Intermediate commit. Transforming single script into individual steps.

.gitignore

@@ -0,0 +1 @@
+.DS_Store

install_script.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# ------------------------------------------------------------------------
+# PACKAGE LIST: register all new dependent tools and libs here. Order
+# is important, the first in the list gets installed first
+# ------------------------------------------------------------------------
+tool_list="gcc intel cmake"
+mpi_list="mpich openmpi intelmpi"
+math_list="mkl acml openblas"
+lib_list="fftw libint libxc libgrpp libxsmm cosma scalapack elpa cusolvermp plumed \
+          spfft spla ptscotch superlu pexsi quip gsl spglib hdf5 libvdwxc sirius
+          libvori libtorch deepmd"
+package_list="${tool_list} ${mpi_list} ${math_list} ${lib_list}"
+# ------------------------------------------------------------------------
+
+# first set everything to __DONTUSE__
+for ii in ${package_list}; do
+  eval with_${ii}="__DONTUSE__"
+done
+
+# ------------------------------------------------------------------------
+# Work out default settings
+# ------------------------------------------------------------------------
+
+# tools to turn on by default:
+with_gcc="__SYSTEM__"
+
+if [ "COMPILER" = intel ]; then
+    ./install_intel.sh
+elif [ "COMPILER" = llvm ]; then
+    ./install_llvm.sh
+elif [ "COMPILER" = clang]; then
+    ./install_llvm.sh
+else
+    ./install_gcc.sh
+fi
+
+

make_cluster.sh

@@ -13,146 +13,19 @@ else
     echo "This script is not the top-level bash file being run."
 fi
 
-## INSTALL GCC FROM SOURCE
+./scripts/install_gcc.sh
-GCC_BUILD_DIR=${BUILD_LOCATION}/gcc
-GCC_INSTALL_DIR=${INSTALL_LOCATION}/gcc
-mkdir -p ${GCC_INSTALL_DIR}
-mkdir gcc-${GCC_VERSION}-build
 
-GCC_VERSION=7.5.0
+./scripts/install_env-modules.sh
-cd ${GCC_BUILD_DIR}
 
-wget ftp://ftp.gnu.org/gnu/gcc/gcc-${GCC_VERSION}/gcc-${GCC_VERSION}.tar.gz
+./scripts/install_openssl.sh
-tar -xf gcc-${GCC_VERSION}.tar.gz
-mv gcc-${GCC_VERSION} gcc-${GCC_VERSION}-source
-cd gcc-${GCC_VERSION}-source
-./contrib/download_prerequisites
-cd ../gcc-${GCC_VERSION}-build
-${GCC_BUILD_DIR}/gcc-${GCC_VERSION}-source/configure --prefix=${GCC_INSTALL_DIR}/${GCC_VERSION} --enable-languages=c,c++,fortran,go --enable-lto --disable-multilib --enable-checking=release --enable-threads=posix --enable-libstdcxx-debug --enable-__cxa_atexit --enable-plugins --enable-bootstrap
-make -j$(nproc)
-make -j$(nproc) check
-make install
 
-## INSTALL ENVIRONMENT MODULES FROM SOURCE
+./scripts/stage0/install_qt.sh
-MODULES_BUILD_DIR=${BUILD_LOCATION}
-MODULES_INSTALL_DIR=${INSTALL_LOCATION}/modules
-mkdir -p ${MODULES_BUILD_DIR}
-mkdir -p ${MODULES_INSTALL_DIR}
 
-MODULES_VERSION=5.3.1
+./scripts/stage0/install_cmake.sh
 
-cd ${MODULES_BUILD_DIR}
+./scripts/stage0/install_git.sh
-curl -LJO https://github.com/cea-hpc/modules/releases/download/v${MODULES_VERSION}/modules-${MODULES_VERSION}.tar.gz
-tar -xf modules-${MODULES_VERSION}.tar.gz
-cd modules-${MODULES_VERSION}
-mkdir build && cd build
-./configure --prefix=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION} --modulefilesdir=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/modulefiles
-make -j$(nproc)
-make install
-ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.sh /etc/profile.d/modules.sh
-ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.csh /etc/profile.d/modules.csh
 
-## INSTALL OPENSSL FOR CMAKE
+./scripts/stage0/install_llvm.sh
-SSL_BUILD_DIR=${BUILD_LOCATION}/openssl
-SSL_INSTALL_DIR=${INSTALL_LOCATION}/openssl
-mkdir -p ${SSL_BUILD_DIR}
-mkdir -p ${SSL_INSTALL_DIR}
-
-SSL_VERSION=1.1.1w
-
-cd ${SSL_BUILD_DIR}
-wget -c https://www.openssl.org/source/openssl-${SSL_VERSION}.tar.gz
-tar -xf openssl-${SSL_VERSION}.tar.gz
-cd openssl-${SSL_VERSION}
-mkdir build && cd build
-../config --prefix=${SSL_INSTALL_DIR}/${SSL_VERSION} --openssldir=${SSL_INSTALL_DIR}/${SSL_VERSION}
-make -j$(nproc)
-make -j$(nproc) test
-make install
-
-## INSTALL Qt FOR CMAKE-GUI
-QT_BUILD_DIR=${BUILD_LOCATION}/qt
-QT_INSTALL_DIR=${INSTALL_LOCATION}/qt
-mkdir -p ${QT_BUILD_DIR}
-mkdir -p ${QT_INSTALL_DIR}
-
-## SOME COMBINATION WILL INSTALL GL
-install build-essential libgl1-mesa-dev libglu1-mesa-dev libglut-dev libgl2-mesa-dev libdrm-dev
-
-QT_VERSION=5.15.12
-QT_MAJOR_VERSION=$(echo ${QT_VERSION} | cut -d. -f1-2)
-
-cd ${QT_BUILD_DIR}
-wget -c https://download.qt.io/official_releases/qt/${QT_MAJOR_VERSION}/${QT_VERSION}/single/qt-everywhere-opensource-src-${QT_VERSION}.tar.xz
-tar -xf qt-everywhere-opensource-src-${QT_VERSION}.tar.xz
-cd qt-everywhere-opensource-src-${QT_VERSION}
-mkdir build && cd build
-../configure -prefix ${QT_INSTALL_DIR}/${QT_VERSION} -make tests -release -opensource -confirm-license
-##### THIS COMMAND NEEDS TO BE FINISHED#####
-
-## INSTALL CMAKE FROM SOURCE
-CMAKE_BUILD_DIR=${BUILD_LOCATION}/cmake
-CMAKE_INSTALL_DIR=${INSTALL_LOCATION}/cmake
-mkdir -p ${CMAKE_BUILD_DIR}
-mkdir -p ${CMAKE_INSTALL_DIR}
-
-VERSIONS=(3.5.2
-3.12.4
-3.17.5
-3.21.3
-3.24.4
-3.28.1)
-
-OPENSSL_ROOT_DIR=${SSL_INSTALL_DIR}/${SSL_VERSION}
-for CMAKE_VERSION in "${strings[@]}"; do
-# CMAKE_VERSION=3.21.3
-CMAKE_MAJOR_VERSION=$(echo ${CMAKE_VERSION} | cut -d. -f1-2)
-cd ${CMAKE_BUILD_DIR}
-wget -c http://www.cmake.org/files/v${CMAKE_MAJOR_VERSION}/cmake-${CMAKE_VERSION}.tar.gz
-tar -xf cmake-${CMAKE_VERSION}.tar.gz
-mkdir -p cmake-${CMAKE_VERSION}/build && cd cmake-${CMAKE_VERSION}/build
-
-../configure --prefix=${CMAKE_INSTALL_DIR}/${CMAKE_VERSION} --parallel=$(nproc)
-make -j$(nproc)
-make install
-done
-
-## INSTALL GIT FROM SOURCE
-GIT_BUILD_DIR=${BUILD_LOCATION}/git
-GIT_INSTALL_DIR=${INSTALL_LOCATION}/git
-mkdir -p ${GIT_BUILD_DIR}
-mkdir -p ${GIT_INSTALL_DIR}
-
-GIT_VERSION=2.11.3
-
-cd ${GIT_BUILD_DIR}
-wget -c https://mirrors.edge.kernel.org/pub/software/scm/git/git-${GIT_VERSION}.tar.gz
-tar -xzf git-${GIT_VERSION}.tar.gz
-cd git-${GIT_VERSION}
-make configure
-./configure --prefix=${GIT_INSTALL_DIR}/${GIT_VERSION}
-make -j$(nproc)
-make -j$(nproc) test
-make install
-
-## INSTALL LLVM FROM SOURCE
-LLVM_BUILD_DIR=${BUILD_LOCATION}/llvm
-LLVM_INSTALL_DIR=${INSTALL_LOCATION}/llvm
-mkdir -p ${LLVM_BUILD_DIR}
-mkdir -p ${LLVM_INSTALL_DIR}
-
-LLVM_VERSION=13.0.0
-
-git clone https://github.com/llvm/llvm-project.git ${LLVM_BUILD_DIR}/llvm-${LLVM_VERSION}
-cd ${LLVM_BUILD_DIR}/llvm-${LLVM_VERSION}
-git checkout llvmorg-${LLVM_VERSION}
-mkdir build && cd build
-cmake -S llvm -B build -G "Unix Makefiles" \
-    -DLLVM_ENABLE_PROJECTS="clang;clang-tools-extra;compiler-rt;libcxx;libcxxabi;libunwind;lld;lldb;openmp;parallel-libs;polly" \
-    -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${LLVM_INSTALL_DIR}/${LLVM_VERSION} \
-    -DLLVM_INSTALL_UTILS=ON llvm
-make -j$(nproc)
-make install
 
 ## INSTALL OPENMPI FROM SOURCE
 module load gcc/${GCC_VERSION} cmake/${CMAKE_VERSION}

scripts/stage0/install_binutils.sh

@@ -0,0 +1,5 @@
+
+BINUTILS_VERSION=2.35
+
+wget -c https://ftp.gnu.org/gnu/binutils/binutils-${BINUTILS_VERSION}.tar.gz
+tar -xf binutils-${BINUTILS_VERSION}.tar.gz

scripts/stage0/install_cmake.sh

@@ -0,0 +1,26 @@
+## INSTALL CMAKE FROM SOURCE
+CMAKE_BUILD_DIR=${BUILD_LOCATION}/cmake
+CMAKE_INSTALL_DIR=${INSTALL_LOCATION}/cmake
+mkdir -p ${CMAKE_BUILD_DIR}
+mkdir -p ${CMAKE_INSTALL_DIR}
+
+VERSIONS=(3.5.2
+3.12.4
+3.17.5
+3.21.3
+3.24.4
+3.28.1)
+
+OPENSSL_ROOT_DIR=${SSL_INSTALL_DIR}/${SSL_VERSION}
+for CMAKE_VERSION in "${strings[@]}"; do
+    # CMAKE_VERSION=3.21.3
+    CMAKE_MAJOR_VERSION=$(echo ${CMAKE_VERSION} | cut -d. -f1-2)
+    cd ${CMAKE_BUILD_DIR}
+    wget -c http://www.cmake.org/files/v${CMAKE_MAJOR_VERSION}/cmake-${CMAKE_VERSION}.tar.gz
+    tar -xf cmake-${CMAKE_VERSION}.tar.gz
+    mkdir -p cmake-${CMAKE_VERSION}/build && cd cmake-${CMAKE_VERSION}/build
+
+    ../configure --prefix=${CMAKE_INSTALL_DIR}/${CMAKE_VERSION} --parallel=$(nproc)
+    make -j$(nproc)
+    make install
+done

scripts/stage0/install_env-modules.sh

@@ -0,0 +1,17 @@
+MODULES_VERSION=5.3.1
+
+MODULES_BUILD_DIR=${BUILD_LOCATION}
+MODULES_INSTALL_DIR=${INSTALL_LOCATION}/modules
+mkdir -p ${MODULES_BUILD_DIR}
+mkdir -p ${MODULES_INSTALL_DIR}
+
+cd ${MODULES_BUILD_DIR}
+curl -LJO https://github.com/cea-hpc/modules/releases/download/v${MODULES_VERSION}/modules-${MODULES_VERSION}.tar.gz
+tar -xf modules-${MODULES_VERSION}.tar.gz
+cd modules-${MODULES_VERSION}
+mkdir build && cd build
+./configure --prefix=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION} --modulefilesdir=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/modulefiles
+make -j$(nproc)
+make install
+ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.sh /etc/profile.d/modules.sh
+ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.csh /etc/profile.d/modules.csh

scripts/stage0/install_gcc.sh

@@ -0,0 +1,45 @@
+#!/bin/bash -e
+
+[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
+SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
+
+VERSIONS=(4.4.7
+4.6.2
+4.8.5
+4.9.3
+5.1.0
+5.2.0
+5.4.0
+6.1.0
+6.3.0
+7.1.0
+7.5.0
+8.4.0
+9.1.0
+10.2.0
+10.3.0
+11.2.0
+12.3.0
+13.1.0)
+
+source "${SCRIPT_DIR}"/common_vars.sh
+
+GCC_VERSION=7.5.0
+
+GCC_BUILD_DIR=${BUILD_LOCATION}/gcc
+GCC_INSTALL_DIR=${INSTALL_LOCATION}/gcc
+mkdir -p ${GCC_INSTALL_DIR}
+mkdir gcc-${GCC_VERSION}-build
+
+cd ${GCC_BUILD_DIR}
+
+wget ftp://ftp.gnu.org/gnu/gcc/gcc-${GCC_VERSION}/gcc-${GCC_VERSION}.tar.gz
+tar -xf gcc-${GCC_VERSION}.tar.gz
+mv gcc-${GCC_VERSION} gcc-${GCC_VERSION}-source
+cd gcc-${GCC_VERSION}-source
+./contrib/download_prerequisites
+cd ../gcc-${GCC_VERSION}-build
+${GCC_BUILD_DIR}/gcc-${GCC_VERSION}-source/configure --prefix=${GCC_INSTALL_DIR}/${GCC_VERSION} --enable-languages=c,c++,fortran,go --enable-lto --disable-multilib --enable-checking=release --enable-threads=posix --enable-libstdcxx-debug --enable-__cxa_atexit --enable-plugins --enable-bootstrap
+make -j$(nproc)
+make -j$(nproc) check
+make install

scripts/stage0/install_git.sh

@@ -0,0 +1,17 @@
+## INSTALL GIT FROM SOURCE
+GIT_BUILD_DIR=${BUILD_LOCATION}/git
+GIT_INSTALL_DIR=${INSTALL_LOCATION}/git
+mkdir -p ${GIT_BUILD_DIR}
+mkdir -p ${GIT_INSTALL_DIR}
+
+GIT_VERSION=2.11.3
+
+cd ${GIT_BUILD_DIR}
+wget -c https://mirrors.edge.kernel.org/pub/software/scm/git/git-${GIT_VERSION}.tar.gz
+tar -xzf git-${GIT_VERSION}.tar.gz
+cd git-${GIT_VERSION}
+make configure
+./configure --prefix=${GIT_INSTALL_DIR}/${GIT_VERSION}
+make -j$(nproc)
+make -j$(nproc) test
+make install

scripts/stage0/install_intel.sh

@@ -0,0 +1,44 @@
+#!/bin/bash -e
+
+# TODO: Review and if possible fix shellcheck errors.
+# shellcheck disable=all
+
+[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=${0}
+SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
+
+INTEL_CFLAGS=""
+INTEL_LDFLAGS=""
+INTEL_LIBS=""
+
+echo "==================== Finding Intel compiler from system paths ===================="
+if [ "${intel_classic}" = "yes" ]; then
+    check_command icc "intel" && CC="$(realpath $(command -v icc))" || exit 1
+    check_command icpc "intel" && CXX="$(realpath $(command -v icpc))" || exit 1
+    check_command ifort "intel" && FC="$(realpath $(command -v ifort))" || exit 1
+else
+    check_command icx "intel" && CC="$(realpath $(command -v icx))" || exit 1
+    check_command icpx "intel" && CXX="$(realpath $(command -v icpx))" || exit 1
+    check_command ifort "intel" && FC="$(realpath $(command -v ifort))" || exit 1
+fi
+F90="${FC}"
+F77="${FC}"
+
+echo "CC  is ${CC}"
+echo "CXX is ${CXX}"
+echo "FC  is ${FC}"
+
+export CC="${CC}"
+export CXX="${CXX}"
+export FC="${FC}"
+export F90="${F90}"
+export F77="${F77}"
+
+export PATH=${pkg_install_dir}/bin:${PATH}
+export LD_LIBRARY_PATH=${pkg_install_dir}/lib:${LD_LIBRARY_PATH}
+export LD_RUN_PATH=${pkg_install_dir}/lib:${LD_RUN_PATH}
+export LIBRARY_PATH=${pkg_install_dir}/lib:${LIBRARY_PATH}
+export CPATH=${pkg_install_dir}/include:${CPATH}
+
+export INTEL_CFLAGS="${INTEL_CFLAGS}"
+export INTEL_LDFLAGS="${INTEL_LDFLAGS}"
+export INTEL_LIBS="${INTEL_LIBS}"

scripts/stage0/install_llvm.sh

@@ -0,0 +1,18 @@
+## INSTALL LLVM FROM SOURCE
+LLVM_BUILD_DIR=${BUILD_LOCATION}/llvm
+LLVM_INSTALL_DIR=${INSTALL_LOCATION}/llvm
+mkdir -p ${LLVM_BUILD_DIR}
+mkdir -p ${LLVM_INSTALL_DIR}
+
+LLVM_VERSION=13.0.0
+
+git clone https://github.com/llvm/llvm-project.git ${LLVM_BUILD_DIR}/llvm-${LLVM_VERSION}
+cd ${LLVM_BUILD_DIR}/llvm-${LLVM_VERSION}
+git checkout llvmorg-${LLVM_VERSION}
+mkdir build && cd build
+cmake -S llvm -B build -G "Unix Makefiles" \
+    -DLLVM_ENABLE_PROJECTS="clang;clang-tools-extra;compiler-rt;libcxx;libcxxabi;libunwind;lld;lldb;openmp;parallel-libs;polly" \
+    -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${LLVM_INSTALL_DIR}/${LLVM_VERSION} \
+    -DLLVM_INSTALL_UTILS=ON llvm
+make -j$(nproc)
+make install

scripts/stage0/install_openssl.sh

@@ -0,0 +1,16 @@
+SSL_VERSION=1.1.1w
+
+SSL_BUILD_DIR=${BUILD_LOCATION}/openssl
+SSL_INSTALL_DIR=${INSTALL_LOCATION}/openssl
+mkdir -p ${SSL_BUILD_DIR}
+mkdir -p ${SSL_INSTALL_DIR}
+
+cd ${SSL_BUILD_DIR}
+wget -c https://www.openssl.org/source/openssl-${SSL_VERSION}.tar.gz
+tar -xf openssl-${SSL_VERSION}.tar.gz
+cd openssl-${SSL_VERSION}
+mkdir build && cd build
+../config --prefix=${SSL_INSTALL_DIR}/${SSL_VERSION} --openssldir=${SSL_INSTALL_DIR}/${SSL_VERSION}
+make -j$(nproc)
+make -j$(nproc) test
+make install

scripts/stage0/install_qt.sh

@@ -0,0 +1,21 @@
+## INSTALL Qt FOR CMAKE-GUI
+QT_BUILD_DIR=${BUILD_LOCATION}/qt
+QT_INSTALL_DIR=${INSTALL_LOCATION}/qt
+mkdir -p ${QT_BUILD_DIR}
+mkdir -p ${QT_INSTALL_DIR}
+
+## SOME COMBINATION WILL INSTALL GL
+# install build-essential libgl1-mesa-dev libglu1-mesa-dev libglut-dev libgl2-mesa-dev libdrm-dev
+
+# wget -c https://qt.mirror.constant.com/archive/online_installers/4.6/qt-unified-linux-x64-4.6.1-online.run
+
+QT_VERSION=5.15.12
+QT_MAJOR_VERSION=$(echo ${QT_VERSION} | cut -d. -f1-2)
+
+cd ${QT_BUILD_DIR}
+wget -c https://download.qt.io/official_releases/qt/${QT_MAJOR_VERSION}/${QT_VERSION}/single/qt-everywhere-opensource-src-${QT_VERSION}.tar.xz
+tar -xf qt-everywhere-opensource-src-${QT_VERSION}.tar.xz
+cd qt-everywhere-opensource-src-${QT_VERSION}
+mkdir build && cd build
+../configure -prefix ${QT_INSTALL_DIR}/${QT_VERSION} -make tests -release -opensource -confirm-license
+##### THIS COMMAND NEEDS TO BE FINISHED#####

scripts/stage0/install_stage0.sh

@@ -0,0 +1,17 @@
+#!/bin/bash -e
+
+# TODO: Review and if possible fix shellcheck errors.
+# shellcheck disable=all
+
+./scripts/stage0/install_env-modules.sh
+./scripts/stage0/install_gcc.sh
+./scripts/stage0/install_binutils.sh
+./scripts/stage0/install_llvm.sh
+./scripts/stage0/install_intel.sh
+./scripts/stage0/setup_buildtools.sh
+./scripts/stage0/install_openssl.sh
+./scripts/stage0/install_git.sh
+./scripts/stage0/install_qt.sh
+./scripts/stage0/install_cmake.sh
+
+#EOF

scripts/stage0/setup_buildtools.sh

@@ -0,0 +1,72 @@
+#!/bin/bash -e
+
+# TODO: Review and if possible fix shellcheck errors.
+# shellcheck disable=all
+
+[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
+SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
+
+source ${SCRIPT_DIR}/common_vars.sh
+source ${SCRIPT_DIR}/tool_kit.sh
+source ${SCRIPT_DIR}/signal_trap.sh
+source ${INSTALLDIR}/toolchain.conf
+source ${INSTALLDIR}/toolchain.env
+
+for ii in $tool_list; do
+  load "${BUILDDIR}/setup_${ii}"
+done
+
+# ------------------------------------------------------------------------
+# Install or compile packages using newly installed tools
+# ------------------------------------------------------------------------
+
+# Setup compiler flags, leading to nice stack traces on crashes but still optimised
+if [ "${with_intel}" != "__DONTUSE__" ]; then
+  CFLAGS="-O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback"
+  if [ "${TARGET_CPU}" = "native" ]; then
+    CFLAGS="${CFLAGS} -xHost"
+  elif [ "${TARGET_CPU}" = "generic" ]; then
+    CFLAGS="${CFLAGS} -mtune=${TARGET_CPU}"
+  else
+    CFLAGS="${CFLAGS} -march=${TARGET_CPU} -mtune=${TARGET_CPU}"
+  fi
+  FFLAGS="${CFLAGS}"
+else
+  CFLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g"
+  if [ "${TARGET_CPU}" = "generic" ]; then
+    CFLAGS="${CFLAGS} -mtune=generic ${TSANFLAGS}"
+  else
+    CFLAGS="${CFLAGS} -march=${TARGET_CPU} -mtune=${TARGET_CPU} ${TSANFLAGS}"
+  fi
+  FFLAGS="${CFLAGS} -fbacktrace"
+fi
+CXXFLAGS="${CFLAGS}"
+F77FLAGS="${FFLAGS}"
+F90FLAGS="${FFLAGS}"
+FCFLAGS="${FFLAGS}"
+
+if [ "${with_intel}" == "__DONTUSE__" ]; then
+  export CFLAGS="$(allowed_gcc_flags ${CFLAGS})"
+  export FFLAGS="$(allowed_gfortran_flags ${FFLAGS})"
+  export F77FLAGS="$(allowed_gfortran_flags ${F77FLAGS})"
+  export F90FLAGS="$(allowed_gfortran_flags ${F90FLAGS})"
+  export FCFLAGS="$(allowed_gfortran_flags ${FCFLAGS})"
+  export CXXFLAGS="$(allowed_gxx_flags ${CXXFLAGS})"
+else
+  # TODO Check functions for allowed Intel compiler flags
+  export CFLAGS
+  export FFLAGS
+  export F77FLAGS
+  export F90FLAGS
+  export FCFLAGS
+  export CXXFLAGS
+fi
+export LDFLAGS="${TSANFLAGS}"
+
+# get system arch information using OpenBLAS prebuild
+${SCRIPTDIR}/get_openblas_arch.sh
+load "${BUILDDIR}/openblas_arch"
+
+write_toolchain_env "${INSTALLDIR}"
+
+#EOF

scripts/stage1/install_openmpi.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+if [[ "$BASH_SOURCE" == "$0" ]]; then
+    BUILD_LOCATION=${PWD}
+    INSTALL_LOCATION=/people/parl703
+    TARGET_CPU="native"
+    CFLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g -march=${TARGET_CPU} -mtune=${TARGET_CPU}"
+    FFLAGS="${CFLAGS} -fbacktrace"
+    CXXFLAGS="${CFLAGS}"
+    F77FLAGS="${FFLAGS}"
+    F90FLAGS="${FFLAGS}"
+    FCFLAGS="${FFLAGS}"
+    LOG_LINES=200
+else
+    source ${BUILD_LOCATION}/build.env
+    ROOT=${PWD}
+fi
+
+MPI_VERSION=4.1.5
+
+OPENMPI_BUILD_DIR=${BUILD_LOCATION}/openmpi
+OPENMPI_INSTALL_DIR=${INSTALL_LOCATION}/openmpi/${MPI_VERSION}
+mkdir -p ${OPENMPI_BUILD_DIR}
+mkdir -p ${OPENMPI_INSTALL_DIR}
+
+cd ${OPENMPI_BUILD_DIR}
+wget -c https://www.openmpi.org/openmpi-${MPI_VERSION}.tar.gz
+tar -xf openmpi-${MPI_VERSION}.tar.gz
+cd openmpi-${MPI_VERSION}
+mkdir build && cd build
+
+if [ "MPI_ENABLED" = false ]; then
+    exit 1
+fi
+
+echo ${FFTW_INSTALL_DIR}
+./configure --prefix=${FFTW_INSTALL_DIR} ${FFTW_FLAGS}
+make -j$(nproc)
+make -j$(nproc) check > check.log 2>&1 || tail -n ${LOG_LINES} check.log
+make -j$(nproc) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
+
+if [[ "$BASH_SOURCE" != "$0" ]]; then
+    cd ${ROOT}
+else
+    echo "Exiting ..."
+fi

scripts/stage3/install_fftw.sh

@@ -5,6 +5,7 @@ if [[ "$BASH_SOURCE" == "$0" ]]; then
     INSTALL_LOCATION=/avfs/people/parl703
     LOG_LINES=200
 else
+    source ${BUILD_LOCATION}/build.env
     ROOT=${PWD}
 fi
 

scripts/tool_kit.sh

@@ -0,0 +1,102 @@
+find_mpi() {
+  # for MPI, we try to detect system MPI variant
+  if (command -v mpiexec > /dev/null 2>&1); then
+    export MPI_ENABLED = true
+    # check if we are dealing with openmpi, mpich or intelmpi
+    if (mpiexec --version 2>&1 | grep -s -q "HYDRA"); then
+      echo "MPI is detected and it appears to be MPICH"
+      export MPI_MODE="mpich"
+      # check openmpi version as reported by mpiexec
+      export MPI_VERSION=$(mpiexec --version | grep "Version:" | awk '{print $2}')
+      with_mpich="__SYSTEM__"
+    elif (mpiexec --version 2>&1 | grep -s -q "OpenRTE"); then
+      echo "MPI is detected and it appears to be OpenMPI"
+      export MPI_MODE="openmpi"
+      # check openmpi version as reported by mpiexec
+      export MPI_VERSION=$(mpiexec --version 2>&1 | grep "(Open MPI)" | awk '{print $4}')
+      with_openmpi="__SYSTEM__"
+    elif (mpiexec --version 2>&1 | grep -s -q "Intel"); then
+      echo "MPI is detected and it appears to be Intel MPI"
+      export MPI_MODE="intelmpi"
+      # check intelmpi version as reported by mpiicc
+      export MPI_VERSION=$(mpiexec --version | grep "Version" | awk '{print $8"."$10}')
+      with_intelmpi="__SYSTEM__"
+    else # default to mpich
+      echo "MPI is detected and defaults to MPICH"
+      export MPI_MODE="mpich"
+      with_mpich="__SYSTEM__"
+    fi
+  else
+    report_warning $LINENO "No MPI installation detected (ignore this message in Cray Linux Environment or when MPI installation was requested)."
+    export MPI_MODE=""
+  fi
+}
+
+# helper routine to check integrity of downloaded files
+checksum() {
+  local __filename=$1
+  local __sha256=$2
+  local __shasum_command='sha256sum'
+  # check if we have sha256sum command, Mac OS X does not have
+  # sha256sum, but has an equivalent with shasum -a 256
+  command -v "$__shasum_command" > /dev/null 2>&1 ||
+    __shasum_command="shasum -a 256"
+  if echo "$__sha256  $__filename" | ${__shasum_command} --check; then
+    echo "Checksum of $__filename Ok"
+  else
+    rm -v ${__filename}
+    report_error "Checksum of $__filename could not be verified, abort."
+    return 1
+  fi
+}
+
+# verify the checksums inside the given checksum file
+verify_checksums() {
+  local __checksum_file=$1
+  local __shasum_command='sha256sum'
+
+  # check if we have sha256sum command, Mac OS X does not have
+  # sha256sum, but has an equivalent with shasum -a 256
+  command -v "$__shasum_command" > /dev/null 2>&1 ||
+    __shasum_command="shasum -a 256"
+
+  ${__shasum_command} --check "${__checksum_file}" > /dev/null 2>&1
+}
+
+# write a checksum file $1 containing checksums for each given file $2, $3, ... (plus the $VERSION_FILE)
+write_checksums() {
+  local __checksum_file=$1
+  shift # remove output file from arguments to be able to pass them along properly quoted
+  local __shasum_command='sha256sum'
+
+  # check if we have sha256sum command, Mac OS X does not have
+  # sha256sum, but has an equivalent with shasum -a 256
+  command -v "$__shasum_command" > /dev/null 2>&1 ||
+    __shasum_command="shasum -a 256"
+
+  ${__shasum_command} "${VERSION_FILE}" "$@" > "${__checksum_file}"
+}
+
+# generate a filtered toolchain.env
+write_toolchain_env() {
+  local __installdir=$1
+
+  # run the following in a subshell to not affect the currently running shell
+  # we do not need to achieve complete filtering, it is sufficient to
+  # remove problematic variables (TERM/TERMCAP/COLORTERM) which may trigger
+  # 'too many arguments' (since the environment vars are stored in the same memory block as command line arguments)
+  # or which may not be valid anymore the next time the user runs the toolchain scripts,
+  # like the proxy vars which may affect fetching tarballs
+  (
+    unset COLORTERM DISPLAY EDITOR LESS LESSOPEN LOGNAME LS_COLORS PAGER
+    unset TERM TERMCAP USER
+    unset ftp_proxy http_proxy no_proxy
+    unset GPG_AGENT_INFO SSH_AGENT_PID SSH_AUTH_SOCK SSH_CLIENT SSH_CONNECTION SSH_TTY
+    unset LS_COLORS LS_OPTIONS
+    unset STY WINDOW XAUTHORITY
+    unset XDG_CURRENT_DESKTOP XDG_RUNTIME_DIR XDG_SEAT XDG_SESSION_CLASS XDG_SESSION_DESKTOP XDG_SESSION_ID XDG_SESSION_TYPE XDG_VTNR XDG_CONFIG_DIRS XDG_DATA_DIRS
+    unset DBUS_SESSION_BUS_ADDRESS
+
+    export -p
+  ) > "${__installdir}/toolchain.env"
+}