diff options
| author | Larry Knox <lrknox@hdfgroup.org> | 2021-02-08 16:56:16 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-02-08 16:56:16 (GMT) |
| commit | 22c67ff6570f16050f0a5654cf1c84df917bb598 (patch) | |
| tree | 38fb63aa498b250c2543fe7e22a511706de96a42 /examples | |
| parent | 551f15f8ae02ca9c995619b216121081eb07633e (diff) | |
| download | hdf5-hdf5-1_8_22.zip hdf5-hdf5-1_8_22.tar.gz hdf5-hdf5-1_8_22.tar.bz2 | |
1.8/master (#317)hdf5-1_8_22
* Revert incorrect bool type
* Correct grep text for filter test
* Check sizeof type to use correct ref_type
* h5dump reg ref chnages has no error file
* Fix comment
* Remove unneeded files
* Verify the decoded version for "all" and "none" selection.
* Remove double entry
* Add missing include
* Snapshot version 1.8 release 22 (snap4)
Update version to 1.8-snap5
* Fixes for test failures with --disable-tests --disable-tools options.
Don't test ph5diff if tests are disabled.
* Correct conditions for parallel builds with and without tests.
* Snapshot version 1.8 release 22 (snap5)
Update version to 1.8.22-snap6
* TRILAB-192 merging warnings changes from develop
* Autotools reconfigure update
* Restore page ejects.
* Restore page eject chars
* Fix orphaned token
* Update LT files
* Correct extra flags and merge TRILAB-24
* Update release note for CMake warnings
* H5repack bug fixes from develop
* TRILAB-192 - merge changes from develop
Single source, config files, for warnings for both autotools and CMake.
Update CMake libraries, tools, tests to use correct flags.
* Add missing m4 file
* Remove 128bit config check fo 1.8
* TRILAB-192 update LTparse files
* A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails.
The code to fix the problem is the same as what is done in H5D__open_oid().
* Add missing " and update function calls incorrectly
named load_gcc_arguments.
Commit changes to gnu-cxxflags to remove unmatched " and to gnu-fflags
to not add C warnings flags to H5_FCFLAGS.
* TRILAB-192 - cleanup edits and match CMake CXX to autotools
* Fix shadowed type
* TRILAB-192 correct fortran commands
* TRILAB-192 version of std=f2008 special check
* Fix shadow variable
* Add prefix_relto_examplesdir function to set relative path to h5c++.
* TRILAB-192 - parser files cannot handle this warning
* Parallel Fortran tests now use the MPI module instead of including
mpif.h.
* Don't add general warnings flags for unsupported old versions of gcc and
g++ (older than gcc/g++ 4.2).
Correct gnu-cxxflags to determine warnings flags to be added based on
C++ compiler version instead of C compiler version.
* Snapshot version 1.8 release 22 (snap6)
Update version to 1.8.22-snap7
* TRILAB-244 separate CXX warnings and errors from C
* Fix NoFilter build
* Move ADD_H5_FLAGS macro from *CompilerFlags.cmake files to
config/cmake_ext_mod/HDFMacros.cmake for common use.
* Restrict errors to gcc 4.8 and above.
* OESS-65 replace szip with aec szip
* Correct CMake version
* Correct -Werror=unused-variable
* Add -Werror= flags to lists displayed in libhdf5.settings.
* Fix -Werror=unused-variable
* More fixes for unused variable
* Resolve warning errors from -Werror= flags:
-Werror=bad-function-cast
-Werror=bad-function-cast
-Werror=implicit-function-declaration
-Werror=nested-externs
* Remove verbose assignments in smoke_check 3 and 5 functions.
* Update to use optimization flags, C++ error flags, and correct
libhdf5.settings.in to remove unworkable changes.
* Update config/gnu-cxxflags.
* Add missing headers
* Fix ifort warning flag.
Restore AC_DEFUN([PAC_PROG_FC_DEFAULT_REALisDBLE] in m4/aclocal_fc.m4.
Add --enable-symbols, --enable-profiling, and --enable-optimization
options to autotools configure; all configure flags for
--enable-production and --disable-production should match HDF5 1.10 and
1.12 production and debug default flags.
* Add github actions file
* Correct path
* OESS-65 Fix packaging
* Update reference name
* Correct filename
* disable pr action and enable fail fast
* Snapshot 1.8.22-snap7
Update version to 1.8.22-snap8.
* Correct mingw path
* Correct mingw paths
* Revise gnu-*flags and cmake/HDF*CompilerFlags.cmake files to add warning
flags for GCC compilers version 4.8 and above.
Removed files from gnu-warnings that only apply to versions < 4.8.
Consolidated warnings from versions < 4.8 that apply to versions >= 4.8
into the 4.8 warnings files.
* Update MANIFEST for removal of older warnings files.
* Yanked all MPI-1 calls
Added batch scripts in bin/batch.
* Snapshot 1.8.22-snap8.
Update version to 1.8.22-snap9.
* Squashed commit of the following:
commit 45b0cbc71929930a874e1c09e0770aa64d0ae697
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Thu Apr 23 13:14:56 2020 -0500
Add C++ warnings treated as error for autotools builds.
commit 6debcddcc766601799d5bd661bd60946f951a07e
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jun 19 16:50:03 2020 -0500
Remove tests for develop branch from testh5cc.sh.in.
Add @H5_ECXXFLAGS@ to AM_CXXFLAGS.
commit fed497e7f207313b2a133d3b68c942b7d7104b90
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jun 12 15:06:39 2020 -0500
Merge pull request #2646 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '998c6470d78e14228695419c3b514c35ecf3d69e':
Remove unnecessary version conditions for Clang compilers.
commit 92e52ce5c211bd1d3991a3b8bb67287ac7b652aa
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jun 10 18:53:45 2020 -0500
Merge pull request #2639 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'a33667faf226f5d8c9633bf537893e8fce1bf1f6':
Add c++ to --enable-sanitize-checks option.
commit 2e802534fb997b81fa98fdd1c7d97d4310898e0d
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jun 10 15:18:36 2020 -0500
Merge pull request #2633 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '20eab963899841c9a003baebead8e3bc07d9e127':
Remove duplicate entries in MANIFEST.
Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers.
Update new clang files to not pick up clang as vendor for pgCC. Add new files to MANIFEST Temporary demotion of 2 -Werror warning flags that fail on macos 10.12 Remove Production flag unknown to Apple clang.
commit 96ef60a58a23847a7da89a891f2415055ec2ab60
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Mon Jun 8 16:24:49 2020 -0500
Merge pull request #2631 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'b942a4d8a3e27317cac50ce37ff5302d477664d8':
Clean up code to get clang version in config/linux-gnulibc1
commit 8a7c687da568e8b50b38fa53da1ca63759be6ec4
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Mon Jun 8 11:42:37 2020 -0500
Merge pull request #2623 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'c7626f79fdee4eee13925e240ef41e61f3367eab':
Add flags from config/clang-warnings/*general files to H5 C and CXX flags for all versions of Clang and Clang++ compilers. Switched from cut to awk in testcheck_version.sh.in to avoid dependence on tab vs. " " in version definitions in H5public.h.
Add files for adding warning flags for clang compilers in autotools configure.
commit db3ef7ff3c1ed79167cecef831501411cff8291f
Merge: 5a0f8d7 f9f1310
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jun 19 14:46:22 2020 -0500
Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12
commit 5a0f8d7940ae57b445f545a0abd7e303ce6924ee
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jun 10 20:15:41 2020 -0500
Merge pull request #2636 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:HDFFV-11000-update-testh5cc.sh.in-for-version to develop
* commit '5c0bd670d6e9919c463fbc05de99e2ba55b0761e':
Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags.
HDFFV-11000: update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop.
* Update configure and Makefile.ins after bin/reconfigure.
* Fix MANIFEST
* Fix HDFFV-10591
Description:
h52gif produced a segfault when a buffer overflow occurred because
the data size was corrupted and became very large. This commit added
a check on the data size against the buffer size to prevent the segfault.
It also added error reporting to h52gif to display an error message
instead of silently exiting when the failure occurred.
Platforms tested:
Linux/64 (jelly)
* Snapshot 1.8.22-snap9. Update version to 1.8.22-snap10.
* Merge pull request #2686 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '800f93f7c994f88dfa716746153ded4b1e690e3a':
Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
* Regenerate configure.
* Merge from 1.10-1.12-dev - LT parse needs update
* Incorporate pull request #2693 from develop for the fix to HDFFV-11080:
(1) Patch up the file pointer when reading attribute of variable length datatype
(2) Test to verify the fix when doing multiple threads
(3) Update MANIFEST
(4) Add new test to Cmake
* Switch bison and flex update of LT files from bin/genltanalyse to
bin/genparser, and from automatically updating the LT files whenever
reconfigure is run to running only on man<F12>ual command.
* Update hl/sr/H5LT files.
Add bin/genparser to MANIFEST; remove bin/genltanalyze.
* Fix to the merge of PR #2708 for HDFFV-11080 to the 1.8 branch.
Need to checkin test/Makefile.in for the new file added.
* Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
Description:
When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump produced a segfault on one file and a
memcpy parameter overlap on another file. This commit added checks
that detect a read pass the end of the buffer to prevent these error
conditions.
Platforms tested:
Linux/64 (jelly)
* Fixed typo
* Check for header szlib.h only when libsz passes AC_CHECK_LIB, so that
H5_HAVE_SALIB_H is not defined when szip is not enabled, to prevent
compile failures for incompatible szlib.
* HDFFV-11127 - force RTLD_LOCAL in dlopen
* spelling
* Remove extra parens
* Remove unnecessary assignment freom configure.ac.
* Add hypen to subrelease regex
* Add special case when H5_VERS_SUBRELEASE is 0
* Revert H5_VERS_SUBRELEASE check
* The version string has a second use for packaging
* MinGW uses "MinGW Makefiles"
* Snapshot 1.8.22-snap10. Update version to 1.8.22-snap11.
* Merge clang-format changes from develop
* remove stray file
* Source formatted
* Add options to github actions.
* Add back file, remove py file
* HDFFV-11096 Correct h5dump usage text
* Update formating
* remove autogen for 1.8 branch
* Fix comment whitespace
* Change '==' to 'eq' in test script
* Merge from develop
github updates
bin scripts
parser updates
* Snapshot 1.8.22-snap11. Update version to 1.8.22-snap12.
* Merge from 1.10
Comments, whitespace
Simple init and if block brackets.
Minimal code changes limited to return value and spelling
* Update autotools files
* Update FD source
* More merges from 1.10 comments and inits
* Comment fixes
* Fix macro argument
* Remove autogen file and cache dir
* Revert autotools files to previous version
* Correct boolean value and missing define
* URL and options corrections
* revert autoconf files
* Fix compile issues with vfd drivers.
* Fix HDFS test
* Remove extra #endif
* Move init above execution
* Multiple changes to bring branch up-to-date (#87)
Correct TARGET variable and CMake config file location.
Add option to allow filter plugins to be built inline.
Update CMake tools macros.
* hdf5 1 8 release text (#113)
* Multiple changes to bring branch up-to-date
Correct TARGET variable and CMake config file location.
Add option to allow filter plugins to be built inline.
Update CMake tools macros.
* release text updates - mostly whitespace
* Fixed HDFFV-10480 and HDFFV-11159 (#145)
* Fixed HDFFV-10480 and HDFFV-11159
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode and
A user's patch was applied to this previously, but it is redone
for a more correct fix, that is the check now accounted for the
previous advance of the buffer pointer.
Platforms tested:
Linux/64 (jelly)
* Fixed typo
* Update HDF5 1.8 copyright headers with updated copyright URL (#148)
* Update URL for COPYING file in copyright headers.
* Make fortran copyright headers uniformly spaced.
* Update url for Copyright file in c++/src/footer.html.
* OESS-98 Update plugin build option (#171)
* 1.8 has extra fortran CMake option (#176)
* 1.8 has extra fortran CMake option
* Update license URL
* OESS-98 fix tools test for plugins (#180)
* Hdf5 1 8 (#169)
* Fixed HDFFV-10480 and HDFFV-11159
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode and
A user's patch was applied to this previously, but it is redone
for a more correct fix, that is the check now accounted for the
previous advance of the buffer pointer.
Platforms tested:
Linux/64 (jelly)
* Fixed typo
* Fixed HDFFV-11150
Description
Replaced an HDassert with a check for null pointer in H5O_dec_rc() to
catch null pointer in corrupted data situation.
Reversed the fix in svn-r24463 in which a check for null pointer prior
to calling H5O_dec_rc()
Platforms tested:
Linux/64 (jelly)
* HDF5 1 8 fix fortran build on macs (#186)
* Correct fortran and shared libs option
* Fix for no shared fortran build
* OESS-98 fix hdf5 link target (#191)
* Partial changes to RELEASE.txt for release. (#185)
* Partial changes to RELEASE.txt for release.
* Update supported and tested platforms.
* Update version to 1.8.22-12.
* close #195. (#196)
* Update HDF5PluginMacros.cmake
* Update HDF5PluginMacros.cmake
* Update directory for SZ filter in HDF5PluginMacros.cmake.
Updates for release:
Switch configure default to production mode.
Set HDF5_GENERATE_HEADERS to OFF.
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Restores maintainer mode in the autotools (#200) (#203)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Hdf5 1 8 22 (#212)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Brings ttsafe_attr_vlen.c changes from develop (#214)
Fixes exposed pthread problem on Windows.
* Update SO numbers for Hdf5 1 8 22 (#215)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Hdf5 1 8 22 (#224)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Update CMake/HDF5Examples version in bin/release
* Update CMake/HDF5Examples version number in bin/release (#225)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Fixed typo in an error message. (#228)
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* Bring 3 small changes from Hdf5 1.8 to 1.8.22 (#241)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Stat st blocks fix 1822 (#251)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* Fixes Autotools detection of the st_blocks field in stat (#246)
* Fixes Autotools detection of the st_blocks field in stat
The Autotools and CMake will now both correctly determine if the
stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS
appropriately.
* Fixes a typo in configure.ac
* Restore lines in RELEASE.txt.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Stat st blocks fix 1822 (#256)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* Fixes Autotools detection of the st_blocks field in stat (#246)
* Fixes Autotools detection of the st_blocks field in stat
The Autotools and CMake will now both correctly determine if the
stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS
appropriately.
* Fixes a typo in configure.ac
* Restore lines in RELEASE.txt.
* Updated configure with reconfigure.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* RELEASE.txt cleanup.
* Hdf5 1 8 22 (#261)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Hdf5 1 8 22 (#266)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Hdf5 1 8 22 - Reverts lock/unlock callback signature to 1.8.21 version (#267)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Update version in H5public.h
* Hdf5 1 8 22 (#269)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Update version in H5public.h
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Set version 1.8.22 for release.
* dd RELEASE.txt entry for HDFFV-10741.
* Hdf5 1 8 22 (#279)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Update version in H5public.h
* Set version 1.8.22 for release.
* dd RELEASE.txt entry for HDFFV-10741.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) (#277)
* Cache the pointer to the next point to process after the last call to
H5S__get_select_elem_pointlist. This allows the normal process of
iterating over the points in batches to be much more efficient, as the
library does not need to traverse the entirety of the preceding points
every time the funciton is re-entered.
* Update RELEASE.txt for point selection iteration performance fix.
* Hdf5 1 8 22 (#281)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Update version in H5public.h
* Set version 1.8.22 for release.
* dd RELEASE.txt entry for HDFFV-10741.
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) (#277)
* Cache the pointer to the next point to process after the last call to
H5S__get_select_elem_pointlist. This allows the normal process of
iterating over the points in batches to be much more efficient, as the
library does not need to traverse the entirety of the preceding points
every time the funciton is re-entered.
* Update RELEASE.txt for point selection iteration performance fix.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
* Hdf5 1 8 22 (#284)
* Fixed typo in an error message.
* Updated for HDFFV-11150, HDFFV-10480, and HDFFV-11159
* Update "Support for New Platforms and Compilers" section in RELEASE.txt;
add check_version workaround for binary compatibility to "Known
Problems".
* Add SUSE Linux to tested platforms.
* Update numbers in config/lt_vers.am and run bin/reconfigure for so
numbers.
* Update version in 3 files missed by merge.
Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
Co-authored-by: Vailin Choi <vchoi@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: hdftest <hdftest@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Diffstat (limited to 'examples')
35 files changed, 2156 insertions, 2272 deletions
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt index d643f35..467dfa4 100644 --- a/examples/CMakeLists.txt +++ b/examples/CMakeLists.txt @@ -1,10 +1,5 @@ -cmake_minimum_required (VERSION 3.10) -PROJECT (HDF5_EXAMPLES) - -#----------------------------------------------------------------------------- -# Apply Definitions to compiler in this directory and below -#----------------------------------------------------------------------------- -add_definitions (${HDF_EXTRA_C_FLAGS}) +cmake_minimum_required (VERSION 3.12) +project (HDF5_EXAMPLES C) #----------------------------------------------------------------------------- # Define Sources @@ -38,30 +33,44 @@ set (examples foreach (example ${examples}) add_executable (${example} ${HDF5_EXAMPLES_SOURCE_DIR}/${example}.c) - TARGET_C_PROPERTIES (${example} STATIC " " " ") - target_link_libraries (${example} ${HDF5_LIB_TARGET}) + target_include_directories (${example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + if (NOT BUILD_SHARED_LIBS) + TARGET_C_PROPERTIES (${example} STATIC) + target_link_libraries (${example} PRIVATE ${HDF5_LIB_TARGET}) + else () + TARGET_C_PROPERTIES (${example} SHARED) + target_link_libraries (${example} PRIVATE ${HDF5_LIBSH_TARGET}) + endif () set_target_properties (${example} PROPERTIES FOLDER examples) - if (BUILD_SHARED_LIBS) - add_executable (${example}-shared ${HDF5_EXAMPLES_SOURCE_DIR}/${example}.c) - TARGET_C_PROPERTIES (${example}-shared SHARED " " " ") - target_link_libraries (${example}-shared ${HDF5_LIBSH_TARGET}) - set_target_properties (${example}-shared PROPERTIES FOLDER examples) + + #----------------------------------------------------------------------------- + # Add Target to clang-format + #----------------------------------------------------------------------------- + if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_EXAMPLES_${example}_FORMAT ${example}) endif () endforeach () if (H5_HAVE_PARALLEL) add_executable (ph5example ${HDF5_EXAMPLES_SOURCE_DIR}/ph5example.c) - TARGET_C_PROPERTIES (ph5example STATIC " " " ") - target_link_libraries (ph5example ${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES}) + target_include_directories (ph5example PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + if (NOT BUILD_SHARED_LIBS) + TARGET_C_PROPERTIES (ph5example STATIC) + target_link_libraries (ph5example PRIVATE ${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES}) + else () + TARGET_C_PROPERTIES (ph5example SHARED) + target_link_libraries (ph5example PRIVATE ${HDF5_LIBSH_TARGET} ${MPI_C_LIBRARIES}) + endif () set_target_properties (ph5example PROPERTIES FOLDER examples) - if (BUILD_SHARED_LIBS) - add_executable (ph5example-shared ${HDF5_EXAMPLES_SOURCE_DIR}/ph5example.c) - TARGET_C_PROPERTIES (ph5example-shared SHARED " " " ") - target_link_libraries (ph5example-shared ${HDF5_LIBSH_TARGET} ${MPI_C_LIBRARIES}) - set_target_properties (ph5example-shared PROPERTIES FOLDER examples) + + #----------------------------------------------------------------------------- + # Add Target to clang-format + #----------------------------------------------------------------------------- + if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_EXAMPLES_ph5example_FORMAT ph5example) endif () endif () -if (BUILD_TESTING) +if (BUILD_TESTING AND HDF5_TEST_EXAMPLES) include (CMakeTests.cmake) endif () diff --git a/examples/CMakeTests.cmake b/examples/CMakeTests.cmake index 592f762..d2b7e56 100644 --- a/examples/CMakeTests.cmake +++ b/examples/CMakeTests.cmake @@ -5,7 +5,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # @@ -15,59 +15,56 @@ ### T E S T I N G ### ############################################################################## ############################################################################## - file (MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/red ${PROJECT_BINARY_DIR}/blue ${PROJECT_BINARY_DIR}/u2w) - if (BUILD_SHARED_LIBS) - file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/H5EX-shared") - file (MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/H5EX-shared/red ${PROJECT_BINARY_DIR}/H5EX-shared/blue ${PROJECT_BINARY_DIR}/H5EX-shared/u2w) - endif () +file (MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/red ${PROJECT_BINARY_DIR}/blue ${PROJECT_BINARY_DIR}/u2w) + +set (test_ex_CLEANFILES + Attributes.h5 + btrees_file.h5 + cmprss.h5 + default_file.h5 + dset.h5 + extend.h5 + extlink_prefix_source.h5 + extlink_source.h5 + extlink_target.h5 + group.h5 + groups.h5 + hard_link.h5 + mount1.h5 + mount2.h5 + one_index_file.h5 + only_dspaces_and_attrs_file.h5 + only_huge_mesgs_file.h5 + REF_REG.h5 + refere.h5 + SDS.h5 + SDScompound.h5 + SDSextendible.h5 + Select.h5 + separate_indexes_file.h5 + small_lists_file.h5 + soft_link.h5 + subset.h5 + unix2win.h5 + blue/prefix_target.h5 + red/prefix_target.h5 + u2w/u2w_target.h5 +) +if (HDF5_TEST_SERIAL) # Remove any output file left over from previous test run add_test ( NAME EXAMPLES-clear-objects - COMMAND ${CMAKE_COMMAND} - -E remove - Attributes.h5 - btrees_file.h5 - cmprss.h5 - default_file.h5 - dset.h5 - extend.h5 - extlink_prefix_source.h5 - extlink_source.h5 - extlink_target.h5 - group.h5 - groups.h5 - hard_link.h5 - mount1.h5 - mount2.h5 - one_index_file.h5 - only_dspaces_and_attrs_file.h5 - only_huge_mesgs_file.h5 - REF_REG.h5 - refere.h5 - SDS.h5 - SDScompound.h5 - SDSextendible.h5 - Select.h5 - separate_indexes_file.h5 - small_lists_file.h5 - soft_link.h5 - subset.h5 - unix2win.h5 - blue/prefix_target.h5 - red/prefix_target.h5 - u2w/u2w_target.h5 + COMMAND ${CMAKE_COMMAND} -E remove ${test_ex_CLEANFILES} ) - if (NOT "${last_test}" STREQUAL "") - set_tests_properties (EXAMPLES-clear-objects PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "EXAMPLES-clear-objects") + set_tests_properties (EXAMPLES-clear-objects PROPERTIES FIXTURES_SETUP clear_EXAMPLES) foreach (example ${examples}) if (HDF5_ENABLE_USING_MEMCHECKER) - add_test (NAME EXAMPLES-${example} COMMAND $<TARGET_FILE:${example}>) + add_test (NAME EXAMPLES-${example} COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:${example}>) else () add_test (NAME EXAMPLES-${example} COMMAND "${CMAKE_COMMAND}" + -D "TEST_EMULATOR=${CMAKE_CROSSCOMPILING_EMULATOR}" -D "TEST_PROGRAM=$<TARGET_FILE:${example}>" -D "TEST_ARGS:STRING=" -D "TEST_EXPECT=0" @@ -78,119 +75,32 @@ -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" ) endif () - if (NOT "${last_test}" STREQUAL "") + set_tests_properties (EXAMPLES-${example} PROPERTIES FIXTURES_REQUIRED clear_EXAMPLES) + if (last_test) set_tests_properties (EXAMPLES-${example} PROPERTIES DEPENDS ${last_test}) endif () set (last_test "EXAMPLES-${example}") endforeach () +endif () - if (BUILD_SHARED_LIBS) - # Remove any output file left over from previous test run - add_test ( - NAME EXAMPLES-shared-clear-objects - COMMAND ${CMAKE_COMMAND} - -E remove - Attributes.h5 - btrees_file.h5 - cmprss.h5 - default_file.h5 - dset.h5 - extend.h5 - extlink_prefix_source.h5 - extlink_source.h5 - extlink_target.h5 - group.h5 - groups.h5 - hard_link.h5 - mount1.h5 - mount2.h5 - one_index_file.h5 - only_dspaces_and_attrs_file.h5 - only_huge_mesgs_file.h5 - REF_REG.h5 - refere.h5 - SDS.h5 - SDScompound.h5 - SDSextendible.h5 - Select.h5 - separate_indexes_file.h5 - small_lists_file.h5 - soft_link.h5 - subset.h5 - unix2win.h5 - blue/prefix_target.h5 - red/prefix_target.h5 - u2w/u2w_target.h5 - WORKING_DIRECTORY - ${PROJECT_BINARY_DIR}/H5EX-shared +### Windows pops up a modal permission dialog on this test +if (H5_HAVE_PARALLEL AND HDF5_TEST_PARALLEL AND NOT WIN32) + if (HDF5_ENABLE_USING_MEMCHECKER) + add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:ph5example> ${MPIEXEC_POSTFLAGS}) + else () + add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND "${CMAKE_COMMAND}" + -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${MPIEXEC_MAX_NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:ph5example>;${MPIEXEC_POSTFLAGS}" + -D "TEST_ARGS:STRING=" + -D "TEST_EXPECT=0" + -D "TEST_OUTPUT=ph5example.out" + -D "TEST_REFERENCE:STRING=PHDF5 tests finished with no errors" + -D "TEST_FILTER:STRING=PHDF5 tests finished with no errors" + -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" + -P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake" ) - if (NOT "${last_test}" STREQUAL "") - set_tests_properties (EXAMPLES-shared-clear-objects PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "EXAMPLES-shared-clear-objects") - - foreach (example ${examples}) - if (HDF5_ENABLE_USING_MEMCHECKER) - add_test (NAME EXAMPLES-shared-${example} COMMAND $<TARGET_FILE:${example}-shared>) - else () - add_test (NAME EXAMPLES-shared-${example} COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$<TARGET_FILE:${example}>" - -D "TEST_ARGS:STRING=" - -D "TEST_EXPECT=0" - -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_OUTPUT=${example}.txt" - #-D "TEST_REFERENCE=${example}.out" - -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/H5EX-shared" - -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" - ) - endif () - set_tests_properties (EXAMPLES-shared-${example} PROPERTIES WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/H5EX-shared) - if (NOT "${last_test}" STREQUAL "") - set_tests_properties (EXAMPLES-shared-${example} PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "EXAMPLES-shared-${example}") - endforeach () endif () - -### Windows pops up a modal permission dialog on this test - if (H5_HAVE_PARALLEL AND NOT WIN32) - if (HDF5_ENABLE_USING_MEMCHECKER) - add_test (NAME EXAMPLES-ph5example COMMAND $<TARGET_FILE:ph5example>) - else () - add_test (NAME EXAMPLES-ph5example COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$<TARGET_FILE:ph5example>" - -D "TEST_ARGS:STRING=" - -D "TEST_EXPECT=0" - -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_OUTPUT=ph5example.txt" - #-D "TEST_REFERENCE=ph5example.out" - -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" - -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" - ) - endif () - if (NOT "${last_test}" STREQUAL "") - set_tests_properties (EXAMPLES-ph5example PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "EXAMPLES-ph5example") - if (BUILD_SHARED_LIBS) - if (HDF5_ENABLE_USING_MEMCHECKER) - add_test (NAME EXAMPLES-shared-ph5example COMMAND $<TARGET_FILE:ph5example-shared>) - else () - add_test (NAME EXAMPLES-shared-ph5example COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$<TARGET_FILE:ph5example-shared>" - -D "TEST_ARGS:STRING=" - -D "TEST_EXPECT=0" - -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_OUTPUT=ph5example-shared.txt" - #-D "TEST_REFERENCE=ph5example-shared.out" - -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/H5EX-shared" - -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" - ) - endif () - set_tests_properties (EXAMPLES-shared-ph5example PROPERTIES WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/H5EX-shared) - if (NOT "${last_test}" STREQUAL "") - set_tests_properties (EXAMPLES-shared-ph5example PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "EXAMPLES-shared-ph5example") - endif () + if (last_test) + set_tests_properties (MPI_TEST_EXAMPLES-ph5example PROPERTIES DEPENDS ${last_test}) endif () + set (last_test "MPI_TEST_EXAMPLES-ph5example") +endif () diff --git a/examples/Makefile.am b/examples/Makefile.am index f737814..4f004bf 100644 --- a/examples/Makefile.am +++ b/examples/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## @@ -80,8 +80,8 @@ CHECK_CLEANFILES+=$(EXTLINK_DIRS) # Example directory # Note: no '/' after DESTDIR. Explanation in commence.am -EXAMPLEDIR=${DESTDIR}$(exec_prefix)/share/hdf5_examples/c -EXAMPLETOPDIR=${DESTDIR}$(exec_prefix)/share/hdf5_examples +EXAMPLEDIR=$(examplesdir)/c +EXAMPLETOPDIR=$(examplesdir) # List dependencies for each program. Normally, automake would take # care of this for us, but if we tell automake about the programs it diff --git a/examples/Makefile.in b/examples/Makefile.in index 76cf389..dfe4e14 100644 --- a/examples/Makefile.in +++ b/examples/Makefile.in @@ -22,7 +22,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # @@ -353,9 +353,9 @@ AMTAR = @AMTAR@ # AM_CFLAGS is an automake construct which should be used by Makefiles # instead of CFLAGS, as CFLAGS is reserved solely for the user to define. # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well. -AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@ +AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@ @H5_ECFLAGS@ AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@ +AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@ @H5_ECXXFLAGS@ AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@ AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ @@ -370,6 +370,7 @@ CC = @CC@ CCDEPMODE = @CCDEPMODE@ CC_VERSION = @CC_VERSION@ CFLAGS = @CFLAGS@ +CLANG_SANITIZE_CHECKS = @CLANG_SANITIZE_CHECKS@ CLEARFILEBUF = @CLEARFILEBUF@ CODESTACK = @CODESTACK@ CONFIG_DATE = @CONFIG_DATE@ @@ -388,6 +389,7 @@ DEFAULT_API_VERSION = @DEFAULT_API_VERSION@ DEFS = @DEFS@ DEPDIR = @DEPDIR@ DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@ +DEV_WARNINGS = @DEV_WARNINGS@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ DSYMUTIL = @DSYMUTIL@ @@ -415,6 +417,8 @@ GREP = @GREP@ H5_CFLAGS = @H5_CFLAGS@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ +H5_ECFLAGS = @H5_ECFLAGS@ +H5_ECXXFLAGS = @H5_ECXXFLAGS@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ H5_LDFLAGS = @H5_LDFLAGS@ @@ -422,9 +426,12 @@ H5_VERSION = @H5_VERSION@ HADDR_T = @HADDR_T@ HAVE_DMALLOC = @HAVE_DMALLOC@ HAVE_FORTRAN_2003 = @HAVE_FORTRAN_2003@ +HAVE_LIBHDFS = @HAVE_LIBHDFS@ HAVE_PTHREAD = @HAVE_PTHREAD@ HDF5_HL = @HDF5_HL@ HDF5_INTERFACES = @HDF5_INTERFACES@ +HDF5_TESTS = @HDF5_TESTS@ +HDF5_TOOLS = @HDF5_TOOLS@ HDF_CXX = @HDF_CXX@ HDF_FORTRAN = @HDF_FORTRAN@ HDF_FORTRAN2003 = @HDF_FORTRAN2003@ @@ -440,6 +447,7 @@ INSTALL_SCRIPT = @INSTALL_SCRIPT@ INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ INSTRUMENT = @INSTRUMENT@ INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@ +JNI_LDFLAGS = @JNI_LDFLAGS@ LD = @LD@ LDFLAGS = @LDFLAGS@ LIBOBJS = @LIBOBJS@ @@ -461,6 +469,7 @@ NMEDIT = @NMEDIT@ OBJDUMP = @OBJDUMP@ OBJECT_NAMELEN_DEFAULT_F = @OBJECT_NAMELEN_DEFAULT_F@ OBJEXT = @OBJEXT@ +OPTIMIZATION = @OPTIMIZATION@ OTOOL = @OTOOL@ OTOOL64 = @OTOOL64@ PACKAGE = @PACKAGE@ @@ -473,8 +482,10 @@ PACKAGE_VERSION = @PACKAGE_VERSION@ PARALLEL = @PARALLEL@ PATH_SEPARATOR = @PATH_SEPARATOR@ PERL = @PERL@ +PROFILING = @PROFILING@ RANLIB = @RANLIB@ ROOT = @ROOT@ +ROS3_VFD = @ROS3_VFD@ RUNPARALLEL = @RUNPARALLEL@ RUNSERIAL = @RUNSERIAL@ R_INTEGER = @R_INTEGER@ @@ -488,6 +499,7 @@ STATIC_EXEC = @STATIC_EXEC@ STATIC_SHARED = @STATIC_SHARED@ STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@ STRIP = @STRIP@ +SYMBOLS = @SYMBOLS@ TESTPARALLEL = @TESTPARALLEL@ THREADSAFE = @THREADSAFE@ TIME = @TIME@ @@ -529,6 +541,7 @@ docdir = $(exec_prefix)/doc dvidir = @dvidir@ enable_shared = @enable_shared@ enable_static = @enable_static@ +examplesdir = @examplesdir@ exec_prefix = @exec_prefix@ fortran_linux_linker_option = @fortran_linux_linker_option@ host = @host@ @@ -647,8 +660,8 @@ EXTLINK_DIRS = red blue u2w # Example directory # Note: no '/' after DESTDIR. Explanation in commence.am -EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/c -EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples +EXAMPLEDIR = $(examplesdir)/c +EXAMPLETOPDIR = $(examplesdir) @BUILD_SHARED_SZIP_CONDITIONAL_TRUE@LD_LIBRARY_PATH = $(LL_PATH) # Assume that all tests in this directory are examples, and tell @@ -659,11 +672,11 @@ EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA) MOSTLYCLEANFILES = *.raw *.meta *.o CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA) -# Automake needs to be taught how to build lib, dyn, progs, and tests targets. +# Automake needs to be taught how to build lib, progs and tests targets. # These will be filled in automatically for the most part (e.g., # lib_LIBRARIES are built for lib target), but EXTRA_LIB, EXTRA_PROG, and # EXTRA_TEST variables are supplied to allow the user to force targets to -# be built at certain times. +# be built at certain times. LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES) \ $(noinst_LTLIBRARIES) $(check_LIBRARIES) $(check_LTLIBRARIES) $(EXTRA_LIB) @@ -1162,6 +1175,7 @@ installcheck-local: (cd $(EXAMPLEDIR); \ /bin/sh ./$(TEST_EXAMPLES_SCRIPT);) \ fi + # lib/progs/tests targets recurse into subdirectories. build-* targets # build files in this directory. build-lib: $(LIB) @@ -1197,7 +1211,7 @@ all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS) # make install-doc doesn't do anything outside of doc directory, but # Makefiles should recognize it. # UPDATE: docs no longer reside in this build tree, so this target -# is depreciated. +# is deprecated. install-doc uninstall-doc: @echo "Nothing to be done." @@ -1358,7 +1372,7 @@ build-check-p: $(LIB) $(PROGS) $(chk_TESTS) echo "**** Hint ****"; \ echo "Parallel test files reside in the current directory" \ "by default."; \ - echo "Set HDF5_PARAPREFIX to use another directory. E.g.,"; \ + echo "Set HDF5_PARAPREFIX to use another directory. e.g.,"; \ echo " HDF5_PARAPREFIX=/PFS/user/me"; \ echo " export HDF5_PARAPREFIX"; \ echo " make check"; \ diff --git a/examples/README b/examples/README index 0550b15..e0a3364 100644 --- a/examples/README +++ b/examples/README @@ -2,7 +2,7 @@ This directory contains example programs for the installed APIs and scripts to compile and run them. Examples in the c and hl/c subdirectories are always -installed, and those in fortan, hl/fortran, c++ and hl/c++ will be installed +installed, and those in fortran, hl/fortran, c++ and hl/c++ will be installed when fortran or c++ are enabled. Running the run-all-ex.sh script in this directory will run the scripts and in diff --git a/examples/h5_attribute.c b/examples/h5_attribute.c index 335f9c2..d88f589 100644 --- a/examples/h5_attribute.c +++ b/examples/h5_attribute.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -29,193 +29,192 @@ #define H5FILE_NAME "Attributes.h5" -#define RANK 1 /* Rank and size of the dataset */ -#define SIZE 7 +#define RANK 1 /* Rank and size of the dataset */ +#define SIZE 7 -#define ARANK 2 /* Rank and dimension sizes of the first dataset attribute */ +#define ARANK 2 /* Rank and dimension sizes of the first dataset attribute */ #define ADIM1 2 #define ADIM2 3 -#define ANAME "Float attribute" /* Name of the array attribute */ +#define ANAME "Float attribute" /* Name of the array attribute */ #define ANAMES "Character attribute" /* Name of the string attribute */ static herr_t attr_info(hid_t loc_id, const char *name, const H5A_info_t *ainfo, void *opdata); - /* Operator function */ +/* Operator function */ int -main (void) +main(void) { - hid_t file, dataset; /* File and dataset identifiers */ - - hid_t fid; /* Dataspace identifier */ - hid_t attr1, attr2, attr3; /* Attribute identifiers */ - hid_t attr; - hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */ - hid_t atype, atype_mem; /* Attribute type */ - H5T_class_t type_class; - - hsize_t fdim[] = {SIZE}; - hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */ - - float matrix[ADIM1][ADIM2]; /* Attribute data */ - - herr_t ret; /* Return value */ - H5O_info_t oinfo; /* Object info */ - unsigned i, j; /* Counters */ - char string_out[80]; /* Buffer to read string attribute back */ - int point_out; /* Buffer to read scalar attribute back */ - - /* - * Data initialization. - */ - int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */ - int point = 1; /* Value of the scalar attribute */ - char string[] = "ABCD"; /* Value of the string attribute */ - - - for (i=0; i < ADIM1; i++) { /* Values of the array attribute */ - for (j=0; j < ADIM2; j++) - matrix[i][j] = -1.; - } - - /* - * Create a file. - */ - file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Create the dataspace for the dataset in the file. - */ - fid = H5Screate(H5S_SIMPLE); - ret = H5Sset_extent_simple(fid, RANK, fdim, NULL); - - /* - * Create the dataset in the file. - */ - dataset = H5Dcreate2(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Write data to the dataset. - */ - ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector); - - /* - * Create dataspace for the first attribute. - */ - aid1 = H5Screate(H5S_SIMPLE); - ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL); - - /* - * Create array attribute. - */ - attr1 = H5Acreate2(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Write array attribute. - */ - ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix); - - /* - * Create scalar attribute. - */ - aid2 = H5Screate(H5S_SCALAR); - attr2 = H5Acreate2(dataset, "Integer attribute", H5T_NATIVE_INT, aid2, - H5P_DEFAULT, H5P_DEFAULT); - - /* - * Write scalar attribute. - */ - ret = H5Awrite(attr2, H5T_NATIVE_INT, &point); - - /* - * Create string attribute. - */ - aid3 = H5Screate(H5S_SCALAR); - atype = H5Tcopy(H5T_C_S1); - H5Tset_size(atype, 5); - H5Tset_strpad(atype,H5T_STR_NULLTERM); - attr3 = H5Acreate2(dataset, ANAMES, atype, aid3, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Write string attribute. - */ - ret = H5Awrite(attr3, atype, string); - - /* - * Close attribute and file dataspaces, and datatype. - */ - ret = H5Sclose(aid1); - ret = H5Sclose(aid2); - ret = H5Sclose(aid3); - ret = H5Sclose(fid); - ret = H5Tclose(atype); - - /* - * Close the attributes. - */ - ret = H5Aclose(attr1); - ret = H5Aclose(attr2); - ret = H5Aclose(attr3); - - /* - * Close the dataset. - */ - ret = H5Dclose(dataset); - - /* - * Close the file. - */ - ret = H5Fclose(file); - - /* - * Reopen the file. - */ - file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT); - - /* - * Open the dataset. - */ - dataset = H5Dopen2(file, "Dataset", H5P_DEFAULT); - - /* - * Attach to the scalar attribute using attribute name, then read and - * display its value. - */ - attr = H5Aopen(dataset, "Integer attribute", H5P_DEFAULT); - ret = H5Aread(attr, H5T_NATIVE_INT, &point_out); - printf("The value of the attribute \"Integer attribute\" is %d \n", point_out); - ret = H5Aclose(attr); - - /* - * Find string attribute by iterating through all attributes - */ - ret = H5Oget_info(dataset, &oinfo); - for(i = 0; i < (unsigned)oinfo.num_attrs; i++) { - attr = H5Aopen_by_idx(dataset, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)i, H5P_DEFAULT, H5P_DEFAULT); - atype = H5Aget_type(attr); - type_class = H5Tget_class(atype); - if (type_class == H5T_STRING) { - atype_mem = H5Tget_native_type(atype, H5T_DIR_ASCEND); - ret = H5Aread(attr, atype_mem, string_out); - printf("Found string attribute; its index is %d , value = %s \n", i, string_out); - ret = H5Tclose(atype_mem); - } - ret = H5Aclose(attr); - ret = H5Tclose(atype); + hid_t file, dataset; /* File and dataset identifiers */ + + hid_t fid; /* Dataspace identifier */ + hid_t attr1, attr2, attr3; /* Attribute identifiers */ + hid_t attr; + hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */ + hid_t atype, atype_mem; /* Attribute type */ + H5T_class_t type_class; + + hsize_t fdim[] = {SIZE}; + hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */ + + float matrix[ADIM1][ADIM2]; /* Attribute data */ + + herr_t ret; /* Return value */ + H5O_info_t oinfo; /* Object info */ + unsigned i, j; /* Counters */ + char string_out[80]; /* Buffer to read string attribute back */ + int point_out; /* Buffer to read scalar attribute back */ + + /* + * Data initialization. + */ + int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */ + int point = 1; /* Value of the scalar attribute */ + char string[] = "ABCD"; /* Value of the string attribute */ + + for (i = 0; i < ADIM1; i++) { /* Values of the array attribute */ + for (j = 0; j < ADIM2; j++) + matrix[i][j] = -1.; + } + + /* + * Create a file. + */ + file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Create the dataspace for the dataset in the file. + */ + fid = H5Screate(H5S_SIMPLE); + ret = H5Sset_extent_simple(fid, RANK, fdim, NULL); + + /* + * Create the dataset in the file. + */ + dataset = H5Dcreate2(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Write data to the dataset. + */ + ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, vector); + + /* + * Create dataspace for the first attribute. + */ + aid1 = H5Screate(H5S_SIMPLE); + ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL); + + /* + * Create array attribute. + */ + attr1 = H5Acreate2(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Write array attribute. + */ + ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix); + + /* + * Create scalar attribute. + */ + aid2 = H5Screate(H5S_SCALAR); + attr2 = H5Acreate2(dataset, "Integer attribute", H5T_NATIVE_INT, aid2, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Write scalar attribute. + */ + ret = H5Awrite(attr2, H5T_NATIVE_INT, &point); + + /* + * Create string attribute. + */ + aid3 = H5Screate(H5S_SCALAR); + atype = H5Tcopy(H5T_C_S1); + H5Tset_size(atype, 5); + H5Tset_strpad(atype, H5T_STR_NULLTERM); + attr3 = H5Acreate2(dataset, ANAMES, atype, aid3, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Write string attribute. + */ + ret = H5Awrite(attr3, atype, string); + + /* + * Close attribute and file dataspaces, and datatype. + */ + ret = H5Sclose(aid1); + ret = H5Sclose(aid2); + ret = H5Sclose(aid3); + ret = H5Sclose(fid); + ret = H5Tclose(atype); + + /* + * Close the attributes. + */ + ret = H5Aclose(attr1); + ret = H5Aclose(attr2); + ret = H5Aclose(attr3); + + /* + * Close the dataset. + */ + ret = H5Dclose(dataset); + + /* + * Close the file. + */ + ret = H5Fclose(file); + + /* + * Reopen the file. + */ + file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT); + + /* + * Open the dataset. + */ + dataset = H5Dopen2(file, "Dataset", H5P_DEFAULT); + + /* + * Attach to the scalar attribute using attribute name, then read and + * display its value. + */ + attr = H5Aopen(dataset, "Integer attribute", H5P_DEFAULT); + ret = H5Aread(attr, H5T_NATIVE_INT, &point_out); + printf("The value of the attribute \"Integer attribute\" is %d \n", point_out); + ret = H5Aclose(attr); + + /* + * Find string attribute by iterating through all attributes + */ + ret = H5Oget_info(dataset, &oinfo); + for (i = 0; i < (unsigned)oinfo.num_attrs; i++) { + attr = H5Aopen_by_idx(dataset, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)i, H5P_DEFAULT, + H5P_DEFAULT); + atype = H5Aget_type(attr); + type_class = H5Tget_class(atype); + if (type_class == H5T_STRING) { + atype_mem = H5Tget_native_type(atype, H5T_DIR_ASCEND); + ret = H5Aread(attr, atype_mem, string_out); + printf("Found string attribute; its index is %d , value = %s \n", i, string_out); + ret = H5Tclose(atype_mem); + } + ret = H5Aclose(attr); + ret = H5Tclose(atype); } - /* - * Get attribute info using iteration function. - */ + /* + * Get attribute info using iteration function. + */ ret = H5Aiterate2(dataset, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_info, NULL); - /* - * Close the dataset and the file. - */ - H5Dclose(dataset); - H5Fclose(file); + /* + * Close the dataset and the file. + */ + H5Dclose(dataset); + H5Fclose(file); - return 0; + return 0; } /* @@ -224,13 +223,13 @@ main (void) static herr_t attr_info(hid_t loc_id, const char *name, const H5A_info_t *ainfo, void *opdata) { - hid_t attr, atype, aspace; /* Attribute, datatype and dataspace identifiers */ - int rank; + hid_t attr, atype, aspace; /* Attribute, datatype and dataspace identifiers */ + int rank; hsize_t sdim[64]; - herr_t ret; - int i; - size_t npoints; /* Number of elements in the array attribute. */ - float *float_array; /* Pointer to the array attribute. */ + herr_t ret; + int i; + size_t npoints; /* Number of elements in the array attribute. */ + float * float_array; /* Pointer to the array attribute. */ /* avoid warnings */ opdata = opdata; @@ -250,17 +249,17 @@ attr_info(hid_t loc_id, const char *name, const H5A_info_t *ainfo, void *opdata) */ atype = H5Aget_type(attr); aspace = H5Aget_space(attr); - rank = H5Sget_simple_extent_ndims(aspace); - ret = H5Sget_simple_extent_dims(aspace, sdim, NULL); + rank = H5Sget_simple_extent_ndims(aspace); + ret = H5Sget_simple_extent_dims(aspace, sdim, NULL); /* * Display rank and dimension sizes for the array attribute. */ - if(rank > 0) { + if (rank > 0) { printf("Rank : %d \n", rank); printf("Dimension sizes : "); - for (i=0; i< rank; i++) + for (i = 0; i < rank; i++) printf("%d ", (int)sdim[i]); printf("\n"); } @@ -271,11 +270,11 @@ attr_info(hid_t loc_id, const char *name, const H5A_info_t *ainfo, void *opdata) if (H5T_FLOAT == H5Tget_class(atype)) { printf("Type : FLOAT \n"); - npoints = H5Sget_simple_extent_npoints(aspace); - float_array = (float *)malloc(sizeof(float)*(int)npoints); - ret = H5Aread(attr, atype, float_array); + npoints = H5Sget_simple_extent_npoints(aspace); + float_array = (float *)malloc(sizeof(float) * (int)npoints); + ret = H5Aread(attr, atype, float_array); printf("Values : "); - for( i = 0; i < (int)npoints; i++) + for (i = 0; i < (int)npoints; i++) printf("%f ", float_array[i]); printf("\n"); free(float_array); @@ -290,4 +289,3 @@ attr_info(hid_t loc_id, const char *name, const H5A_info_t *ainfo, void *opdata) return 0; } - diff --git a/examples/h5_chunk_read.c b/examples/h5_chunk_read.c index c3455f4..408a844 100644 --- a/examples/h5_chunk_read.c +++ b/examples/h5_chunk_read.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -18,68 +18,66 @@ #include "hdf5.h" -#define H5FILE_NAME "SDSextendible.h5" +#define H5FILE_NAME "SDSextendible.h5" #define DATASETNAME "ExtendibleArray" -#define RANK 2 -#define RANKC 1 -#define NX 10 -#define NY 5 +#define RANK 2 +#define RANKC 1 +#define NX 10 +#define NY 5 int -main (void) +main(void) { - hid_t file; /* handles */ - hid_t dataset; - hid_t filespace; - hid_t memspace; - hid_t cparms; - hsize_t dims[2]; /* dataset and chunk dimensions*/ - hsize_t chunk_dims[2]; - hsize_t col_dims[1]; - hsize_t count[2]; - hsize_t offset[2]; - - herr_t status, status_n; - - int data_out[NX][NY]; /* buffer for dataset to be read */ - int chunk_out[2][5]; /* buffer for chunk to be read */ - int column[10]; /* buffer for column to be read */ - int rank, rank_chunk; - int i, j; - - + hid_t file; /* handles */ + hid_t dataset; + hid_t filespace; + hid_t memspace; + hid_t cparms; + hsize_t dims[2]; /* dataset and chunk dimensions*/ + hsize_t chunk_dims[2]; + hsize_t col_dims[1]; + hsize_t count[2]; + hsize_t offset[2]; + + herr_t status, status_n; + + int data_out[NX][NY]; /* buffer for dataset to be read */ + int chunk_out[2][5]; /* buffer for chunk to be read */ + int column[10]; /* buffer for column to be read */ + int rank, rank_chunk; + int i, j; /* * Open the file and the dataset. */ - file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT); + file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT); dataset = H5Dopen2(file, DATASETNAME, H5P_DEFAULT); /* * Get dataset rank and dimension. */ - filespace = H5Dget_space(dataset); /* Get filespace handle first. */ + filespace = H5Dget_space(dataset); /* Get filespace handle first. */ rank = H5Sget_simple_extent_ndims(filespace); status_n = H5Sget_simple_extent_dims(filespace, dims, NULL); - printf("dataset rank %d, dimensions %lu x %lu\n", - rank, (unsigned long)(dims[0]), (unsigned long)(dims[1])); + printf("dataset rank %d, dimensions %lu x %lu\n", rank, (unsigned long)(dims[0]), + (unsigned long)(dims[1])); /* * Define the memory space to read dataset. */ - memspace = H5Screate_simple(RANK,dims,NULL); + memspace = H5Screate_simple(RANK, dims, NULL); /* * Read dataset back and display. */ - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, data_out); + status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, data_out); printf("\n"); printf("Dataset: \n"); for (j = 0; j < dims[0]; j++) { - for (i = 0; i < dims[1]; i++) printf("%d ", data_out[j][i]); - printf("\n"); + for (i = 0; i < dims[1]; i++) + printf("%d ", data_out[j][i]); + printf("\n"); } /* @@ -110,7 +108,7 @@ main (void) * and read it into column array. */ col_dims[0] = 10; - memspace = H5Screate_simple(RANKC, col_dims, NULL); + memspace = H5Screate_simple(RANKC, col_dims, NULL); /* * Define the column (hyperslab) to read. @@ -119,14 +117,12 @@ main (void) offset[1] = 2; count[0] = 10; count[1] = 1; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - count, NULL); - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, column); + status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL); + status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, column); printf("\n"); printf("Third column: \n"); for (i = 0; i < 10; i++) { - printf("%d \n", column[i]); + printf("%d \n", column[i]); } /* @@ -153,19 +149,19 @@ main (void) */ cparms = H5Dget_create_plist(dataset); /* Get properties handle first. */ - if (H5D_CHUNKED == H5Pget_layout(cparms)) { + if (H5D_CHUNKED == H5Pget_layout(cparms)) { - /* - * Get chunking information: rank and dimensions - */ - rank_chunk = H5Pget_chunk(cparms, 2, chunk_dims); - printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk, - (unsigned long)(chunk_dims[0]), (unsigned long)(chunk_dims[1])); + /* + * Get chunking information: rank and dimensions + */ + rank_chunk = H5Pget_chunk(cparms, 2, chunk_dims); + printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk, (unsigned long)(chunk_dims[0]), + (unsigned long)(chunk_dims[1])); /* * Define the memory space to read a chunk. */ - memspace = H5Screate_simple(rank_chunk,chunk_dims,NULL); + memspace = H5Screate_simple(rank_chunk, chunk_dims, NULL); /* * Define chunk in the file (hyperslab) to read. @@ -174,18 +170,17 @@ main (void) offset[1] = 0; count[0] = chunk_dims[0]; count[1] = chunk_dims[1]; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - count, NULL); + status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL); /* * Read chunk back and display. */ - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, chunk_out); + status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, chunk_out); printf("\n"); printf("Chunk: \n"); for (j = 0; j < chunk_dims[0]; j++) { - for (i = 0; i < chunk_dims[1]; i++) printf("%d ", chunk_out[j][i]); + for (i = 0; i < chunk_dims[1]; i++) + printf("%d ", chunk_out[j][i]); printf("\n"); } /* diff --git a/examples/h5_cmprss.c b/examples/h5_cmprss.c index ebc7712..59a59f5 100644 --- a/examples/h5_cmprss.c +++ b/examples/h5_cmprss.c @@ -6,118 +6,116 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/* +/* * This example illustrates how to create a compressed dataset. * It is used in the HDF5 Tutorial. - */ + */ #include "hdf5.h" -#define FILE "cmprss.h5" -#define RANK 2 -#define DIM0 100 -#define DIM1 20 - -int main () { +#define FILE "cmprss.h5" +#define RANK 2 +#define DIM0 100 +#define DIM1 20 - hid_t file_id, dataset_id, dataspace_id; /* identifiers */ - hid_t plist_id; +int +main() +{ - size_t nelmts; - unsigned flags, filter_info; + hid_t file_id, dataset_id, dataspace_id; /* identifiers */ + hid_t plist_id; + + size_t nelmts; + unsigned flags, filter_info; H5Z_filter_t filter_type; - herr_t status; - hsize_t dims[2]; - hsize_t cdims[2]; - - int idx; - int i,j, numfilt; - int buf[DIM0][DIM1]; - int rbuf [DIM0][DIM1]; + herr_t status; + hsize_t dims[2]; + hsize_t cdims[2]; + + int i, j, numfilt; + int buf[DIM0][DIM1]; + int rbuf[DIM0][DIM1]; - /* Uncomment these variables to use SZIP compression + /* Uncomment these variables to use SZIP compression unsigned szip_options_mask; unsigned szip_pixels_per_block; */ /* Create a file. */ - file_id = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - + file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); /* Create dataset "Compressed Data" in the group using absolute name. */ - dims[0] = DIM0; - dims[1] = DIM1; - dataspace_id = H5Screate_simple (RANK, dims, NULL); + dims[0] = DIM0; + dims[1] = DIM1; + dataspace_id = H5Screate_simple(RANK, dims, NULL); - plist_id = H5Pcreate (H5P_DATASET_CREATE); + plist_id = H5Pcreate(H5P_DATASET_CREATE); /* Dataset must be chunked for compression */ cdims[0] = 20; cdims[1] = 20; - status = H5Pset_chunk (plist_id, 2, cdims); + status = H5Pset_chunk(plist_id, 2, cdims); /* Set ZLIB / DEFLATE Compression using compression level 6. - * To use SZIP Compression comment out these lines. - */ - status = H5Pset_deflate (plist_id, 6); + * To use SZIP Compression comment out these lines. + */ + status = H5Pset_deflate(plist_id, 6); - /* Uncomment these lines to set SZIP Compression + /* Uncomment these lines to set SZIP Compression szip_options_mask = H5_SZIP_NN_OPTION_MASK; szip_pixels_per_block = 16; status = H5Pset_szip (plist_id, szip_options_mask, szip_pixels_per_block); */ - - dataset_id = H5Dcreate2 (file_id, "Compressed_Data", H5T_STD_I32BE, - dataspace_id, H5P_DEFAULT, plist_id, H5P_DEFAULT); - for (i = 0; i< DIM0; i++) - for (j=0; j<DIM1; j++) - buf[i][j] = i+j; + dataset_id = H5Dcreate2(file_id, "Compressed_Data", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, plist_id, + H5P_DEFAULT); - status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + for (i = 0; i < DIM0; i++) + for (j = 0; j < DIM1; j++) + buf[i][j] = i + j; - status = H5Sclose (dataspace_id); - status = H5Dclose (dataset_id); - status = H5Pclose (plist_id); - status = H5Fclose (file_id); + status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + + status = H5Sclose(dataspace_id); + status = H5Dclose(dataset_id); + status = H5Pclose(plist_id); + status = H5Fclose(file_id); /* Now reopen the file and dataset in the file. */ - file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT); - dataset_id = H5Dopen2 (file_id, "Compressed_Data", H5P_DEFAULT); + file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); + dataset_id = H5Dopen2(file_id, "Compressed_Data", H5P_DEFAULT); /* Retrieve filter information. */ - plist_id = H5Dget_create_plist (dataset_id); - - numfilt = H5Pget_nfilters (plist_id); - printf ("Number of filters associated with dataset: %i\n", numfilt); - - for (i=0; i<numfilt; i++) { - nelmts = 0; - filter_type = H5Pget_filter2 (plist_id, 0, &flags, &nelmts, NULL, 0, NULL, - &filter_info); - printf ("Filter Type: "); - switch (filter_type) { - case H5Z_FILTER_DEFLATE: - printf ("H5Z_FILTER_DEFLATE\n"); - break; - case H5Z_FILTER_SZIP: - printf ("H5Z_FILTER_SZIP\n"); - break; - default: - printf ("Other filter type included.\n"); - } + plist_id = H5Dget_create_plist(dataset_id); + + numfilt = H5Pget_nfilters(plist_id); + printf("Number of filters associated with dataset: %i\n", numfilt); + + for (i = 0; i < numfilt; i++) { + nelmts = 0; + filter_type = H5Pget_filter2(plist_id, 0, &flags, &nelmts, NULL, 0, NULL, &filter_info); + printf("Filter Type: "); + switch (filter_type) { + case H5Z_FILTER_DEFLATE: + printf("H5Z_FILTER_DEFLATE\n"); + break; + case H5Z_FILTER_SZIP: + printf("H5Z_FILTER_SZIP\n"); + break; + default: + printf("Other filter type included.\n"); + } } - status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, rbuf); - - status = H5Dclose (dataset_id); - status = H5Pclose (plist_id); - status = H5Fclose (file_id); + status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rbuf); + + status = H5Dclose(dataset_id); + status = H5Pclose(plist_id); + status = H5Fclose(file_id); } diff --git a/examples/h5_compound.c b/examples/h5_compound.c index b3b3a4a..093852d 100644 --- a/examples/h5_compound.c +++ b/examples/h5_compound.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -19,10 +19,10 @@ #include "hdf5.h" -#define H5FILE_NAME "SDScompound.h5" -#define DATASETNAME "ArrayOfStructures" -#define LENGTH 10 -#define RANK 1 +#define H5FILE_NAME "SDScompound.h5" +#define DATASETNAME "ArrayOfStructures" +#define LENGTH 10 +#define RANK 1 int main(void) @@ -30,38 +30,37 @@ main(void) /* First structure and dataset*/ typedef struct s1_t { - int a; - float b; - double c; + int a; + float b; + double c; } s1_t; - s1_t s1[LENGTH]; - hid_t s1_tid; /* File datatype identifier */ + s1_t s1[LENGTH]; + hid_t s1_tid; /* File datatype identifier */ /* Second structure (subset of s1_t) and dataset*/ typedef struct s2_t { - double c; - int a; + double c; + int a; } s2_t; - s2_t s2[LENGTH]; - hid_t s2_tid; /* Memory datatype handle */ + s2_t s2[LENGTH]; + hid_t s2_tid; /* Memory datatype handle */ /* Third "structure" ( will be used to read float field of s1) */ - hid_t s3_tid; /* Memory datatype handle */ - float s3[LENGTH]; - - int i; - hid_t file, dataset, space; /* Handles */ - herr_t status; - hsize_t dim[] = {LENGTH}; /* Dataspace dimensions */ + hid_t s3_tid; /* Memory datatype handle */ + float s3[LENGTH]; + int i; + hid_t file, dataset, space; /* Handles */ + herr_t status; + hsize_t dim[] = {LENGTH}; /* Dataspace dimensions */ /* * Initialize the data */ - for (i = 0; i< LENGTH; i++) { + for (i = 0; i < LENGTH; i++) { s1[i].a = i; - s1[i].b = i*i; - s1[i].c = 1./(i+1); + s1[i].b = i * i; + s1[i].c = 1. / (i + 1); } /* @@ -77,7 +76,7 @@ main(void) /* * Create the memory data type. */ - s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t)); + s1_tid = H5Tcreate(H5T_COMPOUND, sizeof(s1_t)); H5Tinsert(s1_tid, "a_name", HOFFSET(s1_t, a), H5T_NATIVE_INT); H5Tinsert(s1_tid, "c_name", HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE); H5Tinsert(s1_tid, "b_name", HOFFSET(s1_t, b), H5T_NATIVE_FLOAT); @@ -126,12 +125,14 @@ main(void) */ printf("\n"); printf("Field c : \n"); - for( i = 0; i < LENGTH; i++) printf("%.4f ", s2[i].c); + for (i = 0; i < LENGTH; i++) + printf("%.4f ", s2[i].c); printf("\n"); printf("\n"); printf("Field a : \n"); - for( i = 0; i < LENGTH; i++) printf("%d ", s2[i].a); + for (i = 0; i < LENGTH; i++) + printf("%d ", s2[i].a); printf("\n"); /* @@ -151,7 +152,8 @@ main(void) */ printf("\n"); printf("Field b : \n"); - for( i = 0; i < LENGTH; i++) printf("%.4f ", s3[i]); + for (i = 0; i < LENGTH; i++) + printf("%.4f ", s3[i]); printf("\n"); /* diff --git a/examples/h5_crtatt.c b/examples/h5_crtatt.c index ade17ba..3edc75d 100644 --- a/examples/h5_crtatt.c +++ b/examples/h5_crtatt.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -19,43 +19,44 @@ #include "hdf5.h" #define FILE "dset.h5" -int main() { +int +main() +{ - hid_t file_id, dataset_id, attribute_id, dataspace_id; /* identifiers */ - hsize_t dims; - int attr_data[2]; - herr_t status; + hid_t file_id, dataset_id, attribute_id, dataspace_id; /* identifiers */ + hsize_t dims; + int attr_data[2]; + herr_t status; - /* Initialize the attribute data. */ - attr_data[0] = 100; - attr_data[1] = 200; + /* Initialize the attribute data. */ + attr_data[0] = 100; + attr_data[1] = 200; - /* Open an existing file. */ - file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); + /* Open an existing file. */ + file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); - /* Open an existing dataset. */ - dataset_id = H5Dopen2(file_id, "/dset", H5P_DEFAULT); + /* Open an existing dataset. */ + dataset_id = H5Dopen2(file_id, "/dset", H5P_DEFAULT); - /* Create the data space for the attribute. */ - dims = 2; - dataspace_id = H5Screate_simple(1, &dims, NULL); + /* Create the data space for the attribute. */ + dims = 2; + dataspace_id = H5Screate_simple(1, &dims, NULL); - /* Create a dataset attribute. */ - attribute_id = H5Acreate2 (dataset_id, "Units", H5T_STD_I32BE, dataspace_id, - H5P_DEFAULT, H5P_DEFAULT); + /* Create a dataset attribute. */ + attribute_id = H5Acreate2(dataset_id, "Units", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT); - /* Write the attribute data. */ - status = H5Awrite(attribute_id, H5T_NATIVE_INT, attr_data); + /* Write the attribute data. */ + status = H5Awrite(attribute_id, H5T_NATIVE_INT, attr_data); - /* Close the attribute. */ - status = H5Aclose(attribute_id); + /* Close the attribute. */ + status = H5Aclose(attribute_id); - /* Close the dataspace. */ - status = H5Sclose(dataspace_id); + /* Close the dataspace. */ + status = H5Sclose(dataspace_id); - /* Close to the dataset. */ - status = H5Dclose(dataset_id); + /* Close to the dataset. */ + status = H5Dclose(dataset_id); - /* Close the file. */ - status = H5Fclose(file_id); + /* Close the file. */ + status = H5Fclose(file_id); } diff --git a/examples/h5_crtdat.c b/examples/h5_crtdat.c index 4a876d2..4450367 100644 --- a/examples/h5_crtdat.c +++ b/examples/h5_crtdat.c @@ -6,44 +6,45 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* - * This example illustrates how to create a dataset that is a 4 x 6 + * This example illustrates how to create a dataset that is a 4 x 6 * array. It is used in the HDF5 Tutorial. */ #include "hdf5.h" #define FILE "dset.h5" -int main() { +int +main() +{ - hid_t file_id, dataset_id, dataspace_id; /* identifiers */ - hsize_t dims[2]; - herr_t status; + hid_t file_id, dataset_id, dataspace_id; /* identifiers */ + hsize_t dims[2]; + herr_t status; - /* Create a new file using default properties. */ - file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + /* Create a new file using default properties. */ + file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - /* Create the data space for the dataset. */ - dims[0] = 4; - dims[1] = 6; - dataspace_id = H5Screate_simple(2, dims, NULL); + /* Create the data space for the dataset. */ + dims[0] = 4; + dims[1] = 6; + dataspace_id = H5Screate_simple(2, dims, NULL); - /* Create the dataset. */ - dataset_id = H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create the dataset. */ + dataset_id = + H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - /* End access to the dataset and release resources used by it. */ - status = H5Dclose(dataset_id); + /* End access to the dataset and release resources used by it. */ + status = H5Dclose(dataset_id); - /* Terminate access to the data space. */ - status = H5Sclose(dataspace_id); + /* Terminate access to the data space. */ + status = H5Sclose(dataspace_id); - /* Close the file. */ - status = H5Fclose(file_id); + /* Close the file. */ + status = H5Fclose(file_id); } - diff --git a/examples/h5_crtgrp.c b/examples/h5_crtgrp.c index 89bddce..abddf09 100644 --- a/examples/h5_crtgrp.c +++ b/examples/h5_crtgrp.c @@ -6,33 +6,35 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* - * This example illustrates how to create and close a group. + * This example illustrates how to create and close a group. * It is used in the HDF5 Tutorial. */ #include "hdf5.h" #define FILE "group.h5" -int main() { +int +main() +{ - hid_t file_id, group_id; /* identifiers */ - herr_t status; + hid_t file_id, group_id; /* identifiers */ + herr_t status; - /* Create a new file using default properties. */ - file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + /* Create a new file using default properties. */ + file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - /* Create a group named "/MyGroup" in the file. */ - group_id = H5Gcreate2(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create a group named "/MyGroup" in the file. */ + group_id = H5Gcreate2(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - /* Close the group. */ - status = H5Gclose(group_id); + /* Close the group. */ + status = H5Gclose(group_id); - /* Terminate access to the file. */ - status = H5Fclose(file_id); + /* Terminate access to the file. */ + status = H5Fclose(file_id); } diff --git a/examples/h5_crtgrpar.c b/examples/h5_crtgrpar.c index 6f8c6e8..a4d5f38 100644 --- a/examples/h5_crtgrpar.c +++ b/examples/h5_crtgrpar.c @@ -6,41 +6,43 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* - * This example illustrates the creation of groups using absolute and + * This example illustrates the creation of groups using absolute and * relative names. It is used in the HDF5 Tutorial. */ #include "hdf5.h" #define FILE "groups.h5" -int main() { +int +main() +{ - hid_t file_id, group1_id, group2_id, group3_id; /* identifiers */ - herr_t status; + hid_t file_id, group1_id, group2_id, group3_id; /* identifiers */ + herr_t status; - /* Create a new file using default properties. */ - file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + /* Create a new file using default properties. */ + file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - /* Create group "MyGroup" in the root group using absolute name. */ - group1_id = H5Gcreate2(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create group "MyGroup" in the root group using absolute name. */ + group1_id = H5Gcreate2(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - /* Create group "Group_A" in group "MyGroup" using absolute name. */ - group2_id = H5Gcreate2(file_id, "/MyGroup/Group_A", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create group "Group_A" in group "MyGroup" using absolute name. */ + group2_id = H5Gcreate2(file_id, "/MyGroup/Group_A", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - /* Create group "Group_B" in group "MyGroup" using relative name. */ - group3_id = H5Gcreate2(group1_id, "Group_B", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create group "Group_B" in group "MyGroup" using relative name. */ + group3_id = H5Gcreate2(group1_id, "Group_B", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - /* Close groups. */ - status = H5Gclose(group1_id); - status = H5Gclose(group2_id); - status = H5Gclose(group3_id); + /* Close groups. */ + status = H5Gclose(group1_id); + status = H5Gclose(group2_id); + status = H5Gclose(group3_id); - /* Close the file. */ - status = H5Fclose(file_id); + /* Close the file. */ + status = H5Fclose(file_id); } diff --git a/examples/h5_crtgrpd.c b/examples/h5_crtgrpd.c index 35c4389..3095aa0 100644 --- a/examples/h5_crtgrpd.c +++ b/examples/h5_crtgrpd.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -19,71 +19,70 @@ #include "hdf5.h" #define FILE "groups.h5" -int main() { +int +main() +{ - hid_t file_id, group_id, dataset_id, dataspace_id; /* identifiers */ - hsize_t dims[2]; - herr_t status; - int i, j, dset1_data[3][3], dset2_data[2][10]; + hid_t file_id, group_id, dataset_id, dataspace_id; /* identifiers */ + hsize_t dims[2]; + herr_t status; + int i, j, dset1_data[3][3], dset2_data[2][10]; - /* Initialize the first dataset. */ - for (i = 0; i < 3; i++) - for (j = 0; j < 3; j++) - dset1_data[i][j] = j + 1; + /* Initialize the first dataset. */ + for (i = 0; i < 3; i++) + for (j = 0; j < 3; j++) + dset1_data[i][j] = j + 1; - /* Initialize the second dataset. */ - for (i = 0; i < 2; i++) - for (j = 0; j < 10; j++) - dset2_data[i][j] = j + 1; + /* Initialize the second dataset. */ + for (i = 0; i < 2; i++) + for (j = 0; j < 10; j++) + dset2_data[i][j] = j + 1; - /* Open an existing file. */ - file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); + /* Open an existing file. */ + file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); - /* Create the data space for the first dataset. */ - dims[0] = 3; - dims[1] = 3; - dataspace_id = H5Screate_simple(2, dims, NULL); + /* Create the data space for the first dataset. */ + dims[0] = 3; + dims[1] = 3; + dataspace_id = H5Screate_simple(2, dims, NULL); - /* Create a dataset in group "MyGroup". */ - dataset_id = H5Dcreate2(file_id, "/MyGroup/dset1", H5T_STD_I32BE, dataspace_id, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create a dataset in group "MyGroup". */ + dataset_id = H5Dcreate2(file_id, "/MyGroup/dset1", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT); - /* Write the first dataset. */ - status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, - dset1_data); + /* Write the first dataset. */ + status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset1_data); - /* Close the data space for the first dataset. */ - status = H5Sclose(dataspace_id); + /* Close the data space for the first dataset. */ + status = H5Sclose(dataspace_id); - /* Close the first dataset. */ - status = H5Dclose(dataset_id); + /* Close the first dataset. */ + status = H5Dclose(dataset_id); - /* Open an existing group of the specified file. */ - group_id = H5Gopen2(file_id, "/MyGroup/Group_A", H5P_DEFAULT); + /* Open an existing group of the specified file. */ + group_id = H5Gopen2(file_id, "/MyGroup/Group_A", H5P_DEFAULT); - /* Create the data space for the second dataset. */ - dims[0] = 2; - dims[1] = 10; - dataspace_id = H5Screate_simple(2, dims, NULL); + /* Create the data space for the second dataset. */ + dims[0] = 2; + dims[1] = 10; + dataspace_id = H5Screate_simple(2, dims, NULL); - /* Create the second dataset in group "Group_A". */ - dataset_id = H5Dcreate2(group_id, "dset2", H5T_STD_I32BE, dataspace_id, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + /* Create the second dataset in group "Group_A". */ + dataset_id = + H5Dcreate2(group_id, "dset2", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - /* Write the second dataset. */ - status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, - dset2_data); + /* Write the second dataset. */ + status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2_data); - /* Close the data space for the second dataset. */ - status = H5Sclose(dataspace_id); + /* Close the data space for the second dataset. */ + status = H5Sclose(dataspace_id); - /* Close the second dataset */ - status = H5Dclose(dataset_id); + /* Close the second dataset */ + status = H5Dclose(dataset_id); - /* Close the group. */ - status = H5Gclose(group_id); + /* Close the group. */ + status = H5Gclose(group_id); - /* Close the file. */ - status = H5Fclose(file_id); + /* Close the file. */ + status = H5Fclose(file_id); } - diff --git a/examples/h5_drivers.c b/examples/h5_drivers.c index 43c1fc7..bd57004 100644 --- a/examples/h5_drivers.c +++ b/examples/h5_drivers.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -22,13 +22,12 @@ #include "stdlib.h" /* global variables */ -int cleanup_g = -1; /* whether to clean. Init to not set. */ +int cleanup_g = -1; /* whether to clean. Init to not set. */ /* prototypes */ void cleanup(const char *); void split_file(void); - /* * Cleanup a file unless $HDF5_NOCLEANUP is set. */ @@ -36,12 +35,11 @@ void cleanup(const char *filename) { if (cleanup_g == -1) - cleanup_g = getenv("HDF5_NOCLEANUP") ? 0 : 1; + cleanup_g = getenv("HDF5_NOCLEANUP") ? 0 : 1; if (cleanup_g) - remove(filename); + remove(filename); } - /* * This shows how to use the split file driver. */ @@ -55,7 +53,7 @@ split_file(void) /* the metadata and rawdata files. */ fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT); - fid=H5Fcreate("Station1",H5F_ACC_TRUNC,H5P_DEFAULT,fapl); + fid = H5Fcreate("Station1", H5F_ACC_TRUNC, H5P_DEFAULT, fapl); /* using the file ... */ H5Fclose(fid); H5Pclose(fapl); @@ -68,7 +66,7 @@ split_file(void) /* the metadata and rawdata files. */ fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "/tmp/%s-r.h5", H5P_DEFAULT); - fid=H5Fcreate("PointA",H5F_ACC_TRUNC,H5P_DEFAULT,fapl); + fid = H5Fcreate("PointA", H5F_ACC_TRUNC, H5P_DEFAULT, fapl); /* using the file ... */ H5Fclose(fid); H5Pclose(fapl); @@ -81,7 +79,7 @@ split_file(void) /* the metadata and rawdata files. */ fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_split(fapl, NULL, H5P_DEFAULT, NULL, H5P_DEFAULT); - fid=H5Fcreate("Measure",H5F_ACC_TRUNC,H5P_DEFAULT,fapl); + fid = H5Fcreate("Measure", H5F_ACC_TRUNC, H5P_DEFAULT, fapl); /* using the file ... */ H5Fclose(fid); H5Pclose(fapl); @@ -90,13 +88,12 @@ split_file(void) cleanup("Measure.raw"); } - /* Main Body */ int -main (void) +main(void) { split_file(); - return(0); + return (0); } diff --git a/examples/h5_dtransform.c b/examples/h5_dtransform.c index 0b718ad..a364ec1 100644 --- a/examples/h5_dtransform.c +++ b/examples/h5_dtransform.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -33,50 +33,48 @@ #include "hdf5.h" -#define ROWS 12 -#define COLS 18 +#define ROWS 12 +#define COLS 18 +/* clang-format off */ const float windchillF[ROWS][COLS] = - { {36.0, 31.0, 25.0, 19.0, 13.0, 7.0, 1.0, -5.0, -11.0, -16.0, -22.0, -28.0, -34.0, -40.0, -46.0, -52.0, -57.0, -63.0 }, - {34.0, 27.0, 21.0, 15.0, 9.0, 3.0, -4.0, -10.0, -16.0, -22.0, -28.0, -35.0, -41.0, -47.0, -53.0, -59.0, -66.0, -72.0 } , - {32.0, 25.0, 19.0, 13.0, 6.0, 0.0, -7.0, -13.0, -19.0, -26.0, -32.0, -39.0, -45.0, -51.0, -58.0, -64.0, -71.0, -77.0 }, - {30.0, 24.0, 17.0, 11.0, 4.0, -2.0, -9.0, -15.0, -22.0, -29.0, -35.0, -42.0, -48.0, -55.0, -61.0, -68.0, -74.0, -81.0 }, - {29.0, 23.0, 16.0, 9.0, 3.0, -4.0, -11.0, -17.0, -24.0, -31.0, -37.0, -44.0, -51.0, -58.0, -64.0, -71.0, -78.0, -84.0 }, - {28.0, 22.0, 15.0, 8.0, 1.0, -5.0, -12.0, -19.0, -26.0, -33.0, -39.0, -46.0, -53.0, -60.0, -67.0, -73.0, -80.0, -87.0 }, - {28.0, 21.0, 14.0, 7.0, 0.0, -7.0, -14.0, -21.0, -27.0, -34.0, -41.0, -48.0, -55.0, -62.0, -69.0, -76.0, -82.0, -89.0 }, - {27.0, 20.0, 13.0, 6.0, -1.0, -8.0, -15.0, -22.0, -29.0, -36.0, -43.0, -50.0, -57.0, -64.0, -71.0, -78.0, -84.0, -91.0 }, - {26.0, 19.0, 12.0, 5.0, -2.0, -9.0, -16.0, -23.0, -30.0, -37.0, -44.0, -51.0, -58.0, -65.0, -72.0, -79.0, -86.0, -93.0 }, + { {36.0, 31.0, 25.0, 19.0, 13.0, 7.0, 1.0, -5.0, -11.0, -16.0, -22.0, -28.0, -34.0, -40.0, -46.0, -52.0, -57.0, -63.0}, + {34.0, 27.0, 21.0, 15.0, 9.0, 3.0, -4.0, -10.0, -16.0, -22.0, -28.0, -35.0, -41.0, -47.0, -53.0, -59.0, -66.0, -72.0}, + {32.0, 25.0, 19.0, 13.0, 6.0, 0.0, -7.0, -13.0, -19.0, -26.0, -32.0, -39.0, -45.0, -51.0, -58.0, -64.0, -71.0, -77.0}, + {30.0, 24.0, 17.0, 11.0, 4.0, -2.0, -9.0, -15.0, -22.0, -29.0, -35.0, -42.0, -48.0, -55.0, -61.0, -68.0, -74.0, -81.0}, + {29.0, 23.0, 16.0, 9.0, 3.0, -4.0, -11.0, -17.0, -24.0, -31.0, -37.0, -44.0, -51.0, -58.0, -64.0, -71.0, -78.0, -84.0}, + {28.0, 22.0, 15.0, 8.0, 1.0, -5.0, -12.0, -19.0, -26.0, -33.0, -39.0, -46.0, -53.0, -60.0, -67.0, -73.0, -80.0, -87.0}, + {28.0, 21.0, 14.0, 7.0, 0.0, -7.0, -14.0, -21.0, -27.0, -34.0, -41.0, -48.0, -55.0, -62.0, -69.0, -76.0, -82.0, -89.0}, + {27.0, 20.0, 13.0, 6.0, -1.0, -8.0, -15.0, -22.0, -29.0, -36.0, -43.0, -50.0, -57.0, -64.0, -71.0, -78.0, -84.0, -91.0}, + {26.0, 19.0, 12.0, 5.0, -2.0, -9.0, -16.0, -23.0, -30.0, -37.0, -44.0, -51.0, -58.0, -65.0, -72.0, -79.0, -86.0, -93.0}, {26.0, 19.0, 12.0, 4.0, -3.0, -10.0, -17.0, -24.0, -31.0, -38.0, -45.0, -52.0, -60.0, -67.0, -74.0, -81.0, -88.0, -95.0}, {25.0, 18.0, 11.0, 4.0, -3.0, -11.0, -18.0, -25.0, -32.0, -39.0, -46.0, -54.0, -61.0, -68.0, -75.0, -82.0, -89.0, -97.0}, {25.0, 17.0, 10.0, 3.0, -4.0, -11.0, -19.0, -26.0, -33.0, -40.0, -48.0, -55.0, -62.0, -69.0, -76.0, -84.0, -91.0, -98.0} }; +/* clang-format on */ -#define PRINT(array) \ -{ \ - for(i=0; i<ROWS; i++) \ - { \ - for(j=0; j<COLS; j++) \ - printf("%6.2f ", array[i][j]); \ - printf("\n"); \ - } \ -} - - - +#define PRINT(array) \ + { \ + for (i = 0; i < ROWS; i++) { \ + for (j = 0; j < COLS; j++) \ + printf("%6.2f ", array[i][j]); \ + printf("\n"); \ + } \ + } int -main (void) +main(void) { - hid_t file, dataset; /* file and dataset handles */ - hid_t dataspace; /* handles */ - hsize_t dimsf[2]; /* dataset dimensions */ + hid_t file, dataset; /* file and dataset handles */ + hid_t dataspace; /* handles */ + hsize_t dimsf[2]; /* dataset dimensions */ herr_t status; - hid_t dxpl_id_f_to_c, dxpl_id_c_to_f; /* data transform handles */ - const char* f_to_c = "(5/9.0)*(x-32)"; - const char* c_to_f = "(9/5.0)*x + 32"; - char* transform; - float windchillC[ROWS][COLS]; - int i,j, transform_size; + hid_t dxpl_id_f_to_c, dxpl_id_c_to_f; /* data transform handles */ + const char *f_to_c = "(5/9.0)*(x-32)"; + const char *c_to_f = "(9/5.0)*x + 32"; + char * transform; + float windchillC[ROWS][COLS]; + int i, j, transform_size; /* * Create a new file using H5F_ACC_TRUNC access, @@ -89,28 +87,25 @@ main (void) * Describe the size of the array and create the data space for fixed * size dataset. */ - dimsf[0] = ROWS; - dimsf[1] = COLS; + dimsf[0] = ROWS; + dimsf[1] = COLS; dataspace = H5Screate_simple(2, dimsf, NULL); /* * Create a new dataset within the file using defined dataspace and * datatype and default dataset creation properties. */ - dataset = H5Dcreate2(file, "data_no_trans", H5T_NATIVE_FLOAT, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dataset = + H5Dcreate2(file, "data_no_trans", H5T_NATIVE_FLOAT, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); printf("\nOriginal Data: \n"); PRINT(windchillF); - - - -/**************** PART 1 **************/ + /**************** PART 1 **************/ /* * Write the data to the dataset using default transfer properties (ie, no transform set) */ - status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, windchillF); + status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, windchillF); /* Create the dataset transfer property list */ dxpl_id_f_to_c = H5Pcreate(H5P_DATASET_XFER); @@ -125,13 +120,11 @@ main (void) printf("\nData with no write transform, but a read transform: \n"); PRINT(windchillC); - -/**************** PART 2 **************/ + /**************** PART 2 **************/ /* * Write the data to the dataset with the f_to_c transform set */ - status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, - dxpl_id_f_to_c, windchillF); + status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, dxpl_id_f_to_c, windchillF); /* Read out the data with the default transfer list (ie, no transform set) */ H5Dread(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, windchillC); @@ -140,8 +133,7 @@ main (void) printf("\nData with write transform, but no read transform: \n"); PRINT(windchillC); -/************** PART 3 ***************/ - + /************** PART 3 ***************/ /* Create the dataset transfer property list */ dxpl_id_c_to_f = H5Pcreate(H5P_DATASET_XFER); @@ -149,12 +141,10 @@ main (void) /* Set the data transform to be used on the read*/ H5Pset_data_transform(dxpl_id_c_to_f, c_to_f); - /* * Write the data to the dataset using the f_to_c transform */ - status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, - dxpl_id_f_to_c, windchillF); + status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, dxpl_id_f_to_c, windchillF); /* Read the data with the c_to_f data transform */ H5Dread(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, dxpl_id_c_to_f, windchillC); @@ -163,10 +153,10 @@ main (void) printf("\nData with both read and write data transform: \n"); PRINT(windchillC); -/************** PART 4 **************/ + /************** PART 4 **************/ transform_size = H5Pget_data_transform(dxpl_id_f_to_c, NULL, 0); - transform = (char*) malloc(transform_size+1); - H5Pget_data_transform(dxpl_id_f_to_c, transform, transform_size+1); + transform = (char *)malloc(transform_size + 1); + H5Pget_data_transform(dxpl_id_f_to_c, transform, transform_size + 1); printf("\nTransform string (from dxpl_id_f_to_c) is: %s\n", transform); diff --git a/examples/h5_elink_unix2win.c b/examples/h5_elink_unix2win.c index df52015..bc2e246 100644 --- a/examples/h5_elink_unix2win.c +++ b/examples/h5_elink_unix2win.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -27,7 +27,6 @@ #include <stdlib.h> #include <string.h> - /* "Windows to Unix" traversal function for external links * * Translates a filename stored in Unix format to Windows format by replacing @@ -37,45 +36,44 @@ * Note that this may not be necessary on your system; many Windows systems can * understand Unix paths. */ -static hid_t elink_unix2win_trav(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id) +static hid_t +elink_unix2win_trav(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, + hid_t lapl_id) { - hid_t fid; - const char *file_name; - const char *obj_name; - char *new_fname = NULL; /* Buffer allocated to hold Unix file path */ - ssize_t prefix_len; /* External link prefix length */ - size_t fname_len; - size_t start_pos; /* Initial position in new_fname buffer */ - size_t x; /* Counter variable */ - hid_t ret_value = -1; + hid_t fid; + const char *file_name; + const char *obj_name; + char * new_fname = NULL; /* Buffer allocated to hold Unix file path */ + ssize_t prefix_len; /* External link prefix length */ + size_t fname_len; + size_t start_pos; /* Initial position in new_fname buffer */ + size_t x; /* Counter variable */ + hid_t ret_value = -1; printf("Converting Unix path to Windows path.\n"); - if(H5Lunpack_elink_val(udata, udata_size, NULL, &file_name, &obj_name) < 0) + if (H5Lunpack_elink_val(udata, udata_size, NULL, &file_name, &obj_name) < 0) goto error; fname_len = strlen(file_name); /* See if the external link prefix property is set */ - if((prefix_len = H5Pget_elink_prefix(lapl_id, NULL, 0)) < 0) + if ((prefix_len = H5Pget_elink_prefix(lapl_id, NULL, 0)) < 0) goto error; /* If so, prepend it to the filename. We assume that the prefix * is in the correct format for the current file system. */ - if(prefix_len > 0) - { + if (prefix_len > 0) { /* Allocate a buffer to hold the filename plus prefix */ new_fname = malloc(prefix_len + fname_len + 1); /* Copy the prefix into the buffer */ - if(H5Pget_elink_prefix(lapl_id, new_fname, (size_t)(prefix_len + 1)) < 0) + if (H5Pget_elink_prefix(lapl_id, new_fname, (size_t)(prefix_len + 1)) < 0) goto error; start_pos = prefix_len; } - else - { + else { /* Allocate a buffer to hold just the filename */ new_fname = malloc(fname_len + 1); start_pos = 0; @@ -84,9 +82,8 @@ static hid_t elink_unix2win_trav(const char *link_name, hid_t cur_group, /* We should now copy file_name into new_fname starting at position pos. * We'll convert '/' characters into '\' characters as we go. */ - for(x=0; file_name[x] != '\0'; x++) - { - if(file_name[x] == '/') + for (x = 0; file_name[x] != '\0'; x++) { + if (file_name[x] == '/') new_fname[x + start_pos] = '\\'; else new_fname[x + start_pos] = file_name[x]; @@ -94,38 +91,37 @@ static hid_t elink_unix2win_trav(const char *link_name, hid_t cur_group, new_fname[x + start_pos] = '\0'; /* Now open the file and object within it */ - if((fid = H5Fopen(new_fname, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) + if ((fid = H5Fopen(new_fname, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) goto error; ret_value = H5Oopen(fid, obj_name, lapl_id); /* If this fails, our return value will be negative. */ - if(H5Fclose(fid) < 0) + if (H5Fclose(fid) < 0) goto error; /* Free file name if it's been allocated */ - if(new_fname) + if (new_fname) free(new_fname); return ret_value; error: /* Free file name if it's been allocated */ - if(new_fname) + if (new_fname) free(new_fname); return -1; } const H5L_class_t elink_unix2win_class[1] = {{ - H5L_LINK_CLASS_T_VERS, /* H5L_class_t version */ - H5L_TYPE_EXTERNAL, /* Link type id number */ - "unix2win external link", /* Link class name for debugging */ - NULL, /* Creation callback */ - NULL, /* Move callback */ - NULL, /* Copy callback */ - elink_unix2win_trav, /* The actual traversal function */ - NULL, /* Deletion callback */ - NULL /* Query callback */ + H5L_LINK_CLASS_T_VERS, /* H5L_class_t version */ + H5L_TYPE_EXTERNAL, /* Link type id number */ + "unix2win external link", /* Link class name for debugging */ + NULL, /* Creation callback */ + NULL, /* Move callback */ + NULL, /* Copy callback */ + elink_unix2win_trav, /* The actual traversal function */ + NULL, /* Deletion callback */ + NULL /* Query callback */ }}; - /* The example function. * Creates a file named "unix2win.h5" with an external link pointing to * the file "u2w/u2w_target.h5". @@ -136,55 +132,65 @@ const H5L_class_t elink_unix2win_class[1] = {{ static int unix2win_example(void) { - hid_t fid = (-1); /* File ID */ - hid_t gid = (-1); /* Group ID */ + hid_t fid = (-1); /* File ID */ + hid_t gid = (-1); /* Group ID */ /* Create the target file. */ #ifdef H5_HAVE_WIN32_API - if((fid=H5Fcreate("u2w\\u2w_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0) goto error; + if ((fid = H5Fcreate("u2w\\u2w_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto error; #else - if((fid=H5Fcreate("u2w/u2w_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0) goto error; + if ((fid = H5Fcreate("u2w/u2w_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto error; #endif - if(H5Fclose(fid) < 0) goto error; + if (H5Fclose(fid) < 0) + goto error; /* Create the source file with an external link in Windows format */ - if((fid=H5Fcreate("unix2win.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0) goto error; + if ((fid = H5Fcreate("unix2win.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto error; /* Create the external link */ - if(H5Lcreate_external("u2w/../u2w/u2w_target.h5", "/", fid, "ext_link", H5P_DEFAULT, H5P_DEFAULT) < 0) goto error; + if (H5Lcreate_external("u2w/../u2w/u2w_target.h5", "/", fid, "ext_link", H5P_DEFAULT, H5P_DEFAULT) < 0) + goto error; - /* If we are not on Windows, assume we are on a Unix-y filesystem and - * follow the external link normally. - * If we are on Windows, register the unix2win traversal function so - * that external links can be traversed. - */ + /* If we are not on Windows, assume we are on a Unix-y filesystem and + * follow the external link normally. + * If we are on Windows, register the unix2win traversal function so + * that external links can be traversed. + */ #ifdef H5_HAVE_WIN32_API /* Register the elink_unix2win class defined above to replace default * external links */ - if(H5Lregister(elink_unix2win_class) < 0) goto error; + if (H5Lregister(elink_unix2win_class) < 0) + goto error; #endif /* Now follow the link */ - if((gid = H5Gopen2(fid, "ext_link", H5P_DEFAULT)) < 0) goto error; + if ((gid = H5Gopen2(fid, "ext_link", H5P_DEFAULT)) < 0) + goto error; printf("Successfully followed external link.\n"); /* Close the group and the file */ - if(H5Gclose(gid) <0) goto error; - if(H5Fclose(fid) <0) goto error; + if (H5Gclose(gid) < 0) + goto error; + if (H5Fclose(fid) < 0) + goto error; return 0; - error: +error: printf("Error!\n"); - H5E_BEGIN_TRY { - H5Gclose (gid); - H5Fclose (fid); - } H5E_END_TRY; + H5E_BEGIN_TRY + { + H5Gclose(gid); + H5Fclose(fid); + } + H5E_END_TRY; return -1; } - /* Main function * @@ -193,12 +199,10 @@ unix2win_example(void) int main(void) { - int ret; + int ret; printf("Testing unix2win external links.\n"); ret = unix2win_example(); return ret; } - - diff --git a/examples/h5_extend.c b/examples/h5_extend.c index 6e3cff2..5807694 100644 --- a/examples/h5_extend.c +++ b/examples/h5_extend.c @@ -6,139 +6,126 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* - * This example how to work with extendible datasets. The dataset + * This example how to work with extendible datasets. The dataset * must be chunked in order to be extendible. - * + * * It is used in the HDF5 Tutorial. */ - #include "hdf5.h" #define FILENAME "extend.h5" #define DATASETNAME "ExtendibleArray" -#define RANK 2 +#define RANK 2 int -main (void) +main(void) { - hid_t file; /* handles */ - hid_t dataspace, dataset; - hid_t filespace, memspace; - hid_t prop; - - hsize_t dims[2] = {3, 3}; /* dataset dimensions at creation time */ - hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; - herr_t status; - hsize_t chunk_dims[2] = {2, 5}; - int data[3][3] = { {1, 1, 1}, /* data to write */ - {1, 1, 1}, - {1, 1, 1} }; + hid_t file; /* handles */ + hid_t dataspace, dataset; + hid_t filespace, memspace; + hid_t prop; + + hsize_t dims[2] = {3, 3}; /* dataset dimensions at creation time */ + hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; + herr_t status; + hsize_t chunk_dims[2] = {2, 5}; + int data[3][3] = {{1, 1, 1}, /* data to write */ + {1, 1, 1}, + {1, 1, 1}}; /* Variables used in extending and writing to the extended portion of dataset */ - hsize_t size[2]; - hsize_t offset[2]; - hsize_t dimsext[2] = {7, 3}; /* extend dimensions */ - int dataext[7][3] = { {2, 3, 4}, - {2, 3, 4}, - {2, 3, 4}, - {2, 3, 4}, - {2, 3, 4}, - {2, 3, 4}, - {2, 3, 4} }; + hsize_t size[2]; + hsize_t offset[2]; + hsize_t dimsext[2] = {7, 3}; /* extend dimensions */ + int dataext[7][3] = {{2, 3, 4}, {2, 3, 4}, {2, 3, 4}, {2, 3, 4}, {2, 3, 4}, {2, 3, 4}, {2, 3, 4}}; /* Variables used in reading data back */ - hsize_t chunk_dimsr[2]; - hsize_t dimsr[2]; - hsize_t i, j; - int rdata[10][3]; - herr_t status_n; - int rank, rank_chunk; + hsize_t chunk_dimsr[2]; + hsize_t dimsr[2]; + hsize_t i, j; + int rdata[10][3]; + herr_t status_n; + int rank, rank_chunk; /* Create the data space with unlimited dimensions. */ - dataspace = H5Screate_simple (RANK, dims, maxdims); + dataspace = H5Screate_simple(RANK, dims, maxdims); /* Create a new file. If file exists its contents will be overwritten. */ - file = H5Fcreate (FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + file = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); /* Modify dataset creation properties, i.e. enable chunking */ - prop = H5Pcreate (H5P_DATASET_CREATE); - status = H5Pset_chunk (prop, RANK, chunk_dims); + prop = H5Pcreate(H5P_DATASET_CREATE); + status = H5Pset_chunk(prop, RANK, chunk_dims); - /* Create a new dataset within the file using chunk + /* Create a new dataset within the file using chunk creation properties. */ - dataset = H5Dcreate2 (file, DATASETNAME, H5T_NATIVE_INT, dataspace, - H5P_DEFAULT, prop, H5P_DEFAULT); + dataset = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, prop, H5P_DEFAULT); /* Write data to dataset */ - status = H5Dwrite (dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, data); + status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); /* Extend the dataset. Dataset becomes 10 x 3 */ - size[0] = dims[0]+ dimsext[0]; + size[0] = dims[0] + dimsext[0]; size[1] = dims[1]; - status = H5Dset_extent (dataset, size); + status = H5Dset_extent(dataset, size); /* Select a hyperslab in extended portion of dataset */ - filespace = H5Dget_space (dataset); + filespace = H5Dget_space(dataset); offset[0] = 3; offset[1] = 0; - status = H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, - dimsext, NULL); + status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, dimsext, NULL); /* Define memory space */ - memspace = H5Screate_simple (RANK, dimsext, NULL); + memspace = H5Screate_simple(RANK, dimsext, NULL); /* Write the data to the extended portion of dataset */ - status = H5Dwrite (dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, dataext); + status = H5Dwrite(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, dataext); /* Close resources */ - status = H5Dclose (dataset); - status = H5Pclose (prop); - status = H5Sclose (dataspace); - status = H5Sclose (memspace); - status = H5Sclose (filespace); - status = H5Fclose (file); + status = H5Dclose(dataset); + status = H5Pclose(prop); + status = H5Sclose(dataspace); + status = H5Sclose(memspace); + status = H5Sclose(filespace); + status = H5Fclose(file); /******************************************** * Re-open the file and read the data back. * ********************************************/ - file = H5Fopen (FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT); - dataset = H5Dopen2 (file, DATASETNAME, H5P_DEFAULT); + file = H5Fopen(FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT); + dataset = H5Dopen2(file, DATASETNAME, H5P_DEFAULT); - filespace = H5Dget_space (dataset); - rank = H5Sget_simple_extent_ndims (filespace); - status_n = H5Sget_simple_extent_dims (filespace, dimsr, NULL); + filespace = H5Dget_space(dataset); + rank = H5Sget_simple_extent_ndims(filespace); + status_n = H5Sget_simple_extent_dims(filespace, dimsr, NULL); - prop = H5Dget_create_plist (dataset); + prop = H5Dget_create_plist(dataset); - if (H5D_CHUNKED == H5Pget_layout (prop)) - rank_chunk = H5Pget_chunk (prop, rank, chunk_dimsr); + if (H5D_CHUNKED == H5Pget_layout(prop)) + rank_chunk = H5Pget_chunk(prop, rank, chunk_dimsr); - memspace = H5Screate_simple (rank, dimsr, NULL); - status = H5Dread (dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, rdata); + memspace = H5Screate_simple(rank, dimsr, NULL); + status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, rdata); printf("\n"); printf("Dataset: \n"); - for (j = 0; j < dimsr[0]; j++) - { - for (i = 0; i < dimsr[1]; i++) - printf("%d ", rdata[j][i]); - printf("\n"); + for (j = 0; j < dimsr[0]; j++) { + for (i = 0; i < dimsr[1]; i++) + printf("%d ", rdata[j][i]); + printf("\n"); } - status = H5Pclose (prop); - status = H5Dclose (dataset); - status = H5Sclose (filespace); - status = H5Sclose (memspace); - status = H5Fclose (file); + status = H5Pclose(prop); + status = H5Dclose(dataset); + status = H5Sclose(filespace); + status = H5Sclose(memspace); + status = H5Fclose(file); } diff --git a/examples/h5_extend_write.c b/examples/h5_extend_write.c index 4abda30..f5db1cf 100644 --- a/examples/h5_extend_write.c +++ b/examples/h5_extend_write.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -20,43 +20,42 @@ #include "hdf5.h" -#define H5FILE_NAME "SDSextendible.h5" +#define H5FILE_NAME "SDSextendible.h5" #define DATASETNAME "ExtendibleArray" -#define RANK 2 -#define NX 10 -#define NY 5 +#define RANK 2 +#define NX 10 +#define NY 5 int -main (void) +main(void) { - hid_t file; /* handles */ - hid_t dataspace, dataset; - hid_t filespace; - hid_t cparms; - hsize_t dims[2] = { 3, 3}; /* - * dataset dimensions - * at the creation time - */ - hsize_t dims1[2] = { 3, 3}; /* data1 dimensions */ - hsize_t dims2[2] = { 7, 1}; /* data2 dimensions */ - hsize_t dims3[2] = { 2, 2}; /* data3 dimensions */ + hid_t file; /* handles */ + hid_t dataspace, dataset; + hid_t filespace; + hid_t cparms; + hsize_t dims[2] = {3, 3}; /* + * dataset dimensions + * at the creation time + */ + hsize_t dims1[2] = {3, 3}; /* data1 dimensions */ + hsize_t dims2[2] = {7, 1}; /* data2 dimensions */ + hsize_t dims3[2] = {2, 2}; /* data3 dimensions */ - hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; - hsize_t chunk_dims[2] ={2, 5}; - hsize_t size[2]; - hsize_t offset[2]; + hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; + hsize_t chunk_dims[2] = {2, 5}; + hsize_t size[2]; + hsize_t offset[2]; - herr_t status; + herr_t status; - int data1[3][3] = { {1, 1, 1}, /* data to write */ - {1, 1, 1}, - {1, 1, 1} }; + int data1[3][3] = {{1, 1, 1}, /* data to write */ + {1, 1, 1}, + {1, 1, 1}}; - int data2[7] = { 2, 2, 2, 2, 2, 2, 2}; + int data2[7] = {2, 2, 2, 2, 2, 2, 2}; - int data3[2][2] = { {3, 3}, - {3, 3} }; - int fillvalue = 0; + int data3[2][2] = {{3, 3}, {3, 3}}; + int fillvalue = 0; /* * Create the data space with unlimited dimensions. @@ -72,22 +71,21 @@ main (void) * Modify dataset creation properties, i.e. enable chunking. */ cparms = H5Pcreate(H5P_DATASET_CREATE); - status = H5Pset_chunk( cparms, RANK, chunk_dims); - status = H5Pset_fill_value (cparms, H5T_NATIVE_INT, &fillvalue ); + status = H5Pset_chunk(cparms, RANK, chunk_dims); + status = H5Pset_fill_value(cparms, H5T_NATIVE_INT, &fillvalue); /* * Create a new dataset within the file using cparms * creation properties. */ - dataset = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, - cparms, H5P_DEFAULT); + dataset = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms, H5P_DEFAULT); /* * Extend the dataset. This call assures that dataset is at least 3 x 3. */ - size[0] = 3; - size[1] = 3; - status = H5Dset_extent(dataset, size); + size[0] = 3; + size[1] = 3; + status = H5Dset_extent(dataset, size); /* * Select a hyperslab. @@ -95,22 +93,20 @@ main (void) filespace = H5Dget_space(dataset); offset[0] = 0; offset[1] = 0; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - dims1, NULL); + status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, dims1, NULL); /* * Write the data to the hyperslab. */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, - H5P_DEFAULT, data1); + status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, H5P_DEFAULT, data1); /* * Extend the dataset. Dataset becomes 10 x 3. */ - dims[0] = dims1[0] + dims2[0]; - size[0] = dims[0]; - size[1] = dims[1]; - status = H5Dset_extent(dataset, size); + dims[0] = dims1[0] + dims2[0]; + size[0] = dims[0]; + size[1] = dims[1]; + status = H5Dset_extent(dataset, size); /* * Select a hyperslab. @@ -118,8 +114,7 @@ main (void) filespace = H5Dget_space(dataset); offset[0] = 3; offset[1] = 0; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - dims2, NULL); + status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, dims2, NULL); /* * Define memory space @@ -129,16 +124,15 @@ main (void) /* * Write the data to the hyperslab. */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, - H5P_DEFAULT, data2); + status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, H5P_DEFAULT, data2); /* * Extend the dataset. Dataset becomes 10 x 5. */ - dims[1] = dims1[1] + dims3[1]; - size[0] = dims[0]; - size[1] = dims[1]; - status = H5Dset_extent(dataset, size); + dims[1] = dims1[1] + dims3[1]; + size[0] = dims[0]; + size[1] = dims[1]; + status = H5Dset_extent(dataset, size); /* * Select a hyperslab @@ -146,8 +140,7 @@ main (void) filespace = H5Dget_space(dataset); offset[0] = 0; offset[1] = 3; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - dims3, NULL); + status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, dims3, NULL); /* * Define memory space. @@ -157,8 +150,7 @@ main (void) /* * Write the data to the hyperslab. */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, - H5P_DEFAULT, data3); + status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, H5P_DEFAULT, data3); /* * Resulting dataset diff --git a/examples/h5_extlink.c b/examples/h5_extlink.c index ba632f5..341bea5 100644 --- a/examples/h5_extlink.c +++ b/examples/h5_extlink.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -26,37 +26,36 @@ #define PREFIX_SOURCE_FILE "extlink_prefix_source.h5" -#define SOFT_LINK_FILE "soft_link.h5" -#define SOFT_LINK_NAME "soft_link_to_group" +#define SOFT_LINK_FILE "soft_link.h5" +#define SOFT_LINK_NAME "soft_link_to_group" #define UD_SOFT_LINK_NAME "ud_soft_link" -#define TARGET_GROUP "target_group" +#define TARGET_GROUP "target_group" #define UD_SOFT_CLASS 65 -#define HARD_LINK_FILE "hard_link.h5" -#define HARD_LINK_NAME "hard_link_to_group" +#define HARD_LINK_FILE "hard_link.h5" +#define HARD_LINK_NAME "hard_link_to_group" #define UD_HARD_LINK_NAME "ud_hard_link" #define UD_HARD_CLASS 66 #define PLIST_LINK_PROP "plist_link_prop" -#define UD_PLIST_CLASS 66 +#define UD_PLIST_CLASS 66 - - /* Basic external link example * * Creates two files and uses an external link to access an object in the * second file from the first file. */ -static void extlink_example(void) +static void +extlink_example(void) { hid_t source_file_id, targ_file_id; hid_t group_id, group2_id; /* Create two files, a source and a target */ source_file_id = H5Fcreate(SOURCE_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - targ_file_id = H5Fcreate(TARGET_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + targ_file_id = H5Fcreate(TARGET_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); /* Create a group in the target file for the external link to point to. */ group_id = H5Gcreate2(targ_file_id, "target_group", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); @@ -96,7 +95,6 @@ static void extlink_example(void) */ } - /* External link prefix example * * Uses a group access property list to set a "prefix" for the filenames @@ -109,7 +107,8 @@ static void extlink_example(void) * where it is run (so to run this example on Unix, first mkdir red and mkdir * blue). */ -static void extlink_prefix_example(void) +static void +extlink_prefix_example(void) { hid_t source_file_id, red_file_id, blue_file_id; hid_t group_id, group2_id; @@ -119,14 +118,15 @@ static void extlink_prefix_example(void) * the same name, but one will be located in the red directory and one will * be located in the blue directory */ source_file_id = H5Fcreate(PREFIX_SOURCE_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - red_file_id = H5Fcreate("red/prefix_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - blue_file_id = H5Fcreate("blue/prefix_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + red_file_id = H5Fcreate("red/prefix_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + blue_file_id = H5Fcreate("blue/prefix_target.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); /* This test needs a red and a blue directory in the filesystem. If they're not present, * trying to create the files above will fail. */ - if(red_file_id < 0 || blue_file_id < 0) - printf("This test requires directories named 'red' and 'blue' to exist. Did you forget to create them?\n"); + if (red_file_id < 0 || blue_file_id < 0) + printf("This test requires directories named 'red' and 'blue' to exist. Did you forget to create " + "them?\n"); /* Create an external link in the source file pointing to the root group of * a file named prefix_target.h5. This file doesn't exist in the current @@ -163,7 +163,7 @@ static void extlink_prefix_example(void) * directory. */ H5Pset_elink_prefix(gapl_id, "blue/"); - group_id = H5Gopen2(source_file_id, "ext_link", gapl_id); + group_id = H5Gopen2(source_file_id, "ext_link", gapl_id); group2_id = H5Gcreate2(group_id, "sky blue", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); /* Close both groups. */ @@ -171,7 +171,7 @@ static void extlink_prefix_example(void) H5Gclose(group_id); /* Each file has had a group created inside it using the same external link. */ - group_id = H5Gopen2(red_file_id, "pink", H5P_DEFAULT); + group_id = H5Gopen2(red_file_id, "pink", H5P_DEFAULT); group2_id = H5Gopen2(blue_file_id, "sky blue", H5P_DEFAULT); /* Clean up our open IDs */ @@ -189,7 +189,6 @@ static void extlink_prefix_example(void) */ } - /* Soft Link example * * Create a new class of user-defined links that behave like HDF5's built-in @@ -207,10 +206,11 @@ static void extlink_prefix_example(void) * We might also have wanted to supply a creation callback that checks * that a path was supplied in the udata. */ -static hid_t UD_soft_traverse(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id); +static hid_t UD_soft_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, + hid_t lapl_id); -static void soft_link_example(void) +static void +soft_link_example(void) { hid_t file_id; hid_t group_id; @@ -220,27 +220,26 @@ static void soft_link_example(void) * callback. */ const H5L_class_t UD_soft_class[1] = {{ - H5L_LINK_CLASS_T_VERS, /* Version number for this struct. - * This field is always H5L_LINK_CLASS_T_VERS */ - (H5L_type_t)UD_SOFT_CLASS, /* Link class id number. This can be any - * value between H5L_TYPE_UD_MIN (64) and - * H5L_TYPE_MAX (255). It should be a - * value that isn't already being used by - * another kind of link. We'll use 65. */ - "UD_soft_link", /* Link class name for debugging */ - NULL, /* Creation callback */ - NULL, /* Move callback */ - NULL, /* Copy callback */ - UD_soft_traverse, /* The actual traversal function */ - NULL, /* Deletion callback */ - NULL /* Query callback */ + H5L_LINK_CLASS_T_VERS, /* Version number for this struct. + * This field is always H5L_LINK_CLASS_T_VERS */ + (H5L_type_t)UD_SOFT_CLASS, /* Link class id number. This can be any + * value between H5L_TYPE_UD_MIN (64) and + * H5L_TYPE_MAX (255). It should be a + * value that isn't already being used by + * another kind of link. We'll use 65. */ + "UD_soft_link", /* Link class name for debugging */ + NULL, /* Creation callback */ + NULL, /* Move callback */ + NULL, /* Copy callback */ + UD_soft_traverse, /* The actual traversal function */ + NULL, /* Deletion callback */ + NULL /* Query callback */ }}; - /* First, create a file and an object within the file for the link to * point to. */ - file_id = H5Fcreate(SOFT_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + file_id = H5Fcreate(SOFT_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); group_id = H5Gcreate2(file_id, TARGET_GROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); H5Gclose(group_id); @@ -275,12 +274,12 @@ static void soft_link_example(void) * The actual traversal function simply needs to open the correct object by * name and return its ID. */ - -static hid_t UD_soft_traverse(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id) + +static hid_t +UD_soft_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, hid_t lapl_id) { - const char *target = (const char *) udata; - hid_t ret_value; + const char *target = (const char *)udata; + hid_t ret_value; /* Pass the udata straight through to HDF5. If it's invalid, let HDF5 * return an error. @@ -289,7 +288,6 @@ static hid_t UD_soft_traverse(const char *link_name, hid_t cur_group, return ret_value; } - /* Hard Link example * * Create a new class of user-defined links that behave like HDF5's built-in @@ -305,17 +303,17 @@ static hid_t UD_soft_traverse(const char *link_name, hid_t cur_group, * To keep the example simple, these links don't have a query callback. * Generally, real link classes should always be query-able. */ -static herr_t UD_hard_create(const char *link_name, hid_t loc_group, - const void *udata, size_t udata_size, hid_t lcpl_id); -static herr_t UD_hard_delete(const char *link_name, hid_t loc_group, - const void *udata, size_t udata_size); -static hid_t UD_hard_traverse(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id); - -static void hard_link_example(void) +static herr_t UD_hard_create(const char *link_name, hid_t loc_group, const void *udata, size_t udata_size, + hid_t lcpl_id); +static herr_t UD_hard_delete(const char *link_name, hid_t loc_group, const void *udata, size_t udata_size); +static hid_t UD_hard_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, + hid_t lapl_id); + +static void +hard_link_example(void) { - hid_t file_id; - hid_t group_id; + hid_t file_id; + hid_t group_id; H5L_info_t li; /* Define the link class that we'll use to register "user-defined hard * links" using the callbacks we defined above. @@ -323,27 +321,26 @@ static void hard_link_example(void) * callback. */ const H5L_class_t UD_hard_class[1] = {{ - H5L_LINK_CLASS_T_VERS, /* Version number for this struct. - * This field is always H5L_LINK_CLASS_T_VERS */ - (H5L_type_t)UD_HARD_CLASS, /* Link class id number. This can be any - * value between H5L_TYPE_UD_MIN (64) and - * H5L_TYPE_MAX (255). It should be a - * value that isn't already being used by - * another kind of link. We'll use 66. */ - "UD_hard_link", /* Link class name for debugging */ - UD_hard_create, /* Creation callback */ - NULL, /* Move callback */ - NULL, /* Copy callback */ - UD_hard_traverse, /* The actual traversal function */ - UD_hard_delete, /* Deletion callback */ - NULL /* Query callback */ + H5L_LINK_CLASS_T_VERS, /* Version number for this struct. + * This field is always H5L_LINK_CLASS_T_VERS */ + (H5L_type_t)UD_HARD_CLASS, /* Link class id number. This can be any + * value between H5L_TYPE_UD_MIN (64) and + * H5L_TYPE_MAX (255). It should be a + * value that isn't already being used by + * another kind of link. We'll use 66. */ + "UD_hard_link", /* Link class name for debugging */ + UD_hard_create, /* Creation callback */ + NULL, /* Move callback */ + NULL, /* Copy callback */ + UD_hard_traverse, /* The actual traversal function */ + UD_hard_delete, /* Deletion callback */ + NULL /* Query callback */ }}; - /* First, create a file and an object within the file for the link to * point to. */ - file_id = H5Fcreate(HARD_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + file_id = H5Fcreate(HARD_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); group_id = H5Gcreate2(file_id, TARGET_GROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); H5Gclose(group_id); @@ -366,8 +363,8 @@ static void hard_link_example(void) /* Now create a user-defined link. We give it the group's address * as its udata. */ - H5Lcreate_ud(file_id, UD_HARD_LINK_NAME, (H5L_type_t)UD_HARD_CLASS, &(li.u.address), - sizeof(li.u.address), H5P_DEFAULT, H5P_DEFAULT); + H5Lcreate_ud(file_id, UD_HARD_LINK_NAME, (H5L_type_t)UD_HARD_CLASS, &(li.u.address), sizeof(li.u.address), + H5P_DEFAULT, H5P_DEFAULT); /* The UD hard link has now incremented the group's reference count * like a normal hard link would. This means that we can unlink the @@ -401,42 +398,39 @@ static void hard_link_example(void) * If this function returns a negative value, the call to H5Lcreate_ud() * will also return failure and the link will not be created. */ -static herr_t UD_hard_create(const char *link_name, hid_t loc_group, - const void *udata, size_t udata_size, hid_t lcpl_id) +static herr_t +UD_hard_create(const char *link_name, hid_t loc_group, const void *udata, size_t udata_size, hid_t lcpl_id) { haddr_t addr; - hid_t target_obj = -1; - herr_t ret_value = 0; + hid_t target_obj = -1; + herr_t ret_value = 0; /* Make sure that the address passed in looks valid */ - if(udata_size != sizeof(haddr_t)) - { - ret_value = -1; - goto done; + if (udata_size != sizeof(haddr_t)) { + ret_value = -1; + goto done; } - addr = *((const haddr_t *) udata); + addr = *((const haddr_t *)udata); /* Open the object this link points to so that we can increment * its reference count. This also ensures that the address passed * in points to a real object (although this check is not perfect!) */ - target_obj= H5Oopen_by_addr(loc_group, addr); - if(target_obj < 0) - { - ret_value = -1; - goto done; + target_obj = H5Oopen_by_addr(loc_group, addr); + if (target_obj < 0) { + ret_value = -1; + goto done; } /* Increment the reference count of the target object */ - if(H5Oincr_refcount(target_obj) < 0) - { - ret_value = -1; - goto done; + if (H5Oincr_refcount(target_obj) < 0) { + ret_value = -1; + goto done; } done: /* Close the target object if we opened it */ - if(target_obj >= 0) + if (target_obj >= 0) H5Oclose(target_obj); return ret_value; } @@ -445,42 +439,39 @@ done: * Since the creation function increments the object's reference count, it's * important to decrement it again when the link is deleted. */ -static herr_t UD_hard_delete(const char *link_name, hid_t loc_group, - const void *udata, size_t udata_size) +static herr_t +UD_hard_delete(const char *link_name, hid_t loc_group, const void *udata, size_t udata_size) { haddr_t addr; - hid_t target_obj = -1; - herr_t ret_value = 0; + hid_t target_obj = -1; + herr_t ret_value = 0; /* Sanity check; we have already verified the udata's size in the creation * callback. */ - if(udata_size != sizeof(haddr_t)) - { - ret_value = -1; - goto done; + if (udata_size != sizeof(haddr_t)) { + ret_value = -1; + goto done; } - addr = *((const haddr_t *) udata); + addr = *((const haddr_t *)udata); /* Open the object this link points to */ - target_obj= H5Oopen_by_addr(loc_group, addr); - if(target_obj < 0) - { - ret_value = -1; - goto done; + target_obj = H5Oopen_by_addr(loc_group, addr); + if (target_obj < 0) { + ret_value = -1; + goto done; } /* Decrement the reference count of the target object */ - if(H5Odecr_refcount(target_obj) < 0) - { - ret_value = -1; - goto done; + if (H5Odecr_refcount(target_obj) < 0) { + ret_value = -1; + goto done; } done: /* Close the target object if we opened it */ - if(target_obj >= 0) + if (target_obj >= 0) H5Oclose(target_obj); return ret_value; } @@ -489,19 +480,19 @@ done: * The actual traversal function simply needs to open the correct object and * return its ID. */ -static hid_t UD_hard_traverse(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id) +static hid_t +UD_hard_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, hid_t lapl_id) { - haddr_t addr; - hid_t ret_value = -1; + haddr_t addr; + hid_t ret_value = -1; /* Sanity check; we have already verified the udata's size in the creation * callback. */ - if(udata_size != sizeof(haddr_t)) - return -1; + if (udata_size != sizeof(haddr_t)) + return -1; - addr = *((const haddr_t *) udata); + addr = *((const haddr_t *)udata); /* Open the object by address. If H5Oopen_by_addr fails, ret_value will * be negative to indicate that the traversal function failed. @@ -511,8 +502,6 @@ static hid_t UD_hard_traverse(const char *link_name, hid_t cur_group, return ret_value; } - - /* Plist example * * Create a new class of user-defined links that open objects within a file @@ -526,10 +515,11 @@ static hid_t UD_hard_traverse(const char *link_name, hid_t cur_group, * These are defined after the example below. * These links have no udata, so they don't need a query function. */ -static hid_t UD_plist_traverse(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id); +static hid_t UD_plist_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, + hid_t lapl_id); -static void plist_link_example(void) +static void +plist_link_example(void) { hid_t file_id; hid_t group_id, group2_id; @@ -558,11 +548,10 @@ static void plist_link_example(void) NULL /* Query callback */ }}; - /* First, create a file and two objects within the file for the link to * point to. */ - file_id = H5Fcreate(HARD_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + file_id = H5Fcreate(HARD_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); group_id = H5Gcreate2(file_id, "group_1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); H5Gclose(group_id); group_id = H5Gcreate2(file_id, "group_1/group_2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); @@ -570,8 +559,7 @@ static void plist_link_example(void) /* Register "plist links" and create one. It has no udata at all. */ H5Lregister(UD_plist_class); - H5Lcreate_ud(file_id, "plist_link", (H5L_type_t)UD_PLIST_CLASS, NULL, 0, - H5P_DEFAULT, H5P_DEFAULT); + H5Lcreate_ud(file_id, "plist_link", (H5L_type_t)UD_PLIST_CLASS, NULL, 0, H5P_DEFAULT, H5P_DEFAULT); /* Create a group access property list to pass in the target for the * plist link. @@ -617,17 +605,17 @@ static void plist_link_example(void) /* UD_plist_traverse * Open a path passed in through the property list. */ -static hid_t UD_plist_traverse(const char *link_name, hid_t cur_group, - const void *udata, size_t udata_size, hid_t lapl_id) +static hid_t +UD_plist_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t udata_size, hid_t lapl_id) { - char * path; - hid_t ret_value = -1; + char *path; + hid_t ret_value = -1; /* If the link property isn't set or can't be found, traversal fails. */ - if(H5Pexist(lapl_id, PLIST_LINK_PROP) < 0) + if (H5Pexist(lapl_id, PLIST_LINK_PROP) < 0) goto error; - if(H5Pget(lapl_id, PLIST_LINK_PROP, &path) < 0) + if (H5Pget(lapl_id, PLIST_LINK_PROP, &path) < 0) goto error; /* Open the object by address. If H5Oopen_by_addr fails, ret_value will @@ -641,13 +629,11 @@ error: return -1; } - - /* Main function * * Invokes the example functions. */ - int +int main(void) { printf("Testing basic external links.\n"); @@ -667,5 +653,3 @@ main(void) return 0; } - - diff --git a/examples/h5_group.c b/examples/h5_group.c index 8e89165..59b0422 100644 --- a/examples/h5_group.c +++ b/examples/h5_group.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -19,31 +19,29 @@ * in the root group and in the created group. */ - #include "hdf5.h" - -#define H5FILE_NAME "group.h5" -#define RANK 2 +#define H5FILE_NAME "group.h5" +#define RANK 2 static herr_t file_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, - void *opdata); /* Link iteration operator function */ + void *opdata); /* Link iteration operator function */ static herr_t group_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, - void *opdata); /* Link iteration operator function */ + void *opdata); /* Link iteration operator function */ int main(void) { - hid_t file; - hid_t grp; - hid_t dataset, dataspace; - hid_t plist; + hid_t file; + hid_t grp; + hid_t dataset, dataspace; + hid_t plist; - herr_t status; - hsize_t dims[2]; - hsize_t cdims[2]; + herr_t status; + hsize_t dims[2]; + hsize_t cdims[2]; - int idx_f, idx_g; + int idx_f, idx_g; /* * Create a file. @@ -61,16 +59,16 @@ main(void) * GZIP compression with the compression effort set to 6. * Note that compression can be used only when dataset is chunked. */ - dims[0] = 1000; - dims[1] = 20; - cdims[0] = 20; - cdims[1] = 20; + dims[0] = 1000; + dims[1] = 20; + cdims[0] = 20; + cdims[1] = 20; dataspace = H5Screate_simple(RANK, dims, NULL); plist = H5Pcreate(H5P_DATASET_CREATE); - H5Pset_chunk(plist, 2, cdims); - H5Pset_deflate( plist, 6); - dataset = H5Dcreate2(file, "/Data/Compressed_Data", H5T_NATIVE_INT, - dataspace, H5P_DEFAULT, plist, H5P_DEFAULT); + H5Pset_chunk(plist, 2, cdims); + H5Pset_deflate(plist, 6); + dataset = + H5Dcreate2(file, "/Data/Compressed_Data", H5T_NATIVE_INT, dataspace, H5P_DEFAULT, plist, H5P_DEFAULT); /* * Close the first dataset . */ @@ -80,11 +78,11 @@ main(void) /* * Create the second dataset. */ - dims[0] = 500; - dims[1] = 20; + dims[0] = 500; + dims[1] = 20; dataspace = H5Screate_simple(RANK, dims, NULL); - dataset = H5Dcreate2(file, "/Data/Float_Data", H5T_NATIVE_FLOAT, - dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dataset = H5Dcreate2(file, "/Data/Float_Data", H5T_NATIVE_FLOAT, dataspace, H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT); /* *Close the second dataset and file. @@ -105,7 +103,8 @@ main(void) * Access "Compressed_Data" dataset in the group. */ dataset = H5Dopen2(grp, "Compressed_Data", H5P_DEFAULT); - if( dataset < 0) printf(" Dataset 'Compressed-Data' is not found. \n"); + if (dataset < 0) + printf(" Dataset 'Compressed-Data' is not found. \n"); printf("\"/Data/Compressed_Data\" dataset is open \n"); /* @@ -123,7 +122,8 @@ main(void) * hard link "Data_new". */ dataset = H5Dopen2(file, "/Data_new/Compressed_Data", H5P_DEFAULT); - if( dataset < 0) printf(" Dataset is not found. \n"); + if (dataset < 0) + printf(" Dataset is not found. \n"); printf("\"/Data_new/Compressed_Data\" dataset is open \n"); /* @@ -131,7 +131,6 @@ main(void) */ status = H5Dclose(dataset); - /* * Use iterator to see the names of the objects in the root group. */ @@ -141,10 +140,10 @@ main(void) * Unlink name "Data" and use iterator to see the names * of the objects in the file root direvtory. */ - if(H5Ldelete(file, "Data", H5P_DEFAULT) < 0) - printf(" H5Ldelete failed \n"); + if (H5Ldelete(file, "Data", H5P_DEFAULT) < 0) + printf(" H5Ldelete failed \n"); else - printf("\"Data\" is unlinked \n"); + printf("\"Data\" is unlinked \n"); idx_f = H5Literate(file, H5_INDEX_NAME, H5_ITER_INC, NULL, file_info, NULL); @@ -152,7 +151,8 @@ main(void) * Use iterator to see the names of the objects in the group * /Data_new. */ - idx_g = H5Literate_by_name(grp, "/Data_new", H5_INDEX_NAME, H5_ITER_INC, NULL, group_info, NULL, H5P_DEFAULT); + idx_g = + H5Literate_by_name(grp, "/Data_new", H5_INDEX_NAME, H5_ITER_INC, NULL, group_info, NULL, H5P_DEFAULT); /* * Close the file. @@ -173,7 +173,7 @@ file_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, void *opdata) /* avoid compiler warnings */ loc_id = loc_id; opdata = opdata; - linfo = linfo; + linfo = linfo; /* * Display group name. The name is passed to the function by @@ -184,23 +184,22 @@ file_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, void *opdata) return 0; } - /* * Operator function. */ static herr_t group_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, void *opdata) { - hid_t did; /* dataset identifier */ - hid_t tid; /* datatype identifier */ + hid_t did; /* dataset identifier */ + hid_t tid; /* datatype identifier */ H5T_class_t t_class; - hid_t pid; /* data_property identifier */ - hsize_t chunk_dims_out[2]; - int rank_chunk; + hid_t pid; /* data_property identifier */ + hsize_t chunk_dims_out[2]; + int rank_chunk; /* avoid warnings */ opdata = opdata; - linfo = linfo; + linfo = linfo; /* * Open the datasets using their names. @@ -215,38 +214,37 @@ group_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, void *opdata /* * Display dataset information. */ - tid = H5Dget_type(did); /* get datatype*/ + tid = H5Dget_type(did); /* get datatype*/ pid = H5Dget_create_plist(did); /* get creation property list */ /* * Check if dataset is chunked. */ - if(H5D_CHUNKED == H5Pget_layout(pid)) { + if (H5D_CHUNKED == H5Pget_layout(pid)) { /* * get chunking information: rank and dimensions. */ rank_chunk = H5Pget_chunk(pid, 2, chunk_dims_out); - printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk, - (unsigned long)(chunk_dims_out[0]), - (unsigned long)(chunk_dims_out[1])); + printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk, (unsigned long)(chunk_dims_out[0]), + (unsigned long)(chunk_dims_out[1])); } else { t_class = H5Tget_class(tid); - if(t_class < 0) { + if (t_class < 0) { puts(" Invalid datatype.\n"); } else { - if(t_class == H5T_INTEGER) + if (t_class == H5T_INTEGER) puts(" Datatype is 'H5T_NATIVE_INTEGER'.\n"); - if(t_class == H5T_FLOAT) + if (t_class == H5T_FLOAT) puts(" Datatype is 'H5T_NATIVE_FLOAT'.\n"); - if(t_class == H5T_STRING) + if (t_class == H5T_STRING) puts(" Datatype is 'H5T_NATIVE_STRING'.\n"); - if(t_class == H5T_BITFIELD) + if (t_class == H5T_BITFIELD) puts(" Datatype is 'H5T_NATIVE_BITFIELD'.\n"); - if(t_class == H5T_OPAQUE) + if (t_class == H5T_OPAQUE) puts(" Datatype is 'H5T_NATIVE_OPAQUE'.\n"); - if(t_class == H5T_COMPOUND) + if (t_class == H5T_COMPOUND) puts(" Datatype is 'H5T_NATIVE_COMPOUND'.\n"); } } @@ -256,4 +254,3 @@ group_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, void *opdata H5Tclose(tid); return 0; } - diff --git a/examples/h5_interm_group.c b/examples/h5_interm_group.c index 6507fd1..c2cafa6 100644 --- a/examples/h5_interm_group.c +++ b/examples/h5_interm_group.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -16,27 +16,24 @@ * all intermediate groups. */ - #include "hdf5.h" - -#define H5FILE_NAME "interm_group.h5" -#define TRUE 1 -#define FALSE 0 +#define H5FILE_NAME "interm_group.h5" +#define TRUE 1 +#define FALSE 0 int main(void) { - hid_t file; - hid_t g1_id, g2_id, g3_id; - hid_t grp_crt_plist; + hid_t file; + hid_t g1_id, g2_id, g3_id; + hid_t grp_crt_plist; H5G_info_t g2_info; - char name[3]; - - herr_t status; - int i; + char name[3]; + herr_t status; + int i; /* * Create a file using the default properties. @@ -59,53 +56,44 @@ main(void) /* * Check if group /G1 exists in the file. */ - if(H5Lexists(file, "/G1", H5P_DEFAULT) !=FALSE) - printf("Group /G1 exists in the file\n"); + if (H5Lexists(file, "/G1", H5P_DEFAULT) != FALSE) + printf("Group /G1 exists in the file\n"); /* * Check that group G2/G3 exists in /G1 and if not create it using * intermediate group creation property. */ g1_id = H5Gopen2(file, "/G1", H5P_DEFAULT); -/* Next commented call causes error stack to be printed out; the next one - * works fine; is it a bug or a feature? EIP 04-25-07 -*/ -/* if (H5Lexists(g1_id, "G2/G3", H5P_DEFAULT) !=TRUE) { */ - if (H5Lexists(g1_id, "G2", H5P_DEFAULT) !=TRUE) { - - grp_crt_plist = H5Pcreate(H5P_LINK_CREATE); - - /* Set flag for intermediate group creation */ - status = H5Pset_create_intermediate_group(grp_crt_plist, TRUE); - g3_id = H5Gcreate2(g1_id, "G2/G3", grp_crt_plist, H5P_DEFAULT, H5P_DEFAULT); - H5Gclose(g3_id); + /* Next commented call causes error stack to be printed out; the next one + * works fine; is it a bug or a feature? EIP 04-25-07 + */ + /* if (H5Lexists(g1_id, "G2/G3", H5P_DEFAULT) !=TRUE) { */ + if (H5Lexists(g1_id, "G2", H5P_DEFAULT) != TRUE) { + + grp_crt_plist = H5Pcreate(H5P_LINK_CREATE); + + /* Set flag for intermediate group creation */ + status = H5Pset_create_intermediate_group(grp_crt_plist, TRUE); + g3_id = H5Gcreate2(g1_id, "G2/G3", grp_crt_plist, H5P_DEFAULT, H5P_DEFAULT); + H5Gclose(g3_id); } H5Gclose(g1_id); - /* Now check if group /G1/G2 exists in the file, then open it and print * its members names */ if (H5Lexists(file, "/G1/G2", H5P_DEFAULT)) { - g2_id = H5Gopen2(file, "/G1/G2", H5P_DEFAULT); - status = H5Gget_info(g2_id, &g2_info); - printf("Group /G1/G2 has %d member(s)\n", (int)g2_info.nlinks); + g2_id = H5Gopen2(file, "/G1/G2", H5P_DEFAULT); + status = H5Gget_info(g2_id, &g2_info); + printf("Group /G1/G2 has %d member(s)\n", (int)g2_info.nlinks); - for (i=0; i < (int)g2_info.nlinks; i++) { - H5Lget_name_by_idx(g2_id, ".", H5_INDEX_NAME, H5_ITER_NATIVE, (hsize_t)i, - name, 3, H5P_DEFAULT); - printf("Object's name is %s\n", name); - - } - H5Gclose(g2_id); + for (i = 0; i < (int)g2_info.nlinks; i++) { + H5Lget_name_by_idx(g2_id, ".", H5_INDEX_NAME, H5_ITER_NATIVE, (hsize_t)i, name, 3, H5P_DEFAULT); + printf("Object's name is %s\n", name); + } + H5Gclose(g2_id); } H5Fclose(file); return 0; } - - - - - - diff --git a/examples/h5_mount.c b/examples/h5_mount.c index a2e16c5..e984d5b 100644 --- a/examples/h5_mount.c +++ b/examples/h5_mount.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -25,107 +25,105 @@ #define FILE2 "mount2.h5" #define RANK 2 -#define NX 4 -#define NY 5 +#define NX 4 +#define NY 5 -int main(void) +int +main(void) { - hid_t fid1, fid2, gid; /* Files and group identifiers */ - hid_t did, tid, sid; /* Dataset and datatype identifiers */ - - herr_t status; - hsize_t dims[] = {NX,NY}; /* Dataset dimensions */ - - int i, j; - int bm[NX][NY], bm_out[NX][NY]; /* Data buffers */ - - /* - * Initialization of buffer matrix "bm" - */ - for(i =0; i < NX; i++) - for(j = 0; j < NY; j++) - bm[i][j] = i + j; - - /* - * Create first file and a group in it. - */ - fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - gid = H5Gcreate2(fid1, "/G", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Close group and file - */ - H5Gclose(gid); - H5Fclose(fid1); - - /* - * Create second file and dataset "D" in it. - */ - fid2 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - dims[0] = NX; - dims[1] = NY; - sid = H5Screate_simple(RANK, dims, NULL); - did = H5Dcreate2(fid2, "D", H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Write data to the dataset. - */ - status = H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, bm); - - /* - * Close all identifiers. - */ - H5Sclose(sid); - H5Dclose(did); - H5Fclose(fid2); - - /* - * Reopen both files - */ - fid1 = H5Fopen(FILE1, H5F_ACC_RDONLY, H5P_DEFAULT); - fid2 = H5Fopen(FILE2, H5F_ACC_RDONLY, H5P_DEFAULT); - - /* - * Mount second file under G in the first file. - */ - H5Fmount(fid1, "/G", fid2, H5P_DEFAULT); - - /* - * Access dataset D in the first file under /G/D name. - */ - did = H5Dopen2(fid1, "/G/D", H5P_DEFAULT); - tid = H5Dget_type(did); - status = H5Dread(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, bm_out); - - /* - * Print out the data. - */ - for(i=0; i<NX; i++){ - for(j=0; j<NY; j++) - printf(" %d", bm_out[i][j]); - printf("\n"); - } - - /* - * Close all identifers - */ - H5Tclose(tid); - H5Dclose(did); - - /* - * Unmounting second file - */ - H5Funmount(fid1, "/G"); - - /* - * Close both files - */ - H5Fclose(fid1); - H5Fclose(fid2); - - return 0; + hid_t fid1, fid2, gid; /* Files and group identifiers */ + hid_t did, tid, sid; /* Dataset and datatype identifiers */ + + herr_t status; + hsize_t dims[] = {NX, NY}; /* Dataset dimensions */ + + int i, j; + int bm[NX][NY], bm_out[NX][NY]; /* Data buffers */ + + /* + * Initialization of buffer matrix "bm" + */ + for (i = 0; i < NX; i++) + for (j = 0; j < NY; j++) + bm[i][j] = i + j; + + /* + * Create first file and a group in it. + */ + fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + gid = H5Gcreate2(fid1, "/G", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Close group and file + */ + H5Gclose(gid); + H5Fclose(fid1); + + /* + * Create second file and dataset "D" in it. + */ + fid2 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + dims[0] = NX; + dims[1] = NY; + sid = H5Screate_simple(RANK, dims, NULL); + did = H5Dcreate2(fid2, "D", H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Write data to the dataset. + */ + status = H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, bm); + + /* + * Close all identifiers. + */ + H5Sclose(sid); + H5Dclose(did); + H5Fclose(fid2); + + /* + * Reopen both files + */ + fid1 = H5Fopen(FILE1, H5F_ACC_RDONLY, H5P_DEFAULT); + fid2 = H5Fopen(FILE2, H5F_ACC_RDONLY, H5P_DEFAULT); + + /* + * Mount second file under G in the first file. + */ + H5Fmount(fid1, "/G", fid2, H5P_DEFAULT); + + /* + * Access dataset D in the first file under /G/D name. + */ + did = H5Dopen2(fid1, "/G/D", H5P_DEFAULT); + tid = H5Dget_type(did); + status = H5Dread(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, bm_out); + + /* + * Print out the data. + */ + for (i = 0; i < NX; i++) { + for (j = 0; j < NY; j++) + printf(" %d", bm_out[i][j]); + printf("\n"); + } + + /* + * Close all identifers + */ + H5Tclose(tid); + H5Dclose(did); + + /* + * Unmounting second file + */ + H5Funmount(fid1, "/G"); + + /* + * Close both files + */ + H5Fclose(fid1); + H5Fclose(fid2); + + return 0; } - - - diff --git a/examples/h5_rdwt.c b/examples/h5_rdwt.c index 6cd7f0f..ba5ddae 100644 --- a/examples/h5_rdwt.c +++ b/examples/h5_rdwt.c @@ -6,12 +6,12 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/* +/* * This example illustrates how to write and read data in an existing * dataset. It is used in the HDF5 Tutorial. */ @@ -19,33 +19,33 @@ #include "hdf5.h" #define FILE "dset.h5" -int main() { +int +main() +{ - hid_t file_id, dataset_id; /* identifiers */ - herr_t status; - int i, j, dset_data[4][6]; + hid_t file_id, dataset_id; /* identifiers */ + herr_t status; + int i, j, dset_data[4][6]; - /* Initialize the dataset. */ - for (i = 0; i < 4; i++) - for (j = 0; j < 6; j++) - dset_data[i][j] = i * 6 + j + 1; + /* Initialize the dataset. */ + for (i = 0; i < 4; i++) + for (j = 0; j < 6; j++) + dset_data[i][j] = i * 6 + j + 1; - /* Open an existing file. */ - file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); + /* Open an existing file. */ + file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); - /* Open an existing dataset. */ - dataset_id = H5Dopen2(file_id, "/dset", H5P_DEFAULT); + /* Open an existing dataset. */ + dataset_id = H5Dopen2(file_id, "/dset", H5P_DEFAULT); - /* Write the dataset. */ - status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, - dset_data); + /* Write the dataset. */ + status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_data); - status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, - dset_data); + status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_data); - /* Close the dataset. */ - status = H5Dclose(dataset_id); + /* Close the dataset. */ + status = H5Dclose(dataset_id); - /* Close the file. */ - status = H5Fclose(file_id); + /* Close the file. */ + status = H5Fclose(file_id); } diff --git a/examples/h5_read.c b/examples/h5_read.c index 7fd8ad4..afd3b14 100644 --- a/examples/h5_read.c +++ b/examples/h5_read.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -20,71 +20,73 @@ #include "hdf5.h" -#define H5FILE_NAME "SDS.h5" +#define H5FILE_NAME "SDS.h5" #define DATASETNAME "IntArray" -#define NX_SUB 3 /* hyperslab dimensions */ -#define NY_SUB 4 -#define NX 7 /* output buffer dimensions */ -#define NY 7 -#define NZ 3 -#define RANK 2 -#define RANK_OUT 3 +#define NX_SUB 3 /* hyperslab dimensions */ +#define NY_SUB 4 +#define NX 7 /* output buffer dimensions */ +#define NY 7 +#define NZ 3 +#define RANK 2 +#define RANK_OUT 3 int -main (void) +main(void) { - hid_t file, dataset; /* handles */ + hid_t file, dataset; /* handles */ hid_t datatype, dataspace; hid_t memspace; - H5T_class_t t_class; /* data type class */ - H5T_order_t order; /* data order */ - size_t size; /* - * size of the data element - * stored in file - */ - hsize_t dimsm[3]; /* memory space dimensions */ - hsize_t dims_out[2]; /* dataset dimensions */ - herr_t status; - - int data_out[NX][NY][NZ ]; /* output buffer */ - - hsize_t count[2]; /* size of the hyperslab in the file */ - hsize_t offset[2]; /* hyperslab offset in the file */ - hsize_t count_out[3]; /* size of the hyperslab in memory */ - hsize_t offset_out[3]; /* hyperslab offset in memory */ - int i, j, k, status_n, rank; + H5T_class_t t_class; /* data type class */ + H5T_order_t order; /* data order */ + size_t size; /* + * size of the data element + * stored in file + */ + hsize_t dimsm[3]; /* memory space dimensions */ + hsize_t dims_out[2]; /* dataset dimensions */ + herr_t status; + + int data_out[NX][NY][NZ]; /* output buffer */ + + hsize_t count[2]; /* size of the hyperslab in the file */ + hsize_t offset[2]; /* hyperslab offset in the file */ + hsize_t count_out[3]; /* size of the hyperslab in memory */ + hsize_t offset_out[3]; /* hyperslab offset in memory */ + int i, j, k, status_n, rank; for (j = 0; j < NX; j++) { - for (i = 0; i < NY; i++) { - for (k = 0; k < NZ ; k++) - data_out[j][i][k] = 0; - } + for (i = 0; i < NY; i++) { + for (k = 0; k < NZ; k++) + data_out[j][i][k] = 0; + } } /* * Open the file and the dataset. */ - file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT); + file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT); dataset = H5Dopen2(file, DATASETNAME, H5P_DEFAULT); /* * Get datatype and dataspace handles and then query * dataset class, order, size, rank and dimensions. */ - datatype = H5Dget_type(dataset); /* datatype handle */ - t_class = H5Tget_class(datatype); - if (t_class == H5T_INTEGER) printf("Data set has INTEGER type \n"); - order = H5Tget_order(datatype); - if (order == H5T_ORDER_LE) printf("Little endian order \n"); - - size = H5Tget_size(datatype); + datatype = H5Dget_type(dataset); /* datatype handle */ + t_class = H5Tget_class(datatype); + if (t_class == H5T_INTEGER) + printf("Data set has INTEGER type \n"); + order = H5Tget_order(datatype); + if (order == H5T_ORDER_LE) + printf("Little endian order \n"); + + size = H5Tget_size(datatype); printf(" Data size is %d \n", (int)size); - dataspace = H5Dget_space(dataset); /* dataspace handle */ + dataspace = H5Dget_space(dataset); /* dataspace handle */ rank = H5Sget_simple_extent_ndims(dataspace); status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL); - printf("rank %d, dimensions %lu x %lu \n", rank, - (unsigned long)(dims_out[0]), (unsigned long)(dims_out[1])); + printf("rank %d, dimensions %lu x %lu \n", rank, (unsigned long)(dims_out[0]), + (unsigned long)(dims_out[1])); /* * Define hyperslab in the dataset. @@ -93,16 +95,15 @@ main (void) offset[1] = 2; count[0] = NX_SUB; count[1] = NY_SUB; - status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, - count, NULL); + status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL); /* * Define the memory dataspace. */ dimsm[0] = NX; dimsm[1] = NY; - dimsm[2] = NZ ; - memspace = H5Screate_simple(RANK_OUT,dimsm,NULL); + dimsm[2] = NZ; + memspace = H5Screate_simple(RANK_OUT, dimsm, NULL); /* * Define memory hyperslab. @@ -113,18 +114,17 @@ main (void) count_out[0] = NX_SUB; count_out[1] = NY_SUB; count_out[2] = 1; - status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, - count_out, NULL); + status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, count_out, NULL); /* * Read data from hyperslab in the file into the hyperslab in * memory and display. */ - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace, - H5P_DEFAULT, data_out); + status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace, H5P_DEFAULT, data_out); for (j = 0; j < NX; j++) { - for (i = 0; i < NY; i++) printf("%d ", data_out[j][i][0]); - printf("\n"); + for (i = 0; i < NY; i++) + printf("%d ", data_out[j][i][0]); + printf("\n"); } /* * 0 0 0 0 0 0 0 diff --git a/examples/h5_ref2reg.c b/examples/h5_ref2reg.c index d045db1..6e635b6 100644 --- a/examples/h5_ref2reg.c +++ b/examples/h5_ref2reg.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -26,33 +26,34 @@ #include "hdf5.h" -#define filename "REF_REG.h5" +#define filename "REF_REG.h5" #define dsetnamev "MATRIX" #define dsetnamer "REGION_REFERENCES" -int main(void) +int +main(void) { - hid_t file_id; /* file identifier */ - hid_t space_id; /* dataspace identifiers */ - hid_t spacer_id; - hid_t dsetv_id; /*dataset identifiers*/ - hid_t dsetr_id; - hsize_t dims[2] = {2,9}; - hsize_t dimsr[1] = {2}; - int rank = 2; - int rankr =1; - herr_t status; + hid_t file_id; /* file identifier */ + hid_t space_id; /* dataspace identifiers */ + hid_t spacer_id; + hid_t dsetv_id; /*dataset identifiers*/ + hid_t dsetr_id; + hsize_t dims[2] = {2, 9}; + hsize_t dimsr[1] = {2}; + int rank = 2; + int rankr = 1; + herr_t status; hdset_reg_ref_t ref[2]; hdset_reg_ref_t ref_out[2]; - int data[2][9] = {{1,1,2,3,3,4,5,5,6},{1,2,2,3,4,4,5,6,6}}; - int data_out[2][9] = {{0,0,0,0,0,0,0,0,0},{0,0,0,0,0,0,0,0,0}}; - hsize_t start[2]; - hsize_t count[2]; - hsize_t coord[2][3] = {{0, 0, 1}, {6, 0, 8}}; - unsigned num_points = 3; - int i, j; - size_t name_size1, name_size2; - char buf1[10], buf2[10]; + int data[2][9] = {{1, 1, 2, 3, 3, 4, 5, 5, 6}, {1, 2, 2, 3, 4, 4, 5, 6, 6}}; + int data_out[2][9] = {{0, 0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 0, 0, 0, 0, 0, 0, 0}}; + hsize_t start[2]; + hsize_t count[2]; + hsize_t coord[2][3] = {{0, 0, 1}, {6, 0, 8}}; + unsigned num_points = 3; + int i, j; + size_t name_size1, name_size2; + char buf1[10], buf2[10]; /* * Create file with default file access and file creation properties. @@ -62,24 +63,26 @@ int main(void) /* * Create dataspace for datasets. */ - space_id = H5Screate_simple(rank, dims, NULL); + space_id = H5Screate_simple(rank, dims, NULL); spacer_id = H5Screate_simple(rankr, dimsr, NULL); /* * Create integer dataset. */ - dsetv_id = H5Dcreate2(file_id, dsetnamev, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dsetv_id = + H5Dcreate2(file_id, dsetnamev, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); /* * Write data to the dataset. */ - status = H5Dwrite(dsetv_id, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT,data); + status = H5Dwrite(dsetv_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); status = H5Dclose(dsetv_id); /* * Dataset with references. */ - dsetr_id = H5Dcreate2(file_id, dsetnamer, H5T_STD_REF_DSETREG, spacer_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dsetr_id = + H5Dcreate2(file_id, dsetnamer, H5T_STD_REF_DSETREG, spacer_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); /* * Create a reference to the hyperslab. @@ -88,8 +91,8 @@ int main(void) start[1] = 3; count[0] = 2; count[1] = 3; - status = H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, NULL, count, NULL); - status = H5Rcreate(&ref[0], file_id, dsetnamev, H5R_DATASET_REGION, space_id); + status = H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, NULL, count, NULL); + status = H5Rcreate(&ref[0], file_id, dsetnamev, H5R_DATASET_REGION, space_id); /* * Create a reference to elements selection. @@ -101,7 +104,7 @@ int main(void) /* * Write dataset with the references. */ - status = H5Dwrite(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,ref); + status = H5Dwrite(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref); /* * Close all objects. @@ -114,7 +117,7 @@ int main(void) /* * Reopen the file to read selections back. */ - file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT); + file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT); /* * Reopen the dataset with object references and read references @@ -122,8 +125,7 @@ int main(void) */ dsetr_id = H5Dopen2(file_id, dsetnamer, H5P_DEFAULT); - status = H5Dread(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, - H5P_DEFAULT, ref_out); + status = H5Dread(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_out); /* * Dereference the first reference. @@ -133,26 +135,26 @@ int main(void) * Get name of the dataset the first region reference points to * using H5Rget_name */ - name_size1 = H5Rget_name(dsetr_id, H5R_DATASET_REGION, &ref_out[0], (char*)buf1, 10); - printf(" Dataset's name (returned by H5Rget_name) the reference points to is %s, name length is %d\n", buf1, (int)name_size1); + name_size1 = H5Rget_name(dsetr_id, H5R_DATASET_REGION, &ref_out[0], (char *)buf1, 10); + printf(" Dataset's name (returned by H5Rget_name) the reference points to is %s, name length is %d\n", + buf1, (int)name_size1); /* * Get name of the dataset the first region reference points to * using H5Iget_name */ - name_size2 = H5Iget_name(dsetv_id, (char*)buf2, 10); - printf(" Dataset's name (returned by H5Iget_name) the reference points to is %s, name length is %d\n", buf2, (int)name_size2); + name_size2 = H5Iget_name(dsetv_id, (char *)buf2, 10); + printf(" Dataset's name (returned by H5Iget_name) the reference points to is %s, name length is %d\n", + buf2, (int)name_size2); - space_id = H5Rget_region(dsetr_id, H5R_DATASET_REGION,&ref_out[0]); + space_id = H5Rget_region(dsetr_id, H5R_DATASET_REGION, &ref_out[0]); /* * Read and display hyperslab selection from the dataset. */ - status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id, - H5P_DEFAULT, data_out); + status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id, H5P_DEFAULT, data_out); printf("Selected hyperslab: "); - for (i = 0; i <= 1; i++) - { + for (i = 0; i <= 1; i++) { printf("\n"); for (j = 0; j <= 8; j++) printf("%d ", data_out[i][j]); @@ -176,17 +178,15 @@ int main(void) * Dereference the second reference. */ dsetv_id = H5Rdereference(dsetr_id, H5R_DATASET_REGION, &ref_out[1]); - space_id = H5Rget_region(dsetv_id, H5R_DATASET_REGION,&ref_out[1]); + space_id = H5Rget_region(dsetv_id, H5R_DATASET_REGION, &ref_out[1]); /* * Read selected data from the dataset. */ - status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id, - H5P_DEFAULT, data_out); + status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id, H5P_DEFAULT, data_out); printf("Selected points: "); - for (i = 0; i <= 1; i++) - { + for (i = 0; i <= 1; i++) { printf("\n"); for (j = 0; j <= 8; j++) printf("%d ", data_out[i][j]); @@ -203,6 +203,3 @@ int main(void) return 0; } - - - diff --git a/examples/h5_reference.c b/examples/h5_reference.c index c73ce89..72cc8a3 100644 --- a/examples/h5_reference.c +++ b/examples/h5_reference.c @@ -6,20 +6,20 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - /* - * This program illustrates how references to objects can be used. - * Program creates a dataset and a group in a file. It also creates - * second dataset, and references to the first dataset and the group - * are stored in it. - * Program reopens the file and reads dataset with the references. - * References are used to open the objects. Information about the - * objects is displayed. - */ +/* + * This program illustrates how references to objects can be used. + * Program creates a dataset and a group in a file. It also creates + * second dataset, and references to the first dataset and the group + * are stored in it. + * Program reopens the file and reads dataset with the references. + * References are used to open the objects. Information about the + * objects is displayed. + */ #include <stdlib.h> @@ -28,120 +28,119 @@ #define H5FILE_NAME "refere.h5" int -main(void) { - hid_t fid; /* File, group, datasets, datatypes */ - hid_t gid_a; /* and dataspaces identifiers */ - hid_t did_b, sid_b, tid_b; - hid_t did_r, tid_r, sid_r; - H5O_type_t obj_type; - herr_t status; - - hobj_ref_t *wbuf; /* buffer to write to disk */ - hobj_ref_t *rbuf; /* buffer to read from disk */ - - - hsize_t dim_r[1]; - hsize_t dim_b[2]; - - /* - * Create a file using default properties. - */ - fid = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Create group "A" in the file. - */ - gid_a = H5Gcreate2(fid, "A", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Create dataset "B" in the file. - */ - dim_b[0] = 2; - dim_b[1] = 6; - sid_b = H5Screate_simple(2, dim_b, NULL); - did_b = H5Dcreate2(fid, "B", H5T_NATIVE_FLOAT, sid_b, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Create dataset "R" to store references to the objects "A" and "B". - */ - dim_r[0] = 2; - sid_r = H5Screate_simple(1, dim_r, NULL); - tid_r = H5Tcopy(H5T_STD_REF_OBJ); - did_r = H5Dcreate2(fid, "R", tid_r, sid_r, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Allocate write and read buffers. - */ - wbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2); - rbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2); - - /* - * Create references to the group "A" and dataset "B" - * and store them in the wbuf. - */ - H5Rcreate(&wbuf[0], fid, "A", H5R_OBJECT, (hid_t)-1); - H5Rcreate(&wbuf[1], fid, "B", H5R_OBJECT, (hid_t)-1); - - /* - * Write dataset R using default transfer properties. - */ - status = H5Dwrite(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf); - - /* - * Close all objects. - */ - H5Gclose(gid_a); - - H5Sclose(sid_b); - H5Dclose(did_b); - - H5Tclose(tid_r); - H5Sclose(sid_r); - H5Dclose(did_r); - - H5Fclose(fid); - - /* - * Reopen the file. - */ - fid = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT); - - /* - * Open and read dataset "R". - */ - did_r = H5Dopen2(fid, "R", H5P_DEFAULT); - status = H5Dread(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, rbuf); - - /* - * Find the type of referenced objects. - */ +main(void) +{ + hid_t fid; /* File, group, datasets, datatypes */ + hid_t gid_a; /* and dataspaces identifiers */ + hid_t did_b, sid_b, tid_b; + hid_t did_r, tid_r, sid_r; + H5O_type_t obj_type; + herr_t status; + + hobj_ref_t *wbuf; /* buffer to write to disk */ + hobj_ref_t *rbuf; /* buffer to read from disk */ + + hsize_t dim_r[1]; + hsize_t dim_b[2]; + + /* + * Create a file using default properties. + */ + fid = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Create group "A" in the file. + */ + gid_a = H5Gcreate2(fid, "A", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Create dataset "B" in the file. + */ + dim_b[0] = 2; + dim_b[1] = 6; + sid_b = H5Screate_simple(2, dim_b, NULL); + did_b = H5Dcreate2(fid, "B", H5T_NATIVE_FLOAT, sid_b, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Create dataset "R" to store references to the objects "A" and "B". + */ + dim_r[0] = 2; + sid_r = H5Screate_simple(1, dim_r, NULL); + tid_r = H5Tcopy(H5T_STD_REF_OBJ); + did_r = H5Dcreate2(fid, "R", tid_r, sid_r, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Allocate write and read buffers. + */ + wbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2); + rbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2); + + /* + * Create references to the group "A" and dataset "B" + * and store them in the wbuf. + */ + H5Rcreate(&wbuf[0], fid, "A", H5R_OBJECT, (hid_t)-1); + H5Rcreate(&wbuf[1], fid, "B", H5R_OBJECT, (hid_t)-1); + + /* + * Write dataset R using default transfer properties. + */ + status = H5Dwrite(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf); + + /* + * Close all objects. + */ + H5Gclose(gid_a); + + H5Sclose(sid_b); + H5Dclose(did_b); + + H5Tclose(tid_r); + H5Sclose(sid_r); + H5Dclose(did_r); + + H5Fclose(fid); + + /* + * Reopen the file. + */ + fid = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT); + + /* + * Open and read dataset "R". + */ + did_r = H5Dopen2(fid, "R", H5P_DEFAULT); + status = H5Dread(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, rbuf); + + /* + * Find the type of referenced objects. + */ status = H5Rget_obj_type2(did_r, H5R_OBJECT, &rbuf[0], &obj_type); - if(obj_type == H5O_TYPE_GROUP) + if (obj_type == H5O_TYPE_GROUP) printf("First dereferenced object is a group. \n"); status = H5Rget_obj_type2(did_r, H5R_OBJECT, &rbuf[1], &obj_type); - if(obj_type == H5O_TYPE_DATASET) + if (obj_type == H5O_TYPE_DATASET) printf("Second dereferenced object is a dataset. \n"); - /* - * Get datatype of the dataset "B" - */ - did_b = H5Rdereference(did_r, H5R_OBJECT, &rbuf[1]); - tid_b = H5Dget_type(did_b); - if(H5Tequal(tid_b, H5T_NATIVE_FLOAT)) - printf("Datatype of the dataset is H5T_NATIVE_FLOAT.\n"); - printf("\n"); - - /* - * Close all objects and free memory buffers. - */ - H5Dclose(did_r); - H5Dclose(did_b); - H5Tclose(tid_b); - H5Fclose(fid); - free(rbuf); - free(wbuf); - - return 0; - } - + /* + * Get datatype of the dataset "B" + */ + did_b = H5Rdereference(did_r, H5R_OBJECT, &rbuf[1]); + tid_b = H5Dget_type(did_b); + if (H5Tequal(tid_b, H5T_NATIVE_FLOAT)) + printf("Datatype of the dataset is H5T_NATIVE_FLOAT.\n"); + printf("\n"); + + /* + * Close all objects and free memory buffers. + */ + H5Dclose(did_r); + H5Dclose(did_b); + H5Tclose(tid_b); + H5Fclose(fid); + free(rbuf); + free(wbuf); + + return 0; +} diff --git a/examples/h5_select.c b/examples/h5_select.c index bbc877c..e8aeb50 100644 --- a/examples/h5_select.c +++ b/examples/h5_select.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -26,78 +26,80 @@ #define H5FILE_NAME "Select.h5" -#define MSPACE1_RANK 1 /* Rank of the first dataset in memory */ -#define MSPACE1_DIM 50 /* Dataset size in memory */ +#define MSPACE1_RANK 1 /* Rank of the first dataset in memory */ +#define MSPACE1_DIM 50 /* Dataset size in memory */ -#define MSPACE2_RANK 1 /* Rank of the second dataset in memory */ -#define MSPACE2_DIM 4 /* Dataset size in memory */ +#define MSPACE2_RANK 1 /* Rank of the second dataset in memory */ +#define MSPACE2_DIM 4 /* Dataset size in memory */ -#define FSPACE_RANK 2 /* Dataset rank as it is stored in the file */ -#define FSPACE_DIM1 8 /* Dimension sizes of the dataset as it is - stored in the file */ -#define FSPACE_DIM2 12 +#define FSPACE_RANK 2 /* Dataset rank as it is stored in the file */ +#define FSPACE_DIM1 \ + 8 /* Dimension sizes of the dataset as it is \ + stored in the file */ +#define FSPACE_DIM2 12 - /* We will read dataset back from the file - to the dataset in memory with these - dataspace parameters. */ -#define MSPACE_RANK 2 -#define MSPACE_DIM1 8 -#define MSPACE_DIM2 9 +/* We will read dataset back from the file + to the dataset in memory with these + dataspace parameters. */ +#define MSPACE_RANK 2 +#define MSPACE_DIM1 8 +#define MSPACE_DIM2 9 -#define NPOINTS 4 /* Number of points that will be selected - and overwritten */ +#define NPOINTS \ + 4 /* Number of points that will be selected \ + and overwritten */ int -main (void) +main(void) { - hid_t file, dataset; /* File and dataset identifiers */ - hid_t mid1, mid2, mid, fid; /* Dataspace identifiers */ - hid_t plist; /* Dataset property list identifier */ + hid_t file, dataset; /* File and dataset identifiers */ + hid_t mid1, mid2, mid, fid; /* Dataspace identifiers */ + hid_t plist; /* Dataset property list identifier */ - hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset + hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset (in memory) */ - hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset + hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset (in memory */ - hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2}; - /* Dimension sizes of the dataset (on disk) */ - hsize_t mdim[] = {MSPACE_DIM1, MSPACE_DIM2}; /* Dimension sizes of the - dataset in memory when we - read selection from the - dataset on the disk */ - - hsize_t start[2]; /* Start of hyperslab */ - hsize_t stride[2]; /* Stride of hyperslab */ - hsize_t count[2]; /* Block count */ - hsize_t block[2]; /* Block sizes */ - - hsize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points - from the file dataspace */ - herr_t ret; - unsigned i,j; - int fillvalue = 0; /* Fill value for the dataset */ - - int matrix_out[MSPACE_DIM1][MSPACE_DIM2]; /* Buffer to read from the - dataset */ - int vector[MSPACE1_DIM]; - int values[] = {53, 59, 61, 67}; /* New values to be written */ - - /* - * Buffers' initialization. - */ - vector[0] = vector[MSPACE1_DIM - 1] = -1; - for(i = 1; i < MSPACE1_DIM - 1; i++) - vector[i] = i; - - /* - * Create a file. - */ - file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Create property list for a dataset and set up fill values. - */ - plist = H5Pcreate(H5P_DATASET_CREATE); - ret = H5Pset_fill_value(plist, H5T_NATIVE_INT, &fillvalue); + hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2}; + /* Dimension sizes of the dataset (on disk) */ + hsize_t mdim[] = {MSPACE_DIM1, MSPACE_DIM2}; /* Dimension sizes of the + dataset in memory when we + read selection from the + dataset on the disk */ + + hsize_t start[2]; /* Start of hyperslab */ + hsize_t stride[2]; /* Stride of hyperslab */ + hsize_t count[2]; /* Block count */ + hsize_t block[2]; /* Block sizes */ + + hsize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points + from the file dataspace */ + herr_t ret; + unsigned i, j; + int fillvalue = 0; /* Fill value for the dataset */ + + int matrix_out[MSPACE_DIM1][MSPACE_DIM2]; /* Buffer to read from the + dataset */ + int vector[MSPACE1_DIM]; + int values[] = {53, 59, 61, 67}; /* New values to be written */ + + /* + * Buffers' initialization. + */ + vector[0] = vector[MSPACE1_DIM - 1] = -1; + for (i = 1; i < MSPACE1_DIM - 1; i++) + vector[i] = i; + + /* + * Create a file. + */ + file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + + /* + * Create property list for a dataset and set up fill values. + */ + plist = H5Pcreate(H5P_DATASET_CREATE); + ret = H5Pset_fill_value(plist, H5T_NATIVE_INT, &fillvalue); /* * Create dataspace for the dataset in the file. @@ -114,11 +116,15 @@ main (void) * Select hyperslab for the dataset in the file, using 3x2 blocks, * (4,3) stride and (2,4) count starting at the position (0,1). */ - start[0] = 0; start[1] = 1; - stride[0] = 4; stride[1] = 3; - count[0] = 2; count[1] = 4; - block[0] = 3; block[1] = 2; - ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block); + start[0] = 0; + start[1] = 1; + stride[0] = 4; + stride[1] = 3; + count[0] = 2; + count[1] = 4; + block[0] = 3; + block[1] = 2; + ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block); /* * Create dataspace for the first dataset. @@ -134,7 +140,7 @@ main (void) stride[0] = 1; count[0] = 48; block[0] = 1; - ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block); + ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block); /* * Write selection from the vector buffer to the dataset in the file. @@ -149,7 +155,7 @@ main (void) * 0 41 42 0 43 44 0 45 46 0 47 48 * 0 0 0 0 0 0 0 0 0 0 0 0 */ - ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector); + ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector); /* * Reset the selection for the file dataspace fid. @@ -164,10 +170,14 @@ main (void) /* * Select sequence of NPOINTS points in the file dataspace. */ - coord[0][0] = 0; coord[0][1] = 0; - coord[1][0] = 3; coord[1][1] = 3; - coord[2][0] = 3; coord[2][1] = 5; - coord[3][0] = 5; coord[3][1] = 6; + coord[0][0] = 0; + coord[0][1] = 0; + coord[1][0] = 3; + coord[1][1] = 3; + coord[2][0] = 3; + coord[2][1] = 5; + coord[3][0] = 5; + coord[3][1] = 6; ret = H5Sselect_elements(fid, H5S_SELECT_SET, NPOINTS, (const hsize_t *)coord); @@ -229,11 +239,15 @@ main (void) * 0 59 0 61 * */ - start[0] = 1; start[1] = 2; - block[0] = 1; block[1] = 1; - stride[0] = 1; stride[1] = 1; - count[0] = 3; count[1] = 4; - ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block); + start[0] = 1; + start[1] = 2; + block[0] = 1; + block[1] = 1; + stride[0] = 1; + stride[1] = 1; + count[0] = 3; + count[1] = 4; + ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block); /* * Add second selected hyperslab to the selection. @@ -248,11 +262,15 @@ main (void) * 19 20 * 0 61 */ - start[0] = 2; start[1] = 4; - block[0] = 1; block[1] = 1; - stride[0] = 1; stride[1] = 1; - count[0] = 6; count[1] = 5; - ret = H5Sselect_hyperslab(fid, H5S_SELECT_OR, start, stride, count, block); + start[0] = 2; + start[1] = 4; + block[0] = 1; + block[1] = 1; + stride[0] = 1; + stride[1] = 1; + count[0] = 6; + count[1] = 5; + ret = H5Sselect_hyperslab(fid, H5S_SELECT_OR, start, stride, count, block); /* * Create memory dataspace. @@ -263,30 +281,37 @@ main (void) * Select two hyperslabs in memory. Hyperslabs has the same * size and shape as the selected hyperslabs for the file dataspace. */ - start[0] = 0; start[1] = 0; - block[0] = 1; block[1] = 1; - stride[0] = 1; stride[1] = 1; - count[0] = 3; count[1] = 4; - ret = H5Sselect_hyperslab(mid, H5S_SELECT_SET, start, stride, count, block); - - start[0] = 1; start[1] = 2; - block[0] = 1; block[1] = 1; - stride[0] = 1; stride[1] = 1; - count[0] = 6; count[1] = 5; - ret = H5Sselect_hyperslab(mid, H5S_SELECT_OR, start, stride, count, block); + start[0] = 0; + start[1] = 0; + block[0] = 1; + block[1] = 1; + stride[0] = 1; + stride[1] = 1; + count[0] = 3; + count[1] = 4; + ret = H5Sselect_hyperslab(mid, H5S_SELECT_SET, start, stride, count, block); + + start[0] = 1; + start[1] = 2; + block[0] = 1; + block[1] = 1; + stride[0] = 1; + stride[1] = 1; + count[0] = 6; + count[1] = 5; + ret = H5Sselect_hyperslab(mid, H5S_SELECT_OR, start, stride, count, block); /* * Initialize data buffer. */ for (i = 0; i < MSPACE_DIM1; i++) { - for (j = 0; j < MSPACE_DIM2; j++) + for (j = 0; j < MSPACE_DIM2; j++) matrix_out[i][j] = 0; } /* * Read data back to the buffer matrix_out. */ - ret = H5Dread(dataset, H5T_NATIVE_INT, mid, fid, - H5P_DEFAULT, matrix_out); + ret = H5Dread(dataset, H5T_NATIVE_INT, mid, fid, H5P_DEFAULT, matrix_out); /* * Display the result. Memory dataset is: @@ -300,8 +325,8 @@ main (void) * 0 0 0 0 0 0 0 0 0 * 0 0 0 0 0 0 0 0 0 */ - for(i = 0; i < MSPACE_DIM1; i++) { - for(j = 0; j < MSPACE_DIM2; j++) + for (i = 0; i < MSPACE_DIM1; i++) { + for (j = 0; j < MSPACE_DIM2; j++) printf("%3d ", matrix_out[i][j]); printf("\n"); } @@ -329,4 +354,3 @@ main (void) return 0; } - diff --git a/examples/h5_shared_mesg.c b/examples/h5_shared_mesg.c index 4e1f92a..0f623b9 100644 --- a/examples/h5_shared_mesg.c +++ b/examples/h5_shared_mesg.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -27,29 +27,13 @@ #include "hdf5.h" #define NUM_DATASETS 40 -const char* DSETNAME[] = { - "dataset0", "dataset1", - "dataset2", "dataset3", - "dataset4", "dataset5", - "dataset6", "dataset7", - "dataset8", "dataset9", - "dataset10", "dataset11", - "dataset12", "dataset13", - "dataset14", "dataset15", - "dataset16", "dataset17", - "dataset18", "dataset19", - "dataset20", "dataset21", - "dataset22", "dataset23", - "dataset24", "dataset25", - "dataset26", "dataset27", - "dataset28", "dataset29", - "dataset30", "dataset31", - "dataset32", "dataset33", - "dataset34", "dataset35", - "dataset36", "dataset37", - "dataset38", "dataset39", - NULL -}; +const char *DSETNAME[] = {"dataset0", "dataset1", "dataset2", "dataset3", "dataset4", "dataset5", + "dataset6", "dataset7", "dataset8", "dataset9", "dataset10", "dataset11", + "dataset12", "dataset13", "dataset14", "dataset15", "dataset16", "dataset17", + "dataset18", "dataset19", "dataset20", "dataset21", "dataset22", "dataset23", + "dataset24", "dataset25", "dataset26", "dataset27", "dataset28", "dataset29", + "dataset30", "dataset31", "dataset32", "dataset33", "dataset34", "dataset35", + "dataset36", "dataset37", "dataset38", "dataset39", NULL}; herr_t create_standard_file(const char *filename, hid_t fcpl); @@ -61,21 +45,24 @@ herr_t create_standard_file(const char *filename, hid_t fcpl); * *------------------------------------------------------------------------- */ -int main(void) +int +main(void) { - hid_t fcpl_id; + hid_t fcpl_id; herr_t ret; /* Create a file creation property list */ fcpl_id = H5Pcreate(H5P_FILE_CREATE); - if(fcpl_id < 0) goto error; + if (fcpl_id < 0) + goto error; /* The file creation property list is the default list right now. * Create a file using it (this is the same as creating a file with * H5P_DEFAULT). Implicit shared messages will be disabled. */ ret = create_standard_file("default_file.h5", fcpl_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* There are five kinds of messages that can be shared: datatypes, * dataspaces, attributes, fill values, and filter pipelines. @@ -86,7 +73,8 @@ int main(void) */ /* To begin with, use only one index. */ ret = H5Pset_shared_mesg_nindexes(fcpl_id, 1); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* Each index has a "minimum message size" for a message of that * type to be shared. Since sharing a message creates some overhead, @@ -111,7 +99,8 @@ int main(void) * shared in this single index. */ ret = H5Pset_shared_mesg_index(fcpl_id, 0, H5O_SHMESG_ALL_FLAG, 40); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* The other property that can be set for shared messages is the * list/B-tree cutoff for the indexes. @@ -128,7 +117,8 @@ int main(void) * second the minimum B-tree size. */ ret = H5Pset_shared_mesg_phase_change(fcpl_id, 30, 20); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* Now create a file with this property list. After the FCPL is used, * everything is automatic; messages will be shared and this will be @@ -137,7 +127,8 @@ int main(void) * written later. */ ret = create_standard_file("one_index_file.h5", fcpl_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* Now try some variations on this. The FCPL hasn't been closed, so * we don't need to re-create it. @@ -147,36 +138,42 @@ int main(void) * overhead). */ ret = H5Pset_shared_mesg_index(fcpl_id, 0, H5O_SHMESG_ALL_FLAG, 1000); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = create_standard_file("only_huge_mesgs_file.h5", fcpl_id); - if(ret < 0) goto error; - + if (ret < 0) + goto error; /* Or, suppose we only wanted to shared dataspaces and * attributes (which might make sense if we were going to use committed * datatypes). We could change the flags on the index: */ ret = H5Pset_shared_mesg_index(fcpl_id, 0, H5O_SHMESG_SDSPACE_FLAG | H5O_SHMESG_ATTR_FLAG, 40); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = create_standard_file("only_dspaces_and_attrs_file.h5", fcpl_id); - if(ret < 0) goto error; - + if (ret < 0) + goto error; /* We could create a second index and put attributes in it to separate them * from datatypes and dataspaces (and then run some performance metrics to * see whether this improved caching performance). */ ret = H5Pset_shared_mesg_nindexes(fcpl_id, 2); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Pset_shared_mesg_index(fcpl_id, 0, H5O_SHMESG_DTYPE_FLAG | H5O_SHMESG_SDSPACE_FLAG, 40); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Pset_shared_mesg_index(fcpl_id, 1, H5O_SHMESG_ATTR_FLAG, 40); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = create_standard_file("separate_indexes_file.h5", fcpl_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* We can try twiddling the "phase change" values and see what it does to * the file size. Since there's only a few different messages (two @@ -184,25 +181,30 @@ int main(void) * save some space. */ ret = H5Pset_shared_mesg_nindexes(fcpl_id, 1); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Pset_shared_mesg_index(fcpl_id, 0, H5O_SHMESG_ALL_FLAG, 40); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Pset_shared_mesg_phase_change(fcpl_id, 5, 0); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = create_standard_file("small_lists_file.h5", fcpl_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* Or we could create indexes that are never lists, but are created as * B-trees. We do this by setting the "maximum list size" to zero. */ ret = H5Pset_shared_mesg_phase_change(fcpl_id, 0, 0); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = create_standard_file("btrees_file.h5", fcpl_id); - if(ret < 0) goto error; - + if (ret < 0) + goto error; /* Obviously there are a lot more permutations of these options possible. * Performance will often be a tradeoff of speed for space, but will @@ -212,10 +214,10 @@ int main(void) * Please let The HDF Group (help@hdfgroup.org) know what you find! */ - /* Close the property list */ ret = H5Pclose(fcpl_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; return 0; error: @@ -238,21 +240,22 @@ error: herr_t create_standard_file(const char *filename, hid_t fcpl_id) { - hid_t file_id=-1; - hid_t type_id=-1, temp_type_id=-1; - hsize_t dims[] = {10, 9, 8, 7, 6, 5, 4, 3, 2, 1}; - hid_t space_id=-1; - hid_t attr_type_id = -1; - hid_t attr_space_id = -1; - int attr_data[] = {1,2,3,4,5,6,7,8,9,0}; - hid_t dset_id=-1; - hid_t attr_id=-1; - int x; - herr_t ret; + hid_t file_id = -1; + hid_t type_id = -1, temp_type_id = -1; + hsize_t dims[] = {10, 9, 8, 7, 6, 5, 4, 3, 2, 1}; + hid_t space_id = -1; + hid_t attr_type_id = -1; + hid_t attr_space_id = -1; + int attr_data[] = {1, 2, 3, 4, 5, 6, 7, 8, 9, 0}; + hid_t dset_id = -1; + hid_t attr_id = -1; + int x; + herr_t ret; /* Create the file */ file_id = H5Fcreate(filename, H5F_ACC_TRUNC, fcpl_id, H5P_DEFAULT); - if(file_id < 0) goto error; + if (file_id < 0) + goto error; /* Create the datatype we'll be using. Generally, sharing messages * is most useful when the message is complex and takes more space on @@ -260,66 +263,80 @@ create_standard_file(const char *filename, hid_t fcpl_id) * However, any type can be shared. */ temp_type_id = H5Tarray_create2(H5T_NATIVE_INT, 2, dims); - if(temp_type_id < 0) goto error; - type_id = H5Tarray_create2(temp_type_id, 2, dims); - if(type_id < 0) goto error; + if (temp_type_id < 0) + goto error; + type_id = H5Tarray_create2(temp_type_id, 2, dims); + if (type_id < 0) + goto error; ret = H5Tclose(temp_type_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; /* Create the dataspace we'll be using. * Again, create a more complex dataspace so that more space will * be saved when we share it. */ space_id = H5Screate_simple(10, dims, dims); - if(space_id < 0) goto error; + if (space_id < 0) + goto error; /* Create a datatype and dataspace for the attributes we'll be creating. * The datatype will be a single integer, and each attribute will hold * 10 integers. */ attr_type_id = H5Tcopy(H5T_NATIVE_INT); - if(attr_type_id < 0) goto error; + if (attr_type_id < 0) + goto error; attr_space_id = H5Screate_simple(1, dims, dims); - if(attr_space_id < 0) goto error; - + if (attr_space_id < 0) + goto error; /* Begin using the messages many times. Do this by creating datasets * that use this datatype, dataspace, and have this attribute. */ - for(x = 0; x < NUM_DATASETS; ++x) { - /* Create a dataset */ - dset_id = H5Dcreate2(file_id, DSETNAME[x], type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - if(dset_id < 0) goto error; - - /* Create an attribute on the dataset */ - attr_id = H5Acreate2(dset_id, "attr_name", attr_type_id, attr_space_id, H5P_DEFAULT, H5P_DEFAULT); - if(attr_id < 0) goto error; - - /* Write data to the attribute */ - ret = H5Awrite(attr_id, H5T_NATIVE_INT, attr_data); - if(ret < 0) goto error; - - ret = H5Aclose(attr_id); - if(ret < 0) goto error; - ret = H5Dclose(dset_id); - if(ret < 0) goto error; + for (x = 0; x < NUM_DATASETS; ++x) { + /* Create a dataset */ + dset_id = H5Dcreate2(file_id, DSETNAME[x], type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (dset_id < 0) + goto error; + + /* Create an attribute on the dataset */ + attr_id = H5Acreate2(dset_id, "attr_name", attr_type_id, attr_space_id, H5P_DEFAULT, H5P_DEFAULT); + if (attr_id < 0) + goto error; + + /* Write data to the attribute */ + ret = H5Awrite(attr_id, H5T_NATIVE_INT, attr_data); + if (ret < 0) + goto error; + + ret = H5Aclose(attr_id); + if (ret < 0) + goto error; + ret = H5Dclose(dset_id); + if (ret < 0) + goto error; } /* Close all open IDs */ ret = H5Tclose(attr_type_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Sclose(attr_space_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Tclose(type_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Sclose(space_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; ret = H5Fclose(file_id); - if(ret < 0) goto error; + if (ret < 0) + goto error; return 0; error: return -1; } - diff --git a/examples/h5_subset.c b/examples/h5_subset.c index 904d3f8..3580046 100644 --- a/examples/h5_subset.c +++ b/examples/h5_subset.c @@ -6,102 +6,97 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/* - * This example illustrates how to read/write a subset of data (a slab) +/* + * This example illustrates how to read/write a subset of data (a slab) * from/to a dataset in an HDF5 file. It is used in the HDF5 Tutorial. */ - + #include "hdf5.h" #define FILE "subset.h5" -#define DATASETNAME "IntArray" -#define RANK 2 - -#define DIM0_SUB 3 /* subset dimensions */ -#define DIM1_SUB 4 +#define DATASETNAME "IntArray" +#define RANK 2 +#define DIM0_SUB 3 /* subset dimensions */ +#define DIM1_SUB 4 -#define DIM0 8 /* size of dataset */ -#define DIM1 10 +#define DIM0 8 /* size of dataset */ +#define DIM1 10 int -main (void) +main(void) { - hsize_t dims[2], dimsm[2]; - int data[DIM0][DIM1]; /* data to write */ - int sdata[DIM0_SUB][DIM1_SUB]; /* subset to write */ - int rdata[DIM0][DIM1]; /* buffer for read */ - - hid_t file_id, dataset_id; /* handles */ - hid_t dataspace_id, memspace_id; - - herr_t status; - - hsize_t count[2]; /* size of subset in the file */ - hsize_t offset[2]; /* subset offset in the file */ - hsize_t stride[2]; - hsize_t block[2]; - int i, j; - - + hsize_t dims[2], dimsm[2]; + int data[DIM0][DIM1]; /* data to write */ + int sdata[DIM0_SUB][DIM1_SUB]; /* subset to write */ + int rdata[DIM0][DIM1]; /* buffer for read */ + + hid_t file_id, dataset_id; /* handles */ + hid_t dataspace_id, memspace_id; + + herr_t status; + + hsize_t count[2]; /* size of subset in the file */ + hsize_t offset[2]; /* subset offset in the file */ + hsize_t stride[2]; + hsize_t block[2]; + int i, j; + /***************************************************************** * Create a new file with default creation and access properties.* * Then create a dataset and write data to it and close the file * * and dataset. * *****************************************************************/ - file_id = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - dims[0] = DIM0; - dims[1] = DIM1; - dataspace_id = H5Screate_simple (RANK, dims, NULL); + file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - dataset_id = H5Dcreate2 (file_id, DATASETNAME, H5T_STD_I32BE, dataspace_id, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dims[0] = DIM0; + dims[1] = DIM1; + dataspace_id = H5Screate_simple(RANK, dims, NULL); + dataset_id = + H5Dcreate2(file_id, DATASETNAME, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); for (j = 0; j < DIM0; j++) { - for (i = 0; i < DIM1; i++) - if (i< (DIM1/2)) - data[j][i] = 1; + for (i = 0; i < DIM1; i++) + if (i < (DIM1 / 2)) + data[j][i] = 1; else - data[j][i] = 2; - } + data[j][i] = 2; + } - status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, data); + status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); - printf ("\nData Written to File:\n"); - for (i = 0; i<DIM0; i++){ - for (j = 0; j<DIM1; j++) - printf (" %i", data[i][j]); - printf ("\n"); + printf("\nData Written to File:\n"); + for (i = 0; i < DIM0; i++) { + for (j = 0; j < DIM1; j++) + printf(" %i", data[i][j]); + printf("\n"); } - status = H5Sclose (dataspace_id); - status = H5Dclose (dataset_id); - status = H5Fclose (file_id); - + status = H5Sclose(dataspace_id); + status = H5Dclose(dataset_id); + status = H5Fclose(file_id); /***************************************************** * Reopen the file and dataset and write a subset of * - * values to the dataset. + * values to the dataset. *****************************************************/ - file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT); - dataset_id = H5Dopen2 (file_id, DATASETNAME, H5P_DEFAULT); + file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT); + dataset_id = H5Dopen2(file_id, DATASETNAME, H5P_DEFAULT); /* Specify size and shape of subset to write. */ offset[0] = 1; offset[1] = 2; - count[0] = DIM0_SUB; - count[1] = DIM1_SUB; + count[0] = DIM0_SUB; + count[1] = DIM1_SUB; stride[0] = 1; stride[1] = 1; @@ -109,43 +104,39 @@ main (void) block[0] = 1; block[1] = 1; - /* Create memory space with size of subset. Get file dataspace + /* Create memory space with size of subset. Get file dataspace and select subset from file dataspace. */ - dimsm[0] = DIM0_SUB; - dimsm[1] = DIM1_SUB; - memspace_id = H5Screate_simple (RANK, dimsm, NULL); + dimsm[0] = DIM0_SUB; + dimsm[1] = DIM1_SUB; + memspace_id = H5Screate_simple(RANK, dimsm, NULL); - dataspace_id = H5Dget_space (dataset_id); - status = H5Sselect_hyperslab (dataspace_id, H5S_SELECT_SET, offset, - stride, count, block); + dataspace_id = H5Dget_space(dataset_id); + status = H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, offset, stride, count, block); - /* Write a subset of data to the dataset, then read the + /* Write a subset of data to the dataset, then read the entire dataset back from the file. */ - printf ("\nWrite subset to file specifying:\n"); - printf (" offset=1x2 stride=1x1 count=3x4 block=1x1\n"); + printf("\nWrite subset to file specifying:\n"); + printf(" offset=1x2 stride=1x1 count=3x4 block=1x1\n"); for (j = 0; j < DIM0_SUB; j++) { - for (i = 0; i < DIM1_SUB; i++) - sdata[j][i] = 5; - } - - status = H5Dwrite (dataset_id, H5T_NATIVE_INT, memspace_id, - dataspace_id, H5P_DEFAULT, sdata); - - status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, rdata); - - printf ("\nData in File after Subset is Written:\n"); - for (i = 0; i<DIM0; i++){ - for (j = 0; j<DIM1; j++) - printf (" %i", rdata[i][j]); - printf ("\n"); + for (i = 0; i < DIM1_SUB; i++) + sdata[j][i] = 5; + } + + status = H5Dwrite(dataset_id, H5T_NATIVE_INT, memspace_id, dataspace_id, H5P_DEFAULT, sdata); + + status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata); + + printf("\nData in File after Subset is Written:\n"); + for (i = 0; i < DIM0; i++) { + for (j = 0; j < DIM1; j++) + printf(" %i", rdata[i][j]); + printf("\n"); } - status = H5Sclose (memspace_id); - status = H5Sclose (dataspace_id); - status = H5Dclose (dataset_id); - status = H5Fclose (file_id); - + status = H5Sclose(memspace_id); + status = H5Sclose(dataspace_id); + status = H5Dclose(dataset_id); + status = H5Fclose(file_id); } diff --git a/examples/h5_write.c b/examples/h5_write.c index 1a7cfe7..c2bf136 100644 --- a/examples/h5_write.c +++ b/examples/h5_write.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -18,28 +18,28 @@ #include "hdf5.h" -#define H5FILE_NAME "SDS.h5" +#define H5FILE_NAME "SDS.h5" #define DATASETNAME "IntArray" -#define NX 5 /* dataset dimensions */ -#define NY 6 -#define RANK 2 +#define NX 5 /* dataset dimensions */ +#define NY 6 +#define RANK 2 int -main (void) +main(void) { - hid_t file, dataset; /* file and dataset handles */ - hid_t datatype, dataspace; /* handles */ - hsize_t dimsf[2]; /* dataset dimensions */ - herr_t status; - int data[NX][NY]; /* data to write */ - int i, j; + hid_t file, dataset; /* file and dataset handles */ + hid_t datatype, dataspace; /* handles */ + hsize_t dimsf[2]; /* dataset dimensions */ + herr_t status; + int data[NX][NY]; /* data to write */ + int i, j; /* * Data and output buffer initialization. */ - for(j = 0; j < NX; j++) - for(i = 0; i < NY; i++) - data[j][i] = i + j; + for (j = 0; j < NX; j++) + for (i = 0; i < NY; i++) + data[j][i] = i + j; /* * 0 1 2 3 4 5 * 1 2 3 4 5 6 @@ -59,8 +59,8 @@ main (void) * Describe the size of the array and create the data space for fixed * size dataset. */ - dimsf[0] = NX; - dimsf[1] = NY; + dimsf[0] = NX; + dimsf[1] = NY; dataspace = H5Screate_simple(RANK, dimsf, NULL); /* @@ -68,14 +68,13 @@ main (void) * We will store little endian INT numbers. */ datatype = H5Tcopy(H5T_NATIVE_INT); - status = H5Tset_order(datatype, H5T_ORDER_LE); + status = H5Tset_order(datatype, H5T_ORDER_LE); /* * Create a new dataset within the file using defined dataspace and * datatype and default dataset creation properties. */ - dataset = H5Dcreate2(file, DATASETNAME, datatype, dataspace, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dataset = H5Dcreate2(file, DATASETNAME, datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); /* * Write the data to the dataset using default transfer properties. @@ -92,4 +91,3 @@ main (void) return 0; } - diff --git a/examples/ph5example.c b/examples/ph5example.c index d718479..a5f3c75 100644 --- a/examples/ph5example.c +++ b/examples/ph5example.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -46,69 +46,73 @@ /* Define some handy debugging shorthands, routines, ... */ /* debugging tools */ -#define MESG(x)\ - if (verbose) printf("%s\n", x);\ - -#define MPI_BANNER(mesg)\ - {printf("--------------------------------\n");\ - printf("Proc %d: ", mpi_rank); \ - printf("*** %s\n", mesg);\ - printf("--------------------------------\n");} +#define MESG(x) \ + if (verbose) \ + printf("%s\n", x); + +#define MPI_BANNER(mesg) \ + { \ + printf("--------------------------------\n"); \ + printf("Proc %d: ", mpi_rank); \ + printf("*** %s\n", mesg); \ + printf("--------------------------------\n"); \ + } -#define SYNC(comm)\ - {MPI_BANNER("doing a SYNC"); MPI_Barrier(comm); MPI_BANNER("SYNC DONE");} +#define SYNC(comm) \ + { \ + MPI_BANNER("doing a SYNC"); \ + MPI_Barrier(comm); \ + MPI_BANNER("SYNC DONE"); \ + } /* End of Define some handy debugging shorthands, routines, ... */ /* Constants definitions */ /* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */ -#define SPACE1_DIM1 24 -#define SPACE1_DIM2 24 -#define SPACE1_RANK 2 -#define DATASETNAME1 "Data1" -#define DATASETNAME2 "Data2" -#define DATASETNAME3 "Data3" +#define SPACE1_DIM1 24 +#define SPACE1_DIM2 24 +#define SPACE1_RANK 2 +#define DATASETNAME1 "Data1" +#define DATASETNAME2 "Data2" +#define DATASETNAME3 "Data3" /* hyperslab layout styles */ -#define BYROW 1 /* divide into slabs of rows */ -#define BYCOL 2 /* divide into blocks of columns */ - -#define PARAPREFIX "HDF5_PARAPREFIX" /* file prefix environment variable name */ +#define BYROW 1 /* divide into slabs of rows */ +#define BYCOL 2 /* divide into blocks of columns */ +#define PARAPREFIX "HDF5_PARAPREFIX" /* file prefix environment variable name */ /* dataset data type. Int's can be easily octo dumped. */ typedef int DATATYPE; /* global variables */ -int nerrors = 0; /* errors count */ +int nerrors = 0; /* errors count */ #ifndef PATH_MAX -#define PATH_MAX 512 -#endif /* !PATH_MAX */ -char testfiles[2][PATH_MAX]; +#define PATH_MAX 512 +#endif /* !PATH_MAX */ +char testfiles[2][PATH_MAX]; - -int mpi_size, mpi_rank; /* mpi variables */ +int mpi_size, mpi_rank; /* mpi variables */ /* option flags */ -int verbose = 0; /* verbose, default as no. */ -int doread=1; /* read test */ -int dowrite=1; /* write test */ -int docleanup=1; /* cleanup */ +int verbose = 0; /* verbose, default as no. */ +int doread = 1; /* read test */ +int dowrite = 1; /* write test */ +int docleanup = 1; /* cleanup */ /* Prototypes */ void slab_set(hsize_t start[], hsize_t count[], hsize_t stride[], int mode); -void dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset); -void dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset); -int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original); +void dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset); +void dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset); +int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original); void phdf5writeInd(char *filename); void phdf5readInd(char *filename); void phdf5writeAll(char *filename); void phdf5readAll(char *filename); void test_split_comm_access(char filenames[][PATH_MAX]); -int parse_options(int argc, char **argv); +int parse_options(int argc, char **argv); void usage(void); -int mkfilenames(char *prefix); +int mkfilenames(char *prefix); void cleanup(void); - /* * Setup the dimensions of the hyperslab. * Two modes--by rows or by columns. @@ -117,113 +121,110 @@ void cleanup(void); void slab_set(hsize_t start[], hsize_t count[], hsize_t stride[], int mode) { - switch (mode){ - case BYROW: - /* Each process takes a slabs of rows. */ - stride[0] = 1; - stride[1] = 1; - count[0] = SPACE1_DIM1/mpi_size; - count[1] = SPACE1_DIM2; - start[0] = mpi_rank*count[0]; - start[1] = 0; - break; - case BYCOL: - /* Each process takes a block of columns. */ - stride[0] = 1; - stride[1] = 1; - count[0] = SPACE1_DIM1; - count[1] = SPACE1_DIM2/mpi_size; - start[0] = 0; - start[1] = mpi_rank*count[1]; - break; - default: - /* Unknown mode. Set it to cover the whole dataset. */ - printf("unknown slab_set mode (%d)\n", mode); - stride[0] = 1; - stride[1] = 1; - count[0] = SPACE1_DIM1; - count[1] = SPACE1_DIM2; - start[0] = 0; - start[1] = 0; - break; + switch (mode) { + case BYROW: + /* Each process takes a slabs of rows. */ + stride[0] = 1; + stride[1] = 1; + count[0] = SPACE1_DIM1 / mpi_size; + count[1] = SPACE1_DIM2; + start[0] = mpi_rank * count[0]; + start[1] = 0; + break; + case BYCOL: + /* Each process takes a block of columns. */ + stride[0] = 1; + stride[1] = 1; + count[0] = SPACE1_DIM1; + count[1] = SPACE1_DIM2 / mpi_size; + start[0] = 0; + start[1] = mpi_rank * count[1]; + break; + default: + /* Unknown mode. Set it to cover the whole dataset. */ + printf("unknown slab_set mode (%d)\n", mode); + stride[0] = 1; + stride[1] = 1; + count[0] = SPACE1_DIM1; + count[1] = SPACE1_DIM2; + start[0] = 0; + start[1] = 0; + break; } } - /* * Fill the dataset with trivial data for testing. * Assume dimension rank is 2 and data is stored contiguous. */ void -dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset) +dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset) { DATATYPE *dataptr = dataset; - hsize_t i, j; + hsize_t i, j; /* put some trivial data in the data_array */ - for (i=0; i < count[0]; i++){ - for (j=0; j < count[1]; j++){ - *dataptr++ = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1); - } + for (i = 0; i < count[0]; i++) { + for (j = 0; j < count[1]; j++) { + *dataptr++ = (i * stride[0] + start[0]) * 100 + (j * stride[1] + start[1] + 1); + } } } - /* * Print the content of the dataset. */ -void dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset) +void +dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset) { DATATYPE *dataptr = dataset; - hsize_t i, j; + hsize_t i, j; /* print the slab read */ - for (i=0; i < count[0]; i++){ - printf("Row %lu: ", (unsigned long)(i*stride[0]+start[0])); - for (j=0; j < count[1]; j++){ - printf("%03d ", *dataptr++); - } - printf("\n"); + for (i = 0; i < count[0]; i++) { + printf("Row %lu: ", (unsigned long)(i * stride[0] + start[0])); + for (j = 0; j < count[1]; j++) { + printf("%03d ", *dataptr++); + } + printf("\n"); } } - /* * Print the content of the dataset. */ -int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original) +int +dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original) { -#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */ +#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */ hsize_t i, j; - int nerr; + int nerr; /* print it if verbose */ if (verbose) - dataset_print(start, count, stride, dataset); + dataset_print(start, count, stride, dataset); nerr = 0; - for (i=0; i < count[0]; i++){ - for (j=0; j < count[1]; j++){ - if (*dataset++ != *original++){ - nerr++; - if (nerr <= MAX_ERR_REPORT){ - printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n", - (unsigned long)i, (unsigned long)j, - (unsigned long)(i*stride[0]+start[0]), (unsigned long)(j*stride[1]+start[1]), - *(dataset-1), *(original-1)); - } - } - } + for (i = 0; i < count[0]; i++) { + for (j = 0; j < count[1]; j++) { + if (*dataset++ != *original++) { + nerr++; + if (nerr <= MAX_ERR_REPORT) { + printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n", + (unsigned long)i, (unsigned long)j, (unsigned long)(i * stride[0] + start[0]), + (unsigned long)(j * stride[1] + start[1]), *(dataset - 1), *(original - 1)); + } + } + } } if (nerr > MAX_ERR_REPORT) - printf("[more errors ...]\n"); + printf("[more errors ...]\n"); if (nerr) - printf("%d errors found in dataset_vrfy\n", nerr); - return(nerr); + printf("%d errors found in dataset_vrfy\n", nerr); + return (nerr); } - /* * Example of using the parallel HDF5 library to create two datasets * in one HDF5 files with parallel MPIO access support. @@ -235,32 +236,31 @@ int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *d void phdf5writeInd(char *filename) { - hid_t fid1; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t sid1; /* Dataspace ID */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - hsize_t dims1[SPACE1_RANK] = - {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ + hid_t fid1; /* HDF5 file IDs */ + hid_t acc_tpl1; /* File access templates */ + hid_t sid1; /* Dataspace ID */ + hid_t file_dataspace; /* File dataspace ID */ + hid_t mem_dataspace; /* memory dataspace ID */ + hid_t dataset1, dataset2; /* Dataset ID */ + hsize_t dims1[SPACE1_RANK] = {SPACE1_DIM1, SPACE1_DIM2}; /* dataspace dim sizes */ + DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - herr_t ret; /* Generic return value */ + herr_t ret; /* Generic return value */ MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; if (verbose) - printf("Independent write test on file %s\n", filename); + printf("Independent write test on file %s\n", filename); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template with parallel IO access. */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); + acc_tpl1 = H5Pcreate(H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); MESG("H5Pcreate access succeed"); /* set Parallel access with communicator */ @@ -277,70 +277,60 @@ phdf5writeInd(char *filename) ret = H5Pclose(acc_tpl1); assert(ret != FAIL); - /* -------------------------- * Define the dimensions of the overall datasets * and the slabs local to the MPI process. * ------------------------- */ /* setup dimensionality object */ sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL); - assert (sid1 != FAIL); + assert(sid1 != FAIL); MESG("H5Screate_simple succeed"); - /* create a dataset collectively */ - dataset1 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dataset1 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset1 != FAIL); MESG("H5Dcreate2 succeed"); /* create another dataset collectively */ - dataset2 = H5Dcreate2(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + dataset2 = H5Dcreate2(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset2 != FAIL); MESG("H5Dcreate2 succeed"); - - /* set up dimensions of the slab this process accesses */ - start[0] = mpi_rank*SPACE1_DIM1/mpi_size; - start[1] = 0; - count[0] = SPACE1_DIM1/mpi_size; - count[1] = SPACE1_DIM2; + start[0] = mpi_rank * SPACE1_DIM1 / mpi_size; + start[1] = 0; + count[0] = SPACE1_DIM1 / mpi_size; + count[1] = SPACE1_DIM2; stride[0] = 1; - stride[1] =1; -if (verbose) - printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", - (unsigned long)start[0], (unsigned long)start[1], - (unsigned long)count[0], (unsigned long)count[1], - (unsigned long)(count[0]*count[1])); + stride[1] = 1; + if (verbose) + printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], + (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)(count[0] * count[1])); /* put some trivial data in the data_array */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); + file_dataspace = H5Dget_space(dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); - ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, NULL); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - assert (mem_dataspace != FAIL); + mem_dataspace = H5Screate_simple(SPACE1_RANK, count, NULL); + assert(mem_dataspace != FAIL); /* write data independently */ - ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); + ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); /* write data independently */ - ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); + ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); @@ -348,10 +338,10 @@ if (verbose) H5Sclose(file_dataspace); /* close dataset collectively */ - ret=H5Dclose(dataset1); + ret = H5Dclose(dataset1); assert(ret != FAIL); MESG("H5Dclose1 succeed"); - ret=H5Dclose(dataset2); + ret = H5Dclose(dataset2); assert(ret != FAIL); MESG("H5Dclose2 succeed"); @@ -366,39 +356,38 @@ if (verbose) void phdf5readInd(char *filename) { - hid_t fid1; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ + hid_t fid1; /* HDF5 file IDs */ + hid_t acc_tpl1; /* File access templates */ + hid_t file_dataspace; /* File dataspace ID */ + hid_t mem_dataspace; /* memory dataspace ID */ + hid_t dataset1, dataset2; /* Dataset ID */ + DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ + DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ - hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - herr_t ret; /* Generic return value */ + herr_t ret; /* Generic return value */ MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; if (verbose) - printf("Independent read test on file %s\n", filename); + printf("Independent read test on file %s\n", filename); /* setup file access template */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); + acc_tpl1 = H5Pcreate(H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); /* set Parallel access with communicator */ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info); assert(ret != FAIL); - /* open the file collectively */ - fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1); + fid1 = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl1); assert(fid1 != FAIL); /* Release file-access template */ - ret=H5Pclose(acc_tpl1); + ret = H5Pclose(acc_tpl1); assert(ret != FAIL); /* open the dataset1 collectively */ @@ -409,37 +398,33 @@ phdf5readInd(char *filename) dataset2 = H5Dopen2(fid1, DATASETNAME1, H5P_DEFAULT); assert(dataset2 != FAIL); - /* set up dimensions of the slab this process accesses */ - start[0] = mpi_rank*SPACE1_DIM1/mpi_size; - start[1] = 0; - count[0] = SPACE1_DIM1/mpi_size; - count[1] = SPACE1_DIM2; + start[0] = mpi_rank * SPACE1_DIM1 / mpi_size; + start[1] = 0; + count[0] = SPACE1_DIM1 / mpi_size; + count[1] = SPACE1_DIM2; stride[0] = 1; - stride[1] =1; -if (verbose) - printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", - (unsigned long)start[0], (unsigned long)start[1], - (unsigned long)count[0], (unsigned long)count[1], - (unsigned long)(count[0]*count[1])); + stride[1] = 1; + if (verbose) + printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], + (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)(count[0] * count[1])); /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); + file_dataspace = H5Dget_space(dataset1); assert(file_dataspace != FAIL); - ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, NULL); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - assert (mem_dataspace != FAIL); + mem_dataspace = H5Screate_simple(SPACE1_RANK, count, NULL); + assert(mem_dataspace != FAIL); /* fill dataset with test data */ dataset_fill(start, count, stride, &data_origin1[0][0]); /* read data independently */ - ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); + ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); assert(ret != FAIL); /* verify the read data with original expected data */ @@ -447,8 +432,7 @@ if (verbose) assert(ret != FAIL); /* read data independently */ - ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - H5P_DEFAULT, data_array1); + ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); assert(ret != FAIL); /* verify the read data with original expected data */ @@ -456,9 +440,9 @@ if (verbose) assert(ret == 0); /* close dataset collectively */ - ret=H5Dclose(dataset1); + ret = H5Dclose(dataset1); assert(ret != FAIL); - ret=H5Dclose(dataset2); + ret = H5Dclose(dataset2); assert(ret != FAIL); /* release all IDs created */ @@ -468,7 +452,6 @@ if (verbose) H5Fclose(fid1); } - /* * Example of using the parallel HDF5 library to create two datasets * in one HDF5 file with collective parallel access support. @@ -481,33 +464,32 @@ if (verbose) void phdf5writeAll(char *filename) { - hid_t fid1; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t xfer_plist; /* Dataset transfer properties list */ - hid_t sid1; /* Dataspace ID */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - hsize_t dims1[SPACE1_RANK] = - {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - - hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - - herr_t ret; /* Generic return value */ + hid_t fid1; /* HDF5 file IDs */ + hid_t acc_tpl1; /* File access templates */ + hid_t xfer_plist; /* Dataset transfer properties list */ + hid_t sid1; /* Dataspace ID */ + hid_t file_dataspace; /* File dataspace ID */ + hid_t mem_dataspace; /* memory dataspace ID */ + hid_t dataset1, dataset2; /* Dataset ID */ + hsize_t dims1[SPACE1_RANK] = {SPACE1_DIM1, SPACE1_DIM2}; /* dataspace dim sizes */ + DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ + + hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ + + herr_t ret; /* Generic return value */ MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; if (verbose) - printf("Collective write test on file %s\n", filename); + printf("Collective write test on file %s\n", filename); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template with parallel IO access. */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); + acc_tpl1 = H5Pcreate(H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); MESG("H5Pcreate access succeed"); /* set Parallel access with communicator */ @@ -516,25 +498,23 @@ phdf5writeAll(char *filename) MESG("H5Pset_fapl_mpio succeed"); /* create the file collectively */ - fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1); + fid1 = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl1); assert(fid1 != FAIL); MESG("H5Fcreate succeed"); /* Release file-access template */ - ret=H5Pclose(acc_tpl1); + ret = H5Pclose(acc_tpl1); assert(ret != FAIL); - /* -------------------------- * Define the dimensions of the overall datasets * and create the dataset * ------------------------- */ /* setup dimensionality object */ - sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL); - assert (sid1 != FAIL); + sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL); + assert(sid1 != FAIL); MESG("H5Screate_simple succeed"); - /* create a dataset collectively */ dataset1 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); assert(dataset1 != FAIL); @@ -551,43 +531,40 @@ phdf5writeAll(char *filename) /* Dataset1: each process takes a block of rows. */ slab_set(start, count, stride, BYROW); -if (verbose) - printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", - (unsigned long)start[0], (unsigned long)start[1], - (unsigned long)count[0], (unsigned long)count[1], - (unsigned long)(count[0]*count[1])); + if (verbose) + printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], + (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)(count[0] * count[1])); /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); + file_dataspace = H5Dget_space(dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); - ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, NULL); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - assert (mem_dataspace != FAIL); + mem_dataspace = H5Screate_simple(SPACE1_RANK, count, NULL); + assert(mem_dataspace != FAIL); /* fill the local slab with some trivial data */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); - if (verbose){ - MESG("data_array created"); - dataset_print(start, count, stride, &data_array1[0][0]); + if (verbose) { + MESG("data_array created"); + dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); + xfer_plist = H5Pcreate(H5P_DATASET_XFER); assert(xfer_plist != FAIL); - ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* write data collectively */ - ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); + ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); @@ -600,51 +577,48 @@ if (verbose) /* Dataset2: each process takes a block of columns. */ slab_set(start, count, stride, BYCOL); -if (verbose) - printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", - (unsigned long)start[0], (unsigned long)start[1], - (unsigned long)count[0], (unsigned long)count[1], - (unsigned long)(count[0]*count[1])); + if (verbose) + printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], + (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)(count[0] * count[1])); /* put some trivial data in the data_array */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); - if (verbose){ - MESG("data_array created"); - dataset_print(start, count, stride, &data_array1[0][0]); + if (verbose) { + MESG("data_array created"); + dataset_print(start, count, stride, &data_array1[0][0]); } /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); + file_dataspace = H5Dget_space(dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); - ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, NULL); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - assert (mem_dataspace != FAIL); + mem_dataspace = H5Screate_simple(SPACE1_RANK, count, NULL); + assert(mem_dataspace != FAIL); /* fill the local slab with some trivial data */ dataset_fill(start, count, stride, &data_array1[0][0]); MESG("data_array initialized"); - if (verbose){ - MESG("data_array created"); - dataset_print(start, count, stride, &data_array1[0][0]); + if (verbose) { + MESG("data_array created"); + dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); + xfer_plist = H5Pcreate(H5P_DATASET_XFER); assert(xfer_plist != FAIL); - ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* write data independently */ - ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); + ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dwrite succeed"); @@ -653,14 +627,13 @@ if (verbose) H5Sclose(mem_dataspace); H5Pclose(xfer_plist); - /* * All writes completed. Close datasets collectively */ - ret=H5Dclose(dataset1); + ret = H5Dclose(dataset1); assert(ret != FAIL); MESG("H5Dclose1 succeed"); - ret=H5Dclose(dataset2); + ret = H5Dclose(dataset2); assert(ret != FAIL); MESG("H5Dclose2 succeed"); @@ -683,31 +656,31 @@ if (verbose) void phdf5readAll(char *filename) { - hid_t fid1; /* HDF5 file IDs */ - hid_t acc_tpl1; /* File access templates */ - hid_t xfer_plist; /* Dataset transfer properties list */ - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ - DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ - DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ + hid_t fid1; /* HDF5 file IDs */ + hid_t acc_tpl1; /* File access templates */ + hid_t xfer_plist; /* Dataset transfer properties list */ + hid_t file_dataspace; /* File dataspace ID */ + hid_t mem_dataspace; /* memory dataspace ID */ + hid_t dataset1, dataset2; /* Dataset ID */ + DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */ + DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */ - hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ - hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t start[SPACE1_RANK]; /* for hyperslab setting */ + hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */ - herr_t ret; /* Generic return value */ + herr_t ret; /* Generic return value */ MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; if (verbose) - printf("Collective read test on file %s\n", filename); + printf("Collective read test on file %s\n", filename); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template with parallel IO access. */ - acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS); + acc_tpl1 = H5Pcreate(H5P_FILE_ACCESS); assert(acc_tpl1 != FAIL); MESG("H5Pcreate access succeed"); /* set Parallel access with communicator */ @@ -716,15 +689,14 @@ phdf5readAll(char *filename) MESG("H5Pset_fapl_mpio succeed"); /* open the file collectively */ - fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1); + fid1 = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl1); assert(fid1 != FAIL); MESG("H5Fopen succeed"); /* Release file-access template */ - ret=H5Pclose(acc_tpl1); + ret = H5Pclose(acc_tpl1); assert(ret != FAIL); - /* -------------------------- * Open the datasets in it * ------------------------- */ @@ -744,43 +716,40 @@ phdf5readAll(char *filename) /* Dataset1: each process takes a block of columns. */ slab_set(start, count, stride, BYCOL); -if (verbose) - printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", - (unsigned long)start[0], (unsigned long)start[1], - (unsigned long)count[0], (unsigned long)count[1], - (unsigned long)(count[0]*count[1])); + if (verbose) + printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], + (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)(count[0] * count[1])); /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); + file_dataspace = H5Dget_space(dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); - ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, NULL); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - assert (mem_dataspace != FAIL); + mem_dataspace = H5Screate_simple(SPACE1_RANK, count, NULL); + assert(mem_dataspace != FAIL); /* fill dataset with test data */ dataset_fill(start, count, stride, &data_origin1[0][0]); MESG("data_array initialized"); - if (verbose){ - MESG("data_array created"); - dataset_print(start, count, stride, &data_array1[0][0]); + if (verbose) { + MESG("data_array created"); + dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); + xfer_plist = H5Pcreate(H5P_DATASET_XFER); assert(xfer_plist != FAIL); - ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* read data collectively */ - ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); + ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dread succeed"); @@ -797,43 +766,40 @@ if (verbose) /* Dataset2: each process takes a block of rows. */ slab_set(start, count, stride, BYROW); -if (verbose) - printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", - (unsigned long)start[0], (unsigned long)start[1], - (unsigned long)count[0], (unsigned long)count[1], - (unsigned long)(count[0]*count[1])); + if (verbose) + printf("start[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], + (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)(count[0] * count[1])); /* create a file dataspace independently */ - file_dataspace = H5Dget_space (dataset1); + file_dataspace = H5Dget_space(dataset1); assert(file_dataspace != FAIL); MESG("H5Dget_space succeed"); - ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, NULL); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); assert(ret != FAIL); MESG("H5Sset_hyperslab succeed"); /* create a memory dataspace independently */ - mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL); - assert (mem_dataspace != FAIL); + mem_dataspace = H5Screate_simple(SPACE1_RANK, count, NULL); + assert(mem_dataspace != FAIL); /* fill dataset with test data */ dataset_fill(start, count, stride, &data_origin1[0][0]); MESG("data_array initialized"); - if (verbose){ - MESG("data_array created"); - dataset_print(start, count, stride, &data_array1[0][0]); + if (verbose) { + MESG("data_array created"); + dataset_print(start, count, stride, &data_array1[0][0]); } /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); + xfer_plist = H5Pcreate(H5P_DATASET_XFER); assert(xfer_plist != FAIL); - ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); assert(ret != FAIL); MESG("H5Pcreate xfer succeed"); /* read data independently */ - ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, - xfer_plist, data_array1); + ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); assert(ret != FAIL); MESG("H5Dread succeed"); @@ -846,14 +812,13 @@ if (verbose) H5Sclose(mem_dataspace); H5Pclose(xfer_plist); - /* * All reads completed. Close datasets collectively */ - ret=H5Dclose(dataset1); + ret = H5Dclose(dataset1); assert(ret != FAIL); MESG("H5Dclose1 succeed"); - ret=H5Dclose(dataset2); + ret = H5Dclose(dataset2); assert(ret != FAIL); MESG("H5Dclose2 succeed"); @@ -877,51 +842,51 @@ test_split_comm_access(char filenames[][PATH_MAX]) { MPI_Comm comm; MPI_Info info = MPI_INFO_NULL; - int color, mrc; - int newrank, newprocs; - hid_t fid; /* file IDs */ - hid_t acc_tpl; /* File access properties */ - herr_t ret; /* generic return value */ + int color, mrc; + int newrank, newprocs; + hid_t fid; /* file IDs */ + hid_t acc_tpl; /* File access properties */ + herr_t ret; /* generic return value */ if (verbose) - printf("Independent write test on file %s %s\n", - filenames[0], filenames[1]); - - color = mpi_rank%2; - mrc = MPI_Comm_split (MPI_COMM_WORLD, color, mpi_rank, &comm); - assert(mrc==MPI_SUCCESS); - MPI_Comm_size(comm,&newprocs); - MPI_Comm_rank(comm,&newrank); - - if (color){ - /* odd-rank processes */ - mrc = MPI_Barrier(comm); - assert(mrc==MPI_SUCCESS); - }else{ - /* even-rank processes */ - /* setup file access template */ - acc_tpl = H5Pcreate (H5P_FILE_ACCESS); - assert(acc_tpl != FAIL); - - /* set Parallel access with communicator */ - ret = H5Pset_fapl_mpio(acc_tpl, comm, info); - assert(ret != FAIL); - - /* create the file collectively */ - fid=H5Fcreate(filenames[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl); - assert(fid != FAIL); - MESG("H5Fcreate succeed"); - - /* Release file-access template */ - ret=H5Pclose(acc_tpl); - assert(ret != FAIL); - - ret=H5Fclose(fid); - assert(ret != FAIL); + printf("Independent write test on file %s %s\n", filenames[0], filenames[1]); + + color = mpi_rank % 2; + mrc = MPI_Comm_split(MPI_COMM_WORLD, color, mpi_rank, &comm); + assert(mrc == MPI_SUCCESS); + MPI_Comm_size(comm, &newprocs); + MPI_Comm_rank(comm, &newrank); + + if (color) { + /* odd-rank processes */ + mrc = MPI_Barrier(comm); + assert(mrc == MPI_SUCCESS); } - if (mpi_rank == 0){ - mrc = MPI_File_delete(filenames[color], info); - assert(mrc==MPI_SUCCESS); + else { + /* even-rank processes */ + /* setup file access template */ + acc_tpl = H5Pcreate(H5P_FILE_ACCESS); + assert(acc_tpl != FAIL); + + /* set Parallel access with communicator */ + ret = H5Pset_fapl_mpio(acc_tpl, comm, info); + assert(ret != FAIL); + + /* create the file collectively */ + fid = H5Fcreate(filenames[color], H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); + assert(fid != FAIL); + MESG("H5Fcreate succeed"); + + /* Release file-access template */ + ret = H5Pclose(acc_tpl); + assert(ret != FAIL); + + ret = H5Fclose(fid); + assert(ret != FAIL); + } + if (mpi_rank == 0) { + mrc = MPI_File_delete(filenames[color], info); + assert(mrc == MPI_SUCCESS); } } @@ -944,7 +909,6 @@ usage(void) printf("\n"); } - /* * compose the test filename with the prefix supplied. * return code: 0 if no error @@ -953,88 +917,93 @@ usage(void) int mkfilenames(char *prefix) { - int i, n; + int i, n; size_t strsize; /* filename will be prefix/ParaEgN.h5 where N is 0 to 9. */ /* So, string must be big enough to hold the prefix, / and 10 more chars */ /* and the terminating null. */ strsize = strlen(prefix) + 12; - if (strsize > PATH_MAX){ - printf("File prefix too long; Use a short path name.\n"); - return(1); + if (strsize > PATH_MAX) { + printf("File prefix too long; Use a short path name.\n"); + return (1); } - n = sizeof(testfiles)/sizeof(testfiles[0]); - if (n > 9){ - printf("Warning: Too many entries in testfiles. " - "Need to adjust the code to accommodate the large size.\n"); + n = sizeof(testfiles) / sizeof(testfiles[0]); + if (n > 9) { + printf("Warning: Too many entries in testfiles. " + "Need to adjust the code to accommodate the large size.\n"); } - for (i=0; i<n; i++){ - sprintf(testfiles[i], "%s/ParaEg%d.h5", prefix, i); + for (i = 0; i < n; i++) { + sprintf(testfiles[i], "%s/ParaEg%d.h5", prefix, i); } - return(0); - + return (0); } - /* * parse the command line options */ int -parse_options(int argc, char **argv){ +parse_options(int argc, char **argv) +{ int i, n; /* initialize testfiles to nulls */ - n = sizeof(testfiles)/sizeof(testfiles[0]); - for (i=0; i<n; i++){ - testfiles[i][0] = '\0'; + n = sizeof(testfiles) / sizeof(testfiles[0]); + for (i = 0; i < n; i++) { + testfiles[i][0] = '\0'; } - while (--argc){ - if (**(++argv) != '-'){ - break; - }else{ - switch(*(*argv+1)){ - case 'f': ++argv; - if (--argc < 1){ - usage(); - nerrors++; - return(1); - } - if (mkfilenames(*argv)){ - nerrors++; - return(1); - } - break; - case 'c': docleanup = 0; /* no cleanup */ - break; - case 'r': doread = 0; - break; - case 'w': dowrite = 0; - break; - case 'v': verbose = 1; - break; - default: usage(); - nerrors++; - return(1); - } - } + while (--argc) { + if (**(++argv) != '-') { + break; + } + else { + switch (*(*argv + 1)) { + case 'f': + ++argv; + if (--argc < 1) { + usage(); + nerrors++; + return (1); + } + if (mkfilenames(*argv)) { + nerrors++; + return (1); + } + break; + case 'c': + docleanup = 0; /* no cleanup */ + break; + case 'r': + doread = 0; + break; + case 'w': + dowrite = 0; + break; + case 'v': + verbose = 1; + break; + default: + usage(); + nerrors++; + return (1); + } + } } /* check the file prefix */ - if (testfiles[0][0] == '\0'){ - /* try get it from environment variable HDF5_PARAPREFIX */ - char *env; - char *env_default = "."; /* default to current directory */ - if ((env=getenv(PARAPREFIX))==NULL){ - env = env_default; - } - mkfilenames(env); + if (testfiles[0][0] == '\0') { + /* try get it from environment variable HDF5_PARAPREFIX */ + char *env; + char *env_default = "."; /* default to current directory */ + if ((env = getenv(PARAPREFIX)) == NULL) { + env = env_default; + } + mkfilenames(env); } - return(0); + return (0); } - /* * cleanup test files created */ @@ -1043,88 +1012,87 @@ cleanup(void) { int i, n; - n = sizeof(testfiles)/sizeof(testfiles[0]); - for (i=0; i<n; i++){ - MPI_File_delete(testfiles[i], MPI_INFO_NULL); + n = sizeof(testfiles) / sizeof(testfiles[0]); + for (i = 0; i < n; i++) { + MPI_File_delete(testfiles[i], MPI_INFO_NULL); } } - /* Main Program */ int main(int argc, char **argv) { - int mpi_namelen; + int mpi_namelen; char mpi_name[MPI_MAX_PROCESSOR_NAME]; - int i, n; + int i, n; - MPI_Init(&argc,&argv); - MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); - MPI_Get_processor_name(mpi_name,&mpi_namelen); + MPI_Init(&argc, &argv); + MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); + MPI_Get_processor_name(mpi_name, &mpi_namelen); /* Make sure datasets can be divided into equal chunks by the processes */ - if ((SPACE1_DIM1 % mpi_size) || (SPACE1_DIM2 % mpi_size)){ - printf("DIM1(%d) and DIM2(%d) must be multiples of processes (%d)\n", - SPACE1_DIM1, SPACE1_DIM2, mpi_size); - nerrors++; - goto finish; + if ((SPACE1_DIM1 % mpi_size) || (SPACE1_DIM2 % mpi_size)) { + printf("DIM1(%d) and DIM2(%d) must be multiples of processes (%d)\n", SPACE1_DIM1, SPACE1_DIM2, + mpi_size); + nerrors++; + goto finish; } if (parse_options(argc, argv) != 0) - goto finish; + goto finish; /* show test file names */ - if (mpi_rank == 0){ - n = sizeof(testfiles)/sizeof(testfiles[0]); - printf("Parallel test files are:\n"); - for (i=0; i<n; i++){ - printf(" %s\n", testfiles[i]); - } + if (mpi_rank == 0) { + n = sizeof(testfiles) / sizeof(testfiles[0]); + printf("Parallel test files are:\n"); + for (i = 0; i < n; i++) { + printf(" %s\n", testfiles[i]); + } } - if (dowrite){ - MPI_BANNER("testing PHDF5 dataset using split communicators..."); - test_split_comm_access(testfiles); - MPI_BANNER("testing PHDF5 dataset independent write..."); - phdf5writeInd(testfiles[0]); - MPI_BANNER("testing PHDF5 dataset collective write..."); - phdf5writeAll(testfiles[1]); + if (dowrite) { + MPI_BANNER("testing PHDF5 dataset using split communicators..."); + test_split_comm_access(testfiles); + MPI_BANNER("testing PHDF5 dataset independent write..."); + phdf5writeInd(testfiles[0]); + MPI_BANNER("testing PHDF5 dataset collective write..."); + phdf5writeAll(testfiles[1]); } - if (doread){ - MPI_BANNER("testing PHDF5 dataset independent read..."); - phdf5readInd(testfiles[0]); - MPI_BANNER("testing PHDF5 dataset collective read..."); - phdf5readAll(testfiles[1]); + if (doread) { + MPI_BANNER("testing PHDF5 dataset independent read..."); + phdf5readInd(testfiles[0]); + MPI_BANNER("testing PHDF5 dataset collective read..."); + phdf5readAll(testfiles[1]); } - if (!(dowrite || doread)){ - usage(); - nerrors++; + if (!(dowrite || doread)) { + usage(); + nerrors++; } finish: - if (mpi_rank == 0){ /* only process 0 reports */ - if (nerrors) - printf("***PHDF5 tests detected %d errors***\n", nerrors); - else{ - printf("===================================\n"); - printf("PHDF5 tests finished with no errors\n"); - printf("===================================\n"); - } + if (mpi_rank == 0) { /* only process 0 reports */ + if (nerrors) + printf("***PHDF5 tests detected %d errors***\n", nerrors); + else { + printf("===================================\n"); + printf("PHDF5 tests finished with no errors\n"); + printf("===================================\n"); + } } if (docleanup) - cleanup(); + cleanup(); MPI_Finalize(); - return(nerrors); + return (nerrors); } -#else /* H5_HAVE_PARALLEL */ +#else /* H5_HAVE_PARALLEL */ /* dummy program since H5_HAVE_PARALLE is not configured in */ int main(void) { -printf("No PHDF5 example because parallel is not configured in\n"); -return(0); + printf("No PHDF5 example because parallel is not configured in\n"); + return (0); } #endif /* H5_HAVE_PARALLEL */ diff --git a/examples/run-all-ex.sh b/examples/run-all-ex.sh index 878e0f8..afd4308 100755 --- a/examples/run-all-ex.sh +++ b/examples/run-all-ex.sh @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. diff --git a/examples/run-c-ex.sh.in b/examples/run-c-ex.sh.in index a684a38..dc3f7ae 100644 --- a/examples/run-c-ex.sh.in +++ b/examples/run-c-ex.sh.in @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. @@ -18,7 +18,7 @@ # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # This script will compile and run the c examples from source files installed # -# in .../share/hdf5_examples/c using h5cc or h5pc. The order for running # +# in @examplesdir@/c using h5cc or h5pc. The order for running # # programs with RunTest in the MAIN section below is taken from the Makefile. # # The order is important since some of the test programs use data files created # # by earlier test programs. Any future additions should be placed accordingly. # @@ -28,10 +28,33 @@ # Initializations EXIT_SUCCESS=0 EXIT_FAILURE=1 - + +# +# Try to derive the path to the installation $prefix established +# by ./configure relative to the examples directory established by +# ./configure. If successful, set `prefix_relto_examplesdir` to the +# relative path. Otherwise, set `prefix_relto_examplesdir` to the +# absolute installation $prefix. +# +# This script uses the value of `prefix` in the user's environment, if +# it is set, below. The content of $() is evaluated in a sub-shell, so +# if `prefix` is set in the user's environment, the shell statements in +# $() won't clobbered it. +# +prefix_relto_examplesdir=$( +prefix=@prefix@ +examplesdir=@examplesdir@ +if [ ${examplesdir##${prefix}/} != ${examplesdir} ]; then + echo $(echo ${examplesdir##${prefix}/} | \ + sed 's,[^/][^/]*,..,g') +else + echo $prefix +fi +) + # Where the tool is installed. # default is relative path to installed location of the tools -prefix="${prefix:-../../../}" +prefix="${prefix:-../${prefix_relto_examplesdir}}" PARALLEL=@PARALLEL@ # Am I in parallel mode? AR="@AR@" RANLIB="@RANLIB@" diff --git a/examples/testh5cc.sh.in b/examples/testh5cc.sh.in index 4e898c1..71254d2 100644 --- a/examples/testh5cc.sh.in +++ b/examples/testh5cc.sh.in @@ -7,7 +7,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # @@ -29,8 +29,7 @@ EXIT_SUCCESS=0 EXIT_FAILURE=1 # Where the tool is installed. -# Note: no '/' after DESTDIR. Explanation in commence.am -prefix="${prefix:-${DESTDIR}@prefix@}" +prefix="${prefix:-@prefix@}" PARALLEL=@PARALLEL@ # Am I in parallel mode? AR="@AR@" RANLIB="@RANLIB@" |