mirror of
https://github.com/cp2k/cp2k.git
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make_cp2k.sh 0.6: Add MPI flag and revise flag parsing
Add entrypoint script file
This commit is contained in:
Matthias Krack
parent
ccfa571fc8
commit
ca3340cbb5
1 changed files with 167 additions and 43 deletions
210
make_cp2k.sh
210
make_cp2k.sh
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@ -47,7 +47,7 @@
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# Authors: Matthias Krack (MK)
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# Version: 0.4
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# Version: 0.6
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# History: - Creation (19.12.2025, MK)
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# - Version 0.1: First working version (09.01.2026, MK)
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@ -55,6 +55,7 @@
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# - Version 0.3: Add no_externals flag and perform more checks (21.01.2026, MK)
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# - Version 0.4: Improve error handling and provide more hints (22.01.2026, MK)
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# - Version 0.5: Adapt script for use within a container (24.01.2026, MK)
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# - Version 0.6: Add MPI flag and revise flag parsing (27.01.2026, MK)
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# set -uo pipefail # can be useful for debugging this script
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@ -119,6 +120,7 @@ BUILD_TYPE="${BUILD_TYPE:-Release}"
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HAS_PODMAN="no"
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HELP="no"
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INSTALL_MESSAGE="NEVER"
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MPI_MODE="psmp"
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if command -v nproc &> /dev/null; then
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MAX_PROCS=$(nproc)
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NUM_PROCS=${NUM_PROCS:-${MAX_PROCS}}
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@ -128,7 +130,7 @@ else
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fi
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RUN_TEST="no"
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TESTOPTS=""
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USE_EXTERNALS="yes"
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USE_EXTERNALS="no"
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VERBOSE=0
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VERBOSE_FLAG="--quiet"
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VERBOSE_MAKEFILE="OFF"
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@ -150,7 +152,12 @@ while [[ $# -gt 0 ]]; do
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shift 2
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;;
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-cv | --cp2k_version)
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CP2K_VERSION="${2}"
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if (($# > 1)); then
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CP2K_VERSION="${2}"
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else
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echo "ERROR: No argument found for flag \"${1}\" (choose psmp or ssmp)"
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${EXIT_CMD} 1
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fi
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shift 2
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;;
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-h | --help)
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@ -158,7 +165,12 @@ while [[ $# -gt 0 ]]; do
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shift 1
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;;
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-ip | --install_path | --install_prefix)
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INSTALL_PREFIX="${2}"
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if (($# > 1)); then
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INSTALL_PREFIX="${2}"
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else
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echo "ERROR: No install path argument found for flag \"${1}\""
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${EXIT_CMD} 1
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fi
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shift 2
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;;
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-j)
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@ -171,7 +183,7 @@ while [[ $# -gt 0 ]]; do
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shift 2
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;;
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*)
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echo "The -j flag can only be followed by an integer number, found \"${2}\""
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echo "ERROR: The -j flag can only be followed by an integer number, found \"${2}\""
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${EXIT_CMD} 1
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;;
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esac
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@ -180,15 +192,31 @@ while [[ $# -gt 0 ]]; do
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NUM_PROCS="${1#-j}"
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shift 1
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;;
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-ne | --no_externals)
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USE_EXTERNALS="no"
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shift 1
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-mpi | --mpi_mode)
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if (($# > 1)); then
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MPI_MODE="${2}"
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else
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echo "ERROR: No argument found for flag \"${1}\""
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echo " The MPI type is required (mpich | no | openmpi)"
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${EXIT_CMD} 1
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fi
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shift 2
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;;
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-t | --test)
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RUN_TEST="yes"
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TESTOPTS="${2}"
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if (($# > 1)); then
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TESTOPTS="${2}"
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else
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echo "ERROR: No argument found for flag \"${1}\""
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echo " A string argument with the TESTOPTS (even an empty one \"\") is required"
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${EXIT_CMD} 1
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fi
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shift 2
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;;
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-ue | --use_externals)
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USE_EXTERNALS="yes"
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shift 1
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;;
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-v | --verbose)
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VERBOSE=1
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INSTALL_MESSAGE="LAZY"
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@ -197,11 +225,11 @@ while [[ $# -gt 0 ]]; do
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shift 1
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;;
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--)
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shift
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shift 1
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break
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;;
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-*)
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echo "ERROR: Unknown option ${1} specified"
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echo "ERROR: Unknown option \"${1}\" specified"
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${EXIT_CMD} 1
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;;
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*)
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@ -211,14 +239,21 @@ while [[ $# -gt 0 ]]; do
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done
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NUM_PROCS=$(awk '{print $1+0}' <<< "${NUM_PROCS}")
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export BUILD_TYPE HAS_PODMAN INSTALL_MESSAGE NUM_PROCS RUN_TEST TESTOPTS VERBOSE VERBOSE_FLAG VERBOSE_MAKEFILE
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export BUILD_TYPE HAS_PODMAN INSTALL_MESSAGE MPI_MODE NUM_PROCS RUN_TEST TESTOPTS VERBOSE VERBOSE_FLAG VERBOSE_MAKEFILE
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# Show help if requested
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if [[ "${HELP}" == "yes" ]]; then
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echo ""
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echo "Usage: ${SCRIPT_NAME} [-bd|--build_deps] [-bt|--build_type (Debug|Release|RelWithDebInfo)]"
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echo " [-cv|--cp2k_version (psmp|ssmp)] [-h|--help] [-ip|--install_path PATH]"
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echo " [-j #processes] [-ne|--no_externals] [-t|test \"TESTOPTS\"] [-v|--verbose]"
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echo "Usage: ${SCRIPT_NAME} [-bd|--build_deps]"
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echo " [-bt|--build_type (Debug | Release | RelWithDebInfo)]"
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echo " [-cv|--cp2k_version (psmp | ssmp)]"
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echo " [-h|--help]"
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echo " [-ip|--install_path PATH]"
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echo " [-j #PROCESSES]"
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echo " [-mpi|--mpi_mode (mpich | no | openmpi)]"
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echo " [-t|test \"TESTOPTS\"]"
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echo " [-ue|--use_externals]"
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echo " [-v|--verbose]"
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echo ""
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echo "Flags:"
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echo " --build_deps : Force a rebuild of all CP2K dependencies from scratch (removes the spack folder)"
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@ -227,10 +262,11 @@ if [[ "${HELP}" == "yes" ]]; then
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echo " --help : Print this help information"
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echo " --install_path : Define the CP2K installation path (default: ./install"
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echo " -j : Number of processes used in parallel"
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echo " --no_externals : Do not use external packages installed on the system. This results in longer build times,"
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echo " but it can help to resolve conflicts with outdated packages on the host system, e.g. old"
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echo " python or gcc versions"
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echo " --mpi_mode : Set preferred MPI mode (default: \"mpich\")"
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echo " --test : Perform a regression test run after a successful build"
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echo " --use_externals: Use external packages installed on the host system. This can result in faster build times,"
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echo " but it can also cause conflicts with outdated packages on the host system, e.g. old"
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echo " python or gcc versions"
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echo " --verbose : Write verbose output"
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echo ""
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echo "Hints:"
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@ -241,10 +277,12 @@ if [[ "${HELP}" == "yes" ]]; then
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${EXIT_CMD} 0
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fi
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echo ""
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echo "CMAKE_BUILD_TYPE = ${BUILD_TYPE}"
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echo "CP2K_VERSION = ${CP2K_VERSION}"
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echo "INSTALL_PREFIX = ${INSTALL_PREFIX}"
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echo "INSTALL_MESSAGE = ${INSTALL_MESSAGE}"
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echo "MPI_MODE = ${MPI_MODE}"
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echo "NUM_PROCS = ${NUM_PROCS} (processes)"
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echo "RUN_TEST = ${RUN_TEST}"
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if [[ "${RUN_TEST}" == "yes" ]]; then
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@ -257,6 +295,7 @@ echo "VERBOSE = ${VERBOSE}"
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if (($# > 0)); then
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echo "Remaining args =" "$@" "(not used)"
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fi
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echo ""
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# Check if a valid number of processes is requested
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if ((NUM_PROCS < 1)); then
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@ -272,7 +311,28 @@ case "${BUILD_TYPE}" in
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true
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;;
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*)
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echo -e "\nERROR: Invalid CMake build type \"${BUILD_TYPE}\" selected"
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echo "ERROR: Invalid CMake build type \"${BUILD_TYPE}\" selected"
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${EXIT_CMD} 1
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;;
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esac
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# Check if a valid MPI type is selected
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case "${MPI_MODE}" in
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mpich | openmpi)
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if [[ "${CP2K_VERSION}" == "ssmp" ]]; then
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echo "ERROR: MPI type \"${MPI_MODE}\" specified for building a serial CP2K binary"
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${EXIT_CMD} 1
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fi
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;;
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no)
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if [[ "${CP2K_VERSION}" == "psmp" ]]; then
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echo "ERROR: MPI type \"${MPI_MODE}\" specified for building an MPI-parallel CP2K binary"
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${EXIT_CMD} 1
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fi
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;;
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*)
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echo "ERROR: Invalid MPI type \"${MPI_MODE}\" selected"
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echo " Choose from (mpich | no | openmpi)"
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${EXIT_CMD} 1
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;;
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esac
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@ -295,6 +355,9 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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mkdir -p "${SPACK_BUILD_PATH}"
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cd "${SPACK_BUILD_PATH}" || ${EXIT_CMD} 1
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# Reset the spack environment
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unset SPACK_ENV
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# Install Spack
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((VERBOSE > 0)) && echo "Installing Spack ${SPACK_VERSION}"
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export SPACK_REPO="https://github.com/spack/spack"
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@ -316,12 +379,12 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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echo "Installing virtual environment for Python packages"
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if ! python3 -m venv "${SPACK_BUILD_PATH}/venv"; then
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echo "ERROR: The creation of a virtual environment (venv) for Python packages failed"
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${EXIT_CMD} 1
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cd "${CP2K_ROOT}" || ${EXIT_CMD} 1 && ${EXIT_CMD} 1
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fi
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export PATH="${SPACK_BUILD_PATH}/venv/bin:${PATH}"
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else
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echo "ERROR: python3 -m venv was not found"
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${EXIT_CMD} 1
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cd "${CP2K_ROOT}" || ${EXIT_CMD} 1 && ${EXIT_CMD} 1
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fi
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# Upgrade pip and install boto3
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@ -331,7 +394,7 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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python3 -m pip install "${VERBOSE_FLAG}" boto3==1.38.11 google-cloud-storage==3.1.0
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else
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echo "ERROR: python3 -m pip was not found"
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${EXIT_CMD} 1
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cd "${CP2K_ROOT}" || ${EXIT_CMD} 1 && ${EXIT_CMD} 1
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fi
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# Install Spack packages
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@ -342,6 +405,9 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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tar -xzf "v${SPACK_PACKAGES_VERSION}.tar.gz"
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rm -f "v${SPACK_PACKAGES_VERSION}.tar.gz"
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# Return from spack folder after all installations are done
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cd "${CP2K_ROOT}" || ${EXIT_CMD} 1
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# Initialize Spack shell hooks
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source "${SPACK_ROOT}/share/spack/setup-env.sh"
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@ -358,8 +424,8 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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HAS_PODMAN="yes"
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else
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echo "INFO: podman was not found"
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echo "INFO: Install the package podman to take advantage of a local spack cache"
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echo "INFO: This accelerates a rebuild of the CP2K dependencies, significantly"
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echo " Install the package podman to take advantage of a local spack cache"
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echo " This accelerates a rebuild of the CP2K dependencies, significantly"
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fi
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fi
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@ -367,6 +433,7 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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if [[ ! -f /run/.containerenv ]] && [[ "${HAS_PODMAN}" == "yes" ]]; then
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if ! "${CP2K_ROOT}"/tools/docker/spack_cache_start.sh; then
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echo "ERROR: Could not start (new) spack cache"
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echo ""
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echo "An error message starting with \"Error: initial journal cursor: ...\" indicates that the"
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echo "journald logging does not work. Try to switch podman (3.x) to file-based logs by creating"
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echo "the file \"~/.config/containers/containers.conf\" with the following two lines:"
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@ -393,19 +460,34 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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-e "/\"build_type=/s|build_type=[^\"]*|build_type=${BUILD_TYPE}|" \
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"${CP2K_ROOT}/tools/spack/cp2k_deps_${CP2K_VERSION}.yaml" > "${CP2K_CONFIG_FILE}"
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# Activate CP2K environment if needed
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# Apply selected MPI type if needed
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# MPICH is selected by default for psmp and no change needed for ssmp
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if [[ "${MPI_MODE}" == "openmpi" ]]; then
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sed -E -e '/\s*-\s+"mpich@/ s/^ /#/' \
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-E -e '/\s*#\s*-\s+"openmpi@/ s/#/ /' \
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-E -e '/\s*-\s+mpich/ s/mpich$/openmpi/' \
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-i "${CP2K_CONFIG_FILE}"
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fi
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# Create CP2K environment if needed
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if spack env list | grep -q "${CP2K_ENV}"; then
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if [[ "${SPACK_ENV:-}" == "${CP2K_ENV}" ]]; then
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echo "The Spack environment \"${CP2K_ENV}\" exists and is activated"
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else
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echo "The Spack environment \"${CP2K_ENV}\" exists but is NOT activated"
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spack env activate "${CP2K_ENV}"
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echo "The Spack environment \"${CP2K_ENV}\" has been activated"
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if [[ -n "${SPACK_ENV}" ]]; then
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echo "The Spack environment \"${CP2K_ENV}\" exists already"
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fi
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else
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echo "The Spack environment \"${CP2K_ENV}\" does NOT exist"
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spack env create "${CP2K_ENV}" "${CP2K_CONFIG_FILE}" && spack env activate "${CP2K_ENV}"
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echo "The Spack environment \"${CP2K_ENV}\" has been created and activated"
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if ! spack env create "${CP2K_ENV}" "${CP2K_CONFIG_FILE}"; then
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echo "ERROR: The creation of the Spack environment \"${CP2K_ENV}\" failed"
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${EXIT_CMD} 1
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fi
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fi
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# Activate CP2K environment if needed
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if spack env activate "${CP2K_ENV}"; then
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echo "The Spack environment \"${CP2K_ENV}\" has been activated"
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else
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echo "ERROR: The activation of the Spack environment \"${CP2K_ENV}\" failed"
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${EXIT_CMD} 1
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fi
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# Add Spack packages builtin repository when missing
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@ -436,15 +518,17 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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# Find all external packages
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if [[ "${USE_EXTERNALS}" == "yes" ]]; then
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if ! spack -C "${SPACK_USER_CONFIG_PATH}" external find --not-buildable; then
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echo "ERROR: The detection of externals by spack failed"
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echo -e "\nERROR: The detection of externals by spack failed"
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${EXIT_CMD} 1
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fi
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fi
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# Concretize CP2K dependencies
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if ! spack -e "${CP2K_ENV}" --no-user-config --no-system-config concretize --fresh; then
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echo ""
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echo "HINT: The --no_externals flag can help to resolve conflicts with outdated"
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echo " packages on the host system, e.g. old python or gcc versions"
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echo ""
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${EXIT_CMD} 1
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fi
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@ -464,8 +548,6 @@ if [[ ! -d "${SPACK_BUILD_PATH}" ]]; then
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${EXIT_CMD} 1
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fi
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cd "${CP2K_ROOT}" || ${EXIT_CMD} 1
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else
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# Initialize Spack shell hooks
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@ -477,8 +559,15 @@ fi
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### Build CP2K ###
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spack env list
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spack env status
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if ! spack env list | grep -q "${CP2K_ENV}"; then
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echo "ERROR: No Spack environment \"${CP2K_ENV}\" found"
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${EXIT_CMD} 1
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else
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spack env list
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spack env status
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fi
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# Activate spack environment
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eval "$(spack env activate --sh ${CP2K_ENV})"
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# CMake configuration step
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@ -553,7 +642,7 @@ echo -e '\n*** Installing CP2K ***\n'
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cmake --install "${CMAKE_BUILD_PATH}" |& tee "${CMAKE_BUILD_PATH}"/install.log
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EXIT_CODE=${PIPESTATUS[0]}
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if ((EXIT_CODE != 0)); then
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echo "ERROR: The CMake installation step failed with the error code ${EXIT_CODE}"
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echo -e "\nERROR: The CMake installation step failed with the error code ${EXIT_CODE}"
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${EXIT_CMD} "${EXIT_CODE}"
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fi
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@ -591,18 +680,53 @@ if ldd "${INSTALL_PREFIX}/bin/cp2k.${CP2K_VERSION}" | grep -q "not found"; then
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fi
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export LD_LIBRARY_PATH
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# Prepare script to run the regression tests
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# Create links to CP2K binaries
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cd "${INSTALL_PREFIX}"/bin || ${EXIT_CMD} 1
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ln -sf cp2k."${CP2K_VERSION}" cp2k
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ln -sf cp2k."${CP2K_VERSION}" cp2k."${CP2K_VERSION/smp/opt}"
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ln -sf cp2k."${CP2K_VERSION}" cp2k_shell
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cd "${CP2K_ROOT}" || ${EXIT_CMD} 1
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# Allow to run as root within a container with OpenMPI
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if [[ "${MPI_MODE}" == "openmpi" ]] && [[ -f /run/.containerenv ]]; then
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OMPI_VARS="export OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 OMPI_MCA_plm_rsh_agent=/bin/false"
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else
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OMPI_VARS=""
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fi
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# Assemble flags for running the regression tests
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TESTOPTS="--cp2kdatadir ${INSTALL_PREFIX}/share/cp2k/data --maxtasks ${NUM_PROCS} --workbasedir ${INSTALL_PREFIX}/regtesting ${TESTOPTS}"
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cat << *** > "${INSTALL_PREFIX}"/bin/run_tests
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if [[ -f /run/.containerenv ]]; then
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# Create entrypoint script file when building within a container
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cat << *** > "${INSTALL_PREFIX}"/bin/entrypoint.sh
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#!/bin/bash
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ulimit -c 0 -s unlimited
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${OMPI_VARS}
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export OMP_STACKSIZE=64M
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export PATH=${INSTALL_PREFIX}/bin:${PATH}
|
||||
export LD_LIBRARY_PATH=${INSTALL_PREFIX}/lib:${LD_LIBRARY_PATH}
|
||||
ldd "${INSTALL_PREFIX}/bin/cp2k.${CP2K_VERSION}" | grep "not found" | sort | uniq
|
||||
exec "\$@"
|
||||
***
|
||||
chmod 750 "${INSTALL_PREFIX}"/bin/entrypoint.sh
|
||||
else
|
||||
# Otherwise put the environment setup in the regression test launch script
|
||||
cat << *** > "${INSTALL_PREFIX}"/bin/run_tests
|
||||
#!/bin/bash
|
||||
ulimit -c 0 -s unlimited
|
||||
${OMPI_VARS}
|
||||
export OMP_STACKSIZE=64M
|
||||
export PATH=${INSTALL_PREFIX}/bin:${PATH}
|
||||
export LD_LIBRARY_PATH=${INSTALL_PREFIX}/lib:${LD_LIBRARY_PATH}
|
||||
***
|
||||
fi
|
||||
|
||||
# Create shortcut for launching the regression tests
|
||||
cat << *** >> "${INSTALL_PREFIX}"/bin/run_tests
|
||||
ldd ${INSTALL_PREFIX}/bin/cp2k.${CP2K_VERSION} | grep "not found" | sort | uniq
|
||||
${CP2K_ROOT}/tests/do_regtest.py ${TESTOPTS} \$* ${INSTALL_PREFIX}/bin ${CP2K_VERSION}
|
||||
***
|
||||
chmod 750 "${INSTALL_PREFIX}/bin/run_tests"
|
||||
chmod 750 "${INSTALL_PREFIX}"/bin/run_tests
|
||||
|
||||
# Optionally, launch test run
|
||||
if [[ "${RUN_TEST}" == "yes" ]]; then
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue