diff options
85 files changed, 1218 insertions, 451 deletions
diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake index 71dabb1..5a89564 100644 --- a/CMakeFilters.cmake +++ b/CMakeFilters.cmake @@ -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 ${SZIP_URL} not found") + endif () else () set (ZLIB_USE_EXTERNAL 0) set (SZIP_USE_EXTERNAL 0) diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake index 464477b..7a0746a 100644 --- a/CMakeInstallation.cmake +++ b/CMakeInstallation.cmake @@ -134,7 +134,7 @@ install ( ) #----------------------------------------------------------------------------- -# Configure the HDF518_Examples.cmake file and the examples +# Configure the HDF5_Examples.cmake file and the examples #----------------------------------------------------------------------------- option (HDF5_PACK_EXAMPLES "Package the HDF5 Library Examples Compressed File" OFF) if (HDF5_PACK_EXAMPLES) diff --git a/CMakeLists.txt b/CMakeLists.txt index a16cb08..b9cdf4d 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -482,6 +482,15 @@ if (HDF5_MEMORY_ALLOC_SANITY_CHECK) endif () #----------------------------------------------------------------------------- +# Option to enable/disable using pread/pwrite for VFDs +#----------------------------------------------------------------------------- +option (HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON) +mark_as_advanced (HDF5_ENABLE_PREADWRITE) +if (HDF5_ENABLE_PREADWRITE AND H5_HAVE_PREAD AND H5_HAVE_PWRITE) + set (H5_HAVE_PREADWRITE 1) +endif () + +#----------------------------------------------------------------------------- # Option to use deprecated public API symbols #----------------------------------------------------------------------------- option (HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols" ON) @@ -749,6 +758,11 @@ if (BUILD_TESTING) "Timeout in seconds for each test (default 1200=20minutes)" ) + # Generate a list of timeouts based on DART_TESTING_TIMEOUT + math (EXPR CTEST_SHORT_TIMEOUT "${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) @@ -826,9 +840,6 @@ 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 ${CMAKE_Fortran_COMPILER_ID}") @@ -841,10 +852,8 @@ if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/for include (${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 @@ -93,6 +93,10 @@ ./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 @@ -100,6 +104,9 @@ ./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_ @@ -469,6 +476,7 @@ ./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 @@ -1074,6 +1082,7 @@ ./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 @@ -3267,7 +3276,6 @@ # CMake-specific Examples Files ./config/cmake/HDF5_Examples.cmake.in -./config/cmake/HDF518_Examples.cmake.in ./release_docs/USING_CMake_Examples.txt ./CMakeLists.txt @@ -3378,6 +3386,8 @@ ./config/cmake/scripts/CTestScript.cmake ./config/cmake/scripts/HDF5config.cmake ./config/cmake/scripts/HDF5options.cmake +./config/cmake/scripts/HPC/par-HDF5options.cmake +./config/cmake/scripts/HPC/ser-HDF5options.cmake # Files generated by autogen ./aclocal.m4 diff --git a/bin/batch/cori_ctestP.sl.in.cmake b/bin/batch/cori_ctestP.sl.in.cmake new file mode 100644 index 0000000..6aa4916 --- /dev/null +++ b/bin/batch/cori_ctestP.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -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" + diff --git a/bin/batch/cori_ctestS.sl.in.cmake b/bin/batch/cori_ctestS.sl.in.cmake new file mode 100644 index 0000000..cf68826 --- /dev/null +++ b/bin/batch/cori_ctestS.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -C Release -j 32 -T test" + +echo "Run $CMD. Test output will be in build/ctestS.out" +$CMD >& ctestS.out +echo "Done running $CMD" diff --git a/bin/batch/cori_knl_ctestP.sl.in.cmake b/bin/batch/cori_knl_ctestP.sl.in.cmake new file mode 100644 index 0000000..90dd52a --- /dev/null +++ b/bin/batch/cori_knl_ctestP.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -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" + diff --git a/bin/batch/cori_knl_ctestS.sl.in.cmake b/bin/batch/cori_knl_ctestS.sl.in.cmake new file mode 100644 index 0000000..7db4483 --- /dev/null +++ b/bin/batch/cori_knl_ctestS.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -C Release -j 32 -T test" + +echo "Run $CMD. Test output will be in build/ctestS.out" +$CMD >& ctestS.out +echo "Done running $CMD" diff --git a/bin/batch/ctestP.sl.in.cmake b/bin/batch/ctestP.sl.in.cmake index 230a642..9fed14d 100644 --- a/bin/batch/ctestP.sl.in.cmake +++ b/bin/batch/ctestP.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -E t_cache_image -C Release -T test" echo "Run $CMD. Test output will be in build/ctestP.out" $CMD >& ctestP.out diff --git a/bin/batch/ctestS.lsf.in.cmake b/bin/batch/ctestS.lsf.in.cmake index 5692574..7ef5af5 100644 --- a/bin/batch/ctestS.lsf.in.cmake +++ b/bin/batch/ctestS.lsf.in.cmake @@ -11,7 +11,7 @@ cd @HDF5_BINARY_DIR@ echo "Run command. Test output will be in build/ctestS.out" -ctest . -E 'TEST_PAR|H5DIFF|PERFORM' -C Release -j 32 -T test >& ctestS.out +ctest . -E 'TEST_PAR|PH5DIFF|PERFORM' -C Release -j 32 -T test >& ctestS.out ##$CMD >& ctestS.out echo "Done running command." diff --git a/bin/batch/ctestS.sl.in.cmake b/bin/batch/ctestS.sl.in.cmake index 9802e13..98c1bcd 100644 --- a/bin/batch/ctestS.sl.in.cmake +++ b/bin/batch/ctestS.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -C Release -j 32 -T test" echo "Run $CMD. Test output will be in build/ctestS.out" $CMD >& ctestS.out diff --git a/bin/batch/knl_ctestP.sl.in.cmake b/bin/batch/knl_ctestP.sl.in.cmake index 687804b..5c7c83f 100644 --- a/bin/batch/knl_ctestP.sl.in.cmake +++ b/bin/batch/knl_ctestP.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -E t_cache_image -C Release -T test" echo "Run $CMD. Test output will be in build/ctestP.out" $CMD >& ctestP.out diff --git a/bin/batch/knl_ctestS.sl.in.cmake b/bin/batch/knl_ctestS.sl.in.cmake index de1335c..0dae31f 100644 --- a/bin/batch/knl_ctestS.sl.in.cmake +++ b/bin/batch/knl_ctestS.sl.in.cmake @@ -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 TEST_PAR|PH5DIFF|PERFORM|ph5example -C Release -j 32 -T test" echo "Run $CMD. Test output will be in build/ctestS.out" $CMD >& ctestS.out diff --git a/bin/batch/ray_ctestP.lsf.in.cmake b/bin/batch/ray_ctestP.lsf.in.cmake new file mode 100644 index 0000000..6b5316a --- /dev/null +++ b/bin/batch/ray_ctestP.lsf.in.cmake @@ -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 $LSB_JOBID + +cd @HDF5_BINARY_DIR@ +echo "Run parallel test command. Test output will be in build/ctestP.out" +ctest . -R 'TEST_PAR|PH5DIFF|PERFORM|ph5example' -E t_cache_image -C Release -T test >& ctestP.out + +echo "Done running ctest parallel command." diff --git a/bin/batch/ray_ctestS.lsf.in.cmake b/bin/batch/ray_ctestS.lsf.in.cmake new file mode 100644 index 0000000..d23a513 --- /dev/null +++ b/bin/batch/ray_ctestS.lsf.in.cmake @@ -0,0 +1,18 @@ +#!/bin/tcsh +### LSF syntax +#BSUB -n 1 #number of nodes +#BSUB -W 29 #walltime in minutes +#BSUB -G guests #account +#BSUB -e ctestSerrors.txt #stderr +#BSUB -o ctestSoutput.txt #stdout +#BSUB -J hdf5_ctestS #job +##BSUB -q pbatch #queue to use +#BSUB -q pdebug + +cd @HDF5_BINARY_DIR@ +echo "Run command. Test output will be in build/ctestS.out" +ctest . -E 'TEST_PAR|PH5DIFF|PERFORM|ph5example' -C Release -j 32 -T test >& ctestS.out + +##$CMD >& ctestS.out +echo "Done running command." + diff --git a/bin/batch/raybsub b/bin/batch/raybsub new file mode 100755 index 0000000..19dceef --- /dev/null +++ b/bin/batch/raybsub @@ -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 diff --git a/bin/release b/bin/release index e43be17..96c2e78 100755 --- a/bin/release +++ b/bin/release @@ -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 diff --git a/c++/test/CMakeVFDTests.cmake b/c++/test/CMakeVFDTests.cmake index 996a20f..6a8ce2c 100644 --- a/c++/test/CMakeVFDTests.cmake +++ b/c++/test/CMakeVFDTests.cmake @@ -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 () diff --git a/config/cmake/CTestCustom.cmake b/config/cmake/CTestCustom.cmake index 33e6d4c..27eaa56 100644 --- a/config/cmake/CTestCustom.cmake +++ b/config/cmake/CTestCustom.cmake @@ -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 @@ -307,6 +311,11 @@ 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 ######### diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in index a740df2..273adb5 100644 --- a/config/cmake/H5pubconf.h.in +++ b/config/cmake/H5pubconf.h.in @@ -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@ diff --git a/config/cmake/HDF518_Examples.cmake.in b/config/cmake/HDF518_Examples.cmake.in deleted file mode 100644 index ba79ef2..0000000 --- a/config/cmake/HDF518_Examples.cmake.in +++ /dev/null @@ -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() diff --git a/config/cmake/HDF5Macros.cmake b/config/cmake/HDF5Macros.cmake index 6c203e2..007bc29 100644 --- a/config/cmake/HDF5Macros.cmake +++ b/config/cmake/HDF5Macros.cmake @@ -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 ${HDF5_BUILD_WITH_INSTALL_NAME} diff --git a/config/cmake/HDF5UseFortran.cmake b/config/cmake/HDF5UseFortran.cmake index a24b2e1..6b77ca4 100644 --- a/config/cmake/HDF5UseFortran.cmake +++ b/config/cmake/HDF5UseFortran.cmake @@ -57,8 +57,8 @@ endmacro () # Read source line beginning at the line matching Input:"START" and ending at the line matching Input:"END" macro (READ_SOURCE SOURCE_START SOURCE_END RETURN_VAR) - file (READ "${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 () diff --git a/config/cmake/HDF5_Examples.cmake.in b/config/cmake/HDF5_Examples.cmake.in index d30f2ab..bac174a 100644 --- a/config/cmake/HDF5_Examples.cmake.in +++ b/config/cmake/HDF5_Examples.cmake.in @@ -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() ############################################################################################################### diff --git a/config/cmake/jrunTest.cmake b/config/cmake/jrunTest.cmake index 43aef22..23f297c 100644 --- a/config/cmake/jrunTest.cmake +++ b/config/cmake/jrunTest.cmake @@ -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 (NOT str_act STREQUAL "") 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 (NOT ${str_act} STREQUAL "") 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 ${TEST_FILTER}") endif () endif () diff --git a/config/cmake/patch.xml b/config/cmake/patch.xml index 70571c5..1bdff3e 100644 --- a/config/cmake/patch.xml +++ b/config/cmake/patch.xml @@ -1,5 +1,5 @@ <CPackWiXPatch> - <CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll"> + <CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll"> <Environment Id="PATH" Name="PATH" Value="[CM_DP_libraries.bin]" @@ -7,5 +7,5 @@ Part="last" Action="set" System="yes"/> - </CPackWiXFragment> + </CPackWiXFragment> </CPackWiXPatch> diff --git a/config/cmake/scripts/CTestScript.cmake b/config/cmake/scripts/CTestScript.cmake index eb466d2..0e2afc7 100644 --- a/config/cmake/scripts/CTestScript.cmake +++ b/config/cmake/scripts/CTestScript.cmake @@ -277,7 +277,11 @@ message (STATUS "Dashboard script configuration:\n${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) diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake index dd3b17c..1d8d501 100644 --- a/config/cmake/scripts/HDF5config.cmake +++ b/config/cmake/scripts/HDF5config.cmake @@ -43,6 +43,7 @@ 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 if (DEFINED CTEST_SCRIPT_ARG) # transform ctest script arguments of the form # script.ctest,var1=value1,var2=value2 @@ -169,7 +170,10 @@ endif () ################################################################### ######### Following is for submission to CDash ############ ################################################################### -set (MODEL "Experimental") +if (NOT DEFINED MODEL) + set (MODEL "Experimental") +endif () + ################################################################### ################################################################### diff --git a/config/cmake/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake index d4cc996..45877d7 100644 --- a/config/cmake/scripts/HDF5options.cmake +++ b/config/cmake/scripts/HDF5options.cmake @@ -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 diff --git a/config/cmake/scripts/HPC/par-HDF5options.cmake b/config/cmake/scripts/HPC/par-HDF5options.cmake new file mode 100644 index 0000000..c7b22b9 --- /dev/null +++ b/config/cmake/scripts/HPC/par-HDF5options.cmake @@ -0,0 +1,126 @@ +# +# 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 "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ### +############################################################################################# + +### uncomment/comment and change the following lines for other configuration options + +############################################################################################# +#### maximum parallel processor count for build and test #### +set (MAX_PROC_COUNT 8) + +############################################################################################# +#### alternate toolsets #### +#set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 17.0") + +############################################################################################# +#### Only build static libraries #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF") +#### Add PICC option on linux/mac #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_ANSI_CFLAGS:STRING=-fPIC") + +############################################################################################# +#### fortran enabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON") +#### fortran disabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") + +############################################################################################# +#### java enabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON") +#### java disabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF") + +############################################################################################# +### change install prefix (default use INSTALLDIR value) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=${INSTALLDIR}") + +############################################################################################# +#### ext libraries #### + +### ext libs from tgz +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}") +### ext libs from git +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT") +### ext libs on system +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include") + +### disable using ext zlib +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF") +### disable using ext szip +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF") + +#### package examples #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.12.4-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}") + +############################################################################################# +### enable parallel builds + +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") + +############################################################################################# +### enable thread-safety builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=ON") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_HL_LIB:BOOL=OFF") + +############################################################################################# +### disable test program builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF") + +############################################################################################# +### disable packaging + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON") +### Create install package with external libraries (szip, zlib) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON") + + +#options to run test scripts in batch commands +set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch") +set (LOCAL_BATCH_TEST "TRUE") +set (LOCAL_BATCH_SCRIPT_NAME "ctestS.sl") +set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "ctestP.sl") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_TEST:BOOL=ON") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=ctestS.sl") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=ctestP.sl") +set (ADD_BUILD_OPTIONS "${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") + + +############################################################################################# +### use a toolchain file + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/GCC.cmake") + +#some additions and alternatives to cross compile on haswell for knl +#set (COMPILENODE_HWCOMPILE_MODULE "craype-haswell") +#set (COMPUTENODE_HWCOMPILE_MODULE "craype-mic-knl") +#set (SITE_BUILDNAME_SUFFIX "knl-intel17-SHARED" +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=knl_ctestS.sl") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=knl_ctestP.sl") +############################################################################################# diff --git a/config/cmake/scripts/HPC/ser-HDF5options.cmake b/config/cmake/scripts/HPC/ser-HDF5options.cmake new file mode 100644 index 0000000..7f2e96f --- /dev/null +++ b/config/cmake/scripts/HPC/ser-HDF5options.cmake @@ -0,0 +1,119 @@ +# +# Copyright by The HDF Group. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. +# +############################################################################################# +#### Change default configuration of options in config/cmake/cacheinit.cmake file ### +#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ### +############################################################################################# + +### uncomment/comment and change the following lines for other configuration options + +############################################################################################# +#### maximum parallel processor count for build and test #### +#set (MAX_PROC_COUNT 8) + +############################################################################################# +#### alternate toolsets #### +#set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 17.0") + +############################################################################################# +#### Only build static libraries #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF") +#### Add PICC option on linux/mac #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_ANSI_CFLAGS:STRING=-fPIC") + +############################################################################################# +#### fortran enabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON") +#### fortran disabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") + +############################################################################################# +#### java enabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON") +#### java disabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF") + +############################################################################################# +### change install prefix (default use INSTALLDIR value) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=${INSTALLDIR}") + +############################################################################################# +#### ext libraries #### + +### ext libs from tgz +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}") +### ext libs from git +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT") +### ext libs on system +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include") + +### disable using ext zlib +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF") +### disable using ext szip +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF") +#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-1.12.4-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}") + +############################################################################################# +### enable parallel builds + +#set (ADD_BUILD_OPTIONS "${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 "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF") + +############################################################################################# +### enable thread-safety builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=ON") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_HL_LIB:BOOL=OFF") + +############################################################################################# +### disable test program builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF") + +############################################################################################# +### disable packaging + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON") +### Create install package with external libraries (szip, zlib) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON") + +#options to run test scripts in batch commands +set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch") +set (LOCAL_BATCH_TEST "TRUE") +set (LOCAL_BATCH_SCRIPT_NAME "ctestS.sl") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_TEST:BOOL=ON") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=ctestS.sl") + +############################################################################################# +### use a toolchain file + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/GCC.cmake") + +#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 (SITE_BUILDNAME_SUFFIX "knl-intel17-SHARED" +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=knl_ctestS.sl") + +############################################################################################# diff --git a/config/cmake/vfdTest.cmake b/config/cmake/vfdTest.cmake index 95a4c40..b616958 100644 --- a/config/cmake/vfdTest.cmake +++ b/config/cmake/vfdTest.cmake @@ -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) diff --git a/config/cmake/volTest.cmake b/config/cmake/volTest.cmake index 27da8a5..d8c82a4 100644 --- a/config/cmake/volTest.cmake +++ b/config/cmake/volTest.cmake @@ -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) diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake index c24c1f8..986280f 100644 --- a/config/cmake_ext_mod/ConfigureChecks.cmake +++ b/config/cmake_ext_mod/ConfigureChecks.cmake @@ -274,10 +274,12 @@ if (NOT WINDOWS) # 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 - set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200112L) + set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) # Need to add this so that O_DIRECT is visible for the direct # VFD on Linux systems. @@ -506,6 +508,8 @@ 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) diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake index 147ae2f..2f4ce52 100644 --- a/config/cmake_ext_mod/HDFMacros.cmake +++ b/config/cmake_ext_mod/HDFMacros.cmake @@ -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 () diff --git a/config/cmake_ext_mod/grepTest.cmake b/config/cmake_ext_mod/grepTest.cmake index b812d73..1417204 100644 --- a/config/cmake_ext_mod/grepTest.cmake +++ b/config/cmake_ext_mod/grepTest.cmake @@ -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 () diff --git a/config/cmake_ext_mod/runTest.cmake b/config/cmake_ext_mod/runTest.cmake index 4ac1dc8..48402a2 100644 --- a/config/cmake_ext_mod/runTest.cmake +++ b/config/cmake_ext_mod/runTest.cmake @@ -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 (NOT ${TEST_FIND_RESULT} STREQUAL "0") +if (TEST_FIND_RESULT GREATER 0) string (REGEX REPLACE "^.*_pmi_alps[^\n]+\n" "" TEST_STREAM "${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 (NOT str_act STREQUAL "") 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 (NOT ${str_act} STREQUAL "") 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 ${TEST_FILTER}") endif () endif () diff --git a/config/toolchain/crayle.cmake b/config/toolchain/crayle.cmake index 47d8afc..159f43a 100644 --- a/config/toolchain/crayle.cmake +++ b/config/toolchain/crayle.cmake @@ -15,7 +15,6 @@ set(HDF5_USE_PREGEN OFF) #set(HDF5_USE_PREGEN_DIR "/lscratch1/lknox/HDF5_1_10_4/CMake-hdf5-1.10.4") # option to generate H5Tinit.c by running H5detect on knl compute node during build -set(HDF5_BATCH_H5DETECT ON) -set(HDF5_BATCH_CMD "sbatch") -set(HDF5_BATCH_H5DETECT_SCRIPT "knl_H5detect.sl") -set(MPIEXEC_EXECUTABLE "srun") +#set(HDF5_BATCH_H5DETECT ON) +#set(HDF5_BATCH_CMD "sbatch") +#set(HDF5_BATCH_H5DETECT_SCRIPT "knl_H5detect.sl") diff --git a/configure.ac b/configure.ac index 63268b1..be43eed 100644 --- a/configure.ac +++ b/configure.ac @@ -1130,11 +1130,12 @@ case "$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 $H5_CPPFLAGS" ## Need to add this so that O_DIRECT is visible for the direct ## VFD on Linux systems. @@ -3345,6 +3346,47 @@ esac ## ---------------------------------------------------------------------- +## Enable use of pread/pwrite instead of read/write in certain VFDs. +## +AC_SUBST([PREADWRITE]) + +## Check these first to avoid interspersed output in the AC_ARG_ENABLE line +## below. (Probably overkill to check for both, but we'll be extra careful) +PREADWRITE_HAVE_BOTH=yes +AC_CHECK_FUNC([pread], [], [PREADWRITE_HAVE_BOTH=no]) +AC_CHECK_FUNC([pwrite], [], [PREADWRITE_HAVE_BOTH=no]) + +AC_MSG_CHECKING([whether to use pread/pwrite instead of read/write in certain VFDs]) +AC_ARG_ENABLE([preadwrite], + [AS_HELP_STRING([--enable-preadwrite], + [Enable using pread/pwrite instead of read/write in sec2/log/core VFDs. + [default=yes if pread/pwrite are present]])], + [PREADWRITE=$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 ## AC_MSG_CHECKING([whether to have library information embedded in the executables]) diff --git a/examples/CMakeTests.cmake b/examples/CMakeTests.cmake index 6b4504b..dd1e03b 100644 --- a/examples/CMakeTests.cmake +++ b/examples/CMakeTests.cmake @@ -181,17 +181,17 @@ ### 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 EXAMPLES_PAR-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=$<TARGET_FILE:ph5example>" + -D "TEST_PROGRAM=${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 "") @@ -200,17 +200,17 @@ set (last_test "EXAMPLES_PAR-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 EXAMPLES_PAR-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=$<TARGET_FILE:ph5example-shared>" + -D "TEST_PROGRAM=${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) diff --git a/fortran/examples/CMakeTests.cmake b/fortran/examples/CMakeTests.cmake index c3d94b4..323cf91 100644 --- a/fortran/examples/CMakeTests.cmake +++ b/fortran/examples/CMakeTests.cmake @@ -109,48 +109,46 @@ foreach (example ${examples}) 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 (NOT "${last_test}" STREQUAL "") + set_tests_properties (f03_ex_${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 ${last_test}) + set_tests_properties (f03_ex-shared_${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> ${MPIEXEC_POSTFLAGS}) diff --git a/fortran/examples/run-fortran-ex.sh.in b/fortran/examples/run-fortran-ex.sh.in index da0c357..aa17f89 100644 --- a/fortran/examples/run-fortran-ex.sh.in +++ b/fortran/examples/run-fortran-ex.sh.in @@ -61,8 +61,6 @@ RunTest() ./$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 $EXIT_VALUE diff --git a/fortran/src/CMakeLists.txt b/fortran/src/CMakeLists.txt index 025fab5..f71e820 100644 --- a/fortran/src/CMakeLists.txt +++ b/fortran/src/CMakeLists.txt @@ -9,11 +9,7 @@ if (WIN32) if (NOT H5_HAVE_PARALLEL) set (H5_NOPAREXP ";") endif () - if (NOT HDF5_ENABLE_F2003) - set (H5_NOF03EXP ";") - else () - set (H5_F03EXP ";") - endif () + set (H5_F03EXP ";") configure_file (${HDF5_F90_SRC_SOURCE_DIR}/hdf5_fortrandll.def.in ${HDF5_F90_SRC_BINARY_DIR}/hdf5_fortrandll.def @ONLY) endif () endif () diff --git a/fortran/test/CMakeTests.cmake b/fortran/test/CMakeTests.cmake index 4d06359..2824ef7 100644 --- a/fortran/test/CMakeTests.cmake +++ b/fortran/test/CMakeTests.cmake @@ -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>) diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 807c613..19ca83b 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -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 diff --git a/java/src/hdf/overview.html b/java/src/hdf/overview.html index edb1b76..e3a032b 100644 --- a/java/src/hdf/overview.html +++ b/java/src/hdf/overview.html @@ -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> diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt index 26cf3ce..233c2cc 100644 --- a/release_docs/INSTALL_CMake.txt +++ b/release_docs/INSTALL_CMake.txt @@ -635,6 +635,7 @@ HDF5_ENABLE_DIRECT_VFD "Build the Direct I/O Virtual File Driver" HDF5_ENABLE_EMBEDDED_LIBINFO "embed library info into executables" ON HDF5_ENABLE_HSIZET "Enable datasets larger than memory" ON HDF5_ENABLE_PARALLEL "Enable parallel build (requires MPI)" OFF +HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON HDF5_ENABLE_TRACE "Enable API tracing capability" OFF HDF5_ENABLE_USING_MEMCHECKER "Indicate that a memory checker is used" OFF HDF5_GENERATE_HEADERS "Rebuild Generated Files" ON diff --git a/release_docs/README_HPC b/release_docs/README_HPC new file mode 100644 index 0000000..bdeab67 --- /dev/null +++ b/release_docs/README_HPC @@ -0,0 +1,79 @@ +HDF5 version 1.11.4 currently under development + +HDF5 source tar files with the HPC prefix are intended for use on clusters where +configuration and build steps will be done on a login node and executable and +lib files that are built will be run on compute nodes. + +Note these differences from the regular CMake tar and zip files: + - Test programs produced by this tar file will be run using batch scripts. + - Serial and parallel HDF5options.cmake files, using parallel options by default. + +Note also that options are now available in HDF5 source to facilitate use of +toolchain files for using cross compilers available on login nodes to compile +HDF5 for compute nodes. + +Instructions to configure build and test HDF5 using CMake: + +1. The cmake version must be 3.10 or later (cmake --version). +2. Load or switch modules and set CC, FC, CXX for compilers desired. +3. run build-unix.sh to configure, build, test and package HDF5 with CMake. + +Contents: + +build-unix.sh Simple script for running CMake to configure, build, + test, and package HDF5. +CTestScript.cmake CMake script to configure, build, test and package + HDF5. +hdf5-<version> HDF5 source for <version>. +HDF5config.cmake CMake script to configure, build, test and package + HDF5. +HDF5Examples Source for HDF5 Examples. +HDF5options.cmake symlink to parallel or serial HDF5options.cmake files. + Default is parallel file, which builds and tests both + serial and parallel C and Fortran wrappers. + To build serial only, C Fortran and C++ wrappers, delete + The HDF5options.cmake link and run + 'ln -s ser-HDF5options.cmake HDF5options.cmake' to switch. +par-HDF5options.cmake Options file for HDF5 serial and parallel build and test. +ser-HDF5options.cmake Options file for HDF5 serial only build and test. +SZip.tar.gz Source for building SZip. +ZLib.tar.gz Source for buildng Zlib. + + +To cross compile with this HPC-CMake tar.gz HDF5 source file: +On Cray XC40 haswell login node for knl compute nodes using CMake and Cray modules: + 1. Uncomment line in HDF5options.txt to use a toolchain file - line 106 for + config/toolchain/crayle.cmake. + 2. Uncomment lines 110, 111, and 115 - 122 of HDF5options.cmake. + Line 110 allows configuring to complete on the haswell node. + Line 111 switches the compiler to build files for knl nodes. + Lines 115 - 122 set up test files to use sbatch to run build tests + in batch jobs on a knl compute node with 6 processes. + 3. Compiler module may be the default PrgEnv-intel/6.0.4 to use + intel/18.0.2 or other intel, PrgEnv-cray/6.0.4 to use cce/8.7.4, + or PrgEnv-gnu/6.0.4 for GCC compilers. PrgEnv-pgi/6.0.4 is also + available but has not been tested with this tar file. + 4. These CMake options are set in config/toolchain/crayle.cmake: + set(CMAKE_SYSTEM_NAME Linux) + set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment") + set(CMAKE_C_COMPILER cc) + set(CMAKE_CXX_COMPILER c++) + set(CMAKE_Fortran_COMPILER ftn) + set(CMAKE_CROSSCOMPILING_EMULATOR "") + + 5. Settings for two other cross-compiling options are also in the + config/toolchain files which do not seem to be necessary with the + Cray PrgEnv-* modules + a. HDF5_USE_PREGEN. This option, along with the HDF5_USE_PREGEN_DIR + CMake variable would allow the use of an appropriate H5Tinit.c + file with type information generated on a compute node to be used + when cross compiling for those compute nodes. The use of the + variables in lines 110 and 111 of HDF5options.cmake file seem to + preclude needing this option with the available Cray modules and + CMake options. + b. HDF5_BATCH_H5DETECT and associated CMake variables. This option + when properly configured will run H5detect in a batch job on a + compute node at the beginning of the CMake build process. It + was also found to be unnecessary with the available Cray modules + and CMake options. +- diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 2dfcfc1..ef3bda0 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -264,6 +264,22 @@ Bug Fixes since HDF5-1.10.3 release Library ------- + - Performance issue when closing an object + + The slow down is due to the search of the "tag_list" to find + out the "corked" status of an object and "uncork" it if so. + + Improve porformance by skipping the search of the "tag_list" + if there are no "corked" objects when closing an object. + + (VC - 2019/2/6) + + - Fixed a potential invalid memory access and failure that could occur when + decoding an unknown object header message (from a future version of the + library). + + (NAF - 2019/01/07) + - Deleting attributes in dense storage The library aborts with "infinite loop closing library" after @@ -395,6 +411,11 @@ Bug Fixes since HDF5-1.10.3 release Testing ------- + - Fixed a test failure in testpar/t_dset.c caused by + the test trying to use the parallel filters feature + on MPI-2 implementations. + + (JTH, 2019/2/7) Bug Fixes since HDF5-1.10.2 release ================================== @@ -637,6 +658,15 @@ Bug Fixes since HDF5-1.10.2 release Testing ------- + - The dt_arith test failed on IBM Power8 and Power9 machines when testing + conversions from or to long double types, especially when special values + such as infinity or NAN were involved. In some cases the results differed + by extremely small amounts from those on other machines, while some other + tests resulted in segmentation faults. These conversion tests with long + double types have been disabled for ppc64 machines until the problems are + better understood and can be properly addressed. + + (SRL - 2019/01/07, TRILAB-98) Supported Platforms =================== diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index ff7402b..6b105a9 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -944,6 +944,12 @@ if (BUILD_SHARED_LIBS) endif () if (LOCAL_BATCH_TEST) + if ("${LOCAL_BATCH_SCRIPT_COMMAND}" STREQUAL "raybsub") + configure_file ( + ${HDF5_SOURCE_DIR}/bin/batch/${LOCAL_BATCH_SCRIPT_COMMAND} + ${HDF5_BINARY_DIR}/${LOCAL_BATCH_SCRIPT_COMMAND} ESCAPE_QUOTES @ONLY + ) + endif () if (LOCAL_BATCH_SCRIPT_NAME) configure_file ( ${HDF5_SOURCE_DIR}/bin/batch/${LOCAL_BATCH_SCRIPT_NAME}.in.cmake @@ -1612,7 +1612,7 @@ H5AC_unprotect(H5F_t *f, const H5AC_class_t *type, haddr_t addr, void *thing, done: /* If currently logging, generate a message */ if(f->shared->cache->log_info->logging) - if(H5C_log_write_unprotect_entry_msg(f->shared->cache, (H5AC_info_t *)thing, type->id, flags, ret_value) < 0) + if(H5C_log_write_unprotect_entry_msg(f->shared->cache, addr, type->id, flags, ret_value) < 0) HDONE_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "unable to emit log message") FUNC_LEAVE_NOAPI(ret_value) @@ -2403,8 +2403,18 @@ H5AC_cork(H5F_t *f, haddr_t obj_addr, unsigned action, hbool_t *corked) HDassert(H5F_addr_defined(obj_addr)); HDassert(action == H5AC__SET_CORK || action == H5AC__UNCORK || action == H5AC__GET_CORKED); - if(action == H5AC__GET_CORKED) - HDassert(corked); + /* Skip the search on "tag_list" when there are no "corked" objects. + * This is done to mitigate the slow down when closing objects. + * Re-visit this optimization when we optimize tag info management + * in the future. + */ + if(action == H5AC__GET_CORKED) { + HDassert(corked); + if(H5C_get_num_objs_corked(f->shared->cache) == 0) { + *corked = FALSE; + HGOTO_DONE(SUCCEED) + } + } if(H5C_cork(f->shared->cache, obj_addr, action, corked) < 0) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Cannot perform the cork action") @@ -327,6 +327,7 @@ H5C_create(size_t max_cache_size, /* Tagging Field Initializations */ cache_ptr->ignore_tags = FALSE; + cache_ptr->num_objs_corked = 0; cache_ptr->slist_changed = FALSE; cache_ptr->slist_len = 0; @@ -7729,6 +7730,8 @@ H5C_cork(H5C_t *cache_ptr, haddr_t obj_addr, unsigned action, hbool_t *corked) /* Set the corked status for the entire object */ tag_info->corked = TRUE; + cache_ptr->num_objs_corked++; + } /* end if */ else { /* Sanity check */ @@ -7740,6 +7743,7 @@ H5C_cork(H5C_t *cache_ptr, haddr_t obj_addr, unsigned action, hbool_t *corked) /* Set the corked status for the entire object */ tag_info->corked = FALSE; + cache_ptr->num_objs_corked--; /* Remove the tag info from the tag list, if there's no more entries with this tag */ if(0 == tag_info->entry_cnt) { diff --git a/src/H5Clog.c b/src/H5Clog.c index 0ae7f13..cf9b7e8 100644 --- a/src/H5Clog.c +++ b/src/H5Clog.c @@ -887,7 +887,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, +H5C_log_write_unprotect_entry_msg(H5C_t *cache, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value) { herr_t ret_value = SUCCEED; @@ -898,9 +898,8 @@ H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, HDassert(cache); /* Write a log message */ - HDassert(entry); if(cache->log_info->cls->write_unprotect_entry_log_msg) - if(cache->log_info->cls->write_unprotect_entry_log_msg(cache->log_info->udata, entry, type_id, flags, fxn_ret_value) < 0) + if(cache->log_info->cls->write_unprotect_entry_log_msg(cache->log_info->udata, address, type_id, flags, fxn_ret_value) < 0) HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "log-specific unprotect entry call failed") done: diff --git a/src/H5Clog.h b/src/H5Clog.h index 9ba6786..0235c4a 100644 --- a/src/H5Clog.h +++ b/src/H5Clog.h @@ -59,7 +59,7 @@ typedef struct H5C_log_class_t { herr_t (*write_resize_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); herr_t (*write_unpin_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); herr_t (*write_destroy_fd_log_msg)(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); - herr_t (*write_unprotect_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); + herr_t (*write_unprotect_entry_log_msg)(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); herr_t (*write_set_cache_config_log_msg)(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value); herr_t (*write_remove_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); @@ -102,7 +102,7 @@ H5_DLL herr_t H5C_log_write_protect_entry_msg(H5C_t *cache, const H5C_cache_entr H5_DLL herr_t H5C_log_write_resize_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_unpin_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_destroy_fd_msg(H5C_t *cache, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); -H5_DLL herr_t H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); +H5_DLL herr_t H5C_log_write_unprotect_entry_msg(H5C_t *cache, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_set_cache_config_msg(H5C_t *cache, const H5AC_cache_config_t *config, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_remove_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); diff --git a/src/H5Clog_json.c b/src/H5Clog_json.c index ccfa222..dd9e9b2 100644 --- a/src/H5Clog_json.c +++ b/src/H5Clog_json.c @@ -41,7 +41,7 @@ /****************/ /* Max log message size */ -#define H5C_MAX_JSON_LOG_MSG_SIZE 128 +#define H5C_MAX_JSON_LOG_MSG_SIZE 1024 /******************/ @@ -87,7 +87,7 @@ static herr_t H5C__json_write_protect_entry_log_msg(void *udata, const H5C_cache static herr_t H5C__json_write_resize_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); static herr_t H5C__json_write_unpin_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); static herr_t H5C__json_write_destroy_fd_log_msg(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); -static herr_t H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); +static herr_t H5C__json_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); static herr_t H5C__json_write_set_cache_config_log_msg(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value); static herr_t H5C__json_write_remove_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); @@ -1232,7 +1232,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, +H5C__json_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value) { H5C_log_json_udata_t *json_udata = (H5C_log_json_udata_t *)(udata); @@ -1243,7 +1243,6 @@ H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *en /* Sanity checks */ HDassert(json_udata); HDassert(json_udata->message); - HDassert(entry); /* Create the log message string */ HDsnprintf(json_udata->message, H5C_MAX_JSON_LOG_MSG_SIZE, @@ -1257,7 +1256,7 @@ H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *en \"returned\":%d\ },\n\ " - , (long long)HDtime(NULL), (unsigned long)entry->addr, + , (long long)HDtime(NULL), (unsigned long)address, type_id, flags, (int)fxn_ret_value); /* Write the log message to the file */ diff --git a/src/H5Clog_trace.c b/src/H5Clog_trace.c index f7d6889..7c1305c 100644 --- a/src/H5Clog_trace.c +++ b/src/H5Clog_trace.c @@ -82,7 +82,7 @@ static herr_t H5C__trace_write_protect_entry_log_msg(void *udata, const H5C_cach static herr_t H5C__trace_write_resize_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); static herr_t H5C__trace_write_unpin_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); static herr_t H5C__trace_write_destroy_fd_log_msg(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); -static herr_t H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); +static herr_t H5C__trace_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); static herr_t H5C__trace_write_set_cache_config_log_msg(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value); static herr_t H5C__trace_write_remove_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); @@ -872,7 +872,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, +H5C__trace_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value) { H5C_log_trace_udata_t *trace_udata = (H5C_log_trace_udata_t *)(udata); @@ -883,11 +883,10 @@ H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *e /* Sanity checks */ HDassert(trace_udata); HDassert(trace_udata->message); - HDassert(entry); /* Create the log message string */ HDsnprintf(trace_udata->message, H5C_MAX_TRACE_LOG_MSG_SIZE, "H5AC_unprotect 0x%lx %d 0x%x %d\n", - (unsigned long)(entry->addr), type_id, flags, (int)fxn_ret_value); + (unsigned long)(address), type_id, flags, (int)fxn_ret_value); /* Write the log message to the file */ if(H5C__trace_write_log_message(trace_udata) < 0) diff --git a/src/H5Cpkg.h b/src/H5Cpkg.h index 9201afb..9156c0d 100644 --- a/src/H5Cpkg.h +++ b/src/H5Cpkg.h @@ -3823,6 +3823,13 @@ typedef struct H5C_tag_info_t { * * ignore_tags: Boolean flag to disable tag validation during entry insertion. * + * num_objs_corked: Unsigned integer field containing the number of objects + * that are "corked". The "corked" status of an object is + * found by searching the "tag_list". This field is added + * for optimization so that the skip list search on "tag_list" + * can be skipped if this field is zero, i.e. no "corked" + * objects. + * * When a cache entry is protected, it must be removed from the LRU * list(s) as it cannot be either flushed or evicted until it is unprotected. * The following fields are used to implement the protected list (pl). @@ -4693,6 +4700,7 @@ struct H5C_t { /* Fields for maintaining list of tagged entries */ H5SL_t * tag_list; hbool_t ignore_tags; + uint32_t num_objs_corked; /* Fields for tracking protected entries */ uint32_t pl_len; diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h index c39c1df..d4ed6fc 100644 --- a/src/H5Cprivate.h +++ b/src/H5Cprivate.h @@ -2301,6 +2301,7 @@ H5_DLL herr_t H5C_validate_resize_config(H5C_auto_size_ctl_t *config_ptr, unsigned int tests); H5_DLL herr_t H5C_ignore_tags(H5C_t *cache_ptr); H5_DLL hbool_t H5C_get_ignore_tags(const H5C_t *cache_ptr); +H5_DLL uint32_t H5C_get_num_objs_corked(const H5C_t *cache_ptr); H5_DLL herr_t H5C_retag_entries(H5C_t * cache_ptr, haddr_t src_tag, haddr_t dest_tag); H5_DLL herr_t H5C_cork(H5C_t *cache_ptr, haddr_t obj_addr, unsigned action, hbool_t *corked); H5_DLL herr_t H5C_get_entry_ring(const H5F_t *f, haddr_t addr, H5C_ring_t *ring); diff --git a/src/H5Ctag.c b/src/H5Ctag.c index 0f08ede..807e68d 100644 --- a/src/H5Ctag.c +++ b/src/H5Ctag.c @@ -175,6 +175,32 @@ H5C_get_ignore_tags(const H5C_t *cache_ptr) /*------------------------------------------------------------------------- * + * Function: H5C_get_num_objs_corked + * + * Purpose: Retrieve the 'num_objs_corked' field for the cache + * + * Return: 'num_objs_corked' value (can't fail) + * + * Programmer: Vailin Choi; Feb 2019 + * + *------------------------------------------------------------------------- + */ +uint32_t +H5C_get_num_objs_corked(const H5C_t *cache_ptr) +{ + FUNC_ENTER_NOAPI_NOERR + + /* Sanity checks */ + HDassert(cache_ptr); + HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); + + /* Return value for num_objs_corked */ + FUNC_LEAVE_NOAPI(cache_ptr->num_objs_corked) +} /* H5C_get_num_objs_corked */ + + +/*------------------------------------------------------------------------- + * * Function: H5C__tag_entry * * Purpose: Tags an entry with the provided tag (contained in the API context). diff --git a/src/H5Dio.c b/src/H5Dio.c index 607bfcf..2f87e38 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -1031,16 +1031,13 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, if(type_info->request_nelmts == 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small") - /* - * Get a temporary buffer for type conversion unless the app has already + /* Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a - * buffer which is the exact size, we allocate the target size. The - * malloc() is usually less resource-intensive if we allocate/free the - * same size over and over. + * buffer which is the exact size, we allocate the target size. */ if(NULL == (type_info->tconv_buf = (uint8_t *)tconv_buf)) { /* Allocate temporary buffer */ - if(NULL == (type_info->tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size))) + if(NULL == (type_info->tconv_buf = H5FL_BLK_CALLOC(type_conv, target_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion") type_info->tconv_buf_allocated = TRUE; } /* end if */ @@ -1484,7 +1484,7 @@ done: * * Purpose: Prints the error stack in some default way. This is just a * convenience function for H5Ewalk() with a function that - * prints error messages. Users are encouraged to write there + * prints error messages. Users are encouraged to write their * own more specific error handlers. * * Return: SUCCEED/FAIL @@ -1566,8 +1566,8 @@ H5Ewalk2(hid_t err_stack, H5E_direction_t direction, H5E_walk2_t stack_func, voi /* Walk the error stack */ op.vers = 2; op.u.func2 = stack_func; - if(H5E__walk(estack, direction, &op, client_data) < 0) - HGOTO_ERROR(H5E_ERROR, H5E_CANTLIST, FAIL, "can't walk error stack") + if((ret_value = H5E__walk(estack, direction, &op, client_data)) < 0) + HERROR(H5E_ERROR, H5E_CANTLIST, "can't walk error stack"); done: FUNC_LEAVE_API(ret_value) diff --git a/src/H5Eint.c b/src/H5Eint.c index 540c9b1..66653ca 100644 --- a/src/H5Eint.c +++ b/src/H5Eint.c @@ -422,7 +422,7 @@ done: * Purpose: Private function to print the error stack in some default * way. This is just a convenience function for H5Ewalk() and * H5Ewalk2() with a function that prints error messages. - * Users are encouraged to write there own more specific error + * Users are encouraged to write their own more specific error * handlers. * * Return: SUCCEED/FAIL @@ -511,10 +511,9 @@ H5E__walk(const H5E_t *estack, H5E_direction_t direction, const H5E_walk_op_t *o void *client_data) { int i; /* Local index variable */ - herr_t status; /* Status from callback function */ - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = H5_ITER_CONT; /* Return value */ - FUNC_ENTER_PACKAGE + FUNC_ENTER_PACKAGE_NOERR /* Sanity check */ HDassert(estack); @@ -530,9 +529,9 @@ H5E__walk(const H5E_t *estack, H5E_direction_t direction, const H5E_walk_op_t *o if(op->u.func1) { H5E_error1_t old_err; - status = SUCCEED; + ret_value = SUCCEED; if(H5E_WALK_UPWARD == direction) { - for(i = 0; i < (int)estack->nused && status >= 0; i++) { + for(i = 0; i < (int)estack->nused && ret_value == H5_ITER_CONT; i++) { /* Point to each error record on the stack and pass it to callback function.*/ old_err.maj_num = estack->slot[i].maj_num; old_err.min_num = estack->slot[i].min_num; @@ -541,12 +540,12 @@ H5E__walk(const H5E_t *estack, H5E_direction_t direction, const H5E_walk_op_t *o old_err.desc = estack->slot[i].desc; old_err.line = estack->slot[i].line; - status = (op->u.func1)(i, &old_err, client_data); + ret_value = (op->u.func1)(i, &old_err, client_data); } /* end for */ } /* end if */ else { H5_CHECK_OVERFLOW(estack->nused - 1, size_t, int); - for(i = (int)(estack->nused - 1); i >= 0 && status >= 0; i--) { + for(i = (int)(estack->nused - 1); i >= 0 && ret_value == H5_ITER_CONT; i--) { /* Point to each error record on the stack and pass it to callback function.*/ old_err.maj_num = estack->slot[i].maj_num; old_err.min_num = estack->slot[i].min_num; @@ -555,12 +554,12 @@ H5E__walk(const H5E_t *estack, H5E_direction_t direction, const H5E_walk_op_t *o old_err.desc = estack->slot[i].desc; old_err.line = estack->slot[i].line; - status = (op->u.func1)((int)(estack->nused - (size_t)(i + 1)), &old_err, client_data); + ret_value = (op->u.func1)((int)(estack->nused - (size_t)(i + 1)), &old_err, client_data); } /* end for */ } /* end else */ - if(status < 0) - HGOTO_ERROR(H5E_ERROR, H5E_CANTLIST, FAIL, "can't walk error stack") + if(ret_value < 0) + HERROR(H5E_ERROR, H5E_CANTLIST, "can't walk error stack"); } /* end if */ #else /* H5_NO_DEPRECATED_SYMBOLS */ HDassert(0 && "version 1 error stack walk without deprecated symbols!"); @@ -569,23 +568,22 @@ H5E__walk(const H5E_t *estack, H5E_direction_t direction, const H5E_walk_op_t *o else { HDassert(op->vers == 2); if(op->u.func2) { - status = SUCCEED; + ret_value = SUCCEED; if(H5E_WALK_UPWARD == direction) { - for(i = 0; i < (int)estack->nused && status >= 0; i++) - status = (op->u.func2)((unsigned)i, estack->slot + i, client_data); + for(i = 0; i < (int)estack->nused && ret_value == H5_ITER_CONT; i++) + ret_value = (op->u.func2)((unsigned)i, estack->slot + i, client_data); } /* end if */ else { H5_CHECK_OVERFLOW(estack->nused - 1, size_t, int); - for(i = (int)(estack->nused - 1); i >= 0 && status >= 0; i--) - status = (op->u.func2)((unsigned)(estack->nused - (size_t)(i + 1)), estack->slot + i, client_data); + for(i = (int)(estack->nused - 1); i >= 0 && ret_value == H5_ITER_CONT; i--) + ret_value = (op->u.func2)((unsigned)(estack->nused - (size_t)(i + 1)), estack->slot + i, client_data); } /* end else */ - if(status < 0) - HGOTO_ERROR(H5E_ERROR, H5E_CANTLIST, FAIL, "can't walk error stack") + if(ret_value < 0) + HERROR(H5E_ERROR, H5E_CANTLIST, "can't walk error stack"); } /* end if */ } /* end else */ -done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5E__walk() */ diff --git a/src/H5FDcore.c b/src/H5FDcore.c index ed05e95..d1a17cd 100644 --- a/src/H5FDcore.c +++ b/src/H5FDcore.c @@ -348,14 +348,17 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size) HDassert(file); - /* Write to backing store */ - if((off_t)addr != HDlseek(file->fd, (off_t)addr, SEEK_SET)) +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pwrite) */ + if((HDoff_t)addr != HDlseek(file->fd, (off_t)addr, SEEK_SET)) HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "error seeking in backing store") +#endif /* H5_HAVE_PREADWRITE */ while (size > 0) { h5_posix_io_t bytes_in = 0; /* # of bytes to write */ h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */ + HDoff_t offset = (HDoff_t)addr; /* Trying to write more bytes than the return type can handle is * undefined behavior in POSIX. @@ -366,15 +369,21 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size) bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_wrote = HDpwrite(file->fd, ptr, bytes_in, offset); + offset += bytes_wrote; +#else bytes_wrote = HDwrite(file->fd, ptr, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_wrote && EINTR == errno); if(-1 == bytes_wrote) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset); } /* end if */ HDassert(bytes_wrote > 0); @@ -852,6 +861,7 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr while(size > 0) { h5_posix_io_t bytes_in = 0; /* # of bytes to read */ h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + HDoff_t offset = (HDoff_t)0; /* Trying to read more bytes than the return type can handle is * undefined behavior in POSIX. @@ -862,15 +872,21 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_read = HDpread(file->fd, mem, bytes_in, offset); + offset += bytes_read; +#else bytes_read = HDread(file->fd, mem, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_read && EINTR == errno); if(-1 == bytes_read) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset); } /* end if */ HDassert(bytes_read >= 0); diff --git a/src/H5FDlog.c b/src/H5FDlog.c index 97d1b41..655d7d3 100644 --- a/src/H5FDlog.c +++ b/src/H5FDlog.c @@ -1191,7 +1191,8 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd } /* end if */ } /* end if */ - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pread) */ if(addr != file->pos || OP_READ != file->op) { #ifdef H5_HAVE_GETTIMEOFDAY if(file->fa.flags & H5FD_LOG_TIME_SEEK) @@ -1234,6 +1235,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd #endif /* H5_HAVE_GETTIMEOFDAY */ } /* end if */ } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* * Read data, being careful of interrupted system calls, partial results, @@ -1247,6 +1249,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd h5_posix_io_t bytes_in = 0; /* # of bytes to read */ h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + HDoff_t offset = (HDoff_t)addr; /* Trying to read more bytes than the return type can handle is * undefined behavior in POSIX. @@ -1257,18 +1260,24 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_read = HDpread(file->fd, buf, bytes_in, offset); + offset += bytes_read; +#else bytes_read = HDread(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_read && EINTR == errno); if(-1 == bytes_read) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); if(file->fa.flags & H5FD_LOG_LOC_READ) HDfprintf(file->logfp, "Error! Reading: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size); - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset); } /* end if */ if(0 == bytes_read) { @@ -1398,7 +1407,8 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had file->nwrite[tmp_addr++]++; } /* end if */ - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pwrite) */ if(addr != file->pos || OP_WRITE != file->op) { #ifdef H5_HAVE_GETTIMEOFDAY if(file->fa.flags & H5FD_LOG_TIME_SEEK) @@ -1441,6 +1451,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had #endif /* H5_HAVE_GETTIMEOFDAY */ } /* end if */ } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* * Write the data, being careful of interrupted system calls and partial @@ -1454,6 +1465,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had h5_posix_io_t bytes_in = 0; /* # of bytes to write */ h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */ + HDoff_t offset = (HDoff_t)addr; /* Trying to write more bytes than the return type can handle is * undefined behavior in POSIX. @@ -1464,18 +1476,24 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset); + offset += bytes_wrote; +#else bytes_wrote = HDwrite(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_wrote && EINTR == errno); if(-1 == bytes_wrote) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); if(file->fa.flags & H5FD_LOG_LOC_WRITE) HDfprintf(file->logfp, "Error! Writing: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size); - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset); } /* end if */ HDassert(bytes_wrote > 0); diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c index c507387..0054a86 100644 --- a/src/H5FDsec2.c +++ b/src/H5FDsec2.c @@ -682,11 +682,13 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS if(REGION_OVERFLOW(addr, size)) HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu", (unsigned long long)addr) - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pread) */ if(addr != file->pos || OP_READ != file->op) { if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0) HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* Read data, being careful of interrupted system calls, partial results, * and the end of the file. @@ -694,7 +696,8 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS while(size > 0) { h5_posix_io_t bytes_in = 0; /* # of bytes to read */ - h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + HDoff_t offset = (HDoff_t)addr; /* Trying to read more bytes than the return type can handle is * undefined behavior in POSIX. @@ -705,15 +708,21 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_read = HDpread(file->fd, buf, bytes_in, offset); + offset += bytes_read; +#else bytes_read = HDread(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_read && EINTR == errno); if(-1 == bytes_read) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset); } /* end if */ if(0 == bytes_read) { @@ -777,11 +786,13 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if(REGION_OVERFLOW(addr, size)) HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu, size = %llu", (unsigned long long)addr, (unsigned long long)size) - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pwrite) */ if(addr != file->pos || OP_WRITE != file->op) { if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0) HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* Write the data, being careful of interrupted system calls and partial * results @@ -790,6 +801,7 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU h5_posix_io_t bytes_in = 0; /* # of bytes to write */ h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */ + HDoff_t offset = (HDoff_t)addr; /* Trying to write more bytes than the return type can handle is * undefined behavior in POSIX. @@ -800,15 +812,21 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset); + offset += bytes_wrote; +#else bytes_wrote = HDwrite(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_wrote && EINTR == errno); if(-1 == bytes_wrote) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset); } /* end if */ HDassert(bytes_wrote > 0); diff --git a/src/H5Oattr.c b/src/H5Oattr.c index c93bf32..c420046 100644 --- a/src/H5Oattr.c +++ b/src/H5Oattr.c @@ -176,7 +176,12 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, /* Decode and store the name */ if(NULL == (attr->shared->name = H5MM_strdup((const char *)p))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Make an attempt to detect corrupted name or name length - HDFFV-10588 */ + if(name_len != (HDstrlen(attr->shared->name) + 1)) + HGOTO_ERROR(H5E_ATTR, H5E_CANTDECODE, NULL, "attribute name has different length than stored length") + if(attr->shared->version < H5O_ATTR_VERSION_2) p += H5O_ALIGN_OLD(name_len); /* advance the memory pointer */ else diff --git a/src/H5VLcallback.c b/src/H5VLcallback.c index 811162d..2d6ac33 100644 --- a/src/H5VLcallback.c +++ b/src/H5VLcallback.c @@ -829,7 +829,8 @@ done: *------------------------------------------------------------------------- */ void * -H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, void *obj) +H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, void *obj, + H5I_type_t obj_type) { void *ret_value = SUCCEED; /* Return value */ @@ -842,7 +843,7 @@ H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, void *obj) /* Only wrap object if there's a wrap context */ if(wrap_ctx) { /* Ask the connector to wrap the object */ - if(NULL == (ret_value = (connector->wrap_object)(obj, wrap_ctx))) + if(NULL == (ret_value = (connector->wrap_object)(obj, obj_type, wrap_ctx))) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, NULL, "can't wrap object") } /* end if */ else @@ -864,13 +865,13 @@ done: *--------------------------------------------------------------------------- */ void * -H5VLwrap_object(void *obj, hid_t connector_id, void *wrap_ctx) +H5VLwrap_object(void *obj, H5I_type_t obj_type, hid_t connector_id, void *wrap_ctx) { H5VL_class_t *cls; /* VOL connector's class struct */ void *ret_value = NULL; /* Return value */ FUNC_ENTER_API_NOINIT - H5TRACE3("*x", "*xi*x", obj, connector_id, wrap_ctx); + H5TRACE4("*x", "*xIti*x", obj, obj_type, connector_id, wrap_ctx); /* Check args and get class pointer */ if(NULL == obj) @@ -879,7 +880,7 @@ H5VLwrap_object(void *obj, hid_t connector_id, void *wrap_ctx) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a VOL connector ID") /* Wrap the object */ - if(NULL == (ret_value = H5VL_wrap_object(cls, wrap_ctx, obj))) + if(NULL == (ret_value = H5VL_wrap_object(cls, wrap_ctx, obj, obj_type))) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, NULL, "unable to wrap object") done: diff --git a/src/H5VLint.c b/src/H5VLint.c index bdb2908..f22fdb6 100644 --- a/src/H5VLint.c +++ b/src/H5VLint.c @@ -65,7 +65,7 @@ typedef struct H5VL_wrap_ctx_t { /* Local Prototypes */ /********************/ static herr_t H5VL__free_cls(H5VL_class_t *cls); -static void *H5VL__wrap_obj(void *obj); +static void *H5VL__wrap_obj(void *obj, H5I_type_t obj_type); static H5VL_object_t *H5VL__new_vol_obj(H5I_type_t type, void *object, H5VL_t *vol_connector, hbool_t wrap_obj); static void *H5VL__object(hid_t id, H5I_type_t obj_type); @@ -248,7 +248,7 @@ done: *------------------------------------------------------------------------- */ static void * -H5VL__wrap_obj(void *obj) +H5VL__wrap_obj(void *obj, H5I_type_t obj_type) { H5VL_wrap_ctx_t *vol_wrap_ctx = NULL; /* Object wrapping context */ void *ret_value = NULL; /* Return value */ @@ -265,7 +265,7 @@ H5VL__wrap_obj(void *obj) /* If there is a VOL object wrapping context, wrap the object */ if(vol_wrap_ctx) { /* Wrap object, using the VOL callback */ - if(NULL == (ret_value = H5VL_wrap_object(vol_wrap_ctx->connector->cls, vol_wrap_ctx->obj_wrap_ctx, obj))) + if(NULL == (ret_value = H5VL_wrap_object(vol_wrap_ctx->connector->cls, vol_wrap_ctx->obj_wrap_ctx, obj, obj_type))) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, NULL, "can't wrap object") } /* end if */ else @@ -310,7 +310,7 @@ H5VL__new_vol_obj(H5I_type_t type, void *object, H5VL_t *vol_connector, hbool_t HGOTO_ERROR(H5E_VOL, H5E_CANTALLOC, NULL, "can't allocate memory for VOL object") new_vol_obj->connector = vol_connector; if(wrap_obj) { - if(NULL == (new_vol_obj->data = H5VL__wrap_obj(object))) + if(NULL == (new_vol_obj->data = H5VL__wrap_obj(object, type))) HGOTO_ERROR(H5E_VOL, H5E_CANTCREATE, NULL, "can't wrap library object") } /* end if */ else @@ -1099,7 +1099,7 @@ H5VL_wrap_register(H5I_type_t type, void *obj, hbool_t app_ref) HGOTO_ERROR(H5E_VOL, H5E_BADTYPE, H5I_INVALID_HID, "can't wrap an uncommitted datatype") /* Wrap the object with VOL connector info */ - if(NULL == (new_obj = H5VL__wrap_obj(obj))) + if(NULL == (new_obj = H5VL__wrap_obj(obj, type))) HGOTO_ERROR(H5E_VOL, H5E_CANTCREATE, H5I_INVALID_HID, "can't wrap library object") /* Retrieve the VOL object wrapping context */ diff --git a/src/H5VLpassthru.c b/src/H5VLpassthru.c index 13d8d8e..f7f9058 100644 --- a/src/H5VLpassthru.c +++ b/src/H5VLpassthru.c @@ -90,7 +90,8 @@ static herr_t H5VL_pass_through_str_to_info(const char *str, void **info); static void *H5VL_pass_through_get_object(const void *obj); static herr_t H5VL_pass_through_get_wrap_ctx(const void *obj, void **wrap_ctx); static herr_t H5VL_pass_through_free_wrap_ctx(void *obj); -static void *H5VL_pass_through_wrap_object(void *obj, void *wrap_ctx); +static void *H5VL_pass_through_wrap_object(void *obj, H5I_type_t obj_type, + void *wrap_ctx); /* Attribute callbacks */ static void *H5VL_pass_through_attr_create(void *obj, const H5VL_loc_params_t *loc_params, const char *name, hid_t acpl_id, hid_t aapl_id, hid_t dxpl_id, void **req); @@ -660,7 +661,7 @@ H5VL_pass_through_get_wrap_ctx(const void *obj, void **wrap_ctx) *--------------------------------------------------------------------------- */ static void * -H5VL_pass_through_wrap_object(void *obj, void *_wrap_ctx) +H5VL_pass_through_wrap_object(void *obj, H5I_type_t obj_type, void *_wrap_ctx) { H5VL_pass_through_wrap_ctx_t *wrap_ctx = (H5VL_pass_through_wrap_ctx_t *)_wrap_ctx; H5VL_pass_through_t *new_obj; @@ -671,7 +672,7 @@ H5VL_pass_through_wrap_object(void *obj, void *_wrap_ctx) #endif /* Wrap the object with the underlying VOL */ - under = H5VLwrap_object(obj, wrap_ctx->under_vol_id, wrap_ctx->under_wrap_ctx); + under = H5VLwrap_object(obj, obj_type, wrap_ctx->under_vol_id, wrap_ctx->under_wrap_ctx); if(under) new_obj = H5VL_pass_through_new_obj(under, wrap_ctx->under_vol_id); else diff --git a/src/H5VLprivate.h b/src/H5VLprivate.h index ef5a81e..283c77a 100644 --- a/src/H5VLprivate.h +++ b/src/H5VLprivate.h @@ -95,7 +95,7 @@ H5_DLL herr_t H5VL_free_wrap_ctx(const H5VL_class_t *connector, void *wrap_ctx); H5_DLL herr_t H5VL_set_vol_wrapper(void *obj, const H5VL_t *vol_connector); H5_DLL herr_t H5VL_reset_vol_wrapper(void); H5_DLL void * H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, - void *obj); + void *obj, H5I_type_t obj_type); /* ID registration functions */ H5_DLL hid_t H5VL_register(H5I_type_t type, void *object, H5VL_t *vol_connector, hbool_t app_ref); diff --git a/src/H5VLpublic.h b/src/H5VLpublic.h index dd1ed54..6ea9fc1 100644 --- a/src/H5VLpublic.h +++ b/src/H5VLpublic.h @@ -22,6 +22,7 @@ #include "H5Apublic.h" /* Attributes */ #include "H5ESpublic.h" /* Event Stack */ #include "H5Fpublic.h" /* Files */ +#include "H5Ipublic.h" /* IDs */ #include "H5Lpublic.h" /* Links */ #include "H5Opublic.h" /* Objects */ #include "H5Rpublic.h" /* References */ @@ -383,7 +384,7 @@ typedef struct H5VL_class_t { herr_t (*str_to_info)(const char *str, void **info); /* Callback to deserialize a string into connector's info */ void * (*get_object)(const void *obj); /* Callback to retrieve underlying object */ herr_t (*get_wrap_ctx)(const void *obj, void **wrap_ctx); /* Callback to retrieve the object wrapping context for the connector */ - void* (*wrap_object)(void *obj, void *wrap_ctx); /* Callback to wrap a library object */ + void* (*wrap_object)(void *obj, H5I_type_t obj_type, void *wrap_ctx); /* Callback to wrap a library object */ herr_t (*free_wrap_ctx)(void *wrap_ctx); /* Callback to release the object wrapping context for the connector */ /* Data Model */ @@ -450,7 +451,8 @@ H5_DLL herr_t H5VLconnector_info_to_str(const void *info, hid_t connector_id, ch H5_DLL herr_t H5VLconnector_str_to_info(const char *str, hid_t connector_id, void **info); H5_DLL void *H5VLget_object(void *obj, hid_t connector_id); H5_DLL herr_t H5VLget_wrap_ctx(void *obj, hid_t connector_id, void **wrap_ctx); -H5_DLL void *H5VLwrap_object(void *obj, hid_t connector_id, void *wrap_ctx); +H5_DLL void *H5VLwrap_object(void *obj, H5I_type_t obj_type, hid_t connector_id, + void *wrap_ctx); H5_DLL herr_t H5VLfree_wrap_ctx(void *wrap_ctx, hid_t connector_id); /* Public wrappers for attribute callbacks */ diff --git a/src/H5private.h b/src/H5private.h index f58faec..8b6253d 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -1156,6 +1156,9 @@ typedef off_t h5_stat_size_t; #ifndef HDpowf #define HDpowf(X,Y) powf(X,Y) #endif /* HDpowf */ +#ifndef HDpread + #define HDpread(F,B,C,O) pread(F,B,C,O) +#endif /* HDpread */ #ifndef HDprintf #define HDprintf(...) HDfprintf(stdout, __VA_ARGS__) #endif /* HDprintf */ @@ -1168,6 +1171,9 @@ typedef off_t h5_stat_size_t; #ifndef HDputs #define HDputs(S) puts(S) #endif /* HDputs */ +#ifndef HDpwrite + #define HDpwrite(F,B,C,O) pwrite(F,B,C,O) +#endif /* HDpwrite */ #ifndef HDqsort #define HDqsort(M,N,Z,F) qsort(M,N,Z,F) #endif /* HDqsort*/ diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake index c0d4813..ba72e3a 100644 --- a/test/CMakeTests.cmake +++ b/test/CMakeTests.cmake @@ -171,6 +171,7 @@ set (HDF5_REFERENCE_TEST_FILES le_data.h5 le_extlink1.h5 le_extlink2.h5 + memleak_H5O_dtype_decode_helper_H5Odtype.h5 mergemsg.h5 multi_file_v16-r.h5 multi_file_v16-s.h5 @@ -586,10 +587,10 @@ foreach (test ${H5_TESTS}) endif () endforeach () -set_tests_properties (H5TEST-fheap PROPERTIES TIMEOUT 1800) -set_tests_properties (H5TEST-big PROPERTIES TIMEOUT 1800) -set_tests_properties (H5TEST-btree2 PROPERTIES TIMEOUT 1800) -set_tests_properties (H5TEST-objcopy PROPERTIES TIMEOUT 1800) +set_tests_properties (H5TEST-fheap PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) +set_tests_properties (H5TEST-big PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) +set_tests_properties (H5TEST-btree2 PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) +set_tests_properties (H5TEST-objcopy PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) if (BUILD_SHARED_LIBS) # Remove any output file left over from previous test run @@ -628,10 +629,10 @@ if (BUILD_SHARED_LIBS) endif () endforeach () - set_tests_properties (H5TEST-shared-fheap PROPERTIES TIMEOUT 1800) - set_tests_properties (H5TEST-shared-big PROPERTIES TIMEOUT 1800) - set_tests_properties (H5TEST-shared-btree2 PROPERTIES TIMEOUT 1800) - set_tests_properties (H5TEST-shared-objcopy PROPERTIES TIMEOUT 1800) + set_tests_properties (H5TEST-shared-fheap PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) + set_tests_properties (H5TEST-shared-big PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) + set_tests_properties (H5TEST-shared-btree2 PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) + set_tests_properties (H5TEST-shared-objcopy PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () #-- Adding test for cache @@ -663,7 +664,7 @@ if (NOT CYGWIN) ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/H5TEST;HDF5TestExpress=${HDF_TEST_EXPRESS}" WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST ) - set_tests_properties (H5TEST-cache PROPERTIES TIMEOUT 1800) + set_tests_properties (H5TEST-cache PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () #-- Adding test for cache_image @@ -713,7 +714,7 @@ if (BUILD_SHARED_LIBS) ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/H5TEST-shared;HDF5TestExpress=${HDF_TEST_EXPRESS}" WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST-shared ) - set_tests_properties (H5TEST-shared-cache PROPERTIES TIMEOUT 1800) + set_tests_properties (H5TEST-shared-cache PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () endif () diff --git a/test/CMakeVFDTests.cmake b/test/CMakeVFDTests.cmake index be02110..9f03c40 100644 --- a/test/CMakeVFDTests.cmake +++ b/test/CMakeVFDTests.cmake @@ -263,17 +263,17 @@ endif () set_tests_properties (VFD-${vfdname}-flush2 PROPERTIES DEPENDS VFD-${vfdname}-flush1) set_tests_properties (VFD-${vfdname}-flush1 PROPERTIES TIMEOUT 10) set_tests_properties (VFD-${vfdname}-flush2 PROPERTIES TIMEOUT 10) - set_tests_properties (VFD-${vfdname}-istore PROPERTIES TIMEOUT 1800) + set_tests_properties (VFD-${vfdname}-istore PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) if (NOT CYGWIN) - set_tests_properties (VFD-${vfdname}-cache PROPERTIES TIMEOUT 1800) + set_tests_properties (VFD-${vfdname}-cache PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () if (BUILD_SHARED_LIBS) set_tests_properties (VFD-${vfdname}-flush2-shared PROPERTIES DEPENDS VFD-${vfdname}-flush1-shared) set_tests_properties (VFD-${vfdname}-flush1-shared PROPERTIES TIMEOUT 10) set_tests_properties (VFD-${vfdname}-flush2-shared PROPERTIES TIMEOUT 10) - set_tests_properties (VFD-${vfdname}-istore-shared PROPERTIES TIMEOUT 1800) + set_tests_properties (VFD-${vfdname}-istore-shared PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) if (NOT CYGWIN AND NOT WIN32) - set_tests_properties (VFD-${vfdname}-cache-shared PROPERTIES TIMEOUT 1800) + set_tests_properties (VFD-${vfdname}-cache-shared PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () endif () if (HDF5_TEST_FHEAP_VFD) @@ -288,7 +288,7 @@ endif () -P "${HDF_RESOURCES_DIR}/vfdTest.cmake" ) set_tests_properties (VFD-${vfdname}-fheap PROPERTIES - TIMEOUT 1800 + TIMEOUT ${CTEST_VERY_LONG_TIMEOUT} ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/${vfdname};HDF5TestExpress=${HDF_TEST_EXPRESS}" WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/${vfdname} ) @@ -304,7 +304,7 @@ endif () -P "${HDF_RESOURCES_DIR}/vfdTest.cmake" ) set_tests_properties (VFD-${vfdname}-fheap-shared PROPERTIES - TIMEOUT 1800 + TIMEOUT ${CTEST_VERY_LONG_TIMEOUT} ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/${vfdname}-shared;HDF5TestExpress=${HDF_TEST_EXPRESS}" WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/${vfdname}-shared ) diff --git a/test/CMakeVOLTests.cmake b/test/CMakeVOLTests.cmake index 39fa2a6..fdd7ba0 100644 --- a/test/CMakeVOLTests.cmake +++ b/test/CMakeVOLTests.cmake @@ -262,17 +262,17 @@ endif () set_tests_properties (VOL-${volname}-flush2 PROPERTIES DEPENDS VOL-${volname}-flush1) set_tests_properties (VOL-${volname}-flush1 PROPERTIES TIMEOUT 10) set_tests_properties (VOL-${volname}-flush2 PROPERTIES TIMEOUT 10) - set_tests_properties (VOL-${volname}-istore PROPERTIES TIMEOUT 1800) + set_tests_properties (VOL-${volname}-istore PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) if (NOT CYGWIN) - set_tests_properties (VOL-${volname}-cache PROPERTIES TIMEOUT 1800) + set_tests_properties (VOL-${volname}-cache PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () if (BUILD_SHARED_LIBS) set_tests_properties (VOL-${volname}-flush2-shared PROPERTIES DEPENDS VOL-${volname}-flush1-shared) set_tests_properties (VOL-${volname}-flush1-shared PROPERTIES TIMEOUT 10) set_tests_properties (VOL-${volname}-flush2-shared PROPERTIES TIMEOUT 10) - set_tests_properties (VOL-${volname}-istore-shared PROPERTIES TIMEOUT 1800) + set_tests_properties (VOL-${volname}-istore-shared PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) if (NOT CYGWIN AND NOT WIN32) - set_tests_properties (VOL-${volname}-cache-shared PROPERTIES TIMEOUT 1800) + set_tests_properties (VOL-${volname}-cache-shared PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) endif () endif () if (HDF5_TEST_FHEAP_VOL) @@ -287,7 +287,7 @@ endif () -P "${HDF_RESOURCES_DIR}/volTest.cmake" ) set_tests_properties (VOL-${volname}-fheap PROPERTIES - TIMEOUT 1800 + TIMEOUT ${CTEST_VERY_LONG_TIMEOUT} ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/${volname};HDF5TestExpress=${HDF_TEST_EXPRESS}" WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/${volname} ) @@ -303,7 +303,7 @@ endif () -P "${HDF_RESOURCES_DIR}/volTest.cmake" ) set_tests_properties (VOL-${volname}-fheap-shared PROPERTIES - TIMEOUT 1800 + TIMEOUT ${CTEST_VERY_LONG_TIMEOUT} ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/${volname}-shared;HDF5TestExpress=${HDF_TEST_EXPRESS}" WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/${volname}-shared ) diff --git a/test/cache_image.c b/test/cache_image.c index 10c37f0..ee49502 100644 --- a/test/cache_image.c +++ b/test/cache_image.c @@ -713,6 +713,9 @@ open_hdf5_file(hbool_t create_file, hbool_t mdci_sbem_expected, file_id = H5Fopen(hdf_file_name, H5F_ACC_RDWR, fapl_id); } + /* tidy up */ + H5Pclose(fapl_id); + if ( file_id < 0 ) { pass = FALSE; @@ -4720,7 +4723,7 @@ cache_image_smoke_check_4(hbool_t single_file_vfd) *------------------------------------------------------------------------- */ -#define MAX_NUM_GROUPS 128 +#define MAX_NUM_GROUPS 64 static unsigned cache_image_smoke_check_5(hbool_t single_file_vfd) @@ -4756,12 +4759,16 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) /* setup the file name */ if ( pass ) { - if ( h5_fixname(FILENAMES[0], H5P_DEFAULT, filename, sizeof(filename)) + hid_t fapl_id = h5_fileaccess(); + + if ( h5_fixname(FILENAMES[0], fapl_id, filename, sizeof(filename)) == NULL ) { pass = FALSE; failure_mssg = "h5_fixname() failed.\n"; } + + H5Pclose(fapl_id); } if ( show_progress ) diff --git a/test/cork.c b/test/cork.c index dceaf5a..240be77 100644 --- a/test/cork.c +++ b/test/cork.c @@ -286,19 +286,19 @@ static unsigned verify_obj_dset_cork(hbool_t swmr) { /* Variable Declarations */ - hid_t fid = -1; /* File ID */ + hid_t fid = -1; /* File ID */ hid_t fapl = -1; /* File access property list */ hid_t aid = -1; /* Attribute ID */ hid_t sid = -1, sid2 = -1; /* Dataspace IDs */ hid_t did = -1, did2 = -1; /* Dataset IDs */ hid_t oid = -1; /* Object ID */ - hid_t dcpl2; /* Dataset creation property list */ + hid_t dcpl2; /* Dataset creation property list */ int i = 0; /* Local index variable */ - hsize_t dim[1] = {100}; /* Dataset dimension size */ + hsize_t dim[1] = {100}; /* Dataset dimension size */ hsize_t chunk_dim[1] = {7}; /* Dataset chunk dimension size */ H5O_info_t oinfo, oinfo2; /* Object metadata information */ char attrname[500]; /* Name of attribute */ - unsigned flags; /* File access flags */ + unsigned flags; /* File access flags */ if(swmr) { TESTING("cork status for dataset objects with attributes (SWMR)"); @@ -341,7 +341,7 @@ verify_obj_dset_cork(hbool_t swmr) TEST_ERROR /* Attach and write to an attribute to the dataset: DSET */ - if((aid = H5Acreate2(did, ATTR, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if((aid = H5Acreate2(did, ATTR, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR /* Verify cork status of the dataset: DSET */ @@ -380,11 +380,11 @@ verify_obj_dset_cork(hbool_t swmr) TEST_ERROR /* Attach 8 attributes to the dataset */ - for(i = 0;i < 8; i++) { - sprintf(attrname, "attr %d", i); - if((aid = H5Acreate2(did2, attrname, H5T_NATIVE_UINT, sid2, H5P_DEFAULT, H5P_DEFAULT)) < 0) + for(i = 0; i < 8; i++) { + HDsprintf(attrname, "attr %d", i); + if((aid = H5Acreate2(did2, attrname, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR - if(H5Awrite(aid, H5T_NATIVE_UINT, &i) < 0) + if(H5Awrite(aid, H5T_NATIVE_INT, &i) < 0) TEST_ERROR if(H5Aclose(aid) < 0) TEST_ERROR diff --git a/test/direct_chunk.c b/test/direct_chunk.c index 2ef38ea..2edfe64 100644 --- a/test/direct_chunk.c +++ b/test/direct_chunk.c @@ -1910,10 +1910,10 @@ test_read_unallocated_chunk (hid_t file) goto error; /* Write a single chunk to intialize the chunk storage */ - HDmemset(&chunk_dims, 0, sizeof(chunk_dims)); + HDmemset(direct_buf, 0, CHUNK_NX * CHUNK_NY * sizeof(int)); offset[0] = 0; offset[1] = 0; - if(H5Dwrite_chunk(dataset, dxpl, filter_mask, offset, chunk_nbytes, &chunk_dims) < 0) + if(H5Dwrite_chunk(dataset, dxpl, filter_mask, offset, chunk_nbytes, direct_buf) < 0) goto error; /* Attempt to read each chunk in the dataset. Chunks are not allocated, diff --git a/test/memleak_H5O_dtype_decode_helper_H5Odtype.h5 b/test/memleak_H5O_dtype_decode_helper_H5Odtype.h5 Binary files differnew file mode 100644 index 0000000..b5980b7 --- /dev/null +++ b/test/memleak_H5O_dtype_decode_helper_H5Odtype.h5 diff --git a/test/titerate.c b/test/titerate.c index de652a7..87ddfb8 100644 --- a/test/titerate.c +++ b/test/titerate.c @@ -20,6 +20,7 @@ *************************************************************/ #include "testhdf5.h" +#include "H5srcdir.h" #define DATAFILE "titerate.h5" @@ -53,6 +54,17 @@ typedef struct { iter_enum command; /* The type of return value */ } iter_info; +/* Definition for test_corrupted_attnamelen */ +#define CORRUPTED_ATNAMELEN_FILE "memleak_H5O_dtype_decode_helper_H5Odtype.h5" +#define DSET_NAME "image" +typedef struct searched_err_t { + char message[256]; + bool found; +} searched_err_t; + +/* Call back function for test_corrupted_attnamelen */ +static int find_err_msg_cb(unsigned n, const H5E_error2_t *err_desc, void *_client_data); + /* Local functions */ int iter_strcmp(const void *s1, const void *s2); int iter_strcmp2(const void *s1, const void *s2); @@ -915,6 +927,92 @@ static void test_links(hid_t fapl) CHECK(ret, FAIL, "H5Fclose"); } /* test_links() */ +/*------------------------------------------------------------------------- + * Function: find_err_msg_cb + * + * Purpose: Callback function to find the given error message. + * Helper function for test_corrupted_attnamelen(). + * + * Return: H5_ITER_STOP when the message is found + * H5_ITER_CONT, otherwise + * + *------------------------------------------------------------------------- + */ +static int +find_err_msg_cb(unsigned n, const H5E_error2_t *err_desc, void *_client_data) +{ + int status = H5_ITER_CONT; + searched_err_t *searched_err = (searched_err_t *)_client_data; + + if (searched_err == NULL) + return -1; + + /* If the searched error message is found, stop the iteration */ + if (err_desc->desc != NULL && strcmp(err_desc->desc, searched_err->message) == 0) + { + searched_err->found = true; + status = H5_ITER_STOP; + } + return status; +} /* end find_err_msg_cb() */ + +/************************************************************************** +** +** test_corrupted_attnamelen(): Test the fix for the JIRA issue HDFFV-10588, +** where corrupted attribute's name length can be +** detected and invalid read can be avoided. +** +**************************************************************************/ +static void test_corrupted_attnamelen(void) +{ + hid_t fid = -1; /* File ID */ + hid_t did = -1; /* Dataset ID */ + searched_err_t err_caught; /* Data to be passed to callback func */ + int err_status; /* Status returned by H5Aiterate2 */ + herr_t ret; /* Return value */ + const char *testfile = H5_get_srcdir_filename(CORRUPTED_ATNAMELEN_FILE); /* Corrected test file name */ + + const char *err_message = "attribute name has different length than stored length"; + /* the error message produced when the failure occurs */ + + /* Output message about test being performed */ + MESSAGE(5, ("Testing the Handling of Corrupted Attribute's Name Length\n")); + + fid = H5Fopen(testfile, H5F_ACC_RDONLY, H5P_DEFAULT); + CHECK(fid, FAIL, "H5Fopen"); + + /* Open the dataset */ + did = H5Dopen2(fid, DSET_NAME, H5P_DEFAULT); + CHECK(did, FAIL, "H5Dopen2"); + + /* Call H5Aiterate2 to trigger the failure in HDFFV-10588. Failure should + occur in the decoding stage, so some arguments are not needed. */ + err_status = H5Aiterate2(did, H5_INDEX_NAME, H5_ITER_INC, NULL, NULL, NULL); + + /* Make sure the intended error was caught */ + if(err_status == -1) + { + /* Initialize client data */ + HDstrcpy(err_caught.message, err_message); + err_caught.found = false; + + /* Look for the correct error message */ + ret = H5Ewalk2(H5E_DEFAULT, H5E_WALK_UPWARD, find_err_msg_cb, &err_caught); + CHECK(ret, FAIL, "H5Ewalk2"); + + /* Fail if the indicated message is not found */ + CHECK(err_caught.found, false, "test_corrupted_attnamelen: Expected error not found"); + } + + /* Close the dataset and file */ + ret = H5Dclose(did); + CHECK(ret, FAIL, "H5Dclose"); + + ret = H5Fclose(fid); + CHECK(ret, FAIL, "H5Fclose"); + +} /* test_corrupted_attnamelen() */ + /**************************************************************** ** ** test_iterate(): Main iteration testing routine. @@ -951,6 +1049,9 @@ test_iterate(void) test_links(new_format ? fapl2 : fapl); /* Test soft and hard link iteration */ } /* end for */ + /* Test the fix for issue HDFFV-10588 */ + test_corrupted_attnamelen(); + /* Close FAPLs */ ret = H5Pclose(fapl); CHECK(ret, FAIL, "H5Pclose"); diff --git a/testpar/t_dset.c b/testpar/t_dset.c index 35501d8..d4e556d 100644 --- a/testpar/t_dset.c +++ b/testpar/t_dset.c @@ -2659,8 +2659,10 @@ compress_readAll(void) nerrors++; } +#if MPI_VERSION >= 3 ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read); VRFY((ret >= 0), "H5Dwrite succeeded"); +#endif ret = H5Pclose(xfer_plist); VRFY((ret >= 0), "H5Pclose succeeded"); diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c index 0092abc..3d9472a 100644 --- a/tools/src/h5repack/h5repack_filters.c +++ b/tools/src/h5repack/h5repack_filters.c @@ -338,12 +338,14 @@ int apply_filters(const char* name, /* object name from traverse list */ sm_nbytes = msize; for (i = rank; i > 0; --i) { - hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; + hsize_t size = 0; + if(sm_nbytes == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "number of bytes per stripmine must be > 0"); + size = H5TOOLS_BUFSIZE / sm_nbytes; if (size == 0) /* datum size > H5TOOLS_BUFSIZE */ size = 1; sm_size[i - 1] = MIN(dims[i - 1], size); sm_nbytes *= sm_size[i - 1]; - HDassert(sm_nbytes > 0); } for (i = 0; i < rank; i++) { diff --git a/tools/test/h5dump/h5dumpgentest.c b/tools/test/h5dump/h5dumpgentest.c index cbbbcfa..946ca04 100644 --- a/tools/test/h5dump/h5dumpgentest.c +++ b/tools/test/h5dump/h5dumpgentest.c @@ -9529,15 +9529,13 @@ gent_intattrscalars(void) } /*------------------------------------------------------------------------- - * Function: gent_packedbits + * Function: gent_intsattrs * - * Purpose: Generate a file to be used in the h5dump packed bits tests. + * Purpose: Generate a file to be used in the h5dump tests. * Four datasets of 1, 2, 4 and 8 bytes of unsigned int types are created. * Four more datasets of 1, 2, 4 and 8 bytes of signed int types are created. * Fill them with raw data such that no bit will be all zero in a dataset. * A dummy dataset of double type is created for failure test. - * Created: Albert Cheng, 2010/5/10. - * Modified: Allen Byrne, 2011/1/5 Use file to test Signed/Unsigned datatypes *------------------------------------------------------------------------- */ static void diff --git a/tools/test/misc/CMakeTestsRepart.cmake b/tools/test/misc/CMakeTestsRepart.cmake index 830de11..8edd243 100644 --- a/tools/test/misc/CMakeTestsRepart.cmake +++ b/tools/test/misc/CMakeTestsRepart.cmake @@ -71,30 +71,37 @@ family_to_single.h5 family_to_sec2.h5 ) - if (NOT "${last_test}" STREQUAL "") - set_tests_properties (H5REPART-clearall-objects PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "H5REPART-clearall-objects") + set_tests_properties (H5REPART-clearall-objects PROPERTIES FIXTURES_SETUP clear_testrepart) # repartition family member size to 20,000 bytes. add_test (NAME H5REPART-h5repart_20K COMMAND $<TARGET_FILE:h5repart> -m 20000 family_file%05d.h5 fst_family%05d.h5) - set_tests_properties (H5REPART-h5repart_20K PROPERTIES DEPENDS H5REPART-clearall-objects) + set_tests_properties (H5REPART-h5repart_20K PROPERTIES + FIXTURES_REQUIRED clear_testrepart + ) # repartition family member size to 5 KB. add_test (NAME H5REPART-h5repart_5K COMMAND $<TARGET_FILE:h5repart> -m 5k family_file%05d.h5 scd_family%05d.h5) - set_tests_properties (H5REPART-h5repart_5K PROPERTIES DEPENDS H5REPART-clearall-objects) + set_tests_properties (H5REPART-h5repart_5K PROPERTIES + FIXTURES_REQUIRED clear_testrepart + ) # convert family file to sec2 file of 20,000 bytes add_test (NAME H5REPART-h5repart_single COMMAND $<TARGET_FILE:h5repart> -m 20000 -family_to_single family_file%05d.h5 family_to_single.h5) - set_tests_properties (H5REPART-h5repart_single PROPERTIES DEPENDS H5REPART-clearall-objects) + set_tests_properties (H5REPART-h5repart_single PROPERTIES + FIXTURES_REQUIRED clear_testrepart + ) # convert family file to sec2 file of 20,000 bytes (old argument) add_test (NAME H5REPART-h5repart_sec2 COMMAND $<TARGET_FILE:h5repart> -m 20000 -family_to_sec2 family_file%05d.h5 family_to_sec2.h5) - set_tests_properties (H5REPART-h5repart_sec2 PROPERTIES DEPENDS H5REPART-clearall-objects) + set_tests_properties (H5REPART-h5repart_sec2 PROPERTIES + FIXTURES_REQUIRED clear_testrepart + ) # test the output files repartitioned above. add_test (NAME H5REPART-h5repart_test COMMAND $<TARGET_FILE:h5repart_test>) - set_tests_properties (H5REPART-h5repart_test PROPERTIES DEPENDS "H5REPART-clearall-objects;H5REPART-h5repart_20K;H5REPART-h5repart_5K;H5REPART-h5repart_sec2") + set_tests_properties (H5REPART-h5repart_test PROPERTIES + DEPENDS "H5REPART-h5repart_20K;H5REPART-h5repart_5K;H5REPART-h5repart_single;H5REPART-h5repart_sec2" + ) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5repart_test diff --git a/tools/test/perform/CMakeTests.cmake b/tools/test/perform/CMakeTests.cmake index 450667a..5abd038 100644 --- a/tools/test/perform/CMakeTests.cmake +++ b/tools/test/perform/CMakeTests.cmake @@ -66,7 +66,7 @@ else () -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" ) endif () -set_tests_properties (PERFORM_h5perf_serial PROPERTIES TIMEOUT 1800) +set_tests_properties (PERFORM_h5perf_serial PROPERTIES TIMEOUT ${CTEST_VERY_LONG_TIMEOUT}) set_tests_properties (PERFORM_h5perf_serial PROPERTIES DEPENDS "PERFORM_h5perform-clearall-objects") if (HDF5_BUILD_PERFORM_STANDALONE) |