CHG: Updated install scripts and configuration for Pleiades

externalpackages/dakota/install-6.2-pleiades.sh

@@ -10,12 +10,12 @@ PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where ext
 
 ## Environment
 #
-export BLAS_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64
-export CXXFLAGS='-std=c++11'
+export BLAS_LIBS="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
+export CXXFLAGS='-std=c++98'
 export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
 export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
 export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
-export LAPACK_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64
+export LAPACK_LIBS="-L${COMP_INTEL_ROOT}/mkl/lib/intel64/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
 
 # Cleanup
 rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
@@ -58,7 +58,7 @@ cmake \
 	-DCMAKE_C_COMPILER=mpicc \
 	-DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \
 	-DCMAKE_CXX_COMPILER=mpicxx \
-	-DCMAKE_Fortran_COMPILER=/usr/bin/gfortran \
+	-DCMAKE_Fortran_COMPILER=gfortran \
 	-DBoost_NO_BOOST_CMAKE=TRUE \
 	-DHAVE_ACRO=OFF \
 	-DHAVE_JEGA=OFF \

externalpackages/gdal/install-3-ghub-workspace_10.sh

@@ -8,7 +8,7 @@ set -eu
 
 ## Constants
 #
-VER="3.5.3"
+VER="3.10.0"
 
 ## Environment
 #

externalpackages/gdal/install-3-linux-python.sh

@@ -8,7 +8,7 @@ set -e
 
 ## Constants
 #
-VER="3.8.4"
+VER="3.10.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/gdal/install"
 

externalpackages/gdal/install-3-linux.sh

@@ -8,7 +8,7 @@ set -e
 
 ## Constants
 #
-VER="3.8.4"
+VER="3.10.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/gdal/install"
 

externalpackages/gdal/install-3-mac-python.sh

@@ -8,7 +8,7 @@ set -e
 
 ## Constants
 #
-VER="3.8.4"
+VER="3.10.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/gdal/install"
 

externalpackages/gdal/install-3-mac.sh

@@ -8,7 +8,7 @@ set -e
 
 ## Constants
 #
-VER="3.8.4"
+VER="3.10.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/gdal/install"
 

externalpackages/gdal/install-3-python-static.sh

@@ -8,7 +8,7 @@ set -e
 
 ## Constants
 #
-VER="3.8.4"
+VER="3.10.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/gdal/install"
 

externalpackages/gdal/install-3-static.sh

@@ -8,7 +8,7 @@ set -e
 
 ## Constants
 #
-VER="3.8.4"
+VER="3.10.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/gdal/install"
 

externalpackages/gmsh/install-4-pleiades.sh

@@ -0,0 +1,84 @@
+#!/bin/bash
+set -e
+
+
+# TODO:
+# - Add support for,
+#	- MUMPS
+#	- PETSc
+# 
+# See Also:
+# - configs/4/static/CMakeLists.txt
+# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
+#
+
+## Constants
+#
+VER="4.12.2"
+
+PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
+
+BLASLAPACK_LIBFLAGS="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
+LIBGFORTRAN_LIBFLAGS="-L${COMP_INTEL_ROOT}/compiler/lib/intel64_lin -lifcore -lifport -lgfortran"
+
+# Environment
+#
+export CXXFLAGS="${CXXFLAGS} -w"
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://gmsh.info/src/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
+
+# Unpack source
+tar -xvzf gmsh-${VER}-source.tgz
+
+# Move source to 'src' directory
+mv gmsh-${VER}-source/* src
+rm -rf gmsh-${VER}-source
+
+# Configure
+#
+# NOTE:
+# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
+# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG 
+#	movies.
+# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not 
+#	importing STEP/IGES files.
+# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we 
+#	do not need to support Apple Touch bar (does not affect compilation on 
+#	Linux).
+#
+cd src
+cmake \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_INSTALL_RPATH="${PREFIX}/lib" \
+	-DCMAKE_BUILD_TYPE=Release \
+	-DENABLE_BUILD_DYNAMIC=1 \
+	-DENABLE_BUILD_SHARED=1 \
+	-DBLAS_LAPACK_LIBRARIES="${BLASLAPACK_LIBFLAGS} ${LIBGFORTRAN_LIBFLAGS}" \
+	-DENABLE_BLAS_LAPACK=1 \
+	-DENABLE_EIGEN=0 \
+	-DENABLE_FLTK=0 \
+	-DENABLE_MPEG_ENCODE=0 \
+	-DENABLE_MPI=1 \
+	-DENABLE_OCC=0 \
+	-DENABLE_TOUCHBAR=0 \
+	-DMETIS_ROOT="${PETSC_DIR}/lib"
+
+# Compile and install
+if [ $# -eq 0 ]; then
+	make
+	make install
+else
+	make -j $1
+	make -j $1 install
+fi
+
+# Make necessary link on RHEL
+if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
+	cd ${PREFIX}
+	ln -s ./lib64 ./lib
+fi

externalpackages/gmt/install-6-pleiades.sh

@@ -0,0 +1,72 @@
+#!/bin/bash
+set -e
+
+
+## Constants
+#
+VER="6.5.0"
+
+PREFIX="${ISSM_DIR}/externalpackages/gmt/install"
+
+BLASLAPACK_LIBFLAGS="-L${COMP_INTEL_ROOT}/mkl/lib/intel64;-lmkl_intel_lp64;-lmkl_sequential;-lmkl_core"
+LIBGFORTRAN_LIBFLAGS="-L${COMP_INTEL_ROOT}/compiler/lib/intel64_lin;-lifcore;-lifport;-lgfortran"
+
+# Environment
+#
+export CC=mpicc
+export CFLAGS="${CFLAGS} -w"
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/GenericMappingTools/gmt/archive/refs/tags/${VER}.tar.gz" "gmt-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf gmt-${VER}.tar.gz
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Move source to 'src' directory
+mv gmt-${VER}/* src
+rm -rf gmt-${VER}
+
+# Copy custom configuration files to source
+cp ./src/cmake/ConfigUserAdvancedTemplate.cmake ./src/cmake/ConfigUser.cmake
+
+# Patch source
+patch ./src/cmake/ConfigUser.cmake < ./configs/${VER%.*}/cmake/ConfigUserAdvancedTemplate.cmake.patch
+
+# Configure
+cd src
+mkdir build
+cd build
+
+# NOTE:
+# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake
+#	that, ostensibly, allows for supplying the path to curl when it is in a
+#	non-standard location. That said, newer versions of CMake will ignore said
+#	variable and instead try to find curl itself. Passing in the two options
+#	below overrides this behavior.
+#
+cmake \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DBLAS_LIBRARIES="${BLASLAPACK_LIBFLAGS};${LIBGFORTRAN_LIBFLAGS}" \
+	-DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
+	-DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \
+	-DLAPACK_LIBRARIES="${BLASLAPACK_LIBFLAGS};${LIBGFORTRAN_LIBFLAGS}" \
+	..
+
+# Compile and install
+if [ $# -eq 0 ]; then
+	make
+	make install
+else
+	make -j $1
+	make -j $1 install
+fi
+
+# Make necessary link on RHEL
+if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
+	cd ${PREFIX}
+	ln -s ./lib64 ./lib
+fi

externalpackages/proj/install-6-static.sh

@@ -4,7 +4,7 @@ set -eu
 
 # Constants
 #
-VER="6.2.1"
+VER="6.3.2"
 
 PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed
 

externalpackages/proj/install-6.sh

@@ -4,7 +4,7 @@ set -eu
 
 # Constants
 #
-VER="6.2.1"
+VER="6.3.2"
 
 PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed
 

externalpackages/semic/install.sh

@@ -4,15 +4,25 @@ set -eu
 
 ## Constants
 #
+VER="1.2"
+
 PREFIX="${ISSM_DIR}/externalpackages/semic/install" # Set to location where external package should be installed
 
 # Cleanup
 rm -rf ${PREFIX} src
-mkdir -p ${PREFIX}/lib
+mkdir -p ${PREFIX} ${PREFIX}/lib src
 
 # Download source
-git clone https://github.com/mkrapp/semic.git src
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/mkrapp/semic/archive/refs/tags/v${VER}.tar.gz" "semic-${VER}.tar.gz"
+
+# Unpack source
+tar -xvzf semic-${VER}.tar.gz
+
+# Move source to 'src' directory
+mv semic-${VER}/* src
+rm -rf semic-${VER}
 
+# Compile and install semic module utils.f90
 if which ifort >/dev/null; then
 	FC="ifort"
 	FFLAGS="-traceback -check all" # -O2 is default 
@@ -25,7 +35,6 @@ else
 	fi
 fi
 
-# Compile and install semic module utils.f90
 cd src/
 (
 cat << EOF