From fb4e5c0570f94d548ade5fb5c16878271f6a06a9 Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Tue, 5 Feb 2019 16:21:29 -0600 Subject: HDFFV-10697 Disable compression option if source unavailable --- CMakeFilters.cmake | 8 ++++++++ config/cmake/scripts/HDF5config.cmake | 6 +++++- release_docs/RELEASE.txt | 7 +++++++ tools/test/h5dump/h5dumpgentest.c | 6 ++---- 4 files changed, 22 insertions(+), 5 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/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake index f8e6f9b..c92fa5b 100755 --- a/config/cmake/scripts/HDF5config.cmake +++ b/config/cmake/scripts/HDF5config.cmake @@ -43,6 +43,7 @@ set (CTEST_SOURCE_VERSEXT "-snap1") #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/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index fd8de96..448ecc3 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -47,6 +47,13 @@ New Features Configuration: ------------- + - Disable SZIP or ZLIB options if TGZ files are not available. + + Changed the TGZ option for SZip and ZLib to disable the options + if the source tar.gz files are not found. + + (ADB - 2019/02/05, HDFFV-10697) + - Rework CMake versioning for OSX platforms. Changed the current_version and compatibility_version flags from optional diff --git a/tools/test/h5dump/h5dumpgentest.c b/tools/test/h5dump/h5dumpgentest.c index aaf5c3e..fe43ecd 100644 --- a/tools/test/h5dump/h5dumpgentest.c +++ b/tools/test/h5dump/h5dumpgentest.c @@ -9528,15 +9528,13 @@ 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 -- cgit v0.12 From 12a0998b04447006b2db28c401c0bd66b00815e6 Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Wed, 6 Feb 2019 08:43:10 -0600 Subject: Update Examples version and references --- bin/release | 224 ++++++++++++++++----------------- config/cmake/HDF518_Examples.cmake.in | 106 ---------------- config/cmake/scripts/HDF5options.cmake | 2 +- 3 files changed, 113 insertions(+), 219 deletions(-) delete mode 100644 config/cmake/HDF518_Examples.cmake.in diff --git a/bin/release b/bin/release index afdbb51..3d1cb26 100755 --- a/bin/release +++ b/bin/release @@ -39,29 +39,29 @@ USAGE() { cat << EOF Usage: $0 -d [--docver BRANCHNAME] [-h] [--nocheck] [--private] ... - -d DIR The name of the directory where the releas(es) should be + -d DIR The name of the directory where the releas(es) should be placed. --docver BRANCHNAME This is added for 1.8 and beyond to get the correct version of documentation files from the hdf5docs repository. BRANCHNAME for v1.8 should be hdf5_1_8. -h print the help page. - --nocheck Ignore errors in MANIFEST file. - --private Make a private release with today's date in version information. - + --nocheck Ignore errors in MANIFEST file. + --private Make a private release with today's date in version information. + This must be run at the top level of the source directory. The other command-line options are the names of the programs to use for compressing the resulting tar archive (if none are given then "tar" is assumed): - tar -- use tar and don't do any compressing. - gzip -- use gzip with "-9" and append ".gz" to the output name. - cmake-tgz -- create a tar file using the gzip default level with a build-unix.sh + tar -- use tar and don't do any compressing. + gzip -- use gzip with "-9" and append ".gz" to the output name. + 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. + 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. + scripts and .bat files to build HDF5 source using CMake on Windows. 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. @@ -114,8 +114,8 @@ EOF tar2zip() { if [ $# -ne 3 ]; then - echo "usage: tar2zip " - return 1 + echo "usage: tar2zip " + return 1 fi ztmpdir=/tmp/ztmpdir$$ mkdir -p $ztmpdir @@ -127,23 +127,23 @@ tar2zip() (cd $ztmpdir; tar xf -) < $tarfile # sanity check if [ ! -d $ztmpdir/$version ]; then - echo "untar did not create $ztmpdir/$version source dir" - # cleanup - rm -rf $ztmpdir - return 1 + echo "untar did not create $ztmpdir/$version source dir" + # cleanup + rm -rf $ztmpdir + return 1 fi # step 2: convert text files # There maybe a simpler way to do this. # options used in unix2dos: - # -k Keep the date stamp + # -k Keep the date stamp # -q quiet mode # grep redirect output to /dev/null because -q or -s are not portable. find $ztmpdir/$version | \ - while read inf; do \ - if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \ - unix2dos -q -k $inf; \ - fi\ - done + while read inf; do \ + if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \ + unix2dos -q -k $inf; \ + fi\ + done # step 3: make zipball # -9 maximum compression # -y Store symbolic links as such in the zip archive @@ -194,8 +194,8 @@ tar2zip() tar2cmakezip() { if [ $# -ne 3 ]; then - echo "usage: tar2cmakezip " - return 1 + echo "usage: tar2cmakezip " + return 1 fi cmziptmpdir=/tmp/cmziptmpdir$$ cmziptmpsubdir=$cmziptmpdir/CMake-$HDF5_VERS @@ -208,10 +208,10 @@ tar2cmakezip() (cd $cmziptmpsubdir; tar xf -) < $tarfile # sanity check if [ ! -d $cmziptmpsubdir/$version ]; then - echo "untar did not create $cmziptmpsubdir/$version source dir" - # cleanup - rm -rf $cmziptmpdir - return 1 + echo "untar did not create $cmziptmpsubdir/$version source dir" + # cleanup + rm -rf $cmziptmpdir + return 1 fi # step 2: add batch file for building CMake on window @@ -225,7 +225,7 @@ 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-1.10.8-Source.tar.gz $cmziptmpsubdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.13-Source.tar.gz $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 @@ -233,15 +233,15 @@ tar2cmakezip() # step 4: convert text files # There maybe a simpler way to do this. # options used in unix2dos: - # -k Keep the date stamp + # -k Keep the date stamp # -q quiet mode # grep redirect output to /dev/null because -q or -s are not portable. find $cmziptmpsubdir/$version | \ - while read inf; do \ - if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \ - unix2dos -q -k $inf; \ - fi\ - done + while read inf; do \ + if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \ + unix2dos -q -k $inf; \ + fi\ + done # step 3: make zipball # -9 maximum compression @@ -293,8 +293,8 @@ tar2cmakezip() tar2cmaketgz() { if [ $# -ne 3 ]; then - echo "usage: tar2cmaketgz " - return 1 + echo "usage: tar2cmaketgz " + return 1 fi cmgztmpdir=/tmp/cmgztmpdir$$ cmgztmpsubdir=$cmgztmpdir/CMake-$HDF5_VERS @@ -307,10 +307,10 @@ tar2cmaketgz() (cd $cmgztmpsubdir; tar xf -) < $tarfile # sanity check if [ ! -d $cmgztmpsubdir/$version ]; then - echo "untar did not create $cmgztmpsubdir/$version source dir" - # cleanup - rm -rf $cmgztmpdir - return 1 + echo "untar did not create $cmgztmpsubdir/$version source dir" + # cleanup + rm -rf $cmgztmpdir + return 1 fi @@ -320,12 +320,12 @@ tar2cmaketgz() # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpsubdir cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir - cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.8-Source.tar.gz $cmgztmpsubdir + cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.13-Source.tar.gz $cmgztmpsubdir cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpsubdir - tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1 - + tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1 + # cleanup rm -rf $cmgztmpdir } @@ -347,7 +347,7 @@ check=yes release_date=`date +%F` today=`date +%Y%m%d` pmode='no' -tmpdir="../#release_tmp.$$" # tmp work directory +tmpdir="../#release_tmp.$$" # tmp work directory DOC_URL=https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git CPPLUS_RM_NAME=cpplus_RM MAINT_MODE_ENABLED="" @@ -364,11 +364,11 @@ fi RESTORE_VERSION() { if [ X-${VERS_OLD} != X- ]; then - echo restoring version information back to $VERS_OLD - rm -f config/lt_vers.am - cp $tmpdir/lt_vers.am config/lt_vers.am - bin/h5vers -s $VERS_OLD - VERS_OLD= + echo restoring version information back to $VERS_OLD + rm -f config/lt_vers.am + cp $tmpdir/lt_vers.am config/lt_vers.am + bin/h5vers -s $VERS_OLD + VERS_OLD= fi } @@ -378,32 +378,32 @@ while [ -n "$1" ]; do arg=$1 shift case "$arg" in - -d) - DEST=$1 - shift - ;; - --nocheck) - check=no - ;; - -h) - USAGE - exit 0 - ;; - --private) - pmode=yes - ;; + -d) + DEST=$1 + shift + ;; + --nocheck) + check=no + ;; + -h) + USAGE + exit 0 + ;; + --private) + pmode=yes + ;; --docver) DOCVERSION=$1 shift ;; - -*) - echo "Unknown switch: $arg" 1>&2 - USAGE - exit 1 - ;; - *) - methods="$methods $arg" - ;; + -*) + echo "Unknown switch: $arg" 1>&2 + USAGE + exit 1 + ;; + *) + methods="$methods $arg" + ;; esac done @@ -453,12 +453,12 @@ if [ "X$fail" = "Xyes" ]; then echo "" echo "Note! If you are running bin/release in a development branch" echo "later than v 1.8 the MANIFEST check is expected to fail when" - echo "autogen.sh has not been run successfully. Either run autogen.sh " + echo "autogen.sh has not been run successfully. Either run autogen.sh " echo "with /usr/hdf/bin/AUTOTOOLS at the beginning of PATH or add the" echo "--nocheck argument to the bin/release command." exit 1 else - echo "Continuing anyway..." + echo "Continuing anyway..." fi fi @@ -492,7 +492,7 @@ test "$verbose" && echo " Running tar..." 1>&2 ( \ cd $tmpdir; \ tar cf $HDF5_VERS.tar $HDF5_VERS/Makefile \ - `sed 's/^\.\//hdf5-'$VERS'\//' $MANIFEST` || exit 1 \ + `sed 's/^\.\//hdf5-'$VERS'\//' $MANIFEST` || exit 1 \ ) # Compress @@ -500,56 +500,56 @@ MD5file=$HDF5_VERS.md5 cp /dev/null $DEST/$MD5file for comp in $methods; do case $comp in - tar) - cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar - (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file) - ;; - gzip) - test "$verbose" && echo " Running gzip..." 1>&2 - gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz - (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file) - ;; + tar) + cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar + (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file) + ;; + gzip) + test "$verbose" && echo " Running gzip..." 1>&2 + gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz + (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file) + ;; cmake-tgz) - test "$verbose" && echo " Creating CMake tar.gz file..." 1>&2 - tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2 - (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file) + test "$verbose" && echo " Creating CMake tar.gz file..." 1>&2 + tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2 + (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file) ;; - bzip2) - test "$verbose" && echo " Running bzip2..." 1>&2 - bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2 - (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file) - ;; - zip) - test "$verbose" && echo " Creating zip ball..." 1>&2 - tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2 - (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file) - ;; + bzip2) + test "$verbose" && echo " Running bzip2..." 1>&2 + bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2 + (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file) + ;; + zip) + test "$verbose" && echo " Creating zip ball..." 1>&2 + tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2 + (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file) + ;; cmake-zip) test "$verbose" && echo " Creating CMake-zip ball..." 1>&2 tar2cmakezip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.zip 1>&2 (cd $DEST; md5sum CMake-$HDF5_VERS.zip >> $MD5file) ;; - doc) + doc) if [ "${DOCVERSION}" = "" ]; then DOCVERSION=master fi - test "$verbose" && echo " Creating docs..." 1>&2 - # Check out docs from git repo - (cd $tmpdir; git clone -q $DOC_URL ${DOCVERSION} > /dev/null) || exit 1 + test "$verbose" && echo " Creating docs..." 1>&2 + # Check out docs from git repo + (cd $tmpdir; git clone -q $DOC_URL ${DOCVERSION} > /dev/null) || exit 1 # Create doxygen C++ RM - (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1 - # Replace version of C++ RM with just-created version - rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1 - mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1 + (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1 + # Replace version of C++ RM with just-created version + rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1 + mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1 # Compress the docs and move them to the release area - mv $tmpdir/${DOCVERSION} $tmpdir/${HDF5_VERS}_docs || exit 1 - (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs) || exit 1 - mv $tmpdir/${HDF5_VERS}_docs.tar $DEST || exit 1 - ;; - *) - echo "***Error*** Unknown method $comp" - exit 1 - ;; + mv $tmpdir/${DOCVERSION} $tmpdir/${HDF5_VERS}_docs || exit 1 + (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs) || exit 1 + mv $tmpdir/${HDF5_VERS}_docs.tar $DEST || exit 1 + ;; + *) + echo "***Error*** Unknown method $comp" + exit 1 + ;; esac done 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/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake index d4cc996..fb191f3 100755 --- a/config/cmake/scripts/HDF5options.cmake +++ b/config/cmake/scripts/HDF5options.cmake @@ -69,7 +69,7 @@ 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 "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.10.13-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}") ############################################################################################# ### enable parallel builds -- cgit v0.12 From a01981ee98917b7df6ffea874113a14d9b697f64 Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Wed, 6 Feb 2019 08:44:05 -0600 Subject: Remove obsolete file --- MANIFEST | 1 - 1 file changed, 1 deletion(-) diff --git a/MANIFEST b/MANIFEST index 5597c64..e2b2e81 100644 --- a/MANIFEST +++ b/MANIFEST @@ -3218,7 +3218,6 @@ # CMake-specific Examples Files ./config/cmake/HDF5_Examples.cmake.in -./config/cmake/HDF518_Examples.cmake.in ./release_docs/USING_CMake_Examples.txt ./CMakeLists.txt -- cgit v0.12 From e9541010eecf7915e0c2de0365a3909516bab65d Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Wed, 6 Feb 2019 08:47:02 -0600 Subject: Remove obsolete reference --- CMakeInstallation.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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) -- cgit v0.12 From fef7d6b0fc387cf793c9a7be1115de82155c2d5e Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Wed, 6 Feb 2019 10:47:11 -0600 Subject: Cleanup F2003 option for CMake --- CMakeLists.txt | 9 +-- config/cmake/scripts/HDF5options.cmake | 4 -- fortran/examples/CMakeTests.cmake | 60 ++++++++--------- fortran/examples/run-fortran-ex.sh.in | 18 +---- fortran/src/CMakeLists.txt | 6 +- fortran/test/CMakeTests.cmake | 70 +++++++++---------- java/src/hdf/hdf5lib/H5.java | 119 +++++++++++++++------------------ 7 files changed, 122 insertions(+), 164 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 7b1a3ba..81d81b6 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -818,9 +818,6 @@ 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 ${CMAKE_Fortran_COMPILER_ID}") @@ -833,10 +830,8 @@ if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/for include (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake) set (LINK_Fortran_LIBS ${LINK_LIBS}) - if (HDF5_ENABLE_F2003) - if (NOT FORTRAN_HAVE_ISO_C_BINDING) - set (HDF5_ENABLE_F2003 OFF) - endif () + if (NOT FORTRAN_HAVE_ISO_C_BINDING) + message (FATAL_ERROR " **** Fortran compiler lacks required Fortran 2003 features; unsupported Fortran 2003 compiler, disable HDF5_BUILD_FORTRAN **** ") endif () # Parallel IO usage requires MPI to be Linked and Included diff --git a/config/cmake/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake index fb191f3..24eaf78 100755 --- a/config/cmake/scripts/HDF5options.cmake +++ b/config/cmake/scripts/HDF5options.cmake @@ -33,12 +33,8 @@ ############################################################################################# #### fortran enabled #### #set (ADD_BUILD_OPTIONS "${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 #### 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 $) + else () + add_test (NAME f03_ex_${example} COMMAND "${CMAKE_COMMAND}" + -D "TEST_PROGRAM=$" + -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 $) + add_test (NAME f03_ex-shared_${example} COMMAND $) else () - add_test (NAME f03_ex_${example} COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$" + add_test (NAME f03_ex-shared_${example} COMMAND "${CMAKE_COMMAND}" + -D "TEST_PROGRAM=$" -D "TEST_ARGS:STRING=" -D "TEST_EXPECT=0" -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_OUTPUT=f03_ex_${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 $) - else () - add_test (NAME f03_ex-shared_${example} COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$" - -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} $ ${MPIEXEC_POSTFLAGS}) diff --git a/fortran/examples/run-fortran-ex.sh.in b/fortran/examples/run-fortran-ex.sh.in index da0c357..aa17f89 100644 --- a/fortran/examples/run-fortran-ex.sh.in +++ b/fortran/examples/run-fortran-ex.sh.in @@ -61,8 +61,6 @@ RunTest() ./$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 $) - else () - add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$" - -D "TEST_ARGS:STRING=" - -D "TEST_EXPECT=0" - -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_REGEX= 0 error.s." - -D "TEST_MATCH= 0 error(s)" - -D "TEST_OUTPUT=fortranlib_test_F03.txt" - #-D "TEST_REFERENCE=fortranlib_test_F03.out" - -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" - -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" - ) - endif () +if (HDF5_ENABLE_USING_MEMCHECKER) + add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND $) +else () + add_test (NAME FORTRAN_fortranlib_test_F03 COMMAND "${CMAKE_COMMAND}" + -D "TEST_PROGRAM=$" + -D "TEST_ARGS:STRING=" + -D "TEST_EXPECT=0" + -D "TEST_SKIP_COMPARE=TRUE" + -D "TEST_REGEX= 0 error.s." + -D "TEST_MATCH= 0 error(s)" + -D "TEST_OUTPUT=fortranlib_test_F03.txt" + #-D "TEST_REFERENCE=fortranlib_test_F03.out" + -D "TEST_FOLDER=${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 $) @@ -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 $) - else () - add_test (NAME FORTRAN_fortranlib_test_F03-shared COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=$" - -D "TEST_ARGS:STRING=" - -D "TEST_EXPECT=0" - -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_REGEX= 0 error.s." - -D "TEST_MATCH= 0 error(s)" - -D "TEST_OUTPUT=fortranlib_test_F03.txt" - #-D "TEST_REFERENCE=fortranlib_test_F03.out" - -D "TEST_FOLDER=${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 $) + else () + add_test (NAME FORTRAN_fortranlib_test_F03-shared COMMAND "${CMAKE_COMMAND}" + -D "TEST_PROGRAM=$" + -D "TEST_ARGS:STRING=" + -D "TEST_EXPECT=0" + -D "TEST_SKIP_COMPARE=TRUE" + -D "TEST_REGEX= 0 error.s." + -D "TEST_MATCH= 0 error(s)" + -D "TEST_OUTPUT=fortranlib_test_F03.txt" + #-D "TEST_REFERENCE=fortranlib_test_F03.out" + -D "TEST_FOLDER=${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 $) diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 03266e6..255a8ec 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -57,19 +57,18 @@ import hdf.hdf5lib.structs.H5O_info_t; /** * This class is the Java interface for the HDF5 library. *

- * This code is the called by Java programs to access the entry points of the HDF5 library. Each - * routine wraps a single HDF5 entry point, generally with the arguments and return codes analogous - * to the C interface. + * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single + * HDF5 entry point, generally with the arguments and return codes analogous to the C interface. *

- * For details of the HDF5 library, see the HDF5 Documentation at: - * http://hdfgroup.org/HDF5/ + * For details of the HDF5 library, see the HDF5 Documentation at: http://hdfgroup.org/HDF5/ *

*

* Mapping of arguments for Java * *

- * In general, arguments to the HDF Java API are straightforward translations from the 'C' API - * described in the HDF Reference Manual. + * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF + * Reference Manual. * * * @@ -109,19 +108,17 @@ import hdf.hdf5lib.structs.H5O_info_t; *
HDF-5 C types to Java types
* General Rules for Passing Arguments and Results *

- * In general, arguments passed IN to Java are the analogous basic types, as above. The - * exception is for arrays, which are discussed below. + * In general, arguments passed IN to Java are the analogous basic types, as above. The exception is for arrays, + * which are discussed below. *

- * The return value of Java methods is also the analogous type, as above. A major exception - * to that rule is that all HDF functions that return SUCCEED/FAIL are declared boolean in - * the Java version, rather than int as in the C. Functions that return a value or else FAIL - * are declared the equivalent to the C function. However, in most cases the Java method will raise - * an exception instead of returning an error code. See Errors and Exceptions - * below. + * The return value of Java methods is also the analogous type, as above. A major exception to that rule is that + * all HDF functions that return SUCCEED/FAIL are declared boolean in the Java version, rather than int as + * in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. However, in most + * cases the Java method will raise an exception instead of returning an error code. See Errors and + * Exceptions below. *

- * Java does not support pass by reference of arguments, so arguments that are returned through - * OUT parameters must be wrapped in an object or array. The Java API for HDF consistently - * wraps arguments in arrays. + * Java does not support pass by reference of arguments, so arguments that are returned through OUT parameters + * must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays. *

* For instance, a function that returns two integers is declared: * @@ -142,14 +139,12 @@ import hdf.hdf5lib.structs.H5O_info_t; * * *

- * All the routines where this convention is used will have specific documentation of the details, - * given below. + * All the routines where this convention is used will have specific documentation of the details, given below. *

* Arrays *

- * 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, + * 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, * * 

  *      herr_t H5Dread(long fid, long filetype, long memtype, long memspace,
@@ -157,45 +152,40 @@ import hdf.hdf5lib.structs.H5O_info_t;
  *
* *

- * where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of - * bytes that is the data for a multi-dimensional array. The other parameters describe the - * dimensions, rank, and datatype of the array on disk (source) and in memory (destination). + * where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that is the + * data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype of the array on + * disk (source) and in memory (destination). *

- * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, - * multidimensional arrays are definitely not layed out contiguously in memory. It would be - * infeasible to declare a separate routine for every combination of number type and dimensionality. - * For that reason, the HDFArray class is used to - * discover the type, shape, and size of the data array at run time, and to convert to and from a - * contiguous array of bytes in synchronized static native C order. + * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, multidimensional + * arrays are definitely not layed out contiguously in memory. It would be infeasible to declare a separate + * routine for every combination of number type and dimensionality. For that reason, the HDFArray class is used to discover the type, shape, and size of the + * data array at run time, and to convert to and from a contiguous array of bytes in synchronized static native C order. *

- * The upshot is that any Java array of numbers (either primitive or sub-classes of type - * Number) can be passed as an ``Object'', and the Java API will translate to and from the - * appropriate packed array of bytes needed by the C library. So the function above would be - * declared: + * The upshot is that any Java array of numbers (either primitive or sub-classes of type Number) can be passed as + * an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes needed by the C + * library. So the function above would be declared: * * 

  * public synchronized static native int H5Dread(long fid, long filetype, long memtype, long memspace, Object data);
  *
- * - * OPEN_IDS.addElement(id); - * - * and the parameter data can be any multi-dimensional array of numbers, such as float[][], - * or int[][][], or Double[][]. + * OPEN_IDS.addElement(id); + + * and the parameter data can be any multi-dimensional array of numbers, such as float[][], or int[][][], or + * Double[][]. *

* HDF-5 Constants *

- * The HDF-5 API defines a set of constants and enumerated values. Most of these values are - * available to Java programs via the class - * HDF5Constants. For example, the parameters for the h5open() call include two numeric - * values, HDFConstants.H5F_ACC_RDWR and HDF5Constants.H5P_DEFAULT. As - * would be expected, these numbers correspond to the C constants H5F_ACC_RDWR and - * H5P_DEFAULT. + * The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs + * via the class HDF5Constants. For example, the parameters for + * the h5open() call include two numeric values, HDFConstants.H5F_ACC_RDWR and + * HDF5Constants.H5P_DEFAULT. As would be expected, these numbers correspond to the C constants + * H5F_ACC_RDWR and H5P_DEFAULT. *

- * The HDF-5 API defines a set of values that describe number types and sizes, such as - * "H5T_NATIVE_INT" and "hsize_t". These values are determined at run time by the HDF-5 C library. - * To support these parameters, the Java class - * HDF5CDataTypes looks up the values when initiated. The values can be accessed as - * public variables of the Java class, such as: + * The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and "hsize_t". + * These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class HDF5CDataTypes looks up the values when initiated. The values + * can be accessed as public variables of the Java class, such as: * * 

  * long data_type = HDF5CDataTypes.JH5T_NATIVE_INT;
@@ -206,21 +196,20 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * 

  * Error handling and Exceptions
  * 

- * 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 for Java programming.
+ * 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
+ * for Java programming.
  * 

- * The exceptions of the JHI5 are organized as sub-classes of the class
- *  HDF5Exception. There are two
- * subclasses of HDF5Exception, 
- * HDF5LibraryException and 
- * HDF5JavaException. The sub-classes of the former represent errors from the HDF-5 C
- * library, while sub-classes of the latter represent errors in the JHI5 wrapper and support code.
+ * The exceptions of the JHI5 are organized as sub-classes of the class  HDF5Exception. There are two subclasses of
+ * HDF5Exception,  HDF5LibraryException
+ * and  HDF5JavaException. The sub-classes of the
+ * former represent errors from the HDF-5 C library, while sub-classes of the latter represent errors in the JHI5
+ * wrapper and support code.
  * 

- * The super-class HDF5LibraryException implements the method
- * 'printStackTrace()', which prints out the HDF-5 error stack, as described in the
- * HDF-5 C API H5Eprint(). This may be used by Java exception handlers to print out
- * the HDF-5 error stack.
+ * The super-class HDF5LibraryException implements the method 'printStackTrace()', which
+ * prints out the HDF-5 error stack, as described in the HDF-5 C API H5Eprint(). This may be used by Java
+ * exception handlers to print out the HDF-5 error stack.
  * 

  *
  * @version HDF5 1.10.5 

-- 
cgit v0.12


From c52df2f5a5a92a83524efc60158f0d20500010e0 Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Wed, 6 Feb 2019 11:01:35 -0600
Subject: Correct name of variable

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 81d81b6..7a69817 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -830,7 +830,7 @@ 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 (NOT FORTRAN_HAVE_ISO_C_BINDING)
+    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 ()
 
-- 
cgit v0.12


From 2a9bd0c431f0c33ac1e85e616b8582978d000086 Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Wed, 6 Feb 2019 16:44:56 -0600
Subject: Refactor TIMEOUT values

---
 c++/test/CMakeVFDTests.cmake        |  2 +-
 test/CMakeTests.cmake               | 20 ++++++++++----------
 test/CMakeVFDTests.cmake            | 12 ++++++------
 tools/test/perform/CMakeTests.cmake |  2 +-
 4 files changed, 18 insertions(+), 18 deletions(-)

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/test/CMakeTests.cmake b/test/CMakeTests.cmake
index 023024e..354c3a4 100644
--- a/test/CMakeTests.cmake
+++ b/test/CMakeTests.cmake
@@ -586,10 +586,10 @@ 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 +628,10 @@ 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 +663,7 @@ 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 +713,7 @@ 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/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)
-- 
cgit v0.12


From 199327b417cd6d6f7e0fe9df27896885829f4f62 Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Wed, 6 Feb 2019 17:03:20 -0600
Subject: Add missing assignments

---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7a69817..8e93231 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -748,6 +748,11 @@ 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)
-- 
cgit v0.12