mirror of
https://github.com/HDFGroup/hdf5.git
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Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_cpp4 into develop
This commit is contained in:
Binh-Minh Ribler
commit
7d9f5ed49a
71
bin/release
71
bin/release
@ -188,45 +188,47 @@ tar2zip()
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# Returns 0 if successful; 1 otherwise
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#
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# need function to create another temporary directory, extract the
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# $tmpdir/$HDF5_VERS.tar into it, add (create) build-unix.sh,
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# CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz and ZLib.tar.gz,
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# and then tar.gz it.
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# $tmpdir/$HDF5_VERS.tar into it, create build-VS*.bat files,
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# add CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz
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# ZLib.tar.gz, HDF5 examples, and then zip it.
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tar2cmakezip()
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{
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if [ $# -ne 3 ]; then
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echo "usage: tar2cmakezip <tarfilename> <tgzfilename>"
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echo "usage: tar2cmakezip <tarfilename> <zipfilename>"
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return 1
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fi
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cmziptmpdir=/tmp/cmziptmpdir$$
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mkdir -p $cmziptmpdir
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cmziptmpsubdir=$cmziptmpdir/CMake-$HDF5_VERS
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mkdir -p $cmziptmpsubdir
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version=$1
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tarfile=$2
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zipfile=$3
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# step 1: untar tarball in cmgztmpdir
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(cd $cmziptmpdir; tar xf -) < $tarfile
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(cd $cmziptmpsubdir; tar xf -) < $tarfile
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# sanity check
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if [ ! -d $cmziptmpdir/$version ]; then
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echo "untar did not create $cmziptmpdir/$version source dir"
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if [ ! -d $cmziptmpsubdir/$version ]; then
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echo "untar did not create $cmziptmpsubdir/$version source dir"
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# cleanup
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rm -rf $cmziptmpdir
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return 1
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fi
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# step 2: add batch file for building CMake on window
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cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2013-32.bat $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2013-64.bat $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2015-32.bat $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2015-64.bat $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2017-32.bat $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2017-64.bat $cmziptmpdir
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(cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2013 -C Release -V -O hdf5.log" > build-VS2013-32.bat; chmod 755 build-VS2013-32.bat)
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(cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201364 -C Release -V -O hdf5.log" > build-VS2013-64.bat; chmod 755 build-VS2013-64.bat)
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(cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2015 -C Release -V -O hdf5.log" > build-VS2015-32.bat; chmod 755 build-VS2015-32.bat)
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(cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201564 -C Release -V -O hdf5.log" > build-VS2015-64.bat; chmod 755 build-VS2015-64.bat)
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(cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2017 -C Release -V -O hdf5.log" > build-VS2017-32.bat; chmod 755 build-VS2017-32.bat)
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(cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201764 -C Release -V -O hdf5.log" > build-VS2017-64.bat; chmod 755 build-VS2017-64.bat)
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# step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
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cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpdir
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cp $cmziptmpdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpdir
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cp $cmziptmpdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpdir
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cp $cmziptmpdir/$version/config/cmake/scripts/HDF5options.cmake $cmziptmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmziptmpsubdir
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cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpsubdir
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cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.8-Source.tar.gz $cmziptmpsubdir
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cp $cmziptmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpsubdir
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cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpsubdir
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cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmziptmpsubdir
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# step 4: convert text files
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# There maybe a simpler way to do this.
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@ -234,12 +236,13 @@ tar2cmakezip()
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# -k Keep the date stamp
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# -q quiet mode
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# grep redirect output to /dev/null because -q or -s are not portable.
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find $cmziptmpdir/$version | \
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find $cmziptmpsubdir/$version | \
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while read inf; do \
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if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
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unix2dos -q -k $inf; \
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fi\
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done
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# step 3: make zipball
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# -9 maximum compression
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# -y Store symbolic links as such in the zip archive
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@ -284,9 +287,9 @@ tar2cmakezip()
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# Returns 0 if successful; 1 otherwise
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#
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# need function to create another temporary directory, extract the
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# $tmpdir/$HDF5_VERS.tar into it, add (create) build-unix.sh,
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# CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz and ZLib.tar.gz,
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# and then tar.gz it.
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# $tmpdir/$HDF5_VERS.tar into it, create build-unix.sh,
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# add CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz
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# ZLib.tar.gz, HDF5 examples, and then tar.gz it.
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tar2cmaketgz()
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{
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if [ $# -ne 3 ]; then
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@ -294,16 +297,17 @@ tar2cmaketgz()
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return 1
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fi
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cmgztmpdir=/tmp/cmgztmpdir$$
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mkdir -p $cmgztmpdir
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cmgztmpsubdir=$cmgztmpdir/CMake-$HDF5_VERS
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mkdir -p $cmgztmpsubdir
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version=$1
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tarfile=$2
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tgzfile=$3
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# step 1: untar tarball in cmgztmpdir
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(cd $cmgztmpdir; tar xf -) < $tarfile
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(cd $cmgztmpsubdir; tar xf -) < $tarfile
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# sanity check
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if [ ! -d $cmgztmpdir/$version ]; then
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echo "untar did not create $cmgztmpdir/$version source dir"
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if [ ! -d $cmgztmpsubdir/$version ]; then
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echo "untar did not create $cmgztmpsubdir/$version source dir"
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# cleanup
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rm -rf $cmgztmpdir
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return 1
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@ -311,14 +315,15 @@ tar2cmaketgz()
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# step 2: add build-unix.sh script
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(cd $cmgztmpdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log" > build-unix.sh; chmod 755 build-unix.sh)
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(cd $cmgztmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log" > build-unix.sh; chmod 755 build-unix.sh)
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# step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
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cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpdir
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cp $cmgztmpdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpdir
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cp $cmgztmpdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpdir
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cp $cmgztmpdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpdir
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cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpsubdir
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cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
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cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.8-Source.tar.gz $cmgztmpsubdir
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cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
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cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
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cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpsubdir
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tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1
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# cleanup
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@ -49,13 +49,14 @@ libhdf5_cpp_la_LIBADD=$(LIBHDF5)
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# Public headers
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include_HEADERS=H5Cpp.h H5AbstractDs.h H5AtomType.h \
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H5Attribute.h H5Classes.h H5CommonFG.h H5CompType.h \
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H5DataSet.h H5DataSpace.h H5DataType.h H5OcreatProp.h \
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H5DaccProp.h H5DcreatProp.h H5DxferProp.h H5EnumType.h \
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H5Exception.h H5FaccProp.h H5FcreatProp.h H5File.h \
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H5FloatType.h H5Group.h H5IdComponent.h H5Include.h \
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H5IntType.h H5LcreatProp.h H5LaccProp.h H5Library.h \
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H5Location.h H5Object.h H5PredType.h H5PropList.h \
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H5StrType.h H5CppDoc.h H5ArrayType.h H5VarLenType.h
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H5DataSet.h H5DataSpace.h H5DataType.h H5OcreatProp.h \
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H5DaccProp.h H5DcreatProp.h \
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H5DxferProp.h H5EnumType.h H5Exception.h H5FaccProp.h \
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H5FcreatProp.h H5File.h H5FloatType.h H5Group.h \
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H5IdComponent.h H5Include.h H5IntType.h H5LcreatProp.h \
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H5LaccProp.h H5Library.h H5Location.h H5Object.h \
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H5PredType.h H5PropList.h H5StrType.h H5CppDoc.h \
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H5ArrayType.h H5VarLenType.h
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# h5c++ and libhdf5.settings are generated during configure. Remove only when
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# distclean.
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@ -85,7 +85,7 @@ case "$cc_vendor-$cc_version" in
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esac
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case "$host_os-$host_cpu" in
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# cygwin needs the "-std-c99" flag removed, so make
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# cygwin needs the "-std=c99" flag removed, so make
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# a specific case for Cygwin without the flag and a default
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# case to add the flag everywhere else
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cygwin-*)
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@ -197,6 +197,44 @@ Bug Fixes since HDF5-1.10.2 release
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(DER - 2018/02/26, HDFFV-10356)
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- A bug was discovered in the parallel library which caused partial
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parallel reads of filtered datasets to return incorrect data. The
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library used the incorrect dataspace for each chunk read, causing
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the selection used in each chunk to be wrong.
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The bug was not caught during testing because all of the current
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tests which do parallel reads of filtered data read all of the data
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using an H5S_ALL selection. Several tests were added which exercise
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partial parallel reads.
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(JTH - 2018/07/16, HDFFV-10467)
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- A bug was discovered in the parallel library which caused parallel
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writes of filtered datasets to trigger an assertion failure in the
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file free space manager.
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This occurred when the filter used caused chunks to repeatedly shrink
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and grow over the course of several dataset writes. The previous chunk
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information, such as the size of the chunk and the offset in the file,
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was being cached and not updated after each write, causing the next write
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to the chunk to retrieve the incorrect cached information and run into
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issues when reallocating space in the file for the chunk.
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(JTH - 2018/07/16, HDFFV-10509)
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- A bug was discovered in the parallel library which caused the
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H5D__mpio_array_gatherv() function to allocate too much memory.
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When the function is called with the 'allgather' parameter set
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to a non-true value, the function will receive data from all MPI
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ranks and gather it to the single rank specied by the 'root'
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parameter. However, the bug in the function caused memory for
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the received data to be allocated on all MPI ranks, not just the
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singular rank specified as the receiver. In some circumstances,
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this would cause an application to fail due to the large amounts
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of memory being allocated.
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(JTH - 2018/07/16, HDFFV-10467)
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Configuration
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-------------
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