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Merge branch 'develop' into c_stdlib_posix_call_cleanup

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This commit is contained in:
Dana Robinson 2019-02-19 14:49:20 -08:00
commit 32ea4e72f1
221 changed files with 25124 additions and 23547 deletions
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8
CMakeFilters.cmake
View File

@ -27,7 +27,15 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
set (TGZPATH ${HDF5_SOURCE_DIR})
endif ()
set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
if (NOT EXISTS "${ZLIB_URL}")
set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
message (STATUS "Filter ZLIB file ${ZLIB_URL} not found")
endif ()
set (SZIP_URL ${TGZPATH}/${SZIP_TGZ_NAME})
if (NOT EXISTS "${SZIP_URL}")
set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
message (STATUS "Filter SZIP file ${SZIP_URL} not found")
endif ()
else ()
set (ZLIB_USE_EXTERNAL 0)
set (SZIP_USE_EXTERNAL 0)

8
CMakeInstallation.cmake
View File

@ -104,6 +104,12 @@ endif ()
# Configure the hdf5-config-version .cmake file for the install directory
#-----------------------------------------------------------------------------
if (NOT HDF5_EXTERNALLY_CONFIGURED)
# 3.11 or greater
#write_basic_package_version_file (
# ${HDF5_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-config-version.cmake
# VERSION ${HDF5_PACKAGE_VERSION}
# COMPATIBILITY SameMinorVersion
#)
configure_file (
${HDF_RESOURCES_DIR}/hdf5-config-version.cmake.in
${HDF5_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-config-version.cmake @ONLY
@ -134,7 +140,7 @@ install (
)
#-----------------------------------------------------------------------------
# Configure the HDF518_Examples.cmake file and the examples
# Configure the HDF5_Examples.cmake file and the examples
#-----------------------------------------------------------------------------
option (HDF5_PACK_EXAMPLES "Package the HDF5 Library Examples Compressed File" OFF)
if (HDF5_PACK_EXAMPLES)

29
CMakeLists.txt
View File

@ -10,7 +10,7 @@ project (HDF5 C)
# set CMAKE_INSTALL_PREFIX to the required install path.
# Make install can be used to install all components for system-wide use.
#
if ("${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
MESSAGE(FATAL_ERROR "\nERROR! ${PROJECT_NAME} DOES NOT SUPPORT IN SOURCE BUILDS!\n"
"CMAKE_CURRENT_SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}"
" == CMAKE_CURRENT_BINARY_DIR=${CMAKE_CURRENT_BINARY_DIR}\n"
@ -314,7 +314,7 @@ set (HDF5_PACKAGE_NAME "HDF5")
set (HDF5_PACKAGE_VERSION "${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}")
set (HDF5_PACKAGE_VERSION_MAJOR "${H5_VERS_MAJOR}.${H5_VERS_MINOR}")
set (HDF5_PACKAGE_VERSION_MINOR "${H5_VERS_RELEASE}")
if (NOT "${H5_VERS_SUBRELEASE}" STREQUAL "")
if (H5_VERS_SUBRELEASE)
set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}-${H5_VERS_SUBRELEASE}")
else ()
set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}")
@ -481,6 +481,15 @@ if (HDF5_MEMORY_ALLOC_SANITY_CHECK)
set (H5_MEMORY_ALLOC_SANITY_CHECK 1)
endif ()
#-----------------------------------------------------------------------------
# Option to enable/disable using pread/pwrite for VFDs
#-----------------------------------------------------------------------------
option (HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON)
mark_as_advanced (HDF5_ENABLE_PREADWRITE)
if (HDF5_ENABLE_PREADWRITE AND H5_HAVE_PREAD AND H5_HAVE_PWRITE)
set (H5_HAVE_PREADWRITE 1)
endif ()
#-----------------------------------------------------------------------------
# Option to use deprecated public API symbols
#-----------------------------------------------------------------------------
@ -749,6 +758,11 @@ if (BUILD_TESTING)
"Timeout in seconds for each test (default 1200=20minutes)"
)
# Generate a list of timeouts based on DART_TESTING_TIMEOUT
math (EXPR CTEST_SHORT_TIMEOUT "${DART_TESTING_TIMEOUT} / 2")
math (EXPR CTEST_LONG_TIMEOUT "${DART_TESTING_TIMEOUT} * 2")
math (EXPR CTEST_VERY_LONG_TIMEOUT "${DART_TESTING_TIMEOUT} * 3")
option (HDF5_TEST_VFD "Execute tests with different VFDs" OFF)
mark_as_advanced (HDF5_TEST_VFD)
if (HDF5_TEST_VFD)
@ -826,25 +840,20 @@ set (H5_FC_FUNC_ "H5_FC_FUNC_(name,NAME) name ## _")
if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/fortran")
option (HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF)
if (HDF5_BUILD_FORTRAN)
option (HDF5_ENABLE_F2003 "Enable FORTRAN 2003 Standard" ON)
include (${HDF_RESOURCES_EXT_DIR}/HDFUseFortran.cmake)
message (STATUS "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
# Building with PGI requires CMake 3.3 or greater because previous versions
# of CMake add the wrong compiler flag for the PGI Fortran compiler.
if ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "PGI" AND "${CMAKE_VERSION}" VERSION_LESS "3.3")
if (CMAKE_Fortran_COMPILER_ID MATCHES "PGI" AND CMAKE_VERSION VERSION_LESS "3.3")
message (FATAL_ERROR " **** PGI FORTRAN REQUIRES CMAKE VERSION 3.3 OR GREATER **** ")
endif ()
include (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake)
set (LINK_Fortran_LIBS ${LINK_LIBS})
if (HDF5_ENABLE_F2003)
if (NOT FORTRAN_HAVE_ISO_C_BINDING)
set (HDF5_ENABLE_F2003 OFF)
endif ()
if (NOT H5_FORTRAN_HAVE_ISO_C_BINDING)
message (FATAL_ERROR " **** Fortran compiler lacks required Fortran 2003 features; unsupported Fortran 2003 compiler, disable HDF5_BUILD_FORTRAN **** ")
endif ()
# Parallel IO usage requires MPI to be Linked and Included

4
CTestConfig.cmake
View File

@ -45,9 +45,9 @@ set (VALGRIND_COMMAND_OPTIONS "-v --tool=memcheck --leak-check=full --track-fds=
set (CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
set (CTEST_MEMORYCHECK_COMMAND_OPTIONS "-v --tool=memcheck --leak-check=full --track-fds=yes --num-callers=50 --show-reachable=yes --track-origins=yes --malloc-fill=0xff --free-fill=0xfe")
set (CTEST_TEST_TIMEOUT 600 CACHE STRING
set (CTEST_TEST_TIMEOUT 1200 CACHE STRING
"Maximum time allowed before CTest will kill the test.")
set (DART_TESTING_TIMEOUT 600 CACHE STRING
set (DART_TESTING_TIMEOUT 1200 CACHE STRING
"Maximum time allowed before CTest will kill the test." FORCE)
SET(CTEST_SUBMIT_RETRY_DELAY 20 CACHE STRING

41
MANIFEST
View File

@ -92,6 +92,10 @@
./bin/timekeeper _DO_NOT_DISTRIBUTE_
./bin/trace
./bin/yodconfigure
./bin/batch/cori_ctestP.sl.in.cmake
./bin/batch/cori_ctestS.sl.in.cmake
./bin/batch/cori_knl_ctestP.sl.in.cmake
./bin/batch/cori_knl_ctestS.sl.in.cmake
./bin/batch/ctestP.lsf.in.cmake
./bin/batch/ctestP.sl.in.cmake
./bin/batch/ctestS.lsf.in.cmake
@ -99,6 +103,9 @@
./bin/batch/knl_ctestP.sl.in.cmake
./bin/batch/knl_ctestS.sl.in.cmake
./bin/batch/knl_H5detect.sl.in.cmake
./bin/batch/ray_ctestP.lsf.in.cmake
./bin/batch/ray_ctestS.lsf.in.cmake
./bin/batch/raybsub
./bin/pkgscrpts/h5rmflags _DO_NOT_DISTRIBUTE_
./bin/pkgscrpts/makeHDF5BinaryTarfiles.pl _DO_NOT_DISTRIBUTE_
./bin/pkgscrpts/makeInternalREADME.pl _DO_NOT_DISTRIBUTE_
@ -455,6 +462,7 @@
./release_docs/INSTALL_Warnings.txt
./release_docs/INSTALL_Windows.txt
./release_docs/RELEASE.txt
./release_docs/README_HPC
./release_docs/USING_HDF5_CMake.txt
./release_docs/USING_HDF5_VS.txt
@ -1057,6 +1065,7 @@
./test/le_extlink2.h5
./test/lheap.c
./test/links.c
./test/memleak_H5O_dtype_decode_helper_H5Odtype.h5
./test/mergemsg.h5
./test/mf.c
./test/mount.c
@ -2891,6 +2900,32 @@
./java/src/jni/h5oImp.h
./java/src/jni/h5pImp.c
./java/src/jni/h5pImp.h
./java/src/jni/h5pACPLImp.c
./java/src/jni/h5pACPLImp.h
./java/src/jni/h5pDAPLImp.c
./java/src/jni/h5pDAPLImp.h
./java/src/jni/h5pDCPLImp.c
./java/src/jni/h5pDCPLImp.h
./java/src/jni/h5pDXPLImp.c
./java/src/jni/h5pDXPLImp.h
./java/src/jni/h5pFAPLImp.c
./java/src/jni/h5pFAPLImp.h
./java/src/jni/h5pFCPLImp.c
./java/src/jni/h5pFCPLImp.h
./java/src/jni/h5pGAPLImp.c
./java/src/jni/h5pGAPLImp.h
./java/src/jni/h5pGCPLImp.c
./java/src/jni/h5pGCPLImp.h
./java/src/jni/h5pLAPLImp.c
./java/src/jni/h5pLAPLImp.h
./java/src/jni/h5pLCPLImp.c
./java/src/jni/h5pLCPLImp.h
./java/src/jni/h5pOCPLImp.c
./java/src/jni/h5pOCPLImp.h
./java/src/jni/h5pOCpyPLImp.c
./java/src/jni/h5pOCpyPLImp.h
./java/src/jni/h5pStrCPLImp.c
./java/src/jni/h5pStrCPLImp.h
./java/src/jni/h5plImp.c
./java/src/jni/h5plImp.h
./java/src/jni/h5rImp.c
@ -3250,7 +3285,6 @@
# CMake-specific Examples Files
./config/cmake/HDF5_Examples.cmake.in
./config/cmake/HDF518_Examples.cmake.in
./release_docs/USING_CMake_Examples.txt
./CMakeLists.txt
@ -3362,6 +3396,11 @@
./config/cmake/scripts/HDF5config.cmake
./config/cmake/scripts/HDF5options.cmake
# CMake-specific HPC Scripts
./config/cmake/scripts/HPC/sbatch-HDF5options.cmake
./config/cmake/scripts/HPC/bsub-HDF5options.cmake
./config/cmake/scripts/HPC/raybsub-HDF5options.cmake
# Files generated by autogen
./aclocal.m4
./bin/compile

17
bin/batch/cori_ctestP.sl.in.cmake Normal file
View File

@ -0,0 +1,17 @@
#!/bin/bash
#SBATCH -C haswell
#SBATCH --nodes=1
#SBATCH -t 00:30:00
#SBATCH --mail-type=BEGIN,END,FAIL
##SBATCH --mail-user=<username>@sandia.gov
#SBATCH --export=ALL
#SBATCH --job-name=h5_ctestP
cd @HDF5_BINARY_DIR@
CMD="ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test"
echo "Run $CMD. Test output will be in build/ctestP.out"
$CMD >& ctestP.out
echo "Done running $CMD"

16
bin/batch/cori_ctestS.sl.in.cmake Normal file
View File

@ -0,0 +1,16 @@
#!/bin/bash
#SBATCH -C haswell
#SBATCH --nodes=1
#SBATCH -t 00:30:00
#SBATCH --mail-type=BEGIN,END,FAIL
##SBATCH --mail-user=<username>@sandia.gov
#SBATCH --export=ALL
#SBATCH --job-name=h5_ctestS
cd @HDF5_BINARY_DIR@
CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
echo "Run $CMD. Test output will be in build/ctestS.out"
$CMD >& ctestS.out
echo "Done running $CMD"

17
bin/batch/cori_knl_ctestP.sl.in.cmake Normal file
View File

@ -0,0 +1,17 @@
#!/bin/bash
#SBATCH -C knl,quad,cache
#SBATCH --nodes=1
#SBATCH -t 00:30:00
#SBATCH --mail-type=BEGIN,END,FAIL
##SBATCH --mail-user=<username>@sandia.gov
#SBATCH --export=ALL
#SBATCH --job-name=h5_ctestP
cd @HDF5_BINARY_DIR@
CMD="ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test"
echo "Run $CMD. Test output will be in build/ctestP.out"
$CMD >& ctestP.out
echo "Done running $CMD"

16
bin/batch/cori_knl_ctestS.sl.in.cmake Normal file
View File

@ -0,0 +1,16 @@
#!/bin/bash
#SBATCH -C knl,quad,cache
#SBATCH --nodes=1
#SBATCH -t 00:30:00
#SBATCH --mail-type=BEGIN,END,FAIL
##SBATCH --mail-user=<username>@sandia.gov
#SBATCH --export=ALL
#SBATCH --job-name=h5_ctestS
cd @HDF5_BINARY_DIR@
CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
echo "Run $CMD. Test output will be in build/ctestS.out"
$CMD >& ctestS.out
echo "Done running $CMD"

4
bin/batch/ctestP.sl.in.cmake
View File

@ -5,10 +5,10 @@
#SBATCH --mail-type=BEGIN,END,FAIL
##SBATCH --mail-user=<username>@sandia.gov
#SBATCH --export=ALL
#SBATCH --job-name=h5_ctestS
#SBATCH --job-name=h5_ctestP
cd @HDF5_BINARY_DIR@
CMD="ctest . -R TEST_PAR|PH5DIFF|PERFORM -E t_cache_image -C Release -T test"
CMD="ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test"
echo "Run $CMD. Test output will be in build/ctestP.out"
$CMD >& ctestP.out

2
bin/batch/ctestS.lsf.in.cmake
View File

@ -11,7 +11,7 @@
cd @HDF5_BINARY_DIR@
echo "Run command. Test output will be in build/ctestS.out"
ctest . -E 'TEST_PAR|H5DIFF|PERFORM' -C Release -j 32 -T test >& ctestS.out
ctest . -E 'TEST_PAR|PH5DIFF|PERFORM' -C Release -j 32 -T test >& ctestS.out
##$CMD >& ctestS.out
echo "Done running command."

2
bin/batch/ctestS.sl.in.cmake
View File

@ -8,7 +8,7 @@
#SBATCH --job-name=h5_ctestS
cd @HDF5_BINARY_DIR@
CMD="ctest . -E TEST_PAR|H5DIFF|PERFORM -C Release -j 32 -T test"
CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
echo "Run $CMD. Test output will be in build/ctestS.out"
$CMD >& ctestS.out

4
bin/batch/knl_ctestP.sl.in.cmake
View File

@ -1,6 +1,6 @@
#!/bin/bash
#SBATCH -C knl,quad,cache
#SBATCH -p knl -C quad,cache
#SBATCH --nodes=1
#SBATCH -t 00:30:00
#SBATCH --mail-type=BEGIN,END,FAIL
@ -10,7 +10,7 @@
cd @HDF5_BINARY_DIR@
#run parallel tests except t_cache_image test
CMD="ctest . -R TEST_PAR|PH5DIFF|PERFORM -E t_cache_image -C Release -T test"
CMD="ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test"
echo "Run $CMD. Test output will be in build/ctestP.out"
$CMD >& ctestP.out

4
bin/batch/knl_ctestS.sl.in.cmake
View File

@ -1,6 +1,6 @@
#!/bin/bash
#SBATCH -C knl,quad,cache
#SBATCH -p knl -C quad,cache
#SBATCH --nodes=1
#SBATCH -t 00:30:00
#SBATCH --mail-type=BEGIN,END,FAIL
@ -9,7 +9,7 @@
#SBATCH --job-name=h5_ctestS
cd @HDF5_BINARY_DIR@
CMD="ctest . -E TEST_PAR|H5DIFF|PERFORM -C Release -j 32 -T test"
CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
echo "Run $CMD. Test output will be in build/ctestS.out"
$CMD >& ctestS.out

20
bin/batch/ray_ctestP.lsf.in.cmake Normal file
View File

@ -0,0 +1,20 @@
#!/bin/tcsh
### LSF syntax
#BSUB -n 6 #number of nodes
#BSUB -R "span[ptile=6]"
#BSUB -W 30 #walltime in minutes
#BSUB -G guests #account
#BSUB -e ctestPerrors.txt #stderr
#BSUB -o ctestPoutput.txt #stdout
#BSUB -J hdf5_ctestP #job
##BSUB -q pbatch #queue to use
#BSUB -q pdebug
##date; hostname
##echo -n 'JobID is '; echo $LSB_JOBID
cd @HDF5_BINARY_DIR@
echo "Run parallel test command. Test output will be in build/ctestP.out"
ctest . -R 'MPI_TEST_' -E t_cache_image -C Release -T test >& ctestP.out
echo "Done running ctest parallel command."

18
bin/batch/ray_ctestS.lsf.in.cmake Normal file
View File

@ -0,0 +1,18 @@
#!/bin/tcsh
### LSF syntax
#BSUB -n 1 #number of nodes
#BSUB -W 29 #walltime in minutes
#BSUB -G guests #account
#BSUB -e ctestSerrors.txt #stderr
#BSUB -o ctestSoutput.txt #stdout
#BSUB -J hdf5_ctestS #job
##BSUB -q pbatch #queue to use
#BSUB -q pdebug
cd @HDF5_BINARY_DIR@
echo "Run command. Test output will be in build/ctestS.out"
ctest . -E 'MPI_TEST_' -C Release -j 32 -T test >& ctestS.out
##$CMD >& ctestS.out
echo "Done running command."

7
bin/batch/raybsub Executable file
View File

@ -0,0 +1,7 @@
#!/bin/tcsh
# ray.llnl.gov requires a '<' with bsub for submitting .lsf batch jobs.
# CMake is reluctant to pass the '<', so we put it in this script and use
# the script to submit the bsub command on ray.
bsub < $1

110
bin/release
View File

@ -55,13 +55,21 @@ for compressing the resulting tar archive (if none are given then
tar -- use tar and don't do any compressing.
gzip -- use gzip with "-9" and append ".gz" to the output name.
bzip2 -- use bzip2 with "-9" and append ".bz2" to the output name.
zip -- convert all text files to DOS style and form a zip file for Windows use.
cmake-tgz -- create a tar file using the gzip default level with a build-unix.sh
command file and all other CMake files needed to build HDF5 source
using CMake on unix machines.
bzip2 -- use bzip2 with "-9" and append ".bz2" to the output name.
zip -- convert all text files to DOS style and form a zip file for Windows use.
cmake-zip -- convert all text files to DOS style and create a zip file inluding cmake
scripts and .bat files to build HDF5 source using CMake on Windows.
hpc-cmake-tgz
-- create a tar file using the gzip default level with a build-unix.sh
command file and all other CMake files needed to build HDF5 source
using CMake on unix machines, with HDF5options.cmake files for serial
and parallel builds on machines requiring batch jobs to run tests.
The default is for parallel build, with serial only build by changing
the HDF5options.cmake symlink to ser-HDF5options.cmake. More
information is available in the README_HPC file.
doc -- produce the latest doc tree in addition to the archive.
An md5 checksum is produced for each archive created and stored in the md5 file.
@ -225,7 +233,7 @@ tar2cmakezip()
# step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.10-Source.tar.gz $cmziptmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.12.4-Source.zip $cmziptmpsubdir
cp $cmziptmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpsubdir
cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpsubdir
cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmziptmpsubdir
@ -256,7 +264,7 @@ tar2cmakezip()
}
# Function name: tar2cmaketgz
# Convert the release tarball to a Windows zipball with files to run CMake build.
# Convert the release tarball to a gzipped tar file with files to run CMake build.
#
# Programmer: Larry Knox
# Creation date: 2017-02-20
@ -320,7 +328,7 @@ tar2cmaketgz()
# step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.10-Source.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.12.4-Source.tar.gz $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpsubdir
@ -330,6 +338,93 @@ tar2cmaketgz()
rm -rf $cmgztmpdir
}
# Function name: tar2hpccmaketgz
# Convert the release tarball to a gzipped tarfile with files to run CMake build
# and HDF5options.cmake files for parallel or serial only builds where build
# tests are run on compute nodes using batch scripts.
#
# Programmer: Larry Knox
# Creation date: 2019-01-28
#
# Modifications
#
# Steps:
# 1. untar the tarball in a temporary directory;
# Note: do this in a temporary directory to avoid changing
# the original source directory which may be around.
# 2. add build-unix.sh script.
# 3. add SZIP.tar.gz, ZLib.tar.gz and cmake files to top level directory.
# 4. create gzipped tar file with these contents:
# build-unix.sh script
# hdf5-<version> source code directory extracted from tar file
# CTestScript.cmake cmake file copied from <hdf5 source code>/config/cmake/scripts
# HDF5config.cmake cmake file copied from <hdf5 source code>/config/cmake/scripts
# HDF5options.cmake cmake file copied from <hdf5 source code>/config/cmake/scripts
# SZip.tar.gz copied from /mnt/scr1/pre-release/hdf5/CMake
# ZLib.tar.gz copied from /mnt/scr1/pre-release/hdf5/CMake
#
# 5. For HPC-CMake tgz file the following are also needed in the top-level directory:
# README_HPC copied from release_docs
# ser-HDF5options.cmake copied from <hdf5 source code>/config/cmake/scripts/HPC
# par-HDF5options.cmake copied from <hdf5 source code>/config/cmake/scripts/HPC
# HDF5options.cmake symlink to par-HDF5options.cmake
#
# Parameters:
# $1 version
# $2 release tarball
# $3 output zipball file name
#
# Returns 0 if successful; 1 otherwise
#
# need function to create another temporary directory, extract the
# $tmpdir/$HDF5_VERS.tar into it, create build-unix.sh,
# add CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz
# ZLib.tar.gz, HDF5 examples, and then tar.gz it.
tar2hpccmaketgz()
{
if [ $# -ne 3 ]; then
echo "usage: tar2hpccmaketgz <tarfilename> <tgzfilename>"
return 1
fi
cmgztmpdir=/tmp/cmgztmpdir$$
cmgztmpsubdir=$cmgztmpdir/HPC-CMake-$HDF5_VERS
mkdir -p $cmgztmpsubdir
version=$1
tarfile=$2
tgzfile=$3
# step 1: untar tarball in cmgztmpdir
(cd $cmgztmpsubdir; tar xf -) < $tarfile
# sanity check
if [ ! -d $cmgztmpsubdir/$version ]; then
echo "untar did not create $cmgztmpsubdir/$version source dir"
# cleanup
rm -rf $cmgztmpdir
return 1
fi
# step 2: add build-unix.sh script
(cd $cmgztmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log" > build-unix.sh; chmod 755 build-unix.sh)
# step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.12.4-Source.tar.gz $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/release_docs/README_HPC $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HPC/ser-HDF5options.cmake $cmgztmpsubdir
cp $cmgztmpsubdir/$version/config/cmake/scripts/HPC/par-HDF5options.cmake $cmgztmpsubdir
(cd $cmgztmpsubdir; ln -s par-HDF5options.cmake HDF5options.cmake)
tar czf $DEST/HPC-CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1
# cleanup
rm -rf $cmgztmpdir
}
# This command must be run at the top level of the hdf5 source directory.
# Verify this requirement.
if [ ! \( -f configure.ac -a -f bin/release \) ]; then
@ -514,6 +609,11 @@ for comp in $methods; do
tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
(cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file)
;;
hpc-cmake-tgz)
test "$verbose" && echo " Creating HPC-CMake tar.gz file..." 1>&2
tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
(cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file)
;;
bzip2)
test "$verbose" && echo " Running bzip2..." 1>&2
bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2

8
c++/examples/CMakeTests.cmake
View File

@ -26,7 +26,7 @@
SDSextendible.h5
Select.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (CPP_ex-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "CPP_ex-clear-objects")
@ -46,7 +46,7 @@
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (CPP_ex_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "CPP_ex_${example}")
@ -66,7 +66,7 @@
h5tutr_groups.h5
h5tutr_subset.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (CPP_ex_tutr-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "CPP_ex_tutr-clear-objects")
@ -86,7 +86,7 @@
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (CPP_ex_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "CPP_ex_${example}")

11
c++/src/H5LaccProp.h
View File

@ -12,9 +12,6 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
// Class LinkAccPropList represents the HDF5 file access property list and
// inherits from DataType.
#ifndef __H5LinkAccPropList_H
#define __H5LinkAccPropList_H
@ -22,15 +19,15 @@ namespace H5 {
/*! \class LinkAccPropList
\brief Class LinkAccPropList inherits from PropList and provides
wrappers for the HDF5 file access property list.
wrappers for the HDF5 link access property list.
*/
// Inheritance: PropList -> IdComponent
class H5_DLLCPP LinkAccPropList : public PropList {
public:
///\brief Default file access property list.
///\brief Default link access property list.
static const LinkAccPropList& DEFAULT;
// Creates a file access property list.
// Creates a link access property list.
LinkAccPropList();
///\brief Returns this class name.
@ -39,7 +36,7 @@ class H5_DLLCPP LinkAccPropList : public PropList {
// Copy constructor: same as the original LinkAccPropList.
LinkAccPropList(const LinkAccPropList& original);
// Creates a copy of an existing file access property list
// Creates a copy of an existing link access property list
// using the property list id.
LinkAccPropList (const hid_t plist_id);

11
c++/src/H5LcreatProp.h
View File

@ -12,9 +12,6 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
// Class LinkCreatPropList represents the HDF5 file access property list and
// inherits from DataType.
#ifndef __H5LinkCreatPropList_H
#define __H5LinkCreatPropList_H
@ -22,15 +19,15 @@ namespace H5 {
/*! \class LinkCreatPropList
\brief Class LinkCreatPropList inherits from PropList and provides
wrappers for the HDF5 file access property list.
wrappers for the HDF5 link creation property list.
*/
// Inheritance: PropList -> IdComponent
class H5_DLLCPP LinkCreatPropList : public PropList {
public:
///\brief Default file access property list.
///\brief Default link creation property list.
static const LinkCreatPropList& DEFAULT;
// Creates a file access property list.
// Creates a link creation property list.
LinkCreatPropList();
///\brief Returns this class name.
@ -39,7 +36,7 @@ class H5_DLLCPP LinkCreatPropList : public PropList {
// Copy constructor: same as the original LinkCreatPropList.
LinkCreatPropList(const LinkCreatPropList& original);
// Creates a copy of an existing file access property list
// Creates a copy of an existing link creation property list
// using the property list id.
LinkCreatPropList (const hid_t plist_id);

73
c++/src/H5Object.cpp
View File

@ -40,9 +40,8 @@
namespace H5 {
#ifndef DOXYGEN_SHOULD_SKIP_THIS
// userAttrOpWrpr simply interfaces between the user's function and the
// C library function H5Aiterate2; used to resolve the different prototype
// problem. May be moved to Iterator later.
// userAttrOpWrpr interfaces between the user's function and the
// C library function H5Aiterate2
extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
const H5A_info_t *ainfo, void *op_data)
{
@ -52,6 +51,17 @@ extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
return 0;
}
// userVisitOpWrpr interfaces between the user's function and the
// C library function H5Ovisit2
extern "C" herr_t userVisitOpWrpr(hid_t obj_id, const char *attr_name,
const H5O_info_t *obj_info, void *op_data)
{
H5std_string s_attr_name = H5std_string(attr_name);
UserData4Visit* myData = reinterpret_cast<UserData4Visit *> (op_data);
int status = myData->op(*myData->obj, s_attr_name, obj_info, myData->opData);
return status;
}
//--------------------------------------------------------------------------
// Function: H5Object default constructor (protected)
// Programmer Binh-Minh Ribler - 2000
@ -197,8 +207,6 @@ Attribute H5Object::openAttribute(const unsigned int idx) const
///\par Description
/// The signature of user_op is
/// void (*)(H5::H5Location&, H5std_string, void*).
/// For information, please refer to the H5Aiterate2 API in
/// the HDF5 C Reference Manual.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int H5Object::iterateAttrs(attr_operator_t user_op, unsigned *_idx, void *op_data)
@ -227,6 +235,61 @@ int H5Object::iterateAttrs(attr_operator_t user_op, unsigned *_idx, void *op_dat
throw AttributeIException(inMemFunc("iterateAttrs"), "H5Aiterate2 failed");
}
//--------------------------------------------------------------------------
// Function: H5Object::visit
///\brief Recursively visits all HDF5 objects accessible from this object.
///\param idx_type - IN: Type of index; valid values include:
/// \li \c H5_INDEX_NAME
/// \li \c H5_INDEX_CRT_ORDER
///\param order - IN: Order in which index is traversed; valid values include:
/// \li \c H5_ITER_DEC
/// \li \c H5_ITER_INC
/// \li \c H5_ITER_NATIVE
///\param user_op - IN: Callback function passing data regarding the
/// object to the calling application
///\param *op_data - IN: User-defined pointer to data required by the
/// application for its processing of the object
///\param fields - IN: Flags specifying the fields to be retrieved
/// to the callback op via the H5O_info_t argument.
/// \li \c H5O_INFO_BASIC fileno, addr, type, and rc fields
/// \li \c H5O_INFO_TIME atime, mtime, ctime, and btime fields
/// \li \c H5O_INFO_NUM_ATTRS num_attrs field
/// \li \c H5O_INFO_HDR hdr field
/// \li \c H5O_INFO_META_SIZE meta_size field
/// \li \c H5O_INFO_ALL H5O_INFO_BASIC | H5O_INFO_TIME | H5O_INFO_NUM_ATTRS | H5O_INFO_HDR | H5O_INFO_META_SIZE
///\return
/// \li On success:
/// \li the return value of the first operator that returns a positive value
/// \li zero if all members were processed with no operator returning non-zero
/// \li On failure:
/// \li an exception Exception will be thrown if something went
/// wrong within the library or the operator failed
///\exception H5::Exception
///\par Description
/// For information, please refer to the H5Ovisit2 API in the HDF5
/// C Reference Manual.
// Programmer Binh-Minh Ribler - Feb, 2019
//--------------------------------------------------------------------------
void H5Object::visit(H5_index_t idx_type, H5_iter_order_t order, visit_operator_t user_op, void *op_data, unsigned int fields)
{
// Store the user's function and data
UserData4Visit* userData = new UserData4Visit;
userData->opData = op_data;
userData->op = user_op;
userData->obj = this;
// Call the C API passing in op wrapper and info
herr_t ret_value = H5Ovisit2(getId(), idx_type, order, userVisitOpWrpr, static_cast<void *>(userData), fields);
// Release memory
delete userData;
// Throw exception if H5Ovisit2 failed, which could be a failure in
// the library or in the call back operator
if (ret_value < 0)
throw Exception(inMemFunc("visit"), "H5Ovisit2 failed");
}
//--------------------------------------------------------------------------
// Function: H5Object::objVersion
///\brief Returns the header version of this HDF5 object.

26
c++/src/H5Object.h
View File

@ -40,16 +40,30 @@ namespace H5 {
// Inheritance: H5Location -> IdComponent
// Define the operator function pointer for H5Aiterate().
typedef void (*attr_operator_t)(H5Object& loc/*in*/,
const H5std_string attr_name/*in*/,
void *operator_data/*in,out*/);
typedef void (*attr_operator_t)(H5Object& loc,
const H5std_string attr_name,
void *operator_data);
// Define the operator function pointer for H5Ovisit2().
typedef int (*visit_operator_t)(H5Object& obj,
const H5std_string attr_name,
const H5O_info_t *oinfo,
void *operator_data);
// User data for attribute iteration
class UserData4Aiterate {
public:
attr_operator_t op;
void* opData;
H5Object* location;
H5Object* location; // Consider changing to H5Location
};
// User data for visit iteration
class UserData4Visit {
public:
visit_operator_t op;
void* opData;
H5Object* obj;
};
class H5_DLLCPP H5Object : public H5Location {
@ -71,6 +85,9 @@ class H5_DLLCPP H5Object : public H5Location {
// Iterate user's function over the attributes of this object.
int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
// Recursively visit elements reachable from this object.
void visit(H5_index_t idx_type, H5_iter_order_t order, visit_operator_t user_op, void *op_data, unsigned int fields);
// Returns the object header version of an object
unsigned objVersion() const;
@ -98,6 +115,7 @@ class H5_DLLCPP H5Object : public H5Location {
ssize_t getObjName(H5std_string& obj_name, size_t len = 0) const;
H5std_string getObjName() const;
#ifndef DOXYGEN_SHOULD_SKIP_THIS
protected:

2
c++/test/CMakeVFDTests.cmake
View File

@ -55,7 +55,7 @@
-P "${HDF_RESOURCES_DIR}/vfdTest.cmake"
)
set_tests_properties (CPP_VFD-${vfdname}-cpp_testhdf5 PROPERTIES DEPENDS CPP_VFD-${vfdname}-cpp_testhdf5-clear-objects)
set_tests_properties (CPP_VFD-${vfdname}-cpp_testhdf5 PROPERTIES TIMEOUT 30)
set_tests_properties (CPP_VFD-${vfdname}-cpp_testhdf5 PROPERTIES TIMEOUT ${CTEST_SHORT_TIMEOUT})
endif ()
endmacro ()

3
c++/test/tarray.cpp
View File

@ -286,7 +286,7 @@ H5::DataType getArr()
*dims = 5;
H5::ArrayType ret;
ret = H5::ArrayType(H5::PredType::NATIVE_INT, 1, dims);
delete[] dims;
delete dims;
return ret;
}
@ -371,7 +371,6 @@ static void test_array_info()
s1_t rdata[SPACE1_DIM1][ARRAY1_DIM1]; // Information read in
hsize_t sdims1[] = {SPACE1_DIM1};
hsize_t tdims1[] = {ARRAY1_DIM1};
int nmemb; // Number of compound members
int ii; // counting variables
hsize_t idxi, idxj, idxk; // dimension indicing variables
H5T_class_t mclass; // Datatype class for field

416
c++/test/tlinks.cpp
View File

@ -31,288 +31,27 @@ using namespace H5;
#include "h5test.h"
#include "h5cpputil.h" // C++ utilility header file
// A lot of the definition inherited from C test links.c is left here until
// the H5L API is implemented and tests are completed - BMR 10/19/2009
/*
* This file needs to access private information from the H5G package.
* This file also needs to access the group testing code.
*/
//#define H5G_FRIEND
//#define H5G_TESTING
//#include "h5test.h"
//#include "H5Gpkg.h" /* Groups */
//#include "H5Iprivate.h" /* IDs */
//#include "H5Lprivate.h" /* Links */
/* File for external link test. Created with gen_udlinks.c */
#define LINKED_FILE "be_extlink2.h5"
#if 0
const char *FILENAME[] = {
"links0",
"links1",
"links2",
"links3",
"links4a", /* 4 */
"links4b", /* 5 */
"links4c", /* 6 */
"links4d", /* 7 */
"links5", /* 8 */
"links6", /* 9 */
"links7", /* 10 */
"links8", /* 11 */
"extlinks0", /* 12: main files */
"tmp/extlinks0", /* 13: */
"extlinks1", /* 14: target files */
"tmp/extlinks1", /* 15: */
"extlinks2", /* 16: */
"tmp/extlinks2", /* 17: */
"extlinks3", /* 18: */
"tmp/extlinks3", /* 19: */
"extlinks4", /* 20: */
"tmp/extlinks4", /* 21: */
"extlinks5", /* 22: */
"tmp/extlinks6", /* 23: */
"extlinks7", /* 24: */
"tmp/extlinks7", /* 25: */
"tmp/extlinks8", /* 26: */
"extlinks9", /* 27: */
"tmp/extlinks9", /* 28: */
"extlinks10", /* 29: */ /* TESTS for windows */
"tmp/extlinks10", /* 30: */
"tmp/extlinks11", /* 31: */
"tmp/extlinks12", /* 32: */
"extlinks13", /* 33: */
"tmp/extlinks13", /* 34: */
"tmp/extlinks14", /* 35: */
"tmp/extlinks15", /* 36: */
"extlinks16A", /* 37: */ /* TESTS for H5P_set_elink_fapl */
"extlinks16B", /* 38: */
"extlinks17", /* 39: */
"extlinks18A", /* 40: */
"extlinks18B", /* 41: */
"extlinks19A", /* 42: */
"extlinks19B", /* 43: */
"extlinks20", /* 44: */
NULL
};
#endif // 0
#define TMPDIR "tmp"
#define FAMILY_SIZE 1024
#define CORE_INCREMENT 1024
#define NUM400 400
/* do not do check_all_closed() for "ext*" files and "tmp/ext*" */
#define EXTSTOP 12
#define LINK_BUF_SIZE 1024
#define NAME_BUF_SIZE 1024
#define MAX_NAME_LEN ((64*1024)+1024)
/* Link type IDs */
#define UD_HARD_TYPE 201
#define UD_CB_TYPE H5L_TYPE_MAX
#define UD_PLIST_TYPE 128
#define UD_CBFAIL_TYPE UD_PLIST_TYPE
#define UD_ERROR_TYPE 189
#define UD_BAD_TYPE1 H5L_TYPE_HARD
#define UD_BAD_TYPE2 (H5L_TYPE_UD_MIN - 5)
#define UD_BAD_VERS (H5L_LINK_CLASS_T_VERS + 1)
#define DEST_PROP_NAME "destination_group"
#define REREG_TARGET_NAME "rereg_target"
#define UD_CB_LINK_NAME "ud_callback_link"
#define NEW_UD_CB_LINK_NAME "ud_callback_link2"
#define UD_CB_TARGET "ud_target"
#define UD_CB_TARGET_LEN 10
#define LE_FILENAME "le_extlink1.h5"
#define BE_FILENAME "be_extlink1.h5"
#define ELINK_CB_FAM_SIZE (hsize_t) 100
#define H5L_DIM1 100
#define H5L_DIM2 100
/* Creation order macros */
#define CORDER_SOFT_GROUP_NAME "corder_soft_group"
#define CORDER_NLINKS 18
/* Timestamp macros */
#define TIMESTAMP_GROUP_1 "timestamp1"
#define TIMESTAMP_GROUP_2 "timestamp2"
/* Link iteration struct */
typedef struct {
H5_iter_order_t order; /* Direction of iteration */
unsigned ncalled; /* # of times callback is entered */
unsigned nskipped; /* # of links skipped */
int stop; /* # of iterations to stop after */
int64_t curr; /* Current creation order value */
size_t max_visit; /* Size of "visited link" flag array */
hbool_t *visited; /* Pointer to array of "visited link" flags */
} link_iter_info_t;
#if 0
/* Link visit structs */
typedef struct {
const char *path; /* Path to link */
H5L_type_t type; /* Type of link */
} link_visit_t;
static const link_visit_t lvisit0[] = {
{"Dataset_zero", H5L_TYPE_HARD},
{"Group1", H5L_TYPE_HARD},
{"Group1/Dataset_one", H5L_TYPE_HARD},
{"Group1/Group2", H5L_TYPE_HARD},
{"Group1/Group2/Dataset_two", H5L_TYPE_HARD},
{"Group1/Group2/Type_two", H5L_TYPE_HARD},
{"Group1/Group2/hard_zero", H5L_TYPE_HARD},
{"Group1/Type_one", H5L_TYPE_HARD},
{"Group1/hard_one", H5L_TYPE_HARD},
{"Type_zero", H5L_TYPE_HARD},
{"ext_dangle", H5L_TYPE_EXTERNAL},
{"ext_one", H5L_TYPE_EXTERNAL},
{"hard_one", H5L_TYPE_HARD},
{"hard_two", H5L_TYPE_HARD},
{"hard_zero", H5L_TYPE_HARD},
{"soft_dangle", H5L_TYPE_SOFT},
{"soft_one", H5L_TYPE_SOFT},
{"soft_two", H5L_TYPE_SOFT}
};
static const link_visit_t lvisit1[] = {
{"Dataset_one", H5L_TYPE_HARD},
{"Group2", H5L_TYPE_HARD},
{"Group2/Dataset_two", H5L_TYPE_HARD},
{"Group2/Type_two", H5L_TYPE_HARD},
{"Group2/hard_zero", H5L_TYPE_HARD},
{"Group2/hard_zero/Dataset_zero", H5L_TYPE_HARD},
{"Group2/hard_zero/Group1", H5L_TYPE_HARD},
{"Group2/hard_zero/Type_zero", H5L_TYPE_HARD},
{"Group2/hard_zero/ext_dangle", H5L_TYPE_EXTERNAL},
{"Group2/hard_zero/ext_one", H5L_TYPE_EXTERNAL},
{"Group2/hard_zero/hard_one", H5L_TYPE_HARD},
{"Group2/hard_zero/hard_two", H5L_TYPE_HARD},
{"Group2/hard_zero/hard_zero", H5L_TYPE_HARD},
{"Group2/hard_zero/soft_dangle", H5L_TYPE_SOFT},
{"Group2/hard_zero/soft_one", H5L_TYPE_SOFT},
{"Group2/hard_zero/soft_two", H5L_TYPE_SOFT},
{"Type_one", H5L_TYPE_HARD},
{"hard_one", H5L_TYPE_HARD}
};
static const link_visit_t lvisit2[] = {
{"Dataset_two", H5L_TYPE_HARD},
{"Type_two", H5L_TYPE_HARD},
{"hard_zero", H5L_TYPE_HARD},
{"hard_zero/Dataset_zero", H5L_TYPE_HARD},
{"hard_zero/Group1", H5L_TYPE_HARD},
{"hard_zero/Group1/Dataset_one", H5L_TYPE_HARD},
{"hard_zero/Group1/Group2", H5L_TYPE_HARD},
{"hard_zero/Group1/Type_one", H5L_TYPE_HARD},
{"hard_zero/Group1/hard_one", H5L_TYPE_HARD},
{"hard_zero/Type_zero", H5L_TYPE_HARD},
{"hard_zero/ext_dangle", H5L_TYPE_EXTERNAL},
{"hard_zero/ext_one", H5L_TYPE_EXTERNAL},
{"hard_zero/hard_one", H5L_TYPE_HARD},
{"hard_zero/hard_two", H5L_TYPE_HARD},
{"hard_zero/hard_zero", H5L_TYPE_HARD},
{"hard_zero/soft_dangle", H5L_TYPE_SOFT},
{"hard_zero/soft_one", H5L_TYPE_SOFT},
{"hard_zero/soft_two", H5L_TYPE_SOFT}
};
typedef struct {
unsigned idx; /* Index in link visit structure */
const link_visit_t *info; /* Pointer to the link visit structure to use */
} lvisit_ud_t;
/* Object visit structs */
// Object visit structs
typedef struct {
const char *path; /* Path to object */
H5O_type_t type; /* Type of object */
} obj_visit_t;
static const obj_visit_t ovisit0_old[] = {
{".", H5O_TYPE_GROUP},
{"Dataset_zero", H5O_TYPE_DATASET},
{"Group1", H5O_TYPE_GROUP},
{"Group1/Dataset_one", H5O_TYPE_DATASET},
{"Group1/Group2", H5O_TYPE_GROUP},
{"Group1/Group2/Dataset_two", H5O_TYPE_DATASET},
{"Group1/Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
{"Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
{"Type_zero", H5O_TYPE_NAMED_DATATYPE}
};
static const obj_visit_t ovisit0_new[] = {
{".", H5O_TYPE_GROUP},
{"Dataset_zero", H5O_TYPE_DATASET},
{"Group1", H5O_TYPE_GROUP},
{"Group1/Dataset_one", H5O_TYPE_DATASET},
{"Group1/Group2", H5O_TYPE_GROUP},
{"Group1/Group2/Dataset_two", H5O_TYPE_DATASET},
{"Group1/Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
{"Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
{"Type_zero", H5O_TYPE_NAMED_DATATYPE}
};
static const obj_visit_t ovisit1_old[] = {
{".", H5O_TYPE_GROUP},
{"Dataset_one", H5O_TYPE_DATASET},
{"Group2", H5O_TYPE_GROUP},
{"Group2/Dataset_two", H5O_TYPE_DATASET},
{"Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
{"Group2/hard_zero", H5O_TYPE_GROUP},
{"Group2/hard_zero/Dataset_zero", H5O_TYPE_DATASET},
{"Group2/hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE},
{"Type_one", H5O_TYPE_NAMED_DATATYPE}
};
static const obj_visit_t ovisit1_new[] = {
{".", H5O_TYPE_GROUP},
{"Dataset_one", H5O_TYPE_DATASET},
{"Group2", H5O_TYPE_GROUP},
{"Group2/Dataset_two", H5O_TYPE_DATASET},
{"Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
{"Group2/hard_zero", H5O_TYPE_GROUP},
{"Group2/hard_zero/Dataset_zero", H5O_TYPE_DATASET},
{"Group2/hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE},
{"Type_one", H5O_TYPE_NAMED_DATATYPE}
};
static const obj_visit_t ovisit2_old[] = {
{".", H5O_TYPE_GROUP},
{"Dataset_two", H5O_TYPE_DATASET},
{"Type_two", H5O_TYPE_NAMED_DATATYPE},
{"hard_zero", H5O_TYPE_GROUP},
{"hard_zero/Dataset_zero", H5O_TYPE_DATASET},
{"hard_zero/Group1", H5O_TYPE_GROUP},
{"hard_zero/Group1/Dataset_one", H5O_TYPE_DATASET},
{"hard_zero/Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
{"hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE}
};
static const obj_visit_t ovisit2_new[] = {
{".", H5O_TYPE_GROUP},
{"Dataset_two", H5O_TYPE_DATASET},
{"Type_two", H5O_TYPE_NAMED_DATATYPE},
{"hard_zero", H5O_TYPE_GROUP},
{"hard_zero/Dataset_zero", H5O_TYPE_DATASET},
{"hard_zero/Group1", H5O_TYPE_GROUP},
{"hard_zero/Group1/Dataset_one", H5O_TYPE_DATASET},
{"hard_zero/Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
{"hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE}
};
// User data for callback function
typedef struct {
unsigned idx; /* Index in object visit structure */
const obj_visit_t *info; /* Pointer to the object visit structure to use */
} ovisit_ud_t;
#endif
static const char *FILENAME[] = {
"link0",
"link1.h5",
"link2.h5",
"visit",
NULL
};
@ -841,6 +580,140 @@ static void test_num_links(hid_t fapl_id, hbool_t new_format)
}
} // test_num_links
// Data for visit on the file
static const obj_visit_t file_visit[] = {
{".", H5O_TYPE_GROUP},
{"Data", H5O_TYPE_GROUP},
{"Data/Compressed_Data", H5O_TYPE_DATASET},
{"Data/Float_Data", H5O_TYPE_DATASET},
};
// Data for visit on the group
static const obj_visit_t group_visit[] = {
{".", H5O_TYPE_GROUP},
{"Compressed_Data", H5O_TYPE_DATASET},
{"Float_Data", H5O_TYPE_DATASET},
};
const H5std_string FILE_NAME("tvisit.h5");
const H5std_string GROUP_NAME("/Data");
const H5std_string DSET1_NAME("/Data/Compressed_Data");
const H5std_string DSET2_NAME("/Data/Float_Data");
const int RANK = 2;
const int DIM1 = 2;
// Operator function
static int visit_obj_cb(H5Object& obj, const H5std_string name, const H5O_info_t *oinfo, void *_op_data)
{
ovisit_ud_t *op_data = static_cast <ovisit_ud_t *>(_op_data);
// Check for correct object information
if(strcmp(op_data->info[op_data->idx].path, name.c_str())) return(H5_ITER_ERROR);
if(op_data->info[op_data->idx].type != oinfo->type) return(H5_ITER_ERROR);
// Advance to next location
op_data->idx++;
return(H5_ITER_CONT);
}
/*-------------------------------------------------------------------------
* Function: test_visit
*
* Purpose Test H5Object::visit
*
* Return None
*
* February 8, 2019
*-------------------------------------------------------------------------
*/
static void test_visit(hid_t fapl_id, hbool_t new_format)
{
hsize_t dims[2];
hsize_t cdims[2];
char filename[NAME_BUF_SIZE];
if(new_format)
SUBTEST("H5Object::visit (w/new group format)")
else
SUBTEST("H5Object::visit")
try
{
// Use the file access template id to create a file access prop. list
FileAccPropList fapl(fapl_id);
// Build the hdf5 file name and create the file
h5_fixname(FILENAME[3], fapl_id, filename, sizeof filename);
H5File *file = new H5File(filename, H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, fapl);
// Create a group
Group* group = new Group(file->createGroup(GROUP_NAME));
// Create a chunked/compressed dataset within this group specified by path
dims[0] = 20;
dims[1] = 2;
cdims[0] = 2;
cdims[1] = 2;
DataSpace *dataspace = new DataSpace(RANK, dims); // create new dspace
DSetCreatPropList ds_creatplist; // create dataset creation prop list
ds_creatplist.setChunk(2, cdims); // then modify it for compression
ds_creatplist.setDeflate(6);
DataSet* dataset = new DataSet(file->createDataSet(DSET1_NAME,
PredType::NATIVE_INT, *dataspace, ds_creatplist));
delete dataset;
delete dataspace;
// Create another dataset
dims[0] = 5;
dims[1] = 2;
dataspace = new DataSpace(RANK, dims); // create second dspace
dataset = new DataSet(file->createDataSet(DSET2_NAME,
PredType::NATIVE_FLOAT, *dataspace));
// Close everything
delete dataset;
delete dataspace;
delete group;
delete file;
// Reopen the file and group in the file.
file = new H5File(filename, H5F_ACC_RDWR);
group = new Group(file->openGroup("Data"));
// Open the group
dataset = new DataSet(group->openDataSet(DSET2_NAME));
delete dataset;
// Visit objects in the file
ovisit_ud_t udata; /* User-data for visiting */
udata.idx = 0;
udata.info = file_visit;
file->visit(H5_INDEX_NAME, H5_ITER_INC, visit_obj_cb, &udata, H5O_INFO_BASIC);
// Visit objects in the group
udata.idx = 0;
udata.info = group_visit;
group->visit(H5_INDEX_NAME, H5_ITER_INC, visit_obj_cb, &udata, H5O_INFO_BASIC);
// Close the group and file.
delete group;
delete file;
PASSED();
} // end of try block
catch (Exception& E)
{
cerr << "in catch" << endl;
issue_fail_msg("test_visit()", __LINE__, __FILE__, E.getCDetailMsg());
}
} // test_visit()
/*-------------------------------------------------------------------------
* Function: test_links
@ -858,7 +731,8 @@ void test_links()
hid_t fapl_id, fapl2_id; /* File access property lists */
unsigned new_format; /* Whether to use the new format or not */
fapl_id = h5_fileaccess();
if((fapl_id = h5_fileaccess()) < 0)
throw Exception("test_links", "Unable to get file access property list");
// Output message about test being performed
MESSAGE(5, ("Testing Various Links\n"));
@ -891,24 +765,18 @@ void test_links()
test_move(my_fapl_id, new_format);
test_copy(my_fapl_id, new_format);
test_lcpl(my_fapl_id, new_format);
test_visit(my_fapl_id, new_format);
} /* end for */
/* Close 2nd FAPL */
H5Pclose(fapl2_id);
h5_clean_files(FILENAME, fapl_id);
/* Test that external links can be used after a library reset. MUST be
* called last so the reset doesn't interfere with the property lists. This
* routine will delete its own file. */
/* nerrors += external_reset_register() < 0 ? 1 : 0;
*/
}
catch (Exception& E)
{
issue_fail_msg("test_links()", __LINE__, __FILE__, E.getCDetailMsg());
}
}
@ -926,7 +794,3 @@ void cleanup_links()
HDremove(FILENAME[0]);
HDremove(FILENAME[1]);
}

19
config/cmake/CTestCustom.cmake
View File

@ -41,16 +41,20 @@ set (CTEST_CUSTOM_MEMCHECK_IGNORE
H5TEST-err_compat #uses runTest.cmake
H5TEST-links_env #uses runTest.cmake
H5TEST-testlibinfo #uses grepTest.cmake
H5TEST-clear-testhdf5-objects
#########
H5TEST-clear-objects
H5TEST-clear-cache-objects
H5TEST-clear-cache_api-objects
H5TEST-clear-cache_image-objects
H5TEST-clear-cache_tagging-objects
H5TEST-clear-del_many_dense_attrs-objects
H5TEST-clear-err_compat-objects
H5TEST-clear-error_test-objects
H5TEST-clear-filenotclosed-objects
H5TEST-clear-flush-objects
H5TEST-clear-links_env-objects
H5TEST-clear-testflushrefresh-objects
H5TEST-clear-testhdf5-objects
H5TEST-clear-ttsafe-objects
PERFORM_h5perform-clear-objects
HL_TOOLS-clear-objects
@ -60,11 +64,19 @@ set (CTEST_CUSTOM_MEMCHECK_IGNORE
CPP_testhdf5-clear-objects
######### tools/h5clear #########
H5CLEAR-clearall-objects
H5CLEAR-copy_h5clear_fsm_persist_equal.h5
H5CLEAR-copy_h5clear_fsm_persist_greater.h5
H5CLEAR-copy_h5clear_fsm_persist_less.h5
H5CLEAR-copy_h5clear_fsm_persist_noclose.h5
H5CLEAR-copy_h5clear_fsm_persist_user_equal.h5
H5CLEAR-copy_h5clear_fsm_persist_user_greater.h5
H5CLEAR-copy_h5clear_fsm_persist_user_less.h5
H5CLEAR-copy_h5clear_log_v3.h5
H5CLEAR-copy_h5clear_mdc_image.h5
H5CLEAR-copy_h5clear_sec2_v0.h5
H5CLEAR-copy_h5clear_sec2_v2.h5
H5CLEAR-copy_h5clear_sec2_v3.h5
H5CLEAR-copy_h5clear_status_noclear.h5
H5CLEAR-copy_latest_h5clear_log_v3.h5
H5CLEAR-copy_latest_h5clear_sec2_v3.h5
H5CLEAR-copy_mod_h5clear_mdc_image.h5
@ -307,6 +319,11 @@ set (CTEST_CUSTOM_MEMCHECK_IGNORE
H5REPACK_VERIFY_LAYOUT_ALL-layout_short_switches #uses grepTest.cmake
H5REPACK-plugin
H5REPACK_CMP-plugin_zero
#########
ADD_H5_VERIFY_INVALIDBOUNDS-h5repack-latest_latest_invalid-clear-objects
H5REPACK_VERIFY_SUPERBLOCK-SB_IS_0-clear-objects
H5REPACK_VERIFY_SUPERBLOCK-SB_IS_2-clear-objects
H5REPACK_VERIFY_SUPERBLOCK-SB_IS_3-clear-objects
######### tools/h5stat #########
H5STAT-clearall-objects
######### tools/misc #########

3
config/cmake/H5pubconf.h.in
View File

@ -267,6 +267,9 @@
/* Define if we have parallel support */
#cmakedefine H5_HAVE_PARALLEL @H5_HAVE_PARALLEL@
/* Define if both pread and pwrite exist. */
#cmakedefine H5_HAVE_PREADWRITE @H5_HAVE_PREADWRITE@
/* Define to 1 if you have the <pthread.h> header file. */
#cmakedefine H5_HAVE_PTHREAD_H @H5_HAVE_PTHREAD_H@

106
config/cmake/HDF518_Examples.cmake.in
View File

@ -1,106 +0,0 @@
#
# Copyright by The HDF Group.
# All rights reserved.
#
# 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.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
cmake_minimum_required (VERSION 3.10)
###############################################################################################################
# This script will build and run the examples from a folder
# Execute from a command line:
# ctest -S HDF518_Examples.cmake,OPTION=VALUE -C Release -VV -O test.log
###############################################################################################################
set(CTEST_CMAKE_GENERATOR "@CMAKE_GENERATOR@")
if("@CMAKE_GENERATOR_TOOLSET@")
set(CMAKE_GENERATOR_TOOLSET "@CMAKE_GENERATOR_TOOLSET@")
endif()
set(CTEST_DASHBOARD_ROOT ${CTEST_SCRIPT_DIRECTORY})
# handle input parameters to script.
#INSTALLDIR - HDF5-1.8 root folder
#CTEST_CONFIGURATION_TYPE - Release, Debug, RelWithDebInfo
#CTEST_SOURCE_NAME - name of source folder; HDF5Examples
if(DEFINED CTEST_SCRIPT_ARG)
# transform ctest script arguments of the form
# script.ctest,var1=value1,var2=value2
# to variables with the respective names set to the respective values
string(REPLACE "," ";" script_args "${CTEST_SCRIPT_ARG}")
foreach(current_var ${script_args})
if("${current_var}" MATCHES "^([^=]+)=(.+)$")
set("${CMAKE_MATCH_1}" "${CMAKE_MATCH_2}")
endif()
endforeach()
endif()
###################################################################
### Following Line is one of [Release, RelWithDebInfo, Debug] #####
set(CTEST_CONFIGURATION_TYPE "$ENV{CMAKE_CONFIG_TYPE}")
if(NOT DEFINED CTEST_CONFIGURATION_TYPE)
set(CTEST_CONFIGURATION_TYPE "Release")
endif()
set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCTEST_CONFIGURATION_TYPE:STRING=${CTEST_CONFIGURATION_TYPE}")
##################################################################
if(NOT DEFINED INSTALLDIR)
set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
endif()
if(NOT DEFINED CTEST_SOURCE_NAME)
set(CTEST_SOURCE_NAME "HDF5Examples")
endif()
if(NOT DEFINED HDF_LOCAL)
set(CDASH_LOCAL "NO")
else()
set(CDASH_LOCAL "YES")
endif()
if(NOT DEFINED CTEST_SITE)
set(CTEST_SITE "local")
endif()
if(NOT DEFINED CTEST_BUILD_NAME)
set(CTEST_BUILD_NAME "examples")
endif()
set(BUILD_OPTIONS "${BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDNAME:STRING=${CTEST_BUILD_NAME}")
#TAR_SOURCE - name of tarfile
#if(NOT DEFINED TAR_SOURCE)
# set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.2.1-Source")
#endif()
###############################################################################################################
if(WIN32)
set(SITE_OS_NAME "Windows")
set(ENV{HDF5_DIR} "${INSTALLDIR}/cmake")
set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}\\build)
set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}\\${CTEST_SOURCE_NAME}")
set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}\\${CTEST_BINARY_NAME}")
else()
set(ENV{HDF5_DIR} "${INSTALLDIR}/share/cmake")
set(ENV{LD_LIBRARY_PATH} "${INSTALLDIR}/lib")
set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}/build)
set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_SOURCE_NAME}")
set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_BINARY_NAME}")
endif()
if(${CDASH_LOCAL})
set(BUILD_OPTIONS "${BUILD_OPTIONS} -DCDASH_LOCAL:BOOL=ON")
endif()
set(BUILD_OPTIONS "${BUILD_OPTIONS} -DHDF5_PACKAGE_NAME:STRING=@HDF5_PACKAGE@@HDF_PACKAGE_EXT@")
###############################################################################################################
# For any comments please contact cdashhelp@hdfgroup.org
#
###############################################################################################################
if(WIN32)
include(${CTEST_SCRIPT_DIRECTORY}\\HDF5_Examples_options.cmake)
include(${CTEST_SCRIPT_DIRECTORY}\\CTestScript.cmake)
else()
include(${CTEST_SCRIPT_DIRECTORY}/HDF5_Examples_options.cmake)
include(${CTEST_SCRIPT_DIRECTORY}/CTestScript.cmake)
endif()

10
config/cmake/HDF5Macros.cmake
View File

@ -15,6 +15,8 @@ macro (H5_SET_LIB_OPTIONS libtarget libname libtype libpackage)
# SOVERSION passed in ARGN when shared
if (${libtype} MATCHES "SHARED")
set (PACKAGE_SOVERSION ${HDF5_${libpackage}_PACKAGE_SOVERSION})
set (PACKAGE_COMPATIBILITY ${H5_${libpackage}_SOVERS_INTERFACE}.0.0)
set (PACKAGE_CURRENT ${H5_${libpackage}_SOVERS_INTERFACE}.${H5_${libpackage}_SOVERS_MINOR}.0)
if (WIN32)
set (LIBHDF_VERSION ${HDF5_PACKAGE_VERSION_MAJOR})
else ()
@ -26,6 +28,11 @@ macro (H5_SET_LIB_OPTIONS libtarget libname libtype libpackage)
else ()
set_target_properties (${libtarget} PROPERTIES SOVERSION ${LIBHDF_VERSION})
endif ()
if (CMAKE_C_OSX_CURRENT_VERSION_FLAG)
set_property(TARGET ${libtarget} APPEND PROPERTY
LINK_FLAGS "${CMAKE_C_OSX_CURRENT_VERSION_FLAG}${PACKAGE_CURRENT} ${CMAKE_C_OSX_COMPATIBILITY_VERSION_FLAG}${PACKAGE_COMPATIBILITY}"
)
endif ()
endif ()
HDF_SET_LIB_OPTIONS (${libtarget} ${LIB_OUT_NAME} ${libtype})
@ -33,9 +40,6 @@ macro (H5_SET_LIB_OPTIONS libtarget libname libtype libpackage)
if (APPLE)
option (HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path" OFF)
if (HDF5_BUILD_WITH_INSTALL_NAME)
set_property(TARGET ${libtarget} APPEND PROPERTY
LINK_FLAGS "-current_version ${HDF5_PACKAGE_VERSION} -compatibility_version ${HDF5_PACKAGE_VERSION}"
)
set_target_properties (${libtarget} PROPERTIES
INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib"
BUILD_WITH_INSTALL_RPATH ${HDF5_BUILD_WITH_INSTALL_NAME}

6
config/cmake/HDF5UseFortran.cmake
View File

@ -57,8 +57,8 @@ endmacro ()
# Read source line beginning at the line matching Input:"START" and ending at the line matching Input:"END"
macro (READ_SOURCE SOURCE_START SOURCE_END RETURN_VAR)
file (READ "${HDF5_SOURCE_DIR}/m4/aclocal_fc.f90" SOURCE_CODE)
string (REGEX MATCH "${SOURCE_START}[\\\t\\\n\\\r[].+]*${SOURCE_END}" SOURCE_CODE ${SOURCE_CODE})
file (READ "${HDF5_SOURCE_DIR}/m4/aclocal_fc.f90" SOURCE_MASTER)
string (REGEX MATCH "${SOURCE_START}[\\\t\\\n\\\r[].+]*${SOURCE_END}" SOURCE_CODE ${SOURCE_MASTER})
set (RETURN_VAR "${SOURCE_CODE}")
endmacro ()
@ -234,7 +234,7 @@ foreach (KIND ${VAR} )
set (pack_real_sizeof "${pack_real_sizeof} ${PROG_OUTPUT1},")
endforeach ()
if (pack_int_sizeof STREQUAL "")
if (pack_real_sizeof STREQUAL "")
message (FATAL_ERROR "Failed to find available REAL KINDs for Fortran")
endif ()

8
config/cmake/HDF5_Examples.cmake.in
View File

@ -48,7 +48,11 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCTEST_CONFIGURATION_TYPE:STRING=${
##################################################################
if(NOT DEFINED INSTALLDIR)
set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
if(WIN32)
set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
else()
set(INSTALLDIR "@CMAKE_INSTALL_PREFIX@")
endif()
endif()
if(NOT DEFINED CTEST_SOURCE_NAME)
@ -70,7 +74,7 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDN
#TAR_SOURCE - name of tarfile
#if(NOT DEFINED TAR_SOURCE)
# set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.10.10-Source")
# set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.12.4-Source")
#endif()
###############################################################################################################

46
config/cmake/hdf5-config-version.cmake.in
View File

@ -21,38 +21,38 @@
set (PACKAGE_VERSION "@HDF5_VERSION_STRING@")
if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}" )
if(PACKAGE_VERSION VERSION_LESS PACKAGE_FIND_VERSION)
set(PACKAGE_VERSION_COMPATIBLE FALSE)
else ()
if ("${PACKAGE_FIND_VERSION_MAJOR}" STREQUAL "@H5_VERS_MAJOR@")
else()
if("@H5_VERS_MAJOR@.@H5_VERS_MINOR@" MATCHES "^([0-9]+)\\.([0-9]+)")
set(CVF_VERSION_MAJOR "${CMAKE_MATCH_1}")
set(CVF_VERSION_MINOR "${CMAKE_MATCH_2}")
else()
set(CVF_VERSION_MAJOR "@HDF5_VERSION_STRING@")
set(CVF_VERSION_MINOR "")
endif()
# exact match for version @H5_VERS_MAJOR@.@H5_VERS_MINOR@
if ("${PACKAGE_FIND_VERSION_MINOR}" STREQUAL "@H5_VERS_MINOR@")
if((PACKAGE_FIND_VERSION_MAJOR STREQUAL CVF_VERSION_MAJOR) AND
(PACKAGE_FIND_VERSION_MINOR STREQUAL CVF_VERSION_MINOR))
set(PACKAGE_VERSION_COMPATIBLE TRUE)
else()
set(PACKAGE_VERSION_COMPATIBLE FALSE)
endif()
# compatible with any version @H5_VERS_MAJOR@.@H5_VERS_MINOR@.x
set (PACKAGE_VERSION_COMPATIBLE TRUE)
if(PACKAGE_FIND_VERSION STREQUAL PACKAGE_VERSION)
set(PACKAGE_VERSION_EXACT TRUE)
endif()
endif()
if ("${PACKAGE_FIND_VERSION_PATCH}" STREQUAL "@H5_VERS_RELEASE@")
set (PACKAGE_VERSION_EXACT TRUE)
if ("${PACKAGE_FIND_VERSION_TWEAK}" STREQUAL "@H5_VERS_SUBRELEASE@")
# not using this yet
endif ()
endif ()
else ()
set (PACKAGE_VERSION_COMPATIBLE FALSE)
endif ()
endif ()
endif ()
# if the installed or the using project don't have CMAKE_SIZEOF_VOID_P set, ignore it:
if("${CMAKE_SIZEOF_VOID_P}" STREQUAL "" OR "@CMAKE_SIZEOF_VOID_P@" STREQUAL "")
if("${CMAKE_SIZEOF_VOID_P}" STREQUAL "" OR "@CMAKE_SIZEOF_VOID_P@" STREQUAL "")
return()
endif ()
endif()
# check that the installed version has the same 32/64bit-ness as the one which is currently searching:
if(NOT "${CMAKE_SIZEOF_VOID_P}" STREQUAL "@CMAKE_SIZEOF_VOID_P@")
if(NOT CMAKE_SIZEOF_VOID_P STREQUAL "@CMAKE_SIZEOF_VOID_P@")
math(EXPR installedBits "@CMAKE_SIZEOF_VOID_P@ * 8")
set(PACKAGE_VERSION "${PACKAGE_VERSION} (${installedBits}bit)")
set(PACKAGE_VERSION_UNSUITABLE TRUE)
endif ()
endif()

29
config/cmake/hdf5-config.cmake.in
View File

@ -38,6 +38,7 @@ set (${HDF5_PACKAGE_NAME}_BUILD_CPP_LIB @HDF5_BUILD_CPP_LIB@)
set (${HDF5_PACKAGE_NAME}_BUILD_JAVA @HDF5_BUILD_JAVA@)
set (${HDF5_PACKAGE_NAME}_BUILD_TOOLS @HDF5_BUILD_TOOLS@)
set (${HDF5_PACKAGE_NAME}_BUILD_HL_LIB @HDF5_BUILD_HL_LIB@)
set (${HDF5_PACKAGE_NAME}_ENABLE_THREADSAFE @HDF5_ENABLE_THREADSAFE@)
set (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT @HDF5_ENABLE_Z_LIB_SUPPORT@)
set (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT @HDF5_ENABLE_SZIP_SUPPORT@)
set (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_ENCODING @HDF5_ENABLE_SZIP_ENCODING@)
@ -45,6 +46,8 @@ set (${HDF5_PACKAGE_NAME}_BUILD_SHARED_LIBS @BUILD_SHARED_LIBS@)
set (${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS @HDF5_PACKAGE_EXTLIBS@)
set (${HDF5_PACKAGE_NAME}_EXPORT_LIBRARIES @HDF5_LIBRARIES_TO_EXPORT@)
set (${HDF5_PACKAGE_NAME}_TOOLSET "@CMAKE_GENERATOR_TOOLSET@")
set (${HDF5_PACKAGE_NAME}_DEFAULT_API_VERSION "@DEFAULT_API_VERSION@")
set (${HDF5_PACKAGE_NAME}_PARALLEL_FILTERED_WRITES "@PARALLEL_FILTERED_WRITES@")
#-----------------------------------------------------------------------------
# Dependencies
@ -124,14 +127,14 @@ endif ()
# Handle requested components:
list (REMOVE_DUPLICATES ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS)
foreach (comp IN LISTS ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS)
if (${comp} STREQUAL "shared")
if (comp STREQUAL "shared")
list (REMOVE_ITEM ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS ${comp})
set (${HDF5_PACKAGE_NAME}_LIB_TYPE ${${HDF5_PACKAGE_NAME}_LIB_TYPE} ${comp})
if (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN)
set (${HDF5_PACKAGE_NAME}_INCLUDE_DIR_FORTRAN "@PACKAGE_INCLUDE_INSTALL_DIR@/shared")
endif ()
elseif (${comp} STREQUAL "static")
elseif (comp STREQUAL "static")
list (REMOVE_ITEM ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS ${comp})
set (${HDF5_PACKAGE_NAME}_LIB_TYPE ${${HDF5_PACKAGE_NAME}_LIB_TYPE} ${comp})
@ -143,32 +146,32 @@ endforeach ()
foreach (libtype IN LISTS ${HDF5_PACKAGE_NAME}_LIB_TYPE)
foreach (comp IN LISTS ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS)
set (hdf5_comp2)
if (${comp} STREQUAL "C")
if (comp STREQUAL "C")
set (hdf5_comp "hdf5")
elseif (${comp} STREQUAL "CXX")
elseif (comp STREQUAL "CXX")
set (hdf5_comp "hdf5_cpp")
elseif (${comp} STREQUAL "HL")
elseif (comp STREQUAL "HL")
set (hdf5_comp "hdf5_hl")
elseif (${comp} STREQUAL "CXX_HL")
elseif (comp STREQUAL "CXX_HL")
set (hdf5_comp "hdf5_hl_cpp")
elseif (${comp} STREQUAL "Java")
elseif (comp STREQUAL "Java")
set (hdf5_comp "hdf5_java")
elseif (${comp} STREQUAL "Tools")
elseif (comp STREQUAL "Tools")
set (hdf5_comp "hdf5_tools")
elseif (${comp} STREQUAL "Fortran")
elseif (comp STREQUAL "Fortran")
set (hdf5_comp2 "hdf5_f90cstub")
set (hdf5_comp "hdf5_fortran")
elseif (${comp} STREQUAL "Fortran_HL")
elseif (comp STREQUAL "Fortran_HL")
set (hdf5_comp2 "hdf5_hl_f90cstub")
set (hdf5_comp "hdf5_hl_fortran")
endif ()
if (${comp} STREQUAL "Java")
if (comp STREQUAL "Java")
list (FIND ${HDF5_PACKAGE_NAME}_EXPORT_LIBRARIES "${hdf5_comp}" HAVE_COMP)
else ()
list (FIND ${HDF5_PACKAGE_NAME}_EXPORT_LIBRARIES "${hdf5_comp}-${libtype}" HAVE_COMP)
endif ()
if (${HAVE_COMP} LESS 0)
if (${comp} STREQUAL "Java")
if (comp STREQUAL "Java")
set (${HDF5_PACKAGE_NAME}_${comp}_FOUND 0)
else ()
set (${HDF5_PACKAGE_NAME}_${libtype}_${comp}_FOUND 0)
@ -183,7 +186,7 @@ foreach (libtype IN LISTS ${HDF5_PACKAGE_NAME}_LIB_TYPE)
string(TOUPPER ${HDF5_PACKAGE_NAME}_${comp}_${libtype}_LIBRARY COMP_LIBRARY)
set (${COMP_LIBRARY} ${${COMP_LIBRARY}} @HDF5_PACKAGE@::${hdf5_comp2}-${libtype} @HDF5_PACKAGE@::${hdf5_comp}-${libtype})
endif ()
elseif (${comp} STREQUAL "Java")
elseif (comp STREQUAL "Java")
set (${HDF5_PACKAGE_NAME}_${comp}_FOUND 1)
string(TOUPPER ${HDF5_PACKAGE_NAME}_${comp}_LIBRARY COMP_LIBRARY)
set (${COMP_LIBRARY} ${${COMP_LIBRARY}} hdf5::${hdf5_comp})

46
config/cmake/jrunTest.cmake
View File

@ -77,10 +77,10 @@ if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}.err)
endif ()
if (NOT ERROR_APPEND)
# append error output to the stdout output file
# write back to original .err file
file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT}.err "${TEST_STREAM}")
else ()
# write back to original .err file
# append error output to the stdout output file
file (APPEND ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_STREAM}")
endif ()
endif ()
@ -110,8 +110,8 @@ if (TEST_MASK_ERROR)
endif ()
endif ()
# if the return value is !=0 bail out
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
# if the return value is !=expected bail out
if (NOT TEST_RESULT EQUAL TEST_EXPECT)
message (STATUS "ERROR OUTPUT: ${TEST_STREAM}")
message (FATAL_ERROR "Failed: Test program ${TEST_PROGRAM} exited != 0.\n${TEST_ERROR}")
endif ()
@ -131,33 +131,33 @@ if (NOT TEST_SKIP_COMPARE)
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_FOLDER}/${TEST_REFERENCE}
RESULT_VARIABLE TEST_RESULT
)
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} test_ref)
list (LENGTH test_ref len_ref)
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
if (len_act GREATER 0 AND len_ref GREATER 0)
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
list (GET test_ref ${line} str_ref)
if (NOT "${str_act}" STREQUAL "${str_ref}")
if (NOT "${str_act}" STREQUAL "")
if (NOT str_act STREQUAL str_ref)
if (str_act)
set (TEST_RESULT 1)
message ("line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
endif ()
endif ()
endforeach ()
else ()
if ("${len_act}" STREQUAL "0")
if (len_act EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT} is empty")
endif ()
if ("${len_ref}" STREQUAL "0")
if (len_ref EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_REFERENCE} is empty")
endif ()
endif ()
if (NOT "${len_act}" STREQUAL "${len_ref}")
if (NOT len_act EQUAL len_ref)
set (TEST_RESULT 1)
endif ()
endif ()
@ -165,7 +165,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_OUTPUT} did not match ${TEST_REFERENCE}")
endif ()
endif ()
@ -182,34 +182,34 @@ if (NOT TEST_SKIP_COMPARE)
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT}.err ${TEST_FOLDER}/${TEST_ERRREF}
RESULT_VARIABLE TEST_RESULT
)
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT}.err test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_ERRREF} test_ref)
list (LENGTH test_ref len_ref)
math (EXPR _FP_LEN "${len_ref} - 1")
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
if (len_act GREATER 0 AND len_ref GREATER 0)
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
list (GET test_ref ${line} str_ref)
if (NOT "${str_act}" STREQUAL "${str_ref}")
if (NOT "${str_act}" STREQUAL "")
if (NOT str_act STREQUAL str_ref)
if (str_act)
set (TEST_RESULT 1)
message ("line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
endif ()
endif ()
endforeach ()
else ()
if ("${len_act}" STREQUAL "0")
if (len_act EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT}.err is empty")
endif ()
if ("${len_ref}" STREQUAL "0")
if (len_ref EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_ERRREF} is empty")
endif ()
endif ()
if (NOT "${len_act}" STREQUAL "${len_ref}")
if (NOT len_act EQUAL len_ref)
set (TEST_RESULT 1)
endif ()
endif ()
@ -217,7 +217,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The error output of ${TEST_OUTPUT}.err did not match ${TEST_ERRREF}")
endif ()
endif ()
@ -230,15 +230,15 @@ if (TEST_GREP_COMPARE)
# TEST_REFERENCE should always be matched
string (REGEX MATCH "${TEST_REFERENCE}" TEST_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT)
if ("${TEST_RESULT}" STREQUAL "0")
if (NOT TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
endif ()
string (REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM})
if ("${TEST_EXPECT}" STREQUAL "1")
if (TEST_EXPECT)
# TEST_EXPECT (1) interperts TEST_FILTER as NOT to match
string (LENGTH "${TEST_MATCH}" TEST_RESULT)
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_FILTER}")
endif ()
endif ()

4
config/cmake/patch.xml
View File

@ -1,5 +1,5 @@
<CPackWiXPatch>
<CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
<CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
<Environment Id="PATH"
Name="PATH"
Value="[CM_DP_libraries.bin]"
@ -7,5 +7,5 @@
Part="last"
Action="set"
System="yes"/>
</CPackWiXFragment>
</CPackWiXFragment>
</CPackWiXPatch>

14
config/cmake/scripts/CTestScript.cmake
View File

@ -257,7 +257,7 @@ message (STATUS "Dashboard script configuration:\n${vars}\n")
# On Cray XC40, configuring fails in the Fortran section when using the craype-mic-knl module.
# When the configure phase is done with the craype-haswell module and the build phase is done
# with the craype-mic-knl module, configure succeeds and tests pass on the knl compute nodes
# for Intel, Cray, GCC and Clang compilers. If the variables aren't set or if not
# for Intel, Cray, GCC and Clang compilers. If the variables aren't set or if not
# cross compiling, the module switch will not occur.
if (CMAKE_CROSSCOMPILING AND COMPILENODE_HWCOMPILE_MODULE AND COMPUTENODE_HWCOMPILE_MODULE)
execute_process (COMMAND module switch ${COMPILENODE_HWCOMPILE_MODULE} ${COMPUTENODE_HWCOMPILE_MODULE})
@ -277,7 +277,11 @@ message (STATUS "Dashboard script configuration:\n${vars}\n")
ctest_test (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND ${ctest_test_args} RETURN_VALUE res)
else ()
file(STRINGS ${CTEST_BINARY_DIRECTORY}/Testing/TAG TAG_CONTENTS REGEX "^2([0-9]+)[-]([0-9]+)$")
execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME})
if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "raybsub")
execute_process (COMMAND ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME})
else ()
execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME})
endif ()
message(STATUS "Check for existence of ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml")
execute_process(COMMAND ls ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml RESULT_VARIABLE result OUTPUT_QUIET ERROR_QUIET)
while(result)
@ -292,7 +296,11 @@ message (STATUS "Dashboard script configuration:\n${vars}\n")
file (RENAME ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/SerialTest.xml)
file (RENAME ${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastTest_${TAG_CONTENTS}.log ${CTEST_BINARY_DIRECTORY}/Testing/Temporary/LastTest_${TAG_CONTENTS}_Serial.log)
unset(result CACHE)
execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_PARALLEL_NAME})
if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "raybsub")
execute_process (COMMAND ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_PARALLEL_NAME})
else ()
execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_PARALLEL_NAME})
endif ()
message(STATUS "Check for existence of ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml")
execute_process(COMMAND ls ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml RESULT_VARIABLE result OUTPUT_QUIET ERROR_QUIET)
while(result)

157
config/cmake/scripts/HDF5config.cmake
View File

@ -43,6 +43,9 @@ set (CTEST_SOURCE_VERSEXT "")
#INSTALLDIR - HDF5-1.10.0 root folder
#CTEST_CONFIGURATION_TYPE - Release, Debug, RelWithDebInfo
#CTEST_SOURCE_NAME - name of source folder; HDF5-1.10.0
#MODEL - CDash group name
#HPC - run alternate configurations for HPC machines; sbatch, bsub, raybsub
#MPI - enable MPI;
if (DEFINED CTEST_SCRIPT_ARG)
# transform ctest script arguments of the form
# script.ctest,var1=value1,var2=value2
@ -55,6 +58,11 @@ if (DEFINED CTEST_SCRIPT_ARG)
endforeach ()
endif ()
#HPC - run alternate configurations for HPC machines
if (DEFINED HPC)
set (BUILD_GENERATOR "Unix")
endif ()
# build generator must be defined
if (NOT DEFINED BUILD_GENERATOR)
message (FATAL_ERROR "BUILD_GENERATOR must be defined - Unix, VS2017, or VS201764, VS2015, VS201564, VS2013, VS201364")
@ -92,84 +100,95 @@ endif ()
###################################################################
######### Following describes compiler ############
if (WIN32)
set (SITE_OS_NAME "Windows")
set (SITE_OS_VERSION "WIN7")
if (${BUILD_GENERATOR} STREQUAL "VS201764")
set (CTEST_CMAKE_GENERATOR "Visual Studio 15 2017 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2017")
set (SITE_COMPILER_VERSION "15")
elseif (${BUILD_GENERATOR} STREQUAL "VS2017")
set (CTEST_CMAKE_GENERATOR "Visual Studio 15 2017")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2017")
set (SITE_COMPILER_VERSION "15")
elseif (${BUILD_GENERATOR} STREQUAL "VS201564")
set (CTEST_CMAKE_GENERATOR "Visual Studio 14 2015 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2015")
set (SITE_COMPILER_VERSION "14")
elseif (${BUILD_GENERATOR} STREQUAL "VS2015")
set (CTEST_CMAKE_GENERATOR "Visual Studio 14 2015")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2015")
set (SITE_COMPILER_VERSION "14")
elseif (${BUILD_GENERATOR} STREQUAL "VS201364")
set (CTEST_CMAKE_GENERATOR "Visual Studio 12 2013 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2013")
set (SITE_COMPILER_VERSION "12")
elseif (${BUILD_GENERATOR} STREQUAL "VS2013")
set (CTEST_CMAKE_GENERATOR "Visual Studio 12 2013")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2013")
set (SITE_COMPILER_VERSION "12")
elseif (${BUILD_GENERATOR} STREQUAL "VS201264")
set (CTEST_CMAKE_GENERATOR "Visual Studio 11 2012 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2012")
set (SITE_COMPILER_VERSION "11")
elseif (${BUILD_GENERATOR} STREQUAL "VS2012")
set (CTEST_CMAKE_GENERATOR "Visual Studio 11 2012")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2012")
set (SITE_COMPILER_VERSION "11")
else ()
message (FATAL_ERROR "Invalid BUILD_GENERATOR must be - Unix, VS2017, or VS201764, VS2015, VS201564, VS2013, VS201364")
if (NOT DEFINED HPC)
if (NOT DEFINED BUILD_GENERATOR)
message (FATAL_ERROR "BUILD_GENERATOR must be defined - Unix, VS2017, or VS201764, VS2015, VS201564, VS2013, VS201364")
endif ()
if (WIN32)
set (SITE_OS_NAME "Windows")
set (SITE_OS_VERSION "WIN7")
if (BUILD_GENERATOR STREQUAL "VS201764")
set (CTEST_CMAKE_GENERATOR "Visual Studio 15 2017 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2017")
set (SITE_COMPILER_VERSION "15")
elseif (BUILD_GENERATOR STREQUAL "VS2017")
set (CTEST_CMAKE_GENERATOR "Visual Studio 15 2017")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2017")
set (SITE_COMPILER_VERSION "15")
elseif (BUILD_GENERATOR STREQUAL "VS201564")
set (CTEST_CMAKE_GENERATOR "Visual Studio 14 2015 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2015")
set (SITE_COMPILER_VERSION "14")
elseif (BUILD_GENERATOR STREQUAL "VS2015")
set (CTEST_CMAKE_GENERATOR "Visual Studio 14 2015")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2015")
set (SITE_COMPILER_VERSION "14")
elseif (BUILD_GENERATOR STREQUAL "VS201364")
set (CTEST_CMAKE_GENERATOR "Visual Studio 12 2013 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2013")
set (SITE_COMPILER_VERSION "12")
elseif (BUILD_GENERATOR STREQUAL "VS2013")
set (CTEST_CMAKE_GENERATOR "Visual Studio 12 2013")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2013")
set (SITE_COMPILER_VERSION "12")
elseif (BUILD_GENERATOR STREQUAL "VS201264")
set (CTEST_CMAKE_GENERATOR "Visual Studio 11 2012 Win64")
set (SITE_OS_BITS "64")
set (SITE_COMPILER_NAME "vs2012")
set (SITE_COMPILER_VERSION "11")
elseif (BUILD_GENERATOR STREQUAL "VS2012")
set (CTEST_CMAKE_GENERATOR "Visual Studio 11 2012")
set (SITE_OS_BITS "32")
set (SITE_COMPILER_NAME "vs2012")
set (SITE_COMPILER_VERSION "11")
else ()
message (FATAL_ERROR "Invalid BUILD_GENERATOR must be - Unix, VS2017, or VS201764, VS2015, VS201564, VS2013, VS201364")
endif ()
## Set the following to unique id your computer ##
set (CTEST_SITE "WIN7${BUILD_GENERATOR}.XXXX")
else ()
set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
## Set the following to unique id your computer ##
if (APPLE)
set (CTEST_SITE "MAC.XXXX")
else ()
set (CTEST_SITE "LINUX.XXXX")
endif ()
if (APPLE)
execute_process (COMMAND xcrun --find cc OUTPUT_VARIABLE XCODE_CC OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process (COMMAND xcrun --find c++ OUTPUT_VARIABLE XCODE_CXX OUTPUT_STRIP_TRAILING_WHITESPACE)
set (ENV{CC} "${XCODE_CC}")
set (ENV{CXX} "${XCODE_CXX}")
set (CTEST_USE_LAUNCHERS 1)
set (RR_WARNINGS_COMMON "-Wno-format-nonliteral -Wno-cast-align -Wno-unused -Wno-unused-variable -Wno-unused-function -Wno-self-assign -Wno-unused-parameter -Wno-sign-compare")
set (RR_WARNINGS_C "${RR_WARNINGS_COMMON} -Wno-deprecated-declarations -Wno-uninitialized")
set (RR_WARNINGS_CXX "${RR_WARNINGS_COMMON} -Woverloaded-virtual -Wshadow -Wwrite-strings -Wc++11-compat")
set (RR_FLAGS_COMMON "-g -O0 -fstack-protector-all -D_FORTIFY_SOURCE=2")
set (RR_FLAGS_C "${RR_FLAGS_COMMON}")
set (RR_FLAGS_CXX "${RR_FLAGS_COMMON}")
set (ENV{CFLAGS} "${RR_WARNINGS_C} ${RR_FLAGS_C}")
set (ENV{CXXFLAGS} "${RR_WARNINGS_CXX} ${RR_FLAGS_CXX}")
endif ()
endif ()
## Set the following to unique id your computer ##
set (CTEST_SITE "WIN7${BUILD_GENERATOR}.XXXX")
else ()
set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
## Set the following to unique id your computer ##
if (APPLE)
set (CTEST_SITE "MAC.XXXX")
else ()
set (CTEST_SITE "LINUX.XXXX")
endif ()
if (APPLE)
execute_process (COMMAND xcrun --find cc OUTPUT_VARIABLE XCODE_CC OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process (COMMAND xcrun --find c++ OUTPUT_VARIABLE XCODE_CXX OUTPUT_STRIP_TRAILING_WHITESPACE)
set (ENV{CC} "${XCODE_CC}")
set (ENV{CXX} "${XCODE_CXX}")
set (CTEST_USE_LAUNCHERS 1)
set (RR_WARNINGS_COMMON "-Wno-format-nonliteral -Wno-cast-align -Wno-unused -Wno-unused-variable -Wno-unused-function -Wno-self-assign -Wno-unused-parameter -Wno-sign-compare")
set (RR_WARNINGS_C "${RR_WARNINGS_COMMON} -Wno-deprecated-declarations -Wno-uninitialized")
set (RR_WARNINGS_CXX "${RR_WARNINGS_COMMON} -Woverloaded-virtual -Wshadow -Wwrite-strings -Wc++11-compat")
set (RR_FLAGS_COMMON "-g -O0 -fstack-protector-all -D_FORTIFY_SOURCE=2")
set (RR_FLAGS_C "${RR_FLAGS_COMMON}")
set (RR_FLAGS_CXX "${RR_FLAGS_COMMON}")
set (ENV{CFLAGS} "${RR_WARNINGS_C} ${RR_FLAGS_C}")
set (ENV{CXXFLAGS} "${RR_WARNINGS_CXX} ${RR_FLAGS_CXX}")
endif ()
include (${CTEST_SOURCE_DIRECTORY}/config/cmake/scripts/HPC/${HPC}-HDF5options.cmake)
endif ()
###################################################################
###################################################################
######### Following is for submission to CDash ############
###################################################################
set (MODEL "Experimental")
if (NOT DEFINED MODEL)
set (MODEL "Experimental")
endif ()
###################################################################
###################################################################

6
config/cmake/scripts/HDF5options.cmake
View File

@ -33,12 +33,8 @@
#############################################################################################
#### fortran enabled ####
#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON")
### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN
#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=ON")
#### fortran disabled ####
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF")
### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=OFF")
#############################################################################################
#### java enabled ####
@ -69,7 +65,7 @@ set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRIN
#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
#### package examples ####
#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.10.9-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}")
#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.12.4-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}")
#############################################################################################
### enable parallel builds

40
config/cmake/scripts/HPC/bsub-HDF5options.cmake Normal file
View File

@ -0,0 +1,40 @@
#
# Copyright by The HDF Group.
# All rights reserved.
#
# 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.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
#############################################################################################
#### Change default configuration of options in config/cmake/cacheinit.cmake file ###
#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ###
#############################################################################################
### uncomment/comment and change the following lines for other configuration options
#############################################################################################
### enable parallel builds
if (DEFINED MPI)
# maximum parallel processor count for build and test ####
set (MAX_PROC_COUNT 8)
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=ON")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF")
endif ()
#############################################################################################
### options to run test scripts in batch commands
set (LOCAL_BATCH_SCRIPT_COMMAND "bsub")
set (LOCAL_BATCH_TEST "TRUE")
set (LOCAL_BATCH_SCRIPT_NAME "ctestS.lsf")
set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "ctestP.lsf")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_TEST:BOOL=ON")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=${LOCAL_BATCH_SCRIPT_NAME}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=${LOCAL_BATCH_SCRIPT_PARALLEL_NAME}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=srun")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_NUMPROC_FLAG:STRING=-n")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_MAX_NUMPROCS:STRING=6")

41
config/cmake/scripts/HPC/raybsub-HDF5options.cmake Normal file
View File

@ -0,0 +1,41 @@
#
# Copyright by The HDF Group.
# All rights reserved.
#
# 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.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
#############################################################################################
#### Change default configuration of options in config/cmake/cacheinit.cmake file ###
#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ###
#############################################################################################
### uncomment/comment and change the following lines for other configuration options
#############################################################################################
### enable parallel builds
if (DEFINED MPI)
# maximum parallel processor count for build and test ####
set (MAX_PROC_COUNT 8)
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=ON")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF")
endif ()
#############################################################################################
### options to run test scripts in batch commands
set (LOCAL_BATCH_SCRIPT_COMMAND "raybsub")
set (LOCAL_BATCH_TEST "TRUE")
set (LOCAL_BATCH_SCRIPT_NAME "ray_ctestS.lsf")
set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "ray_ctestP.lsf")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_TEST:BOOL=ON")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_COMMAND:STRING=${LOCAL_BATCH_SCRIPT_COMMAND}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=${LOCAL_BATCH_SCRIPT_NAME}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=${LOCAL_BATCH_SCRIPT_PARALLEL_NAME}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=mpirun")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_NUMPROC_FLAG:STRING=-np")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_MAX_NUMPROCS:STRING=6")

52
config/cmake/scripts/HPC/sbatch-HDF5options.cmake Normal file
View File

@ -0,0 +1,52 @@
#
# Copyright by The HDF Group.
# All rights reserved.
#
# 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.
# If you do not have access to either file, you may request a copy from
# help@hdfgroup.org.
#
#############################################################################################
#### Change default configuration of options in config/cmake/cacheinit.cmake file ###
#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ###
#############################################################################################
### uncomment/comment and change the following lines for other configuration options
#############################################################################################
### enable parallel builds
if (DEFINED MPI)
# maximum parallel processor count for build and test ####
set (MAX_PROC_COUNT 8)
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=ON")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF")
endif ()
#############################################################################################
### options to run test scripts in batch commands
if (DEFINED KNL)
### some additions and alternatives to cross compile on haswell for knl
set (COMPILENODE_HWCOMPILE_MODULE "craype-haswell")
set (COMPUTENODE_HWCOMPILE_MODULE "craype-mic-knl")
set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl")
set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake")
else ()
set (LOCAL_BATCH_SCRIPT_NAME "ctestS.sl")
set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "ctestP.sl")
endif ()
set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch")
set (LOCAL_BATCH_TEST "TRUE")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_TEST:BOOL=ON")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=${LOCAL_BATCH_SCRIPT_NAME}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=${LOCAL_BATCH_SCRIPT_PARALLEL_NAME}")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=srun")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_NUMPROC_FLAG:STRING=-n")
set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_MAX_NUMPROCS:STRING=6")
#############################################################################################
#############################################################################################

8
config/cmake/userblockTest.cmake
View File

@ -62,7 +62,7 @@ if (TEST_CHECKUB STREQUAL "YES")
OUTPUT_VARIABLE TEST_OUT
ERROR_VARIABLE TEST_ERROR
)
if (NOT ${TEST_RESULT} STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} ${TEST_OFILE} is: ${TEST_ERROR}")
endif ()
file (READ ${TEST_HFILE}.len.txt TEST_O_STRING_LEN)
@ -70,7 +70,7 @@ if (TEST_CHECKUB STREQUAL "YES")
math( EXPR TEST_STRING_SIZE "${TEST_U_STRING_LEN} + ${TEST_O_STRING_LEN}" )
if (NOT TEST_O_STRING_LEN STREQUAL "0")
if (TEST_O_STRING_LEN)
#$JAM_BIN/getub -c $s2 $origfile > $cmpfile
EXECUTE_PROCESS (
COMMAND ${TEST_GET_PROGRAM} -c ${TEST_O_STRING_LEN} ${TEST_OFILE}
@ -108,7 +108,7 @@ if (TEST_CHECKUB STREQUAL "YES")
message (STATUS "COMPARE Result: ${TEST_RESULT}: ${TEST_STRING_SIZE}=${TEST_U_STRING_LEN}+${TEST_O_STRING_LEN}")
# if the return value is !=${TEST_EXPECT} bail out
if (NOT ${TEST_RESULT} STREQUAL ${TEST_EXPECT})
if (NOT TEST_RESULT EQUAL TEST_EXPECT)
message (FATAL_ERROR "Failed: The output of ${TEST_HFILE}-ub did not match ${TEST_HFILE}.\n${TEST_ERROR}")
endif ()
else ()
@ -121,7 +121,7 @@ else ()
OUTPUT_VARIABLE TEST_OUT
ERROR_VARIABLE TEST_ERROR
)
if (NOT TEST_H_STRING_LEN STREQUAL "0")
if (TEST_H_STRING_LEN)
message (FATAL_ERROR "Failed: The output of ${TEST_HFILE} was NOT empty")
endif ()
endif ()

2
config/cmake/vfdTest.cmake
View File

@ -60,7 +60,7 @@ if (ERROR_APPEND AND EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}_${TEST_VFD}.err)
endif ()
# if the return value is !=${TEST_EXPECT} bail out
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
if (NOT TEST_RESULT EQUAL TEST_EXPECT)
if (NOT TEST_NOERRDISPLAY)
if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}_${TEST_VFD}.out)
file (READ ${TEST_FOLDER}/${TEST_OUTPUT}_${TEST_VFD}.out TEST_STREAM)

2
config/cmake/volTest.cmake
View File

@ -60,7 +60,7 @@ if (ERROR_APPEND AND EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}.err)
endif ()
# if the return value is !=${TEST_EXPECT} bail out
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
if (NOT TEST_RESULT EQUAL TEST_EXPECT)
if (NOT TEST_NOERRDISPLAY)
if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}.out)
file (READ ${TEST_FOLDER}/${TEST_OUTPUT}.out TEST_STREAM)

14
config/cmake_ext_mod/ConfigureChecks.cmake
View File

@ -229,7 +229,7 @@ macro (HDF_FUNCTION_TEST OTHER_TEST)
endif ()
#message (STATUS "Performing ${OTHER_TEST}")
TRY_COMPILE (${OTHER_TEST}
try_compile (${OTHER_TEST}
${CMAKE_BINARY_DIR}
${HDF_RESOURCES_EXT_DIR}/HDFTests.c
COMPILE_DEFINITIONS "${MACRO_CHECK_FUNCTION_DEFINITIONS}"
@ -286,7 +286,7 @@ if (NOT WINDOWS)
option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON)
if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN)
set (msg "Performing TEST_LFS_WORKS")
TRY_RUN (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE
try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE
${CMAKE_BINARY_DIR}
${HDF_RESOURCES_EXT_DIR}/HDFTests.c
COMPILE_DEFINITIONS "-DTEST_LFS_WORKS"
@ -443,7 +443,7 @@ if (NOT WINDOWS)
# Check a bunch of time functions
#-----------------------------------------------------------------------------
CHECK_FUNCTION_EXISTS (gettimeofday ${HDF_PREFIX}_HAVE_GETTIMEOFDAY)
foreach (test
foreach (time_test
HAVE_TM_GMTOFF
HAVE___TM_GMTOFF
# HAVE_TIMEZONE
@ -453,7 +453,7 @@ if (NOT WINDOWS)
HAVE_TM_ZONE
HAVE_STRUCT_TM_TM_ZONE
)
HDF_FUNCTION_TEST (${test})
HDF_FUNCTION_TEST (${time_test})
endforeach ()
if (NOT CYGWIN AND NOT MINGW)
HDF_FUNCTION_TEST (HAVE_TIMEZONE)
@ -506,6 +506,8 @@ CHECK_FUNCTION_EXISTS (lround ${HDF_PREFIX}_HAVE_LROUND)
CHECK_FUNCTION_EXISTS (lroundf ${HDF_PREFIX}_HAVE_LROUNDF)
CHECK_FUNCTION_EXISTS (lstat ${HDF_PREFIX}_HAVE_LSTAT)
CHECK_FUNCTION_EXISTS (pread ${HDF_PREFIX}_HAVE_PREAD)
CHECK_FUNCTION_EXISTS (pwrite ${HDF_PREFIX}_HAVE_PWRITE)
CHECK_FUNCTION_EXISTS (rand_r ${HDF_PREFIX}_HAVE_RAND_R)
CHECK_FUNCTION_EXISTS (random ${HDF_PREFIX}_HAVE_RANDOM)
CHECK_FUNCTION_EXISTS (round ${HDF_PREFIX}_HAVE_ROUND)
@ -555,7 +557,7 @@ endif ()
# Check a bunch of other functions
#-----------------------------------------------------------------------------
if (NOT WINDOWS)
foreach (test
foreach (other_test
HAVE_ATTRIBUTE
HAVE_C99_FUNC
# STDC_HEADERS
@ -564,7 +566,7 @@ if (NOT WINDOWS)
SYSTEM_SCOPE_THREADS
HAVE_SOCKLEN_T
)
HDF_FUNCTION_TEST (${test})
HDF_FUNCTION_TEST (${other_test})
endforeach ()
endif ()

6
config/cmake_ext_mod/HDFMacros.cmake
View File

@ -14,7 +14,7 @@
macro (SET_HDF_BUILD_TYPE)
get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(_isMultiConfig)
set(HDF_CFG_NAME ${CTEST_CONFIGURATION_TYPE})
set(HDF_CFG_NAME ${CMAKE_BUILD_TYPE})
set(HDF_BUILD_TYPE ${CMAKE_CFG_INTDIR})
set(HDF_CFG_BUILD_TYPE \${CMAKE_INSTALL_CONFIG_NAME})
else()
@ -170,7 +170,7 @@ macro (HDF_IMPORT_SET_LIB_OPTIONS libtarget libname libtype libversion)
if (${importtype} MATCHES "IMPORT")
set (importprefix "${CMAKE_STATIC_LIBRARY_PREFIX}")
endif ()
if (${CMAKE_BUILD_TYPE} MATCHES "Debug")
if (${HDF_CFG_NAME} MATCHES "Debug")
set (IMPORT_LIB_NAME ${LIB_DEBUG_NAME})
else ()
set (IMPORT_LIB_NAME ${LIB_RELEASE_NAME})
@ -273,7 +273,7 @@ macro (HDF_README_PROPERTIES target_fortran)
set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO 2015")
else ()
set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO 2017")
endif ()
endif ()
else ()
set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO ${CMAKE_C_COMPILER_VERSION}")
endif ()

4
config/cmake_ext_mod/HDFUseCXX.cmake
View File

@ -96,7 +96,7 @@ endmacro ()
# Check a bunch of cxx functions
#-----------------------------------------------------------------------------
if (CMAKE_CXX_COMPILER_LOADED)
foreach (test
foreach (cxx_test
OLD_HEADER_FILENAME
HDF_NO_NAMESPACE
HDF_NO_STD
@ -104,6 +104,6 @@ if (CMAKE_CXX_COMPILER_LOADED)
NO_STATIC_CAST
CXX_HAVE_OFFSETOF
)
HDF_CXX_FUNCTION_TEST (${test})
HDF_CXX_FUNCTION_TEST (${cxx_test})
endforeach ()
endif ()

8
config/cmake_ext_mod/grepTest.cmake
View File

@ -57,15 +57,15 @@ file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
# TEST_REFERENCE should always be matched
string (REGEX MATCH "${TEST_REFERENCE}" TEST_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT)
if ("${TEST_RESULT}" STREQUAL "0")
if (NOT TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
endif ()
string (REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM})
if ("${TEST_EXPECT}" STREQUAL "1")
# TEST_EXPECT (1) interperts TEST_FILTER as NOT to match
if (TEST_EXPECT)
# TEST_EXPECT (1) interprets TEST_FILTER as; NOT to match
string (LENGTH "${TEST_MATCH}" TEST_RESULT)
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_FILTER}")
endif ()
endif ()

46
config/cmake_ext_mod/runTest.cmake
View File

@ -80,7 +80,7 @@ if (TEST_REGEX)
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
string (REGEX MATCH "${TEST_REGEX}" REGEX_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${REGEX_MATCH}" "${TEST_MATCH}" REGEX_RESULT)
if ("${REGEX_RESULT}" STREQUAL "0")
if (NOT REGEX_RESULT)
message (STATUS "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_MATCH}")
endif ()
endif ()
@ -111,7 +111,7 @@ if (TEST_APPEND)
endif ()
# if the return value is !=${TEST_EXPECT} bail out
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
if (NOT TEST_RESULT EQUAL TEST_EXPECT)
if (NOT TEST_NOERRDISPLAY)
if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT})
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
@ -126,7 +126,7 @@ message (STATUS "COMMAND Error: ${TEST_ERROR}")
# remove special output
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
string (FIND TEST_STREAM "_pmi_alps" "${TEST_FIND_RESULT}")
if ("${TEST_FIND_RESULT}" GREATER "0")
if (TEST_FIND_RESULT GREATER 0)
string (REGEX REPLACE "^.*_pmi_alps[^\n]+\n" "" TEST_STREAM "${TEST_STREAM}")
file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_STREAM})
endif ()
@ -207,33 +207,33 @@ if (NOT TEST_SKIP_COMPARE)
endif ()
endif ()
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} test_ref)
list (LENGTH test_ref len_ref)
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
if (len_act GREATER 0 AND len_ref GREATER 0)
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
list (GET test_ref ${line} str_ref)
if (NOT "${str_act}" STREQUAL "${str_ref}")
if (NOT "${str_act}" STREQUAL "")
if (NOT str_act STREQUAL str_ref)
if (str_act)
set (TEST_RESULT 1)
message ("line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
endif ()
endif ()
endforeach ()
else ()
if ("${len_act}" STREQUAL "0")
if (len_act EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT} is empty")
endif ()
if ("${len_ref}" STREQUAL "0")
if (len_ref EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_REFERENCE} is empty")
endif ()
endif ()
if (NOT "${len_act}" STREQUAL "${len_ref}")
if (NOT len_act EQUAL len_ref)
set (TEST_RESULT 1)
endif ()
endif ()
@ -241,7 +241,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_OUTPUT} did not match ${TEST_REFERENCE}")
endif ()
endif ()
@ -258,34 +258,34 @@ if (NOT TEST_SKIP_COMPARE)
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT}.err ${TEST_FOLDER}/${TEST_ERRREF}
RESULT_VARIABLE TEST_RESULT
)
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT}.err test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_ERRREF} test_ref)
list (LENGTH test_ref len_ref)
math (EXPR _FP_LEN "${len_ref} - 1")
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
if (len_act GREATER 0 AND len_ref GREATER 0)
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
list (GET test_ref ${line} str_ref)
if (NOT "${str_act}" STREQUAL "${str_ref}")
if (NOT "${str_act}" STREQUAL "")
if (NOT str_act STREQUAL str_ref)
if (str_act)
set (TEST_RESULT 1)
message ("line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
endif ()
endif ()
endforeach ()
else ()
if ("${len_act}" STREQUAL "0")
if (len_act EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT}.err is empty")
endif ()
if ("${len_ref}" STREQUAL "0")
if (len_ref EQUAL 0)
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_ERRREF} is empty")
endif ()
endif ()
if (NOT "${len_act}" STREQUAL "${len_ref}")
if (NOT len_act EQUAL len_ref)
set (TEST_RESULT 1)
endif ()
endif ()
@ -293,7 +293,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The error output of ${TEST_OUTPUT}.err did not match ${TEST_ERRREF}")
endif ()
endif ()
@ -306,15 +306,15 @@ if (TEST_GREP_COMPARE)
# TEST_REFERENCE should always be matched
string (REGEX MATCH "${TEST_REFERENCE}" TEST_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT)
if ("${TEST_RESULT}" STREQUAL "0")
if (NOT TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
endif ()
string (REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM})
if ("${TEST_EXPECT}" STREQUAL "1")
# TEST_EXPECT (1) interperts TEST_FILTER as NOT to match
if (TEST_EXPECT)
# TEST_EXPECT (1) interprets TEST_FILTER as; NOT to match
string (LENGTH "${TEST_MATCH}" TEST_RESULT)
if (NOT "${TEST_RESULT}" STREQUAL "0")
if (TEST_RESULT)
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_FILTER}")
endif ()
endif ()

11
config/toolchain/crayle.cmake
View File

@ -8,14 +8,3 @@ set(CMAKE_Fortran_COMPILER ftn)
# the following is used if cross-compiling
set(CMAKE_CROSSCOMPILING_EMULATOR "")
# option to use pre-generated H5Tinit.c file
set(HDF5_USE_PREGEN OFF)
# directory where H5Tinit.c file will be found
#set(HDF5_USE_PREGEN_DIR "/lscratch1/lknox/HDF5_1_10_4/CMake-hdf5-1.10.4")
# option to generate H5Tinit.c by running H5detect on knl compute node during build
set(HDF5_BATCH_H5DETECT ON)
set(HDF5_BATCH_CMD "sbatch")
set(HDF5_BATCH_H5DETECT_SCRIPT "knl_H5detect.sl")
set(MPIEXEC_EXECUTABLE "srun")

46
configure.ac
View File

@ -1130,11 +1130,12 @@ case "$host_cpu-$host_vendor-$host_os" in
## functionality so clock_gettime and CLOCK_MONOTONIC are defined
## correctly. This was later updated to 200112L so that
## posix_memalign() is visible for the direct VFD code on Linux
## systems.
## systems. Even later, this was changed to 200809L to support
## pread/pwrite in VFDs.
##
## POSIX feature information can be found in the gcc manual at:
## http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html
H5_CPPFLAGS="-D_POSIX_C_SOURCE=200112L $H5_CPPFLAGS"
H5_CPPFLAGS="-D_POSIX_C_SOURCE=200809L $H5_CPPFLAGS"
## Need to add this so that O_DIRECT is visible for the direct
## VFD on Linux systems.
@ -3265,6 +3266,47 @@ case "X-$STRICT_FORMAT_CHECKS" in
esac
## ----------------------------------------------------------------------
## Enable use of pread/pwrite instead of read/write in certain VFDs.
##
AC_SUBST([PREADWRITE])
## Check these first to avoid interspersed output in the AC_ARG_ENABLE line
## below. (Probably overkill to check for both, but we'll be extra careful)
PREADWRITE_HAVE_BOTH=yes
AC_CHECK_FUNC([pread], [], [PREADWRITE_HAVE_BOTH=no])
AC_CHECK_FUNC([pwrite], [], [PREADWRITE_HAVE_BOTH=no])
AC_MSG_CHECKING([whether to use pread/pwrite instead of read/write in certain VFDs])
AC_ARG_ENABLE([preadwrite],
[AS_HELP_STRING([--enable-preadwrite],
[Enable using pread/pwrite instead of read/write in sec2/log/core VFDs.
[default=yes if pread/pwrite are present]])],
[PREADWRITE=$enableval])
## Set the default level.
if test "X-$PREADWRITE" = X- ; then
PREADWRITE=yes
fi
case "X-$PREADWRITE" in
X-yes)
if test "X-$PREADWRITE_HAVE_BOTH" = "X-yes"; then
AC_DEFINE([HAVE_PREADWRITE], [1], [Define if both pread and pwrite exist.])
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
fi
;;
X-no)
AC_MSG_RESULT([no])
;;
*)
AC_MSG_ERROR([Unrecognized value: $PREADWRITE])
;;
esac
## ----------------------------------------------------------------------
## Enable embedded library information
##

50
examples/CMakeTests.cmake
View File

@ -71,7 +71,7 @@
vds-simpleIO.h5
vds-eiger.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (EXAMPLES-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "EXAMPLES-clear-objects")
@ -91,7 +91,7 @@
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (EXAMPLES-${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "EXAMPLES-${example}")
@ -150,7 +150,7 @@
WORKING_DIRECTORY
${PROJECT_BINARY_DIR}/H5EX-shared
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (EXAMPLES-shared-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "EXAMPLES-shared-clear-objects")
@ -171,7 +171,7 @@
)
endif ()
set_tests_properties (EXAMPLES-shared-${example} PROPERTIES WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/H5EX-shared)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (EXAMPLES-shared-${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "EXAMPLES-shared-${example}")
@ -181,42 +181,42 @@
### 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_PAR-ph5example COMMAND $<TARGET_FILE:ph5example>)
add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:ph5example> ${MPIEXEC_POSTFLAGS})
else ()
add_test (NAME EXAMPLES_PAR-ph5example COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:ph5example>"
add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND "${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_SKIP_COMPARE=TRUE"
-D "TEST_OUTPUT=ph5example.txt"
#-D "TEST_REFERENCE=ph5example.out"
-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}/runTest.cmake"
-P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
set_tests_properties (EXAMPLES_PAR-ph5example PROPERTIES DEPENDS ${last_test})
if (last_test)
set_tests_properties (MPI_TEST_EXAMPLES-ph5example PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "EXAMPLES_PAR-ph5example")
set (last_test "MPI_TEST_EXAMPLES-ph5example")
if (BUILD_SHARED_LIBS)
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME EXAMPLES_PAR-shared-ph5example COMMAND $<TARGET_FILE:ph5example-shared>)
add_test (NAME MPI_TEST_EXAMPLES-shared-ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:ph5example-shared> ${MPIEXEC_POSTFLAGS})
else ()
add_test (NAME EXAMPLES_PAR-shared-ph5example COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:ph5example-shared>"
add_test (NAME MPI_TEST_EXAMPLES-shared-ph5example COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${MPIEXEC_MAX_NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:ph5example-shared>;${MPIEXEC_POSTFLAGS}"
-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_OUTPUT=ph5example-shared.out"
-D "TEST_REFERENCE:STRING=PHDF5 tests finished with no errors"
-D "TEST_FILTER:STRING=PHDF5 tests finished with no errors"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/H5EX-shared"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
-P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake"
)
endif ()
set_tests_properties (EXAMPLES_PAR-shared-ph5example PROPERTIES WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/H5EX-shared)
if (NOT "${last_test}" STREQUAL "")
set_tests_properties (EXAMPLES_PAR-shared-ph5example PROPERTIES DEPENDS ${last_test})
set_tests_properties (MPI_TEST_EXAMPLES-shared-ph5example PROPERTIES WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/H5EX-shared)
if (last_test)
set_tests_properties (MPI_TEST_EXAMPLES-shared-ph5example PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "EXAMPLES_PAR-shared-ph5example")
set (last_test "MPI_TEST_EXAMPLES-shared-ph5example")
endif ()
endif ()

74
fortran/examples/CMakeTests.cmake
View File

@ -37,7 +37,7 @@
SDScompound.h5
test.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (f90_ex-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f90_ex-clear-objects")
@ -62,7 +62,7 @@
SDScompound.h5
test.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (f90_ex-shared-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f90_ex-shared-clear-objects")
@ -83,7 +83,7 @@ foreach (example ${examples})
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (f90_ex_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f90_ex_${example}")
@ -102,59 +102,57 @@ foreach (example ${examples})
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (f90_ex-shared_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f90_ex-shared_${example}")
endif ()
endforeach ()
if (HDF5_ENABLE_F2003)
foreach (example ${F2003_examples})
foreach (example ${F2003_examples})
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME f03_ex_${example} COMMAND $<TARGET_FILE:f03_ex_${example}>)
else ()
add_test (NAME f03_ex_${example} COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:f03_ex_${example}>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_OUTPUT=f03_ex_${example}.txt"
#-D "TEST_REFERENCE=f03_ex_${example}.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (last_test)
set_tests_properties (f03_ex_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f03_ex_${example}")
if (BUILD_SHARED_LIBS)
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME f03_ex_${example} COMMAND $<TARGET_FILE:f03_ex_${example}>)
add_test (NAME f03_ex-shared_${example} COMMAND $<TARGET_FILE:f03_ex_${example}-shared>)
else ()
add_test (NAME f03_ex_${example} COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:f03_ex_${example}>"
add_test (NAME f03_ex-shared_${example} COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:f03_ex_${example}-shared>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_OUTPUT=f03_ex_${example}.txt"
#-D "TEST_REFERENCE=f03_ex_${example}.out"
-D "TEST_OUTPUT=f03_ex_${example}-shared.txt"
#-D "TEST_REFERENCE=f03_ex_${example}-shared.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
set_tests_properties (f03_ex_${example} PROPERTIES DEPENDS ${last_test})
if (last_test)
set_tests_properties (f03_ex-shared_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f03_ex_${example}")
if (BUILD_SHARED_LIBS)
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME f03_ex-shared_${example} COMMAND $<TARGET_FILE:f03_ex_${example}-shared>)
else ()
add_test (NAME f03_ex-shared_${example} COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:f03_ex_${example}-shared>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_OUTPUT=f03_ex_${example}-shared.txt"
#-D "TEST_REFERENCE=f03_ex_${example}-shared.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
set_tests_properties (f03_ex-shared_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "f03_ex-shared_${example}")
endif ()
endforeach ()
endif ()
set (last_test "f03_ex-shared_${example}")
endif ()
endforeach ()
if (H5_HAVE_PARALLEL AND MPI_Fortran_FOUND)
add_test (NAME f90_ex_ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:f90_ex_ph5example> ${MPIEXEC_POSTFLAGS})
add_test (NAME MPI_TEST_f90_ex_ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:f90_ex_ph5example> ${MPIEXEC_POSTFLAGS})
if (BUILD_SHARED_LIBS)
add_test (NAME f90_ex-shared_ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:f90_ex_ph5example> ${MPIEXEC_POSTFLAGS})
add_test (NAME MPI_TEST_f90_ex-shared_ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:f90_ex_ph5example> ${MPIEXEC_POSTFLAGS})
endif ()
endif ()

18
fortran/examples/run-fortran-ex.sh.in
View File

@ -61,8 +61,6 @@ RunTest()
./$TEST_EXEC
}
F2003_ENABLED=@HAVE_FORTRAN_2003@
################## MAIN ##################
# Run tests
@ -97,17 +95,8 @@ then
RunTest mountexample &&\
rm mountexample &&\
RunTest compound &&\
rm compound); then
EXIT_VALUE=${EXIT_SUCCESS}
else
EXIT_VALUE=${EXIT_FAILURE}
fi
fi
if [ $EXIT_VALUE -eq ${EXIT_SUCCESS} -a "$F2003_ENABLED" = "yes" ]
then
# Add attention tests for Fortran 2003 features
if (RunTest rwdset_fortran2003 &&\
rm compound &&\
RunTest rwdset_fortran2003 &&\
rm rwdset_fortran2003 &&\
RunTest nested_derived_type &&\
rm nested_derived_type &&\
@ -120,12 +109,11 @@ then
EXIT_VALUE=${EXIT_FAILURE}
fi
fi
# Cleanup
rm *.o
rm *.h5
echo
exit $EXIT_VALUE
exit $EXIT_VALUE

6
fortran/src/CMakeLists.txt
View File

@ -9,11 +9,7 @@ if (WIN32)
if (NOT H5_HAVE_PARALLEL)
set (H5_NOPAREXP ";")
endif ()
if (NOT HDF5_ENABLE_F2003)
set (H5_NOF03EXP ";")
else ()
set (H5_F03EXP ";")
endif ()
set (H5_F03EXP ";")
configure_file (${HDF5_F90_SRC_SOURCE_DIR}/hdf5_fortrandll.def.in ${HDF5_F90_SRC_BINARY_DIR}/hdf5_fortrandll.def @ONLY)
endif ()
endif ()

161
fortran/src/H5Sf.c
View File

@ -995,167 +995,6 @@ done:
}
#ifdef NEW_HYPERSLAB_API
/****if* H5Sf/h5scombine_hyperslab_c
* NAME
* h5scombine_hyperslab_c
* PURPOSE
* Call H5Scombine_hyperslab
* INPUTS
* space_id - identifier of the dataspace
* operator - defines how the new selection is combined
* start - offset of start of hyperslab
* count - number of blocks included in the hyperslab
* stride - hyperslab stride (interval between blocks)
* block - size of block in the hyperslab
* OUTPUTS
* hyper_id - identifier for the new dataspace
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Monday, October 7, 2002
* HISTORY
*
* SOURCE
*/
int_f
h5scombine_hyperslab_c ( hid_t_f *space_id , int_f *op, hsize_t_f *start, hsize_t_f *count, hsize_t_f *stride, hsize_t_f *block, hid_t_f *hyper_id)
/******/
{
int ret_value = -1;
hid_t c_space_id;
hid_t c_hyper_id;
hsize_t *c_start = NULL;
hsize_t *c_count = NULL;
hsize_t *c_stride = NULL;
hsize_t *c_block = NULL;
H5S_seloper_t c_op;
herr_t status;
int rank;
int i;
rank = H5Sget_simple_extent_ndims(*space_id);
if (rank < 0 ) return ret_value;
c_start = (hsize_t *)HDmalloc(sizeof(hsize_t)*rank);
if (c_start == NULL) goto DONE;
c_count = (hsize_t *)HDmalloc(sizeof(hsize_t)*rank);
if (c_count == NULL) goto DONE;
c_stride = (hsize_t *)HDmalloc(sizeof(hsize_t)*rank);
if (c_stride == NULL) goto DONE;
c_block = (hsize_t *)HDmalloc(sizeof(hsize_t)*rank);
if (c_block == NULL) goto DONE;
/*
* Reverse dimensions due to C-FORTRAN storage order.
*/
for (i=0; i < rank; i++) {
int t= (rank - i) - 1;
c_start[i] = (hsize_t)start[t];
c_count[i] = (hsize_t)count[t];
c_stride[i] = (hsize_t)stride[t];
c_block[i] = (hsize_t)block[t];
}
c_op = (H5S_seloper_t)*op;
c_space_id = (hid_t)*space_id;
c_hyper_id = H5Scombine_hyperslab(c_space_id, c_op, c_start, c_stride, c_count, c_block);
if ( c_hyper_id < 0 ) goto DONE;
*hyper_id = (hid_t_f)c_hyper_id;
ret_value = 0;
DONE:
if(c_start != NULL) HDfree(c_start);
if(c_count != NULL) HDfree(c_count);
if(c_stride!= NULL) HDfree(c_stride);
if(c_block != NULL) HDfree(c_block);
return ret_value;
}
/****if* H5Sf/h5scombine_select_c
* NAME
* h5scombine_select_c
* PURPOSE
* Call H5Scombine_ select
* INPUTS
* space1_id - identifier of the first dataspace
* operator - defines how the new selection is combined
* space2_id - identifier of the second dataspace
* OUTPUTS
* ds_id - identifier for the new dataspace
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Monday, October 7, 2002
* HISTORY
*
* SOURCE
*/
int_f
h5scombine_select_c ( hid_t_f *space1_id , int_f *op, hid_t_f *space2_id, hid_t_f *ds_id)
/******/
{
int ret_value = -1;
hid_t c_space1_id;
hid_t c_space2_id;
hid_t c_ds_id;
H5S_seloper_t c_op;
c_op = (H5S_seloper_t)*op;
c_space1_id = (hid_t)*space1_id;
c_space2_id = (hid_t)*space2_id;
c_ds_id = H5Scombine_select(c_space1_id, c_op, c_space2_id);
if ( c_ds_id < 0 ) return ret_value;
*ds_id = (hid_t_f)c_ds_id;
ret_value = 0;
return ret_value;
}
/****if* H5Sf/h5sselect_select_c
* NAME
* h5sselect_select_c
* PURPOSE
* Call H5Sselect_ select
* INPUTS
* space1_id - identifier of the first dataspace to modify
* operator - defines how the new selection is combined
* space2_id - identifier of the second dataspace
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Monday, October 7, 2002
* HISTORY
*
* SOURCE
*/
int_f
h5sselect_select_c ( hid_t_f *space1_id , int_f *op, hid_t_f *space2_id)
/******/
{
int ret_value = -1;
hid_t c_space1_id;
hid_t c_space2_id;
H5S_seloper_t c_op;
c_op = (H5S_seloper_t)*op;
c_space1_id = (hid_t)*space1_id;
c_space2_id = (hid_t)*space2_id;
if( H5Sselect_select(c_space1_id, c_op, c_space2_id)< 0) return ret_value;
ret_value = 0;
return ret_value;
}
#endif /*NEW_HYPERSLAB_API*/
/****if* H5Sf/h5sget_select_type_c
* NAME
* h5sget_select_type_c

304
fortran/src/H5Sff.F90
View File

@ -1275,310 +1275,6 @@ CONTAINS
DEALLOCATE(def_stride)
END SUBROUTINE h5sselect_hyperslab_f
! !$!
! !$!****s* H5S/h5scombine_hyperslab_f
! !$!
! !$! NAME
! !$! h5scombine_hyperslab_f
! !$!
! !$! PURPOSE
! !$! Combine a hyperslab selection with the current
! !$! selection for a dataspace
! !$!
! !$! INPUTS
! !$! space_id - dataspace of selection to use
! !$! operator - flag, valid values are:
! !$! H5S_SELECT_NOOP_F
! !$! H5S_SELECT_SET_F
! !$! H5S_SELECT_OR_F
! !$! H5S_SELECT_AND_F
! !$! H5S_SELECT_XOR_F
! !$! H5S_SELECT_NOTB_F
! !$! H5S_SELECT_NOTA_F
! !$! H5S_SELECT_APPEND_F
! !$! H5S_SELECT_PREPEND_F
! !$! start - array with hyperslab offsets
! !$! count - number of blocks included in the
! !$! hyperslab
! !$! OUTPUTS
! !$! hyper_id - identifier for the new hyperslab
! !$! hdferr: - error code
! !$! Success: 0
! !$! Failure: -1
! !$! OPTIONAL PARAMETERS
! !$! stride - array with hyperslab strides
! !$! block - array with hyperslab block sizes
! !$!
! !$! AUTHOR
! !$! Elena Pourmal
! !$! October 7, 2002
! !$!
! !$! HISTORY
! !$!
! !$!
! !$! NOTES
! !$! Commented out until 1.6 ? 10/08/2002
! !$!
! !$! SOURCE
! SUBROUTINE h5scombine_hyperslab_f(space_id, operator, start, count, &
! hyper_id, hdferr, stride, block)
! IMPLICIT NONE
! INTEGER(HID_T), INTENT(IN) :: space_id ! Dataspace identifier
! INTEGER, INTENT(IN) :: operator ! Flag, valid values are:
! H5S_SELECT_NOOP_F
! H5S_SELECT_SET_F
! H5S_SELECT_OR_F
! H5S_SELECT_AND_F
! H5S_SELECT_XOR_F
! H5S_SELECT_NOTB_F
! H5S_SELECT_NOTA_F
! H5S_SELECT_APPEND_F
! H5S_SELECT_PREPEND_F
!
! INTEGER(HSIZE_T), DIMENSION(*), INTENT(IN) :: start
! Starting coordinates of the hyperslab
! INTEGER(HSIZE_T), DIMENSION(*), INTENT(IN) :: count
! Number of blocks to select
! from dataspace
! INTEGER(HID_T), INTENT(OUT) :: hyper_id ! New hyperslab identifier
! INTEGER, INTENT(OUT) :: hdferr ! Error code
! INTEGER(HSIZE_T), DIMENSION(:), OPTIONAL, INTENT(IN) :: stride
! Array of how many elements to move
! in each direction
! INTEGER(HSIZE_T), DIMENSION(:), OPTIONAL, INTENT(IN) :: block
! Sizes of element block
! INTEGER(HSIZE_T), DIMENSION(:), ALLOCATABLE :: def_block
! INTEGER(HSIZE_T), DIMENSION(:), ALLOCATABLE :: def_stride
! INTEGER :: rank
! INTEGER :: error1, error2
! INTERFACE
! INTEGER FUNCTION h5scombine_hyperslab_c(space_id, operator, &
! start, count, stride, block, hyper_id)
! USE H5GLOBAL
! !DEC$IF DEFINED(HDF5F90_WINDOWS)
! !DEC$ATTRIBUTES C,reference,decorate,alias:'H5SCOMBINE_HYPERSLAB_C'::h5scombine_hyperslab_c
! !DEC$ENDIF
! INTEGER(HID_T), INTENT(IN) :: space_id
! INTEGER, INTENT(IN) :: operator
! INTEGER(HSIZE_T), DIMENSION(*), INTENT(IN) :: start
! INTEGER(HSIZE_T), DIMENSION(*), INTENT(IN) :: count
! INTEGER(HSIZE_T), DIMENSION(*), OPTIONAL, INTENT(IN) :: stride
! INTEGER(HSIZE_T), DIMENSION(*), OPTIONAL, INTENT(IN) :: block
! INTEGER(HID_T), INTENT(OUT) :: hyper_id
! END FUNCTION h5scombine_hyperslab_c
! END INTERFACE
! if (present(stride).and. present(block)) then
! hdferr = h5scombine_hyperslab_c(space_id, operator, start, count, &
! stride, block, hyper_id)
! return
! endif
! Case of optional parameters.
!
! Find the rank of the dataspace to allocate memory for
! default stride and block arrays.
!
! CALL h5sget_simple_extent_ndims_f(space_id, rank, hdferr)
! if( hdferr .EQ. -1) return
!
! if (present(stride).and. .not.present(block)) then
! allocate(def_block(rank), stat=error1)
! if (error1.NE.0) then
! hdferr = -1
! return
! endif
! def_block = 1
! hdferr = h5scombine_hyperslab_c(space_id, operator, start, count, &
! stride, def_block, hyper_id)
! deallocate(def_block)
! return
! endif
! if (.not.present(stride).and. present(block)) then
! allocate(def_stride(rank), stat=error2)
! if (error2.NE.0) then
! hdferr = -1
! return
! endif
! def_stride = 1
! hdferr = h5scombine_hyperslab_c(space_id, operator, start, count, &
! def_stride, block, hyper_id)
! deallocate(def_stride)
! return
! endif
! allocate(def_block(rank), stat=error1)
! allocate(def_stride(rank), stat=error2)
! if ((error1.NE.0) .OR. (error2.NE.0)) then
! hdferr = -1
! return
! endif
! def_block = 1
! def_stride = 1
! hdferr = h5scombine_hyperslab_c(space_id, operator, start, count, &
! def_stride, def_block, hyper_id)
! deallocate(def_block)
! deallocate(def_stride)
! END SUBROUTINE h5scombine_hyperslab_f
! !$!
! !$!****s* H5S/
! !$!
! !$! NAME
! !$! h5scombine_select_f
! !$!
! !$! PURPOSE
! !$! Combine two hyperslab selections with an operation
! !$! and return a dataspace with resulting selection.
! !$!
! !$! INPUTS
! !$! space1_id - dataspace of selection to use
! !$! operator - flag, valid values are:
! !$! H5S_SELECT_NOOP_F
! !$! H5S_SELECT_SET_F
! !$! H5S_SELECT_OR_F
! !$! H5S_SELECT_AND_F
! !$! H5S_SELECT_XOR_F
! !$! H5S_SELECT_NOTB_F
! !$! H5S_SELECT_NOTA_F
! !$! H5S_SELECT_APPEND_F
! !$! H5S_SELECT_PREPEND_F
! !$! space2_id - dataspace of selection to use
! !$! OUTPUTS
! !$! ds_id - idataspace identifier with the new selection
! !$! hdferr: - error code
! !$! Success: 0
! !$! Failure: -1
! !$! OPTIONAL PARAMETERS - NONE
! !$!
! !$! AUTHOR
! !$! Elena Pourmal
! !$! October 7, 2002
! !$!
! !$! HISTORY
! !$!
! !$!
! !$! NOTES commented out until 1.6 release(?) 10/08/2002
! !$!
! ! SOURCE
! !$ SUBROUTINE h5scombine_select_f(space1_id, operator, space2_id, &
! ds_id, hdferr)
! IMPLICIT NONE
! INTEGER(HID_T), INTENT(IN) :: space1_id ! First dataspace identifier
! INTEGER(HID_T), INTENT(IN) :: space2_id ! Second dataspace identifier
! INTEGER, INTENT(IN) :: operator ! Flag, valid values are:
! H5S_SELECT_NOOP_F
! H5S_SELECT_SET_F
! H5S_SELECT_OR_F
! H5S_SELECT_AND_F
! H5S_SELECT_XOR_F
! H5S_SELECT_NOTB_F
! H5S_SELECT_NOTA_F
! H5S_SELECT_APPEND_F
! H5S_SELECT_PREPEND_F
!
! INTEGER(HID_T), INTENT(OUT) :: ds_id ! New dataspace identifier
! INTEGER, INTENT(OUT) :: hdferr ! Error code
!
! INTERFACE
! INTEGER FUNCTION h5scombine_select_c(space1_id, operator, &
! space2_id, ds_id)
! USE H5GLOBAL
! !DEC$IF DEFINED(HDF5F90_WINDOWS)
! !DEC$ATTRIBUTES C,reference,decorate,alias:'H5SCOMBINE_SELECT_C'::h5scombine_select_c
! !DEC$ENDIF
! INTEGER(HID_T), INTENT(IN) :: space1_id
! INTEGER(HID_T), INTENT(IN) :: space2_id
! INTEGER, INTENT(IN) :: operator
! INTEGER(HID_T), INTENT(OUT) :: ds_id
! END FUNCTION h5scombine_select_c
! END INTERFACE
! hdferr = h5scombine_select_c(space1_id, operator, space2_id, &
! ds_id)
! return
! END SUBROUTINE h5scombine_select_f
! !$!
! !$!****s* H5S/
! !$!
! !$! NAME
! !$! h5sselect_select_f
! !$!
! !$! PURPOSE
! !$! Refine a hyperslab selection with an operation
! !$! using second hyperslab
! !$!
! !$! INPUTS
! !$! space1_id - dataspace of selection to modify
! !$! operator - flag, valid values are:
! !$! H5S_SELECT_NOOP_F
! !$! H5S_SELECT_SET_F
! !$! H5S_SELECT_OR_F
! !$! H5S_SELECT_AND_F
! !$! H5S_SELECT_XOR_F
! !$! H5S_SELECT_NOTB_F
! !$! H5S_SELECT_NOTA_F
! !$! H5S_SELECT_APPEND_F
! !$! H5S_SELECT_PREPEND_F
! !$! space2_id - dataspace of selection to use
! !$!
! !$! OUTPUTS
! !$! hdferr: - error code
! !$! Success: 0
! !$! Failure: -1
! !$! OPTIONAL PARAMETERS - NONE
! !$!
! !$! AUTHOR
! !$! Elena Pourmal
! !$! October 7, 2002
! !$!
! !$! HISTORY
! !$!
! !$!
! !$! NOTESCommented out until 1.6 release(?) 10/08/2002 EIP
! !$!
! ! SOURCE
! SUBROUTINE h5sselect_select_f(space1_id, operator, space2_id, &
! hdferr)
! IMPLICIT NONE
! INTEGER(HID_T), INTENT(INOUT) :: space1_id ! Dataspace identifier to
! modify
! INTEGER(HID_T), INTENT(IN) :: space2_id ! Second dataspace identifier
! INTEGER, INTENT(IN) :: operator ! Flag, valid values are:
! H5S_SELECT_NOOP_F
! H5S_SELECT_SET_F
! H5S_SELECT_OR_F
! H5S_SELECT_AND_F
! H5S_SELECT_XOR_F
! H5S_SELECT_NOTB_F
! H5S_SELECT_NOTA_F
! H5S_SELECT_APPEND_F
! H5S_SELECT_PREPEND_F
!
! INTEGER, INTENT(OUT) :: hdferr ! Error code
! INTERFACE
! INTEGER FUNCTION h5sselect_select_c(space1_id, operator, &
! space2_id)
! USE H5GLOBAL
! !DEC$IF DEFINED(HDF5F90_WINDOWS)
! !DEC$ATTRIBUTES C,reference,decorate,alias:'H5SSELECT_SELECT_C'::h5sselect_select_c
! !DEC$ENDIF
! INTEGER(HID_T), INTENT(INOUT) :: space1_id
! INTEGER(HID_T), INTENT(IN) :: space2_id
! INTEGER, INTENT(IN) :: operator
! END FUNCTION h5sselect_select_c
! END INTERFACE
! hdferr = h5sselect_select_c(space1_id, operator, space2_id)
! return
! END SUBROUTINE h5sselect_select_f
!
!****s* H5S/h5sget_select_type_f

3
fortran/src/H5f90proto.h
View File

@ -120,9 +120,6 @@ H5_FCDLL int_f h5sset_extent_none_c( hid_t_f *space_id );
H5_FCDLL int_f h5sselect_hyperslab_c( hid_t_f *space_id , int_f *op, hsize_t_f *start, hsize_t_f *count, hsize_t_f *stride, hsize_t_f *block);
H5_FCDLL int_f h5sget_select_type_c( hid_t_f *space_id , int_f *op);
H5_FCDLL int_f h5sselect_elements_c( hid_t_f *space_id , int_f *op, size_t_f *nelements, hsize_t_f *coord);
H5_FCDLL int_f h5scombine_hyperslab_c( hid_t_f *space_id , int_f *op, hsize_t_f *start, hsize_t_f *count, hsize_t_f *stride, hsize_t_f *block, hid_t_f *hyper_id);
H5_FCDLL int_f h5scombine_select_c( hid_t_f *space1_id , int_f *op, hid_t_f *space2_id, hid_t_f *ds_id);
H5_FCDLL int_f h5sselect_select_c( hid_t_f *space1_id , int_f *op, hid_t_f *space2_id);
H5_FCDLL int_f h5sdecode_c( _fcd buf, hid_t_f *obj_id );
H5_FCDLL int_f h5sencode_c(_fcd buf, hid_t_f *obj_id, size_t_f *nalloc );
H5_FCDLL int_f h5sextent_equal_c( hid_t_f * space1_id, hid_t_f *space2_id, hid_t_f *c_equal);

72
fortran/test/CMakeTests.cmake
View File

@ -58,7 +58,7 @@ add_test (
vds.h5
visit.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (FORTRAN_testhdf5-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "FORTRAN_testhdf5-clear-objects")
@ -103,26 +103,24 @@ endif ()
set_tests_properties (FORTRAN_testhdf5_fortran_1_8 PROPERTIES DEPENDS FORTRAN_testhdf5_fortran)
#-- Adding test for fortranlib_test_F03
if (HDF5_ENABLE_F2003)
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND $<TARGET_FILE:fortranlib_test_F03>)
else ()
add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:fortranlib_test_F03>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_REGEX= 0 error.s."
-D "TEST_MATCH= 0 error(s)"
-D "TEST_OUTPUT=fortranlib_test_F03.txt"
#-D "TEST_REFERENCE=fortranlib_test_F03.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND $<TARGET_FILE:fortranlib_test_F03>)
else ()
add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:fortranlib_test_F03>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_REGEX= 0 error.s."
-D "TEST_MATCH= 0 error(s)"
-D "TEST_OUTPUT=fortranlib_test_F03.txt"
#-D "TEST_REFERENCE=fortranlib_test_F03.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
# set_tests_properties (FORTRAN_fortranlib_test_F03 PROPERTIES PASS_REGULAR_EXPRESSION "[ ]*0 error.s")
set_tests_properties (FORTRAN_fortranlib_test_F03 PROPERTIES DEPENDS FORTRAN_testhdf5_fortran_1_8)
endif ()
#-- Adding test for fflush1
add_test (NAME FORTRAN_fflush1 COMMAND $<TARGET_FILE:fflush1>)
@ -215,26 +213,24 @@ if (BUILD_SHARED_LIBS)
set_tests_properties (FORTRAN_testhdf5_fortran_1_8-shared PROPERTIES DEPENDS FORTRAN_testhdf5_fortran_1_8)
#-- Adding test for fortranlib_test_F03
if (HDF5_ENABLE_F2003)
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME FORTRAN_fortranlib_test_F03-shared COMMAND $<TARGET_FILE:fortranlib_test_F03-shared>)
else ()
add_test (NAME FORTRAN_fortranlib_test_F03-shared COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:fortranlib_test_F03-shared>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_REGEX= 0 error.s."
-D "TEST_MATCH= 0 error(s)"
-D "TEST_OUTPUT=fortranlib_test_F03.txt"
#-D "TEST_REFERENCE=fortranlib_test_F03.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/fshared"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
# set_tests_properties (FORTRAN_fortranlib_test_F03-shared PROPERTIES PASS_REGULAR_EXPRESSION "[ ]*0 error.s")
set_tests_properties (FORTRAN_fortranlib_test_F03-shared PROPERTIES DEPENDS FORTRAN_fortranlib_test_F03)
if (HDF5_ENABLE_USING_MEMCHECKER)
add_test (NAME FORTRAN_fortranlib_test_F03-shared COMMAND $<TARGET_FILE:fortranlib_test_F03-shared>)
else ()
add_test (NAME FORTRAN_fortranlib_test_F03-shared COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:fortranlib_test_F03-shared>"
-D "TEST_ARGS:STRING="
-D "TEST_EXPECT=0"
-D "TEST_SKIP_COMPARE=TRUE"
-D "TEST_REGEX= 0 error.s."
-D "TEST_MATCH= 0 error(s)"
-D "TEST_OUTPUT=fortranlib_test_F03.txt"
#-D "TEST_REFERENCE=fortranlib_test_F03.out"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/fshared"
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
# set_tests_properties (FORTRAN_fortranlib_test_F03-shared PROPERTIES PASS_REGULAR_EXPRESSION "[ ]*0 error.s")
set_tests_properties (FORTRAN_fortranlib_test_F03-shared PROPERTIES DEPENDS FORTRAN_fortranlib_test_F03)
#-- Adding test for fflush1
add_test (NAME FORTRAN_fflush1-shared COMMAND $<TARGET_FILE:fflush1-shared>)

8
fortran/test/tH5P.F90
View File

@ -657,7 +657,7 @@ SUBROUTINE test_chunk_cache(cleanup, total_error)
minimize = .TRUE.
CALL h5pget_dset_no_attrs_hint_f(dcpl, minimize, error)
CALL check("h5pget_dset_no_attrs_hint_f",error,total_error)
if(error .eq. 0 .and. minimize .neqv. .FALSE.) then
if(minimize .neqv. .FALSE.) then
total_error = total_error + 1
write(*,*) "Default dataset minimize flag was incorrect (H5P)"
endif
@ -671,7 +671,7 @@ SUBROUTINE test_chunk_cache(cleanup, total_error)
minimize = .FALSE.
CALL h5pget_dset_no_attrs_hint_f(dcpl, minimize, error)
CALL check("h5pget_dset_no_attrs_hint_f",error,total_error)
if(error .eq. 0 .and. minimize .neqv. .TRUE.) then
if(minimize .neqv. .TRUE.) then
total_error = total_error + 1
write(*,*) "Unable to get correct dataset minimize flag (H5P)"
endif
@ -681,7 +681,7 @@ SUBROUTINE test_chunk_cache(cleanup, total_error)
minimize = .TRUE.
CALL h5fget_dset_no_attrs_hint_f(fid, minimize, error)
CALL check("h5fget_dset_no_attrs_hint_f",error,total_error)
if(error .eq. 0 .and. minimize .neqv. .FALSE.) then
if(minimize .neqv. .FALSE.) then
total_error = total_error + 1
write(*,*) "Default dataset minimize flag was incorrect (H5F)"
endif
@ -695,7 +695,7 @@ SUBROUTINE test_chunk_cache(cleanup, total_error)
minimize = .FALSE.
CALL h5fget_dset_no_attrs_hint_f(fid, minimize, error)
CALL check("h5fget_dset_no_attrs_hint_f",error,total_error)
if(error .eq. 0 .and. minimize .neqv. .TRUE.) then
if(minimize .neqv. .TRUE.) then
total_error = total_error + 1
write(*,*) "Unable to get correct dataset minimize flag (H5F)"
endif

2
fortran/testpar/CMakeTests.cmake
View File

@ -15,4 +15,4 @@
### T E S T I N G ###
##############################################################################
##############################################################################
add_test (NAME FORT_parallel_test COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:parallel_test> ${MPIEXEC_POSTFLAGS})
add_test (NAME MPI_TEST_FORT_parallel_test COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:parallel_test> ${MPIEXEC_POSTFLAGS})

4
hl/examples/CMakeTests.cmake
View File

@ -51,7 +51,7 @@ add_custom_target(hl_ex_ex_ds1_files ALL COMMENT "Copying files needed by hl_ex_
ex_table_12.h5
ex_ds1.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (HL_ex-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "HL_ex-clear-objects")
@ -71,7 +71,7 @@ foreach (example ${examples})
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (HL_ex_${example} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "HL_ex_${example}")

4
hl/fortran/test/CMakeLists.txt
View File

@ -70,8 +70,8 @@ macro (ADD_H5_FORTRAN_EXE file)
endif ()
endmacro ()
foreach (test ${H5_TESTS})
ADD_H5_FORTRAN_EXE(${test})
foreach (h5_test ${H5_TESTS})
ADD_H5_FORTRAN_EXE(${h5_test})
endforeach ()
include (CMakeTests.cmake)

4
hl/fortran/test/CMakeTests.cmake
View File

@ -87,6 +87,6 @@ if (BUILD_SHARED_LIBS)
)
endif ()
foreach (test ${H5_TESTS})
ADD_H5_FORTRAN_TEST(${test})
foreach (h5_test ${H5_TESTS})
ADD_H5_FORTRAN_TEST(${h5_test})
endforeach ()

4
hl/test/CMakeTests.cmake
View File

@ -61,7 +61,7 @@ macro (HL_ADD_TEST hl_name)
-P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (HL_${hl_name} PROPERTIES DEPENDS ${last_test}
ENVIRONMENT "srcdir=${HDF5_HL_TEST_BINARY_DIR}"
WORKING_DIRECTORY ${HDF5_HL_TEST_BINARY_DIR}
@ -104,7 +104,7 @@ add_test (
testfl_packet_table_vlen.h5
test_table.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (HL_test-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "HL_test-clear-objects")

2
hl/tools/h5watch/CMakeTests.cmake
View File

@ -147,7 +147,7 @@ if (NOT SWMR_INCOMPAT)
-E remove
WATCH.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (H5WATCH-clearall-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "H5WATCH-clearall-objects")

11
java/examples/datasets/CMakeLists.txt
View File

@ -71,7 +71,7 @@ foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH})
set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}")
endforeach ()
MACRO (ADD_H5_TEST resultfile resultcode)
macro (ADD_H5_TEST resultfile resultcode)
set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=$<TARGET_PROPERTY:${HDF5_JAVA_JNI_LIB_TARGET},OUTPUT_NAME$<$<CONFIG:Debug>:_DEBUG>>;")
add_test (
NAME JAVA_datasets-${resultfile}
@ -87,16 +87,15 @@ MACRO (ADD_H5_TEST resultfile resultcode)
-D "TEST_REFERENCE=datasets/${resultfile}.txt"
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_datasets-${resultfile} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "JAVA_datasets-${resultfile}")
ENDMACRO ()
endmacro ()
if (BUILD_TESTING)
foreach (example ${HDF_JAVA_EXAMPLES})
if ("${example}" STREQUAL "H5Ex_D_External")
if (example STREQUAL "H5Ex_D_External")
add_test (
NAME JAVA_datasets-${example}-clear-objects
COMMAND ${CMAKE_COMMAND}
@ -112,7 +111,7 @@ if (BUILD_TESTING)
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_datasets-${example}-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
add_test (

4
java/examples/datatypes/CMakeLists.txt
View File

@ -72,7 +72,7 @@ MACRO (ADD_H5_TEST resultfile resultcode)
-D "TEST_REFERENCE=datatypes/${resultfile}.txt"
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_datatypes-${resultfile} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "JAVA_datatypes-${resultfile}")
@ -86,7 +86,7 @@ if (BUILD_TESTING)
-E remove
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_datatypes-${example}-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
add_test (

14
java/examples/groups/CMakeLists.txt
View File

@ -55,7 +55,7 @@ foreach (h5_file ${HDF_JAVA_TEST_FILES})
endforeach ()
add_custom_target(H5Ex_G_Visit_files ALL COMMENT "Copying files needed by H5Ex_G_Visit tests" DEPENDS ${H5Ex_G_Visit_files_list})
MACRO (ADD_H5_TEST resultfile resultcode)
macro (ADD_H5_TEST resultfile resultcode)
set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=$<TARGET_PROPERTY:${HDF5_JAVA_JNI_LIB_TARGET},OUTPUT_NAME$<$<CONFIG:Debug>:_DEBUG>>;")
add_test (
NAME JAVA_groups-${resultfile}
@ -71,16 +71,16 @@ MACRO (ADD_H5_TEST resultfile resultcode)
-D "TEST_REFERENCE=groups/${resultfile}.txt"
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_groups-${resultfile} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "JAVA_groups-${resultfile}")
ENDMACRO ()
endmacro ()
if (BUILD_TESTING)
foreach (example ${HDF_JAVA_EXAMPLES})
if (NOT "${example}" STREQUAL "H5Ex_G_Iterate" AND NOT "${example}" STREQUAL "H5Ex_G_Visit")
if ("${example}" STREQUAL "H5Ex_G_Compact")
if (NOT example STREQUAL "H5Ex_G_Iterate" AND NOT example STREQUAL "H5Ex_G_Visit")
if (example STREQUAL "H5Ex_G_Compact")
add_test (
NAME JAVA_groups-${example}-clear-h5s
COMMAND ${CMAKE_COMMAND}
@ -96,7 +96,7 @@ if (BUILD_TESTING)
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
)
endif ()
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_groups-${example}-clear-h5s PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "JAVA_groups-${example}-clear-h5s")
@ -108,7 +108,7 @@ if (BUILD_TESTING)
${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.groups.${example}.txt
${HDFJAVA_EXAMPLES_GROUPS_BINARY_DIR}/${example}.txt
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_groups-${example}-copy-objects PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "JAVA_groups-${example}-copy-objects")

4
java/examples/intro/CMakeLists.txt
View File

@ -73,7 +73,7 @@ MACRO (ADD_H5_TEST resultfile resultcode)
-D "TEST_REFERENCE=intro/${resultfile}.txt"
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_intro-${resultfile} PROPERTIES DEPENDS ${last_test})
endif ()
set (last_test "JAVA_intro-${resultfile}")
@ -88,7 +88,7 @@ if (BUILD_TESTING)
-E remove
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
)
if (NOT "${last_test}" STREQUAL "")
if (last_test)
set_tests_properties (JAVA_intro-${example}-clear-objects PROPERTIES DEPENDS ${last_test})
endif ()
add_test (

16
java/src/hdf/hdf5lib/H5.java
View File

@ -70,8 +70,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF
* Reference Manual.
*
* <center>
* <table border=2 cellpadding=2>
* <table border=1>
* <caption><b>HDF-5 C types to Java types</b> </caption>
* <tr>
* <td><b>HDF-5</b></td>
@ -107,8 +106,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* <td>Special -- see HDFArray</td>
* </tr>
* </table>
* </center>
* <center> <b>General Rules for Passing Arguments and Results</b> </center>
* <b>General Rules for Passing Arguments and Results</b>
* <p>
* In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is for arrays,
* which are discussed below.
@ -143,7 +141,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* <p>
* All the routines where this convention is used will have specific documentation of the details, given below.
* <p>
* <a NAME="ARRAYS"> <b>Arrays</b> </a>
* <b>Arrays</b>
* <p>
* HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API describes the
* layout of the source and destination, and the data for the array passed as a block of bytes, for instance,
@ -176,7 +174,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or
* Double[][].
* <p>
* <a NAME="CONSTANTS"> <b>HDF-5 Constants</b></a>
* <b>HDF-5 Constants</b>
* <p>
* The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs
* via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, the parameters for
@ -196,7 +194,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* The Java application uses both types of constants the same way, the only difference is that the
* <b><i>HDF5CDataTypes</i></b> may have different values on different platforms.
* <p>
* <a NAME="ERRORS"> <b>Error handling and Exceptions</b></a>
* <b>Error handling and Exceptions</b>
* <p>
* The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted from the
* JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural
@ -3235,6 +3233,8 @@ public class H5 implements java.io.Serializable {
* @param file_id
* IN: Identifier of the target file.
*
* @return true if the file-level is set to create minimized dataset object headers, false if not.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
@ -7000,6 +7000,8 @@ public class H5 implements java.io.Serializable {
* @param dcpl_id
* IN: Dataset creation property list
*
* @return true if the given dcpl is set to create minimized dataset object headers, false if not.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/

3
java/src/hdf/overview.html
View File

@ -90,8 +90,7 @@ like this:
The <i><b>H5</b> </i>class automatically loads the native method implementations
and the HDF5 library.
<h3>
<a NAME="DOWNLOAD"></a>To Obtain</h3>
<h3>To Obtain</h3>
The JHI5 is included with the <a href="https://portal.hdfgroup.org/display/support/Downloads">HDF5</a> library.
</body>

26
java/src/jni/CMakeLists.txt
View File

@ -14,6 +14,19 @@ set (HDF5_JAVA_JNI_CSRCS
${HDF5_JAVA_JNI_SOURCE_DIR}/h5lImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5oImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pACPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pDAPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pDCPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pDXPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pFAPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pFCPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pGAPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pGCPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pLAPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pLCPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pOCPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pOCpyPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pStrCPLImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5plImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5rImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5sImp.c
@ -36,6 +49,19 @@ set (HDF5_JAVA_JNI_CHDRS
${HDF5_JAVA_JNI_SOURCE_DIR}/h5lImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5oImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pACPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pDAPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pDCPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pDXPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pFAPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pFCPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pGAPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pGCPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pLAPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pLCPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pOCPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pOCpyPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5pStrCPLImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5plImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5rImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5sImp.h

5
java/src/jni/Makefile.am
View File

@ -34,7 +34,10 @@ libhdf5_java_la_LDFLAGS = -avoid-version -shared -export-dynamic -version-info $
# Source files for the library
libhdf5_java_la_SOURCES=exceptionImp.c h5Constants.c nativeData.c h5util.c h5Imp.c \
h5aImp.c h5dImp.c h5eImp.c h5fImp.c h5gImp.c h5iImp.c h5lImp.c h5oImp.c \
h5pImp.c h5plImp.c h5rImp.c h5sImp.c h5tImp.c h5vlImp.c h5zImp.c
h5pImp.c h5pACPLImp.c h5pDAPLImp.c h5pDCPLImp.c h5pDXPLImp.c \
h5pFAPLImp.c h5pFCPLImp.c h5pGAPLImp.c h5pGCPLImp.c h5pLAPLImp.c h5pLCPLImp.c \
h5pOCPLImp.c h5pOCpyPLImp.c h5pStrCPLImp.c h5plImp.c h5rImp.c h5sImp.c h5tImp.c \
h5vlImp.c h5zImp.c
# HDF5 Java (JNI) library depends on HDF5 Library.
libhdf5_java_la_LIBADD=$(LIBHDF5)

208
java/src/jni/exceptionImp.c
View File

@ -33,21 +33,14 @@ extern "C" {
#include "h5jni.h"
#include "exceptionImp.h"
extern H5E_auto2_t efunc;
extern void *edata;
extern H5E_auto2_t efunc;
extern void *edata;
/*******************/
/* Local Variables */
/*******************/
/* These types are copied from H5Eprivate.h
* They should be moved to a public include file, and deleted from
* here.
*/
#define H5E_NSLOTS 32 /*number of slots in an error stack */
/*
* The list of error messages in the system is kept as an array of
* error_code/message pairs, one for major error numbers and another for
@ -73,29 +66,29 @@ typedef struct H5E_num_t {
/* Local Macros */
/********************/
#define THROWEXCEPTION(className,args) { \
jclass jc; \
jmethodID jm; \
jobject ex; \
jc = ENVPTR->FindClass(ENVPAR (className)); \
if (jc == NULL) { \
return JNI_FALSE; \
} \
jm = ENVPTR->GetMethodID(ENVPAR jc, "<init>", "(Ljava/lang/String;)V"); \
if (jm == NULL) { \
printf("THROWEXCEPTION FATAL ERROR: GetMethodID failed\n"); \
return JNI_FALSE; \
} \
ex = ENVPTR->NewObjectA (ENVPAR jc, jm, (jvalue*)(args)); \
if (ex == NULL) { \
printf("THROWEXCEPTION FATAL ERROR: %s: Creation failed\n", (className)); \
return JNI_FALSE; \
} \
if (ENVPTR->Throw(ENVPAR (jthrowable)ex) < 0) { \
printf("THROWEXCEPTION FATAL ERROR: %s: Throw failed\n", (className)); \
return JNI_FALSE; \
} \
return JNI_TRUE; \
#define THROWEXCEPTION(className, args) \
{ \
jmethodID jm; \
jclass jc; \
jobject ex; \
\
if (NULL == (jc = ENVPTR->FindClass(ENVONLY, (className)))) \
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); \
\
if (NULL == (jm = ENVPTR->GetMethodID(ENVONLY, jc, "<init>", "(Ljava/lang/String;)V"))) { \
HDprintf("THROWEXCEPTION FATAL ERROR: GetMethodID failed\n"); \
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); \
} \
\
if (NULL == (ex = ENVPTR->NewObjectA(ENVONLY, jc, jm, (jvalue *)(args)))) { \
HDprintf("THROWEXCEPTION FATAL ERROR: Class %s: Creation failed\n", (className)); \
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); \
} \
\
if (ENVPTR->Throw(ENVONLY, (jthrowable)ex) < 0) { \
HDprintf("THROWEXCEPTION FATAL ERROR: Class %s: Throw failed\n", (className)); \
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); \
} \
}
/********************/
@ -112,7 +105,9 @@ walk_error_callback
{
H5E_num_t *err_nums = (H5E_num_t *)_err_nums;
if(err_desc) {
UNUSED(n);
if (err_desc) {
err_nums->maj_num = err_desc->maj_num;
err_nums->min_num = err_desc->min_num;
} /* end if */
@ -130,8 +125,15 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5error_1off
(JNIEnv *env, jclass clss)
{
H5Eget_auto2(H5E_DEFAULT, &efunc, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
UNUSED(env);
UNUSED(clss);
if (H5Eget_auto2(H5E_DEFAULT, &efunc, &edata) < 0)
return -1;
if (H5Eset_auto2(H5E_DEFAULT, NULL, NULL) < 0)
return -1;
return 0;
} /* end Java_hdf_hdf5lib_H5_H5error_1off() */
@ -145,10 +147,12 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5error_1on
(JNIEnv *env, jclass clss)
{
UNUSED(env);
UNUSED(clss);
H5Eset_auto2(H5E_DEFAULT, efunc, edata);
} /* end Java_hdf_hdf5lib_H5_H5error_1on() */
/*
* Class: hdf_hdf5lib_exceptions_HDFLibraryException
* Method: printStackTrace0
@ -163,18 +167,25 @@ Java_hdf_hdf5lib_exceptions_HDF5LibraryException_printStackTrace0
FILE *stream = NULL;
const char *file = NULL;
if(file_name == NULL) {
UNUSED(obj);
if (NULL == file_name) {
H5Eprint2(H5E_DEFAULT, stderr);
} /* end if */
}
else {
file = ENVPTR->GetStringUTFChars(ENVPAR file_name, 0);
stream = HDfopen(file, "a+");
if(stream) {
PIN_JAVA_STRING(ENVONLY, file_name, file, NULL, "printStackTrace0: file name not pinned");
if ((stream = HDfopen(file, "a+"))) {
H5Eprint2(H5E_DEFAULT, stream);
HDfclose(stream);
} /* end if */
ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, file);
} /* end else */
}
}
done:
if (file)
UNPIN_JAVA_STRING(ENVONLY, file_name, file);
return;
} /* end Java_hdf_hdf5lib_exceptions_HDF5LibraryException_printStackTrace0() */
/*
@ -189,10 +200,15 @@ Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMajorErrorNumber
(JNIEnv *env, jobject obj)
{
H5E_num_t err_nums;
UNUSED(env);
UNUSED(obj);
err_nums.maj_num = 0;
err_nums.min_num = 0;
H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums);
if (H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums) < 0)
return -1;
return err_nums.maj_num;
} /* end Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMajorErrorNumber() */
@ -209,27 +225,42 @@ Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMinorErrorNumber
(JNIEnv *env, jobject obj)
{
H5E_num_t err_nums;
UNUSED(env);
UNUSED(obj);
err_nums.maj_num = 0;
err_nums.min_num = 0;
H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums);
if (H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums) < 0)
return -1;
return err_nums.min_num;
} /* end Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMinorErrorNumber() */
/*
* Routine to raise particular Java exceptions from C
* Routine to raise particular Java exceptions from C.
*/
static jboolean
H5JNIErrorClass
(JNIEnv *env, const char *message, const char *className)
{
char *args[2];
jstring str = ENVPTR->NewStringUTF(ENVPAR message);
args[0] = (char *)str;
jstring str;
char *args[2];
jboolean retVal = JNI_FALSE;
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, message)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
args[0] = (char *) str;
args[1] = 0;
THROWEXCEPTION(className, args);
retVal = JNI_TRUE;
done:
return retVal;
} /* end H5JNIErrorClass() */
/*
@ -316,7 +347,7 @@ h5unimplemented
*/
jboolean
h5raiseException
(JNIEnv *env, const char *exception, const char *message)
(JNIEnv *env, const char *message, const char *exception)
{
return H5JNIErrorClass(env, message, exception);
} /* end h5raiseException() */
@ -336,51 +367,76 @@ jboolean
h5libraryError
(JNIEnv *env)
{
char *args[2];
const char *exception = NULL;
char *msg_str = NULL;
int num_errs = 0;
H5E_type_t error_msg_type;
H5E_num_t exceptionNumbers;
jstring str = NULL;
ssize_t msg_size = 0;
hid_t min_num;
hid_t maj_num;
ssize_t msg_size = 0;
H5E_type_t error_msg_type;
jstring str = NULL;
hid_t stk_id = -1;
H5E_num_t exceptionNumbers;
hid_t stk_id = H5I_INVALID_HID;
char *args[2];
char *msg_str = NULL;
jboolean retVal = JNI_FALSE;
exceptionNumbers.maj_num = 0;
exceptionNumbers.min_num = 0;
/* Save current stack contents for future use */
stk_id = H5Eget_current_stack(); /* This will clear current stack */
if(stk_id >= 0)
H5Ewalk2(stk_id, H5E_WALK_DOWNWARD, walk_error_callback, &exceptionNumbers);
if ((stk_id = H5Eget_current_stack()) >= 0)
/* This will clear current stack */
if (H5Ewalk2(stk_id, H5E_WALK_DOWNWARD, walk_error_callback, &exceptionNumbers) < 0)
goto done;
maj_num = exceptionNumbers.maj_num;
min_num = exceptionNumbers.min_num;
/*
* TODO: handle < 0 case.
*/
/*
* No error detected in HDF5 error stack.
*/
if (!maj_num && !min_num)
goto done;
exception = defineHDF5LibraryException(maj_num);
/* get the length of the name */
msg_size = H5Eget_msg(min_num, NULL, NULL, 0);
if(msg_size > 0) {
msg_size++; /* add extra space for the null terminator */
msg_str = (char*)HDcalloc((size_t)msg_size, sizeof(char));
if(msg_str) {
msg_size = H5Eget_msg(min_num, &error_msg_type, (char *)msg_str, (size_t)msg_size);
str = ENVPTR->NewStringUTF(ENVPAR msg_str);
HDfree(msg_str);
} /* end if */
} /* end if */
if ((msg_size = H5Eget_msg(min_num, NULL, NULL, 0)) < 0)
goto done;
if (msg_size > 0) {
if (NULL == (msg_str = (char *) HDcalloc((size_t)msg_size + 1, sizeof(char))))
H5_JNI_FATAL_ERROR(ENVONLY, "h5libraryerror: failed to allocate buffer for error message");
if ((msg_size = H5Eget_msg(min_num, &error_msg_type, msg_str, (size_t)msg_size + 1)) < 0)
goto done;
msg_str[msg_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, msg_str)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else
str = NULL;
if(stk_id >= 0)
if (stk_id >= 0)
H5Eset_current_stack(stk_id);
args[0] = (char *)str;
args[0] = (char *) str;
args[1] = 0;
THROWEXCEPTION(exception, args);
} /* end h5libraryError() */
THROWEXCEPTION(exception, args);
retVal = JNI_TRUE;
done:
if (msg_str)
HDfree(msg_str);
return retVal;
} /* end h5libraryError() */
/*
* defineHDF5LibraryException() returns the name of the sub-class

2
java/src/jni/h5Constants.c
View File

@ -1260,7 +1260,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5VL_1CAP_1FLAG_1THREADSAFE(JNIEnv *env, jclass c
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE(JNIEnv *env, jclass cls) { return H5VL_NATIVE; }
JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE_1NAME(JNIEnv *env, jclass cls) { return (jstring)ENVPTR->NewStringUTF(ENVPAR H5VL_NATIVE_NAME); }
Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE_1NAME(JNIEnv *env, jclass cls) { return (jstring)ENVPTR->NewStringUTF(ENVONLY, H5VL_NATIVE_NAME); }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE_1VALUE(JNIEnv *env, jclass cls) { return H5VL_NATIVE_VALUE; }
JNIEXPORT jint JNICALL

106
java/src/jni/h5Imp.c
View File

@ -35,7 +35,10 @@ extern "C" {
#include "h5jni.h"
#include "h5Imp.h"
extern JavaVM *jvm;
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
/*
* Class: hdf_hdf5lib_H5
@ -46,10 +49,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5open
(JNIEnv *env, jclass clss)
{
herr_t retVal = H5open();
if (retVal < 0)
h5libraryError(env);
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5open()) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5open */
@ -62,10 +69,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5close
(JNIEnv *env, jclass clss)
{
herr_t retVal = H5close();
if (retVal < 0)
h5libraryError(env);
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5close()) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5close */
@ -78,10 +89,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5dont_1atexit
(JNIEnv *env, jclass clss)
{
herr_t retVal = H5dont_atexit();
if (retVal < 0)
h5libraryError(env);
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5dont_atexit()) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5dont_1atexit */
@ -94,29 +109,25 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5get_1libversion
(JNIEnv *env, jclass clss, jintArray libversion)
{
unsigned *theArray = NULL;
herr_t status = -1;
jboolean isCopy;
jboolean libversionArrayIsCopy;
int *libversionArray = NULL;
herr_t status = FAIL;
if (libversion == NULL) {
h5nullArgument(env, "H5get_version: libversion is NULL");
} /* end if */
else {
theArray = (unsigned*)ENVPTR->GetIntArrayElements(ENVPAR libversion, &isCopy);
if (theArray == NULL) {
h5JNIFatalError( env, "H5get_libversion: input not pinned");
} /* end if */
else {
status = H5get_libversion(&(theArray[0]), &(theArray[1]), &(theArray[2]));
UNUSED(clss);
if (status < 0) {
ENVPTR->ReleaseIntArrayElements(ENVPAR libversion, (jint*)theArray, JNI_ABORT);
h5libraryError(env);
} /* end if */
ENVPTR->ReleaseIntArrayElements(ENVPAR libversion, (jint*)theArray,0);
} /* end else */
} /* end else */
return (jint)status;
if (libversion == NULL)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5get_libversion: libversion is NULL");
PIN_INT_ARRAY(ENVONLY, libversion, libversionArray, &libversionArrayIsCopy, "H5get_libversion: libversion input not pinned");
if ((status = H5get_libversion((unsigned *) &(libversionArray[0]), (unsigned *) &(libversionArray[1]), (unsigned *) &(libversionArray[2]))) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (libversionArray)
UNPIN_INT_ARRAY(ENVONLY, libversion, libversionArray, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5get_1libversion */
/*
@ -128,6 +139,9 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5check_1version
(JNIEnv *env, jclass clss, jint majnum, jint minnum, jint relnum)
{
UNUSED(env);
UNUSED(clss);
return (jint)H5check_version((unsigned)majnum, (unsigned)minnum, (unsigned)relnum);
} /* end Java_hdf_hdf5lib_H5_H5check_1version */
@ -141,10 +155,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5garbage_1collect
(JNIEnv *env, jclass clss)
{
herr_t retVal = H5garbage_collect();
if (retVal < 0)
h5libraryError(env);
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5garbage_collect()) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5garbage_1collect */
@ -158,11 +176,15 @@ Java_hdf_hdf5lib_H5_H5set_1free_1list_1limits
(JNIEnv *env, jclass clss, jint reg_global_lim, jint reg_list_lim,
jint arr_global_lim, jint arr_list_lim, jint blk_global_lim, jint blk_list_lim )
{
herr_t retVal = H5set_free_list_limits((int)reg_global_lim, (int)reg_list_lim,
(int)arr_global_lim, (int)arr_list_lim, (int)blk_global_lim, (int)blk_list_lim);
if (retVal < 0)
h5libraryError(env);
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5set_free_list_limits((int)reg_global_lim, (int)reg_list_lim,
(int)arr_global_lim, (int)arr_list_lim, (int)blk_global_lim, (int)blk_list_lim)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5set_1free_1list_1limits */
@ -176,7 +198,13 @@ Java_hdf_hdf5lib_H5_H5is_1library_1threadsafe
(JNIEnv *env, jclass clss)
{
hbool_t is_ts = false;
H5is_library_threadsafe(&is_ts);
UNUSED(clss);
if (H5is_library_threadsafe(&is_ts) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jboolean)is_ts;
} /* end Java_hdf_hdf5lib_H5_H5is_1library_1threadsafe */

2727
java/src/jni/h5aImp.c
View File

File diff suppressed because it is too large Load Diff

2572
java/src/jni/h5dImp.c
View File

File diff suppressed because it is too large Load Diff

576
java/src/jni/h5eImp.c
View File

@ -39,6 +39,9 @@ extern "C" {
#include "h5jni.h"
#include "h5eImp.h"
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
extern JavaVM *jvm;
typedef struct _cb_wrapper {
@ -46,20 +49,6 @@ typedef struct _cb_wrapper {
jobject op_data;
} cb_wrapper;
#ifdef __cplusplus
#define CBENVPTR (cbenv)
#define CBENVPAR
#define JVMPTR (jvm)
#define JVMPAR
#define JVMPAR2
#else /* __cplusplus */
#define CBENVPTR (*cbenv)
#define CBENVPAR cbenv,
#define JVMPTR (*jvm)
#define JVMPAR jvm
#define JVMPAR2 jvm,
#endif /* __cplusplus */
/********************/
/* Local Prototypes */
/********************/
@ -77,12 +66,15 @@ Java_hdf_hdf5lib_H5_H5Eauto_1is_1v2
{
unsigned int is_stack = 0;
if (stk_id < 0) {
h5badArgument(env, "H5Eauto_is_v2: invalid argument");
} /* end if */
else if (H5Eauto_is_v2((hid_t)stk_id, &is_stack) < 0)
h5libraryError(env);
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eauto_is_v2: invalid stack ID");
if (H5Eauto_is_v2((hid_t)stk_id, &is_stack) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jboolean)is_stack;
} /* end Java_hdf_hdf5lib_H5_H5Eauto_1is_1v2 */
@ -95,20 +87,34 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Eregister_1class
(JNIEnv *env, jclass cls, jstring cls_name, jstring lib_name, jstring version)
{
hid_t ret_val = -1;
const char* the_cls_name;
const char* the_lib_name;
const char* the_version;
const char* the_cls_name = NULL;
const char* the_lib_name = NULL;
const char* the_version = NULL;
hid_t ret_val = H5I_INVALID_HID;
PIN_JAVA_STRING_THREE(cls_name, the_cls_name, lib_name, the_lib_name, version, the_version);
if (the_cls_name != NULL && the_lib_name != NULL && the_version != NULL) {
ret_val = H5Eregister_class(the_cls_name, the_lib_name, the_version);
UNUSED(cls);
UNPIN_JAVA_STRING_THREE(cls_name, the_cls_name, lib_name, the_lib_name, version, the_version);
if (NULL == cls_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Eregister_class: class name is NULL");
if (NULL == lib_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Eregister_class: lib name is NULL");
if (NULL == version)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Eregister_class: version string is NULL");
if (ret_val < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, cls_name, the_cls_name, NULL, "H5Eregister_class: class name not pinned");
PIN_JAVA_STRING(ENVONLY, lib_name, the_lib_name, NULL, "H5Eregister_class: lib name not pinned");
PIN_JAVA_STRING(ENVONLY, version, the_version, NULL, "H5Eregister_class: version string not pinned");
if ((ret_val = H5Eregister_class(the_cls_name, the_lib_name, the_version)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (the_version)
UNPIN_JAVA_STRING(ENVONLY, version, the_version);
if (the_lib_name)
UNPIN_JAVA_STRING(ENVONLY, lib_name, the_lib_name);
if (the_cls_name)
UNPIN_JAVA_STRING(ENVONLY, cls_name, the_cls_name);
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Eregister_1class */
@ -122,11 +128,16 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Eunregister_1class
(JNIEnv *env, jclass cls, jlong cls_id)
{
if (cls_id < 0) {
h5badArgument(env, "H5Eunregister_class: invalid argument");
} /* end if */
else if (H5Eunregister_class((hid_t)cls_id) < 0)
h5libraryError(env);
UNUSED(cls);
if (cls_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eunregister_class: invalid error class ID");
if (H5Eunregister_class((hid_t)cls_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Eunregister_1class */
/*
@ -138,11 +149,16 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Eclose_1msg
(JNIEnv *env, jclass cls, jlong err_id)
{
if (err_id < 0) {
h5badArgument(env, "H5Eclose_msg: invalid argument");
} /* end if */
else if (H5Eclose_msg((hid_t)err_id) < 0)
h5libraryError(env);
UNUSED(cls);
if (err_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eclose_msg: invalid error message ID");
if (H5Eclose_msg((hid_t)err_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Eclose_1msg */
/*
@ -154,24 +170,25 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Ecreate_1msg
(JNIEnv *env, jclass cls, jlong err_id, jint msg_type, jstring err_msg)
{
hid_t ret_val = -1;
const char *the_err_msg;
H5E_type_t error_msg_type = (H5E_type_t)msg_type;
const char *the_err_msg = NULL;
hid_t ret_val = H5I_INVALID_HID;
if (err_id < 0) {
h5badArgument(env, "H5Ecreate_msg: invalid argument");
} /* end if */
else {
PIN_JAVA_STRING(err_msg, the_err_msg);
if (the_err_msg != NULL) {
ret_val = H5Ecreate_msg((hid_t)err_id, error_msg_type, the_err_msg);
UNUSED(cls);
UNPIN_JAVA_STRING(err_msg, the_err_msg);
if (err_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Ecreate_msg: invalid error class ID");
if (NULL == err_msg)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Ecreate_msg: error message string is NULL");
if (ret_val < 0)
h5libraryError(env);
}
} /* end else */
PIN_JAVA_STRING(ENVONLY, err_msg, the_err_msg, NULL, "H5Ecreate_msg: error message string not pinned");
if ((ret_val = H5Ecreate_msg((hid_t)err_id, error_msg_type, the_err_msg)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (the_err_msg)
UNPIN_JAVA_STRING(ENVONLY, err_msg, the_err_msg);
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Ecreate_1msg */
@ -185,12 +202,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Ecreate_1stack
(JNIEnv *env, jclass cls)
{
hid_t ret_val = -1;
hid_t ret_val = H5I_INVALID_HID;
ret_val = H5Ecreate_stack();
if (ret_val < 0)
h5libraryError(env);
UNUSED(cls);
if ((ret_val = H5Ecreate_stack()) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Ecreate_1stack */
@ -203,12 +222,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Eget_1current_1stack
(JNIEnv *env, jclass cls)
{
hid_t ret_val = -1;
hid_t ret_val = H5I_INVALID_HID;
ret_val = H5Eget_current_stack();
if (ret_val < 0)
h5libraryError(env);
UNUSED(cls);
if ((ret_val = H5Eget_current_stack()) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Eget_1current_1stack */
@ -221,11 +242,16 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Eclose_1stack
(JNIEnv *env, jclass cls, jlong stk_id)
{
if (stk_id < 0) {
h5badArgument(env, "H5Eclose_stack: invalid argument");
} /* end if */
else if (H5Eclose_stack((hid_t)stk_id) < 0)
h5libraryError(env);
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eclose_stack: invalid error stack ID");
if (H5Eclose_stack((hid_t)stk_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Eclose_1stack */
/*
@ -237,20 +263,24 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Eprint2
(JNIEnv *env, jclass cls, jlong stk_id, jobject stream_obj)
{
herr_t ret_val = -1;
herr_t ret_val = FAIL;
if (stk_id < 0) {
h5badArgument(env, "H5Eprint2: invalid argument");
} /* end if */
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eprint2: invalid error stack ID");
if (!stream_obj) {
if ((ret_val = H5Eprint2((hid_t)stk_id, stdout)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
else {
if(!stream_obj)
ret_val = H5Eprint2((hid_t)stk_id, stdout);
else
ret_val = H5Eprint2((hid_t)stk_id, (FILE*)stream_obj);
if ((ret_val = H5Eprint2((hid_t)stk_id, (FILE *)stream_obj)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (ret_val < 0)
h5libraryError(env);
} /* end else */
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Eprint2 */
/*
@ -262,43 +292,36 @@ JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Eget_1class_1name
(JNIEnv *env, jclass cls, jlong cls_id)
{
char *namePtr;
jstring str = NULL;
ssize_t buf_size;
jstring str = NULL;
ssize_t buf_size;
char *namePtr = NULL;
if (cls_id < 0) {
h5badArgument(env, "H5Eget_class_name: invalid argument");
} /* end if */
else {
/* get the length of the name */
buf_size = H5Eget_class_name((hid_t)cls_id, NULL, 0);
UNUSED(cls);
if (buf_size < 0) {
h5badArgument( env, "H5Eget_class_name: buf_size < 0");
} /* end if */
else if (buf_size == 0) {
h5badArgument( env, "H5Eget_class_name: No class name");
} /* end else if */
else {
buf_size++; /* add extra space for the null terminator */
namePtr = (char*)HDmalloc(sizeof(char) * (size_t)buf_size);
if (namePtr == NULL) {
h5outOfMemory( env, "H5Eget_class_name: malloc failed");
} /* end if */
else {
buf_size = H5Eget_class_name((hid_t)cls_id, (char *)namePtr, (size_t)buf_size);
if (cls_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eget_class_name: invalid error class ID");
/* Get the length of the name */
if ((buf_size = H5Eget_class_name((hid_t)cls_id, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (!buf_size)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eget_class_name: no class name");
if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Eget_class_name: malloc failed");
if ((H5Eget_class_name((hid_t)cls_id, (char *)namePtr, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
namePtr[buf_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (namePtr)
HDfree(namePtr);
if (buf_size < 0) {
HDfree(namePtr);
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR namePtr);
HDfree(namePtr);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return str;
} /* end Java_hdf_hdf5lib_H5_H5Eget_1class_1name */
@ -311,11 +334,16 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Eset_1current_1stack
(JNIEnv *env, jclass cls, jlong stk_id)
{
if (stk_id < 0) {
h5badArgument(env, "H5Eset_current_stack: invalid argument");
} /* end if */
else if (H5Eset_current_stack((hid_t)stk_id) < 0)
h5libraryError(env);
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eset_current_stack: invalid error stack ID");
if (H5Eset_current_stack((hid_t)stk_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Eset_1current_1stack */
/*
@ -327,11 +355,16 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Epop
(JNIEnv *env, jclass cls, jlong stk_id, jlong count)
{
if (stk_id < 0) {
h5badArgument(env, "H5Epop: invalid argument");
} /* end if */
else if (H5Epop((hid_t)stk_id, (size_t)count) < 0)
h5libraryError(env);
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Epop: invalid error stack ID");
if (H5Epop((hid_t)stk_id, (size_t)count) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Epop */
/*
@ -344,35 +377,43 @@ Java_hdf_hdf5lib_H5_H5Epush2
(JNIEnv *env, jclass cls, jlong stk_id, jstring filename, jstring funcname,
jint linenumber, jlong class_id, jlong major_id, jlong minor_id, jstring err_desc)
{
herr_t ret_val = -1;
const char* fName;
const char* fncName;
const char* errMsg;
const char *fName = NULL;
const char *fncName = NULL;
const char *errMsg = NULL;
herr_t ret_val = FAIL;
if (stk_id < 0) {
h5badArgument(env, "H5Epush: invalid argument");
} /* end if */
else if (class_id < 0) {
h5badArgument(env, "H5Epush: invalid class_id argument");
} /* end else if */
else if (major_id < 0) {
h5badArgument(env, "H5Epush: invalid major_id argument");
} /* end else if */
else if (minor_id < 0) {
h5badArgument(env, "H5Epush: invalid minor_id argument");
} /* end else if */
else {
PIN_JAVA_STRING_THREE(filename, fName, funcname, fncName, err_desc, errMsg);
if (fName != NULL && fncName != NULL && errMsg != NULL) {
ret_val = H5Epush2((hid_t)stk_id, fName, fncName, (unsigned)linenumber, (hid_t)class_id,
(hid_t)major_id, (hid_t)minor_id, errMsg);
UNUSED(cls);
UNPIN_JAVA_STRING_THREE(filename, fName, funcname, fncName, err_desc, errMsg);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Epush2: invalid error stack ID");
if (class_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Epush2: invalid error class ID");
if (major_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Epush2: invalid major error class ID");
if (minor_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Epush2: invalid minor error class ID");
if (NULL == filename)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Epush2: filename is NULL");
if (NULL == funcname)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Epush2: function name is NULL");
if (NULL == err_desc)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Epush2: error message is NULL");
if (ret_val < 0)
h5libraryError(env);
}
} /* end else */
PIN_JAVA_STRING(ENVONLY, filename, fName, NULL, "H5Epush2: filename not pinned");
PIN_JAVA_STRING(ENVONLY, funcname, fncName, NULL, "H5Epush2: function name not pinned");
PIN_JAVA_STRING(ENVONLY, err_desc, errMsg, NULL, "H5Epush2: error message not pinned");
if ((ret_val = H5Epush2((hid_t)stk_id, fName, fncName, (unsigned)linenumber, (hid_t)class_id,
(hid_t)major_id, (hid_t)minor_id, errMsg)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (errMsg)
UNPIN_JAVA_STRING(ENVONLY, err_desc, errMsg);
if (fncName)
UNPIN_JAVA_STRING(ENVONLY, funcname, fncName);
if (fName)
UNPIN_JAVA_STRING(ENVONLY, filename, fName);
} /* end Java_hdf_hdf5lib_H5_H5Epush2 */
/*
@ -384,11 +425,16 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Eclear2
(JNIEnv *env, jclass cls, jlong stk_id)
{
if (stk_id < 0) {
h5badArgument(env, "H5Eclear2: invalid argument");
} /* end if */
else if (H5Eclear2((hid_t)stk_id) < 0)
h5libraryError(env);
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eclear2: invalid error stack ID");
if (H5Eclear2((hid_t)stk_id) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Eclear2 */
/*
@ -400,57 +446,45 @@ JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Eget_1msg
(JNIEnv *env, jclass cls, jlong msg_id, jintArray error_msg_type_list)
{
char *namePtr;
jstring str = NULL;
jboolean isCopy;
ssize_t buf_size;
jint *theArray;
H5E_type_t error_msg_type;
H5E_type_t error_msg_type;
jstring str = NULL;
ssize_t buf_size;
jint *theArray = NULL;
char *namePtr = NULL;
if (msg_id < 0) {
h5badArgument(env, "H5Eget_msg: invalid argument");
} /* end if */
else if (error_msg_type_list == NULL) {
h5nullArgument(env, "H5Eget_msg: error_msg_type_list is NULL");
} /* end if */
else {
/* get the length of the name */
buf_size = H5Eget_msg((hid_t)msg_id, NULL, NULL, 0);
UNUSED(cls);
if ((buf_size < 0) || (buf_size == 0)) {
h5JNIFatalError(env, "H5Eget_msg: Invalid message");
} /* end if */
else {
buf_size++; /* add extra space for the null terminator */
namePtr = (char*)HDmalloc(sizeof(char) * (size_t)buf_size);
if (namePtr == NULL) {
h5outOfMemory(env, "H5Eget_msg: malloc failed");
} /* end if */
else {
theArray = (jint*)ENVPTR->GetIntArrayElements(ENVPAR error_msg_type_list, &isCopy);
if (theArray == NULL) {
HDfree(namePtr);
h5JNIFatalError(env, "H5Eget_msg: error_msg_type_list not pinned");
} /* end if */
else {
buf_size = H5Eget_msg((hid_t)msg_id, &error_msg_type, (char *)namePtr, (size_t)buf_size);
if (msg_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eget_msg: invalid error message ID");
if (NULL == error_msg_type_list)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Eget_msg: error_msg_type_list is NULL");
if (buf_size < 0) {
HDfree(namePtr);
ENVPTR->ReleaseIntArrayElements(ENVPAR error_msg_type_list, theArray, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
theArray[0] = error_msg_type;
ENVPTR->ReleaseIntArrayElements(ENVPAR error_msg_type_list, theArray, 0);
/* Get the length of the name */
if ((buf_size = H5Eget_msg((hid_t)msg_id, NULL, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
str = ENVPTR->NewStringUTF(ENVPAR namePtr);
HDfree(namePtr);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
} /* end else */
if (!buf_size)
H5_JNI_FATAL_ERROR(ENVONLY, "H5Eget_msg: invalid message");
if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Eget_msg: malloc failed");
PIN_INT_ARRAY(ENVONLY, error_msg_type_list, theArray, NULL, "H5Eget_msg: error_msg_type_list not pinned");
if ((H5Eget_msg((hid_t)msg_id, &error_msg_type, (char *)namePtr, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
namePtr[buf_size] = '\0';
theArray[0] = error_msg_type;
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (theArray)
UNPIN_INT_ARRAY(ENVONLY, error_msg_type_list, theArray, 0);
if (namePtr)
HDfree(namePtr);
return str;
} /* end Java_hdf_hdf5lib_H5_H5Eget_1msg */
@ -466,14 +500,15 @@ Java_hdf_hdf5lib_H5_H5Eget_1num
{
ssize_t ret_val = -1;
if (stk_id < 0) {
h5badArgument(env, "H5Eget_num: invalid argument");
} /* end if */
else {
ret_val = H5Eget_num((hid_t)stk_id);
if (ret_val < 0)
h5libraryError(env);
} /* end else */
UNUSED(cls);
if (stk_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Eget_num: invalid error stack ID");
if ((ret_val = H5Eget_num((hid_t)stk_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Eget_1num */
@ -481,52 +516,67 @@ static herr_t
H5E_walk_cb
(int nindx, const H5E_error2_t *info, void *cb_data)
{
JNIEnv *cbenv;
jint status = -1;
jclass cls;
jmethodID mid;
jstring str1, str2, str3;
jmethodID constructor;
jvalue args[7];
jobject cb_info_t = NULL;
cb_wrapper *wrapper = (cb_wrapper *)cb_data;
void *op_data = (void *)wrapper->op_data;
jobject visit_callback = wrapper->visit_callback;
jmethodID constructor;
jmethodID mid;
jobject visit_callback = wrapper->visit_callback;
jstring str1, str2, str3;
jobject cb_info_t = NULL;
jvalue args[7];
JNIEnv *cbenv = NULL;
jclass cls;
void *op_data = (void *)wrapper->op_data;
jint status = FAIL;
if (JVMPTR->AttachCurrentThread(JVMPAR, (void **)&cbenv, NULL) < 0) {
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(CBENVONLY, "H5E_walk_cb: failed to attach current thread to JVM");
}
if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cls, "callback", "(ILhdf/hdf5lib/structs/H5E_error2_t;Lhdf/hdf5lib/callbacks/H5E_walk_t;)I")))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
args[0].j = info->cls_id;
args[1].j = info->maj_num;
args[2].j = info->min_num;
args[3].i = (jint)info->line;
if (NULL == (str1 = CBENVPTR->NewStringUTF(CBENVONLY, info->func_name)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
args[4].l = str1;
if (NULL == (str2 = CBENVPTR->NewStringUTF(CBENVONLY, info->file_name)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
args[5].l = str2;
if (NULL == (str3 = CBENVPTR->NewStringUTF(CBENVONLY, info->desc)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
args[6].l = str3;
/* Get a reference to your class if you don't have it already */
if (NULL == (cls = CBENVPTR->FindClass(CBENVONLY, "hdf/hdf5lib/structs/H5E_error2_t")))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
/* get a reference to the constructor; the name is <init> */
if (NULL == (constructor = CBENVPTR->GetMethodID(CBENVONLY, cls, "<init>", "(JJJILjava/lang/String;Ljava/lang/String;Ljava/lang/String;)V")))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL == (cb_info_t = CBENVPTR->NewObjectA(CBENVONLY, cls, constructor, args)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
status = CBENVPTR->CallIntMethod(CBENVONLY, visit_callback, mid, nindx, cb_info_t, op_data);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
done:
if (CBENVONLY)
JVMPTR->DetachCurrentThread(JVMPAR);
if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback);
if (cls != 0) {
mid = CBENVPTR->GetMethodID(CBENVPAR cls, "callback", "(ILhdf/hdf5lib/structs/H5E_error2_t;Lhdf/hdf5lib/callbacks/H5E_walk_t;)I");
if (mid != 0) {
args[0].j = info->cls_id;
args[1].j = info->maj_num;
args[2].j = info->min_num;
args[3].i = (jint)info->line;
str1 = CBENVPTR->NewStringUTF(CBENVPAR info->func_name);
args[4].l = str1;
str2 = CBENVPTR->NewStringUTF(CBENVPAR info->file_name);
args[5].l = str2;
str3 = CBENVPTR->NewStringUTF(CBENVPAR info->desc);
args[6].l = str3;
// get a reference to your class if you don't have it already
cls = CBENVPTR->FindClass(CBENVPAR "hdf/hdf5lib/structs/H5E_error2_t");
if (cls != 0) {
// get a reference to the constructor; the name is <init>
constructor = CBENVPTR->GetMethodID(CBENVPAR cls, "<init>", "(JJJILjava/lang/String;Ljava/lang/String;Ljava/lang/String;)V");
if (constructor != 0) {
cb_info_t = CBENVPTR->NewObjectA(CBENVPAR cls, constructor, args);
if (cb_info_t == NULL) {
printf("FATAL ERROR: hdf/hdf5lib/structs/H5E_error2_t: Creation failed\n");
}
else {
status = CBENVPTR->CallIntMethod(CBENVPAR visit_callback, mid, nindx, cb_info_t, op_data);
}
} /* end if (constructor != 0) */
} /* end if(cls != 0) */
} /* end if (mid != 0) */
} /* end if (cls != 0) */
} /* end if */
JVMPTR->DetachCurrentThread(JVMPAR);
return (herr_t)status;
} /* end H5E_walk_cb */
@ -539,15 +589,23 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Ewalk2
(JNIEnv *env, jclass cls, jlong stk_id, jlong direction, jobject callback_op, jobject op_data)
{
cb_wrapper wrapper = {callback_op, op_data};
cb_wrapper wrapper = { callback_op, op_data };
ENVPTR->GetJavaVM(ENVPAR &jvm);
UNUSED(cls);
if ((op_data == NULL) || (callback_op == NULL)) {
h5nullArgument(env, "H5Ewalk2: op_data or callback_op is NULL");
} /* end if */
else if (H5Ewalk2(stk_id, (H5E_direction_t)direction, (H5E_walk2_t)H5E_walk_cb, (void*)&wrapper) < 0)
h5libraryError(env);
ENVPTR->GetJavaVM(ENVONLY, &jvm);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == op_data)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Ewalk2: op_data is NULL");
if (NULL == callback_op)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Ewalk2: callback_op is NULL");
if (H5Ewalk2(stk_id, (H5E_direction_t)direction, (H5E_walk2_t)H5E_walk_cb, (void *)&wrapper) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end iJava_hdf_hdf5lib_H5_H5Ewalk2f */
#ifdef __cplusplus

597
java/src/jni/h5fImp.c
View File

@ -28,7 +28,10 @@ extern "C" {
#include "h5fImp.h"
#include "h5util.h"
extern JavaVM *jvm;
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
/*
* Class: hdf_hdf5lib_H5
@ -39,18 +42,22 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Fopen
(JNIEnv *env, jclass clss, jstring name, jint flags, jlong access_id)
{
hid_t status = -1;
const char *fileName;
const char *fileName = NULL;
hid_t status = H5I_INVALID_HID;
PIN_JAVA_STRING(name, fileName);
if (fileName != NULL) {
status = H5Fopen(fileName, (unsigned)flags, (hid_t)access_id );
UNUSED(clss);
UNPIN_JAVA_STRING(name, fileName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fopen: file name is NULL");
if (status < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, name, fileName, NULL, "H5Fopen: file name not pinned");
if ((status = H5Fopen(fileName, (unsigned)flags, (hid_t)access_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
return (jlong)status;
} /* end Java_hdf_hdf5lib_H5__1H5Fopen */
@ -64,18 +71,22 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Fcreate
(JNIEnv *env, jclass clss, jstring name, jint flags, jlong create_id, jlong access_id)
{
hid_t status = -1;
const char *fileName;
const char *fileName = NULL;
hid_t status = H5I_INVALID_HID;
PIN_JAVA_STRING(name, fileName);
if (fileName != NULL) {
status = H5Fcreate(fileName, (unsigned)flags, create_id, access_id);
UNUSED(clss);
UNPIN_JAVA_STRING(name, fileName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fcreate: file name is NULL");
if (status < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, name, fileName, NULL, "H5Fcreate: file name not pinned");
if ((status = H5Fcreate(fileName, (unsigned)flags, create_id, access_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
return (jlong)status;
} /* end Java_hdf_hdf5lib_H5__1H5Fcreate */
@ -89,12 +100,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Fflush
(JNIEnv *env, jclass clss, jlong object_id, jint scope)
{
herr_t retVal = -1;
herr_t retVal = FAIL;
retVal = H5Fflush((hid_t)object_id, (H5F_scope_t)scope );
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Fflush((hid_t)object_id, (H5F_scope_t)scope)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Fflush */
@ -107,34 +120,29 @@ JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1name
(JNIEnv *env, jclass cls, jlong file_id)
{
char *namePtr;
jstring str = NULL;
ssize_t buf_size;
jstring str = NULL;
ssize_t buf_size;
char *namePtr = NULL;
/* get the length of the name */
buf_size = H5Fget_name((hid_t)file_id, NULL, 0);
UNUSED(cls);
if (buf_size <= 0) {
h5badArgument(env, "H5Fget_name: buf_size <= 0");
} /* end if */
else {
buf_size++; /* add extra space for the null terminator */
namePtr = (char*)HDmalloc(sizeof(char) * (size_t)buf_size);
if (namePtr == NULL) {
h5outOfMemory(env, "H5Fget_name: malloc failed");
} /* end if */
else {
buf_size = H5Fget_name((hid_t)file_id, namePtr, (size_t)buf_size);
if (buf_size < 0) {
HDfree(namePtr);
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR namePtr);
HDfree(namePtr);
}/* end else */
}/* end else */
}/* end else */
/* Get the length of the name */
if ((buf_size = H5Fget_name((hid_t)file_id, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Fget_name: malloc failed");
if ((H5Fget_name((hid_t)file_id, namePtr, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
namePtr[buf_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (namePtr)
HDfree(namePtr);
return str;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1name */
@ -148,24 +156,29 @@ JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Fis_1hdf5
(JNIEnv *env, jclass clss, jstring name)
{
const char *fileName = NULL;
htri_t bval = JNI_FALSE;
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
h5unimplemented(env, "H5Fis_hdf5: not implemented");
#else
const char *fileName;
PIN_JAVA_STRING(name, fileName);
if (fileName != NULL) {
bval = H5Fis_hdf5(fileName);
UNPIN_JAVA_STRING(name, fileName);
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
h5libraryError(env);
}
H5_UNIMPLEMENTED(ENVONLY, "H5Fis_hdf5: not implemented");
#endif
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fis_hdf5: file name is NULL");
PIN_JAVA_STRING(ENVONLY, name, fileName, NULL, "H5Fis_hdf5: file name not pinned");
if ((bval = H5Fis_hdf5(fileName)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
done:
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Fis_1hdf5 */
@ -178,20 +191,24 @@ JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Fis_1accessible
(JNIEnv *env, jclass clss, jstring name, jlong file_id)
{
const char *fileName = NULL;
htri_t bval = JNI_FALSE;
const char *fileName;
PIN_JAVA_STRING(name, fileName);
if (fileName != NULL) {
bval = H5Fis_accessible(fileName, (hid_t)file_id);
UNUSED(clss);
UNPIN_JAVA_STRING(name, fileName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fis_accessible: file name is NULL");
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, name, fileName, NULL, "H5Fis_accessible: file name not pinned");
if ((bval = H5Fis_accessible(fileName, (hid_t)file_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
done:
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Fis_1accessible */
@ -205,12 +222,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Fget_1create_1plist
(JNIEnv *env, jclass clss, jlong file_id)
{
hid_t retVal = -1;
hid_t retVal = H5I_INVALID_HID;
retVal = H5Fget_create_plist((hid_t)file_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Fget_create_plist((hid_t)file_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Fget_1create_1plist */
@ -223,12 +242,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Fget_1access_1plist
(JNIEnv *env, jclass clss, jlong file_id)
{
hid_t retVal = -1;
hid_t retVal = H5I_INVALID_HID;
retVal = H5Fget_access_plist((hid_t)file_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Fget_access_plist((hid_t)file_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Fget_1access_1plist */
@ -243,9 +264,12 @@ Java_hdf_hdf5lib_H5_H5Fget_1intent
{
unsigned intent = 0;
if (H5Fget_intent((hid_t)file_id, &intent) < 0)
h5libraryError(env);
UNUSED(cls);
if (H5Fget_intent((hid_t)file_id, &intent) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)intent;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1intent */
@ -258,14 +282,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5__1H5Fclose
(JNIEnv *env, jclass clss, jlong file_id)
{
herr_t status = -1;
herr_t status = FAIL;
if (file_id > 0)
status = H5Fclose((hid_t)file_id );
UNUSED(clss);
if (status < 0)
h5libraryError(env);
if ((status = H5Fclose((hid_t)file_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)status;
} /* end Java_hdf_hdf5lib_H5__1H5Fclose */
@ -278,18 +302,22 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Fmount
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong child_id, jlong plist_id)
{
herr_t status = -1;
const char *fileName;
const char *fileName = NULL;
herr_t status = FAIL;
PIN_JAVA_STRING(name, fileName);
if (fileName != NULL) {
status = H5Fmount((hid_t)loc_id, fileName, (hid_t)child_id, (hid_t)plist_id);
UNUSED(clss);
UNPIN_JAVA_STRING(name, fileName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fmount: file name is NULL");
if (status < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, name, fileName, NULL, "H5Fmount: file name not pinned");
if ((status = H5Fmount((hid_t)loc_id, fileName, (hid_t)child_id, (hid_t)plist_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Fmount */
@ -303,18 +331,22 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Funmount
(JNIEnv *env, jclass clss, jlong loc_id, jstring name)
{
herr_t status = -1;
const char *fileName;
const char *fileName = NULL;
herr_t status = FAIL;
PIN_JAVA_STRING(name, fileName);
if (fileName != NULL) {
status = H5Funmount((hid_t)loc_id, fileName);
UNUSED(clss);
UNPIN_JAVA_STRING(name, fileName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Funmount: file name is NULL");
if (status < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, name, fileName, NULL, "H5Funmount: file name not pinned");
if ((status = H5Funmount((hid_t)loc_id, fileName)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Funmount */
@ -328,11 +360,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1freespace
(JNIEnv *env, jclass cls, jlong file_id)
{
hssize_t ret_val = H5Fget_freespace((hid_t)file_id);
hssize_t ret_val = -1;
if (ret_val < 0)
h5libraryError(env);
UNUSED(cls);
if ((ret_val = H5Fget_freespace((hid_t)file_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1freespace */
@ -345,12 +380,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Freopen
(JNIEnv *env, jclass clss, jlong file_id)
{
hid_t retVal = -1;
hid_t retVal = H5I_INVALID_HID;
retVal = H5Freopen((hid_t)file_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Freopen((hid_t)file_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Freopen */
@ -364,47 +401,40 @@ Java_hdf_hdf5lib_H5_H5Fget_1obj_1ids
(JNIEnv *env, jclass cls, jlong file_id, jint types, jlong maxObjs,
jlongArray obj_id_list)
{
ssize_t ret_val = -1;
jlong *obj_id_listP;
jboolean isCopy;
hid_t *id_list;
size_t rank;
size_t i;
jboolean isCopy;
ssize_t ret_val = -1;
size_t i;
jsize rank;
jlong *obj_id_listP = NULL;
hid_t *id_list = NULL;
if (obj_id_list == NULL) {
h5nullArgument(env, "H5Fget_obj_ids: obj_id_list is NULL");
} /* end if */
else {
obj_id_listP = ENVPTR->GetLongArrayElements(ENVPAR obj_id_list, &isCopy);
if (obj_id_listP == NULL) {
h5JNIFatalError(env, "H5Fget_obj_ids: obj_id_list not pinned");
} /* end if */
else {
rank = (size_t)ENVPTR->GetArrayLength(ENVPAR obj_id_list);
UNUSED(cls);
id_list = (hid_t *)HDmalloc(rank * sizeof(hid_t));
if (id_list == NULL) {
ENVPTR->ReleaseLongArrayElements(ENVPAR obj_id_list, obj_id_listP, JNI_ABORT);
h5JNIFatalError(env, "H5Fget_obj_ids: obj_id_list not converted to hid_t");
} /* end if */
else {
ret_val = H5Fget_obj_ids((hid_t)file_id, (unsigned int)types, (size_t)maxObjs, id_list);
if (NULL == obj_id_list)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fget_obj_ids: obj_id_list is NULL");
if (ret_val < 0) {
ENVPTR->ReleaseLongArrayElements(ENVPAR obj_id_list, obj_id_listP, JNI_ABORT);
HDfree(id_list);
h5libraryError(env);
} /* end if */
else {
for (i = 0; i < rank; i++) {
obj_id_listP[i] = (jlong)id_list[i];
} /* end for */
HDfree(id_list);
ENVPTR->ReleaseLongArrayElements(ENVPAR obj_id_list, obj_id_listP, 0);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
PIN_LONG_ARRAY(ENVONLY, obj_id_list, obj_id_listP, &isCopy, "H5Fget_obj_ids: obj_id_list not pinned");
if ((rank = ENVPTR->GetArrayLength(ENVONLY, obj_id_list)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Fget_obj_ids: obj_id_list length < 0");
}
if (NULL == (id_list = (hid_t *) HDmalloc((size_t)rank * sizeof(hid_t))))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Fget_obj_ids: malloc failed");
if ((ret_val = H5Fget_obj_ids((hid_t)file_id, (unsigned int)types, (size_t)maxObjs, id_list)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
for (i = 0; i < (size_t)rank; i++) {
obj_id_listP[i] = (jlong)id_list[i];
} /* end for */
done:
if (id_list)
HDfree(id_list);
if (obj_id_listP)
UNPIN_LONG_ARRAY(ENVONLY, obj_id_list, obj_id_listP, (ret_val < 0) ? JNI_ABORT : 0);
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1obj_1ids */
@ -418,11 +448,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1obj_1count
(JNIEnv *env, jclass cls, jlong file_id, jint types)
{
ssize_t ret_val = H5Fget_obj_count((hid_t)file_id, (unsigned int)types);
ssize_t ret_val = -1;
if (ret_val < 0)
h5libraryError(env);
UNUSED(cls);
if ((ret_val = H5Fget_obj_count((hid_t)file_id, (unsigned int)types)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1obj_1count_1long */
@ -437,9 +470,12 @@ Java_hdf_hdf5lib_H5_H5Fget_1filesize
{
hsize_t size = 0;
if (H5Fget_filesize ((hid_t)file_id, &size) < 0)
h5libraryError(env);
UNUSED(clss);
if (H5Fget_filesize((hid_t)file_id, &size) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong) size;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1filesize */
@ -454,9 +490,12 @@ Java_hdf_hdf5lib_H5_H5Fget_1mdc_1hit_1rate
{
double rate = 0.0;
if (H5Fget_mdc_hit_rate((hid_t)file_id, &rate) < 0)
h5libraryError(env);
UNUSED(cls);
if (H5Fget_mdc_hit_rate((hid_t)file_id, &rate) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jdouble)rate;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1mdc_1hit_1rate */
@ -469,33 +508,37 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1mdc_1size
(JNIEnv *env, jclass cls, jlong file_id, jlongArray metadata_cache)
{
jint size = 0;
jlong *metadata_cache_ptr;
size_t max_size = 0, min_clean_size = 0, cur_size = 0;
int cur_num_entries = -1;
jboolean isCopy;
jboolean isCopy;
size_t max_size = 0, min_clean_size = 0, cur_size = 0;
jlong *metadata_cache_ptr = NULL;
jsize size = 0;
int cur_num_entries = -1;
if (metadata_cache == NULL) {
h5nullArgument(env, "H5Fget_mdc_size: metadata_cache is NULL");
} /* end if */
else {
size = (int)ENVPTR->GetArrayLength(ENVPAR metadata_cache);
if (size < 3) {
h5badArgument(env, "H5Fget_mdc_size: length of metadata_cache < 3.");
} /* end if */
else {
if (H5Fget_mdc_size((hid_t)file_id, &max_size, &min_clean_size, &cur_size, &cur_num_entries) < 0) {
h5libraryError(env);
} /* end if */
else {
metadata_cache_ptr = ENVPTR->GetLongArrayElements(ENVPAR metadata_cache, &isCopy);
metadata_cache_ptr[0] = (jlong)max_size;
metadata_cache_ptr[1] = (jlong)min_clean_size;
metadata_cache_ptr[2] = (jlong)cur_size;
ENVPTR->ReleaseLongArrayElements(ENVPAR metadata_cache, metadata_cache_ptr, 0);
} /* end else */
} /* end else */
} /* end else */
UNUSED(cls);
if (NULL == metadata_cache)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fget_mdc_size: metadata cache array is NULL");
if ((size = ENVPTR->GetArrayLength(ENVONLY, metadata_cache)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Fget_mdc_size: metadata_cache length < 0");
}
if (size < 3)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Fget_mdc_size: length of metadata_cache array < 3");
if (H5Fget_mdc_size((hid_t)file_id, &max_size, &min_clean_size, &cur_size, &cur_num_entries) < 0)
H5_LIBRARY_ERROR(ENVONLY);
PIN_LONG_ARRAY(ENVONLY, metadata_cache, metadata_cache_ptr, &isCopy, "H5Fget_mdc_size: metadata_cache array not pinned");
metadata_cache_ptr[0] = (jlong)max_size;
metadata_cache_ptr[1] = (jlong)min_clean_size;
metadata_cache_ptr[2] = (jlong)cur_size;
done:
if (metadata_cache_ptr)
UNPIN_LONG_ARRAY(ENVONLY, metadata_cache, metadata_cache_ptr, 0);
return (jint)cur_num_entries;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1mdc_1size */
@ -509,31 +552,36 @@ JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1info
(JNIEnv *env, jclass clss, jlong obj_id)
{
H5F_info2_t finfo;
jvalue args[9];
H5F_info2_t finfo;
jobject ihinfobuf;
jvalue args[9];
jobject ret_obj = NULL;
if (H5Fget_info2((hid_t)obj_id, &finfo) < 0) {
h5libraryError(env);
} /* end if */
else {
args[0].j = (jlong)finfo.sohm.msgs_info.index_size;
args[1].j = (jlong)finfo.sohm.msgs_info.heap_size;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5_ih_info_t", "(JJ)V", args);
ihinfobuf = ret_obj;
UNUSED(clss);
args[0].i = (jint)finfo.super.version;
args[1].j = (jlong)finfo.super.super_size;
args[2].j = (jlong)finfo.super.super_ext_size;
args[3].i = (jint)finfo.free.version;
args[4].j = (jlong)finfo.free.meta_size;
args[5].j = (jlong)finfo.free.tot_space;
args[6].j = (jint)finfo.sohm.version;
args[7].j = (jlong)finfo.sohm.hdr_size;
args[8].l = ihinfobuf;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5F_info2_t", "(IJJIJJIJLhdf/hdf5lib/structs/H5_ih_info_t;)V", args);
} /* end else */
if (H5Fget_info2((hid_t)obj_id, &finfo) < 0)
H5_LIBRARY_ERROR(ENVONLY);
args[0].j = (jlong)finfo.sohm.msgs_info.index_size;
args[1].j = (jlong)finfo.sohm.msgs_info.heap_size;
CALL_CONSTRUCTOR(ENVONLY, "hdf/hdf5lib/structs/H5_ih_info_t", "(JJ)V", args, ret_obj);
ihinfobuf = ret_obj;
args[0].i = (jint)finfo.super.version;
args[1].j = (jlong)finfo.super.super_size;
args[2].j = (jlong)finfo.super.super_ext_size;
args[3].i = (jint)finfo.free.version;
args[4].j = (jlong)finfo.free.meta_size;
args[5].j = (jlong)finfo.free.tot_space;
args[6].j = (jint)finfo.sohm.version;
args[7].j = (jlong)finfo.sohm.hdr_size;
args[8].l = ihinfobuf;
CALL_CONSTRUCTOR(ENVONLY, "hdf/hdf5lib/structs/H5F_info2_t", "(IJJIJJIJLhdf/hdf5lib/structs/H5_ih_info_t;)V", args, ret_obj);
done:
return ret_obj;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1info */
@ -546,8 +594,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Freset_1mdc_1hit_1rate_1stats
(JNIEnv *env, jclass cls, jlong file_id)
{
UNUSED(cls);
if (H5Freset_mdc_hit_rate_stats((hid_t)file_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Freset_1mdc_1hit_1rate_1stats */
/*
@ -559,8 +612,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fclear_1elink_1file_1cache
(JNIEnv *env, jclass cls, jlong file_id)
{
UNUSED(cls);
if (H5Fclear_elink_file_cache((hid_t)file_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Fclear_1elink_1file_1cache */
/*
@ -572,8 +630,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fstart_1swmr_1write
(JNIEnv *env, jclass cls, jlong file_id)
{
UNUSED(cls);
if (H5Fstart_swmr_write((hid_t)file_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Fstart_1swmr_1write */
/*
@ -585,8 +648,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fstart_1mdc_1logging
(JNIEnv *env, jclass cls, jlong file_id)
{
UNUSED(cls);
if (H5Fstart_mdc_logging((hid_t)file_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Fstart_1mdc_1logging */
/*
@ -598,8 +666,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fstop_1mdc_1logging
(JNIEnv *env, jclass cls, jlong file_id)
{
UNUSED(cls);
if (H5Fstop_mdc_logging((hid_t)file_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Fstop_1mdc_1logging */
/*
@ -611,32 +684,38 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status
(JNIEnv *env, jclass cls, jlong file_id, jbooleanArray mdc_logging_status)
{
jboolean *mdc_logging_status_ptr = NULL;
jboolean isCopy;
hbool_t is_enabled;
hbool_t is_currently_logging;
jboolean *mdc_logging_status_ptr;
jint size;
jboolean isCopy;
jsize size;
if (mdc_logging_status == NULL) {
h5nullArgument(env, "H5Fget_mdc_logging_status: mdc_logging_status is NULL");
} /* end if */
else {
size = (int)ENVPTR->GetArrayLength(ENVPAR mdc_logging_status);
if (size < 2) {
h5badArgument(env, "H5Fget_mdc_logging_status: length of mdc_logging_status < 2.");
} /* end if */
else {
if (H5Fget_mdc_logging_status((hid_t)file_id, &is_enabled, &is_currently_logging) < 0) {
h5libraryError(env);
} /* end if */
else {
mdc_logging_status_ptr = ENVPTR->GetBooleanArrayElements(ENVPAR mdc_logging_status, &isCopy);
mdc_logging_status_ptr[0] = (jboolean)is_enabled;
mdc_logging_status_ptr[1] = (jboolean)is_currently_logging;
ENVPTR->ReleaseBooleanArrayElements(ENVPAR mdc_logging_status, mdc_logging_status_ptr, 0);
} /* end else */
} /* end else */
} /* end else */
UNUSED(cls);
if (NULL == mdc_logging_status)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fget_mdc_logging_status: mdc_logging_status is NULL");
if ((size = ENVPTR->GetArrayLength(ENVONLY, mdc_logging_status)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Fget_mdc_logging_status: mdc_logging_status length < 0");
}
if (size < 2)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Fget_mdc_logging_status: length of mdc_logging_status < 2");
if (H5Fget_mdc_logging_status((hid_t)file_id, &is_enabled, &is_currently_logging) < 0)
H5_LIBRARY_ERROR(ENVONLY);
PIN_BOOL_ARRAY(ENVONLY, mdc_logging_status, mdc_logging_status_ptr, &isCopy, "H5Fget_mdc_logging_status: mdc_logging_status array not pinned");
mdc_logging_status_ptr[0] = (jboolean)is_enabled;
mdc_logging_status_ptr[1] = (jboolean)is_currently_logging;
done:
if (mdc_logging_status_ptr)
UNPIN_BOOL_ARRAY(ENVONLY, mdc_logging_status, mdc_logging_status_ptr, 0);
return;
} /* end Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status */
/*
@ -648,17 +727,18 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint
(JNIEnv *env, jclass clss, jlong file_id, jboolean minimize)
{
herr_t retVal = -1;
hbool_t minimize_val;
hbool_t minimize_val;
herr_t retVal = FAIL;
if (minimize == JNI_TRUE)
minimize_val = TRUE;
else
minimize_val = FALSE;
UNUSED(clss);
retVal = H5Fset_dset_no_attrs_hint((hid_t)file_id, (hbool_t)minimize_val);
if (retVal < 0)
h5libraryError(env);
minimize_val = (minimize == JNI_TRUE) ? TRUE : FALSE;
if ((retVal = H5Fset_dset_no_attrs_hint((hid_t)file_id, (hbool_t)minimize_val)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
}
/*
@ -670,17 +750,18 @@ JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint
(JNIEnv *env, jclass clss, jlong file_id)
{
hbool_t minimize = FALSE;
jboolean bval = JNI_FALSE;
jboolean bval = JNI_FALSE;
hbool_t minimize = FALSE;
if (H5Fget_dset_no_attrs_hint((hid_t)file_id, (hbool_t *)&minimize) < 0) {
h5libraryError(env);
}
else {
if (minimize == TRUE)
bval = JNI_TRUE;
} /* end else */
UNUSED(clss);
if (H5Fget_dset_no_attrs_hint((hid_t)file_id, (hbool_t *)&minimize) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (minimize == TRUE)
bval = JNI_TRUE;
done:
return bval;
}
@ -693,11 +774,15 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds
(JNIEnv *env, jclass clss, jlong file_id, jint low, jint high)
{
herr_t retVal = -1;
herr_t retVal = FAIL;
retVal = H5Fset_libver_bounds((hid_t)file_id, (H5F_libver_t)low, (H5F_libver_t)high);
if(retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Fset_libver_bounds((hid_t)file_id, (H5F_libver_t)low, (H5F_libver_t)high)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds */

2
java/src/jni/h5fImp.h
View File

@ -72,7 +72,7 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
* Signature: (Ljava/lang/String;J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Fis_1ccessible
Java_hdf_hdf5lib_H5_H5Fis_1accessible
(JNIEnv*, jclass, jstring, jlong);
/*

228
java/src/jni/h5gImp.c
View File

@ -29,7 +29,10 @@ extern "C" {
#include "h5util.h"
#include "h5gImp.h"
extern JavaVM *jvm;
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
/*
* Class: hdf_hdf5lib_H5
@ -40,12 +43,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5__1H5Gclose
(JNIEnv *env, jclass clss, jlong group_id)
{
herr_t retVal = -1;
herr_t retVal = FAIL;
retVal = H5Gclose((hid_t)group_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Gclose((hid_t)group_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Gclose */
@ -63,33 +68,46 @@ jobject
create_H5G_info_t
(JNIEnv *env, H5G_info_t group_info)
{
jclass cls;
jfieldID fid_storage_type, fid_nlinks, fid_max_corder, fid_mounted;
jboolean jmounted;
jclass cls;
jint storage_type;
jobject obj = NULL;
jfieldID fid_storage_type, fid_nlinks, fid_max_corder, fid_mounted;
cls = ENVPTR->FindClass(ENVPAR "hdf/hdf5lib/structs/H5G_info_t");
if (cls != NULL) {
obj = ENVPTR->AllocObject(ENVPAR cls);
if (obj != NULL) {
if ((fid_storage_type = ENVPTR->GetFieldID(ENVPAR cls, "storage_type", "I")) != NULL) {
if ((fid_nlinks = ENVPTR->GetFieldID(ENVPAR cls, "nlinks", "J")) != NULL) {
if ((fid_max_corder = ENVPTR->GetFieldID(ENVPAR cls, "max_corder", "J")) != NULL) {
if ((fid_mounted = ENVPTR->GetFieldID(ENVPAR cls, "mounted", "Z")) != NULL) {
jmounted = (group_info.mounted==0) ? JNI_FALSE : JNI_TRUE;
storage_type = (jint)group_info.storage_type;
if (NULL == (cls = ENVPTR->FindClass(ENVONLY, "hdf/hdf5lib/structs/H5G_info_t")))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetIntField(ENVPAR obj, fid_storage_type, (jint)storage_type);
ENVPTR->SetLongField(ENVPAR obj, fid_nlinks, (jlong)group_info.nlinks);
ENVPTR->SetLongField(ENVPAR obj, fid_max_corder, (jlong)group_info.max_corder);
ENVPTR->SetBooleanField(ENVPAR obj, fid_mounted, jmounted);
}
}
}
}
}
}
if (NULL == (obj = ENVPTR->AllocObject(ENVONLY, cls)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (fid_storage_type = ENVPTR->GetFieldID(ENVONLY, cls, "storage_type", "I")))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (fid_nlinks = ENVPTR->GetFieldID(ENVONLY, cls, "nlinks", "J")))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (fid_max_corder = ENVPTR->GetFieldID(ENVONLY, cls, "max_corder", "J")))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == (fid_mounted = ENVPTR->GetFieldID(ENVONLY, cls, "mounted", "Z")))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
jmounted = (group_info.mounted == 0) ? JNI_FALSE : JNI_TRUE;
storage_type = (jint)group_info.storage_type;
ENVPTR->SetIntField(ENVONLY, obj, fid_storage_type, (jint)storage_type);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetLongField(ENVONLY, obj, fid_nlinks, (jlong)group_info.nlinks);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetLongField(ENVONLY, obj, fid_max_corder, (jlong)group_info.max_corder);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetBooleanField(ENVONLY, obj, fid_mounted, jmounted);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
return obj;
} /* end create_H5G_info_t */
@ -103,17 +121,22 @@ Java_hdf_hdf5lib_H5__1H5Gcreate2
(JNIEnv *env, jclass clss, jlong loc_id, jstring name,
jlong link_plist_id, jlong create_plist_id, jlong access_plist_id)
{
hid_t group_id = -1;
const char *gName;
const char *grpName = NULL;
hid_t group_id = H5I_INVALID_HID;
PIN_JAVA_STRING(name, gName);
if (gName != NULL) {
group_id = H5Gcreate2((hid_t)loc_id, gName, (hid_t)link_plist_id, (hid_t)create_plist_id, (hid_t)access_plist_id );
UNUSED(clss);
UNPIN_JAVA_STRING(name, gName);
if (group_id < 0)
h5libraryError(env);
}
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gcreate2: group name is NULL");
PIN_JAVA_STRING(ENVONLY, name, grpName, NULL, "H5Gcreate2: group name not pinned");
if ((group_id = H5Gcreate2((hid_t)loc_id, grpName, (hid_t)link_plist_id, (hid_t)create_plist_id, (hid_t)access_plist_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (grpName)
UNPIN_JAVA_STRING(ENVONLY, name, grpName);
return (jlong)group_id;
} /* end Java_hdf_hdf5lib_H5__1H5Gcreate2 */
@ -127,12 +150,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Gcreate_1anon
(JNIEnv *env, jclass cls, jlong loc_id, jlong gcpl_id, jlong gapl_id)
{
hid_t group_id = -1;
hid_t group_id = H5I_INVALID_HID;
group_id = H5Gcreate_anon((hid_t)loc_id, (hid_t)gcpl_id, (hid_t)gapl_id);
if (group_id < 0)
h5libraryError(env);
UNUSED(cls);
if ((group_id = H5Gcreate_anon((hid_t)loc_id, (hid_t)gcpl_id, (hid_t)gapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)group_id;
} /* end Java_hdf_hdf5lib_H5__1H5Gcreate_1anon */
@ -145,18 +170,22 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Gopen2
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_plist_id)
{
hid_t group_id = -1;
const char *gName;
const char *grpName = NULL;
hid_t group_id = H5I_INVALID_HID;
PIN_JAVA_STRING(name, gName);
if (gName != NULL) {
group_id = H5Gopen2((hid_t)loc_id, gName, (hid_t)access_plist_id );
UNUSED(clss);
UNPIN_JAVA_STRING(name, gName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gopen2: group name is NULL");
if (group_id < 0)
h5libraryError(env);
}
PIN_JAVA_STRING(ENVONLY, name, grpName, NULL, "H5Gopen2: group name not pinned");
if ((group_id = H5Gopen2((hid_t)loc_id, grpName, (hid_t)access_plist_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (grpName)
UNPIN_JAVA_STRING(ENVONLY, name, grpName);
return (jlong)group_id;
} /* end Java_hdf_hdf5lib_H5__1H5Gopen2 */
@ -171,11 +200,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Gget_1create_1plist
(JNIEnv *env, jclass cls, jlong loc_id)
{
hid_t plist_id = H5Gget_create_plist((hid_t)loc_id);
hid_t plist_id = H5I_INVALID_HID;
if (plist_id < 0)
h5libraryError(env);
UNUSED(cls);
if ((plist_id = H5Gget_create_plist((hid_t)loc_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)plist_id;
} /* end Java_hdf_hdf5lib_H5_H5Gget_1create_1plist */
@ -188,14 +220,18 @@ JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Gget_1info
(JNIEnv *env, jclass cls, jlong loc_id)
{
jobject obj = NULL;
H5G_info_t group_info;
jobject obj = NULL;
UNUSED(cls);
if (H5Gget_info((hid_t)loc_id, &group_info) < 0)
h5libraryError(env);
else
obj = create_H5G_info_t(env, group_info);
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (obj = create_H5G_info_t(env, group_info)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_info: unable to create H5G_info_t object");
done:
return obj;
} /* end Java_hdf_hdf5lib_H5_H5Gget_1info */
@ -208,23 +244,30 @@ JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1name
(JNIEnv *env, jclass cls, jlong loc_id, jstring name, jlong lapl_id)
{
jobject obj = NULL;
herr_t ret_val = -1;
const char *gName;
H5G_info_t group_info;
const char *grpName = NULL;
jobject obj = NULL;
herr_t ret_val = FAIL;
PIN_JAVA_STRING(name, gName);
if (gName != NULL) {
ret_val = H5Gget_info_by_name((hid_t)loc_id, gName, &group_info, (hid_t)lapl_id);
UNUSED(cls);
UNPIN_JAVA_STRING(name, gName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_info_by_name: group name is NULL");
if (ret_val < 0)
h5libraryError(env);
else
obj = create_H5G_info_t(env, group_info);
PIN_JAVA_STRING(ENVONLY, name, grpName, NULL, "H5Gget_info_by_name: group name not pinned");
if ((ret_val = H5Gget_info_by_name((hid_t)loc_id, grpName, &group_info, (hid_t)lapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (obj = create_H5G_info_t(env, group_info))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_info_by_name: unable to create H5G_info_t object");
}
done:
if (grpName)
UNPIN_JAVA_STRING(ENVONLY, name, grpName);
return obj;
} /* end Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1name */
@ -238,26 +281,33 @@ Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx
(JNIEnv *env, jclass cls, jlong loc_id, jstring name, jint index_type,
jint order, jlong n, jlong lapl_id)
{
jobject obj = NULL;
herr_t ret_val = -1;
const char *gName;
H5G_info_t group_info;
H5_index_t cindex_type = (H5_index_t)index_type;
H5_iter_order_t corder = (H5_iter_order_t)order;
H5_iter_order_t corder = (H5_iter_order_t)order;
H5_index_t cindex_type = (H5_index_t)index_type;
H5G_info_t group_info;
const char *grpName = NULL;
jobject obj = NULL;
herr_t ret_val = FAIL;
PIN_JAVA_STRING(name, gName);
if (gName != NULL) {
ret_val = H5Gget_info_by_idx((hid_t)loc_id, gName, cindex_type,
corder, (hsize_t)n, &group_info, (hid_t)lapl_id);
UNUSED(cls);
UNPIN_JAVA_STRING(name, gName);
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_info_by_idx: group name is NULL");
if (ret_val < 0)
h5libraryError(env);
else
obj = create_H5G_info_t(env, group_info);
PIN_JAVA_STRING(ENVONLY, name, grpName, NULL, "H5Gget_info_by_idx: group name not pinned");
if ((ret_val = H5Gget_info_by_idx((hid_t)loc_id, grpName, cindex_type,
corder, (hsize_t)n, &group_info, (hid_t)lapl_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (obj = create_H5G_info_t(env, group_info))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_info_by_idx: unable to create H5G_info_t object");
}
done:
if (grpName)
UNPIN_JAVA_STRING(ENVONLY, name, grpName);
return obj;
} /* end Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx */
@ -270,8 +320,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Gflush
(JNIEnv *env, jclass clss, jlong loc_id)
{
UNUSED(clss);
if (H5Gflush((hid_t)loc_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Gflush */
/*
@ -283,8 +338,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Grefresh
(JNIEnv *env, jclass clss, jlong loc_id)
{
UNUSED(clss);
if (H5Grefresh((hid_t)loc_id) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Grefresh */

227
java/src/jni/h5iImp.c
View File

@ -27,7 +27,10 @@ extern "C" {
#include "h5jni.h"
#include "h5iImp.h"
extern JavaVM *jvm;
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
/*
* Class: hdf_hdf5lib_H5
@ -40,10 +43,12 @@ Java_hdf_hdf5lib_H5_H5Iget_1type
{
H5I_type_t retVal = H5I_BADID;
retVal = H5Iget_type((hid_t)obj_id);
if (retVal == H5I_BADID)
h5libraryError(env);
UNUSED(clss);
if (H5I_BADID == (retVal = H5Iget_type((hid_t)obj_id)))
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1type */
@ -56,32 +61,32 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1name_1long
(JNIEnv *env, jclass clss, jlong obj_id, jobjectArray name, jlong buf_size)
{
char *aName;
jstring str;
hssize_t size = -1;
long bs;
ssize_t size = -1;
jstring str;
char *aName = NULL;
UNUSED(clss);
if (buf_size < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Iget_name_long: buf_size < 0");
if (NULL == (aName = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Iget_name_long: malloc failed");
if ((size = H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size + 1)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
aName[buf_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, aName)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
ENVPTR->SetObjectArrayElement(ENVONLY, name, 0, str);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (aName)
HDfree(aName);
bs = (long)buf_size;
if (bs <= 0) {
h5badArgument(env, "H5Iget_name: buf_size <= 0");
} /* end if */
else {
aName = (char*)HDmalloc(sizeof(char) * (size_t)bs);
if (aName == NULL) {
h5outOfMemory(env, "H5Iget_name: malloc failed");
} /* end if */
else {
size = H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size);
if (size < 0) {
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aName);
ENVPTR->SetObjectArrayElement(ENVPAR name, 0, str);
}
HDfree(aName);
}
}
return (jlong)size;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1name */
@ -95,33 +100,30 @@ JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1name
(JNIEnv *env, jclass clss, jlong obj_id)
{
char *aName;
jstring str = NULL;
ssize_t buf_size;
ssize_t buf_size = -1;
char *aName = NULL;
/* get the length of the name */
buf_size = H5Iget_name((hid_t)obj_id, NULL, 0);
UNUSED(clss);
/* Get the length of the name */
if ((buf_size = H5Iget_name((hid_t)obj_id, NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (aName = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Iget_name: malloc failed");
if (H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size + 1) < 0)
H5_LIBRARY_ERROR(ENVONLY);
aName[buf_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, aName)))
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (aName)
HDfree(aName);
if (buf_size <= 0) {
h5badArgument(env, "H5Iget_name: buf_size <= 0");
} /* end if */
else {
buf_size++; /* add extra space for the null terminator */
aName = (char*)HDmalloc(sizeof(char) * (size_t)buf_size);
if (aName == NULL) {
h5outOfMemory(env, "H5Iget_name: malloc failed");
} /* end if */
else {
buf_size = H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size);
if (buf_size < 0) {
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aName);
}
HDfree(aName);
}
}
return str;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1name */
@ -134,12 +136,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1ref
(JNIEnv *env, jclass clss, jlong obj_id)
{
int retVal = -1;
int retVal = FAIL;
retVal = H5Iget_ref((hid_t)obj_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Iget_ref((hid_t)obj_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1ref */
@ -152,12 +156,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Iinc_1ref
(JNIEnv *env, jclass clss, jlong obj_id)
{
int retVal = -1;
int retVal = FAIL;
retVal = H5Iinc_ref((hid_t)obj_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Iinc_ref((hid_t)obj_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Iinc_1ref */
@ -170,12 +176,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Idec_1ref
(JNIEnv *env, jclass clss, jlong obj_id)
{
int retVal = -1;
int retVal = FAIL;
retVal = H5Idec_ref((hid_t)obj_id);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Idec_ref((hid_t)obj_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Idec_1ref */
@ -189,12 +197,14 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1file_1id
(JNIEnv *env, jclass clss, jlong obj_id)
{
hid_t file_id = -1;
hid_t file_id = H5I_INVALID_HID;
file_id = H5Iget_file_id((hid_t)obj_id);
if (file_id < 0)
h5libraryError(env);
UNUSED(clss);
if ((file_id = H5Iget_file_id((hid_t)obj_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong) file_id;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1file_1id */
@ -207,12 +217,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1type_1ref
(JNIEnv *env, jclass clss, jint type)
{
int retVal = -1;
int retVal = FAIL;
retVal = H5Iget_type_ref((H5I_type_t)type);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Iget_type_ref((H5I_type_t)type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1type_1ref */
@ -225,12 +237,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Idec_1type_1ref
(JNIEnv *env, jclass clss, jint type)
{
int retVal = -1;
int retVal = FAIL;
retVal = H5Idec_type_ref((H5I_type_t)type);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Idec_type_ref((H5I_type_t)type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Idec_1type_1ref */
@ -243,12 +257,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Iinc_1type_1ref
(JNIEnv *env, jclass clss, jint type)
{
int retVal = -1;
int retVal = FAIL;
retVal = H5Iinc_type_ref((H5I_type_t)type);
if (retVal < 0)
h5libraryError(env);
UNUSED(clss);
if ((retVal = H5Iinc_type_ref((H5I_type_t)type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Iinc_1type_1ref */
@ -261,11 +277,14 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Inmembers
(JNIEnv *env, jclass clss, jint type)
{
hsize_t num_members;
hsize_t num_members = 0;
UNUSED(clss);
if (H5Inmembers((H5I_type_t)type, &num_members) < 0)
h5libraryError(env);
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)num_members;
} /* end Java_hdf_hdf5lib_H5_H5Inmembers */
@ -280,12 +299,14 @@ Java_hdf_hdf5lib_H5_H5Iis_1valid
{
htri_t bval = JNI_FALSE;
bval = H5Iis_valid((hid_t)obj_id);
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
h5libraryError(env);
UNUSED(clss);
if ((bval = H5Iis_valid((hid_t)obj_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
done:
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Iis_1valid */
/*
@ -299,12 +320,14 @@ Java_hdf_hdf5lib_H5_H5Itype_1exists
{
htri_t bval = JNI_FALSE;
bval = H5Itype_exists((H5I_type_t)type);
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
h5libraryError(env);
UNUSED(clss);
if ((bval = H5Itype_exists((H5I_type_t)type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
done:
return (jboolean)bval;
} /* end else Java_hdf_hdf5lib_H5_H5Itype_1exists */
@ -317,8 +340,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Iclear_1type
(JNIEnv *env, jclass clss, jint type, jboolean force)
{
if (H5Iclear_type((H5I_type_t)type, (hbool_t)force) < 0)
h5libraryError(env);
UNUSED(clss);
if (H5Iclear_type((H5I_type_t)type, (hbool_t)force) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Iclear_1type */
/*
@ -330,8 +358,13 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Idestroy_1type
(JNIEnv *env, jclass clss, jint type)
{
if (H5Idestroy_type((H5I_type_t)type) < 0)
h5libraryError(env);
UNUSED(clss);
if (H5Idestroy_type((H5I_type_t)type) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Idestroy_1type */
#ifdef __cplusplus

374
java/src/jni/h5jni.h
View File

@ -27,147 +27,299 @@
#ifdef __cplusplus
#define ENVPTR (env)
#define ENVPAR
#define ENVONLY
#define CBENVPTR (cbenv)
#define CBENVPAR
#define CBENVONLY
#define JVMPTR (jvm)
#define JVMPAR
#define JVMPAR2
#else /* __cplusplus */
#define ENVPTR (*env)
#define ENVPAR env,
#define ENVONLY env
#define CBENVPTR (*cbenv)
#define CBENVPAR cbenv,
#define CBENVONLY cbenv
#define JVMPTR (*jvm)
#define JVMPAR jvm
#define JVMPAR2 jvm,
#endif /* __cplusplus */
/*
* Used to silence compiler when a particular
* function parameter is not used.
*/
#define UNUSED(o) (void) o
/* Macros for class access */
/* Calling code must define ret_obj as jobject */
#define CALL_CONSTRUCTOR(classname,classsig,args) { \
jclass cls; \
jmethodID constructor; \
cls = ENVPTR->FindClass(ENVPAR (classname)); \
if (cls == 0) { \
h5JNIFatalError(env, "JNI error: GetObjectClass\n"); \
ret_obj = NULL; \
} \
constructor = ENVPTR->GetMethodID(ENVPAR cls, "<init>", (classsig)); \
if (constructor == 0) { \
h5JNIFatalError(env, "JNI error: GetMethodID failed\n"); \
ret_obj = NULL; \
} \
ret_obj = ENVPTR->NewObjectA(ENVPAR cls, constructor, (args)); \
#define CALL_CONSTRUCTOR(env, classname, classsig, args, ret_obj) \
{ \
jmethodID constructor; \
jclass cls; \
\
if (NULL == (cls = ENVPTR->FindClass(env, (classname)))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, "JNI error: GetObjectClass"); \
} \
if (NULL == (constructor = ENVPTR->GetMethodID(ENVONLY, cls, "<init>", (classsig)))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, "JNI error: GetMethodID failed"); \
} \
if (NULL == (ret_obj = ENVPTR->NewObjectA(ENVONLY, cls, constructor, (args)))) { \
CHECK_JNI_EXCEPTION(env, JNI_FALSE); \
} \
}
/*
* Macros for pinning/unpinning objects.
*/
#define PIN_BYTE_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetByteArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_BYTE_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jbyte *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_BYTE_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseByteArrayElements(env, pinnedArray, (jbyte *) bufToRelease, freeMode); \
}
#define PIN_SHORT_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetShortArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_SHORT_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jshort *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_SHORT_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseShortArrayElements(env, pinnedArray, (jshort *) bufToRelease, freeMode); \
}
#define PIN_INT_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetIntArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_INT_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jint *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_INT_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseIntArrayElements(env, pinnedArray, (jint *) bufToRelease, freeMode); \
}
#define PIN_LONG_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetLongArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_LONG_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jlong *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_LONG_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseLongArrayElements(env, pinnedArray, (jlong *) bufToRelease, freeMode); \
}
#define PIN_FLOAT_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetFloatArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_FLOAT_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jfloat *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_FLOAT_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseFloatArrayElements(env, pinnedArray, (jfloat *) bufToRelease, freeMode); \
}
#define PIN_DOUBLE_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetDoubleArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_DOUBLE_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jdouble *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_DOUBLE_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseDoubleArrayElements(env, pinnedArray, (jdouble *) bufToRelease, freeMode); \
}
#define PIN_BOOL_ARRAY(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = ENVPTR->GetBooleanArrayElements(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define PIN_BOOL_ARRAY_CRITICAL(env, arrayToPin, outBuf, isCopy, failErrMsg) \
{ \
if (NULL == (outBuf = (jboolean *) ENVPTR->GetPrimitiveArrayCritical(env, arrayToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_BOOL_ARRAY(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleaseBooleanArrayElements(env, pinnedArray, (jboolean *) bufToRelease, freeMode); \
}
#define UNPIN_ARRAY_CRITICAL(env, pinnedArray, bufToRelease, freeMode) \
{ \
ENVPTR->ReleasePrimitiveArrayCritical(env, pinnedArray, bufToRelease, freeMode); \
}
/* Macros for string access */
#define PIN_JAVA_STRING(javastr,localstr) { \
jboolean isCopy; \
(localstr) = NULL; \
if ((javastr) == NULL) { \
h5nullArgument(env, "java string is NULL"); \
} \
else { \
(localstr) = ENVPTR->GetStringUTFChars(ENVPAR (javastr), &isCopy); \
if ((localstr) == NULL) { \
h5JNIFatalError(env, "local c string is not pinned"); \
} \
} \
#define PIN_JAVA_STRING(env, stringToPin, outString, isCopy, failErrMsg) \
{ \
if (NULL == (outString = ENVPTR->GetStringUTFChars(env, stringToPin, isCopy))) { \
CHECK_JNI_EXCEPTION(env, JNI_TRUE); \
H5_JNI_FATAL_ERROR(env, failErrMsg); \
} \
}
#define UNPIN_JAVA_STRING(javastr,localstr) { \
ENVPTR->ReleaseStringUTFChars(ENVPAR (javastr), (localstr)); \
#define UNPIN_JAVA_STRING(env, pinnedString, stringToRelease) \
{ \
ENVPTR->ReleaseStringUTFChars(env, pinnedString, stringToRelease); \
}
#define PIN_JAVA_STRING_TWO(javastr,localstr,java2str,local2str) { \
jboolean isCopy; \
(localstr) = NULL; \
(local2str) = NULL; \
if ((javastr) == NULL) { \
h5nullArgument(env, "java string is NULL"); \
} \
else if ((java2str) == NULL) { \
h5nullArgument(env, "second java string is NULL"); \
} \
else { \
(localstr) = ENVPTR->GetStringUTFChars(ENVPAR (javastr), &isCopy); \
if ((localstr) == NULL) { \
h5JNIFatalError(env, "local c string is not pinned"); \
} \
else { \
(local2str) = ENVPTR->GetStringUTFChars(ENVPAR (java2str), &isCopy); \
if ((local2str) == NULL) { \
ENVPTR->ReleaseStringUTFChars(ENVPAR (javastr), (localstr)); \
h5JNIFatalError(env, "second local c string is not pinned"); \
} \
} \
} \
}
#define UNPIN_JAVA_STRING_TWO(javastr,localstr,java2str,local2str) { \
ENVPTR->ReleaseStringUTFChars(ENVPAR (javastr), (localstr)); \
ENVPTR->ReleaseStringUTFChars(ENVPAR (java2str), (local2str)); \
}
#define PIN_JAVA_STRING_THREE(javastr,localstr,java2str,local2str,java3str,local3str) { \
jboolean isCopy; \
(localstr) = NULL; \
(local2str) = NULL; \
(local3str) = NULL; \
if ((javastr) == NULL) { \
h5nullArgument(env, "java string is NULL"); \
} \
else if ((java2str) == NULL) { \
h5nullArgument(env, "second java string is NULL"); \
} \
else if ((java3str) == NULL) { \
h5nullArgument(env, "third java string is NULL"); \
} \
else { \
(localstr) = ENVPTR->GetStringUTFChars(ENVPAR (javastr), &isCopy); \
if ((localstr) == NULL) { \
h5JNIFatalError(env, "local c string is not pinned"); \
} \
else { \
(local2str) = ENVPTR->GetStringUTFChars(ENVPAR (java2str), &isCopy); \
if ((local2str) == NULL) { \
ENVPTR->ReleaseStringUTFChars(ENVPAR (javastr), (localstr)); \
h5JNIFatalError(env, "second local c string is not pinned"); \
} \
else { \
(local3str) = ENVPTR->GetStringUTFChars(ENVPAR (java3str), &isCopy); \
if ((local3str) == NULL) { \
ENVPTR->ReleaseStringUTFChars(ENVPAR (javastr), (localstr)); \
ENVPTR->ReleaseStringUTFChars(ENVPAR (java2str), (local2str)); \
h5JNIFatalError(env, "third local c string is not pinned"); \
} \
} \
} \
} \
}
#define UNPIN_JAVA_STRING_THREE(javastr,localstr,java2str,local2str,java3str,local3str) { \
ENVPTR->ReleaseStringUTFChars(ENVPAR (javastr), (localstr)); \
ENVPTR->ReleaseStringUTFChars(ENVPAR (java2str), (local2str)); \
ENVPTR->ReleaseStringUTFChars(ENVPAR (java3str), (local3str)); \
/*
* Macro to check for a JNI exception after a JNI method is called.
* If an exception occurred, the value of 'clearException' will determine
* whether or not the exception will be cleared in order for the native
* method to do its own error handling.
*
* If the exception does not get cleared, this macro will skip to the
* cleanup+return section of the native method, since at that point
* cleaning up and returning is the only safe thing that can be done.
*/
#define CHECK_JNI_EXCEPTION(env, clearException) \
{ \
if (JNI_TRUE == (*env)->ExceptionCheck(env)) { \
if (JNI_TRUE == clearException) \
(*env)->ExceptionClear(env); \
else \
goto done; \
} \
}
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
extern jboolean h5JNIFatalError(JNIEnv *, const char *);
extern jboolean h5nullArgument(JNIEnv *, const char *);
extern jboolean h5badArgument (JNIEnv *, const char *);
extern jboolean h5outOfMemory (JNIEnv *, const char *);
extern jboolean h5libraryError(JNIEnv *env );
extern jboolean h5raiseException(JNIEnv *, const char *, const char *);
extern jboolean h5JNIFatalError(JNIEnv *env, const char *);
extern jboolean h5nullArgument(JNIEnv *env, const char *);
extern jboolean h5badArgument(JNIEnv *env, const char *);
extern jboolean h5outOfMemory(JNIEnv *env, const char *);
extern jboolean h5libraryError(JNIEnv *env);
extern jboolean h5raiseException(JNIEnv *env, const char *, const char *);
extern jboolean h5unimplemented( JNIEnv *env, const char *functName);
/*
* The following macros are to facilitate immediate cleanup+return
* from a native JNI method when an exception is to be thrown.
* Since, in general, the "cleanup" methods are the only safe JNI
* methods to call once an exception has occurred, we want to immediately
* cleanup and return instead of letting the native method continue.
*
* Note that a native method can clear the exception when one occurs and
* then do its own error handling, but we instead opt to immediately return.
*/
#define H5_JNI_FATAL_ERROR(env, message) \
{ \
h5JNIFatalError(env, message); \
goto done; \
}
#define H5_NULL_ARGUMENT_ERROR(env, message) \
{ \
h5nullArgument(env, message); \
goto done; \
}
#define H5_BAD_ARGUMENT_ERROR(env, message) \
{ \
h5badArgument(env, message); \
goto done; \
}
#define H5_OUT_OF_MEMORY_ERROR(env, message) \
{ \
h5outOfMemory(env, message); \
goto done; \
}
#define H5_LIBRARY_ERROR(env) \
{ \
h5libraryError(env); \
goto done; \
}
#define H5_RAISE_EXCEPTION(env, message, exception) \
{ \
h5raiseException(env, message, exception); \
goto done; \
}
#define H5_UNIMPLEMENTED(env, message) \
{ \
h5unimplemented(env, message); \
goto done; \
}
/* implemented at H5.c */
extern jint get_enum_value(JNIEnv *env, jobject enum_obj);
extern jobject get_enum_object(JNIEnv *env, const char* enum_class_name,

886
java/src/jni/h5lImp.c
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917
java/src/jni/h5oImp.c
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36
java/src/jni/h5pACPLImp.c Normal file
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@ -0,0 +1,36 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* For details of the HDF libraries, see the HDF Documentation at:
* http://hdfgroup.org/HDF5/doc/
*
*/
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <stdlib.h>
#include "hdf5.h"
#include "h5jni.h"
#include "h5pACPLImp.h"
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */

27
java/src/jni/h5pACPLImp.h Normal file
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifndef _Included_hdf_hdf5lib_H5_H5PACPL
#define _Included_hdf_hdf5lib_H5_H5PACPL
#include <jni.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
#endif /* _Included_hdf_hdf5lib_H5_H5PACPL */

325
java/src/jni/h5pDAPLImp.c Normal file
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* For details of the HDF libraries, see the HDF Documentation at:
* http://hdfgroup.org/HDF5/doc/
*
*/
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <stdlib.h>
#include "hdf5.h"
#include "h5jni.h"
#include "h5pDAPLImp.h"
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
extern JavaVM *jvm;
typedef struct _cb_wrapper {
jobject visit_callback;
jobject op_data;
} cb_wrapper;
static herr_t H5D_append_cb(hid_t dataset_id, hsize_t *cur_dims, void *cb_data);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_chunk_cache
* Signature: (JJJD)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1chunk_1cache
(JNIEnv *env, jclass clss, jlong dapl, jlong rdcc_nslots,
jlong rdcc_nbytes, jdouble rdcc_w0)
{
UNUSED(clss);
if (H5Pset_chunk_cache((hid_t)dapl, (size_t)rdcc_nslots, (size_t)rdcc_nbytes, (double) rdcc_w0) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1chunk_1cache */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_chunk_cache
* Signature: (J[J[J[D)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk_1cache
(JNIEnv *env, jclass clss, jlong dapl, jlongArray rdcc_nslots,
jlongArray rdcc_nbytes, jdoubleArray rdcc_w0)
{
jboolean isCopy;
jdouble *w0Array = NULL;
jlong *rdcc_nslotsArray = NULL;
jlong *nbytesArray = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL != rdcc_w0)
PIN_DOUBLE_ARRAY(ENVONLY, rdcc_w0, w0Array, &isCopy, "H5Pget_chunk_cache: rdcc_w0 array not pinned");
if (NULL != rdcc_nslots)
PIN_LONG_ARRAY(ENVONLY, rdcc_nslots, rdcc_nslotsArray, &isCopy, "H5Pget_chunk_cache: rdcc_nslots array not pinned");
if (NULL != rdcc_nbytes)
PIN_LONG_ARRAY(ENVONLY, rdcc_nbytes, nbytesArray, &isCopy, "H5Pget_chunk_cache: nbytesArray array not pinned");
{
/* direct cast (size_t *)variable fails on 32-bit environment */
long long rdcc_nslots_temp = *rdcc_nslotsArray;
long long nbytes_temp = *nbytesArray;
size_t rdcc_nslots_t = (size_t) rdcc_nslots_temp;
size_t nbytes_t = (size_t) nbytes_temp;
if ((status = H5Pget_chunk_cache((hid_t)dapl, &rdcc_nslots_t, &nbytes_t, (double *)w0Array)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
*rdcc_nslotsArray = (jlong)rdcc_nslots_t;
*nbytesArray = (jlong)nbytes_t;
} /* end direct cast special handling */
done:
if (nbytesArray)
UNPIN_LONG_ARRAY(ENVONLY, rdcc_nbytes, nbytesArray, (status < 0) ? JNI_ABORT : 0);
if (rdcc_nslotsArray)
UNPIN_LONG_ARRAY(ENVONLY, rdcc_nslots, rdcc_nslotsArray, (status < 0) ? JNI_ABORT : 0);
if (w0Array)
UNPIN_DOUBLE_ARRAY(ENVONLY, rdcc_w0, w0Array, (status < 0) ? JNI_ABORT : 0);
} /* end Java_hdf_hdf5lib_H5_H5Pget_1chunk_1cache */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_efile_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix
(JNIEnv *env, jclass clss, jlong dapl_id, jstring prefix)
{
const char *extFilePrefix = NULL;
herr_t retVal = FAIL;
UNUSED(clss);
if (NULL == prefix)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pset_efile_prefix: external file prefix is NULL");
PIN_JAVA_STRING(ENVONLY, prefix, extFilePrefix, NULL, "H5Pset_efile_prefix: external file prefix not pinned");
if ((retVal = H5Pset_efile_prefix((hid_t)dapl_id, extFilePrefix)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (extFilePrefix)
UNPIN_JAVA_STRING(ENVONLY, prefix, extFilePrefix);
} /* end Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_efile_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix
(JNIEnv *env, jclass clss, jlong dapl_id)
{
ssize_t prefix_size = -1;
char *pre = NULL;
jstring str = NULL;
UNUSED(clss);
if ((prefix_size = H5Pget_efile_prefix((hid_t)dapl_id, (char *)NULL, 0)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (pre = (char *) HDmalloc(sizeof(char) * (size_t)prefix_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Pget_efile_prefix: memory allocation failed");
if (H5Pget_efile_prefix((hid_t)dapl_id, (char *)pre, (size_t)prefix_size + 1) < 0)
H5_LIBRARY_ERROR(ENVONLY);
pre[(size_t)prefix_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, pre))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(ENVONLY, "H5Pget_efile_prefix: out of memory - unable to construct string from UTF characters");
}
done:
if (pre)
HDfree(pre);
return (jstring)str;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_append_flush
* Signature: (JI[JLjava/lang/Object;Ljava/lang/Object;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1append_1flush
(JNIEnv *env, jclass clss, jlong plist_id, jint ndims, jlongArray boundary, jobject callback_op, jobject op_data)
{
cb_wrapper wrapper = { callback_op, op_data };
herr_t status = FAIL;
UNUSED(clss);
ENVPTR->GetJavaVM(ENVONLY, &jvm);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (NULL == op_data)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pset_append_flush: op_data is NULL");
if (NULL == callback_op)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pset_append_flush: callback_op is NULL");
if ((status = H5Pset_append_flush((hid_t)plist_id, (unsigned)ndims, (const hsize_t *)boundary, (H5D_append_cb_t)H5D_append_cb, (void *)&wrapper)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1append_1flush */
/*
* TODO: H5Pget_append_flush
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_view
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1view
(JNIEnv *env, jclass clss, jlong dapl_id, jint view)
{
UNUSED(clss);
if (H5Pset_virtual_view((hid_t)dapl_id, (H5D_vds_view_t)view) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1virtual_1view */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_view
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1view
(JNIEnv *env, jclass clss, jlong dapl_id)
{
H5D_vds_view_t virtual_view = H5D_VDS_ERROR;
UNUSED(clss);
if (H5Pget_virtual_view((hid_t)dapl_id, &virtual_view) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)virtual_view;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1virtual_1view */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_printf_gap
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1printf_1gap
(JNIEnv *env, jclass clss, jlong dapl_id, jlong gap_size)
{
UNUSED(clss);
if (H5Pset_virtual_printf_gap((hid_t)dapl_id, (hsize_t)gap_size) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1virtual_1printf_1gap */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_printf_gap
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1printf_1gap
(JNIEnv *env, jclass clss, jlong dapl_id)
{
hsize_t gap_size = 0;
UNUSED(clss);
if (H5Pget_virtual_printf_gap((hid_t)dapl_id, &gap_size) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)gap_size;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1virtual_1printf_1gap */
static herr_t
H5D_append_cb
(hid_t dataset_id, hsize_t *cur_dims, void *cb_data)
{
cb_wrapper *wrapper = (cb_wrapper *)cb_data;
jlongArray cur_dimsArray;
jmethodID mid;
jobject visit_callback = wrapper->visit_callback;
jclass cls;
JNIEnv *cbenv = NULL;
void *op_data = (void *)wrapper->op_data;
jint status = -1;
if (JVMPTR->AttachCurrentThread(JVMPAR, (void **)&cbenv, NULL) < 0) {
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(CBENVONLY, "H5D_append_cb: failed to attach current thread to JVM");
}
if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cls, "callback", "(J[JLhdf/hdf5lib/callbacks/H5D_append_t;)I")))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
if (NULL != cur_dims) {
if (NULL == (cur_dimsArray = CBENVPTR->NewLongArray(CBENVONLY, 2)))
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
CBENVPTR->SetLongArrayRegion(CBENVONLY, cur_dimsArray, 0, 2, (const jlong *)cur_dims);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
status = CBENVPTR->CallIntMethod(CBENVONLY, visit_callback, mid, dataset_id, cur_dims, op_data);
CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE);
}
done:
if (CBENVONLY)
JVMPTR->DetachCurrentThread(JVMPAR);
return (herr_t)status;
} /* end H5D_append_cb */
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */

112
java/src/jni/h5pDAPLImp.h Normal file
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifndef _Included_hdf_hdf5lib_H5_H5PDAPL
#define _Included_hdf_hdf5lib_H5_H5PDAPL
#include <jni.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_chunk_cache
* Signature: (JJJD)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1chunk_1cache
(JNIEnv *, jclass, jlong, jlong, jlong, jdouble);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_chunk_cache
* Signature: (J[J[J[D)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk_1cache
(JNIEnv *, jclass, jlong, jlongArray, jlongArray, jdoubleArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_efile_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix
(JNIEnv *, jclass, jlong, jstring);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_efile_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_append_flush
* Signature: (JI[JLjava/lang/Object;Ljava/lang/Object;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1append_1flush
(JNIEnv*, jclass, jlong, jint, jlongArray, jobject, jobject);
/*
* TODO: H5Pget_append_flush
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_view
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1view
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_view
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1view
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_printf_gap
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1printf_1gap
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_printf_gap
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1printf_1gap
(JNIEnv *, jclass, jlong);
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
#endif /* _Included_hdf_hdf5lib_H5_H5PDAPL */

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifndef _Included_hdf_hdf5lib_H5_H5PDCPL
#define _Included_hdf_hdf5lib_H5_H5PDCPL
#include <jni.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_layout
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1layout
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_layout
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1layout
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_chunk
* Signature: (JI[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1chunk
(JNIEnv *, jclass, jlong, jint, jbyteArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_chunk
* Signature: (JI[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk
(JNIEnv *, jclass, jlong, jint, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_chunk_opts
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_chunk_opts
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_dset_no_attrs_hint
* Signature: (JZ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1dset_1no_1attrs_1hint
(JNIEnv *, jclass, jlong, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_dset_no_attrs_hint
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1dset_1no_1attrs_1hint
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_deflate
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1deflate
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fill_value
* Signature: (JJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fill_1value
(JNIEnv *, jclass, jlong, jlong, jbyteArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fill_value
* Signature: (JJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fill_1value
(JNIEnv *, jclass, jlong, jlong, jbyteArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pfill_value_defined
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pfill_1value_1defined
(JNIEnv *, jclass, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fill_time
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fill_1time
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fill_time
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fill_1time
(JNIEnv *, jclass, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_alloc_time
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1alloc_1time
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_alloc_time
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1alloc_1time
(JNIEnv *, jclass, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_filter
* Signature: (JIIJ[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1filter
(JNIEnv *, jclass, jlong, jint, jint, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pall_filters_avail
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pall_1filters_1avail
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_nfilters
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1nfilters
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_filter
* Signature: (JI[I[J[IJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1filter
(JNIEnv *, jclass, jlong, jint, jintArray, jlongArray, jintArray, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_filter2
* Signature: (JI[I[J[IJ[Ljava/lang/String;[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1filter2
(JNIEnv *, jclass, jlong, jint, jintArray, jlongArray, jintArray, jlong, jobjectArray, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_filter_by_id
* Signature: (JI[I[J[IJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1filter_1by_1id
(JNIEnv *, jclass, jlong, jint, jintArray, jlongArray, jintArray, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_filter_by_id2
* Signature: (JI[I[J[IJ[Ljava/lang/String;[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1filter_1by_1id2
(JNIEnv *, jclass, jlong, jint, jintArray, jlongArray, jintArray, jlong, jobjectArray, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pmodify_filter
* Signature: (JIIJ[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pmodify_1filter
(JNIEnv *, jclass, jlong, jint, jint, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Premove_filter
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5P1remove_1filter
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fletcher32
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fletcher32
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_nbit
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1nbit
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_scaleoffset
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1scaleoffset
(JNIEnv *, jclass, jlong, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shuffle
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shuffle
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_szip
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1szip
(JNIEnv *, jclass, jlong, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_external
* Signature: (JLjava/lang/String;JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1external
(JNIEnv *, jclass, jlong, jstring, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_external
* Signature: (JIJ[Ljava/lang/String;[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1external
(JNIEnv *, jclass, jlong, jint, jlong, jobjectArray, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_external_count
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1external_1count
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual
* Signature: (JJLjava/lang/String;Ljava/lang/String;J)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual
(JNIEnv *, jclass, jlong, jlong, jstring, jstring, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_count
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1count
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_dsetname
* Signature: (JJ)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1dsetname
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_filename
* Signature: (JJ)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1filename
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_srcspace
* Signature: (JJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1srcspace
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_vspace
* Signature: (JJ)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1vspace
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix
(JNIEnv *, jclass, jlong, jstring);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix
(JNIEnv *, jclass, jlong);
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
#endif /* _Included_hdf_hdf5lib_H5_H5PDCPL */

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* For details of the HDF libraries, see the HDF Documentation at:
* http://hdfgroup.org/HDF5/doc/
*
*/
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <stdlib.h>
#include "hdf5.h"
#include "h5jni.h"
#include "h5pDXPLImp.h"
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_buffer
* Signature: (JJ[B[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1buffer
(JNIEnv *env, jclass clss, jlong plist, jlong size, jbyteArray tconv, jbyteArray bkg)
{
#ifdef notdef
jboolean isCopy;
jbyte *tconvP = NULL;
jbyte *bkgP = NULL;
#endif
herr_t status = FAIL;
UNUSED(clss);
#ifndef notdef
UNUSED(plist);
UNUSED(size);
UNUSED(tconv);
UNUSED(bkg);
#endif
H5_UNIMPLEMENTED(ENVONLY, "H5Pset_buffer: not implemented");
/* NOTE: DON'T IMPLEMENT THIS!!! */
#ifdef notdef
if (NULL != tconv)
PIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, &isCopy, "H5Pset_buffer: tconv not pinned");
if (NULL != bkg)
PIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, &isCopy, "H5Pset_buffer: bkg not pinned");
if ((status = H5Pset_buffer((hid_t)plist, (size_t)size, tconvP, bkgP)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
#ifdef notdef
if (bkgP)
UNPIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, (status < 0) ? JNI_ABORT : 0);
if (tconvP)
UNPIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, (status < 0) ? JNI_ABORT : 0);
#endif
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1buffer */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_buffer
* Signature: (J[B[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1buffer
(JNIEnv *env, jclass clss, jlong plist, jbyteArray tconv, jbyteArray bkg)
{
#ifdef notdef
jboolean isCopy;
jbyte *tconvP = NULL;
jbyte *bkgP = NULL;
#endif
herr_t status = FAIL;
UNUSED(clss);
#ifndef notdef
UNUSED(plist);
UNUSED(tconv);
UNUSED(bkg);
#endif
H5_UNIMPLEMENTED(ENVONLY, "H5Pget_buffer: not implemented");
/* NOTE: DON'T IMPLEMENT THIS!!! */
#ifdef notdef
if (NULL == tconv)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_buffer: tconv input array is NULL");
if (NULL == bkg)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_buffer: bkg array is NULL");
PIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, &isCopy, "H5Pget_buffer: tconv not pinned");
PIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, &isCopy, "H5Pget_buffer: bkg not pinned");
if ((status = H5Pget_buffer((hid_t)plist, tconvP, bkgP)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
#ifdef notdef
if (bkgP)
UNPIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, (status < 0) ? JNI_ABORT : 0);
if (tconvP)
UNPIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, (status < 0) ? JNI_ABORT : 0);
#endif
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1buffer */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_buffer_size
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1buffer_1size
(JNIEnv *env, jclass clss, jlong plist, jlong size)
{
UNUSED(clss);
if (H5Pset_buffer((hid_t)plist, (size_t)size, NULL, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1buffer_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_buffer_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1buffer_1size
(JNIEnv *env, jclass clss, jlong plist)
{
size_t size = 0;
UNUSED(clss);
if (!(size = H5Pget_buffer((hid_t)plist, NULL, NULL)))
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)size;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1buffer_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_preserve
* Signature: (JZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1preserve
(JNIEnv *env, jclass clss, jlong plist, jboolean status)
{
hbool_t st = JNI_FALSE;
herr_t retVal = FAIL;
UNUSED(clss);
if (JNI_TRUE == status)
st = TRUE;
else if (JNI_FALSE == status)
st = false;
else
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_preserve: status not TRUE or FALSE");
if ((retVal = H5Pset_preserve((hid_t)plist, st)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1preserve */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_preserve
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1preserve
(JNIEnv *env, jclass clss, jlong plist)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pget_preserve((hid_t)plist)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1preserve */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_edc_check
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1edc_1check
(JNIEnv *env, jclass clss, jlong plist, jint check)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pset_edc_check((hid_t)plist, (H5Z_EDC_t)check)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1edc_1check */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_edc_check
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1edc_1check
(JNIEnv *env, jclass clss, jlong plist)
{
H5Z_EDC_t retVal = -1;
UNUSED(clss);
if ((retVal = H5Pget_edc_check((hid_t)plist)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1edc_1check */
/*
* TODO: H5Pset_filter_callback
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_data_transform
* Signature: (JLjava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1data_1transform
(JNIEnv *env, jclass clss, jlong plist_id, jstring expression)
{
const char *express = NULL;
herr_t retVal = FAIL;
UNUSED(clss);
if (NULL == expression)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pset_data_transform: data transform expression is NULL");
PIN_JAVA_STRING(ENVONLY, expression, express, NULL, "H5Pset_data_transform: data transform expression not pinned");
if ((retVal = H5Pset_data_transform((hid_t)plist_id, express)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (express)
UNPIN_JAVA_STRING(ENVONLY, expression, express);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1data_1transform */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_data_transform
* Signature: (J[Ljava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1data_1transform
(JNIEnv *env, jclass clss, jlong plist_id, jobjectArray expression, jlong size)
{
jstring str = NULL;
char *express = NULL;
ssize_t express_size = -1;
UNUSED(clss);
if (size <= 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_data_transform: size <= 0");
if ((express_size = H5Pget_data_transform((hid_t)plist_id, (char *)NULL, (size_t)size)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (NULL == (express = (char *) HDmalloc(sizeof(char) * (size_t)express_size + 1)))
H5_JNI_FATAL_ERROR(ENVONLY, "H5Pget_data_transform: memory allocation failed");
if (H5Pget_data_transform((hid_t)plist_id, express, (size_t)express_size + 1) < 0)
H5_LIBRARY_ERROR(ENVONLY);
express[express_size] = '\0';
if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, express))) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_JNI_FATAL_ERROR(ENVONLY, "H5Pget_data_transform: out of memory - unable to construct string from UTF characters");
}
ENVPTR->SetObjectArrayElement(ENVONLY, expression, 0, str);
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
done:
if (express)
HDfree(express);
return (jlong)express_size;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1data_1transform */
/*
* TODO: H5Pset_type_conv_cb
*/
/*
* TODO: H5Pget_type_conv_cb
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_hyper_vector_size
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size
(JNIEnv *env, jclass clss, jlong plist, jlong vector_size)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pset_hyper_vector_size((hid_t)plist, (size_t)vector_size)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_hyper_vector_size
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size
(JNIEnv *env, jclass clss, jlong plist, jlongArray vector_size)
{
jboolean isCopy;
size_t size;
jlong *theArray = NULL;
herr_t retVal = FAIL;
UNUSED(clss);
if (NULL == vector_size)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_hyper_vector_size: vector_size is NULL");
PIN_LONG_ARRAY(ENVONLY, vector_size, theArray, &isCopy, "H5Pget_hyper_vector_size: vector_size not pinned");
if ((retVal = H5Pget_hyper_vector_size((hid_t)plist, &size)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
theArray[0] = (jlong)size;
done:
if (theArray)
UNPIN_LONG_ARRAY(ENVONLY, vector_size, theArray, (retVal < 0) ? JNI_ABORT : 0);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_btree_ratios
* Signature: (JDDD)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1btree_1ratios
(JNIEnv *env, jclass clss, jlong plist_id, jdouble left, jdouble middle, jdouble right)
{
herr_t status = FAIL;
UNUSED(clss);
if ((status = H5Pset_btree_ratios((hid_t)plist_id, (double)left,(double)middle, (double)right)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1btree_1ratios */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_btree_ratios
* Signature: (J[D[D[D)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios
(JNIEnv *env, jclass clss, jlong plist_id, jdoubleArray left,
jdoubleArray middle, jdoubleArray right)
{
jboolean isCopy;
jdouble *leftP = NULL;
jdouble *middleP = NULL;
jdouble *rightP = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == left)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_btree_ratios: left input array is NULL");
if (NULL == middle)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_btree_ratios: middle input array is NULL");
if (NULL == right)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_btree_ratios: right input array is NULL");
PIN_DOUBLE_ARRAY(ENVONLY, left, leftP, &isCopy, "H5Pget_btree_ratios: left array not pinned");
PIN_DOUBLE_ARRAY(ENVONLY, middle, middleP, &isCopy, "H5Pget_btree_ratios: middle array not pinned");
PIN_DOUBLE_ARRAY(ENVONLY, right, rightP, &isCopy, "H5Pget_btree_ratios: right array not pinned");
if ((status = H5Pget_btree_ratios((hid_t)plist_id, (double *)leftP,
(double *)middleP, (double *)rightP)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (rightP)
UNPIN_DOUBLE_ARRAY(ENVONLY, right, rightP, (status < 0) ? JNI_ABORT : 0);
if (middleP)
UNPIN_DOUBLE_ARRAY(ENVONLY, middle, middleP, (status < 0) ? JNI_ABORT : 0);
if (leftP)
UNPIN_DOUBLE_ARRAY(ENVONLY, left, leftP, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios */
/*
* TODO: H5Pset_vlen_mem_manager
*/
/*
* TODO: H5Pget_vlen_mem_manager
*/
/*
* TODO: H5Pset_dxpl_mpio
*/
/*
* TODO: H5Pget_dxpl_mpio
*/
/*
* TODO: H5Pset_dxpl_mpio_chunk_opt
*/
/*
* TODO: H5Pset_dxpl_mpio_chunk_opt_num
*/
/*
* TODO: H5Pset_dxpl_mpio_chunk_opt_ratio
*/
/*
* TODO: H5Pset_dxpl_mpio_collective_opt
*/
/*
* TODO: H5Pget_mpio_actual_chunk_opt_mode
*/
/*
* TODO: H5Pget_mpio_actual_io_mode
*/
/*
* TODO: H5Pget_mpio_no_collective_cause
*/
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifndef _Included_hdf_hdf5lib_H5_H5PDXPL
#define _Included_hdf_hdf5lib_H5_H5PDXPL
#include <jni.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_buffer
* Signature: (JJ[B[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1buffer
(JNIEnv *, jclass, jlong, jlong, jbyteArray, jbyteArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_buffer
* Signature: (J[B[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1buffer
(JNIEnv *, jclass, jlong, jbyteArray, jbyteArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_buffer_size
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1buffer_1size
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_buffer_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1buffer_1size
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_preserve
* Signature: (JZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1preserve
(JNIEnv *, jclass, jlong, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_preserve
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1preserve
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_edc_check
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1edc_1check
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_edc_check
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1edc_1check
(JNIEnv *, jclass, jlong);
/*
* TODO: H5Pset_filter_callback
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_data_transform
* Signature: (JLjava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1data_1transform
(JNIEnv *, jclass, jlong, jstring);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_data_transform
* Signature: (J[Ljava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1data_1transform
(JNIEnv *, jclass, jlong, jobjectArray, jlong);
/*
* TODO: H5Pset_type_conv_cb
*/
/*
* TODO: H5Pget_type_conv_cb
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_hyper_vector_size
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_hyper_vector_size
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size
(JNIEnv *, jclass, jlong, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_btree_ratios
* Signature: (JDDD)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1btree_1ratios
(JNIEnv *, jclass, jlong, jdouble, jdouble, jdouble);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_btree_ratios
* Signature: (J[D[D[D)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios
(JNIEnv *, jclass, jlong, jdoubleArray, jdoubleArray, jdoubleArray);
/*
* TODO: H5Pset_vlen_mem_manager
*/
/*
* TODO: H5Pget_vlen_mem_manager
*/
/*
* TODO: H5Pset_dxpl_mpio
*/
/*
* TODO: H5Pget_dxpl_mpio
*/
/*
* TODO: H5Pset_dxpl_mpio_chunk_opt
*/
/*
* TODO: H5Pset_dxpl_mpio_chunk_opt_num
*/
/*
* TODO: H5Pset_dxpl_mpio_chunk_opt_ratio
*/
/*
* TODO: H5Pset_dxpl_mpio_collective_opt
*/
/*
* TODO: H5Pget_mpio_actual_chunk_opt_mode
*/
/*
* TODO: H5Pget_mpio_actual_io_mode
*/
/*
* TODO: H5Pget_mpio_no_collective_cause
*/
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
#endif /* _Included_hdf_hdf5lib_H5_H5PDXPL */

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifndef _Included_hdf_hdf5lib_H5_H5PFAPL
#define _Included_hdf_hdf5lib_H5_H5PFAPL
#include <jni.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/*
* TODO: H5Pset_driver
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_driver
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1driver
(JNIEnv *, jclass, jlong);
/*
* TODO: H5Pget_driver_info
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fclose_degree
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fclose_1degree
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fclose_degree
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fclose_1degree
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_core
* Signature: (JJZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1core
(JNIEnv *, jclass, jlong, jlong, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fapl_core
* Signature: (J[J[Z)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fapl_1core
(JNIEnv *, jclass, jlong, jlongArray, jbooleanArray);
/*
* TODO: H5Pset_core_write_tracking
*/
/*
* TODO: H5Pget_core_write_tracking
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_direct
* Signature: (JJJJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1direct
(JNIEnv *, jclass, jlong, jlong, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fapl_direct
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fapl_1direct
(JNIEnv *, jclass, jlong, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_family
* Signature: (JJJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1family
(JNIEnv *, jclass, jlong, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fapl_family
* Signature: (J[J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fapl_1family
(JNIEnv *, jclass, jlong, jlongArray, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_family_offset
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1family_1offset
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_family_offset
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1family_1offset
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_log
* Signature: (JLjava/lang/String;JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1log
(JNIEnv *, jclass, jlong, jstring, jlong, jlong);
/*
* TODO: H5Pset_fapl_mpio
*/
/*
* TODO: H5Pget_fapl_mpio
*/
/*
* TODO: H5Pset_fapl_mpiposix
*/
/*
* TODO: H5Pget_fapl_mpiposix
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_multi
* Signature: (J[I[J[Ljava/lang/String;[JZ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1multi
(JNIEnv *, jclass, jlong, jintArray, jlongArray, jobjectArray, jlongArray, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_fapl_multi
* Signature: (J[I[J[Ljava/lang/String;[J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1fapl_1multi
(JNIEnv *, jclass, jlong, jintArray, jlongArray, jobjectArray, jlongArray);
/*
* TODO: H5Pset_multi_type
*/
/*
* TODO: H5Pget_multi_type
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_split
* Signature: (JLjava/lang/String;JLjava/lang/String;J)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1split
(JNIEnv *, jclass, jlong, jstring, jlong, jstring, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_sec2
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1sec2
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_stdio
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1stdio
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_fapl_windows
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1fapl_1windows
(JNIEnv *, jclass, jlong);
/*
* TODO: H5Pset_file_image
*/
/*
* TODO: H5Pget_file_image
*/
/*
* TODO: H5Pset_file_image_callbacks
*/
/*
* TODO: H5Pget_file_image_callbacks
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_meta_block_size
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1meta_1block_1size
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_meta_block_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1meta_1block_1size
(JNIEnv *, jclass, jlong);
/*
* TODO: H5Pset_page_buffer_size
*/
/*
* TODO: H5Pget_page_buffer_size
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_sieve_buf_size
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1sieve_1buf_1size
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_sieve_buf_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1sieve_1buf_1size
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_alignment
* Signature: (JJJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1alignment
(JNIEnv *, jclass, jlong, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_alignment
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1alignment
(JNIEnv *, jclass, jlong, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_cache
* Signature: (JIJJD)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1cache
(JNIEnv *, jclass, jlong, jint, jlong, jlong, jdouble);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_cache
* Signature: (J[I[J[J[D)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1cache
(JNIEnv *, jclass, jlong, jintArray, jlongArray, jlongArray, jdoubleArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_elink_file_cache_size
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1elink_1file_1cache_1size
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_elink_file_cache_size
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1elink_1file_1cache_1size
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_evict_on_close
* Signature: (JZ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close
(JNIEnv *, jclass, jlong, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_evict_on_close
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_metadata_read_attempts
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_metadata_read_attempts
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1metadata_1read_1attempts
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_mdc_config
* Signature: (JLhdf/hdf5lib/structs/H5AC_cache_config_t;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1mdc_1config
(JNIEnv *, jclass, jlong, jobject);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_mdc_config
* Signature: (J)Lhdf/hdf5lib/structs/H5AC_cache_config_t;
*/
JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1mdc_1config
(JNIEnv *, jclass, jlong);
/*
* TODO: H5Pset_mdc_image_config
*/
/*
* TODO: H5Pget_mdc_image_config
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_mdc_log_options
* Signature: (JZLjava/lang/String;Z)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1mdc_1log_1options
(JNIEnv *, jclass, jlong, jboolean, jstring, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_mdc_log_options
* Signature: (J[Z)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1mdc_1log_1options
(JNIEnv *, jclass, jlong, jbooleanArray);
/*
* TODO: H5Pset_all_coll_metadata_ops
*/
/*
* TODO: H5Pget_all_coll_metadata_ops
*/
/*
* TODO: H5Pset_coll_metadata_write
*/
/*
* TODO: H5Pget_coll_metadata_write
*/
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_gc_references
* Signature: (JZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1gc_1references
(JNIEnv *, jclass, jlong, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_gc_references
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1gc_1references
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_small_data_block_size
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1small_1data_1block_1size
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_small_data_block_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1small_1data_1block_1size
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_libver_bounds
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1libver_1bounds
(JNIEnv *, jclass, jlong, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_libver_bounds
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1libver_1bounds
(JNIEnv *, jclass, jlong, jintArray);
/*
* TODO: H5Pset_object_flush_cb
*/
/*
* TODO: H5Pget_object_flush_cb
*/
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
#endif /* _Included_hdf_hdf5lib_H5_H5PFAPL */

572
java/src/jni/h5pFCPLImp.c Normal file
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@ -0,0 +1,572 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* For details of the HDF libraries, see the HDF Documentation at:
* http://hdfgroup.org/HDF5/doc/
*
*/
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <stdlib.h>
#include "hdf5.h"
#include "h5jni.h"
#include "h5pFCPLImp.h"
/*
* Pointer to the JNI's Virtual Machine; used for callback functions.
*/
/* extern JavaVM *jvm; */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_userblock
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1userblock
(JNIEnv *env, jclass clss, jlong plist, jlong size)
{
long sz = (long) size;
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pset_userblock((hid_t)plist, (hsize_t)sz)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1userblock */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_userblock
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1userblock
(JNIEnv *env, jclass clss, jlong plist, jlongArray size)
{
jboolean isCopy;
hsize_t s;
jlong *theArray = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == size)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_userblock: size is NULL");
PIN_LONG_ARRAY(ENVONLY, size, theArray, &isCopy, "H5Pget_userblock: size not pinned");
if ((status = H5Pget_userblock((hid_t)plist, &s)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
theArray[0] = (jlong)s;
done:
if (theArray)
UNPIN_LONG_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1userblock */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_sizes
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1sizes
(JNIEnv *env, jclass clss, jlong plist, jint sizeof_addr, jint sizeof_size)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pset_sizes((hid_t)plist, (size_t)sizeof_addr, (size_t)sizeof_size)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1sizes */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_sizes
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1sizes
(JNIEnv *env, jclass clss, jlong plist, jlongArray size)
{
jboolean isCopy;
jlong *theArray = NULL;
jsize arrLen;
size_t ss;
size_t sa;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == size)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_sizes: size is NULL");
if ((arrLen = ENVPTR->GetArrayLength(ENVONLY, size)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_sizes: size array length < 0");
}
if (arrLen < 2)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_sizes: size input array < 2 elements");
PIN_LONG_ARRAY(ENVONLY, size, theArray, &isCopy, "H5Pget_sizes: size not pinned");
if ((status = H5Pget_sizes((hid_t)plist, &sa, &ss)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
theArray[0] = (jlong)sa;
theArray[1] = (jlong)ss;
done:
if (theArray)
UNPIN_LONG_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1sizes */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_sym_k
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1sym_1k
(JNIEnv *env, jclass clss, jlong plist, jint ik, jint lk)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pset_sym_k((hid_t)plist, (unsigned)ik, (unsigned)lk)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1sym_1k */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_sym_k
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1sym_1k
(JNIEnv *env, jclass clss, jlong plist, jintArray size)
{
jboolean isCopy;
jsize arrLen;
jint *theArray = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == size)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_sym_k: size is NULL");
if ((arrLen = ENVPTR->GetArrayLength(ENVONLY, size)) < 0) {
CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_sym_k: size array length < 0");
}
if (arrLen < 2)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_sym_k: size < 2 elements");
PIN_INT_ARRAY(ENVONLY, size, theArray, &isCopy, "H5Pget_sym_k: size not pinned");
if ((status = H5Pget_sym_k((hid_t)plist, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1]))) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (theArray)
UNPIN_LONG_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1sym_1k */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_istore_k
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1istore_1k
(JNIEnv *env, jclass clss, jlong plist, jint ik)
{
herr_t retVal = FAIL;
UNUSED(clss);
if ((retVal = H5Pset_istore_k((hid_t)plist, (unsigned)ik)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1istore_1k */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_istore_k
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1istore_1k
(JNIEnv *env, jclass clss, jlong plist, jintArray ik)
{
jboolean isCopy;
jint *theArray = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == ik)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_store_k: ik is NULL");
PIN_INT_ARRAY(ENVONLY, ik, theArray, &isCopy, "H5Pget_store_k: size not pinned");
if ((status = H5Pget_istore_k((hid_t)plist, (unsigned *)&(theArray[0]))) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (theArray)
UNPIN_INT_ARRAY(ENVONLY, ik, theArray, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1istore_1k */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_file_space_page_size
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1file_1space_1page_1size
(JNIEnv *env, jclass clss, jlong fcpl_id, jlong fsp_size)
{
UNUSED(clss);
if (H5Pset_file_space_page_size((hid_t)fcpl_id, (hsize_t)fsp_size) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1file_1space_1page_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_page_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1page_1size
(JNIEnv *env, jclass clss, jlong fcpl_id)
{
hsize_t fsp_size = 0;
UNUSED(clss);
if (H5Pget_file_space_page_size((hid_t)fcpl_id, &fsp_size) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)fsp_size;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1page_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_file_space_strategy
* Signature: (JIZJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1file_1space_1strategy
(JNIEnv *env, jclass clss, jlong fcpl_id, jint strategy, jboolean persist, jlong threshold)
{
UNUSED(clss);
if (H5Pset_file_space_strategy((hid_t)fcpl_id, (H5F_fspace_strategy_t)strategy, (hbool_t)persist, (hsize_t)threshold) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return;
} /* end Java_hdf_hdf5lib_H5_H5Pset_file_space_strategy */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_strategy
* Signature: (J[Z[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy
(JNIEnv *env, jclass clss, jlong fcpl_id, jbooleanArray persist, jlongArray threshold)
{
H5F_fspace_strategy_t thestrategy = H5F_FSPACE_STRATEGY_FSM_AGGR; /* Library default */
jboolean isCopy;
jboolean *persistArray = NULL;
jlong *thresholdArray = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (persist)
PIN_BOOL_ARRAY(ENVONLY, persist, persistArray, &isCopy, "H5Pget_file_space: persist not pinned");
if (threshold)
PIN_LONG_ARRAY(ENVONLY, threshold, thresholdArray, &isCopy, "H5Pget_file_space: threshold not pinned");
if ((status = H5Pget_file_space_strategy((hid_t)fcpl_id, &thestrategy, (hbool_t *)persistArray, (hsize_t *)thresholdArray)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (thresholdArray)
UNPIN_LONG_ARRAY(ENVONLY, threshold, thresholdArray, (status < 0) ? JNI_ABORT : 0);
if (persistArray)
UNPIN_BOOL_ARRAY(ENVONLY, persist, persistArray, (status < 0) ? JNI_ABORT : 0);
return (jint)thestrategy;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_strategy_persist
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy_1persist
(JNIEnv *env, jclass clss, jlong fcpl_id)
{
hbool_t persist = FALSE;
herr_t status = FAIL;
UNUSED(clss);
if ((status = H5Pget_file_space_strategy((hid_t)fcpl_id, NULL, &persist, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jboolean)persist;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy_1persist */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_strategy_threshold
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy_1threshold
(JNIEnv *env, jclass clss, jlong fcpl_id)
{
hsize_t threshold = 0;
herr_t status = FAIL;
UNUSED(clss);
if ((status = H5Pget_file_space_strategy((hid_t)fcpl_id, NULL, NULL, &threshold)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jlong)threshold;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1threshold */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shared_mesg_nindexes
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1nindexes
(JNIEnv *env, jclass clss, jlong plist_id, jint nindexes)
{
herr_t retVal = FAIL;
UNUSED(clss);
if (nindexes > H5O_SHMESG_MAX_NINDEXES)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_shared_mesg_nindexes: number of indexes is greater than H5O_SHMESG_MAX_NINDEXES");
if ((retVal = H5Pset_shared_mesg_nindexes((hid_t)plist_id, (unsigned)nindexes)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1nindexes */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_shared_mesg_nindexes
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1nindexes
(JNIEnv *env, jclass clss, jlong fcpl_id)
{
unsigned nindexes;
UNUSED(clss);
if (H5Pget_shared_mesg_nindexes((hid_t)fcpl_id, &nindexes) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)nindexes;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1nindexes */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shared_mesg_index
* Signature: (JIII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1index
(JNIEnv *env, jclass clss, jlong fcpl_id, jint index_num,
jint mesg_type_flags, jint min_mesg_size)
{
unsigned nindexes; /* Number of SOHM indexes */
herr_t retVal = FAIL;
UNUSED(clss);
/* Check arguments */
if ((unsigned) mesg_type_flags > H5O_SHMESG_ALL_FLAG)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_shared_mesg_index: unrecognized flags in mesg_type_flags");
/* Read the current number of indexes */
if (H5Pget_shared_mesg_nindexes((hid_t)fcpl_id, &nindexes) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Range check */
if ((unsigned) index_num >= nindexes)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_shared_mesg_index: index_num is too large; no such index");
if ((retVal = H5Pset_shared_mesg_index((hid_t)fcpl_id, (unsigned)index_num, (unsigned) mesg_type_flags, (unsigned) min_mesg_size)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1index */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_shared_mesg_index
* Signature: (JI[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1index
(JNIEnv *env, jclass clss, jlong fcpl_id, jint index_num, jintArray mesg_info)
{
jboolean isCopy;
unsigned nindexes; /* Number of SOHM indexes */
jint *theArray = NULL;
herr_t retVal = FAIL;
UNUSED(clss);
if (NULL == mesg_info)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_shared_mesg_index: mesg_info is NULL");
/* Read the current number of indexes */
if (H5Pget_shared_mesg_nindexes((hid_t)fcpl_id, &nindexes) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Range check */
if ((unsigned) index_num >= nindexes)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_shared_mesg_index: index_num is too large; no such index");
PIN_INT_ARRAY(ENVONLY, mesg_info, theArray, &isCopy, "H5Pget_shared_mesg_index: input not pinned");
if ((retVal = H5Pget_shared_mesg_index((hid_t)fcpl_id, (unsigned)index_num, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1]))) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (theArray)
UNPIN_INT_ARRAY(ENVONLY, mesg_info, theArray, (retVal < 0) ? JNI_ABORT : 0);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1index */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shared_mesg_phase_change
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1phase_1change
(JNIEnv *env, jclass clss, jlong fcpl_id, jint max_list, jint min_btree)
{
herr_t retVal = FAIL;
UNUSED(clss);
/* Check that values are sensible. The min_btree value must be no greater
* than the max list plus one.
*
* Range check to make certain they will fit into encoded form.
*/
if (max_list + 1 < min_btree)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_shared_mesg_phase_change: minimum B-tree value is greater than maximum list value");
if (max_list > H5O_SHMESG_MAX_LIST_SIZE)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_shared_mesg_phase_change: max list value is larger than H5O_SHMESG_MAX_LIST_SIZE");
if (min_btree > H5O_SHMESG_MAX_LIST_SIZE)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_shared_mesg_phase_change: min btree value is larger than H5O_SHMESG_MAX_LIST_SIZE");
if ((retVal = H5Pset_shared_mesg_phase_change((hid_t)fcpl_id, (unsigned)max_list, (unsigned)min_btree)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1phase_1change */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_shared_mesg_phase_change
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1phase_1change
(JNIEnv *env, jclass clss, jlong fcpl_id, jintArray size)
{
jboolean isCopy;
jint *theArray = NULL;
herr_t retVal = FAIL;
UNUSED(clss);
if (NULL == size)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_shared_mesg_phase_change: size is NULL");
PIN_INT_ARRAY(ENVONLY, size, theArray, &isCopy, "H5Pget_shared_mesg_phase_change: input not pinned");
if ((retVal = H5Pget_shared_mesg_phase_change((hid_t)fcpl_id, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1]))) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (theArray)
UNPIN_INT_ARRAY(ENVONLY, size, theArray, (retVal < 0) ? JNI_ABORT : 0);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1phase_1change */
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */

207
java/src/jni/h5pFCPLImp.h Normal file
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@ -0,0 +1,207 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* 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. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifndef _Included_hdf_hdf5lib_H5_H5PFCPL
#define _Included_hdf_hdf5lib_H5_H5PFCPL
#include <jni.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_userblock
* Signature: (JJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1userblock
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_userblock
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1userblock
(JNIEnv *, jclass, jlong, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_sizes
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1sizes
(JNIEnv *, jclass, jlong, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_sizes
* Signature: (J[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1sizes
(JNIEnv *, jclass, jlong, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_sym_k
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1sym_1k
(JNIEnv *, jclass, jlong, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_sym_k
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1sym_1k
(JNIEnv *, jclass, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_istore_k
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1istore_1k
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_istore_k
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1istore_1k
(JNIEnv *, jclass, jlong, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_file_space_page_size
* Signature: (JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1file_1space_1page_1size
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_page_size
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1page_1size
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_file_space_strategy
* Signature: (JIZJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1file_1space_1strategy
(JNIEnv *, jclass, jlong, jint, jboolean, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_strategy
* Signature: (J[Z[J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy
(JNIEnv *, jclass, jlong, jbooleanArray, jlongArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_strategy_persist
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy_1persist
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_file_space_strategy_threshold
* Signature: (J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1file_1space_1strategy_1threshold
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shared_mesg_nindexes
* Signature: (JI)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1nindexes
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_shared_mesg_nindexes
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1nindexes
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shared_mesg_index
* Signature: (JIII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1index
(JNIEnv *, jclass, jlong, jint, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_shared_mesg_index
* Signature: (JI[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1index
(JNIEnv *, jclass, jlong, jint, jintArray);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_shared_mesg_phase_change
* Signature: (JII)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1phase_1change
(JNIEnv *, jclass, jlong, jint, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_shared_mesg_phase_change
* Signature: (J[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1phase_1change
(JNIEnv *, jclass, jlong, jintArray);
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */
#endif /* _Included_hdf_hdf5lib_H5_H5PFCPL */

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