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * (fix) H5Z_xform_create function and scientific notation (#144) * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * Adds const to a few global variables (#623) * Committing clang-format changes * Adds consts to a few global variables Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Made private my_yyinput function static (#618) This prevents it being exported as a public symbol. * Reduces overly-pedantic casting in the public headers (#644) * Committing clang-format changes * Fixes overly pedantic casting in public headers Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Fixes for a couple of trivial warnings (#676) * Committing clang-format changes * Trivial warning fixes: * Removes an unused done target in H5Tbit.c * Add (void) to quiet "ignored return value" warnings in the generators (which generally ignore errors) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Various CMake changes (#679) * Committing clang-format changes * Several CMake updates: * Removes unused HDF5_ENABLE_HSIZET * Switches TEST_SHELL_SCRIPTS to ON * Sets SH_PROGRAM to bash instead of sh * Set default build type back to RelWithDebInfo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Removes alternative function enter/leave macro scheme (#678)" This reverts commit edddb11b791adbdcaafed3ba718c95dd349a4e9a. * err_compat test cleanup (#681) * Committing clang-format changes * Cleans up err_compat test and output * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Sets the memory alloc sanity check option to disabled in autotools (#686) * Revert "Sets the memory alloc sanity check option to disabled in autotools (#686)" This reverts commit 652ffca58699388fff960c6a92c8ecfd1fc5d19b. (Only for release branch). * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: Jan-Willem Blokland <J.W.S.Blokland@XS4All.nl> Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> Co-authored-by: Sean McBride <sean@rogue-research.com> commit 14794490ec522fbd3ac2faa6efa0920979490fbc Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jul 14 13:50:26 2021 -0500 Update version to 1.10.8-2 after snapshot release of 1.10.8-1 (#838) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. * Snapshot version 1.10 release 8-1. Update version to 1.10.8-2. Squashed commit of the following: commit 60734e63fe077238f10de3d6ca8f037f9a42af89 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 24 14:20:39 2021 -0500 Hdf5 1 10 Fix tools test (#796) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit bfb780a4441e4ef43dd23708d415e5e3b84800f4 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 23 14:11:46 2021 -0500 Hdf5 1 10 Release Note (#786) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 22 07:03:26 2021 -0500 Hdf5 1 10 Update missing release note info. (#778) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb Author: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri Jun 18 06:42:23 2021 -0700 Brings hash table IDs feature from develop/1.12 (#768) * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 17 11:21:43 2021 -0500 Hdf5 1 10 Fix cmake configure path (#762) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 16 15:45:58 2021 -0500 Hdf5 1 10 merge warnings changes (#756) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit e25980e7f35b8508db90648409ba80ee36d61c9e Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 8 14:37:13 2021 -0500 Hdf5 1 10 merges of CMake changes (#738) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jun 3 16:07:23 2021 -0500 Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> * Revert references to SIZE_MAX to ((size_t)(-1)) in C header defines used by c++ code that fail on centos7 when -std=c++11 is not set. * Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (#699) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes pre-C99 build and header cruft (#700) * Committing clang-format changes * Removes pre-C99 build and header cruft * Assumes ANSI C headers exist * Assumes stdbool.h, stdint.h, and inttypes.h are present * Assumes the C++ compiler can handle stdint.h * Removes all work-arounds for missing functionality, especially stdbool.h * Formats source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up type size checks in configure.ac (#702) * Removes some DEC Alpha cruft from H5detect and H5private.h (#708) * Cleans up hsize_t and haddr_t size guessing (#709) * Cleans up definitions of haddr_t and hsize_t + cruft removal * Formatted source * Revert "Cleans up hsize_t and haddr_t size guessing (#709)" This reverts commit be6ad9a7a0f2d08b670fa98bbdd1ba9530c9e89a. * Updates bin/trace script to correctly wrap H5TRACE macros near clang-format column limit (#719) * Removes clang-format comments from H5O.c call * Fixes bin/trace to correctly wrap lines near the clang-format limit * Removed unused variable from bin/trace Conflicts: bin/trace src/H5O.c * Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601) * Committing clang-format changes * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times An internal string is incorrectly freed when the API call is invoked multiple times on a property list, which will usually cause a segfault to occur. On the first call the log location is NULL so the problem doesn't occur. Fixes HDFFV-11239 * Fixes typos Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Conflicts: release_docs/RELEASE.txt * Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607) * Committing clang-format changes * Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid fapl ID This was due to a pointer-containing struct being memset after the first internal API call. If the first call failed, the error condition would check if the pointer was not NULL and then attempt to free it if not. This would lead to the freeing of a wild pointer if an invalid fapl ID were passed in. This was fixed by reordering the memset and adding a test to ensure the problem stays fixed. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Conflicts: release_docs/RELEASE.txt * Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611) * Committing clang-format changes * Fixes incorrect size_hint handling in H5Gcreate1 * Updates the size hint type for group creation * Updates the RELEASE.txt note * Revert "Updates the RELEASE.txt note" This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff. * Reverts previous behavior to use a uint32_t struct field * Updates RELEASE.txt Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Conflicts: src/H5Gdeprec.c * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ (#726) * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ Allows C++ library to be built on older versions of gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Conflicts: src/H5public.h * Remove conflicts from RELEASE.txt * Always include inttypes.h * Moves H5PacketTable default ctor inside source file (#731) * Remove private H5_GCC_DIAG_OFF/ON from standalone program (#734) * Fixes C++ warnings when passing hsize_t values to printf in test code (#745) * Squashed commit of the following: commit 1aa2c3421bef7ccd3610392d06c1856362c37312 Author: Larry Knox <lrknox@hdfgroup.org> Date: Sun Jul 25 21:20:20 2021 -0500 Merge issue 839 develop PRs to hdf5 1 10 - round 2 (#852) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. * Snapshot version 1.10 release 8-1. Update version to 1.10.8-2. Squashed commit of the following: commit 60734e63fe077238f10de3d6ca8f037f9a42af89 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 24 14:20:39 2021 -0500 Hdf5 1 10 Fix tools test (#796) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit bfb780a4441e4ef43dd23708d415e5e3b84800f4 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 23 14:11:46 2021 -0500 Hdf5 1 10 Release Note (#786) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 22 07:03:26 2021 -0500 Hdf5 1 10 Update missing release note info. (#778) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb Author: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri Jun 18 06:42:23 2021 -0700 Brings hash table IDs feature from develop/1.12 (#768) * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 17 11:21:43 2021 -0500 Hdf5 1 10 Fix cmake configure path (#762) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 16 15:45:58 2021 -0500 Hdf5 1 10 merge warnings changes (#756) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit e25980e7f35b8508db90648409ba80ee36d61c9e Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 8 14:37:13 2021 -0500 Hdf5 1 10 merges of CMake changes (#738) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jun 3 16:07:23 2021 -0500 Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> * (fix) Segmentation fault when using a compound type. (#143) * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * (fix) H5Z_xform_create function and scientific notation (#144) * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * Adds const to a few global variables (#623) * Committing clang-format changes * Adds consts to a few global variables Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Made private my_yyinput function static (#618) This prevents it being exported as a public symbol. * Reduces overly-pedantic casting in the public headers (#644) * Committing clang-format changes * Fixes overly pedantic casting in public headers Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Fixes for a couple of trivial warnings (#676) * Committing clang-format changes * Trivial warning fixes: * Removes an unused done target in H5Tbit.c * Add (void) to quiet "ignored return value" warnings in the generators (which generally ignore errors) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Various CMake changes (#679) * Committing clang-format changes * Several CMake updates: * Removes unused HDF5_ENABLE_HSIZET * Switches TEST_SHELL_SCRIPTS to ON * Sets SH_PROGRAM to bash instead of sh * Set default build type back to RelWithDebInfo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Removes alternative function enter/leave macro scheme (#678)" This reverts commit edddb11b791adbdcaafed3ba718c95dd349a4e9a. * err_compat test cleanup (#681) * Committing clang-format changes * Cleans up err_compat test and output * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Sets the memory alloc sanity check option to disabled in autotools (#686) * Revert "Sets the memory alloc sanity check option to disabled in autotools (#686)" This reverts commit 652ffca58699388fff960c6a92c8ecfd1fc5d19b. (Only for release branch). * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Squashed commit of the following: commit e2578640fedf671cf11535cf22313dd477da1165 Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jul 16 10:57:51 2021 -0500 Merge issue 839 changes to hdf5 1 10 (#841) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. * Snapshot version 1.10 release 8-1. Update version to 1.10.8-2. Squashed commit of the following: commit 60734e63fe077238f10de3d6ca8f037f9a42af89 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 24 14:20:39 2021 -0500 Hdf5 1 10 Fix tools test (#796) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit bfb780a4441e4ef43dd23708d415e5e3b84800f4 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 23 14:11:46 2021 -0500 Hdf5 1 10 Release Note (#786) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 22 07:03:26 2021 -0500 Hdf5 1 10 Update missing release note info. (#778) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb Author: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri Jun 18 06:42:23 2021 -0700 Brings hash table IDs feature from develop/1.12 (#768) * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 17 11:21:43 2021 -0500 Hdf5 1 10 Fix cmake configure path (#762) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 16 15:45:58 2021 -0500 Hdf5 1 10 merge warnings changes (#756) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit e25980e7f35b8508db90648409ba80ee36d61c9e Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 8 14:37:13 2021 -0500 Hdf5 1 10 merges of CMake changes (#738) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jun 3 16:07:23 2021 -0500 Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Bmr dev hdffv 11223 (#640) * Fixed HDFFV-11223 (CVE-2018-14460) Description - Added checks against buffer size to prevent segfault, in case of data corruption, for sdim->size and sdim->max. - Renamed data files in an existing test to shorten their length as agreed with other developers previously. Platforms tested: Linux/64 (jelly) * Committing clang-format changes * Updated for test files * Updated for HDFFV-11223 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b50484841118cf633fd6147302a63a30fd746. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> * (fix) Segmentation fault when using a compound type. (#143) * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * (fix) H5Z_xform_create function and scientific notation (#144) * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * Adds const to a few global variables (#623) * Committing clang-format changes * Adds consts to a few global variables Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Made private my_yyinput function static (#618) This prevents it being exported as a public symbol. * Reduces overly-pedantic casting in the public headers (#644) * Committing clang-format changes * Fixes overly pedantic casting in public headers Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Fixes for a couple of trivial warnings (#676) * Committing clang-format changes * Trivial warning fixes: * Removes an unused done target in H5Tbit.c * Add (void) to quiet "ignored return value" warnings in the generators (which generally ignore errors) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Various CMake changes (#679) * Committing clang-format changes * Several CMake updates: * Removes unused HDF5_ENABLE_HSIZET * Switches TEST_SHELL_SCRIPTS to ON * Sets SH_PROGRAM to bash instead of sh * Set default build type back to RelWithDebInfo Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Removes alternative function enter/leave macro scheme (#678)" This reverts commit edddb11b791adbdcaafed3ba718c95dd349a4e9a. * err_compat test cleanup (#681) * Committing clang-format changes * Cleans up err_compat test and output * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Sets the memory alloc sanity check option to disabled in autotools (#686) * Revert "Sets the memory alloc sanity check option to disabled in autotools (#686)" This reverts commit 652ffca58699388fff960c6a92c8ecfd1fc5d19b. (Only for release branch). * Removes alternative function enter/leave macro scheme (#678) * Committing clang-for… * Normalization of H5_nanosleep() with VFD SWMR branch (#746) * Normalization of H5_nanosleep() with VFD SWMR branch * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes some H5SL include statements (#758) * Fixes an array issue flagged by PGI in a C++ test (#763) * Fixes non-C99 format strings in tarray test code (#766) * Removes checks and work-arounds for strtoll and strtoull (#769) * Removes checks and work-arounds for strtoll and strtoull * Removes CMake checks for strtoll and strtoull * Removes checks for (v)snprintf, which are C99 (#772) * Removes outdated checks for ways inline might be defined (#781) These are obsolete now that we require C99. * Removes checks for system(), which is C89/90 (#782) * Cleans up some POSIX header bits in H5private.h (#783) * Further simplifies Autotools type size checks (#789) Also fixes an issue where clock_gettime and difftime are not detected due to earlier simplifications of this code. * Removes ancient Autotools cruft (#790) * Normalization of CMake H5pubconf.h with Autotools (#791) Mostly just moving things around and changing the comments to keep the delta small. The only symbol change is that for curl/curl.h which I changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol is not used in the library and is just an artifact of the checks. * Update initialization of table_id in PacketTable Null constructor for non c++11 clang compiler. * Reorganization of C and POSIX headers in H5public.h & H5private.h (#793) * Reorganization of C and POSIX headers in H5public.h & H5private.h Consolidated and removed duplicates * It turns out Windows has sys/types.h Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Conflicts: src/H5public.h * Removes checks for signal and set/longjmp, which are C89 (#798) Also removes checks for setjmp.h and stddef.h Conflicts: config/cmake/H5pubconf.h.in * Assume frexpl/f and fabsl/f, which are C99 (#799) * Removes obsolete equivalents of C99's __func__ (#800) Conflicts: bin/trace src/H5A.c src/H5D.c src/H5F.c src/H5G.c src/H5L.c src/H5M.c src/H5O.c src/H5R.c src/H5T.c src/H5Tcommit.c src/H5VLcallback.c src/H5private.h tools/test/h5repack/h5repacktst.c * Brings the tools getopt(3) replacement into the main library (#803) * Moves get_option from the tools library to the C library * Adds H5 prefix to get_option call and variables * Renames the H5_get_option long options struct and enum Conflicts: tools/src/h5diff/h5diff_common.c tools/src/h5dump/h5dump.c tools/src/h5repack/h5repack_main.c tools/src/misc/h5mkgrp.c * Committing clang-format changes * Cleans up POSIX/C bits in H5private.h (#804) test/ros3.c and test/s3comms.c each had a 'FUNC' that needed to be '__func__', missed in a previous merge. * Cleans up POSIX/C bits in H5private.h * Assume difftime exists (C89) * Reorg AC_CHECK_HEADERS so headers are in alphabetical order * Split off networking-related AC_CHECK_HEADERS * Remove unused UNAME_CYGWIN from configure.ac * Remove checks for unused sys/timeb.h * Tidying pass over H5private.h HD prefix macros * Tidy H5win32defs.h * Add HD prefix to various scanf calls * Committing clang-format changes * Fixes to the alarm(2) code used in the tests to make Windows happy Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Assume the library has C99 types in C++ type code (#806) * Assume the library has C99 types in C++ type code * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes type guesses when C99 types are missing (#807) * Assume C99 types exist in H5detect.c (#808) * Fixes parallel issues from recent C99 changes (#809) * Fixes parallel issues from recent C99 changes * Adds MPE FUNC --> __func__ changes missed in earlier PRs * Even more missed FUNC --> __func__ macros * Committing clang-format changes * Removes remaining H5_TIME_WITH_SYS_TIME cruft (#810) Mostly from CMake * Remove checks for winsock2.h (#813) This is only needed on Windows and always available, so there's no need to check for it. * Removes develop header cruft (#828) * OESS-168:Remove implicit conversion warnings. (#829) * OESS-168:Remove implicit conversion increases floating-point precision warnings. * OESS-168:Remove clang warnings. * Add support for parallel filters to h5repack (#832) * 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> * 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> * Allow parallel filters feature for comm size of 1 (#840) * Revert "Allow parallel filters feature for comm size of 1 (#840)" This reverts commit 0061341fe2ada7656cd29b2da9d29e4a273f98b5. * Revert "Removes remaining H5_TIME_WITH_SYS_TIME cruft (#810)" This reverts commit 7345be4d67932acfddf8c801827ccdd337bf2286. * Revert "Assume frexpl/f and fabsl/f, which are C99 (#799)" This reverts commit 07b423c1ddd93e6c210b7386d17a33d3da2c95d1. * Revert "Removes outdated checks for ways inline might be defined (#781)" This reverts commit 3b0ce023c7e8c0c87b682a1b3ef55a75e3045a92. * Revert "Removes checks for (v)snprintf, which are C99 (#772)" This reverts commit a99e9fc0890fe0214795ff94ae1b0750d7d877f7. * Revert "Removes checks and work-arounds for strtoll and strtoull (#769)" This reverts commit 2228ecd14b8b9169887da4f5ad4e4558a2d2c7fb. * Revert "Removes ancient Autotools cruft (#790)" This reverts commit c760dfeeb94bfe61ca38cccadd1b28d24c91854e. * Revert "Removes obsolete equivalents of C99's __func__ (#800)" This reverts commit 93fbbf8fd9333d0672f61da6e9f1dc367270e2f1. * Revert "Assume the library has C99 types in C++ type code (#806)" This reverts commit c65d9f3f3c86a1cc133092c80ab99d80901a929d. * Revert "Removes type guesses when C99 types are missing (#807)" This reverts commit 94b18d9be50f43104d3994215a9267ceeea4c0ce. * Revert "Assume C99 types exist in H5detect.c (#808)" This reverts commit 1a9208ae5ac107bd43265f799ac96bd8e093fd82. * Revert "Fixes parallel issues from recent C99 changes (#809)" This reverts commit cb4846a03cf541bf3418b6f0dcfd79295b2a7b32. * Committing clang-format changes * Revert "Cleans up POSIX/C bits in H5private.h (#804)" This reverts commit 641e6f7b4e48710bd8a7a9d386137756d5b8cb73. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: Jan-Willem Blokland <J.W.S.Blokland@XS4All.nl> Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
author: Larry Knox <lrknox@hdfgroup.org> 2021-08-11 12:33:57 (GMT)
committer: GitHub <noreply@github.com> 2021-08-11 12:33:57 (GMT)
commit: c0407bd48f60335218dda35740034ab1b41f8a97 (patch)
tree: ee8b6a9d84741f93790f30e224de3b5195983c92 /tools
parent: da7a4b5849015b3332e83a715935ea2edb8218b8 (diff)
download: hdf5-c0407bd48f60335218dda35740034ab1b41f8a97.zip
hdf5-c0407bd48f60335218dda35740034ab1b41f8a97.tar.gz
hdf5-c0407bd48f60335218dda35740034ab1b41f8a97.tar.bz2
23 files changed, 1009 insertions, 1217 deletions
diff --git a/tools/lib/h5tools_utils.c b/tools/lib/h5tools_utils.c
index 108cd4f..b60ee4f 100644
--- a/tools/lib/h5tools_utils.c
+++ b/tools/lib/h5tools_utils.c
@@ -25,12 +25,8 @@
 #include "H5FDros3.h"
 #endif
 
-/* global variables */
-unsigned h5tools_nCols = 80;
-/* ``get_option'' variables */
-int                opt_err = 1; /*get_option prints errors if this is on */
-int                opt_ind = 1; /*token pointer                          */
-const char *       opt_arg;     /*flag argument (or value)               */
+/* Global variables */
+unsigned           h5tools_nCols    = 80;
 static int         h5tools_d_status = 0;
 static const char *h5tools_progname = "h5tools";
 
@@ -162,167 +158,6 @@ help_ref_msg(FILE *output)
     HDfprintf(output, "see the <%s> entry in the 'HDF5 Reference Manual'.\n", h5tools_getprogname());
 }
 
-/*-------------------------------------------------------------------------
- * Function: get_option
- *
- * Purpose:  Determine the command-line options a user specified. We can
- *           accept both short and long type command-lines.
- *
- * Return:  Success:    The short valued "name" of the command line
- *              parameter or EOF if there are no more
- *              parameters to process.
- *
- *          Failure:    A question mark.
- *-------------------------------------------------------------------------
- */
-int
-get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts)
-{
-    static int sp      = 1;   /* character index in current token */
-    int        opt_opt = '?'; /* option character passed back to user */
-
-    if (sp == 1) {
-        /* check for more flag-like tokens */
-        if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0') {
-            return EOF;
-        }
-        else if (HDstrcmp(argv[opt_ind], "--") == 0) {
-            opt_ind++;
-            return EOF;
-        }
-    }
-
-    if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') {
-        /* long command line option */
-        int        i;
-        const char ch      = '=';
-        char *     arg     = HDstrdup(&argv[opt_ind][2]);
-        size_t     arg_len = 0;
-
-        opt_arg = strchr(&argv[opt_ind][2], ch);
-        arg_len = HDstrlen(&argv[opt_ind][2]);
-        if (opt_arg) {
-            arg_len -= HDstrlen(opt_arg);
-            opt_arg++; /* skip the equal sign */
-        }
-        arg[arg_len] = 0;
-
-        for (i = 0; l_opts && l_opts[i].name; i++) {
-            if (HDstrcmp(arg, l_opts[i].name) == 0) {
-                /* we've found a matching long command line flag */
-                opt_opt = l_opts[i].shortval;
-
-                if (l_opts[i].has_arg != no_arg) {
-                    if (opt_arg == NULL) {
-                        if (l_opts[i].has_arg != optional_arg) {
-                            if (opt_ind < (argc - 1))
-                                if (argv[opt_ind + 1][0] != '-')
-                                    opt_arg = argv[++opt_ind];
-                        }
-                        else if (l_opts[i].has_arg == require_arg) {
-                            if (opt_err)
-                                HDfprintf(rawerrorstream, "%s: option required for \"--%s\" flag\n", argv[0],
-                                          arg);
-
-                            opt_opt = '?';
-                        }
-                    }
-                }
-                else {
-                    if (opt_arg) {
-                        if (opt_err)
-                            HDfprintf(rawerrorstream, "%s: no option required for \"%s\" flag\n", argv[0],
-                                      arg);
-
-                        opt_opt = '?';
-                    }
-                }
-                break;
-            }
-        }
-
-        if (l_opts[i].name == NULL) {
-            /* exhausted all of the l_opts we have and still didn't match */
-            if (opt_err)
-                HDfprintf(rawerrorstream, "%s: unknown option \"%s\"\n", argv[0], arg);
-
-            opt_opt = '?';
-        }
-
-        opt_ind++;
-        sp = 1;
-
-        HDfree(arg);
-    }
-    else {
-        register char *cp; /* pointer into current token */
-
-        /* short command line option */
-        opt_opt = argv[opt_ind][sp];
-
-        if (opt_opt == ':' || (cp = HDstrchr(opts, opt_opt)) == 0) {
-            if (opt_err)
-                HDfprintf(rawerrorstream, "%s: unknown option \"%c\"\n", argv[0], opt_opt);
-
-            /* if no chars left in this token, move to next token */
-            if (argv[opt_ind][++sp] == '\0') {
-                opt_ind++;
-                sp = 1;
-            }
-            return '?';
-        }
-
-        if (*++cp == ':') {
-            /* if a value is expected, get it */
-            if (argv[opt_ind][sp + 1] != '\0') {
-                /* flag value is rest of current token */
-                opt_arg = &argv[opt_ind++][sp + 1];
-            }
-            else if (++opt_ind >= argc) {
-                if (opt_err)
-                    HDfprintf(rawerrorstream, "%s: value expected for option \"%c\"\n", argv[0], opt_opt);
-
-                opt_opt = '?';
-            }
-            else {
-                /* flag value is next token */
-                opt_arg = argv[opt_ind++];
-            }
-
-            sp = 1;
-        }
-        /* wildcard argument */
-        else if (*cp == '*') {
-            /* check the next argument */
-            opt_ind++;
-            /* we do have an extra argument, check if not last */
-            if ((opt_ind + 1) < argc) {
-                if (argv[opt_ind][0] != '-') {
-                    opt_arg = argv[opt_ind++];
-                }
-                else {
-                    opt_arg = NULL;
-                }
-            }
-            else {
-                opt_arg = NULL;
-            }
-        }
-        else {
-            /* set up to look at next char in token, next time */
-            if (argv[opt_ind][++sp] == '\0') {
-                /* no more in current token, so setup next token */
-                opt_ind++;
-                sp = 1;
-            }
-            opt_arg = NULL;
-        }
-    }
-
-    /* return the current flag character found */
-    return opt_opt;
-}
-
 /*****************************************************************************
  *
  * Function: parse_tuple()
diff --git a/tools/lib/h5tools_utils.h b/tools/lib/h5tools_utils.h
index 34ac89b..fed4b52 100644
--- a/tools/lib/h5tools_utils.h
+++ b/tools/lib/h5tools_utils.h
@@ -40,58 +40,6 @@ H5TOOLS_DLLVAR FILE *overflow_file;
 H5TOOLS_DLLVAR hsize_t H5TOOLS_MALLOCSIZE;
 /* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */
 H5TOOLS_DLLVAR hsize_t H5TOOLS_BUFSIZE;
-/*
- * begin get_option section
- */
-H5TOOLS_DLLVAR int         opt_err; /* getoption prints errors if this is on    */
-H5TOOLS_DLLVAR int         opt_ind; /* token pointer                            */
-H5TOOLS_DLLVAR const char *opt_arg; /* flag argument (or value)                 */
-
-enum {
-    no_arg = 0,  /* doesn't take an argument     */
-    require_arg, /* requires an argument          */
-    optional_arg /* argument is optional         */
-};
-
-/*
- * get_option determines which options are specified on the command line and
- * returns a pointer to any arguments possibly associated with the option in
- * the ``opt_arg'' variable. get_option returns the shortname equivalent of
- * the option. The long options are specified in the following way:
- *
- * struct long_options foo[] = {
- *   { "filename", require_arg, 'f' },
- *   { "append", no_arg, 'a' },
- *   { "width", require_arg, 'w' },
- *   { NULL, 0, 0 }
- * };
- *
- * Long named options can have arguments specified as either:
- *
- *   ``--param=arg'' or ``--param arg''
- *
- * Short named options can have arguments specified as either:
- *
- *   ``-w80'' or ``-w 80''
- *
- * and can have more than one short named option specified at one time:
- *
- *   -aw80
- *
- * in which case those options which expect an argument need to come at the
- * end.
- */
-typedef struct long_options {
-    const char *name;     /* name of the long option              */
-    int         has_arg;  /* whether we should look for an arg    */
-    char        shortval; /* the shortname equivalent of long arg
-                           * this gets returned from get_option   */
-} long_options;
-
-H5TOOLS_DLL int get_option(int argc, const char **argv, const char *opt, const struct long_options *l_opt);
-/*
- * end get_option section
- */
 
 /*struct taken from the dumper. needed in table struct*/
 typedef struct obj_t {
diff --git a/tools/lib/io_timer.h b/tools/lib/io_timer.h
index 0269b93..0976804 100644
--- a/tools/lib/io_timer.h
+++ b/tools/lib/io_timer.h
@@ -25,7 +25,7 @@
 #include <time.h>
 #endif
 
-#ifdef H5_HAVE_WINSOCK2_H
+#ifdef H5_HAVE_WIN32_API
 #include <winsock2.h>
 #endif /* H5_HAVE_WINSOCK2_H */
 
diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c
index f618914..4e9a25e 100644
--- a/tools/src/h5copy/h5copy.c
+++ b/tools/src/h5copy/h5copy.c
@@ -19,23 +19,23 @@
 #define PROGRAMNAME "h5copy"
 
 /* command-line options: short and long-named parameters */
-static const char *        s_opts    = "d:f:hi:o:ps:vVE";
-static struct long_options l_opts[]  = {{"destination", require_arg, 'd'},
-                                       {"flag", require_arg, 'f'},
-                                       {"help", no_arg, 'h'},
-                                       {"input", require_arg, 'i'},
-                                       {"output", require_arg, 'o'},
-                                       {"parents", no_arg, 'p'},
-                                       {"source", require_arg, 's'},
-                                       {"verbose", no_arg, 'v'},
-                                       {"version", no_arg, 'V'},
-                                       {"enable-error-stack", no_arg, 'E'},
-                                       {NULL, 0, '\0'}};
-char *                     fname_src = NULL;
-char *                     fname_dst = NULL;
-char *                     oname_src = NULL;
-char *                     oname_dst = NULL;
-char *                     str_flag  = NULL;
+static const char *           s_opts    = "d:f:hi:o:ps:vVE";
+static struct h5_long_options l_opts[]  = {{"destination", require_arg, 'd'},
+                                          {"flag", require_arg, 'f'},
+                                          {"help", no_arg, 'h'},
+                                          {"input", require_arg, 'i'},
+                                          {"output", require_arg, 'o'},
+                                          {"parents", no_arg, 'p'},
+                                          {"source", require_arg, 's'},
+                                          {"verbose", no_arg, 'v'},
+                                          {"version", no_arg, 'V'},
+                                          {"enable-error-stack", no_arg, 'E'},
+                                          {NULL, 0, '\0'}};
+char *                        fname_src = NULL;
+char *                        fname_dst = NULL;
+char *                        oname_src = NULL;
+char *                        oname_dst = NULL;
+char *                        str_flag  = NULL;
 
 /*-------------------------------------------------------------------------
  * Function:    leave
@@ -242,19 +242,19 @@ main(int argc, const char *argv[])
     } /* end if */
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'd':
-                oname_dst = HDstrdup(opt_arg);
+                oname_dst = HDstrdup(H5_optarg);
                 break;
 
             case 'f':
                 /* validate flag */
-                if (parse_flag(opt_arg, &flag) < 0) {
+                if (parse_flag(H5_optarg, &flag) < 0) {
                     usage();
                     leave(EXIT_FAILURE);
                 }
-                str_flag = HDstrdup(opt_arg);
+                str_flag = HDstrdup(H5_optarg);
                 break;
 
             case 'h':
@@ -263,11 +263,11 @@ main(int argc, const char *argv[])
                 break;
 
             case 'i':
-                fname_src = HDstrdup(opt_arg);
+                fname_src = HDstrdup(H5_optarg);
                 break;
 
             case 'o':
-                fname_dst = HDstrdup(opt_arg);
+                fname_dst = HDstrdup(H5_optarg);
                 break;
 
             case 'p':
@@ -275,7 +275,7 @@ main(int argc, const char *argv[])
                 break;
 
             case 's':
-                oname_src = HDstrdup(opt_arg);
+                oname_src = HDstrdup(H5_optarg);
                 break;
 
             case 'V':
diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index e6b384a..b9f64d7 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -25,24 +25,24 @@ static int check_d_input(const char *);
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *        s_opts   = "hVrv*qn:d:p:NcelxE:A:S";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
-                                       {"version", no_arg, 'V'},
-                                       {"report", no_arg, 'r'},
-                                       {"verbose", optional_arg, 'v'},
-                                       {"quiet", no_arg, 'q'},
-                                       {"count", require_arg, 'n'},
-                                       {"delta", require_arg, 'd'},
-                                       {"relative", require_arg, 'p'},
-                                       {"nan", no_arg, 'N'},
-                                       {"compare", no_arg, 'c'},
-                                       {"use-system-epsilon", no_arg, 'e'},
-                                       {"follow-symlinks", no_arg, 'l'},
-                                       {"no-dangling-links", no_arg, 'x'},
-                                       {"exclude-path", require_arg, 'E'},
-                                       {"exclude-attribute", require_arg, 'A'},
-                                       {"enable-error-stack", no_arg, 'S'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "hVrv*qn:d:p:NcelxE:A:S";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+                                          {"version", no_arg, 'V'},
+                                          {"report", no_arg, 'r'},
+                                          {"verbose", optional_arg, 'v'},
+                                          {"quiet", no_arg, 'q'},
+                                          {"count", require_arg, 'n'},
+                                          {"delta", require_arg, 'd'},
+                                          {"relative", require_arg, 'p'},
+                                          {"nan", no_arg, 'N'},
+                                          {"compare", no_arg, 'c'},
+                                          {"use-system-epsilon", no_arg, 'e'},
+                                          {"follow-symlinks", no_arg, 'l'},
+                                          {"no-dangling-links", no_arg, 'x'},
+                                          {"exclude-path", require_arg, 'E'},
+                                          {"exclude-attribute", require_arg, 'A'},
+                                          {"enable-error-stack", no_arg, 'S'},
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function: check_options
@@ -226,7 +226,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
     exclude_attr_head = NULL;
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             default:
                 usage();
@@ -250,20 +250,20 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
                      * special check for short opt
                      */
                     if (!strcmp(argv[i], "-v")) {
-                        if (opt_arg != NULL)
-                            opt_ind--;
+                        if (H5_optarg != NULL)
+                            H5_optind--;
                         opts->mode_verbose_level = 0;
                         break;
                     }
                     else if (!strncmp(argv[i], "-v", (size_t)2)) {
-                        if (opt_arg != NULL)
-                            opt_ind--;
+                        if (H5_optarg != NULL)
+                            H5_optind--;
                         opts->mode_verbose_level = atoi(&argv[i][2]);
                         break;
                     }
                     else {
-                        if (opt_arg != NULL)
-                            opts->mode_verbose_level = HDatoi(opt_arg);
+                        if (H5_optarg != NULL)
+                            opts->mode_verbose_level = HDatoi(H5_optarg);
                         else
                             opts->mode_verbose_level = 0;
                     }
@@ -302,7 +302,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
                 }
 
                 /* init */
-                exclude_node->obj_path = opt_arg;
+                exclude_node->obj_path = H5_optarg;
                 exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
                 exclude_prev           = exclude_head;
 
@@ -330,7 +330,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
                 }
 
                 /* init */
-                exclude_attr_node->obj_path = opt_arg;
+                exclude_attr_node->obj_path = H5_optarg;
                 exclude_attr_node->obj_type = H5TRAV_TYPE_UNKNOWN;
                 exclude_attr_prev           = exclude_attr_head;
 
@@ -350,23 +350,23 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
             case 'd':
                 opts->delta_bool = 1;
 
-                if (check_d_input(opt_arg) == -1) {
-                    HDprintf("<-d %s> is not a valid option\n", opt_arg);
+                if (check_d_input(H5_optarg) == -1) {
+                    HDprintf("<-d %s> is not a valid option\n", H5_optarg);
                     usage();
                     h5diff_exit(EXIT_FAILURE);
                 }
-                opts->delta = HDatof(opt_arg);
+                opts->delta = HDatof(H5_optarg);
                 /* do not check against default, the DBL_EPSILON is being replaced by user */
                 break;
 
             case 'p':
                 opts->percent_bool = 1;
-                if (check_p_input(opt_arg) == -1) {
-                    HDprintf("<-p %s> is not a valid option\n", opt_arg);
+                if (check_p_input(H5_optarg) == -1) {
+                    HDprintf("<-p %s> is not a valid option\n", H5_optarg);
                     usage();
                     h5diff_exit(EXIT_FAILURE);
                 }
-                opts->percent = HDatof(opt_arg);
+                opts->percent = HDatof(H5_optarg);
 
                 /* -p 0 is the same as default */
                 if (H5_DBL_ABS_EQUAL(opts->percent, 0.0))
@@ -375,12 +375,12 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
 
             case 'n':
                 opts->count_bool = 1;
-                if (check_n_input(opt_arg) == -1) {
-                    HDprintf("<-n %s> is not a valid option\n", opt_arg);
+                if (check_n_input(H5_optarg) == -1) {
+                    HDprintf("<-n %s> is not a valid option\n", H5_optarg);
                     usage();
                     h5diff_exit(EXIT_FAILURE);
                 }
-                opts->count = HDstrtoull(opt_arg, NULL, 0);
+                opts->count = HDstrtoull(H5_optarg, NULL, 0);
                 break;
 
             case 'N':
@@ -409,15 +409,15 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
         opts->exclude_attr = exclude_attr_head;
 
     /* check for file names to be processed */
-    if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+    if (argc <= H5_optind || argv[H5_optind + 1] == NULL) {
         error_msg("missing file names\n");
         usage();
         h5diff_exit(EXIT_FAILURE);
     }
 
-    *fname1   = argv[opt_ind];
-    *fname2   = argv[opt_ind + 1];
-    *objname1 = argv[opt_ind + 2];
+    *fname1   = argv[H5_optind];
+    *fname2   = argv[H5_optind + 1];
+    *objname1 = argv[H5_optind + 2];
     H5TOOLS_DEBUG("file1 = %s", *fname1);
     H5TOOLS_DEBUG("file2 = %s", *fname2);
 
@@ -428,8 +428,8 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
     }
     H5TOOLS_DEBUG("objname1 = %s", *objname1);
 
-    if (argv[opt_ind + 3] != NULL) {
-        *objname2 = argv[opt_ind + 3];
+    if (argv[H5_optind + 3] != NULL) {
+        *objname2 = argv[H5_optind + 3];
     }
     else {
         *objname2 = *objname1;
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index cf1f80b..bdd1a41 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -77,129 +77,129 @@ struct handler_t {
  */
 /* The following initialization makes use of C language concatenating */
 /* "xxx" "yyy" into "xxxyyy". */
-static const char *        s_opts   = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:";
-static struct long_options l_opts[] = {{"attribute", require_arg, 'a'},
-                                       {"attribut", require_arg, 'a'},
-                                       {"attribu", require_arg, 'a'},
-                                       {"attrib", require_arg, 'a'},
-                                       {"attri", require_arg, 'a'},
-                                       {"attr", require_arg, 'a'},
-                                       {"att", require_arg, 'a'},
-                                       {"at", require_arg, 'a'},
-                                       {"binary", optional_arg, 'b'},
-                                       {"count", require_arg, 'c'},
-                                       {"coun", require_arg, 'c'},
-                                       {"cou", require_arg, 'c'},
-                                       {"co", require_arg, 'c'},
-                                       {"dataset", require_arg, 'd'},
-                                       {"datase", require_arg, 'd'},
-                                       {"datas", require_arg, 'd'},
-                                       {"escape", no_arg, 'e'},
-                                       {"filedriver", require_arg, 'f'},
-                                       {"filedrive", require_arg, 'f'},
-                                       {"filedriv", require_arg, 'f'},
-                                       {"filedri", require_arg, 'f'},
-                                       {"filedr", require_arg, 'f'},
-                                       {"filed", require_arg, 'f'},
-                                       {"file", require_arg, 'f'},
-                                       {"fil", require_arg, 'f'},
-                                       {"fi", require_arg, 'f'},
-                                       {"group", require_arg, 'g'},
-                                       {"grou", require_arg, 'g'},
-                                       {"gro", require_arg, 'g'},
-                                       {"gr", require_arg, 'g'},
-                                       {"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"object-ids", no_arg, 'i'},
-                                       {"object-id", no_arg, 'i'},
-                                       {"object-i", no_arg, 'i'},
-                                       {"object", no_arg, 'i'},
-                                       {"objec", no_arg, 'i'},
-                                       {"obje", no_arg, 'i'},
-                                       {"obj", no_arg, 'i'},
-                                       {"ob", no_arg, 'i'},
-                                       {"block", require_arg, 'k'},
-                                       {"bloc", require_arg, 'k'},
-                                       {"blo", require_arg, 'k'},
-                                       {"bl", require_arg, 'k'},
-                                       {"soft-link", require_arg, 'l'},
-                                       {"soft-lin", require_arg, 'l'},
-                                       {"soft-li", require_arg, 'l'},
-                                       {"soft-l", require_arg, 'l'},
-                                       {"soft", require_arg, 'l'},
-                                       {"sof", require_arg, 'l'},
-                                       {"format", require_arg, 'm'},
-                                       {"contents", optional_arg, 'n'},
-                                       {"output", optional_arg, 'o'},
-                                       {"outpu", optional_arg, 'o'},
-                                       {"outp", optional_arg, 'o'},
-                                       {"out", optional_arg, 'o'},
-                                       {"ou", optional_arg, 'o'},
-                                       {"properties", no_arg, 'p'},
-                                       {"sort_by", require_arg, 'q'},
-                                       {"string", no_arg, 'r'},
-                                       {"strin", no_arg, 'r'},
-                                       {"start", require_arg, 's'},
-                                       {"star", require_arg, 's'},
-                                       {"sta", require_arg, 's'},
-                                       {"datatype", require_arg, 't'},
-                                       {"datatyp", require_arg, 't'},
-                                       {"dataty", require_arg, 't'},
-                                       {"datat", require_arg, 't'},
-                                       {"use-dtd", no_arg, 'u'},
-                                       {"use-dt", no_arg, 'u'},
-                                       {"use-d", no_arg, 'u'},
-                                       {"use-", no_arg, 'u'},
-                                       {"use", no_arg, 'u'},
-                                       {"us", no_arg, 'u'},
-                                       {"u", no_arg, 'u'},
-                                       {"vds-view-first-missing", no_arg, 'v'},
-                                       {"width", require_arg, 'w'},
-                                       {"widt", require_arg, 'w'},
-                                       {"wid", require_arg, 'w'},
-                                       {"wi", require_arg, 'w'},
-                                       {"xml", no_arg, 'x'},
-                                       {"xm", no_arg, 'x'},
-                                       {"noindex", no_arg, 'y'},
-                                       {"sort_order", require_arg, 'z'},
-                                       {"onlyattr", optional_arg, 'A'},
-                                       {"superblock", no_arg, 'B'},
-                                       {"boot-block", no_arg, 'B'},
-                                       {"boot-bloc", no_arg, 'B'},
-                                       {"boot-blo", no_arg, 'B'},
-                                       {"boot-bl", no_arg, 'B'},
-                                       {"boot-b", no_arg, 'B'},
-                                       {"boot", no_arg, 'B'},
-                                       {"boo", no_arg, 'B'},
-                                       {"bo", no_arg, 'B'},
-                                       {"no-compact-subset", no_arg, 'C'},
-                                       {"xml-dtd", require_arg, 'D'},
-                                       {"xml-dt", require_arg, 'D'},
-                                       {"xml-d", require_arg, 'D'},
-                                       {"enable-error-stack", optional_arg, 'E'},
-                                       {"form", require_arg, 'F'},
-                                       {"vds-gap-size", require_arg, 'G'},
-                                       {"header", no_arg, 'H'},
-                                       {"heade", no_arg, 'H'},
-                                       {"head", no_arg, 'H'},
-                                       {"hea", no_arg, 'H'},
-                                       {"packed-bits", require_arg, 'M'},
-                                       {"any_path", require_arg, 'N'},
-                                       {"ddl", optional_arg, 'O'},
-                                       {"region", no_arg, 'R'},
-                                       {"stride", require_arg, 'S'},
-                                       {"strid", require_arg, 'S'},
-                                       {"version", no_arg, 'V'},
-                                       {"versio", no_arg, 'V'},
-                                       {"versi", no_arg, 'V'},
-                                       {"vers", no_arg, 'V'},
-                                       {"ver", no_arg, 'V'},
-                                       {"ve", no_arg, 'V'},
-                                       {"xml-ns", require_arg, 'X'},
-                                       {"xml-n", require_arg, 'X'},
-                                       {"s3-cred", require_arg, '$'},
-                                       {"hdfs-attrs", require_arg, '#'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:";
+static struct h5_long_options l_opts[] = {{"attribute", require_arg, 'a'},
+                                          {"attribut", require_arg, 'a'},
+                                          {"attribu", require_arg, 'a'},
+                                          {"attrib", require_arg, 'a'},
+                                          {"attri", require_arg, 'a'},
+                                          {"attr", require_arg, 'a'},
+                                          {"att", require_arg, 'a'},
+                                          {"at", require_arg, 'a'},
+                                          {"binary", optional_arg, 'b'},
+                                          {"count", require_arg, 'c'},
+                                          {"coun", require_arg, 'c'},
+                                          {"cou", require_arg, 'c'},
+                                          {"co", require_arg, 'c'},
+                                          {"dataset", require_arg, 'd'},
+                                          {"datase", require_arg, 'd'},
+                                          {"datas", require_arg, 'd'},
+                                          {"escape", no_arg, 'e'},
+                                          {"filedriver", require_arg, 'f'},
+                                          {"filedrive", require_arg, 'f'},
+                                          {"filedriv", require_arg, 'f'},
+                                          {"filedri", require_arg, 'f'},
+                                          {"filedr", require_arg, 'f'},
+                                          {"filed", require_arg, 'f'},
+                                          {"file", require_arg, 'f'},
+                                          {"fil", require_arg, 'f'},
+                                          {"fi", require_arg, 'f'},
+                                          {"group", require_arg, 'g'},
+                                          {"grou", require_arg, 'g'},
+                                          {"gro", require_arg, 'g'},
+                                          {"gr", require_arg, 'g'},
+                                          {"help", no_arg, 'h'},
+                                          {"hel", no_arg, 'h'},
+                                          {"object-ids", no_arg, 'i'},
+                                          {"object-id", no_arg, 'i'},
+                                          {"object-i", no_arg, 'i'},
+                                          {"object", no_arg, 'i'},
+                                          {"objec", no_arg, 'i'},
+                                          {"obje", no_arg, 'i'},
+                                          {"obj", no_arg, 'i'},
+                                          {"ob", no_arg, 'i'},
+                                          {"block", require_arg, 'k'},
+                                          {"bloc", require_arg, 'k'},
+                                          {"blo", require_arg, 'k'},
+                                          {"bl", require_arg, 'k'},
+                                          {"soft-link", require_arg, 'l'},
+                                          {"soft-lin", require_arg, 'l'},
+                                          {"soft-li", require_arg, 'l'},
+                                          {"soft-l", require_arg, 'l'},
+                                          {"soft", require_arg, 'l'},
+                                          {"sof", require_arg, 'l'},
+                                          {"format", require_arg, 'm'},
+                                          {"contents", optional_arg, 'n'},
+                                          {"output", optional_arg, 'o'},
+                                          {"outpu", optional_arg, 'o'},
+                                          {"outp", optional_arg, 'o'},
+                                          {"out", optional_arg, 'o'},
+                                          {"ou", optional_arg, 'o'},
+                                          {"properties", no_arg, 'p'},
+                                          {"sort_by", require_arg, 'q'},
+                                          {"string", no_arg, 'r'},
+                                          {"strin", no_arg, 'r'},
+                                          {"start", require_arg, 's'},
+                                          {"star", require_arg, 's'},
+                                          {"sta", require_arg, 's'},
+                                          {"datatype", require_arg, 't'},
+                                          {"datatyp", require_arg, 't'},
+                                          {"dataty", require_arg, 't'},
+                                          {"datat", require_arg, 't'},
+                                          {"use-dtd", no_arg, 'u'},
+                                          {"use-dt", no_arg, 'u'},
+                                          {"use-d", no_arg, 'u'},
+                                          {"use-", no_arg, 'u'},
+                                          {"use", no_arg, 'u'},
+                                          {"us", no_arg, 'u'},
+                                          {"u", no_arg, 'u'},
+                                          {"vds-view-first-missing", no_arg, 'v'},
+                                          {"width", require_arg, 'w'},
+                                          {"widt", require_arg, 'w'},
+                                          {"wid", require_arg, 'w'},
+                                          {"wi", require_arg, 'w'},
+                                          {"xml", no_arg, 'x'},
+                                          {"xm", no_arg, 'x'},
+                                          {"noindex", no_arg, 'y'},
+                                          {"sort_order", require_arg, 'z'},
+                                          {"onlyattr", optional_arg, 'A'},
+                                          {"superblock", no_arg, 'B'},
+                                          {"boot-block", no_arg, 'B'},
+                                          {"boot-bloc", no_arg, 'B'},
+                                          {"boot-blo", no_arg, 'B'},
+                                          {"boot-bl", no_arg, 'B'},
+                                          {"boot-b", no_arg, 'B'},
+                                          {"boot", no_arg, 'B'},
+                                          {"boo", no_arg, 'B'},
+                                          {"bo", no_arg, 'B'},
+                                          {"no-compact-subset", no_arg, 'C'},
+                                          {"xml-dtd", require_arg, 'D'},
+                                          {"xml-dt", require_arg, 'D'},
+                                          {"xml-d", require_arg, 'D'},
+                                          {"enable-error-stack", optional_arg, 'E'},
+                                          {"form", require_arg, 'F'},
+                                          {"vds-gap-size", require_arg, 'G'},
+                                          {"header", no_arg, 'H'},
+                                          {"heade", no_arg, 'H'},
+                                          {"head", no_arg, 'H'},
+                                          {"hea", no_arg, 'H'},
+                                          {"packed-bits", require_arg, 'M'},
+                                          {"any_path", require_arg, 'N'},
+                                          {"ddl", optional_arg, 'O'},
+                                          {"region", no_arg, 'R'},
+                                          {"stride", require_arg, 'S'},
+                                          {"strid", require_arg, 'S'},
+                                          {"version", no_arg, 'V'},
+                                          {"versio", no_arg, 'V'},
+                                          {"versi", no_arg, 'V'},
+                                          {"vers", no_arg, 'V'},
+                                          {"ver", no_arg, 'V'},
+                                          {"ve", no_arg, 'V'},
+                                          {"xml-ns", require_arg, 'X'},
+                                          {"xml-n", require_arg, 'X'},
+                                          {"s3-cred", require_arg, '$'},
+                                          {"hdfs-attrs", require_arg, '#'},
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function:    leave
@@ -902,7 +902,7 @@ parse_command_line(int argc, const char *argv[])
     }
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
 parse_start:
         switch ((char)opt) {
             case 'R':
@@ -916,8 +916,8 @@ parse_start:
             case 'n':
                 dump_opts.display_fi = TRUE;
                 last_was_dset        = FALSE;
-                if (opt_arg != NULL)
-                    h5trav_set_verbose(HDatoi(opt_arg));
+                if (H5_optarg != NULL)
+                    h5trav_set_verbose(HDatoi(H5_optarg));
                 break;
             case 'p':
                 dump_opts.display_dcpl = TRUE;
@@ -934,8 +934,8 @@ parse_start:
                 last_was_dset               = FALSE;
                 break;
             case 'A':
-                if (opt_arg != NULL) {
-                    if (0 == HDatoi(opt_arg))
+                if (H5_optarg != NULL) {
+                    if (0 == HDatoi(H5_optarg))
                         dump_opts.include_attrs = FALSE;
                 }
                 else {
@@ -959,7 +959,7 @@ parse_start:
                 goto done;
                 break;
             case 'w': {
-                int sh5tools_nCols = HDatoi(opt_arg);
+                int sh5tools_nCols = HDatoi(H5_optarg);
 
                 if (sh5tools_nCols <= 0)
                     h5tools_nCols = 65535;
@@ -973,7 +973,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_paths;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -985,7 +985,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_attributes;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -997,7 +997,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func        = handle_datasets;
-                        hand[i].obj         = HDstrdup(opt_arg);
+                        hand[i].obj         = HDstrdup(H5_optarg);
                         hand[i].subset_info = parse_subset_params(hand[i].obj);
                         last_dset           = &hand[i];
                         break;
@@ -1006,7 +1006,7 @@ parse_start:
                 last_was_dset = TRUE;
                 break;
             case 'f':
-                driver_name_g = opt_arg;
+                driver_name_g = H5_optarg;
                 break;
             case 'g':
                 dump_opts.display_all = 0;
@@ -1014,7 +1014,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_groups;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1026,7 +1026,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_links;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1038,7 +1038,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_datatypes;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1046,7 +1046,7 @@ parse_start:
                 break;
 
             case 'O':
-                if (h5tools_set_output_file(opt_arg, 0) < 0) {
+                if (h5tools_set_output_file(H5_optarg, 0) < 0) {
                     usage(h5tools_getprogname());
                     goto error;
                 }
@@ -1054,20 +1054,20 @@ parse_start:
 
             case 'o':
                 if (bin_output) {
-                    if (h5tools_set_data_output_file(opt_arg, 1) < 0) {
+                    if (h5tools_set_data_output_file(H5_optarg, 1) < 0) {
                         usage(h5tools_getprogname());
                         goto error;
                     }
                 }
                 else {
                     if (dump_opts.display_attr_data && !dump_opts.display_data) {
-                        if (h5tools_set_attr_output_file(opt_arg, 0) < 0) {
+                        if (h5tools_set_attr_output_file(H5_optarg, 0) < 0) {
                             usage(h5tools_getprogname());
                             goto error;
                         }
                     }
                     if (dump_opts.display_data || dump_opts.display_all) {
-                        if (h5tools_set_data_output_file(opt_arg, 0) < 0) {
+                        if (h5tools_set_data_output_file(H5_optarg, 0) < 0) {
                             usage(h5tools_getprogname());
                             goto error;
                         }
@@ -1076,12 +1076,12 @@ parse_start:
 
                 dump_opts.usingdasho = TRUE;
                 last_was_dset        = FALSE;
-                outfname_g           = opt_arg;
+                outfname_g           = H5_optarg;
                 break;
 
             case 'b':
-                if (opt_arg != NULL) {
-                    if ((bin_form = set_binary_form(opt_arg)) < 0) {
+                if (H5_optarg != NULL) {
+                    if ((bin_form = set_binary_form(H5_optarg)) < 0) {
                         /* failed to set binary form */
                         usage(h5tools_getprogname());
                         goto error;
@@ -1100,7 +1100,7 @@ parse_start:
                 break;
 
             case 'q':
-                if ((sort_by = set_sort_by(opt_arg)) < 0) {
+                if ((sort_by = set_sort_by(H5_optarg)) < 0) {
                     /* failed to set "sort by" form */
                     usage(h5tools_getprogname());
                     goto error;
@@ -1108,7 +1108,7 @@ parse_start:
                 break;
 
             case 'z':
-                if ((sort_order = set_sort_order(opt_arg)) < 0) {
+                if ((sort_order = set_sort_order(H5_optarg)) < 0) {
                     /* failed to set "sort order" form */
                     usage(h5tools_getprogname());
                     goto error;
@@ -1120,7 +1120,7 @@ parse_start:
                     error_msg("option \"-%c\" can only be used after --dataset option\n", opt);
                     goto error;
                 }
-                if (parse_mask_list(opt_arg) != SUCCEED) {
+                if (parse_mask_list(H5_optarg) != SUCCEED) {
                     usage(h5tools_getprogname());
                     goto error;
                 }
@@ -1130,7 +1130,7 @@ parse_start:
                 dump_opts.display_vds_first = TRUE;
                 break;
             case 'G':
-                dump_opts.vds_gap_size = HDatoi(opt_arg);
+                dump_opts.vds_gap_size = HDatoi(H5_optarg);
                 if (dump_opts.vds_gap_size < 0) {
                     usage(h5tools_getprogname());
                     goto error;
@@ -1157,13 +1157,13 @@ parse_start:
             case 'D':
                 /* specify alternative XML DTD or schema */
                 /* To Do: check format of this value?  */
-                xml_dtd_uri_g = opt_arg;
+                xml_dtd_uri_g = H5_optarg;
                 h5tools_nCols = 0;
                 break;
 
             case 'm':
                 /* specify alternative floating point printing format */
-                fp_format     = opt_arg;
+                fp_format     = H5_optarg;
                 h5tools_nCols = 0;
                 break;
 
@@ -1174,10 +1174,10 @@ parse_start:
                     usage(h5tools_getprogname());
                     goto error;
                 }
-                if (HDstrcmp(opt_arg, ":") == 0)
+                if (HDstrcmp(H5_optarg, ":") == 0)
                     xmlnsprefix = "";
                 else
-                    xmlnsprefix = opt_arg;
+                    xmlnsprefix = H5_optarg;
                 h5tools_nCols = 0;
                 break;
             /** end XML parameters **/
@@ -1223,33 +1223,33 @@ parse_start:
                                 HDfree(s->start.data);
                                 s->start.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->start);
+                            parse_hsize_list(H5_optarg, &s->start);
                             break;
                         case 'S':
                             if (s->stride.data) {
                                 HDfree(s->stride.data);
                                 s->stride.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->stride);
+                            parse_hsize_list(H5_optarg, &s->stride);
                             break;
                         case 'c':
                             if (s->count.data) {
                                 HDfree(s->count.data);
                                 s->count.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->count);
+                            parse_hsize_list(H5_optarg, &s->count);
                             break;
                         case 'k':
                             if (s->block.data) {
                                 HDfree(s->block.data);
                                 s->block.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->block);
+                            parse_hsize_list(H5_optarg, &s->block);
                             break;
                         default:
                             goto end_collect;
                     }
-                } while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF);
+                } while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF);
 
 end_collect:
                 last_was_dset = FALSE;
@@ -1262,8 +1262,8 @@ end_collect:
                 /** end subsetting parameters **/
 
             case 'E':
-                if (opt_arg != NULL)
-                    enable_error_stack = HDatoi(opt_arg);
+                if (H5_optarg != NULL)
+                    enable_error_stack = HDatoi(H5_optarg);
                 else
                     enable_error_stack = 1;
                 break;
@@ -1279,7 +1279,7 @@ end_collect:
 
             case '$':
 #ifdef H5_HAVE_ROS3_VFD
-                if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &ros3_fa_g) < 0) {
+                if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa_g) < 0) {
                     error_msg("failed to parse S3 VFD credential info\n");
                     usage(h5tools_getprogname());
                     free_handler(hand, argc);
@@ -1296,7 +1296,7 @@ end_collect:
 
             case '#':
 #ifdef H5_HAVE_LIBHDFS
-                if (h5tools_parse_hdfs_fapl_tuple(opt_arg, ',', &hdfs_fa_g) < 0) {
+                if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa_g) < 0) {
                     error_msg("failed to parse HDFS VFD configuration info\n");
                     usage(h5tools_getprogname());
                     free_handler(hand, argc);
@@ -1320,7 +1320,7 @@ end_collect:
 
 parse_end:
     /* check for file name to be processed */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         goto error;
@@ -1412,7 +1412,7 @@ main(int argc, const char *argv[])
         }
     }
 
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         h5tools_setstatus(EXIT_FAILURE);
@@ -1457,8 +1457,8 @@ main(int argc, const char *argv[])
         }
     } /* driver name defined */
 
-    while (opt_ind < argc) {
-        fname = HDstrdup(argv[opt_ind++]);
+    while (H5_optind < argc) {
+        fname = HDstrdup(argv[H5_optind++]);
 
         fid = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id, (fapl_id == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0);
 
diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c
index 9fd68cf..a23a6d8 100644
--- a/tools/src/h5format_convert/h5format_convert.c
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -38,28 +38,28 @@ static int   verbose_g = 0;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *        s_opts   = "hVvd:n";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"he", no_arg, 'h'},
-                                       {"version", no_arg, 'V'},
-                                       {"version", no_arg, 'V'},
-                                       {"versio", no_arg, 'V'},
-                                       {"versi", no_arg, 'V'},
-                                       {"vers", no_arg, 'V'},
-                                       {"verbose", no_arg, 'v'},
-                                       {"verbos", no_arg, 'v'},
-                                       {"verbo", no_arg, 'v'},
-                                       {"verb", no_arg, 'v'},
-                                       {"dname", require_arg, 'd'},
-                                       {"dnam", require_arg, 'd'},
-                                       {"dna", require_arg, 'd'},
-                                       {"dn", require_arg, 'd'},
-                                       {"noop", no_arg, 'n'},
-                                       {"noo", no_arg, 'n'},
-                                       {"no", no_arg, 'n'},
-                                       {"enable-error-stack", no_arg, 'E'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "hVvd:n";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+                                          {"hel", no_arg, 'h'},
+                                          {"he", no_arg, 'h'},
+                                          {"version", no_arg, 'V'},
+                                          {"version", no_arg, 'V'},
+                                          {"versio", no_arg, 'V'},
+                                          {"versi", no_arg, 'V'},
+                                          {"vers", no_arg, 'V'},
+                                          {"verbose", no_arg, 'v'},
+                                          {"verbos", no_arg, 'v'},
+                                          {"verbo", no_arg, 'v'},
+                                          {"verb", no_arg, 'v'},
+                                          {"dname", require_arg, 'd'},
+                                          {"dnam", require_arg, 'd'},
+                                          {"dna", require_arg, 'd'},
+                                          {"dn", require_arg, 'd'},
+                                          {"noop", no_arg, 'n'},
+                                          {"noo", no_arg, 'n'},
+                                          {"no", no_arg, 'n'},
+                                          {"enable-error-stack", no_arg, 'E'},
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function: usage
@@ -123,7 +123,7 @@ parse_command_line(int argc, const char **argv)
     }
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'h':
                 usage(h5tools_getprogname());
@@ -140,11 +140,11 @@ parse_command_line(int argc, const char **argv)
                 break;
 
             case 'd': /* -d dname */
-                if (opt_arg != NULL && *opt_arg)
-                    dname_g = HDstrdup(opt_arg);
+                if (H5_optarg != NULL && *H5_optarg)
+                    dname_g = HDstrdup(H5_optarg);
                 if (dname_g == NULL) {
                     h5tools_setstatus(EXIT_FAILURE);
-                    error_msg("No dataset name\n", opt_arg);
+                    error_msg("No dataset name\n", H5_optarg);
                     usage(h5tools_getprogname());
                     goto error;
                 }
@@ -167,19 +167,19 @@ parse_command_line(int argc, const char **argv)
         } /* switch */
     }     /* while */
 
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         h5tools_setstatus(EXIT_FAILURE);
         goto error;
     }
 
-    fname_g = HDstrdup(argv[opt_ind]);
+    fname_g = HDstrdup(argv[H5_optind]);
 
-    return (0);
+    return 0;
 
 error:
-    return (-1);
+    return -1;
     ;
 } /* parse_command_line() */
 
diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c
index 316356c..8bf53d0 100644
--- a/tools/src/h5jam/h5jam.c
+++ b/tools/src/h5jam/h5jam.c
@@ -34,8 +34,8 @@ char *ub_file     = NULL;
  * parameters. The long-named ones can be partially spelled. When
  * adding more, make sure that they don't clash with each other.
  */
-static const char *        s_opts   = "hi:u:o:c:V"; /* add more later ? */
-static struct long_options l_opts[] = {
+static const char *           s_opts   = "hi:u:o:c:V"; /* add more later ? */
+static struct h5_long_options l_opts[] = {
     {"help", no_arg, 'h'},    {"hel", no_arg, 'h'},   {"i", require_arg, 'i'}, /* input file */
     {"u", require_arg, 'u'},                                                   /* user block file */
     {"o", require_arg, 'o'},                                                   /* output file */
@@ -113,16 +113,16 @@ parse_command_line(int argc, const char *argv[])
     int opt = FALSE;
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'o':
-                output_file = HDstrdup(opt_arg);
+                output_file = HDstrdup(H5_optarg);
                 break;
             case 'i':
-                input_file = HDstrdup(opt_arg);
+                input_file = HDstrdup(H5_optarg);
                 break;
             case 'u':
-                ub_file = HDstrdup(opt_arg);
+                ub_file = HDstrdup(H5_optarg);
                 break;
             case 'c':
                 do_clobber = TRUE;
diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c
index 04fd27a..2cf7702 100644
--- a/tools/src/h5jam/h5unjam.c
+++ b/tools/src/h5jam/h5unjam.c
@@ -35,8 +35,8 @@ char *ub_file     = NULL;
  * parameters. The long-named ones can be partially spelled. When
  * adding more, make sure that they don't clash with each other.
  */
-static const char *        s_opts   = "hu:i:o:d:V";
-static struct long_options l_opts[] = {
+static const char *           s_opts   = "hu:i:o:d:V";
+static struct h5_long_options l_opts[] = {
     {"help", no_arg, 'h'},   {"hel", no_arg, 'h'},  {"i", require_arg, 'i'}, /* input file */
     {"u", require_arg, 'u'},                                                 /* user block file */
     {"o", require_arg, 'o'},                                                 /* output file */
@@ -101,23 +101,23 @@ parse_command_line(int argc, const char *argv[])
     int opt = FALSE;
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'o':
-                output_file = HDstrdup(opt_arg);
+                output_file = HDstrdup(H5_optarg);
                 if (output_file)
                     h5tools_set_data_output_file(output_file, 1);
                 break;
 
             case 'i':
-                input_file = HDstrdup(opt_arg);
+                input_file = HDstrdup(H5_optarg);
                 if (input_file)
                     h5tools_set_input_file(input_file, 1);
                 break;
                 ;
 
             case 'u':
-                ub_file = HDstrdup(opt_arg);
+                ub_file = HDstrdup(H5_optarg);
                 if (ub_file)
                     h5tools_set_output_file(ub_file, 1);
                 else
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index ffb4844..b3c8ffb 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -626,6 +626,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
     hid_t              wtype_id      = H5I_INVALID_HID; /* read/write type ID */
     hid_t              ocpl_id       = H5I_INVALID_HID; /* property to pass copy options */
     hid_t              lcpl_id       = H5I_INVALID_HID; /* link creation property list */
+    hid_t              dxpl_id       = H5I_INVALID_HID; /* dataset transfer property list */
     named_dt_t *       named_dt_head = NULL;            /* Pointer to the stack of named datatypes copied */
     size_t             msize;                           /* size of type */
     hsize_t            nelmts;                          /* number of elements in dataset */
@@ -959,12 +960,27 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                     if (need < H5TOOLS_MALLOCSIZE)
                                         buf = HDmalloc(need);
 
+                                    /* Set up collective write if using filters in parallel */
+                                    {
+#ifdef H5_HAVE_PARALLEL
+                                        hbool_t parallel = (H5FD_MPIO == H5Pget_driver(options->fout_fapl));
+
+                                        if (parallel && apply_s && apply_f) {
+                                            if ((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
+                                                H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed");
+                                            if (H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) < 0)
+                                                H5TOOLS_GOTO_ERROR((-1), "H5Pset_dxpl_mpio failed");
+                                        }
+                                        else
+#endif
+                                            dxpl_id = H5P_DEFAULT;
+                                    }
+
                                     if (buf != NULL) {
                                         if (H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) <
                                             0)
                                             H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
-                                        if (H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) <
-                                            0)
+                                        if (H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0)
                                             H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed");
 
                                         /* Check if we have VL data in the dataset's
@@ -1066,8 +1082,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                             if (H5Dread(dset_in, wtype_id, hslab_space, f_space_id,
                                                         H5P_DEFAULT, hslab_buf) < 0)
                                                 H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
-                                            if (H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id,
-                                                         H5P_DEFAULT, hslab_buf) < 0)
+                                            if (H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, dxpl_id,
+                                                         hslab_buf) < 0)
                                                 H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed");
 
                                             /* reclaim any VL memory, if necessary */
@@ -1347,6 +1363,7 @@ done:
         H5Pclose(dcpl_in);
         H5Pclose(gcpl_in);
         H5Pclose(gcpl_out);
+        H5Pclose(dxpl_id);
         H5Sclose(f_space_id);
         H5Dclose(dset_in);
         H5Dclose(dset_out);
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 01d1b90..13184a5 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -31,38 +31,38 @@ const char *outfile = NULL;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *        s_opts   = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:vz:EG:LM:P:S:T:VXW";
-static struct long_options l_opts[] = {{"alignment", require_arg, 'a'},
-                                       {"block", require_arg, 'b'},
-                                       {"compact", require_arg, 'c'},
-                                       {"indexed", require_arg, 'd'},
-                                       {"file", require_arg, 'e'},
-                                       {"filter", require_arg, 'f'},
-                                       {"help", no_arg, 'h'},
-                                       {"infile", require_arg, 'i'}, /* for backward compability */
-                                       {"low", require_arg, 'j'},
-                                       {"high", require_arg, 'k'},
-                                       {"layout", require_arg, 'l'},
-                                       {"minimum", require_arg, 'm'},
-                                       {"native", no_arg, 'n'},
-                                       {"outfile", require_arg, 'o'}, /* for backward compability */
-                                       {"sort_by", require_arg, 'q'},
-                                       {"ssize", require_arg, 's'},
-                                       {"threshold", require_arg, 't'},
-                                       {"ublock", require_arg, 'u'},
-                                       {"verbose", no_arg, 'v'},
-                                       {"sort_order", require_arg, 'z'},
-                                       {"enable-error-stack", no_arg, 'E'},
-                                       {"fs_pagesize", require_arg, 'G'},
-                                       {"latest", no_arg, 'L'},
-                                       {"metadata_block_size", require_arg, 'M'},
-                                       {"fs_persist", require_arg, 'P'},
-                                       {"fs_strategy", require_arg, 'S'},
-                                       {"fs_threshold", require_arg, 'T'},
-                                       {"version", no_arg, 'V'},
-                                       {"merge", no_arg, 'X'},
-                                       {"prune", no_arg, 'W'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:vz:EG:LM:P:S:T:VXW";
+static struct h5_long_options l_opts[] = {{"alignment", require_arg, 'a'},
+                                          {"block", require_arg, 'b'},
+                                          {"compact", require_arg, 'c'},
+                                          {"indexed", require_arg, 'd'},
+                                          {"file", require_arg, 'e'},
+                                          {"filter", require_arg, 'f'},
+                                          {"help", no_arg, 'h'},
+                                          {"infile", require_arg, 'i'}, /* for backward compability */
+                                          {"low", require_arg, 'j'},
+                                          {"high", require_arg, 'k'},
+                                          {"layout", require_arg, 'l'},
+                                          {"minimum", require_arg, 'm'},
+                                          {"native", no_arg, 'n'},
+                                          {"outfile", require_arg, 'o'}, /* for backward compability */
+                                          {"sort_by", require_arg, 'q'},
+                                          {"ssize", require_arg, 's'},
+                                          {"threshold", require_arg, 't'},
+                                          {"ublock", require_arg, 'u'},
+                                          {"verbose", no_arg, 'v'},
+                                          {"sort_order", require_arg, 'z'},
+                                          {"enable-error-stack", no_arg, 'E'},
+                                          {"fs_pagesize", require_arg, 'G'},
+                                          {"latest", no_arg, 'L'},
+                                          {"metadata_block_size", require_arg, 'M'},
+                                          {"fs_persist", require_arg, 'P'},
+                                          {"fs_strategy", require_arg, 'S'},
+                                          {"fs_threshold", require_arg, 'T'},
+                                          {"version", no_arg, 'V'},
+                                          {"merge", no_arg, 'X'},
+                                          {"prune", no_arg, 'W'},
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function: usage
@@ -462,18 +462,18 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
     int ret_value = 0;
 
     /* parse command line options */
-    while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) {
+    while (EOF != (opt = H5_get_option(argc, argv, s_opts, l_opts))) {
         switch ((char)opt) {
 
             /* -i for backward compatibility */
             case 'i':
-                infile = opt_arg;
+                infile = H5_optarg;
                 has_i++;
                 break;
 
             /* -o for backward compatibility */
             case 'o':
-                outfile = opt_arg;
+                outfile = H5_optarg;
                 has_o++;
                 break;
 
@@ -495,7 +495,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
 
             case 'f':
                 /* parse the -f filter option */
-                if (h5repack_addfilter(opt_arg, options) < 0) {
+                if (h5repack_addfilter(H5_optarg, options) < 0) {
                     error_msg("in parsing filter\n");
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
@@ -505,7 +505,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
 
             case 'l':
                 /* parse the -l layout option */
-                if (h5repack_addlayout(opt_arg, options) < 0) {
+                if (h5repack_addlayout(H5_optarg, options) < 0) {
                     error_msg("in parsing layout\n");
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
@@ -514,9 +514,9 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'm':
-                options->min_comp = HDstrtoull(opt_arg, NULL, 0);
+                options->min_comp = HDstrtoull(H5_optarg, NULL, 0);
                 if ((int)options->min_comp <= 0) {
-                    error_msg("invalid minimum compress size <%s>\n", opt_arg);
+                    error_msg("invalid minimum compress size <%s>\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -524,8 +524,8 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'e':
-                if ((ret_value = read_info(opt_arg, options)) < 0) {
-                    error_msg("failed to read from repack options file <%s>\n", opt_arg);
+                if ((ret_value = read_info(H5_optarg, options)) < 0) {
+                    error_msg("failed to read from repack options file <%s>\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -541,7 +541,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'j':
-                bound = HDatoi(opt_arg);
+                bound = HDatoi(H5_optarg);
                 if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) {
                     error_msg("in parsing low bound\n");
                     h5tools_setstatus(EXIT_FAILURE);
@@ -552,7 +552,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'k':
-                bound = HDatoi(opt_arg);
+                bound = HDatoi(H5_optarg);
                 if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) {
                     error_msg("in parsing high bound\n");
                     h5tools_setstatus(EXIT_FAILURE);
@@ -571,13 +571,13 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'c':
-                options->grp_compact = HDatoi(opt_arg);
+                options->grp_compact = HDatoi(H5_optarg);
                 if (options->grp_compact > 0)
                     options->latest = TRUE; /* must use latest format */
                 break;
 
             case 'd':
-                options->grp_indexed = HDatoi(opt_arg);
+                options->grp_indexed = HDatoi(H5_optarg);
                 if (options->grp_indexed > 0)
                     options->latest = TRUE; /* must use latest format */
                 break;
@@ -585,10 +585,10 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
             case 's': {
                 int   idx       = 0;
                 int   ssize     = 0;
-                char *msgPtr    = HDstrchr(opt_arg, ':');
+                char *msgPtr    = HDstrchr(H5_optarg, ':');
                 options->latest = TRUE; /* must use latest format */
                 if (msgPtr == NULL) {
-                    ssize = HDatoi(opt_arg);
+                    ssize = HDatoi(H5_optarg);
                     for (idx = 0; idx < 5; idx++)
                         options->msg_size[idx] = ssize;
                 }
@@ -597,7 +597,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
 
                     HDstrcpy(msgType, msgPtr + 1);
                     msgPtr[0] = '\0';
-                    ssize     = HDatoi(opt_arg);
+                    ssize     = HDatoi(H5_optarg);
                     if (!HDstrncmp(msgType, "dspace", 6))
                         options->msg_size[0] = ssize;
                     else if (!HDstrncmp(msgType, "dtype", 5))
@@ -612,25 +612,25 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
             } break;
 
             case 'u':
-                options->ublock_filename = opt_arg;
+                options->ublock_filename = H5_optarg;
                 break;
 
             case 'b':
-                options->ublock_size = (hsize_t)HDatol(opt_arg);
+                options->ublock_size = (hsize_t)HDatol(H5_optarg);
                 break;
 
             case 'M':
-                options->meta_block_size = (hsize_t)HDatol(opt_arg);
+                options->meta_block_size = (hsize_t)HDatol(H5_optarg);
                 break;
 
             case 't':
-                options->threshold = (hsize_t)HDatol(opt_arg);
+                options->threshold = (hsize_t)HDatol(H5_optarg);
                 break;
 
             case 'a':
-                options->alignment = HDstrtoull(opt_arg, NULL, 0);
+                options->alignment = HDstrtoull(H5_optarg, NULL, 0);
                 if (options->alignment < 1) {
-                    error_msg("invalid alignment size\n", opt_arg);
+                    error_msg("invalid alignment size\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -640,7 +640,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
             case 'S': {
                 char strategy[MAX_NC_NAME];
 
-                HDstrcpy(strategy, opt_arg);
+                HDstrcpy(strategy, H5_optarg);
                 if (!HDstrcmp(strategy, "FSM_AGGR"))
                     options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR;
                 else if (!HDstrcmp(strategy, "PAGE"))
@@ -650,7 +650,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 else if (!HDstrcmp(strategy, "NONE"))
                     options->fs_strategy = H5F_FSPACE_STRATEGY_NONE;
                 else {
-                    error_msg("invalid file space management strategy\n", opt_arg);
+                    error_msg("invalid file space management strategy\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -661,29 +661,29 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
             } break;
 
             case 'P':
-                options->fs_persist = HDatoi(opt_arg);
+                options->fs_persist = HDatoi(H5_optarg);
                 if (options->fs_persist == 0)
                     /* To distinguish the "specified" zero value */
                     options->fs_persist = -1;
                 break;
 
             case 'T':
-                options->fs_threshold = HDatol(opt_arg);
+                options->fs_threshold = HDatol(H5_optarg);
                 if (options->fs_threshold == 0)
                     /* To distinguish the "specified" zero value */
                     options->fs_threshold = -1;
                 break;
 
             case 'G':
-                options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0);
+                options->fs_pagesize = HDstrtoll(H5_optarg, NULL, 0);
                 if (options->fs_pagesize == 0)
                     /* To distinguish the "specified" zero value */
                     options->fs_pagesize = -1;
                 break;
 
             case 'q':
-                if (H5_INDEX_UNKNOWN == (sort_by = set_sort_by(opt_arg))) {
-                    error_msg("failed to set sort by form <%s>\n", opt_arg);
+                if (H5_INDEX_UNKNOWN == (sort_by = set_sort_by(H5_optarg))) {
+                    error_msg("failed to set sort by form <%s>\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -691,8 +691,8 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'z':
-                if (H5_ITER_UNKNOWN == (sort_order = set_sort_order(opt_arg))) {
-                    error_msg("failed to set sort order form <%s>\n", opt_arg);
+                if (H5_ITER_UNKNOWN == (sort_order = set_sort_order(H5_optarg))) {
+                    error_msg("failed to set sort order form <%s>\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -710,9 +710,9 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
 
     /* If neither -i nor -o given, get in and out files positionally */
     if (0 == (has_i + has_o)) {
-        if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
-            infile  = argv[opt_ind];
-            outfile = argv[opt_ind + 1];
+        if (argv[H5_optind] != NULL && argv[H5_optind + 1] != NULL) {
+            infile  = argv[H5_optind];
+            outfile = argv[H5_optind + 1];
 
             if (!HDstrcmp(infile, outfile)) {
                 error_msg("file names cannot be the same\n");
diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c
index e5b235d..a30aee5 100644
--- a/tools/src/h5stat/h5stat.c
+++ b/tools/src/h5stat/h5stat.c
@@ -171,106 +171,106 @@ struct handler_t {
 
 static const char *s_opts = "Aa:Ddm:EFfhGgl:sSTO:Vw:H:";
 /* e.g. "filemetadata" has to precede "file"; "groupmetadata" has to precede "group" etc. */
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"he", no_arg, 'h'},
-                                       {"filemetadata", no_arg, 'F'},
-                                       {"filemetadat", no_arg, 'F'},
-                                       {"filemetada", no_arg, 'F'},
-                                       {"filemetad", no_arg, 'F'},
-                                       {"filemeta", no_arg, 'F'},
-                                       {"filemet", no_arg, 'F'},
-                                       {"fileme", no_arg, 'F'},
-                                       {"filem", no_arg, 'F'},
-                                       {"file", no_arg, 'f'},
-                                       {"fil", no_arg, 'f'},
-                                       {"fi", no_arg, 'f'},
-                                       {"groupmetadata", no_arg, 'G'},
-                                       {"groupmetadat", no_arg, 'G'},
-                                       {"groupmetada", no_arg, 'G'},
-                                       {"groupmetad", no_arg, 'G'},
-                                       {"groupmeta", no_arg, 'G'},
-                                       {"groupmet", no_arg, 'G'},
-                                       {"groupme", no_arg, 'G'},
-                                       {"groupm", no_arg, 'G'},
-                                       {"group", no_arg, 'g'},
-                                       {"grou", no_arg, 'g'},
-                                       {"gro", no_arg, 'g'},
-                                       {"gr", no_arg, 'g'},
-                                       {"links", require_arg, 'l'},
-                                       {"link", require_arg, 'l'},
-                                       {"lin", require_arg, 'l'},
-                                       {"li", require_arg, 'l'},
-                                       {"dsetmetadata", no_arg, 'D'},
-                                       {"dsetmetadat", no_arg, 'D'},
-                                       {"dsetmetada", no_arg, 'D'},
-                                       {"dsetmetad", no_arg, 'D'},
-                                       {"dsetmeta", no_arg, 'D'},
-                                       {"dsetmet", no_arg, 'D'},
-                                       {"dsetme", no_arg, 'D'},
-                                       {"dsetm", no_arg, 'D'},
-                                       {"dset", no_arg, 'd'},
-                                       {"dse", no_arg, 'd'},
-                                       {"ds", no_arg, 'd'},
-                                       {"dims", require_arg, 'm'},
-                                       {"dim", require_arg, 'm'},
-                                       {"di", require_arg, 'm'},
-                                       {"dtypemetadata", no_arg, 'T'},
-                                       {"dtypemetadat", no_arg, 'T'},
-                                       {"dtypemetada", no_arg, 'T'},
-                                       {"dtypemetad", no_arg, 'T'},
-                                       {"dtypemeta", no_arg, 'T'},
-                                       {"dtypemet", no_arg, 'T'},
-                                       {"dtypeme", no_arg, 'T'},
-                                       {"dtypem", no_arg, 'T'},
-                                       {"dtype", no_arg, 'T'},
-                                       {"dtyp", no_arg, 'T'},
-                                       {"dty", no_arg, 'T'},
-                                       {"dt", no_arg, 'T'},
-                                       {"object", require_arg, 'O'},
-                                       {"objec", require_arg, 'O'},
-                                       {"obje", require_arg, 'O'},
-                                       {"obj", require_arg, 'O'},
-                                       {"ob", require_arg, 'O'},
-                                       {"version", no_arg, 'V'},
-                                       {"versio", no_arg, 'V'},
-                                       {"versi", no_arg, 'V'},
-                                       {"vers", no_arg, 'V'},
-                                       {"ver", no_arg, 'V'},
-                                       {"ve", no_arg, 'V'},
-                                       {"attribute", no_arg, 'A'},
-                                       {"attribut", no_arg, 'A'},
-                                       {"attribu", no_arg, 'A'},
-                                       {"attrib", no_arg, 'A'},
-                                       {"attri", no_arg, 'A'},
-                                       {"attr", no_arg, 'A'},
-                                       {"att", no_arg, 'A'},
-                                       {"at", no_arg, 'A'},
-                                       {"enable-error-stack", no_arg, 'E'},
-                                       {"numattrs", require_arg, 'a'},
-                                       {"numattr", require_arg, 'a'},
-                                       {"numatt", require_arg, 'a'},
-                                       {"numat", require_arg, 'a'},
-                                       {"numa", require_arg, 'a'},
-                                       {"num", require_arg, 'a'},
-                                       {"nu", require_arg, 'a'},
-                                       {"freespace", no_arg, 's'},
-                                       {"freespac", no_arg, 's'},
-                                       {"freespa", no_arg, 's'},
-                                       {"freesp", no_arg, 's'},
-                                       {"frees", no_arg, 's'},
-                                       {"free", no_arg, 's'},
-                                       {"fre", no_arg, 's'},
-                                       {"fr", no_arg, 's'},
-                                       {"summary", no_arg, 'S'},
-                                       {"summar", no_arg, 'S'},
-                                       {"summa", no_arg, 'S'},
-                                       {"summ", no_arg, 'S'},
-                                       {"sum", no_arg, 'S'},
-                                       {"su", no_arg, 'S'},
-                                       {"s3-cred", require_arg, 'w'},
-                                       {"hdfs-attrs", require_arg, 'H'},
-                                       {NULL, 0, '\0'}};
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+                                          {"hel", no_arg, 'h'},
+                                          {"he", no_arg, 'h'},
+                                          {"filemetadata", no_arg, 'F'},
+                                          {"filemetadat", no_arg, 'F'},
+                                          {"filemetada", no_arg, 'F'},
+                                          {"filemetad", no_arg, 'F'},
+                                          {"filemeta", no_arg, 'F'},
+                                          {"filemet", no_arg, 'F'},
+                                          {"fileme", no_arg, 'F'},
+                                          {"filem", no_arg, 'F'},
+                                          {"file", no_arg, 'f'},
+                                          {"fil", no_arg, 'f'},
+                                          {"fi", no_arg, 'f'},
+                                          {"groupmetadata", no_arg, 'G'},
+                                          {"groupmetadat", no_arg, 'G'},
+                                          {"groupmetada", no_arg, 'G'},
+                                          {"groupmetad", no_arg, 'G'},
+                                          {"groupmeta", no_arg, 'G'},
+                                          {"groupmet", no_arg, 'G'},
+                                          {"groupme", no_arg, 'G'},
+                                          {"groupm", no_arg, 'G'},
+                                          {"group", no_arg, 'g'},
+                                          {"grou", no_arg, 'g'},
+                                          {"gro", no_arg, 'g'},
+                                          {"gr", no_arg, 'g'},
+                                          {"links", require_arg, 'l'},
+                                          {"link", require_arg, 'l'},
+                                          {"lin", require_arg, 'l'},
+                                          {"li", require_arg, 'l'},
+                                          {"dsetmetadata", no_arg, 'D'},
+                                          {"dsetmetadat", no_arg, 'D'},
+                                          {"dsetmetada", no_arg, 'D'},
+                                          {"dsetmetad", no_arg, 'D'},
+                                          {"dsetmeta", no_arg, 'D'},
+                                          {"dsetmet", no_arg, 'D'},
+                                          {"dsetme", no_arg, 'D'},
+                                          {"dsetm", no_arg, 'D'},
+                                          {"dset", no_arg, 'd'},
+                                          {"dse", no_arg, 'd'},
+                                          {"ds", no_arg, 'd'},
+                                          {"dims", require_arg, 'm'},
+                                          {"dim", require_arg, 'm'},
+                                          {"di", require_arg, 'm'},
+                                          {"dtypemetadata", no_arg, 'T'},
+                                          {"dtypemetadat", no_arg, 'T'},
+                                          {"dtypemetada", no_arg, 'T'},
+                                          {"dtypemetad", no_arg, 'T'},
+                                          {"dtypemeta", no_arg, 'T'},
+                                          {"dtypemet", no_arg, 'T'},
+                                          {"dtypeme", no_arg, 'T'},
+                                          {"dtypem", no_arg, 'T'},
+                                          {"dtype", no_arg, 'T'},
+                                          {"dtyp", no_arg, 'T'},
+                                          {"dty", no_arg, 'T'},
+                                          {"dt", no_arg, 'T'},
+                                          {"object", require_arg, 'O'},
+                                          {"objec", require_arg, 'O'},
+                                          {"obje", require_arg, 'O'},
+                                          {"obj", require_arg, 'O'},
+                                          {"ob", require_arg, 'O'},
+                                          {"version", no_arg, 'V'},
+                                          {"versio", no_arg, 'V'},
+                                          {"versi", no_arg, 'V'},
+                                          {"vers", no_arg, 'V'},
+                                          {"ver", no_arg, 'V'},
+                                          {"ve", no_arg, 'V'},
+                                          {"attribute", no_arg, 'A'},
+                                          {"attribut", no_arg, 'A'},
+                                          {"attribu", no_arg, 'A'},
+                                          {"attrib", no_arg, 'A'},
+                                          {"attri", no_arg, 'A'},
+                                          {"attr", no_arg, 'A'},
+                                          {"att", no_arg, 'A'},
+                                          {"at", no_arg, 'A'},
+                                          {"enable-error-stack", no_arg, 'E'},
+                                          {"numattrs", require_arg, 'a'},
+                                          {"numattr", require_arg, 'a'},
+                                          {"numatt", require_arg, 'a'},
+                                          {"numat", require_arg, 'a'},
+                                          {"numa", require_arg, 'a'},
+                                          {"num", require_arg, 'a'},
+                                          {"nu", require_arg, 'a'},
+                                          {"freespace", no_arg, 's'},
+                                          {"freespac", no_arg, 's'},
+                                          {"freespa", no_arg, 's'},
+                                          {"freesp", no_arg, 's'},
+                                          {"frees", no_arg, 's'},
+                                          {"free", no_arg, 's'},
+                                          {"fre", no_arg, 's'},
+                                          {"fr", no_arg, 's'},
+                                          {"summary", no_arg, 'S'},
+                                          {"summar", no_arg, 'S'},
+                                          {"summa", no_arg, 'S'},
+                                          {"summ", no_arg, 'S'},
+                                          {"sum", no_arg, 'S'},
+                                          {"su", no_arg, 'S'},
+                                          {"s3-cred", require_arg, 'w'},
+                                          {"hdfs-attrs", require_arg, 'H'},
+                                          {NULL, 0, '\0'}};
 
 static void
 leave(int ret)
@@ -914,7 +914,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
     struct handler_t *hand = NULL;
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'h':
                 usage(h5tools_getprogname());
@@ -953,8 +953,8 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
                 break;
 
             case 'l':
-                if (opt_arg) {
-                    sgroups_threshold = HDatoi(opt_arg);
+                if (H5_optarg) {
+                    sgroups_threshold = HDatoi(H5_optarg);
                     if (sgroups_threshold < 1) {
                         error_msg("Invalid threshold for small groups\n");
                         goto error;
@@ -976,8 +976,8 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
                 break;
 
             case 'm':
-                if (opt_arg) {
-                    sdsets_threshold = HDatoi(opt_arg);
+                if (H5_optarg) {
+                    sdsets_threshold = HDatoi(H5_optarg);
                     if (sdsets_threshold < 1) {
                         error_msg("Invalid threshold for small datasets\n");
                         goto error;
@@ -999,8 +999,8 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
                 break;
 
             case 'a':
-                if (opt_arg) {
-                    sattrs_threshold = HDatoi(opt_arg);
+                if (H5_optarg) {
+                    sattrs_threshold = HDatoi(H5_optarg);
                     if (sattrs_threshold < 1) {
                         error_msg("Invalid threshold for small # of attributes\n");
                         goto error;
@@ -1040,7 +1040,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
 
                 /* Store object names */
                 for (u = 0; u < hand->obj_count; u++)
-                    if (NULL == (hand->obj[u] = HDstrdup(opt_arg))) {
+                    if (NULL == (hand->obj[u] = HDstrdup(H5_optarg))) {
                         error_msg("unable to allocate memory for object name\n");
                         goto error;
                     } /* end if */
@@ -1048,7 +1048,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
 
             case 'w':
 #ifdef H5_HAVE_ROS3_VFD
-                if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &ros3_fa) < 0) {
+                if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa) < 0) {
                     error_msg("failed to parse S3 VFD credential info\n");
                     goto error;
                 }
@@ -1062,7 +1062,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
 
             case 'H':
 #ifdef H5_HAVE_LIBHDFS
-                if (h5tools_parse_hdfs_fapl_tuple(opt_arg, ',', &hdfs_fa) < 0) {
+                if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa) < 0) {
                     error_msg("failed to parse HDFS VFD configuration info\n");
                     goto error;
                 }
@@ -1081,7 +1081,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
     }     /* end while */
 
     /* check for file name to be processed */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         goto error;
@@ -1805,7 +1805,7 @@ main(int argc, const char *argv[])
         }
     }
 
-    fname = argv[opt_ind];
+    fname = argv[H5_optind];
 
     /* Check for filename given */
     if (fname) {
diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c
index ac7c0ca..524ad03 100644
--- a/tools/src/misc/h5clear.c
+++ b/tools/src/misc/h5clear.c
@@ -44,40 +44,40 @@ static hsize_t increment          = DEFAULT_INCREMENT;
 /*
  * Command-line options: only publicize long options
  */
-static const char *        s_opts   = "hVsmzi*";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"he", no_arg, 'h'},
-                                       {"version", no_arg, 'V'},
-                                       {"version", no_arg, 'V'},
-                                       {"versio", no_arg, 'V'},
-                                       {"versi", no_arg, 'V'},
-                                       {"vers", no_arg, 'V'},
-                                       {"status", no_arg, 's'},
-                                       {"statu", no_arg, 's'},
-                                       {"stat", no_arg, 's'},
-                                       {"sta", no_arg, 's'},
-                                       {"st", no_arg, 's'},
-                                       {"image", no_arg, 'm'},
-                                       {"imag", no_arg, 'm'},
-                                       {"ima", no_arg, 'm'},
-                                       {"im", no_arg, 'm'},
-                                       {"filesize", no_arg, 'z'},
-                                       {"filesiz", no_arg, 'z'},
-                                       {"filesi", no_arg, 'z'},
-                                       {"files", no_arg, 'z'},
-                                       {"file", no_arg, 'z'},
-                                       {"fil", no_arg, 'z'},
-                                       {"fi", no_arg, 'z'},
-                                       {"increment", optional_arg, 'i'},
-                                       {"incremen", optional_arg, 'i'},
-                                       {"increme", optional_arg, 'i'},
-                                       {"increm", optional_arg, 'i'},
-                                       {"incre", optional_arg, 'i'},
-                                       {"incr", optional_arg, 'i'},
-                                       {"inc", optional_arg, 'i'},
-                                       {"in", optional_arg, 'i'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "hVsmzi*";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+                                          {"hel", no_arg, 'h'},
+                                          {"he", no_arg, 'h'},
+                                          {"version", no_arg, 'V'},
+                                          {"version", no_arg, 'V'},
+                                          {"versio", no_arg, 'V'},
+                                          {"versi", no_arg, 'V'},
+                                          {"vers", no_arg, 'V'},
+                                          {"status", no_arg, 's'},
+                                          {"statu", no_arg, 's'},
+                                          {"stat", no_arg, 's'},
+                                          {"sta", no_arg, 's'},
+                                          {"st", no_arg, 's'},
+                                          {"image", no_arg, 'm'},
+                                          {"imag", no_arg, 'm'},
+                                          {"ima", no_arg, 'm'},
+                                          {"im", no_arg, 'm'},
+                                          {"filesize", no_arg, 'z'},
+                                          {"filesiz", no_arg, 'z'},
+                                          {"filesi", no_arg, 'z'},
+                                          {"files", no_arg, 'z'},
+                                          {"file", no_arg, 'z'},
+                                          {"fil", no_arg, 'z'},
+                                          {"fi", no_arg, 'z'},
+                                          {"increment", optional_arg, 'i'},
+                                          {"incremen", optional_arg, 'i'},
+                                          {"increme", optional_arg, 'i'},
+                                          {"increm", optional_arg, 'i'},
+                                          {"incre", optional_arg, 'i'},
+                                          {"incr", optional_arg, 'i'},
+                                          {"inc", optional_arg, 'i'},
+                                          {"in", optional_arg, 'i'},
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function:    usage
@@ -150,7 +150,7 @@ parse_command_line(int argc, const char **argv)
     }
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'h':
                 usage(h5tools_getprogname());
@@ -176,12 +176,12 @@ parse_command_line(int argc, const char **argv)
 
             case 'i':
                 increment_eoa_eof = TRUE;
-                if (opt_arg != NULL) {
-                    if (HDatoi(opt_arg) < 0) {
+                if (H5_optarg != NULL) {
+                    if (HDatoi(H5_optarg) < 0) {
                         usage(h5tools_getprogname());
                         goto done;
                     }
-                    increment = (hsize_t)HDatoi(opt_arg);
+                    increment = (hsize_t)HDatoi(H5_optarg);
                 }
                 break;
 
@@ -193,14 +193,14 @@ parse_command_line(int argc, const char **argv)
     }     /* end while */
 
     /* check for file name to be processed */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         h5tools_setstatus(EXIT_FAILURE);
         goto error;
     } /* end if */
 
-    fname_g = HDstrdup(argv[opt_ind]);
+    fname_g = HDstrdup(argv[H5_optind]);
 
 done:
     return (0);
diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c
index 7e92c83..6e4f0a6 100644
--- a/tools/src/misc/h5mkgrp.c
+++ b/tools/src/misc/h5mkgrp.c
@@ -22,10 +22,10 @@
 int d_status = EXIT_SUCCESS;
 
 /* command-line options: short and long-named parameters */
-static const char *        s_opts   = "hlpvV";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},    {"latest", no_arg, 'l'},
-                                       {"parents", no_arg, 'p'}, {"verbose", no_arg, 'v'},
-                                       {"version", no_arg, 'V'}, {NULL, 0, '\0'}};
+static const char *           s_opts   = "hlpvV";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},    {"latest", no_arg, 'l'},
+                                          {"parents", no_arg, 'p'}, {"verbose", no_arg, 'v'},
+                                          {"version", no_arg, 'V'}, {NULL, 0, '\0'}};
 
 /* Command line parameter settings */
 typedef struct mkgrp_opt_t {
@@ -124,7 +124,7 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
     }
 
     /* Parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             /* Display 'help' */
             case 'h':
@@ -161,33 +161,33 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
     }     /* end while */
 
     /* Check for file name to be processed */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         leave(EXIT_FAILURE);
     }
 
     /* Retrieve file name */
-    options->fname = HDstrdup(argv[opt_ind]);
-    opt_ind++;
+    options->fname = HDstrdup(argv[H5_optind]);
+    H5_optind++;
 
     /* Check for group(s) to be created */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing group name(s)\n");
         usage(h5tools_getprogname());
         leave(EXIT_FAILURE);
     }
 
     /* Allocate space for the group name pointers */
-    options->ngroups = (size_t)(argc - opt_ind);
+    options->ngroups = (size_t)(argc - H5_optind);
     options->groups  = (char **)HDmalloc(options->ngroups * sizeof(char *));
 
     /* Retrieve the group names */
     curr_group = 0;
-    while (opt_ind < argc) {
-        options->groups[curr_group] = HDstrdup(argv[opt_ind]);
+    while (H5_optind < argc) {
+        options->groups[curr_group] = HDstrdup(argv[H5_optind]);
         curr_group++;
-        opt_ind++;
+        H5_optind++;
     }
 
     return 0;
diff --git a/tools/test/h5jam/getub.c b/tools/test/h5jam/getub.c
index a9b4437..eae7f15 100644
--- a/tools/test/h5jam/getub.c
+++ b/tools/test/h5jam/getub.c
@@ -21,9 +21,9 @@ void parse_command_line(int argc, const char *argv[]);
 #define PROGRAM_NAME "getub"
 char *nbytes = NULL;
 
-static const char *        s_opts   = "c:";                     /* add more later ? */
-static struct long_options l_opts[] = {{"c", require_arg, 'c'}, /* input file */
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "c:";                     /* add more later ? */
+static struct h5_long_options l_opts[] = {{"c", require_arg, 'c'}, /* input file */
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function:    usage
@@ -57,10 +57,10 @@ parse_command_line(int argc, const char *argv[])
     int opt;
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'c':
-                nbytes = HDstrdup(opt_arg);
+                nbytes = HDstrdup(H5_optarg);
                 break;
             case '?':
             default:
@@ -69,7 +69,7 @@ parse_command_line(int argc, const char *argv[])
         } /* end switch */
     }     /* end while */
 
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         HDexit(EXIT_FAILURE);
@@ -100,13 +100,13 @@ main(int argc, const char *argv[])
         goto error;
     } /* end if */
 
-    if (argc <= (opt_ind)) {
+    if (argc <= (H5_optind)) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         goto error;
     } /* end if */
 
-    filename = HDstrdup(argv[opt_ind]);
+    filename = HDstrdup(argv[H5_optind]);
 
     size = 0;
     if (EOF == (res = sscanf(nbytes, "%u", &size))) {
diff --git a/tools/test/h5jam/tellub.c b/tools/test/h5jam/tellub.c
index 54f545a..46e5ae3 100644
--- a/tools/test/h5jam/tellub.c
+++ b/tools/test/h5jam/tellub.c
@@ -24,8 +24,8 @@
  * parameters. The long-named ones can be partially spelled. When
  * adding more, make sure that they don't clash with each other.
  */
-static const char *        s_opts   = "h";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'}, {"hel", no_arg, 'h'}, {NULL, 0, '\0'}};
+static const char *           s_opts   = "h";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"hel", no_arg, 'h'}, {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function:    usage
@@ -61,7 +61,7 @@ parse_command_line(int argc, const char *argv[])
     int opt;
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'h':
                 usage(h5tools_getprogname());
@@ -75,7 +75,7 @@ parse_command_line(int argc, const char *argv[])
     }
 
     /* check for file name to be processed */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         h5tools_setstatus(EXIT_FAILURE);
@@ -118,14 +118,14 @@ main(int argc, const char *argv[])
     /* enable error reporting if command line option */
     h5tools_error_report();
 
-    if (argc <= (opt_ind)) {
+    if (argc <= (H5_optind)) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
 
-    ifname = HDstrdup(argv[opt_ind]);
+    ifname = HDstrdup(argv[H5_optind]);
 
     testval = H5Fis_hdf5(ifname);
 
diff --git a/tools/test/perform/pio_perf.c b/tools/test/perform/pio_perf.c
index 6fb5043..d38c574 100644
--- a/tools/test/perform/pio_perf.c
+++ b/tools/test/perform/pio_perf.c
@@ -123,12 +123,12 @@ static const char *s_opts = "a:A:B:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:";
 #else
 static const char *s_opts = "a:A:bB:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:";
 #endif /* 1 */
-static struct long_options l_opts[] = {{"align", require_arg, 'a'},
-                                       {"alig", require_arg, 'a'},
-                                       {"ali", require_arg, 'a'},
-                                       {"al", require_arg, 'a'},
-                                       {"api", require_arg, 'A'},
-                                       {"ap", require_arg, 'A'},
+static struct h5_long_options l_opts[] = {{"align", require_arg, 'a'},
+                                          {"alig", require_arg, 'a'},
+                                          {"ali", require_arg, 'a'},
+                                          {"al", require_arg, 'a'},
+                                          {"api", require_arg, 'A'},
+                                          {"ap", require_arg, 'A'},
 #if 0
     /* a sighting of the elusive binary option */
     { "binary", no_arg, 'b' },
@@ -137,133 +137,133 @@ static struct long_options l_opts[] = {{"align", require_arg, 'a'},
     { "bin", no_arg, 'b' },
     { "bi", no_arg, 'b' },
 #endif /* 0 */
-                                       {"block-size", require_arg, 'B'},
-                                       {"block-siz", require_arg, 'B'},
-                                       {"block-si", require_arg, 'B'},
-                                       {"block-s", require_arg, 'B'},
-                                       {"block-", require_arg, 'B'},
-                                       {"block", require_arg, 'B'},
-                                       {"bloc", require_arg, 'B'},
-                                       {"blo", require_arg, 'B'},
-                                       {"bl", require_arg, 'B'},
-                                       {"chunk", no_arg, 'c'},
-                                       {"chun", no_arg, 'c'},
-                                       {"chu", no_arg, 'c'},
-                                       {"ch", no_arg, 'c'},
-                                       {"collective", no_arg, 'C'},
-                                       {"collectiv", no_arg, 'C'},
-                                       {"collecti", no_arg, 'C'},
-                                       {"collect", no_arg, 'C'},
-                                       {"collec", no_arg, 'C'},
-                                       {"colle", no_arg, 'C'},
-                                       {"coll", no_arg, 'C'},
-                                       {"col", no_arg, 'C'},
-                                       {"co", no_arg, 'C'},
-                                       {"debug", require_arg, 'D'},
-                                       {"debu", require_arg, 'D'},
-                                       {"deb", require_arg, 'D'},
-                                       {"de", require_arg, 'D'},
-                                       {"geometry", no_arg, 'g'},
-                                       {"geometr", no_arg, 'g'},
-                                       {"geomet", no_arg, 'g'},
-                                       {"geome", no_arg, 'g'},
-                                       {"geom", no_arg, 'g'},
-                                       {"geo", no_arg, 'g'},
-                                       {"ge", no_arg, 'g'},
-                                       {"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"he", no_arg, 'h'},
-                                       {"interleaved", require_arg, 'I'},
-                                       {"interleave", require_arg, 'I'},
-                                       {"interleav", require_arg, 'I'},
-                                       {"interlea", require_arg, 'I'},
-                                       {"interle", require_arg, 'I'},
-                                       {"interl", require_arg, 'I'},
-                                       {"inter", require_arg, 'I'},
-                                       {"inte", require_arg, 'I'},
-                                       {"int", require_arg, 'I'},
-                                       {"in", require_arg, 'I'},
-                                       {"max-num-processes", require_arg, 'P'},
-                                       {"max-num-processe", require_arg, 'P'},
-                                       {"max-num-process", require_arg, 'P'},
-                                       {"max-num-proces", require_arg, 'P'},
-                                       {"max-num-proce", require_arg, 'P'},
-                                       {"max-num-proc", require_arg, 'P'},
-                                       {"max-num-pro", require_arg, 'P'},
-                                       {"max-num-pr", require_arg, 'P'},
-                                       {"max-num-p", require_arg, 'P'},
-                                       {"min-num-processes", require_arg, 'p'},
-                                       {"min-num-processe", require_arg, 'p'},
-                                       {"min-num-process", require_arg, 'p'},
-                                       {"min-num-proces", require_arg, 'p'},
-                                       {"min-num-proce", require_arg, 'p'},
-                                       {"min-num-proc", require_arg, 'p'},
-                                       {"min-num-pro", require_arg, 'p'},
-                                       {"min-num-pr", require_arg, 'p'},
-                                       {"min-num-p", require_arg, 'p'},
-                                       {"max-xfer-size", require_arg, 'X'},
-                                       {"max-xfer-siz", require_arg, 'X'},
-                                       {"max-xfer-si", require_arg, 'X'},
-                                       {"max-xfer-s", require_arg, 'X'},
-                                       {"max-xfer", require_arg, 'X'},
-                                       {"max-xfe", require_arg, 'X'},
-                                       {"max-xf", require_arg, 'X'},
-                                       {"max-x", require_arg, 'X'},
-                                       {"min-xfer-size", require_arg, 'x'},
-                                       {"min-xfer-siz", require_arg, 'x'},
-                                       {"min-xfer-si", require_arg, 'x'},
-                                       {"min-xfer-s", require_arg, 'x'},
-                                       {"min-xfer", require_arg, 'x'},
-                                       {"min-xfe", require_arg, 'x'},
-                                       {"min-xf", require_arg, 'x'},
-                                       {"min-x", require_arg, 'x'},
-                                       {"num-bytes", require_arg, 'e'},
-                                       {"num-byte", require_arg, 'e'},
-                                       {"num-byt", require_arg, 'e'},
-                                       {"num-by", require_arg, 'e'},
-                                       {"num-b", require_arg, 'e'},
-                                       {"num-dsets", require_arg, 'd'},
-                                       {"num-dset", require_arg, 'd'},
-                                       {"num-dse", require_arg, 'd'},
-                                       {"num-ds", require_arg, 'd'},
-                                       {"num-d", require_arg, 'd'},
-                                       {"num-files", require_arg, 'F'},
-                                       {"num-file", require_arg, 'F'},
-                                       {"num-fil", require_arg, 'F'},
-                                       {"num-fi", require_arg, 'F'},
-                                       {"num-f", require_arg, 'F'},
-                                       {"num-iterations", require_arg, 'i'},
-                                       {"num-iteration", require_arg, 'i'},
-                                       {"num-iteratio", require_arg, 'i'},
-                                       {"num-iterati", require_arg, 'i'},
-                                       {"num-iterat", require_arg, 'i'},
-                                       {"num-itera", require_arg, 'i'},
-                                       {"num-iter", require_arg, 'i'},
-                                       {"num-ite", require_arg, 'i'},
-                                       {"num-it", require_arg, 'i'},
-                                       {"num-i", require_arg, 'i'},
-                                       {"output", require_arg, 'o'},
-                                       {"outpu", require_arg, 'o'},
-                                       {"outp", require_arg, 'o'},
-                                       {"out", require_arg, 'o'},
-                                       {"ou", require_arg, 'o'},
-                                       {"threshold", require_arg, 'T'},
-                                       {"threshol", require_arg, 'T'},
-                                       {"thresho", require_arg, 'T'},
-                                       {"thresh", require_arg, 'T'},
-                                       {"thres", require_arg, 'T'},
-                                       {"thre", require_arg, 'T'},
-                                       {"thr", require_arg, 'T'},
-                                       {"th", require_arg, 'T'},
-                                       {"write-only", require_arg, 'w'},
-                                       {"write-onl", require_arg, 'w'},
-                                       {"write-on", require_arg, 'w'},
-                                       {"write-o", require_arg, 'w'},
-                                       {"write", require_arg, 'w'},
-                                       {"writ", require_arg, 'w'},
-                                       {"wri", require_arg, 'w'},
-                                       {"wr", require_arg, 'w'},
-                                       {NULL, 0, '\0'}};
+                                          {"block-size", require_arg, 'B'},
+                                          {"block-siz", require_arg, 'B'},
+                                          {"block-si", require_arg, 'B'},
+                                          {"block-s", require_arg, 'B'},
+                                          {"block-", require_arg, 'B'},
+                                          {"block", require_arg, 'B'},
+                                          {"bloc", require_arg, 'B'},
+                                          {"blo", require_arg, 'B'},
+                                          {"bl", require_arg, 'B'},
+                                          {"chunk", no_arg, 'c'},
+                                          {"chun", no_arg, 'c'},
+                                          {"chu", no_arg, 'c'},
+                                          {"ch", no_arg, 'c'},
+                                          {"collective", no_arg, 'C'},
+                                          {"collectiv", no_arg, 'C'},
+                                          {"collecti", no_arg, 'C'},
+                                          {"collect", no_arg, 'C'},
+                                          {"collec", no_arg, 'C'},
+                                          {"colle", no_arg, 'C'},
+                                          {"coll", no_arg, 'C'},
+                                          {"col", no_arg, 'C'},
+                                          {"co", no_arg, 'C'},
+                                          {"debug", require_arg, 'D'},
+                                          {"debu", require_arg, 'D'},
+                                          {"deb", require_arg, 'D'},
+                                          {"de", require_arg, 'D'},
+                                          {"geometry", no_arg, 'g'},
+                                          {"geometr", no_arg, 'g'},
+                                          {"geomet", no_arg, 'g'},
+                                          {"geome", no_arg, 'g'},
+                                          {"geom", no_arg, 'g'},
+                                          {"geo", no_arg, 'g'},
+                                          {"ge", no_arg, 'g'},
+                                          {"help", no_arg, 'h'},
+                                          {"hel", no_arg, 'h'},
+                                          {"he", no_arg, 'h'},
+                                          {"interleaved", require_arg, 'I'},
+                                          {"interleave", require_arg, 'I'},
+                                          {"interleav", require_arg, 'I'},
+                                          {"interlea", require_arg, 'I'},
+                                          {"interle", require_arg, 'I'},
+                                          {"interl", require_arg, 'I'},
+                                          {"inter", require_arg, 'I'},
+                                          {"inte", require_arg, 'I'},
+                                          {"int", require_arg, 'I'},
+                                          {"in", require_arg, 'I'},
+                                          {"max-num-processes", require_arg, 'P'},
+                                          {"max-num-processe", require_arg, 'P'},
+                                          {"max-num-process", require_arg, 'P'},
+                                          {"max-num-proces", require_arg, 'P'},
+                                          {"max-num-proce", require_arg, 'P'},
+                                          {"max-num-proc", require_arg, 'P'},
+                                          {"max-num-pro", require_arg, 'P'},
+                                          {"max-num-pr", require_arg, 'P'},
+                                          {"max-num-p", require_arg, 'P'},
+                                          {"min-num-processes", require_arg, 'p'},
+                                          {"min-num-processe", require_arg, 'p'},
+                                          {"min-num-process", require_arg, 'p'},
+                                          {"min-num-proces", require_arg, 'p'},
+                                          {"min-num-proce", require_arg, 'p'},
+                                          {"min-num-proc", require_arg, 'p'},
+                                          {"min-num-pro", require_arg, 'p'},
+                                          {"min-num-pr", require_arg, 'p'},
+                                          {"min-num-p", require_arg, 'p'},
+                                          {"max-xfer-size", require_arg, 'X'},
+                                          {"max-xfer-siz", require_arg, 'X'},
+                                          {"max-xfer-si", require_arg, 'X'},
+                                          {"max-xfer-s", require_arg, 'X'},
+                                          {"max-xfer", require_arg, 'X'},
+                                          {"max-xfe", require_arg, 'X'},
+                                          {"max-xf", require_arg, 'X'},
+                                          {"max-x", require_arg, 'X'},
+                                          {"min-xfer-size", require_arg, 'x'},
+                                          {"min-xfer-siz", require_arg, 'x'},
+                                          {"min-xfer-si", require_arg, 'x'},
+                                          {"min-xfer-s", require_arg, 'x'},
+                                          {"min-xfer", require_arg, 'x'},
+                                          {"min-xfe", require_arg, 'x'},
+                                          {"min-xf", require_arg, 'x'},
+                                          {"min-x", require_arg, 'x'},
+                                          {"num-bytes", require_arg, 'e'},
+                                          {"num-byte", require_arg, 'e'},
+                                          {"num-byt", require_arg, 'e'},
+                                          {"num-by", require_arg, 'e'},
+                                          {"num-b", require_arg, 'e'},
+                                          {"num-dsets", require_arg, 'd'},
+                                          {"num-dset", require_arg, 'd'},
+                                          {"num-dse", require_arg, 'd'},
+                                          {"num-ds", require_arg, 'd'},
+                                          {"num-d", require_arg, 'd'},
+                                          {"num-files", require_arg, 'F'},
+                                          {"num-file", require_arg, 'F'},
+                                          {"num-fil", require_arg, 'F'},
+                                          {"num-fi", require_arg, 'F'},
+                                          {"num-f", require_arg, 'F'},
+                                          {"num-iterations", require_arg, 'i'},
+                                          {"num-iteration", require_arg, 'i'},
+                                          {"num-iteratio", require_arg, 'i'},
+                                          {"num-iterati", require_arg, 'i'},
+                                          {"num-iterat", require_arg, 'i'},
+                                          {"num-itera", require_arg, 'i'},
+                                          {"num-iter", require_arg, 'i'},
+                                          {"num-ite", require_arg, 'i'},
+                                          {"num-it", require_arg, 'i'},
+                                          {"num-i", require_arg, 'i'},
+                                          {"output", require_arg, 'o'},
+                                          {"outpu", require_arg, 'o'},
+                                          {"outp", require_arg, 'o'},
+                                          {"out", require_arg, 'o'},
+                                          {"ou", require_arg, 'o'},
+                                          {"threshold", require_arg, 'T'},
+                                          {"threshol", require_arg, 'T'},
+                                          {"thresho", require_arg, 'T'},
+                                          {"thresh", require_arg, 'T'},
+                                          {"thres", require_arg, 'T'},
+                                          {"thre", require_arg, 'T'},
+                                          {"thr", require_arg, 'T'},
+                                          {"th", require_arg, 'T'},
+                                          {"write-only", require_arg, 'w'},
+                                          {"write-onl", require_arg, 'w'},
+                                          {"write-on", require_arg, 'w'},
+                                          {"write-o", require_arg, 'w'},
+                                          {"write", require_arg, 'w'},
+                                          {"writ", require_arg, 'w'},
+                                          {"wri", require_arg, 'w'},
+                                          {"wr", require_arg, 'w'},
+                                          {NULL, 0, '\0'}};
 
 struct options {
     long        io_types;      /* bitmask of which I/O types to test   */
@@ -1286,13 +1286,13 @@ parse_command_line(int argc, char *argv[])
     cl_opts->h5_write_only = FALSE; /* Do both read and write by default */
     cl_opts->verify        = FALSE; /* No Verify data correctness by default */
 
-    while ((opt = get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'a':
-                cl_opts->h5_alignment = parse_size_directive(opt_arg);
+                cl_opts->h5_alignment = parse_size_directive(H5_optarg);
                 break;
             case 'A': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
 
                 while (end && *end != '\0') {
                     char buf[10];
@@ -1332,7 +1332,7 @@ parse_command_line(int argc, char *argv[])
             break;
 #endif /* 0 */
             case 'B':
-                cl_opts->blk_size = (size_t)parse_size_directive(opt_arg);
+                cl_opts->blk_size = (size_t)parse_size_directive(H5_optarg);
                 break;
             case 'c':
                 /* Turn on chunked HDF5 dataset creation */
@@ -1342,10 +1342,10 @@ parse_command_line(int argc, char *argv[])
                 cl_opts->collective = 1;
                 break;
             case 'd':
-                cl_opts->num_dsets = atoi(opt_arg);
+                cl_opts->num_dsets = atoi(H5_optarg);
                 break;
             case 'D': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
 
                 while (end && *end != '\0') {
                     char buf[10];
@@ -1402,40 +1402,40 @@ parse_command_line(int argc, char *argv[])
 
             break;
             case 'e':
-                cl_opts->num_bpp = parse_size_directive(opt_arg);
+                cl_opts->num_bpp = parse_size_directive(H5_optarg);
                 break;
             case 'F':
-                cl_opts->num_files = HDatoi(opt_arg);
+                cl_opts->num_files = HDatoi(H5_optarg);
                 break;
             case 'g':
                 cl_opts->dim2d = 1;
                 break;
             case 'i':
-                cl_opts->num_iters = HDatoi(opt_arg);
+                cl_opts->num_iters = HDatoi(H5_optarg);
                 break;
             case 'I':
                 cl_opts->interleaved = 1;
                 break;
             case 'o':
-                cl_opts->output_file = opt_arg;
+                cl_opts->output_file = H5_optarg;
                 break;
             case 'p':
-                cl_opts->min_num_procs = HDatoi(opt_arg);
+                cl_opts->min_num_procs = HDatoi(H5_optarg);
                 break;
             case 'P':
-                cl_opts->max_num_procs = HDatoi(opt_arg);
+                cl_opts->max_num_procs = HDatoi(H5_optarg);
                 break;
             case 'T':
-                cl_opts->h5_threshold = parse_size_directive(opt_arg);
+                cl_opts->h5_threshold = parse_size_directive(H5_optarg);
                 break;
             case 'w':
                 cl_opts->h5_write_only = TRUE;
                 break;
             case 'x':
-                cl_opts->min_xfer_size = (size_t)parse_size_directive(opt_arg);
+                cl_opts->min_xfer_size = (size_t)parse_size_directive(H5_optarg);
                 break;
             case 'X':
-                cl_opts->max_xfer_size = (size_t)parse_size_directive(opt_arg);
+                cl_opts->max_xfer_size = (size_t)parse_size_directive(H5_optarg);
                 break;
             case 'h':
             case '?':
diff --git a/tools/test/perform/pio_standalone.c b/tools/test/perform/pio_standalone.c
index 0a9bfc0..ded15a4 100644
--- a/tools/test/perform/pio_standalone.c
+++ b/tools/test/perform/pio_standalone.c
@@ -26,31 +26,26 @@ MPI_Info h5_io_info_g = MPI_INFO_NULL; /* MPI INFO object for IO */
 /* global variables */
 int nCols = 80;
 
-/* ``get_option'' variables */
-int         opt_err = 1; /*get_option prints errors if this is on */
-int         opt_ind = 1; /*token pointer                          */
-const char *opt_arg;     /*flag argument (or value)               */
-
 int
-get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts)
+get_option(int argc, const char **argv, const char *opts, const struct h5_long_options *l_opts)
 {
     static int sp      = 1;   /* character index in current token */
     int        opt_opt = '?'; /* option character passed back to user */
 
     if (sp == 1) {
         /* check for more flag-like tokens */
-        if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0') {
+        if (H5_optind >= argc || argv[H5_optind][0] != '-' || argv[H5_optind][1] == '\0') {
             return EOF;
         }
-        else if (HDstrcmp(argv[opt_ind], "--") == 0) {
-            opt_ind++;
+        else if (HDstrcmp(argv[H5_optind], "--") == 0) {
+            H5_optind++;
             return EOF;
         }
     }
 
-    if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') {
+    if (sp == 1 && argv[H5_optind][0] == '-' && argv[H5_optind][1] == '-') {
         /* long command line option */
-        const char *arg = &argv[opt_ind][2];
+        const char *arg = &argv[H5_optind][2];
         int         i;
 
         for (i = 0; l_opts && l_opts[i].name; i++) {
@@ -62,13 +57,13 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
                 if (l_opts[i].has_arg != no_arg) {
                     if (arg[len] == '=') {
-                        opt_arg = &arg[len + 1];
+                        H5_optarg = &arg[len + 1];
                     }
-                    else if (opt_ind < (argc - 1) && argv[opt_ind + 1][0] != '-') {
-                        opt_arg = argv[++opt_ind];
+                    else if (H5_optind < (argc - 1) && argv[H5_optind + 1][0] != '-') {
+                        H5_optarg = argv[++H5_optind];
                     }
                     else if (l_opts[i].has_arg == require_arg) {
-                        if (opt_err)
+                        if (H5_opterr)
                             HDfprintf(stderr, "%s: option required for \"--%s\" flag\n", argv[0], arg);
 
                         opt_opt = '?';
@@ -76,13 +71,13 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
                 }
                 else {
                     if (arg[len] == '=') {
-                        if (opt_err)
+                        if (H5_opterr)
                             HDfprintf(stderr, "%s: no option required for \"%s\" flag\n", argv[0], arg);
 
                         opt_opt = '?';
                     }
 
-                    opt_arg = NULL;
+                    H5_optarg = NULL;
                 }
 
                 break;
@@ -91,29 +86,29 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
         if (l_opts[i].name == NULL) {
             /* exhausted all of the l_opts we have and still didn't match */
-            if (opt_err)
+            if (H5_opterr)
                 HDfprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
 
             opt_opt = '?';
         }
 
-        opt_ind++;
+        H5_optind++;
         sp = 1;
     }
     else {
         register char *cp; /* pointer into current token */
 
         /* short command line option */
-        opt_opt = argv[opt_ind][sp];
+        opt_opt = argv[H5_optind][sp];
 
         if (opt_opt == ':' || (cp = strchr(opts, opt_opt)) == 0) {
 
-            if (opt_err)
+            if (H5_opterr)
                 HDfprintf(stderr, "%s: unknown option \"%c\"\n", argv[0], opt_opt);
 
             /* if no chars left in this token, move to next token */
-            if (argv[opt_ind][++sp] == '\0') {
-                opt_ind++;
+            if (argv[H5_optind][++sp] == '\0') {
+                H5_optind++;
                 sp = 1;
             }
 
@@ -122,32 +117,32 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
         if (*++cp == ':') {
             /* if a value is expected, get it */
-            if (argv[opt_ind][sp + 1] != '\0') {
+            if (argv[H5_optind][sp + 1] != '\0') {
                 /* flag value is rest of current token */
-                opt_arg = &argv[opt_ind++][sp + 1];
+                H5_optarg = &argv[H5_optind++][sp + 1];
             }
-            else if (++opt_ind >= argc) {
-                if (opt_err)
+            else if (++H5_optind >= argc) {
+                if (H5_opterr)
                     HDfprintf(stderr, "%s: value expected for option \"%c\"\n", argv[0], opt_opt);
 
                 opt_opt = '?';
             }
             else {
                 /* flag value is next token */
-                opt_arg = argv[opt_ind++];
+                H5_optarg = argv[H5_optind++];
             }
 
             sp = 1;
         }
         else {
             /* set up to look at next char in token, next time */
-            if (argv[opt_ind][++sp] == '\0') {
+            if (argv[H5_optind][++sp] == '\0') {
                 /* no more in current token, so setup next token */
-                opt_ind++;
+                H5_optind++;
                 sp = 1;
             }
 
-            opt_arg = NULL;
+            H5_optarg = NULL;
         }
     }
 
diff --git a/tools/test/perform/pio_standalone.h b/tools/test/perform/pio_standalone.h
index 82fabdc..813ad2d 100644
--- a/tools/test/perform/pio_standalone.h
+++ b/tools/test/perform/pio_standalone.h
@@ -471,24 +471,25 @@ void h5_dump_info_object(MPI_Info info);
 
 /** From h5tools_utils.h **/
 
-extern int         opt_err; /* getoption prints errors if this is on    */
-extern int         opt_ind; /* token pointer                            */
-extern const char *opt_arg; /* flag argument (or value)                 */
+H5_DLLVAR int         H5_opterr; /* getoption prints errors if this is on    */
+H5_DLLVAR int         H5_optind; /* token pointer                            */
+H5_DLLVAR const char *H5_optarg; /* flag argument (or value)                 */
 
-enum {
+enum h5_arg_level {
     no_arg = 0,  /* doesn't take an argument     */
     require_arg, /* requires an argument          */
     optional_arg /* argument is optional         */
 };
 
-typedef struct long_options {
-    const char *name;     /* name of the long option              */
-    int         has_arg;  /* whether we should look for an arg    */
-    char        shortval; /* the shortname equivalent of long arg
-                           * this gets returned from get_option   */
-} long_options;
+struct h5_long_options {
+    const char *      name;     /* Name of the long option */
+    enum h5_arg_level has_arg;  /* Whether we should look for an arg */
+    char              shortval; /* The shortname equivalent of long arg
+                                 * this gets returned from get_option
+                                 */
+};
 
-extern int get_option(int argc, const char **argv, const char *opt, const struct long_options *l_opt);
+extern int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt);
 
 extern int nCols; /*max number of columns for outputting  */
 
diff --git a/tools/test/perform/sio_perf.c b/tools/test/perform/sio_perf.c
index fe4e7e7..51a7825 100644
--- a/tools/test/perform/sio_perf.c
+++ b/tools/test/perform/sio_perf.c
@@ -97,13 +97,13 @@ static const char *progname = "h5perf_serial";
  * It seems that only the options that accept additional information
  * such as dataset size (-e) require the colon next to it.
  */
-static const char *        s_opts   = "a:A:B:c:Cd:D:e:F:ghi:Imno:p:P:r:stT:v:wx:X:";
-static struct long_options l_opts[] = {{"align", require_arg, 'a'},
-                                       {"alig", require_arg, 'a'},
-                                       {"ali", require_arg, 'a'},
-                                       {"al", require_arg, 'a'},
-                                       {"api", require_arg, 'A'},
-                                       {"ap", require_arg, 'A'},
+static const char *           s_opts   = "a:A:B:c:Cd:D:e:F:ghi:Imno:p:P:r:stT:v:wx:X:";
+static struct h5_long_options l_opts[] = {{"align", require_arg, 'a'},
+                                          {"alig", require_arg, 'a'},
+                                          {"ali", require_arg, 'a'},
+                                          {"al", require_arg, 'a'},
+                                          {"api", require_arg, 'A'},
+                                          {"ap", require_arg, 'A'},
 #if 0
     /* a sighting of the elusive binary option */
     { "binary", no_arg, 'b' },
@@ -112,156 +112,156 @@ static struct long_options l_opts[] = {{"align", require_arg, 'a'},
     { "bin", no_arg, 'b' },
     { "bi", no_arg, 'b' },
 #endif /* 0 */
-                                       {"block-size", require_arg, 'B'},
-                                       {"block-siz", require_arg, 'B'},
-                                       {"block-si", require_arg, 'B'},
-                                       {"block-s", require_arg, 'B'},
-                                       {"block-", require_arg, 'B'},
-                                       {"block", require_arg, 'B'},
-                                       {"bloc", require_arg, 'B'},
-                                       {"blo", require_arg, 'B'},
-                                       {"bl", require_arg, 'B'},
-                                       {"chunk", no_arg, 'c'},
-                                       {"chun", no_arg, 'c'},
-                                       {"chu", no_arg, 'c'},
-                                       {"ch", no_arg, 'c'},
-                                       {"collective", no_arg, 'C'},
-                                       {"collectiv", no_arg, 'C'},
-                                       {"collecti", no_arg, 'C'},
-                                       {"collect", no_arg, 'C'},
-                                       {"collec", no_arg, 'C'},
-                                       {"colle", no_arg, 'C'},
-                                       {"coll", no_arg, 'C'},
-                                       {"col", no_arg, 'C'},
-                                       {"co", no_arg, 'C'},
-                                       {"debug", require_arg, 'D'},
-                                       {"debu", require_arg, 'D'},
-                                       {"deb", require_arg, 'D'},
-                                       {"de", require_arg, 'D'},
-                                       {"file-driver", require_arg, 'v'},
-                                       {"file-drive", require_arg, 'v'},
-                                       {"file-driv", require_arg, 'v'},
-                                       {"file-dri", require_arg, 'v'},
-                                       {"file-dr", require_arg, 'v'},
-                                       {"file-d", require_arg, 'v'},
-                                       {"file-", require_arg, 'v'},
-                                       {"file", require_arg, 'v'},
-                                       {"fil", require_arg, 'v'},
-                                       {"fi", require_arg, 'v'},
-                                       {"geometry", no_arg, 'g'},
-                                       {"geometr", no_arg, 'g'},
-                                       {"geomet", no_arg, 'g'},
-                                       {"geome", no_arg, 'g'},
-                                       {"geom", no_arg, 'g'},
-                                       {"geo", no_arg, 'g'},
-                                       {"ge", no_arg, 'g'},
-                                       {"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"he", no_arg, 'h'},
-                                       {"interleaved", require_arg, 'I'},
-                                       {"interleave", require_arg, 'I'},
-                                       {"interleav", require_arg, 'I'},
-                                       {"interlea", require_arg, 'I'},
-                                       {"interle", require_arg, 'I'},
-                                       {"interl", require_arg, 'I'},
-                                       {"inter", require_arg, 'I'},
-                                       {"inte", require_arg, 'I'},
-                                       {"int", require_arg, 'I'},
-                                       {"in", require_arg, 'I'},
-                                       {"max-num-processes", require_arg, 'P'},
-                                       {"max-num-processe", require_arg, 'P'},
-                                       {"max-num-process", require_arg, 'P'},
-                                       {"max-num-proces", require_arg, 'P'},
-                                       {"max-num-proce", require_arg, 'P'},
-                                       {"max-num-proc", require_arg, 'P'},
-                                       {"max-num-pro", require_arg, 'P'},
-                                       {"max-num-pr", require_arg, 'P'},
-                                       {"max-num-p", require_arg, 'P'},
-                                       {"min-num-processes", require_arg, 'p'},
-                                       {"min-num-processe", require_arg, 'p'},
-                                       {"min-num-process", require_arg, 'p'},
-                                       {"min-num-proces", require_arg, 'p'},
-                                       {"min-num-proce", require_arg, 'p'},
-                                       {"min-num-proc", require_arg, 'p'},
-                                       {"min-num-pro", require_arg, 'p'},
-                                       {"min-num-pr", require_arg, 'p'},
-                                       {"min-num-p", require_arg, 'p'},
-                                       {"max-xfer-size", require_arg, 'X'},
-                                       {"max-xfer-siz", require_arg, 'X'},
-                                       {"max-xfer-si", require_arg, 'X'},
-                                       {"max-xfer-s", require_arg, 'X'},
-                                       {"max-xfer", require_arg, 'X'},
-                                       {"max-xfe", require_arg, 'X'},
-                                       {"max-xf", require_arg, 'X'},
-                                       {"max-x", require_arg, 'X'},
-                                       {"min-xfer-size", require_arg, 'x'},
-                                       {"min-xfer-siz", require_arg, 'x'},
-                                       {"min-xfer-si", require_arg, 'x'},
-                                       {"min-xfer-s", require_arg, 'x'},
-                                       {"min-xfer", require_arg, 'x'},
-                                       {"min-xfe", require_arg, 'x'},
-                                       {"min-xf", require_arg, 'x'},
-                                       {"min-x", require_arg, 'x'},
-                                       {"num-bytes", require_arg, 'e'},
-                                       {"num-byte", require_arg, 'e'},
-                                       {"num-byt", require_arg, 'e'},
-                                       {"num-by", require_arg, 'e'},
-                                       {"num-b", require_arg, 'e'},
-                                       {"num-dsets", require_arg, 'd'},
-                                       {"num-dset", require_arg, 'd'},
-                                       {"num-dse", require_arg, 'd'},
-                                       {"num-ds", require_arg, 'd'},
-                                       {"num-d", require_arg, 'd'},
-                                       {"num-files", require_arg, 'F'},
-                                       {"num-file", require_arg, 'F'},
-                                       {"num-fil", require_arg, 'F'},
-                                       {"num-fi", require_arg, 'F'},
-                                       {"num-f", require_arg, 'F'},
-                                       {"num-iterations", require_arg, 'i'},
-                                       {"num-iteration", require_arg, 'i'},
-                                       {"num-iteratio", require_arg, 'i'},
-                                       {"num-iterati", require_arg, 'i'},
-                                       {"num-iterat", require_arg, 'i'},
-                                       {"num-itera", require_arg, 'i'},
-                                       {"num-iter", require_arg, 'i'},
-                                       {"num-ite", require_arg, 'i'},
-                                       {"num-it", require_arg, 'i'},
-                                       {"num-i", require_arg, 'i'},
-                                       {"order", require_arg, 'r'},
-                                       {"orde", require_arg, 'r'},
-                                       {"ord", require_arg, 'r'},
-                                       {"or", require_arg, 'r'},
-                                       {"output", require_arg, 'o'},
-                                       {"outpu", require_arg, 'o'},
-                                       {"outp", require_arg, 'o'},
-                                       {"out", require_arg, 'o'},
-                                       {"ou", require_arg, 'o'},
-                                       {"extendable", no_arg, 't'},
-                                       {"extendabl", no_arg, 't'},
-                                       {"extendab", no_arg, 't'},
-                                       {"extenda", no_arg, 't'},
-                                       {"extend", no_arg, 't'},
-                                       {"exten", no_arg, 't'},
-                                       {"exte", no_arg, 't'},
-                                       {"ext", no_arg, 't'},
-                                       {"ex", no_arg, 't'},
-                                       {"threshold", require_arg, 'T'},
-                                       {"threshol", require_arg, 'T'},
-                                       {"thresho", require_arg, 'T'},
-                                       {"thresh", require_arg, 'T'},
-                                       {"thres", require_arg, 'T'},
-                                       {"thre", require_arg, 'T'},
-                                       {"thr", require_arg, 'T'},
-                                       {"th", require_arg, 'T'},
-                                       {"write-only", require_arg, 'w'},
-                                       {"write-onl", require_arg, 'w'},
-                                       {"write-on", require_arg, 'w'},
-                                       {"write-o", require_arg, 'w'},
-                                       {"write", require_arg, 'w'},
-                                       {"writ", require_arg, 'w'},
-                                       {"wri", require_arg, 'w'},
-                                       {"wr", require_arg, 'w'},
-                                       {NULL, 0, '\0'}};
+                                          {"block-size", require_arg, 'B'},
+                                          {"block-siz", require_arg, 'B'},
+                                          {"block-si", require_arg, 'B'},
+                                          {"block-s", require_arg, 'B'},
+                                          {"block-", require_arg, 'B'},
+                                          {"block", require_arg, 'B'},
+                                          {"bloc", require_arg, 'B'},
+                                          {"blo", require_arg, 'B'},
+                                          {"bl", require_arg, 'B'},
+                                          {"chunk", no_arg, 'c'},
+                                          {"chun", no_arg, 'c'},
+                                          {"chu", no_arg, 'c'},
+                                          {"ch", no_arg, 'c'},
+                                          {"collective", no_arg, 'C'},
+                                          {"collectiv", no_arg, 'C'},
+                                          {"collecti", no_arg, 'C'},
+                                          {"collect", no_arg, 'C'},
+                                          {"collec", no_arg, 'C'},
+                                          {"colle", no_arg, 'C'},
+                                          {"coll", no_arg, 'C'},
+                                          {"col", no_arg, 'C'},
+                                          {"co", no_arg, 'C'},
+                                          {"debug", require_arg, 'D'},
+                                          {"debu", require_arg, 'D'},
+                                          {"deb", require_arg, 'D'},
+                                          {"de", require_arg, 'D'},
+                                          {"file-driver", require_arg, 'v'},
+                                          {"file-drive", require_arg, 'v'},
+                                          {"file-driv", require_arg, 'v'},
+                                          {"file-dri", require_arg, 'v'},
+                                          {"file-dr", require_arg, 'v'},
+                                          {"file-d", require_arg, 'v'},
+                                          {"file-", require_arg, 'v'},
+                                          {"file", require_arg, 'v'},
+                                          {"fil", require_arg, 'v'},
+                                          {"fi", require_arg, 'v'},
+                                          {"geometry", no_arg, 'g'},
+                                          {"geometr", no_arg, 'g'},
+                                          {"geomet", no_arg, 'g'},
+                                          {"geome", no_arg, 'g'},
+                                          {"geom", no_arg, 'g'},
+                                          {"geo", no_arg, 'g'},
+                                          {"ge", no_arg, 'g'},
+                                          {"help", no_arg, 'h'},
+                                          {"hel", no_arg, 'h'},
+                                          {"he", no_arg, 'h'},
+                                          {"interleaved", require_arg, 'I'},
+                                          {"interleave", require_arg, 'I'},
+                                          {"interleav", require_arg, 'I'},
+                                          {"interlea", require_arg, 'I'},
+                                          {"interle", require_arg, 'I'},
+                                          {"interl", require_arg, 'I'},
+                                          {"inter", require_arg, 'I'},
+                                          {"inte", require_arg, 'I'},
+                                          {"int", require_arg, 'I'},
+                                          {"in", require_arg, 'I'},
+                                          {"max-num-processes", require_arg, 'P'},
+                                          {"max-num-processe", require_arg, 'P'},
+                                          {"max-num-process", require_arg, 'P'},
+                                          {"max-num-proces", require_arg, 'P'},
+                                          {"max-num-proce", require_arg, 'P'},
+                                          {"max-num-proc", require_arg, 'P'},
+                                          {"max-num-pro", require_arg, 'P'},
+                                          {"max-num-pr", require_arg, 'P'},
+                                          {"max-num-p", require_arg, 'P'},
+                                          {"min-num-processes", require_arg, 'p'},
+                                          {"min-num-processe", require_arg, 'p'},
+                                          {"min-num-process", require_arg, 'p'},
+                                          {"min-num-proces", require_arg, 'p'},
+                                          {"min-num-proce", require_arg, 'p'},
+                                          {"min-num-proc", require_arg, 'p'},
+                                          {"min-num-pro", require_arg, 'p'},
+                                          {"min-num-pr", require_arg, 'p'},
+                                          {"min-num-p", require_arg, 'p'},
+                                          {"max-xfer-size", require_arg, 'X'},
+                                          {"max-xfer-siz", require_arg, 'X'},
+                                          {"max-xfer-si", require_arg, 'X'},
+                                          {"max-xfer-s", require_arg, 'X'},
+                                          {"max-xfer", require_arg, 'X'},
+                                          {"max-xfe", require_arg, 'X'},
+                                          {"max-xf", require_arg, 'X'},
+                                          {"max-x", require_arg, 'X'},
+                                          {"min-xfer-size", require_arg, 'x'},
+                                          {"min-xfer-siz", require_arg, 'x'},
+                                          {"min-xfer-si", require_arg, 'x'},
+                                          {"min-xfer-s", require_arg, 'x'},
+                                          {"min-xfer", require_arg, 'x'},
+                                          {"min-xfe", require_arg, 'x'},
+                                          {"min-xf", require_arg, 'x'},
+                                          {"min-x", require_arg, 'x'},
+                                          {"num-bytes", require_arg, 'e'},
+                                          {"num-byte", require_arg, 'e'},
+                                          {"num-byt", require_arg, 'e'},
+                                          {"num-by", require_arg, 'e'},
+                                          {"num-b", require_arg, 'e'},
+                                          {"num-dsets", require_arg, 'd'},
+                                          {"num-dset", require_arg, 'd'},
+                                          {"num-dse", require_arg, 'd'},
+                                          {"num-ds", require_arg, 'd'},
+                                          {"num-d", require_arg, 'd'},
+                                          {"num-files", require_arg, 'F'},
+                                          {"num-file", require_arg, 'F'},
+                                          {"num-fil", require_arg, 'F'},
+                                          {"num-fi", require_arg, 'F'},
+                                          {"num-f", require_arg, 'F'},
+                                          {"num-iterations", require_arg, 'i'},
+                                          {"num-iteration", require_arg, 'i'},
+                                          {"num-iteratio", require_arg, 'i'},
+                                          {"num-iterati", require_arg, 'i'},
+                                          {"num-iterat", require_arg, 'i'},
+                                          {"num-itera", require_arg, 'i'},
+                                          {"num-iter", require_arg, 'i'},
+                                          {"num-ite", require_arg, 'i'},
+                                          {"num-it", require_arg, 'i'},
+                                          {"num-i", require_arg, 'i'},
+                                          {"order", require_arg, 'r'},
+                                          {"orde", require_arg, 'r'},
+                                          {"ord", require_arg, 'r'},
+                                          {"or", require_arg, 'r'},
+                                          {"output", require_arg, 'o'},
+                                          {"outpu", require_arg, 'o'},
+                                          {"outp", require_arg, 'o'},
+                                          {"out", require_arg, 'o'},
+                                          {"ou", require_arg, 'o'},
+                                          {"extendable", no_arg, 't'},
+                                          {"extendabl", no_arg, 't'},
+                                          {"extendab", no_arg, 't'},
+                                          {"extenda", no_arg, 't'},
+                                          {"extend", no_arg, 't'},
+                                          {"exten", no_arg, 't'},
+                                          {"exte", no_arg, 't'},
+                                          {"ext", no_arg, 't'},
+                                          {"ex", no_arg, 't'},
+                                          {"threshold", require_arg, 'T'},
+                                          {"threshol", require_arg, 'T'},
+                                          {"thresho", require_arg, 'T'},
+                                          {"thresh", require_arg, 'T'},
+                                          {"thres", require_arg, 'T'},
+                                          {"thre", require_arg, 'T'},
+                                          {"thr", require_arg, 'T'},
+                                          {"th", require_arg, 'T'},
+                                          {"write-only", require_arg, 'w'},
+                                          {"write-onl", require_arg, 'w'},
+                                          {"write-on", require_arg, 'w'},
+                                          {"write-o", require_arg, 'w'},
+                                          {"write", require_arg, 'w'},
+                                          {"writ", require_arg, 'w'},
+                                          {"wri", require_arg, 'w'},
+                                          {"wr", require_arg, 'w'},
+                                          {NULL, 0, '\0'}};
 
 struct options {
     long        io_types;            /* bitmask of which I/O types to test   */
@@ -993,19 +993,19 @@ parse_command_line(int argc, const char *argv[])
     cl_opts->h5_extendable = FALSE; /* Use extendable dataset */
     cl_opts->verify        = FALSE; /* No Verify data correctness by default */
 
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'a':
-                cl_opts->h5_alignment = parse_size_directive(opt_arg);
+                cl_opts->h5_alignment = parse_size_directive(H5_optarg);
                 break;
             case 'G':
-                cl_opts->page_size = parse_size_directive(opt_arg);
+                cl_opts->page_size = parse_size_directive(H5_optarg);
                 break;
             case 'b':
-                cl_opts->page_buffer_size = parse_size_directive(opt_arg);
+                cl_opts->page_buffer_size = parse_size_directive(H5_optarg);
                 break;
             case 'A': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
                 while (end && *end != '\0') {
                     char buf[10];
 
@@ -1043,7 +1043,7 @@ parse_command_line(int argc, const char *argv[])
                 /* Turn on chunked HDF5 dataset creation */
                 cl_opts->h5_use_chunks = 1;
                 {
-                    const char *end = opt_arg;
+                    const char *end = H5_optarg;
                     int         j   = 0;
 
                     while (end && *end != '\0') {
@@ -1070,7 +1070,7 @@ parse_command_line(int argc, const char *argv[])
                 break;
 
             case 'D': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
 
                 while (end && *end != '\0') {
                     char buf[10];
@@ -1126,7 +1126,7 @@ parse_command_line(int argc, const char *argv[])
 
             break;
             case 'e': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
                 int         j   = 0;
 
                 while (end && *end != '\0') {
@@ -1153,38 +1153,38 @@ parse_command_line(int argc, const char *argv[])
             break;
 
             case 'i':
-                cl_opts->num_iters = HDatoi(opt_arg);
+                cl_opts->num_iters = HDatoi(H5_optarg);
                 break;
             case 'o':
-                cl_opts->output_file = opt_arg;
+                cl_opts->output_file = H5_optarg;
                 break;
             case 'T':
-                cl_opts->h5_threshold = parse_size_directive(opt_arg);
+                cl_opts->h5_threshold = parse_size_directive(H5_optarg);
                 break;
             case 'v':
-                if (!HDstrcasecmp(opt_arg, "sec2")) {
+                if (!HDstrcasecmp(H5_optarg, "sec2")) {
                     cl_opts->vfd = sec2;
                 }
-                else if (!HDstrcasecmp(opt_arg, "stdio")) {
+                else if (!HDstrcasecmp(H5_optarg, "stdio")) {
                     cl_opts->vfd = stdio;
                 }
-                else if (!HDstrcasecmp(opt_arg, "core")) {
+                else if (!HDstrcasecmp(H5_optarg, "core")) {
                     cl_opts->vfd = core;
                 }
-                else if (!HDstrcasecmp(opt_arg, "split")) {
+                else if (!HDstrcasecmp(H5_optarg, "split")) {
                     cl_opts->vfd = split;
                 }
-                else if (!HDstrcasecmp(opt_arg, "multi")) {
+                else if (!HDstrcasecmp(H5_optarg, "multi")) {
                     cl_opts->vfd = multi;
                 }
-                else if (!HDstrcasecmp(opt_arg, "family")) {
+                else if (!HDstrcasecmp(H5_optarg, "family")) {
                     cl_opts->vfd = family;
                 }
-                else if (!HDstrcasecmp(opt_arg, "direct")) {
+                else if (!HDstrcasecmp(H5_optarg, "direct")) {
                     cl_opts->vfd = direct;
                 }
                 else {
-                    HDfprintf(stderr, "sio_perf: invalid --api option %s\n", opt_arg);
+                    HDfprintf(stderr, "sio_perf: invalid --api option %s\n", H5_optarg);
                     HDexit(EXIT_FAILURE);
                 }
                 break;
@@ -1195,7 +1195,7 @@ parse_command_line(int argc, const char *argv[])
                 cl_opts->h5_extendable = TRUE;
                 break;
             case 'x': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
                 int         j   = 0;
 
                 while (end && *end != '\0') {
@@ -1222,7 +1222,7 @@ parse_command_line(int argc, const char *argv[])
             break;
 
             case 'r': {
-                const char *end = opt_arg;
+                const char *end = H5_optarg;
                 int         j   = 0;
 
                 while (end && *end != '\0') {
diff --git a/tools/test/perform/sio_standalone.c b/tools/test/perform/sio_standalone.c
index abc0777..7c22b53 100644
--- a/tools/test/perform/sio_standalone.c
+++ b/tools/test/perform/sio_standalone.c
@@ -22,31 +22,26 @@
 /* global variables */
 int nCols = 80;
 
-/* ``get_option'' variables */
-int         opt_err = 1; /*get_option prints errors if this is on */
-int         opt_ind = 1; /*token pointer                          */
-const char *opt_arg;     /*flag argument (or value)               */
-
 int
-get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts)
+get_option(int argc, const char **argv, const char *opts, const struct h5_long_options *l_opts)
 {
     static int sp      = 1;   /* character index in current token */
     int        opt_opt = '?'; /* option character passed back to user */
 
     if (sp == 1) {
         /* check for more flag-like tokens */
-        if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0') {
+        if (H5_optind >= argc || argv[H5_optind][0] != '-' || argv[H5_optind][1] == '\0') {
             return EOF;
         }
-        else if (HDstrcmp(argv[opt_ind], "--") == 0) {
-            opt_ind++;
+        else if (HDstrcmp(argv[H5_optind], "--") == 0) {
+            H5_optind++;
             return EOF;
         }
     }
 
-    if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') {
+    if (sp == 1 && argv[H5_optind][0] == '-' && argv[H5_optind][1] == '-') {
         /* long command line option */
-        const char *arg = &argv[opt_ind][2];
+        const char *arg = &argv[H5_optind][2];
         int         i;
 
         for (i = 0; l_opts && l_opts[i].name; i++) {
@@ -58,13 +53,13 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
                 if (l_opts[i].has_arg != no_arg) {
                     if (arg[len] == '=') {
-                        opt_arg = &arg[len + 1];
+                        H5_optarg = &arg[len + 1];
                     }
-                    else if (opt_ind < (argc - 1) && argv[opt_ind + 1][0] != '-') {
-                        opt_arg = argv[++opt_ind];
+                    else if (H5_optind < (argc - 1) && argv[H5_optind + 1][0] != '-') {
+                        H5_optarg = argv[++H5_optind];
                     }
                     else if (l_opts[i].has_arg == require_arg) {
-                        if (opt_err)
+                        if (H5_opterr)
                             HDfprintf(stderr, "%s: option required for \"--%s\" flag\n", argv[0], arg);
 
                         opt_opt = '?';
@@ -72,13 +67,13 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
                 }
                 else {
                     if (arg[len] == '=') {
-                        if (opt_err)
+                        if (H5_opterr)
                             HDfprintf(stderr, "%s: no option required for \"%s\" flag\n", argv[0], arg);
 
                         opt_opt = '?';
                     }
 
-                    opt_arg = NULL;
+                    H5_optarg = NULL;
                 }
 
                 break;
@@ -87,29 +82,29 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
         if (l_opts[i].name == NULL) {
             /* exhausted all of the l_opts we have and still didn't match */
-            if (opt_err)
+            if (H5_opterr)
                 HDfprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
 
             opt_opt = '?';
         }
 
-        opt_ind++;
+        H5_optind++;
         sp = 1;
     }
     else {
         register char *cp; /* pointer into current token */
 
         /* short command line option */
-        opt_opt = argv[opt_ind][sp];
+        opt_opt = argv[H5_optind][sp];
 
         if (opt_opt == ':' || (cp = strchr(opts, opt_opt)) == 0) {
 
-            if (opt_err)
+            if (H5_opterr)
                 HDfprintf(stderr, "%s: unknown option \"%c\"\n", argv[0], opt_opt);
 
             /* if no chars left in this token, move to next token */
-            if (argv[opt_ind][++sp] == '\0') {
-                opt_ind++;
+            if (argv[H5_optind][++sp] == '\0') {
+                H5_optind++;
                 sp = 1;
             }
 
@@ -118,32 +113,32 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
         if (*++cp == ':') {
             /* if a value is expected, get it */
-            if (argv[opt_ind][sp + 1] != '\0') {
+            if (argv[H5_optind][sp + 1] != '\0') {
                 /* flag value is rest of current token */
-                opt_arg = &argv[opt_ind++][sp + 1];
+                H5_optarg = &argv[H5_optind++][sp + 1];
             }
-            else if (++opt_ind >= argc) {
-                if (opt_err)
+            else if (++H5_optind >= argc) {
+                if (H5_opterr)
                     HDfprintf(stderr, "%s: value expected for option \"%c\"\n", argv[0], opt_opt);
 
                 opt_opt = '?';
             }
             else {
                 /* flag value is next token */
-                opt_arg = argv[opt_ind++];
+                H5_optarg = argv[H5_optind++];
             }
 
             sp = 1;
         }
         else {
             /* set up to look at next char in token, next time */
-            if (argv[opt_ind][++sp] == '\0') {
+            if (argv[H5_optind][++sp] == '\0') {
                 /* no more in current token, so setup next token */
-                opt_ind++;
+                H5_optind++;
                 sp = 1;
             }
 
-            opt_arg = NULL;
+            H5_optarg = NULL;
         }
     }
 
diff --git a/tools/test/perform/sio_standalone.h b/tools/test/perform/sio_standalone.h
index 54e82fa..9a2a8c6 100644
--- a/tools/test/perform/sio_standalone.h
+++ b/tools/test/perform/sio_standalone.h
@@ -486,24 +486,25 @@ void h5_dump_info_object(MPI_Info info);
 
 /** From h5tools_utils.h **/
 
-extern int         opt_err; /* getoption prints errors if this is on    */
-extern int         opt_ind; /* token pointer                            */
-extern const char *opt_arg; /* flag argument (or value)                 */
+H5_DLLVAR int         H5_opterr; /* getoption prints errors if this is on    */
+H5_DLLVAR int         H5_optind; /* token pointer                            */
+H5_DLLVAR const char *H5_optarg; /* flag argument (or value)                 */
 
-enum {
+enum h5_arg_level {
     no_arg = 0,  /* doesn't take an argument     */
     require_arg, /* requires an argument          */
     optional_arg /* argument is optional         */
 };
 
-typedef struct long_options {
-    const char *name;     /* name of the long option              */
-    int         has_arg;  /* whether we should look for an arg    */
-    char        shortval; /* the shortname equivalent of long arg
-                           * this gets returned from get_option   */
-} long_options;
+struct h5_long_options {
+    const char *      name;     /* Name of the long option */
+    enum h5_arg_level has_arg;  /* Whether we should look for an arg */
+    char              shortval; /* The shortname equivalent of long arg
+                                 * this gets returned from get_option
+                                 */
+};
 
-extern int get_option(int argc, const char **argv, const char *opt, const struct long_options *l_opt);
+extern int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt);
 
 extern int nCols; /*max number of columns for outputting  */
 
diff --git a/tools/test/perform/zip_perf.c b/tools/test/perform/zip_perf.c
index 517866b..6231587 100644
--- a/tools/test/perform/zip_perf.c
+++ b/tools/test/perform/zip_perf.c
@@ -64,66 +64,66 @@ static void error(const char *fmt, ...);
 static void compress_buffer(Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen);
 
 /* commandline options : long and short form */
-static const char *        s_opts   = "hB:b:c:p:rs:0123456789";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
-                                       {"compressability", require_arg, 'c'},
-                                       {"compressabilit", require_arg, 'c'},
-                                       {"compressabili", require_arg, 'c'},
-                                       {"compressabil", require_arg, 'c'},
-                                       {"compressabi", require_arg, 'c'},
-                                       {"compressab", require_arg, 'c'},
-                                       {"compressa", require_arg, 'c'},
-                                       {"compress", require_arg, 'c'},
-                                       {"compres", require_arg, 'c'},
-                                       {"compre", require_arg, 'c'},
-                                       {"compr", require_arg, 'c'},
-                                       {"comp", require_arg, 'c'},
-                                       {"com", require_arg, 'c'},
-                                       {"co", require_arg, 'c'},
-                                       {"file-size", require_arg, 's'},
-                                       {"file-siz", require_arg, 's'},
-                                       {"file-si", require_arg, 's'},
-                                       {"file-s", require_arg, 's'},
-                                       {"file", require_arg, 's'},
-                                       {"fil", require_arg, 's'},
-                                       {"fi", require_arg, 's'},
-                                       {"max-buffer-size", require_arg, 'B'},
-                                       {"max-buffer-siz", require_arg, 'B'},
-                                       {"max-buffer-si", require_arg, 'B'},
-                                       {"max-buffer-s", require_arg, 'B'},
-                                       {"max-buffer", require_arg, 'B'},
-                                       {"max-buffe", require_arg, 'B'},
-                                       {"max-buff", require_arg, 'B'},
-                                       {"max-buf", require_arg, 'B'},
-                                       {"max-bu", require_arg, 'B'},
-                                       {"max-b", require_arg, 'B'},
-                                       {"max", require_arg, 'B'},
-                                       {"min-buffer-size", require_arg, 'b'},
-                                       {"min-buffer-siz", require_arg, 'b'},
-                                       {"min-buffer-si", require_arg, 'b'},
-                                       {"min-buffer-s", require_arg, 'b'},
-                                       {"min-buffer", require_arg, 'b'},
-                                       {"min-buffe", require_arg, 'b'},
-                                       {"min-buff", require_arg, 'b'},
-                                       {"min-buf", require_arg, 'b'},
-                                       {"min-bu", require_arg, 'b'},
-                                       {"min-b", require_arg, 'b'},
-                                       {"min", require_arg, 'b'},
-                                       {"prefix", require_arg, 'p'},
-                                       {"prefi", require_arg, 'p'},
-                                       {"pref", require_arg, 'p'},
-                                       {"pre", require_arg, 'p'},
-                                       {"pr", require_arg, 'p'},
-                                       {"random-test", no_arg, 'r'},
-                                       {"random-tes", no_arg, 'r'},
-                                       {"random-te", no_arg, 'r'},
-                                       {"random-t", no_arg, 'r'},
-                                       {"random", no_arg, 'r'},
-                                       {"rando", no_arg, 'r'},
-                                       {"rand", no_arg, 'r'},
-                                       {"ran", no_arg, 'r'},
-                                       {"ra", no_arg, 'r'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "hB:b:c:p:rs:0123456789";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+                                          {"compressability", require_arg, 'c'},
+                                          {"compressabilit", require_arg, 'c'},
+                                          {"compressabili", require_arg, 'c'},
+                                          {"compressabil", require_arg, 'c'},
+                                          {"compressabi", require_arg, 'c'},
+                                          {"compressab", require_arg, 'c'},
+                                          {"compressa", require_arg, 'c'},
+                                          {"compress", require_arg, 'c'},
+                                          {"compres", require_arg, 'c'},
+                                          {"compre", require_arg, 'c'},
+                                          {"compr", require_arg, 'c'},
+                                          {"comp", require_arg, 'c'},
+                                          {"com", require_arg, 'c'},
+                                          {"co", require_arg, 'c'},
+                                          {"file-size", require_arg, 's'},
+                                          {"file-siz", require_arg, 's'},
+                                          {"file-si", require_arg, 's'},
+                                          {"file-s", require_arg, 's'},
+                                          {"file", require_arg, 's'},
+                                          {"fil", require_arg, 's'},
+                                          {"fi", require_arg, 's'},
+                                          {"max-buffer-size", require_arg, 'B'},
+                                          {"max-buffer-siz", require_arg, 'B'},
+                                          {"max-buffer-si", require_arg, 'B'},
+                                          {"max-buffer-s", require_arg, 'B'},
+                                          {"max-buffer", require_arg, 'B'},
+                                          {"max-buffe", require_arg, 'B'},
+                                          {"max-buff", require_arg, 'B'},
+                                          {"max-buf", require_arg, 'B'},
+                                          {"max-bu", require_arg, 'B'},
+                                          {"max-b", require_arg, 'B'},
+                                          {"max", require_arg, 'B'},
+                                          {"min-buffer-size", require_arg, 'b'},
+                                          {"min-buffer-siz", require_arg, 'b'},
+                                          {"min-buffer-si", require_arg, 'b'},
+                                          {"min-buffer-s", require_arg, 'b'},
+                                          {"min-buffer", require_arg, 'b'},
+                                          {"min-buffe", require_arg, 'b'},
+                                          {"min-buff", require_arg, 'b'},
+                                          {"min-buf", require_arg, 'b'},
+                                          {"min-bu", require_arg, 'b'},
+                                          {"min-b", require_arg, 'b'},
+                                          {"min", require_arg, 'b'},
+                                          {"prefix", require_arg, 'p'},
+                                          {"prefi", require_arg, 'p'},
+                                          {"pref", require_arg, 'p'},
+                                          {"pre", require_arg, 'p'},
+                                          {"pr", require_arg, 'p'},
+                                          {"random-test", no_arg, 'r'},
+                                          {"random-tes", no_arg, 'r'},
+                                          {"random-te", no_arg, 'r'},
+                                          {"random-t", no_arg, 'r'},
+                                          {"random", no_arg, 'r'},
+                                          {"rando", no_arg, 'r'},
+                                          {"rand", no_arg, 'r'},
+                                          {"ran", no_arg, 'r'},
+                                          {"ra", no_arg, 'r'},
+                                          {NULL, 0, '\0'}};
 
 /*
  * Function:    error
@@ -551,7 +551,7 @@ main(int argc, const char *argv[])
     /* Initialize h5tools lib */
     h5tools_init();
 
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) > 0) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) > 0) {
         switch ((char)opt) {
             case '0':
             case '1':
@@ -566,13 +566,13 @@ main(int argc, const char *argv[])
                 compress_level = opt - '0';
                 break;
             case 'B':
-                max_buf_size = parse_size_directive(opt_arg);
+                max_buf_size = parse_size_directive(H5_optarg);
                 break;
             case 'b':
-                min_buf_size = parse_size_directive(opt_arg);
+                min_buf_size = parse_size_directive(H5_optarg);
                 break;
             case 'c':
-                compress_percent = (int)HDstrtol(opt_arg, NULL, 10);
+                compress_percent = (int)HDstrtol(H5_optarg, NULL, 10);
 
                 if (compress_percent < 0)
                     compress_percent = 0;
@@ -581,13 +581,13 @@ main(int argc, const char *argv[])
 
                 break;
             case 'p':
-                option_prefix = opt_arg;
+                option_prefix = H5_optarg;
                 break;
             case 'r':
                 random_test = TRUE;
                 break;
             case 's':
-                file_size = parse_size_directive(opt_arg);
+                file_size = parse_size_directive(H5_optarg);
                 break;
             case '?':
                 usage();
author	Larry Knox <lrknox@hdfgroup.org>	2021-08-11 12:33:57 (GMT)
committer	GitHub <noreply@github.com>	2021-08-11 12:33:57 (GMT)
commit	c0407bd48f60335218dda35740034ab1b41f8a97 (patch)
tree	ee8b6a9d84741f93790f30e224de3b5195983c92 /tools
parent	da7a4b5849015b3332e83a715935ea2edb8218b8 (diff)
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