diff options
| author | Larry Knox <lrknox@hdfgroup.org> | 2021-07-31 18:48:24 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-07-31 18:48:24 (GMT) |
| commit | 9c0188539decac62881b5530c317947203e6dea3 (patch) | |
| tree | 6f269af6ba8239ca71c1320e56684e01d00b5bfe | |
| parent | d99d6c17c9ad8a92ff3f37f70d30017d6902e4dd (diff) | |
| download | hdf5-9c0188539decac62881b5530c317947203e6dea3.zip hdf5-9c0188539decac62881b5530c317947203e6dea3.tar.gz hdf5-9c0188539decac62881b5530c317947203e6dea3.tar.bz2 | |
Merge pr520 to hdf5 1 10 (#870)
* 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>
* 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.
* Clean up MPI-IO VFD tracing support (#520)
* Clean up tracing support
* Committing clang-format changes
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: Quincey Koziol <koziol@lbl.gov>
| -rw-r--r-- | src/H5FDmpio.c | 593 |
1 files changed, 335 insertions, 258 deletions
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 2dd7fd3..37b3bff 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -42,7 +42,7 @@ static hid_t H5FD_MPIO_g = 0; /* Whether to allow collective I/O operations */ -/* (Value can be set from environment variable also) */ +/* (Can be changed by setting "HDF5_MPI_OPT_TYPES" environment variable to '0' or '1') */ hbool_t H5FD_mpi_opt_types_g = TRUE; /* @@ -72,26 +72,26 @@ typedef struct H5FD_mpio_t { /* Private Prototypes */ /* Callbacks */ -static herr_t H5FD_mpio_term(void); -static void * H5FD_mpio_fapl_get(H5FD_t *_file); -static void * H5FD_mpio_fapl_copy(const void *_old_fa); -static herr_t H5FD_mpio_fapl_free(void *_fa); -static H5FD_t * H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); -static herr_t H5FD_mpio_close(H5FD_t *_file); -static herr_t H5FD_mpio_query(const H5FD_t *_f1, unsigned long *flags); -static haddr_t H5FD_mpio_get_eoa(const H5FD_t *_file, H5FD_mem_t type); -static herr_t H5FD_mpio_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr); -static haddr_t H5FD_mpio_get_eof(const H5FD_t *_file, H5FD_mem_t type); -static herr_t H5FD_mpio_get_handle(H5FD_t *_file, hid_t fapl, void **file_handle); -static herr_t H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, - void *buf); -static herr_t H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, - const void *buf); -static herr_t H5FD_mpio_flush(H5FD_t *_file, hid_t dxpl_id, hbool_t closing); -static herr_t H5FD_mpio_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing); -static int H5FD_mpio_mpi_rank(const H5FD_t *_file); -static int H5FD_mpio_mpi_size(const H5FD_t *_file); -static MPI_Comm H5FD_mpio_communicator(const H5FD_t *_file); +static herr_t H5FD__mpio_term(void); +static void * H5FD__mpio_fapl_get(H5FD_t *_file); +static void * H5FD__mpio_fapl_copy(const void *_old_fa); +static herr_t H5FD__mpio_fapl_free(void *_fa); +static H5FD_t * H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); +static herr_t H5FD__mpio_close(H5FD_t *_file); +static herr_t H5FD__mpio_query(const H5FD_t *_f1, unsigned long *flags); +static haddr_t H5FD__mpio_get_eoa(const H5FD_t *_file, H5FD_mem_t type); +static herr_t H5FD__mpio_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr); +static haddr_t H5FD__mpio_get_eof(const H5FD_t *_file, H5FD_mem_t type); +static herr_t H5FD__mpio_get_handle(H5FD_t *_file, hid_t fapl, void **file_handle); +static herr_t H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, + void *buf); +static herr_t H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, + const void *buf); +static herr_t H5FD__mpio_flush(H5FD_t *_file, hid_t dxpl_id, hbool_t closing); +static herr_t H5FD__mpio_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing); +static int H5FD__mpio_mpi_rank(const H5FD_t *_file); +static int H5FD__mpio_mpi_size(const H5FD_t *_file); +static MPI_Comm H5FD__mpio_communicator(const H5FD_t *_file); /* The MPIO file driver information */ static const H5FD_class_mpi_t H5FD_mpio_g = { @@ -100,59 +100,62 @@ static const H5FD_class_mpi_t H5FD_mpio_g = { "mpio", /*name */ HADDR_MAX, /*maxaddr */ H5F_CLOSE_SEMI, /* fc_degree */ - H5FD_mpio_term, /*terminate */ + H5FD__mpio_term, /*terminate */ NULL, /*sb_size */ NULL, /*sb_encode */ NULL, /*sb_decode */ sizeof(H5FD_mpio_fapl_t), /*fapl_size */ - H5FD_mpio_fapl_get, /*fapl_get */ - H5FD_mpio_fapl_copy, /*fapl_copy */ - H5FD_mpio_fapl_free, /*fapl_free */ + H5FD__mpio_fapl_get, /*fapl_get */ + H5FD__mpio_fapl_copy, /*fapl_copy */ + H5FD__mpio_fapl_free, /*fapl_free */ 0, /*dxpl_size */ NULL, /*dxpl_copy */ NULL, /*dxpl_free */ - H5FD_mpio_open, /*open */ - H5FD_mpio_close, /*close */ + H5FD__mpio_open, /*open */ + H5FD__mpio_close, /*close */ NULL, /*cmp */ - H5FD_mpio_query, /*query */ + H5FD__mpio_query, /*query */ NULL, /*get_type_map */ NULL, /*alloc */ NULL, /*free */ - H5FD_mpio_get_eoa, /*get_eoa */ - H5FD_mpio_set_eoa, /*set_eoa */ - H5FD_mpio_get_eof, /*get_eof */ - H5FD_mpio_get_handle, /*get_handle */ - H5FD_mpio_read, /*read */ - H5FD_mpio_write, /*write */ - H5FD_mpio_flush, /*flush */ - H5FD_mpio_truncate, /*truncate */ + H5FD__mpio_get_eoa, /*get_eoa */ + H5FD__mpio_set_eoa, /*set_eoa */ + H5FD__mpio_get_eof, /*get_eof */ + H5FD__mpio_get_handle, /*get_handle */ + H5FD__mpio_read, /*read */ + H5FD__mpio_write, /*write */ + H5FD__mpio_flush, /*flush */ + H5FD__mpio_truncate, /*truncate */ NULL, /*lock */ NULL, /*unlock */ H5FD_FLMAP_DICHOTOMY /*fl_map */ }, /* End of superclass information */ - H5FD_mpio_mpi_rank, /*get_rank */ - H5FD_mpio_mpi_size, /*get_size */ - H5FD_mpio_communicator /*get_comm */ + H5FD__mpio_mpi_rank, /*get_rank */ + H5FD__mpio_mpi_size, /*get_size */ + H5FD__mpio_communicator /*get_comm */ }; #ifdef H5FDmpio_DEBUG -/* Flags to control debug actions in H5Fmpio. - * Meant to be indexed by characters. - * - * 'c' show result of MPI_Get_count after read - * 'r' show read offset and size - * 't' trace function entry and exit - * 'w' show write offset and size +/* Flags to control debug actions in the MPI-IO VFD. + * (Meant to be indexed by characters) + * + * These flags can be set with either (or both) the environment variable + * "H5FD_mpio_Debug" set to a string containing one or more characters + * (flags) or by setting them as a string value for the + * "H5F_mpio_debug_key" MPI Info key. + * + * Supported characters in 'H5FD_mpio_Debug' string: + * 't' trace function entry and exit + * 'r' show read offset and size + * 'w' show write offset and size + * '0'-'9' only show output from a single MPI rank (ranks 0-9 supported) */ -static int H5FD_mpio_Debug[256] = { - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; +static int H5FD_mpio_debug_flags_s[256]; +static int H5FD_mpio_debug_rank_s = -1; + +/* Indicate if this rank should output tracing info */ +#define H5FD_MPIO_TRACE_THIS_RANK(file) \ + (H5FD_mpio_debug_rank_s < 0 || H5FD_mpio_debug_rank_s == (file)->mpi_rank) #endif /*-------------------------------------------------------------------------- @@ -184,6 +187,41 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5FD__init_package() */ +#ifdef H5FDmpio_DEBUG + +/*--------------------------------------------------------------------------- + * Function: H5FD__mpio_parse_debug_str + * + * Purpose: Parse a string for debugging flags + * + * Returns: N/A + * + * Programmer: Quincey Koziol + * Wednesday, Aug 12, 2020 + * + *--------------------------------------------------------------------------- + */ +static void +H5FD__mpio_parse_debug_str(const char *s) +{ + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(s); + + /* Set debug mask */ + while (*s) { + if ((int)(*s) >= (int)'0' && (int)(*s) <= (int)'9') + H5FD_mpio_debug_rank_s = ((int)*s) - (int)'0'; + else + H5FD_mpio_debug_flags_s[(int)*s]++; + s++; + } /* end while */ + + FUNC_LEAVE_NOAPI_VOID +} /* end H5FD__mpio_parse_debug_str() */ +#endif /* H5FDmpio_DEBUG */ + /*------------------------------------------------------------------------- * Function: H5FD_mpio_init * @@ -201,11 +239,8 @@ done: hid_t H5FD_mpio_init(void) { -#ifdef H5FDmpio_DEBUG static int H5FD_mpio_Debug_inited = 0; -#endif /* H5FDmpio_DEBUG */ - const char *s; /* String for environment variables */ - hid_t ret_value = H5I_INVALID_HID; /* Return value */ + hid_t ret_value = H5I_INVALID_HID; /* Return value */ FUNC_ENTER_NOAPI(H5I_INVALID_HID) @@ -213,28 +248,27 @@ H5FD_mpio_init(void) if (H5I_VFL != H5I_get_type(H5FD_MPIO_g)) H5FD_MPIO_g = H5FD_register((const H5FD_class_t *)&H5FD_mpio_g, sizeof(H5FD_class_mpi_t), FALSE); - /* Allow MPI buf-and-file-type optimizations? */ - s = HDgetenv("HDF5_MPI_OPT_TYPES"); - if (s && HDisdigit(*s)) { - long env_val = HDstrtol(s, NULL, 0); - H5FD_mpi_opt_types_g = (0 == env_val) ? FALSE : TRUE; - } + if (!H5FD_mpio_Debug_inited) { + const char *s; /* String for environment variables */ + + /* Allow MPI buf-and-file-type optimizations? */ + s = HDgetenv("HDF5_MPI_OPT_TYPES"); + if (s && HDisdigit(*s)) + H5FD_mpi_opt_types_g = (0 == HDstrtol(s, NULL, 0)) ? FALSE : TRUE; #ifdef H5FDmpio_DEBUG - if (!H5FD_mpio_Debug_inited) { + /* Clear the flag buffer */ + HDmemset(H5FD_mpio_debug_flags_s, 0, sizeof(H5FD_mpio_debug_flags_s)); + /* Retrieve MPI-IO debugging environment variable */ s = HDgetenv("H5FD_mpio_Debug"); - if (s) { - /* Set debug mask */ - while (*s) { - H5FD_mpio_Debug[(int)*s]++; - s++; - } /* end while */ - } /* end if */ - H5FD_mpio_Debug_inited++; - } /* end if */ + if (s) + H5FD__mpio_parse_debug_str(s); #endif /* H5FDmpio_DEBUG */ + H5FD_mpio_Debug_inited++; + } /* end if */ + /* Set return value */ ret_value = H5FD_MPIO_g; @@ -255,7 +289,7 @@ done: *--------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_term(void) +H5FD__mpio_term(void) { FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -263,7 +297,7 @@ H5FD_mpio_term(void) H5FD_MPIO_g = 0; FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpio_term() */ +} /* end H5FD__mpio_term() */ /*------------------------------------------------------------------------- * Function: H5Pset_fapl_mpio @@ -650,7 +684,7 @@ done: } /* end H5Pset_dxpl_mpio_chunk_opt_ratio() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_fapl_get + * Function: H5FD__mpio_fapl_get * * Purpose: Returns a file access property list which could be used to * create another file the same as this one. @@ -666,11 +700,11 @@ done: *------------------------------------------------------------------------- */ static void * -H5FD_mpio_fapl_get(H5FD_t *_file) +H5FD__mpio_fapl_get(H5FD_t *_file) { - H5FD_mpio_t * file = (H5FD_mpio_t *)_file; - H5FD_mpio_fapl_t *fa = NULL; - void * ret_value; /* Return value */ + H5FD_mpio_t * file = (H5FD_mpio_t *)_file; + H5FD_mpio_fapl_t *fa = NULL; + void * ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI_NOINIT @@ -692,7 +726,7 @@ done: } /*------------------------------------------------------------------------- - * Function: H5FD_mpio_fapl_copy + * Function: H5FD__mpio_fapl_copy * * Purpose: Copies the mpio-specific file access properties. * @@ -706,15 +740,18 @@ done: *------------------------------------------------------------------------- */ static void * -H5FD_mpio_fapl_copy(const void *_old_fa) +H5FD__mpio_fapl_copy(const void *_old_fa) { void * ret_value = NULL; const H5FD_mpio_fapl_t *old_fa = (const H5FD_mpio_fapl_t *)_old_fa; H5FD_mpio_fapl_t * new_fa = NULL; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = H5FD_mpio_debug_flags_s[(int)'t']; +#endif FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) + if (H5FD_mpio_debug_t_flag) HDfprintf(stderr, "enter H5FD_mpio_fapl_copy\n"); #endif @@ -737,14 +774,14 @@ done: } #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) + if (H5FD_mpio_debug_t_flag) HDfprintf(stderr, "leaving H5FD_mpio_fapl_copy\n"); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_fapl_copy() */ +} /* end H5FD__mpio_fapl_copy() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_fapl_free + * Function: H5FD__mpio_fapl_free * * Purpose: Frees the mpio-specific file access properties. * @@ -757,15 +794,18 @@ done: * *------------------------------------------------------------------------- */ -static herr_t -H5FD_mpio_fapl_free(void *_fa) +herr_t +H5FD__mpio_fapl_free(void *_fa) { herr_t ret_value = SUCCEED; H5FD_mpio_fapl_t *fa = (H5FD_mpio_fapl_t *)_fa; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = H5FD_mpio_debug_flags_s[(int)'t']; +#endif FUNC_ENTER_NOAPI_NOINIT_NOERR #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) + if (H5FD_mpio_debug_t_flag) HDfprintf(stderr, "in H5FD_mpio_fapl_free\n"); #endif HDassert(fa); @@ -776,11 +816,11 @@ H5FD_mpio_fapl_free(void *_fa) H5MM_xfree(fa); #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) + if (H5FD_mpio_debug_t_flag) HDfprintf(stderr, "leaving H5FD_mpio_fapl_free\n"); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_fapl_free() */ +} /* end H5FD__mpio_fapl_free() */ /*------------------------------------------------------------------------- * Function: H5FD_set_mpio_atomicity @@ -798,30 +838,27 @@ herr_t H5FD_set_mpio_atomicity(H5FD_t *_file, hbool_t flag) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; - int mpi_code; /* MPI return code */ - int temp_flag; - herr_t ret_value = SUCCEED; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); +#endif + int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif - if (FALSE == flag) - temp_flag = 0; - else - temp_flag = 1; - /* set atomicity value */ - if (MPI_SUCCESS != (mpi_code = MPI_File_set_atomicity(file->f, temp_flag))) + if (MPI_SUCCESS != (mpi_code = MPI_File_set_atomicity(file->f, (int)(flag != FALSE)))) HMPI_GOTO_ERROR(FAIL, "MPI_File_set_atomicity", mpi_code) done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, file->mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) @@ -843,15 +880,18 @@ herr_t H5FD_get_mpio_atomicity(H5FD_t *_file, hbool_t *flag) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; - int mpi_code; /* MPI return code */ int temp_flag; - herr_t ret_value = SUCCEED; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); +#endif + int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif /* Get atomicity value */ @@ -865,8 +905,8 @@ H5FD_get_mpio_atomicity(H5FD_t *_file, hbool_t *flag) done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, file->mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) @@ -891,30 +931,27 @@ done: *------------------------------------------------------------------------- */ static H5FD_t * -H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR_UNUSED maxaddr) +H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR_UNUSED maxaddr) { - H5FD_mpio_t * file = NULL; - MPI_File fh; - unsigned file_opened = 0; /* Flag to indicate that the file was successfully opened */ - int mpi_amode; - int mpi_rank; /* MPI rank of this process */ - int mpi_size; /* Total number of MPI processes */ - int mpi_code; /* mpi return code */ - MPI_Offset size; const H5FD_mpio_fapl_t *fa = NULL; H5FD_mpio_fapl_t _fa; - H5P_genplist_t * plist; /* Property list pointer */ - MPI_Comm comm_dup = MPI_COMM_NULL; - MPI_Info info_dup = MPI_INFO_NULL; - H5FD_t * ret_value; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - + H5FD_mpio_t * file = NULL; /* VFD File struct for new file */ + H5P_genplist_t * plist; /* Property list pointer */ + MPI_Comm comm = MPI_COMM_NULL; /* MPI Communicator, from plist */ + MPI_Info info = MPI_INFO_NULL; /* MPI Info, from plist */ + MPI_File fh; /* MPI file handle */ + hbool_t file_opened = FALSE; /* Flag to indicate that the file was successfully opened */ + int mpi_amode; /* MPI file access flags */ + int mpi_rank = INT_MAX; /* MPI rank of this process */ + int mpi_size; /* Total number of MPI processes */ + MPI_Offset file_size; /* File size (of existing files) */ #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering - name = \"%s\", flags = 0x%x, fapl_id = %d, maxaddr = %lu\n", FUNC, - name, flags, (int)fapl_id, (unsigned long)maxaddr); + hbool_t H5FD_mpio_debug_t_flag = FALSE; #endif + int mpi_code; /* MPI return code */ + H5FD_t *ret_value = NULL; /* Return value */ + + FUNC_ENTER_STATIC /* Get a pointer to the fapl */ if (NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS))) @@ -930,9 +967,17 @@ H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR_ } /* end else */ /* Duplicate communicator and Info object for use by this file. */ - if (FAIL == H5FD_mpi_comm_info_dup(fa->comm, fa->info, &comm_dup, &info_dup)) + if (FAIL == H5FD_mpi_comm_info_dup(fa->comm, fa->info, &comm, &info)) HGOTO_ERROR(H5E_INTERNAL, H5E_CANTCOPY, NULL, "Communicator/Info duplicate failed") +#ifdef H5FDmpio_DEBUG + H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && + (H5FD_mpio_debug_rank_s < 0 || H5FD_mpio_debug_rank_s == mpi_rank)); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering - name = \"%s\", flags = 0x%x, fapl_id = %d, maxaddr = %lu\n", + FUNC, mpi_rank, name, flags, (int)fapl_id, (unsigned long)maxaddr); +#endif + /* Convert HDF5 flags to MPI-IO flags */ /* Some combinations are illegal; let MPI-IO figure it out */ mpi_amode = (flags & H5F_ACC_RDWR) ? MPI_MODE_RDWR : MPI_MODE_RDONLY; @@ -943,65 +988,61 @@ H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR_ #ifdef H5FDmpio_DEBUG /* Check for debug commands in the info parameter */ - if (MPI_INFO_NULL != info_dup) { + if (MPI_INFO_NULL != info) { char debug_str[128]; int flag; - MPI_Info_get(fa->info, H5F_MPIO_DEBUG_KEY, sizeof(debug_str) - 1, debug_str, &flag); - if (flag) { - int i; - - HDfprintf(stdout, "H5FD_mpio debug flags = '%s'\n", debug_str); - for (i = 0; debug_str[i] /*end of string*/ && i < 128 /*just in case*/; ++i) - H5FD_mpio_Debug[(int)debug_str[i]] = 1; - } /* end if */ - } /* end if */ + MPI_Info_get(info, H5F_MPIO_DEBUG_KEY, sizeof(debug_str) - 1, debug_str, &flag); + if (flag) + H5FD__mpio_parse_debug_str(debug_str); + } /* end if */ #endif - if (MPI_SUCCESS != (mpi_code = MPI_File_open(comm_dup, name, mpi_amode, info_dup, &fh))) + if (MPI_SUCCESS != (mpi_code = MPI_File_open(comm, name, mpi_amode, info, &fh))) HMPI_GOTO_ERROR(NULL, "MPI_File_open failed", mpi_code) file_opened = 1; /* Get the MPI rank of this process and the total number of processes */ - if (MPI_SUCCESS != (mpi_code = MPI_Comm_rank(comm_dup, &mpi_rank))) + if (MPI_SUCCESS != (mpi_code = MPI_Comm_rank(comm, &mpi_rank))) HMPI_GOTO_ERROR(NULL, "MPI_Comm_rank failed", mpi_code) - if (MPI_SUCCESS != (mpi_code = MPI_Comm_size(comm_dup, &mpi_size))) + if (MPI_SUCCESS != (mpi_code = MPI_Comm_size(comm, &mpi_size))) HMPI_GOTO_ERROR(NULL, "MPI_Comm_size failed", mpi_code) /* Build the return value and initialize it */ if (NULL == (file = (H5FD_mpio_t *)H5MM_calloc(sizeof(H5FD_mpio_t)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") file->f = fh; - file->comm = comm_dup; - file->info = info_dup; + file->comm = comm; + file->info = info; file->mpi_rank = mpi_rank; file->mpi_size = mpi_size; /* Only processor p0 will get the filesize and broadcast it. */ if (mpi_rank == 0) { - if (MPI_SUCCESS != (mpi_code = MPI_File_get_size(fh, &size))) + if (MPI_SUCCESS != (mpi_code = MPI_File_get_size(fh, &file_size))) HMPI_GOTO_ERROR(NULL, "MPI_File_get_size failed", mpi_code) } /* end if */ /* Broadcast file size */ - if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&size, (int)sizeof(MPI_Offset), MPI_BYTE, 0, comm_dup))) + if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&file_size, (int)sizeof(MPI_Offset), MPI_BYTE, 0, comm))) HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code) /* Determine if the file should be truncated */ - if (size && (flags & H5F_ACC_TRUNC)) { + if (file_size && (flags & H5F_ACC_TRUNC)) { + /* Truncate the file */ if (MPI_SUCCESS != (mpi_code = MPI_File_set_size(fh, (MPI_Offset)0))) HMPI_GOTO_ERROR(NULL, "MPI_File_set_size failed", mpi_code) /* Don't let any proc return until all have truncated the file. */ - if (MPI_SUCCESS != (mpi_code = MPI_Barrier(comm_dup))) + if (MPI_SUCCESS != (mpi_code = MPI_Barrier(comm))) HMPI_GOTO_ERROR(NULL, "MPI_Barrier failed", mpi_code) /* File is zero size now */ - size = 0; + file_size = 0; } /* end if */ /* Set the size of the file (from library's perspective) */ - file->eof = H5FD_mpi_MPIOff_to_haddr(size); + file->eof = H5FD_mpi_MPIOff_to_haddr(file_size); file->local_eof = file->eof; /* Set return value */ @@ -1011,24 +1052,24 @@ done: if (ret_value == NULL) { if (file_opened) MPI_File_close(&fh); - if (MPI_COMM_NULL != comm_dup) - MPI_Comm_free(&comm_dup); - if (MPI_INFO_NULL != info_dup) - MPI_Info_free(&info_dup); + if (MPI_COMM_NULL != comm) + MPI_Comm_free(&comm); + if (MPI_INFO_NULL != info) + MPI_Info_free(&info); if (file) H5MM_xfree(file); } /* end if */ #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_open() */ +} /* end H5FD__mpio_open() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_close + * Function: H5FDi__mpio_close * * Purpose: Closes a file. This is collective. * @@ -1040,17 +1081,21 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_close(H5FD_t *_file) +H5FD__mpio_close(H5FD_t *_file) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; - int mpi_code; /* MPI return code */ - herr_t ret_value = SUCCEED; /* Return value */ +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); + int mpi_rank = file->mpi_rank; +#endif + int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif /* Sanity checks */ @@ -1067,15 +1112,15 @@ H5FD_mpio_close(H5FD_t *_file) done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_close() */ +} /* end H5FD__mpio_close() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_query + * Function: H5FD__mpio_query * * Purpose: Set the flags that this VFL driver is capable of supporting. * (listed in H5FDpublic.h) @@ -1088,7 +1133,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_query(const H5FD_t H5_ATTR_UNUSED *_file, unsigned long *flags /* out */) +H5FD__mpio_query(const H5FD_t H5_ATTR_UNUSED *_file, unsigned long *flags /* out */) { FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -1100,14 +1145,14 @@ H5FD_mpio_query(const H5FD_t H5_ATTR_UNUSED *_file, unsigned long *flags /* out *flags |= H5FD_FEAT_HAS_MPI; /* This driver uses MPI */ *flags |= H5FD_FEAT_ALLOCATE_EARLY; /* Allocate space early instead of late */ *flags |= H5FD_FEAT_DEFAULT_VFD_COMPATIBLE; /* VFD creates a file which can be opened with the default - VFD */ + VFD */ } /* end if */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpio_query() */ +} /* end H5FD__mpio_query() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_get_eoa + * Function: H5FD__mpio_get_eoa * * Purpose: Gets the end-of-address marker for the file. The EOA marker * is the first address past the last byte allocated in the @@ -1122,7 +1167,7 @@ H5FD_mpio_query(const H5FD_t H5_ATTR_UNUSED *_file, unsigned long *flags /* out *------------------------------------------------------------------------- */ static haddr_t -H5FD_mpio_get_eoa(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) +H5FD__mpio_get_eoa(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) { const H5FD_mpio_t *file = (const H5FD_mpio_t *)_file; @@ -1133,10 +1178,10 @@ H5FD_mpio_get_eoa(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) HDassert(H5FD_MPIO == file->pub.driver_id); FUNC_LEAVE_NOAPI(file->eoa) -} /* end H5FD_mpio_get_eoa() */ +} /* end H5FD__mpio_get_eoa() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_set_eoa + * Function: H5FD__mpio_set_eoa * * Purpose: Set the end-of-address marker for the file. This function is * called shortly after an existing HDF5 file is opened in order @@ -1150,7 +1195,7 @@ H5FD_mpio_get_eoa(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_set_eoa(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, haddr_t addr) +H5FD__mpio_set_eoa(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, haddr_t addr) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; @@ -1163,10 +1208,10 @@ H5FD_mpio_set_eoa(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, haddr_t addr) file->eoa = addr; FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpio_set_eoa() */ +} /* end H5FD__mpio_set_eoa() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_get_eof + * Function: H5FD__mpio_get_eof * * Purpose: Gets the end-of-file marker for the file. The EOF marker * is the real size of the file. @@ -1192,7 +1237,7 @@ H5FD_mpio_set_eoa(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, haddr_t addr) *------------------------------------------------------------------------- */ static haddr_t -H5FD_mpio_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) +H5FD__mpio_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) { const H5FD_mpio_t *file = (const H5FD_mpio_t *)_file; @@ -1203,7 +1248,7 @@ H5FD_mpio_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) HDassert(H5FD_MPIO == file->pub.driver_id); FUNC_LEAVE_NOAPI(file->eof) -} /* end H5FD_mpio_get_eof() */ +} /* end H5FD__mpio_get_eof() */ /*------------------------------------------------------------------------- * Function: H5FD_mpio_get_handle @@ -1218,7 +1263,7 @@ H5FD_mpio_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_get_handle(H5FD_t *_file, hid_t H5_ATTR_UNUSED fapl, void **file_handle) +H5FD__mpio_get_handle(H5FD_t *_file, hid_t H5_ATTR_UNUSED fapl, void **file_handle) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; herr_t ret_value = SUCCEED; @@ -1232,10 +1277,10 @@ H5FD_mpio_get_handle(H5FD_t *_file, hid_t H5_ATTR_UNUSED fapl, void **file_handl done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_get_handle() */ +} /* end H5FD__mpio_get_handle() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_get_info + * Function: H5FD__mpio_get_info * * Purpose: Returns the file info of MPIO file driver. * @@ -1247,7 +1292,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_get_info(H5FD_t *_file, void **mpi_info) +H5FD_mpio__get_info(H5FD_t *_file, void **mpi_info) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; herr_t ret_value = SUCCEED; @@ -1262,10 +1307,10 @@ H5FD_mpio_get_info(H5FD_t *_file, void **mpi_info) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5FD_mpio_get_info() */ +} /* H5FD__mpio_get_info() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_read + * Function: H5FD__mpio_read * * Purpose: Reads SIZE bytes of data from FILE beginning at address ADDR * into buffer BUF according to data transfer properties in @@ -1286,13 +1331,12 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, - size_t size, void *buf /*out*/) +H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, + size_t size, void *buf /*out*/) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; MPI_Offset mpi_off; MPI_Status mpi_stat; /* Status from I/O operation */ - int mpi_code; /* mpi return code */ MPI_Datatype buf_type = MPI_BYTE; /* MPI description of the selection in memory */ int size_i; /* Integer copy of 'size' to read */ #if MPI_VERSION >= 3 @@ -1308,13 +1352,18 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS #endif hbool_t use_view_this_time = FALSE; hbool_t rank0_bcast = FALSE; /* If read-with-rank0-and-bcast flag was used */ - herr_t ret_value = SUCCEED; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); + hbool_t H5FD_mpio_debug_r_flag = (H5FD_mpio_debug_flags_s[(int)'r'] && H5FD_MPIO_TRACE_THIS_RANK(file)); +#endif + int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif /* Sanity checks */ @@ -1333,8 +1382,9 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size to size_i") #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'r']) - HDfprintf(stdout, "%s: mpi_off = %ld size_i = %d\n", FUNC, (long)mpi_off, size_i); + if (H5FD_mpio_debug_r_flag) + HDfprintf(stderr, "%s: (%d) mpi_off = %ld size_i = %d\n", FUNC, file->mpi_rank, (long)mpi_off, + size_i); #endif /* Only look for MPI views for raw data transfers */ @@ -1380,8 +1430,8 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS H5FD_mpio_collective_opt_t coll_opt_mode; #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'r']) - HDfprintf(stdout, "%s: using MPIO collective mode\n", FUNC); + if (H5FD_mpio_debug_r_flag) + HDfprintf(stderr, "%s: (%d) using MPIO collective mode\n", FUNC, file->mpi_rank); #endif /* Get the collective_opt property to check whether the application wants to do IO individually. */ if (H5CX_get_mpio_coll_opt(&coll_opt_mode) < 0) @@ -1389,14 +1439,14 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS if (coll_opt_mode == H5FD_MPIO_COLLECTIVE_IO) { #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'r']) - HDfprintf(stdout, "%s: doing MPI collective IO\n", FUNC); + if (H5FD_mpio_debug_r_flag) + HDfprintf(stderr, "%s: (%d) doing MPI collective IO\n", FUNC, file->mpi_rank); #endif /* Check whether we should read from rank 0 and broadcast to other ranks */ if (H5CX_get_mpio_rank0_bcast()) { #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'r']) - HDfprintf(stdout, "%s: doing read-rank0-and-MPI_Bcast\n", FUNC); + if (H5FD_mpio_debug_r_flag) + HDfprintf(stderr, "%s: (%d) doing read-rank0-and-MPI_Bcast\n", FUNC, file->mpi_rank); #endif /* Indicate path we've taken */ rank0_bcast = TRUE; @@ -1415,8 +1465,8 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS } /* end if */ else { #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'r']) - HDfprintf(stdout, "%s: doing MPI independent IO\n", FUNC); + if (H5FD_mpio_debug_r_flag) + HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", FUNC, file->mpi_rank); #endif if (MPI_SUCCESS != @@ -1431,8 +1481,16 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS H5FD_mpi_native_g, file->info))) HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) } /* end if */ - else if (MPI_SUCCESS != (mpi_code = MPI_File_read_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) - HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code) + else { +#ifdef H5FDmpio_DEBUG + if (H5FD_mpio_debug_r_flag) + HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", FUNC, file->mpi_rank); +#endif + + /* Perform independent read operation */ + if (MPI_SUCCESS != (mpi_code = MPI_File_read_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) + HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code) + } /* end else */ /* Only retrieve bytes read if this rank _actually_ participated in I/O */ if (!rank0_bcast || (rank0_bcast && file->mpi_rank == 0)) { @@ -1484,15 +1542,15 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, file->mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_read() */ +} /* end H5FD__mpio_read() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_write + * Function: H5FD__mpio_write * * Purpose: Writes SIZE bytes of data to FILE beginning at address ADDR * from buffer BUF according to data transfer properties in @@ -1513,14 +1571,13 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, size_t size, - const void *buf) +H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, size_t size, + const void *buf) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; MPI_Offset mpi_off; MPI_Status mpi_stat; /* Status from I/O operation */ MPI_Datatype buf_type = MPI_BYTE; /* MPI description of the selection in memory */ - int mpi_code; /* MPI return code */ #if MPI_VERSION >= 3 MPI_Count bytes_written; MPI_Count type_size; /* MPI datatype used for I/O's size */ @@ -1533,13 +1590,18 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha int size_i; hbool_t use_view_this_time = FALSE; H5FD_mpio_xfer_t xfer_mode; /* I/O transfer mode */ - herr_t ret_value = SUCCEED; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); + hbool_t H5FD_mpio_debug_w_flag = (H5FD_mpio_debug_flags_s[(int)'w'] && H5FD_MPIO_TRACE_THIS_RANK(file)); +#endif + int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif /* Sanity checks */ @@ -1561,8 +1623,9 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size to size_i") #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'w']) - HDfprintf(stdout, "%s: mpi_off = %ld size_i = %d\n", FUNC, (long)mpi_off, size_i); + if (H5FD_mpio_debug_w_flag) + HDfprintf(stderr, "%s: (%d) mpi_off = %ld size_i = %d\n", FUNC, file->mpi_rank, (long)mpi_off, + size_i); #endif /* Get the transfer mode from the API context */ @@ -1603,8 +1666,8 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha H5FD_mpio_collective_opt_t coll_opt_mode; #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "H5FD_mpio_write: using MPIO collective mode\n"); + if (H5FD_mpio_debug_w_flag) + HDfprintf(stderr, "%s: (%d) using MPIO collective mode\n", FUNC, file->mpi_rank); #endif /* Get the collective_opt property to check whether the application wants to do IO individually. */ @@ -1613,8 +1676,8 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha if (coll_opt_mode == H5FD_MPIO_COLLECTIVE_IO) { #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "H5FD_mpio_write: doing MPI collective IO\n"); + if (H5FD_mpio_debug_w_flag) + HDfprintf(stderr, "%s: (%d) doing MPI collective IO\n", FUNC, file->mpi_rank); #endif if (MPI_SUCCESS != (mpi_code = MPI_File_write_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) @@ -1624,9 +1687,10 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha if (type != H5FD_MEM_DRAW) HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "Metadata Coll opt property should be collective at this point") + #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "H5FD_mpio_write: doing MPI independent IO\n"); + if (H5FD_mpio_debug_w_flag) + HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", FUNC, file->mpi_rank); #endif if (MPI_SUCCESS != (mpi_code = MPI_File_write_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) @@ -1638,11 +1702,18 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha H5FD_mpi_native_g, file->info))) HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) } /* end if */ - else if (MPI_SUCCESS != - (mpi_code = MPI_File_write_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) - HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at failed", mpi_code) + else { +#ifdef H5FDmpio_DEBUG + if (H5FD_mpio_debug_w_flag) + HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", FUNC, file->mpi_rank); +#endif + + /* Perform independent write operation */ + if (MPI_SUCCESS != (mpi_code = MPI_File_write_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat))) + HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at failed", mpi_code) + } /* end else */ - /* How many bytes were actually written? */ + /* How many bytes were actually written? */ #if MPI_VERSION >= 3 if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&mpi_stat, buf_type, &bytes_written))) #else @@ -1684,15 +1755,15 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving, proc %d: ret_value = %d\n", FUNC, file->mpi_rank, ret_value); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving: ret_value = %d\n", FUNC, file->mpi_rank, ret_value); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_write() */ +} /* end H5FD__mpio_write() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_flush + * Function: H5FD__mpio_flush * * Purpose: Makes sure that all data is on disk. This is collective. * @@ -1704,17 +1775,20 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_flush(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t closing) +H5FD__mpio_flush(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t closing) { H5FD_mpio_t *file = (H5FD_mpio_t *)_file; - int mpi_code; /* mpi return code */ - herr_t ret_value = SUCCEED; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); +#endif + int mpi_code; /* mpi return code */ + herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif /* Sanity checks */ @@ -1728,15 +1802,15 @@ H5FD_mpio_flush(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t closing) done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, file->mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_flush() */ +} /* end H5FD__mpio_flush() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_truncate + * Function: H5FD__mpio_truncate * * Purpose: Make certain the file's size matches it's allocated size * @@ -1758,16 +1832,19 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5FD_mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_UNUSED closing) +H5FD__mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_UNUSED closing) { - H5FD_mpio_t *file = (H5FD_mpio_t *)_file; - herr_t ret_value = SUCCEED; + H5FD_mpio_t *file = (H5FD_mpio_t *)_file; +#ifdef H5FDmpio_DEBUG + hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); +#endif + herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Entering\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Entering\n", FUNC, file->mpi_rank); #endif /* Sanity checks */ @@ -1835,15 +1912,15 @@ H5FD_mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_ done: #ifdef H5FDmpio_DEBUG - if (H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "%s: Leaving\n", FUNC); + if (H5FD_mpio_debug_t_flag) + HDfprintf(stderr, "%s: (%d) Leaving\n", FUNC, file->mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_truncate() */ +} /* end H5FD__mpio_truncate() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_mpi_rank + * Function: H5FD__mpio_mpi_rank * * Purpose: Returns the MPI rank for a process * @@ -1856,7 +1933,7 @@ done: *------------------------------------------------------------------------- */ static int -H5FD_mpio_mpi_rank(const H5FD_t *_file) +H5FD__mpio_mpi_rank(const H5FD_t *_file) { const H5FD_mpio_t *file = (const H5FD_mpio_t *)_file; @@ -1867,10 +1944,10 @@ H5FD_mpio_mpi_rank(const H5FD_t *_file) HDassert(H5FD_MPIO == file->pub.driver_id); FUNC_LEAVE_NOAPI(file->mpi_rank) -} /* end H5FD_mpio_mpi_rank() */ +} /* end H5FD__mpio_mpi_rank() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_mpi_size + * Function: H5FD__mpio_mpi_size * * Purpose: Returns the number of MPI processes * @@ -1883,7 +1960,7 @@ H5FD_mpio_mpi_rank(const H5FD_t *_file) *------------------------------------------------------------------------- */ static int -H5FD_mpio_mpi_size(const H5FD_t *_file) +H5FD__mpio_mpi_size(const H5FD_t *_file) { const H5FD_mpio_t *file = (const H5FD_mpio_t *)_file; @@ -1894,10 +1971,10 @@ H5FD_mpio_mpi_size(const H5FD_t *_file) HDassert(H5FD_MPIO == file->pub.driver_id); FUNC_LEAVE_NOAPI(file->mpi_size) -} /* end H5FD_mpio_mpi_size() */ +} /* end H5FD__mpio_mpi_size() */ /*------------------------------------------------------------------------- - * Function: H5FD_mpio_communicator + * Function: H5FD__mpio_communicator * * Purpose: Returns the MPI communicator for the file. * @@ -1910,7 +1987,7 @@ H5FD_mpio_mpi_size(const H5FD_t *_file) *------------------------------------------------------------------------- */ static MPI_Comm -H5FD_mpio_communicator(const H5FD_t *_file) +H5FD__mpio_communicator(const H5FD_t *_file) { const H5FD_mpio_t *file = (const H5FD_mpio_t *)_file; @@ -1921,6 +1998,6 @@ H5FD_mpio_communicator(const H5FD_t *_file) HDassert(H5FD_MPIO == file->pub.driver_id); FUNC_LEAVE_NOAPI(file->comm) -} /* end H5FD_mpio_communicator() */ +} /* end H5FD__mpio_communicator() */ #endif /* H5_HAVE_PARALLEL */ |