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Louis Nicolas Stenger
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‎.bash_profile‎

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# .bash_profile
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# Get the aliases and functions
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if [ -f ~/.bashrc ]; then
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. ~/.bashrc
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fi
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# User specific environment and startup programs
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export MODULEPATH="/discofs/$(whoami)/opt/software/modulefiles${MODULEPATH:+:$MODULEPATH}"

‎.bashrc‎

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# .bashrc
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# Source global definitions
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if [ -f /etc/bashrc ]; then
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. /etc/bashrc
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fi
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# User specific environment
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if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]]
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then
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PATH="$HOME/.local/bin:$HOME/bin:$PATH"
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fi
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export PATH
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export TZ='Europe/Zurich'
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export SCRATCH="/discofs/$(whoami)"
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export PROJECT="/discofs/$(whoami)"
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# Uncomment the following line if you don't like systemctl's auto-paging feature:
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# export SYSTEMD_PAGER=
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# User specific aliases and functions
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function gbsmoduleload(){
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PETSC_VERSION="${1:-3.19.4}"
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PETSC_COMPILER="${2:-intel}"
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PETSC_OPTLEVEL="${3:-opt}"
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PETSC_MPI='openmpi'
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PETSC_MAJOR_VERSION="$(echo $PETSC_VERSION | cut -d. -f1)"
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PETSC_MODULENAME="petsc/${PETSC_MAJOR_VERSION}/${PETSC_VERSION}/${PETSC_COMPILER}-${PETSC_MPI}-${PETSC_OPTLEVEL}"
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module load "$PETSC_MODULENAME"
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export CC=mpicc CXX=mpicxx FC=mpifort
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}

‎petsc_install.sh‎

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#!/usr/bin/bash
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set -euo pipefail
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IFS=$'\n\t'
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mkdir -p tmp
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export TMP="$(realpath tmp)"
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export TEMP="$TMP"
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export TMPDIR="$TMP"
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INSTALL_ROOT="/discofs/$(whoami)"
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INSTALL_OPT="${INSTALL_ROOT}/opt/software"
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INSTALL_PETSC_COMPILER="intel"
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INSTALL_PETSC_MPI="mpich"
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INSTALL_PETSC_HDF5_FORCE_MODULE=""
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INSTALL_PETSC_HDF5_VERSION="1.13"
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INSTALL_PETSC_OPT="opt" # "opt" or "dbg" or "fast"
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INSTALL_PETSC_VERSION_MAJOR="3"
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INSTALL_PETSC_VERSION_MINOR="19.4"
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INSTALL_PETSC_VERSION="${INSTALL_PETSC_VERSION_MAJOR}.${INSTALL_PETSC_VERSION_MINOR}"
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INSTALL_PETSC_TAG="v${INSTALL_PETSC_VERSION}"
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INSTALL_PETSC_HDF5_MODULENAME="${INSTALL_PETSC_HDF5_FORCE_MODULE:-hdf5/1/${INSTALL_PETSC_HDF5_VERSION}/latest-${INSTALL_PETSC_COMPILER}-${INSTALL_PETSC_MPI}}"
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echo "Using $INSTALL_PETSC_HDF5_MODULENAME as base."
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if [[ ${INSTALL_PETSC_COMPILER} =~ "intel" ]]; then
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mpiicc &>/dev/null && INSTALL_MPICC='mpiicc' || INSTALL_MPICC='mpicc'
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mpiicpc &>/dev/null && INSTALL_MPICXX='mpiicpc' || INSTALL_MPICXX='mpicxx'
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mpiifort &>/dev/null && INSTALL_MPIF90='mpiifort' || INSTALL_MPIF90='mpif90'
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else
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INSTALL_MPICC='mpicc'
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INSTALL_MPICXX='mpicxx'
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INSTALL_MPIF90='mpif90'
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fi
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if [[ ${INSTALL_PETSC_MPI} =~ "mpich" ]]; then
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if [[ ${INSTALL_PETSC_COMPILER} =~ "intel" ]]; then
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export MPICH_CC="icc"
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export MPICH_CXX="icpc"
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export MPICH_FC="ifort"
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fi
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fi
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if [[ ${INSTALL_PETSC_OPT} == "fast" ]]; then
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INSTALL_CFLAGS='-Ofast -DNDEBUG'
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INSTALL_CXXFLAGS="${INSTALL_CFLAGS}"
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INSTALL_FFLAGS="${INSTALL_CFLAGS}"
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INSTALL_PETSC_WITH_DEBUGGING='no'
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elif [[ ${INSTALL_PETSC_OPT} == "opt" ]]; then
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INSTALL_CFLAGS='-O3 -DNDEBUG'
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INSTALL_CXXFLAGS="${INSTALL_CFLAGS}"
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INSTALL_FFLAGS="${INSTALL_CFLAGS}"
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INSTALL_PETSC_WITH_DEBUGGING='no'
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else
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INSTALL_PETSC_OPT='dbg'
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INSTALL_CFLAGS='-g -O0'
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INSTALL_CXXFLAGS="${INSTALL_CFLAGS}"
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INSTALL_FFLAGS="${INSTALL_CFLAGS}"
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INSTALL_PETSC_WITH_DEBUGGING='yes'
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fi
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if [[ ${INSTALL_PETSC_OPT} != "dbg" ]]; then
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if [[ ${INSTALL_PETSC_COMPILER} =~ "intel" ]]; then
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INSTALL_CFLAGS="${INSTALL_CFLAGS} -march=core-avx2 -mtune=core-avx2"
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INSTALL_CXXFLAGS="${INSTALL_CXXFLAGS} -march=core-avx2 -mtune=core-avx2"
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INSTALL_FFLAGS="${INSTALL_FFLAGS} -march=core-avx2 -mtune=core-avx2"
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elif [[ ${INSTALL_PETSC_COMPILER} =~ "aocc" ]]; then
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INSTALL_CFLAGS="${INSTALL_CFLAGS} -march=znver2"
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INSTALL_CXXFLAGS="${INSTALL_CXXFLAGS} -march=znver2"
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INSTALL_FFLAGS="${INSTALL_FFLAGS} -march=znver2"
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else
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INSTALL_CFLAGS="${INSTALL_CFLAGS} -march=znver2 -mtune=native"
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INSTALL_CXXFLAGS="${INSTALL_CXXFLAGS} -march=znver2 -mtune=native"
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INSTALL_FFLAGS="${INSTALL_FFLAGS} -march=znver2 -mtune=native"
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fi
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fi
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if [[ ${INSTALL_PETSC_COMPILER} =~ "intel" ]]; then
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INSTALL_CFLAGS="-diag-disable=10441 ${INSTALL_CFLAGS}"
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INSTALL_CXXFLAGS="-diag-disable=10441 ${INSTALL_CXXFLAGS}"
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fi
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module purge
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module load $INSTALL_PETSC_HDF5_MODULENAME
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IFS=$' \n\t'
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echo "Calling the selected compilers"
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echo " ${INSTALL_MPICC} ${INSTALL_CFLAGS} --version"
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${INSTALL_MPICC} ${INSTALL_CFLAGS} --version
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echo
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echo " ${INSTALL_MPICXX} ${INSTALL_CXXFLAGS} --version"
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${INSTALL_MPICXX} ${INSTALL_CXXFLAGS} --version
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echo
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echo " ${INSTALL_MPIF90} ${INSTALL_FFLAGS} --version"
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${INSTALL_MPIF90} ${INSTALL_FFLAGS} -diag-disable=10006 --version
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echo
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IFS=$'\n\t'
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export PETSC_ARCH="${INSTALL_PETSC_COMPILER}-${INSTALL_PETSC_MPI}-${INSTALL_PETSC_OPT}"
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PETSC_PREFIX="petsc/${INSTALL_PETSC_VERSION_MAJOR}/${INSTALL_PETSC_VERSION}/${PETSC_ARCH}"
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INSTALL_PETSC_FULL_PREFIX="${INSTALL_OPT}/${PETSC_PREFIX}"
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mkdir -p "$INSTALL_PETSC_FULL_PREFIX"
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PETSC_CLONE_DIR="${TMPDIR}/petsc-${INSTALL_PETSC_TAG}"
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rm -rf ${PETSC_CLONE_DIR}
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git clone -b "${INSTALL_PETSC_TAG}" --depth=1 https://gitlab.com/petsc/petsc.git "${PETSC_CLONE_DIR}" || true
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pushd "${PETSC_CLONE_DIR}"
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./configure \
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--prefix="$INSTALL_PETSC_FULL_PREFIX" \
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--with-debugging=${INSTALL_PETSC_WITH_DEBUGGING} \
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--with-batch \
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--with-cc="${INSTALL_MPICC}" \
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--with-cxx="${INSTALL_MPICXX}" \
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--with-fc="${INSTALL_MPIF90}" \
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COPTFLAGS=${INSTALL_CFLAGS} \
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CXXOPTFLAGS=${INSTALL_CXXFLAGS} \
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FOPTFLAGS=${INSTALL_FFLAGS} \
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--download-sowing=yes \
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--download-fblaslapack=yes \
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--download-hypre=yes
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make
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make install
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popd
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MODULE_INSTALL_ROOT="${INSTALL_OPT}/modulefiles"
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MODULEFILE_PATH="${MODULE_INSTALL_ROOT}/${PETSC_PREFIX}"
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MODULEFILE_DIR="$(dirname ${MODULE_INSTALL_ROOT}/${PETSC_PREFIX})"
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mkdir -p "$MODULEFILE_DIR"
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cat > "$MODULEFILE_PATH" <<EOF
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#%Module 1.0
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module load $INSTALL_PETSC_HDF5_MODULENAME
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set prefix $INSTALL_PETSC_FULL_PREFIX
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prepend-path PATH \$prefix/bin
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prepend-path LD_LIBRARY_PATH \$prefix/lib
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prepend-path LD_RUN_PATH \$prefix/lib
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prepend-path PKG_CONFIG_PATH \$prefix/lib/pkgconfig
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prepend-path --delim " " CFLAGS "-I\$prefix/include"
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prepend-path --delim " " CXXFLAGS "-I\$prefix/include"
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prepend-path --delim " " FCFLAGS "-I\$prefix/include"
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prepend-path --delim " " LDFLAGS "-L\$prefix/lib"
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EOF
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echo "PETSc should have been installed."
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echo " Module files are provided with this installation."
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echo " Running the following commands should put PETSc in your PATH:"
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echo
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echo ' export MODULEPATH="'"${MODULE_INSTALL_ROOT}"'${MODULEPATH:+:$MODULEPATH}"'
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echo ' module load petsc'
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echo
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echo ' The first line may be added to your ~/.bash_profile if it works.'
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echo

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