CI: Build without hdf5

sandialabs · Jun 1, 2023 · 1ec8147 · 1ec8147
1 parent 875867c
commit 1ec8147
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Showing 4 changed files with 120 additions and 83 deletions.
diff --git a/TPL/matio/runcmake.sh b/TPL/matio/runcmake.sh
@@ -11,6 +11,14 @@ INSTALL_PATH=${INSTALL_PATH:-${ACCESS}}
 
 rm -f config.cache
 
+HDF5="${HDF5:-YES}"
+if [ "$HDF5" == "YES" ]
+then
+  DEFAULT_VERSION="7.3"
+else
+  DEFAULT_VERSION="5"
+fi
+
 DEBUG="${DEBUG:-NO}"
 if [ "$DEBUG" == "YES" ]
 then
@@ -51,12 +59,12 @@ rm -f config.cache
 cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
          -DBUILD_SHARED_LIBS:BOOL=${SHARED} \
          -DMATIO_SHARED:BOOL=${SHARED} \
-	 -DMATIO_DEFAULT_FILE_VERSION=7.3 \
-         -DMATIO_MAT73:BOOL=ON \
+	 -DMATIO_DEFAULT_FILE_VERSION=${DEFAULT_VERSION} \
+         -DMATIO_MAT73:BOOL=${HDF5} \
          -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} \
          -DCMAKE_INSTALL_LIBDIR:PATH=lib \
 	 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-         -DMATIO_WITH_HDF5:BOOL=ON \
+         -DMATIO_WITH_HDF5:BOOL=${HDF5} \
          -DMATIO_WITH_ZLIB:BOOL=ON \
          -DHDF5_ROOT:PATH=${INSTALL_PATH} \
          -DHDF5_DIR:PATH=${INSTALL_PATH} \

diff --git a/TPL/netcdf/runcmake.sh b/TPL/netcdf/runcmake.sh
@@ -6,6 +6,7 @@ if [ "X$ACCESS" == "X" ] ; then
 fi
 INSTALL_PATH=${INSTALL_PATH:-${ACCESS}}
 
+HDF5="${HDF5:-YES}"
 DEBUG="${DEBUG:-NO}"
 if [ "$DEBUG" == "YES" ]
 then
@@ -28,6 +29,13 @@ else
   EXTRA_DEPS="-DNC_EXTRA_DEPS=-ldl\;-lz"
 fi
 
+if [[ "$HDF5" == "ON" || "$HDF5" == "YES" ]]
+then
+    HDF5_INFO="-DHDF5_ROOT:PATH=${INSTALL_PATH} -DHDF5_DIR:PATH=${INSTALL_PATH} -DENABLE_NETCDF4:BOOL=ON"
+else
+    HDF5_INFO="-DENABLE_HDF5=OFF -DENABLE_NETCDF4:BOOL=OFF"
+fi
+
 NEEDS_ZLIB="${NEEDS_ZLIB:-NO}"
 if [ "$NEEDS_ZLIB" == "YES" ]
 then
@@ -54,7 +62,6 @@ cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
          -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} \
          -DCMAKE_INSTALL_LIBDIR:PATH=lib \
 	 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-         -DENABLE_NETCDF_4:BOOL=ON \
          -DENABLE_PNETCDF:BOOL=${MPI} \
          -DENABLE_CDF5=ON \
          -DENABLE_MMAP:BOOL=ON \
@@ -63,9 +70,8 @@ cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
          ${LOCAL_ZLIB} \
          ${LOCAL_SZIP} \
          ${EXTRA_DEPS} \
-         -DENABLE_CONVERSION_WARNINGS:BOOL=OFF \
-         -DHDF5_ROOT:PATH=${INSTALL_PATH} \
-         -DHDF5_DIR:PATH=${INSTALL_PATH}
+	 ${HDF5_INFO} \
+         -DENABLE_CONVERSION_WARNINGS:BOOL=OFF
 
 echo ""
 echo "         MPI: ${MPI}"

diff --git a/cmake/modules/FindMatio.cmake b/cmake/modules/FindMatio.cmake
@@ -170,7 +170,16 @@ else(Matio_LIBRARIES AND Matio_INCLUDE_DIRS)
     # Need to find the Matio config script to check for HDF5
     message(STATUS "Assuming that Matio requires HDF5")
     if ( NOT TARGET hdf5)
-      add_package_dependency(Matio DEPENDS_ON HDF5)
+     assert_defined(Matio_INCLUDE_DIRS)
+     find_path(inc_path
+        NAMES "matio_pubconf.h"
+        HINTS ${Matio_INCLUDE_DIRS}
+        NO_DEFAULT_PATH)
+     file(STRINGS "${inc_path}/matio_pubconf.h" matio_default_version REGEX " MAT_FT_DEFAULT ")
+     string(REGEX MATCH "4|73" default_version "${matio_default_version}")
+     if (default_version EQUAL 73)
+        add_package_dependency(Matio DEPENDS_ON HDF5)
+     endif()
     endif()
 
 endif(Matio_LIBRARIES AND Matio_INCLUDE_DIRS )    

diff --git a/install-tpl.sh b/install-tpl.sh
@@ -69,8 +69,10 @@ BB=$(check_valid BB)
 CRAY=${CRAY:-NO}
 CRAY=$(check_valid CRAY)
 
-# Which TPLS? (HDF5 and NetCDF always, PnetCDF if MPI=ON)
-CGNS=${CGNS:-YES}
+# Which TPLS? (NetCDF always, PnetCDF if MPI=ON)
+HDF5=${HDF5:-YES}
+HDF5=$(check_valid HDF5)
+CGNS=${CGNS:-${HDF5}}
 CGNS=$(check_valid CGNS)
 
 MATIO=${MATIO:-YES}
@@ -186,6 +188,7 @@ if [ $# -gt 0 ]; then
         echo "   DEBUG        = ${DEBUG}"
         echo "   USE_PROXY    = ${USE_PROXY}"
         echo ""
+        echo "   HDF5         = ${HDF5}"
         echo "   H5VERSION    = ${H5VERSION}"
         echo "   CGNS         = ${CGNS}"
         echo "   MATIO        = ${MATIO}"
@@ -391,80 +394,84 @@ then
 fi
 
 # =================== BUILD HDF5 ===============
-if [ "$FORCE" == "YES" ] || ! [ -e $INSTALL_PATH/lib/libhdf5.${LD_EXT} ]
+if [ "$HDF5" == "YES" ]
 then
-    echo "${txtgrn}+++ HDF5${txtrst}"
-    hdf_suffix=""
-    if [ "${H5VERSION}" == "V18" ]; then
-        hdf_version="1.8.23"
-        hdf_base="1.8"
-    elif [ "${H5VERSION}" == "V110" ]; then
-        hdf_version="1.10.10"
-        hdf_base="1.10"
-    elif [ "${H5VERSION}" == "V112" ]; then
-        hdf_version="1.12.2"
-        hdf_base="1.12"
-    elif [ "${H5VERSION}" == "V113" ]; then
-        hdf_version="1.13.1"
-        hdf_base="1.13"
-    elif [ "${H5VERSION}" == "V114" ]; then
-        hdf_version="1.14.1"
-        hdf_base="1.14"
-	hdf_suffix="-2"
-    elif [ "${H5VERSION}" == "develop" ]; then
-        hdf_version="develop"
-    else
-        echo 1>&2 ${txtred}Invalid HDF5 version specified: ${H5VERSION}.  Must be one of V18, V110, V112. exiting.${txtrst}
-        exit 1
-    fi
-
-    cd $ACCESS || exit
-    cd TPL/hdf5 || exit
-    if [ "$DOWNLOAD" == "YES" ]
-    then
-        echo "${txtgrn}+++ Downloading...${txtrst}"
-        rm -rf hdf5-${hdf_version}${hdf_suffix}
-        rm -f hdf5-${hdf_version}${hdf_suffix}.tar.bz2
-        if [ "${H5VERSION}" == "develop" ]; then
-            git clone https://github.com/HDFGroup/hdf5.git hdf5-develop
-        else
-            wget --no-check-certificate https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${hdf_base}/hdf5-${hdf_version}/src/hdf5-${hdf_version}${hdf_suffix}.tar.bz2
-        fi
-        if [ "${H5VERSION}" != "develop" ]
-        then
-            tar -jxf hdf5-${hdf_version}${hdf_suffix}.tar.bz2
-            rm -f hdf5-${hdf_version}${hdf_suffix}.tar.bz2
-        fi
-    fi
-
-    if [ "$BUILD" == "YES" ]
+    if [ "$FORCE" == "YES" ] || ! [ -e $INSTALL_PATH/lib/libhdf5.${LD_EXT} ]
     then
-        echo "${txtgrn}+++ Configuring, Building, and Installing...${txtrst}"
-        cd hdf5-${hdf_version}${hdf_suffix} || exit
-        rm -rf build
-        mkdir build
-        cd build || exit
-        CRAY=${CRAY} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash -x ../../runcmake.sh
-        #CRAY=${CRAY} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash ../runconfigure.sh
-        if [[ $? != 0 ]]
-        then
-            echo 1>&2 ${txtred}couldn\'t configure hdf5. exiting.${txtrst}
-            exit 1
-        fi
-        make -j${JOBS} && ${SUDO} make "V=${VERBOSE}" install
-        if [[ $? != 0 ]]
-        then
-            echo 1>&2 ${txtred}couldn\'t build hdf5. exiting.${txtrst}
+	echo "${txtgrn}+++ HDF5${txtrst}"
+	hdf_suffix=""
+	if [ "${H5VERSION}" == "V18" ]; then
+            hdf_version="1.8.23"
+            hdf_base="1.8"
+	elif [ "${H5VERSION}" == "V110" ]; then
+            hdf_version="1.10.10"
+            hdf_base="1.10"
+	elif [ "${H5VERSION}" == "V112" ]; then
+            hdf_version="1.12.2"
+            hdf_base="1.12"
+	elif [ "${H5VERSION}" == "V113" ]; then
+            hdf_version="1.13.1"
+            hdf_base="1.13"
+	elif [ "${H5VERSION}" == "V114" ]; then
+            hdf_version="1.14.1"
+            hdf_base="1.14"
+	    hdf_suffix="-2"
+	elif [ "${H5VERSION}" == "develop" ]; then
+            hdf_version="develop"
+	else
+            echo 1>&2 ${txtred}Invalid HDF5 version specified: ${H5VERSION}.  Must be one of V18, V110, V112. exiting.${txtrst}
             exit 1
-        fi
+	fi
+
+	cd $ACCESS || exit
+	cd TPL/hdf5 || exit
+	if [ "$DOWNLOAD" == "YES" ]
+	then
+            echo "${txtgrn}+++ Downloading...${txtrst}"
+            rm -rf hdf5-${hdf_version}${hdf_suffix}
+            rm -f hdf5-${hdf_version}${hdf_suffix}.tar.bz2
+            if [ "${H5VERSION}" == "develop" ]; then
+		git clone https://github.com/HDFGroup/hdf5.git hdf5-develop
+            else
+		wget --no-check-certificate https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${hdf_base}/hdf5-${hdf_version}/src/hdf5-${hdf_version}${hdf_suffix}.tar.bz2
+            fi
+            if [ "${H5VERSION}" != "develop" ]
+            then
+		tar -jxf hdf5-${hdf_version}${hdf_suffix}.tar.bz2
+		rm -f hdf5-${hdf_version}${hdf_suffix}.tar.bz2
+            fi
+	fi
+
+	if [ "$BUILD" == "YES" ]
+	then
+            echo "${txtgrn}+++ Configuring, Building, and Installing...${txtrst}"
+            cd hdf5-${hdf_version}${hdf_suffix} || exit
+            rm -rf build
+            mkdir build
+            cd build || exit
+            CRAY=${CRAY} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash -x ../../runcmake.sh
+            #CRAY=${CRAY} H5VERSION=${H5VERSION} DEBUG=${DEBUG} SHARED=${SHARED} NEEDS_ZLIB=${NEEDS_ZLIB} NEEDS_SZIP=${NEEDS_SZIP} MPI=${MPI} bash ../runconfigure.sh
+            if [[ $? != 0 ]]
+            then
+		echo 1>&2 ${txtred}couldn\'t configure hdf5. exiting.${txtrst}
+		exit 1
+            fi
+            make -j${JOBS} && ${SUDO} make "V=${VERBOSE}" install
+            if [[ $? != 0 ]]
+            then
+		echo 1>&2 ${txtred}couldn\'t build hdf5. exiting.${txtrst}
+		exit 1
+            fi
+	fi
+	# Create default plugin directory...
+	mkdir  ${INSTALL_PATH}/lib/hdf5
+	mkdir  ${INSTALL_PATH}/lib/hdf5/lib
+	mkdir  ${INSTALL_PATH}/lib/hdf5/lib/plugin
+    else
+	echo "${txtylw}+++ HDF5 already installed.  Skipping download and installation.${txtrst}"
     fi
-    # Create default plugin directory...
-    mkdir  ${INSTALL_PATH}/lib/hdf5
-    mkdir  ${INSTALL_PATH}/lib/hdf5/lib
-    mkdir  ${INSTALL_PATH}/lib/hdf5/lib/plugin
-else
-    echo "${txtylw}+++ HDF5 already installed.  Skipping download and installation.${txtrst}"
 fi
+
 # =================== INSTALL PnetCDF if parallel build ===============
 if [ "$MPI" == "YES" ]
 then
@@ -544,8 +551,11 @@ then
         rm -rf build
         mkdir build
         cd build || exit
-        export HDF5_PLUGIN_PATH=${INSTALL_PATH}/lib/hdf5/lib/plugin
-        CRAY=${CRAY} SHARED=${SHARED} DEBUG=${DEBUG} NEEDS_ZLIB=${NEEDS_ZLIB} MPI=${MPI} bash -x ../../runcmake.sh
+	if [ "$HDF5" == "YES" ]
+	then
+           export HDF5_PLUGIN_PATH=${INSTALL_PATH}/lib/hdf5/lib/plugin
+	fi
+        CRAY=${CRAY} SHARED=${SHARED} DEBUG=${DEBUG} HDF5=${HDF5} NEEDS_ZLIB=${NEEDS_ZLIB} MPI=${MPI} bash -x ../../runcmake.sh
         if [[ $? != 0 ]]
         then
             echo 1>&2 ${txtred}couldn\'t configure cmake for NetCDF. exiting.${txtrst}
@@ -563,7 +573,7 @@ else
     echo "${txtylw}+++ NetCDF already installed.  Skipping download and installation.${txtrst}"
 fi
 # =================== INSTALL CGNS ===============
-if [ "$CGNS" == "YES" ]
+if [ "$CGNS" == "YES" ] && [ "$HDF5" == "YES" ]
 then
     if [ "$FORCE" == "YES" ] || ! [ -e $INSTALL_PATH/lib/libcgns.${LD_EXT} ]
     then
@@ -603,6 +613,10 @@ then
         echo "${txtylw}+++ CGNS already installed.  Skipping download and installation.${txtrst}"
     fi
 fi
+if [ "$CGNS" == "YES" ] && [ "$HDF5" == "NO" ]
+then
+    echo "${txtred}+++ CGNS requested, but HDF5 is not enabled.  Cannot build CGNS without HDF5.${txtrst}"
+fi
 
 # =================== INSTALL METIS  ===============
 if [ "$METIS" == "YES" ]
@@ -713,7 +727,7 @@ then
             rm -rf build
             mkdir build
             cd build || exit
-            CRAY=${CRAY} SHARED=${SHARED} DEBUG=${DEBUG} NEEDS_ZLIB=${NEEDS_ZLIB} bash -x ../../runcmake.sh
+            CRAY=${CRAY} SHARED=${SHARED} DEBUG=${DEBUG} NEEDS_ZLIB=${NEEDS_ZLIB} HDF5=${HDF5} bash -x ../../runcmake.sh
             if [[ $? != 0 ]]
             then
                 echo 1>&2 ${txtred}couldn\'t configure MatIO. exiting.${txtrst}