* Tools merges from develop
Brings the tools getopt(3) replacement into the main library (#803)
Perform option arg variables (#834)
Removes unused commented-out code from h5jamgentest.c (#851)
Reorg tools perform to provide h5perf for installation (#884)
* Fix missing files
* Remove empty files
* Remove empty file
* Resync defines
* Fix endif typo
* Add Makfile to list
* Fix typo
* Remove H5_GCC_DIAG_ON line to match removal of H5_GCC_DIAG_OFF line in
sio_engine.c/
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Reorganization of C and POSIX headers in H5public.h & H5private.h (#793)
* Reorganization of C and POSIX headers in H5public.h & H5private.h
Consolidated and removed duplicates
* It turns out Windows has sys/types.h
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Brings the tools getopt(3) replacement into the main library (#803)
* Moves get_option from the tools library to the C library
* Adds H5 prefix to get_option call and variables
* Renames the H5_get_option long options struct and enum
* Remove version-check for relnum in H5check. (#812)
* Remove version-check for relnum in H5check.
* Add in release exception code check
* Fix typos
* Fix more typos
* Rework comments
* format change
* format whitespace
* Library version must be less than or equal to headers
* Need the NOT version of the compare
* Enable release+1 check for PASS
* Add release note
* Update note
* Remove checks for winsock2.h (#813)
This is only needed on Windows and always available, so there's no need
to check for it.
* Removes develop header cruft (#828)
* OESS-168:Remove implicit conversion warnings. (#829)
* OESS-168:Remove implicit conversion increases floating-point precision warnings.
* OESS-168:Remove clang warnings.
* Add support for parallel filters to h5repack (#832)
* Perform option arg variables (#834)
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
* Fix static perform tools compile for arg options
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* OESS-168:Remove clang warnings. (#835)
* OESS-168:Remove implicit conversion increases floating-point precision warnings.
* OESS-168:Remove clang warnings.
* OESS-168:Remove clang warnings.
* Committing clang-format changes
* OESS-168:Remove clang warnings.
* Committing clang-format changes
* OESS-168:Remove clang warning.
* OESS-168:Remove clang warnings.
* OESS-168:Address @byrnHDF review.
* Remove line added to generated hl/src/H5LTanalyze.c file.
Issue #854 created for creating a fix.
* Remove extra whitespace from H5LTanalyze.c.
* Remove extra blank line.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removes unused commented-out code from h5jamgentest.c (#851)
* Updates a comment in H5mpi.c (#863)
MPI_Type_struct() is an MPI-1 call we no longer use.
* Unsigned comparison to 0 warning avoidance (#869)
* Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid
warning that unsigned comparison < 0 is always false, which is known,
but for later versions the comparison can possibly be true.
* Better solution for avoiding warning that unsigned comparison < 0.
* Updates the RELEASE.txt file with a note about the variable-length fill (#871)
value issue. A fix is in progress, but it might be a while before
we have time to finish it up.
* Add parallel version of h5pfc script (#881)
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: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
* Merge workflow and minor changes from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge serval small changes from dev
* fix typo
* Minor non-space formatting changes
* GH #386 copyright corrections for java folder
* revert because logic requires false return
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Remove case statement for H5I_EVENTSET
* Correct call with versioning
* Remove tabs
* Double underscore change
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Added a funtion to reset dataset & hyperslab buffer size for h5repack from an
environment variable.
This is performance debugging purpose for now.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE), cmake
Work for:
HDFFV-7515 - GMQS: h5unjam - incorrect help page and should display when
no file is given.
and
HDFFV-5941 - h5jam: specifying a user block file with a proper HDF5 magic
number will result in a corrupted HDF5 file.
Description:
- Revised command help pages of h5jam and h5unjam. The descriptions
were not up to date and some were missing. (HDFFV-7515)
- Fixed h5jam not to allow specifying an HDF5 formatted file as input
file for -u (user block file) option, because the original HDF5 file
will not be accessible if allows. (HDFFV-5941)
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Wondows)
Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.
Tested:
jam, amani, heiwa
Merge r19290 & r19291 from 1.8 branch to trunk:
r19290:
Correct another error in metadata accumulator dirty region calculations
(this time with a corner case when freeing data in the file).
r19291:
Avoid getting object information for soft/external links if we aren't
going to traverse across the link itself.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Bring Coverity changes from branch to trunk:
r19161:
Fixed the part for matching the subset info with dataset
r19189:
BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset
Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump.
Changed all references to use new data structure.
Added tests for each subset parameter.
r19190:
Added new h5dump ddl files
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(h5committested on branch)
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions
Tested:
Windows, linux
Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Code cleanup & speedup
Description:
Refactor h5dump & related code to be considerably cleaner & faster for
files with large #'s of objects.
Platforms tested:
FreeBS 4.11 (sleipnir)
Linux 2.4
Bug fix
Description:
ph5diff had been hanging in Tflops. Found out that vsnprintf ph5diff
uses was a local coded that did not limit printing according to the size
argument. That resulted in buffer overflow and other problems.
Solution:
Added some sort of size checking in the home-grown vsnprintf and
had ph5diff checked for error return of vsnprintf. Leon also
revamped the ph5diff manager's way of handling communications with
the workers. That eliminated all but the last case of hanging.
Platforms tested:
Tflops.
Misc. update:
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Bug Fix
Description:
There was a problem with having a lot of groups nested together. We
could only handle 1024 characters at most, but, in a parallel program
especially, it could occur that there were lots and lots of groups
and would be more than 1024.
Solution:
I made the "objname" part of the obj_t structure a pointer instead of
a fixed size. Added code to allocate/deallocate the memory we need
for it. Had to fix how the "prefix" was being handled in the h5dump
program. It was also set to only 1024 characters in length. I made it
dynamic.
Added a test case...Go me!
Platforms tested:
Linux, Solaris
New Modules
Description:
Separated the "generic" functions out of the h5tools module into
their own separate module to make things a bit nicer to deal with.
Platforms tested:
Linux
