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Docker: Major refactoring (#87)

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Ole Schütt 2018-11-08 13:56:15 +01:00 • committed by GitHub
parent 30e41bb77a
commit 4a97bb7342
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77 changed files with 1031 additions and 1051 deletions
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tools/docker/.gitignore vendored Normal file
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!/scripts/

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tools/docker/Dockerfile.test_aiida Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_aiida.sh .
RUN ./install_aiida.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_aiida.sh ./
CMD ["./ci_entrypoint.sh", "./test_aiida.sh"]
#EOF

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tools/docker/Dockerfile.test_ase Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_ase.sh .
RUN ./install_ase.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_ase.sh ./
CMD ["./ci_entrypoint.sh", "./test_ase.sh"]
#EOF

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tools/docker/Dockerfile.test_conventions Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_conventions.sh .
RUN ./install_conventions.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_conventions.sh ./
CMD ["./ci_entrypoint.sh", "./test_conventions.sh"]
#EOF

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tools/docker/Dockerfile.test_coverage-pdbg Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local_coverage pdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_coverage.sh ./
CMD ["./ci_entrypoint.sh", "./test_coverage.sh", "pdbg"]
#EOF

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tools/docker/Dockerfile.test_coverage-sdbg Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local_coverage sdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_coverage.sh ./
CMD ["./ci_entrypoint.sh", "./test_coverage.sh", "sdbg"]
#EOF

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tools/docker/Dockerfile.test_farming Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local popt
COPY ./scripts/ci_entrypoint.sh ./scripts/test_farming.sh ./
CMD ["./ci_entrypoint.sh", "./test_farming.sh"]
#EOF

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tools/docker/Dockerfile.test_formatting Normal file
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FROM ubuntu:18.04
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_formatting.sh .
RUN ./install_formatting.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_formatting.sh ./
CMD ["./ci_entrypoint.sh", "./test_formatting.sh"]
#EOF

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tools/docker/Dockerfile.test_i-pi Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_i-pi.sh .
RUN ./install_i-pi.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_i-pi.sh ./
CMD ["./ci_entrypoint.sh", "./test_i-pi.sh"]
#EOF

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tools/docker/Dockerfile.test_manual Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_manual.sh .
RUN ./install_manual.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_manual.sh ./
CMD ["./ci_entrypoint.sh", "./test_manual.sh"]
#EOF

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tools/docker/Dockerfile.test_minimal Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh minimal sdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "minimal", "sdbg"]
#EOF

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tools/docker/Dockerfile.test_pdbg Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local pdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "pdbg"]
#EOF

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tools/docker/Dockerfile.test_popt Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local popt
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "popt"]
#EOF

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tools/docker/Dockerfile.test_psmp Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local psmp
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "psmp"]
#EOF

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tools/docker/Dockerfile.test_python Normal file
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FROM ubuntu:18.04
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_python.sh .
RUN ./install_python.sh
COPY ./scripts/ci_entrypoint.sh ./scripts/test_python.sh ./
CMD ["./ci_entrypoint.sh", "./test_python.sh"]
#EOF

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tools/docker/Dockerfile.test_sdbg Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local sdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "sdbg"]
#EOF

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tools/docker/Dockerfile.test_sopt Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local sopt
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "sopt"]
#EOF

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tools/docker/Dockerfile.test_ssmp Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local ssmp
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "ssmp"]
#EOF

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FROM ubuntu:18.04
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_ubuntu_toolchain.sh .
RUN ./install_ubuntu_toolchain.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local ssmp
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local", "ssmp"]
#EOF

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tools/docker/Dockerfile.test_valgrind-pdbg Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local_valgrind pdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local_valgrind", "pdbg"]
#EOF

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tools/docker/Dockerfile.test_valgrind-sdbg Normal file
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FROM cp2k/toolchain:latest
# author: Ole Schuett
WORKDIR /workspace
COPY ./scripts/install_basics.sh .
RUN ./install_basics.sh
COPY ./scripts/install_regtest.sh .
RUN ./install_regtest.sh local_valgrind sdbg
COPY ./scripts/ci_entrypoint.sh ./scripts/test_regtest.sh ./
CMD ["./ci_entrypoint.sh", "./test_regtest.sh", "local_valgrind", "sdbg"]
#EOF

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tools/docker/build_test.sh
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#!/bin/bash
#!/bin/bash -e
# author: Ole Schuett
@ -13,12 +13,7 @@ TESTNAME=$1
shift
echo "Building ${TESTNAME} ..."
BUILDARGS=""
if [ -f ./test_${TESTNAME}/buildargs.sh ]; then
source ./test_${TESTNAME}/buildargs.sh
fi
set -x
docker build -t img_cp2k_test_${TESTNAME} ${BUILDARGS} "$@" ./test_${TESTNAME}/
docker build -t "img_cp2k_test_${TESTNAME}" "$@" -f "Dockerfile.test_${TESTNAME}" .
#EOF

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tools/docker/exe_psmp/Dockerfile.psmp
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FROM cp2k/toolchain:latest
# author: Ole Schuett
# Has to be build from cp2k root directory:
# docker build -f ./infra/docker/Dockerfile.psmp .
WORKDIR /opt/cp2k/
RUN ln -s /opt/cp2k-toolchain/install/arch/ .
COPY makefiles ./makefiles
COPY tools ./tools
COPY tests ./tests
COPY data ./data
COPY src ./src
ARG REVISION
RUN echo ${REVISION} > ./REVISION
WORKDIR /opt/cp2k/makefiles
RUN ln -sf bash /bin/sh
RUN source /opt/cp2k-toolchain/install/setup && \
make -j VERSION="psmp" cp2k && \
make -j VERSION="psmp" cp2k_shell && \
make VERSION="psmp" clean
ENV PATH="/opt/cp2k/exe/local:${PATH}"
WORKDIR /
#EOF

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tools/docker/regtest/Dockerfile
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FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
ARG ARCH
ARG VERSION
WORKDIR /opt/cp2k-master
# run regtests which lack fixed reference value
# Disable LeakSanitizer during docker build as it requires ptrace capabilities.
RUN source /opt/cp2k-toolchain/install/setup && \
make -j ARCH=${ARCH} VERSION=${VERSION} && \
export LSAN_OPTIONS="detect_leaks=0" && \
make test ARCH=${ARCH} VERSION=${VERSION} TESTOPTS="-restrictdir QS/regtest-almo-md -restrictdir QS/regtest-almo-1 -restrictdir SE/regtest-3-4 -restrictdir QS/regtest-ot-1-vib -restrictdir Fist/regtest-5-vib -restrictdir QS/regtest-optbas -restrictdir TMC/regtest_ana_post_proc" && \
rm -rf lib exe regtesting/${ARCH}/${VERSION}/TEST-*
# install Debian packages
RUN apt-get update && apt-get install -y --no-install-recommends \
rsync \
&& rm -rf /var/lib/apt/lists/*
ARG TESTNAME
ENV TESTNAME=${TESTNAME}
ENV ARCH=${ARCH}
ENV VERSION=${VERSION}
WORKDIR /opt/cp2k_test_${TESTNAME}
COPY ./cmd.sh .
CMD ["./cmd.sh"]
#EOF

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tools/docker/regtest/buildargs.sh
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# author: Ole Schuett
BUILDARGS="$BUILDARGS --build-arg TESTNAME=${TESTNAME}"
if [[ "${TESTNAME}" =~ ^(sopt|ssmp|sdbg|popt|psmp|pdbg)$ ]]; then
BUILDARGS="$BUILDARGS --build-arg ARCH=local --build-arg VERSION=${TESTNAME}"
elif [[ "${TESTNAME}" == "farming" ]]; then
BUILDARGS="$BUILDARGS --build-arg ARCH=local --build-arg VERSION=popt"
elif [[ "${TESTNAME}" == "minimal" ]]; then
BUILDARGS="$BUILDARGS --build-arg ARCH=minimal --build-arg VERSION=sdbg"
elif [[ "${TESTNAME}" =~ ^coverage-(sdbg|pdbg)$ ]]; then
BUILDARGS="$BUILDARGS --build-arg ARCH=local_coverage --build-arg VERSION=${TESTNAME:9}"
elif [[ "${TESTNAME}" =~ ^valgrind-(sdbg|sopt|pdbg|popt)$ ]]; then
BUILDARGS="$BUILDARGS --build-arg ARCH=local_valgrind --build-arg VERSION=${TESTNAME:9}"
else
echo "Unkown test name: ${TESTNAME}"
exit 1
fi
#EOF

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tools/docker/regtest/cmd.sh
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#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--exclude=/regtesting/ \
--exclude=/tools/toolchain/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/build/ \
--exclude=/install/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
echo -e "\n========== Running Regtests =========="
source /opt/cp2k-toolchain/install/setup
cd /opt/cp2k-master
rm -rf obj/${ARCH}/${VERSION}/*.gcda # remove old gcov statistics
if [[ "$TESTNAME" != "farming" ]]; then
make ARCH=${ARCH} VERSION=${VERSION} test TESTOPTS="${TESTOPTS}"
else
make ARCH=${ARCH} VERSION=${VERSION} test TESTOPTS="-farming -skipunittest -skipdir TMC/regtest_ana_on_the_fly -skipdir TMC/regtest_ana_post_proc -skipdir TMC/regtest ${TESTOPTS}"
fi
if [[ "$TESTNAME" == coverage-* ]]; then
# gcov gets stuck on some files...
# Maybe related: https://bugs.launchpad.net/gcc-arm-embedded/+bug/1694644
# As a workaround we'll simply remove the offending files for now.
rm -v /opt/cp2k-master/obj/${ARCH}/${VERSION}/almo_scf_types.gcda
rm -v /opt/cp2k-master/obj/${ARCH}/${VERSION}/dbcsr_tensor_types.gcda
rm -v /opt/cp2k-master/obj/${ARCH}/${VERSION}/mp2_types.gcda
#cd /tmp
#for i in /opt/cp2k-master/obj/${ARCH}/${VERSION}/*.gcda; do
# timeout 30 gcov $i >/dev/null 2>&1 || rm -v $i
#done
# collect coverage stats
mkdir -p /opt/cp2k_test_artifacts/coverage
cd /opt/cp2k_test_artifacts/coverage
lcov --directory /opt/cp2k-master/obj/${ARCH}/${VERSION} --capture --output-file coverage.info > lcov.log
lcov --summary coverage.info
# generate html report
genhtml --title "CP2K Regtests (${CP2K_REVISION})" coverage.info > genhtml.log
# plot
LINE_COV=$(lcov --summary coverage.info | grep lines | awk '{print substr($2, 1, length($2)-1)}')
FUNC_COV=$(lcov --summary coverage.info | grep funct | awk '{print substr($2, 1, length($2)-1)}')
echo 'Plot: name="cov", title="Test Coverage", ylabel="Coverage %"'
echo "PlotPoint: name='lines', plot='cov', label='Lines', y=$LINE_COV, yerr=0"
echo "PlotPoint: name='funcs', plot='cov', label='Functions', y=$FUNC_COV, yerr=0"
fi
#EOF

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tools/docker/run_test.sh
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#!/bin/bash
#!/bin/bash -e
# author: Ole Schuett
@ -13,21 +13,12 @@ TESTNAME=$1
shift
echo "Running ${TESTNAME} ..."
echo -n "StartDate: "
date --utc --rfc-3339=seconds
if git rev-parse; then
git --no-pager log -1 --pretty="%nCommitSHA: %H%nCommitTime: %ci%nCommitAuthor: %an%nCommitSubject: %s%n"
CP2K_REVISION="git:$(git log --pretty=format:'%h' -n 1)"
fi
CP2K_LOCAL=$(realpath ../../)
set -x
# SYS_PTRACE needed by LeakSanitizer.
docker run -i --init --rm --cap-add=SYS_PTRACE --env "CP2K_REVISION=$CP2K_REVISION" --volume ${CP2K_LOCAL}:/opt/cp2k-local/:ro "$@" img_cp2k_test_${TESTNAME}
set +x
echo -n "EndDate: "
date --utc --rfc-3339=seconds
# SYS_PTRACE needed by LeakSanitizer.
docker run -i --init --rm --cap-add=SYS_PTRACE \
--volume "${CP2K_LOCAL}:/mnt/cp2k/:ro" \
"$@" "img_cp2k_test_${TESTNAME}"
#EOF

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tools/docker/scripts/ci_entrypoint.sh Executable file
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#!/bin/bash -e
# author: Ole Schuett
REPORT=/workspace/report.txt
echo -n "StartDate: " > $REPORT
date --utc --rfc-3339=seconds >> $REPORT
# Rsync with common args.
function rsync_changes {
rsync --update \
--delete \
--executability \
--ignore-times \
--verbose \
--recursive \
--checksum \
"$@"
}
# Upload to cloud storage.
function upload_file {
URL=$1
FILE=$2
CONTENT_TYPE=$3
wget -O- --method=PUT --header="content-type: ${CONTENT_TYPE}" --header="cache-control: no-cache" --body-file="${FILE}" "${URL}"
}
# Get cp2k sources.
if [ -n "${GIT_REF}" ]; then
echo -e "\n========== Fetching Git Commit =========="
cd /workspace/cp2k
git fetch origin "${GIT_BRANCH}"
git checkout "${GIT_REF}"
git submodule update --init --recursive
git --no-pager log -1 --pretty='%nCommitSHA: %H%nCommitTime: %ci%nCommitAuthor: %an%nCommitSubject: %s%n' | tee -a $REPORT
elif [ -d /mnt/cp2k ]; then
echo -e "\n========== Copying Changed Files =========="
rsync_changes --exclude="*~" \
--exclude=".*/" \
--exclude="*.py[cod]" \
--exclude="__pycache__" \
--exclude="/obj/" \
--exclude="/lib/" \
--exclude="/exe/" \
--exclude="/regtesting/" \
--exclude="/arch/local*" \
--exclude="/tools/toolchain/build/" \
--exclude="/tools/toolchain/install/" \
/mnt/cp2k/ /workspace/cp2k/
else
echo "Neither GIT_REF nor /mnt/cp2k found - aborting."
exit 255
fi
# Update toolchain.
if [ -d /opt/cp2k-toolchain ]; then
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain
rsync_changes --exclude="/build/" \
--exclude="/install/" \
/workspace/cp2k/tools/toolchain/ /opt/cp2k-toolchain/
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# shellcheck disable=SC2086
./install_cp2k_toolchain.sh ${CP2K_TOOLCHAIN_OPTIONS}
fi
echo -e "\n========== Running Test =========="
cd /workspace
"$@" 2>&1 | tee -a $REPORT & # Launch in the background.
# Upload preliminary report every 30s while test is running.
while jobs %1 &> /dev/null ; do
sleep 1
count=$(( (count + 1) % 30 ))
if (( count == 1 )) && [ -n "${REPORT_UPLOAD_URL}" ]; then
upload_file "${REPORT_UPLOAD_URL}" "${REPORT}" "text/plain;charset=utf-8"
fi
done
# Test has finished.
echo -n "EndDate: " >> $REPORT
date --utc --rfc-3339=seconds >> $REPORT
# Upload final report.
if [ -n "${REPORT_UPLOAD_URL}" ]; then
echo "Uploading report..."
upload_file "${REPORT_UPLOAD_URL}" "${REPORT}" "text/plain;charset=utf-8"
fi
# Upload artifacts.
if [ -n "${ARTIFACTS_UPLOAD_URL}" ] && [ -d /workspace/artifacts ]; then
echo "Uploading artifacts..."
ARTIFACTS_TGZ="/tmp/test_${TESTNAME}_artifacts.tgz"
tar -czf "${ARTIFACTS_TGZ}" -C /workspace/artifacts .
upload_file "${ARTIFACTS_UPLOAD_URL}" "${ARTIFACTS_TGZ}" "application/gzip"
fi
echo "Done :-)"
#EOF

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#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
export DEBIAN_FRONTEND=noninteractive
export DEBCONF_NONINTERACTIVE_SEEN=true
apt-get install -y --no-install-recommends \
build-essential \
python-setuptools \
python-wheel \
python-pip \
python-dev \
postgresql \
sudo \
ssh
rm -rf /var/lib/apt/lists/*
# install python packages
pip install flake8 aiida ase
# create ubuntu user with sudo powers
adduser --disabled-password --gecos "" ubuntu
echo "ubuntu ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# setup arch files
cd /workspace/cp2k/arch
ln -vs /opt/cp2k-toolchain/install/arch/local* .
# pre-build cp2k
cd /workspace/cp2k
make -j VERSION=pdbg
rm -rf lib exe
#EOF

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tools/docker/scripts/install_ase.sh Executable file
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#!/bin/bash -e
# author: Ole Schuett
# install python packages
apt-get update
apt-get install -y --no-install-recommends \
python3 \
python3-dev \
python3-pip \
python3-wheel \
python3-setuptools \
build-essential
rm -rf /var/lib/apt/lists/*
# install python packages
pip3 install numpy scipy matplotlib flask
# clone ase reprository
git clone --depth=1 --single-branch -b master https://gitlab.com/ase/ase.git /opt/ase
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# setup arch files
cd /workspace/cp2k/arch
ln -vs /opt/cp2k-toolchain/install/arch/local* .
# pre-build cp2k
cd /workspace/cp2k
make -j VERSION=pdbg
rm -rf lib exe
#EOF

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tools/docker/scripts/install_basics.sh Executable file
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#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
apt-get install -y --no-install-recommends \
ca-certificates \
python \
git \
nano \
wget \
unzip \
less \
make \
rsync
rm -rf /var/lib/apt/lists/*
# clone cp2k repository
git clone --depth=1 --single-branch -b master https://github.com/cp2k/cp2k.git /workspace/cp2k
#EOF

17
tools/docker/scripts/install_conventions.sh Executable file
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@ -0,0 +1,17 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# setup arch files
cd /workspace/cp2k/arch
ln -vs /opt/cp2k-toolchain/install/arch/local* .
# pre-build cp2k
cd /workspace/cp2k/tools/conventions
./test_conventions.sh
rm -rf ../lib/ ../exe/
#EOF

14
tools/docker/scripts/install_formatting.sh Executable file
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@ -0,0 +1,14 @@
#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
apt-get install -y --no-install-recommends libfindbin-libs-perl
rm -rf /var/lib/apt/lists/*
# pre-run prettify
cd /workspace/cp2k
make -j pretty
#EOF

32
tools/docker/scripts/install_i-pi.sh Executable file
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@ -0,0 +1,32 @@
#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
apt-get install -y --no-install-recommends \
python \
python-pip \
python-wheel \
python-setuptools
rm -rf /var/lib/apt/lists/*
# install python packages
pip install numpy
# clone i-pi repository
git clone --depth=1 --single-branch -b master https://github.com/i-pi/i-pi.git /opt/i-pi
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# setup arch files
cd /workspace/cp2k/arch
ln -vs /opt/cp2k-toolchain/install/arch/local* .
# pre-build cp2k
cd /workspace/cp2k
make -j VERSION=pdbg
rm -rf lib exe
#EOF

24
tools/docker/scripts/install_manual.sh Executable file
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@ -0,0 +1,24 @@
#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
apt-get install -y --no-install-recommends \
default-jre-headless \
libsaxonhe-java
rm -rf /var/lib/apt/lists/*
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# setup arch files
cd /workspace/cp2k/arch
ln -vs /opt/cp2k-toolchain/install/arch/local* .
# pre-build cp2k
cd /workspace/cp2k
make -j VERSION=sopt
rm -rf lib exe
#EOF

36
tools/docker/scripts/install_python.sh Executable file
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@ -0,0 +1,36 @@
#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
apt-get install -y --no-install-recommends \
python \
python3 \
python-pip \
python3-pip \
python-wheel \
python3-wheel \
python-setuptools \
python3-setuptools \
python-dev \
python3-dev \
build-essential
rm -rf /var/lib/apt/lists/*
# install python packages
pip install numpy matplotlib requests
pip3 install numpy matplotlib requests
# install python2.6
cd /tmp
wget -q https://www.python.org/ftp/python/2.6.9/Python-2.6.9.tgz
tar -xzf Python-2.6.9.tgz
pushd Python-2.6.9
./configure
make -j
make install
popd
rm -rf Python-2.6.9*
#EOF

30
tools/docker/scripts/install_regtest.sh Executable file
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@ -0,0 +1,30 @@
#!/bin/bash -e
# author: Ole Schuett
if (( $# != 2 )) ; then
echo "Usage: install_regtest.sh <ARCH> <VERSION>"
exit 1
fi
ARCH=$1
VERSION=$2
# setup arch files
cd /workspace/cp2k/arch
ln -vs /opt/cp2k-toolchain/install/arch/local* .
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
# pre-build cp2k
cd /workspace/cp2k
make -j ARCH="${ARCH}" VERSION="${VERSION}"
# run regtests which lack fixed reference value
# Disable LeakSanitizer during docker build as it requires ptrace capabilities.
export LSAN_OPTIONS="detect_leaks=0"
make test ARCH="${ARCH}" VERSION="${VERSION}" TESTOPTS="-restrictdir QS/regtest-almo-md -restrictdir QS/regtest-almo-1 -restrictdir SE/regtest-3-4 -restrictdir QS/regtest-ot-1-vib -restrictdir Fist/regtest-5-vib -restrictdir QS/regtest-optbas -restrictdir TMC/regtest_ana_post_proc"
rm -rf lib exe "regtesting/${ARCH}/${VERSION}"/TEST-*
#EOF

32
tools/docker/scripts/install_ubuntu_toolchain.sh Executable file
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@ -0,0 +1,32 @@
#!/bin/bash -e
# author: Ole Schuett
# install Ubuntu packages
apt-get update
apt-get install -y --no-install-recommends \
build-essential \
gfortran \
fftw3-dev \
libopenblas-dev \
liblapack-dev \
libint-dev
rm -rf /var/lib/apt/lists/*
# build toolchain relying mostly on ubuntu packages
cp -r /workspace/cp2k/tools/toolchain /opt/cp2k-toolchain/
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh \
--mpi-mode=no \
--with-gcc=system \
--with-binutils=system \
--with-make=system \
--with-fftw=system \
--with-openblas=system \
--with-reflapack=system \
--with-libint=system \
--with-libxc=install \
--with-libxsmm=install
rm -rf ./build
#EOF

53
tools/docker/scripts/test_aiida.sh Executable file
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@ -0,0 +1,53 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Compiling CP2K =========="
cd /workspace/cp2k
make -j VERSION=pdbg cp2k
echo -e "\n========== Installing CP2K =========="
cat > /usr/bin/cp2k << EndOfMessage
#!/bin/bash -e
source /opt/cp2k-toolchain/install/setup
/workspace/cp2k/exe/local/cp2k.pdbg "\$@"
EndOfMessage
chmod +x /usr/bin/cp2k
echo -e "\n========== Installing AiiDA-CP2K plugin =========="
cd /opt/
git clone https://github.com/cp2k/aiida-cp2k.git
pip install ./aiida-cp2k/
echo -e "\n========== Configuring AiiDA =========="
for i in $(dirname "$(which mpirun)")/* ; do ln -sf "$i" /usr/bin/; done
SUDO="sudo -u ubuntu -H"
cd /opt/aiida-cp2k/test/
$SUDO ./configure_aiida.sh
echo -e "\n========== Running AiiDA-CP2K Tests =========="
cd /opt/aiida-cp2k/test/
set +e # disable error trapping for remainder of script
(
set -e # abort on error
$SUDO ./run_tests.sh
)
EXIT_CODE=$?
echo ""
AIIDA_COMMIT=$(git rev-parse --short HEAD)
if (( EXIT_CODE )); then
echo "Summary: Something is wrong with aiida-cp2k commit ${AIIDA_COMMIT}."
echo "Status: FAILED"
else
echo "Summary: aiida-cp2k commit ${AIIDA_COMMIT} works fine."
echo "Status: OK"
fi
#EOF

44
tools/docker/scripts/test_ase.sh Executable file
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@ -0,0 +1,44 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Compiling CP2K =========="
cd /workspace/cp2k
make -j VERSION=pdbg cp2k_shell
echo -e "\n========== Installing ASE =========="
cd /opt/ase/
git pull
pip3 install .
echo -e "\n========== Running ASE Tests =========="
cd /opt/ase/
export ASE_CP2K_COMMAND="mpiexec -np 2 /workspace/cp2k/exe/local/cp2k_shell.pdbg"
set +e # disable error trapping for remainder of script
(
set -e # abort if error is encountered
for i in ./ase/test/cp2k/cp2k_*.py
do
echo "Running $i ..."
python3 "$i"
done
)
EXIT_CODE=$?
echo ""
ASE_REVISION=$(git rev-parse --short HEAD)
if (( EXIT_CODE )); then
echo "Summary: Something is wrong with ASE commit ${ASE_REVISION}."
echo "Status: FAILED"
else
echo "Summary: ASE commit ${ASE_REVISION} works fine."
echo "Status: OK"
fi
#EOF

12
tools/docker/scripts/test_conventions.sh Executable file
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@ -0,0 +1,12 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Running Conventions Test =========="
cd /workspace/cp2k/tools/conventions
./test_conventions.sh #TODO port to Python3
#EOF

49
tools/docker/scripts/test_coverage.sh Executable file
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@ -0,0 +1,49 @@
#!/bin/bash -e
# author: Ole Schuett
if (( $# != 1 )) ; then
echo "Usage: test_coverage.sh <VERSION>"
exit 1
fi
ARCH=local_coverage
VERSION=$1
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Running Regtests =========="
cd /workspace/cp2k
rm -rf "obj/${ARCH}/${VERSION}"/*.gcda # remove old gcov statistics
make ARCH="${ARCH}" VERSION="${VERSION}" TESTOPTS="${TESTOPTS}" test
# gcov gets stuck on some files...
# Maybe related: https://bugs.launchpad.net/gcc-arm-embedded/+bug/1694644
# As a workaround we'll simply remove the offending files for now.
rm -v "/workspace/cp2k/obj/${ARCH}/${VERSION}"/almo_scf_types.gcda
rm -v "/workspace/cp2k/obj/${ARCH}/${VERSION}"/dbcsr_tensor_types.gcda
rm -v "/workspace/cp2k/obj/${ARCH}/${VERSION}"/mp2_types.gcda
#cd /tmp
#for i in /workspace/cp2k/obj/${ARCH}/${VERSION}/*.gcda; do
# timeout 30 gcov $i >/dev/null 2>&1 || rm -v $i
#done
# collect coverage stats
mkdir -p /workspace/artifacts/coverage
cd /workspace/artifacts/coverage
lcov --directory "/workspace/cp2k/obj/${ARCH}/${VERSION}" --capture --output-file coverage.info > lcov.log
lcov --summary coverage.info
# generate html report
genhtml --title "CP2K Regtests (${CP2K_REVISION})" coverage.info > genhtml.log
# plot
LINE_COV=$(lcov --summary coverage.info | grep lines | awk '{print substr($2, 1, length($2)-1)}')
FUNC_COV=$(lcov --summary coverage.info | grep funct | awk '{print substr($2, 1, length($2)-1)}')
echo 'Plot: name="cov", title="Test Coverage", ylabel="Coverage %"'
echo "PlotPoint: name='lines', plot='cov', label='Lines', y=$LINE_COV, yerr=0"
echo "PlotPoint: name='funcs', plot='cov', label='Functions', y=$FUNC_COV, yerr=0"
#EOF

12
tools/docker/scripts/test_farming.sh Executable file
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@ -0,0 +1,12 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Running Regtests =========="
cd /workspace/cp2k
make VERSION=popt test TESTOPTS="-farming -skipunittest -skipdir TMC/regtest_ana_on_the_fly -skipdir TMC/regtest_ana_post_proc -skipdir TMC/regtest ${TESTOPTS}"
#EOF

9
tools/docker/scripts/test_formatting.sh Executable file
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@ -0,0 +1,9 @@
#!/bin/bash -e
# author: Ole Schuett
echo -e "\n========== Running Formatting Test =========="
cd /workspace/cp2k
./tools/formatting/test_formatting.sh
#EOF

53
tools/docker/scripts/test_i-pi.sh Executable file
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@ -0,0 +1,53 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Compiling CP2K =========="
cd /workspace/cp2k
make -j VERSION=pdbg cp2k
echo -e "\n========== Installing i-Pi =========="
cd /opt/i-pi
git pull
pip install .
echo -e "\n========== Running i-Pi Tests =========="
cd /opt/i-pi/examples/cp2k/nvt-cl
set +e # disable error trapping for remainder of script
# launch cp2k
(
mkdir -p run_1
cd run_1
echo 42 > cp2k_exit_code
sleep 2 # give i-pi some time to startup
mpiexec -np 2 /workspace/cp2k/exe/local/cp2k.pdbg ../in.cp2k
echo $? > cp2k_exit_code
) &
# launch i-pi
sed -i "s/total_steps>1000/total_steps>10/" input.xml
/usr/local/bin/i-pi input.xml
IPI_EXIT_CODE=$?
wait # for cp2k to shutdown
CP2K_EXIT_CODE=$(cat ./run_1/cp2k_exit_code)
echo ""
echo "CP2K exit code: ${CP2K_EXIT_CODE}"
echo "i-Pi exit code: ${IPI_EXIT_CODE}"
IPI_REVISION=$(git rev-parse --short HEAD)
if (( IPI_EXIT_CODE )) || (( CP2K_EXIT_CODE )) ; then
echo "Summary: Something is wrong with i-Pi commit ${IPI_REVISION}."
echo "Status: FAILED"
else
echo "Summary: i-Pi commit ${IPI_REVISION} works fine."
echo "Status: OK"
fi
#EOF

43
tools/docker/scripts/test_manual.sh Executable file
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@ -0,0 +1,43 @@
#!/bin/bash -e
# author: Ole Schuett
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Compiling CP2K =========="
cd /workspace/cp2k
touch src/cp2k_info.F # ensure latest REVISION is picked up.
make -j VERSION="sopt" cp2k
echo -e "\n========== Generating Manual =========="
mkdir -p /workspace/artifacts/manual
cd /workspace/artifacts/manual
/workspace/cp2k/exe/local/cp2k.sopt --version
/workspace/cp2k/exe/local/cp2k.sopt --xml
TOOLS=/workspace/cp2k/tools
cp ${TOOLS}/manual/favicon.png .
cp ${TOOLS}/manual/toggle_folding.js .
set +e # disable error trapping for remainder of script
(
set -e # abort if error is encountered
SAXON="java -jar /usr/share/java/Saxon-HE.jar"
$SAXON -o:index.html ./cp2k_input.xml ${TOOLS}/manual/cp2k_input.xsl add_edit_links=yes
$SAXON -o:cp2k.vim ./cp2k_input.xml ${TOOLS}/input_editing/vim/vim.xsl
)
EXIT_CODE=$?
echo ""
if (( EXIT_CODE )); then
echo "Summary: Something is wrong."
echo "Status: FAILED"
else
echo "Summary: Manual generation works fine."
echo "Status: OK"
fi
#EOF

48
tools/docker/test_python/cmd.sh → tools/docker/scripts/test_python.sh
View file

@ -1,62 +1,54 @@
#!/bin/bash
#!/bin/bash -e
# author: Ole Schuett
set -e
run_selftests() {
function run_selftests {
PYTHON=$1
shift
BASEDIR=`pwd`
VERSION=`$PYTHON -V 2>&1 | tr -d '\n'`
SCRIPTS=$2
BASEDIR=$(pwd)
VERSION=$(${PYTHON} -V 2>&1 | tr -d '\n')
echo ""
echo "========== Running ${VERSION} Tests =========="
#find ./src/ ./tools/ -name "*.pyc" -exec rm {} \;
for i in $@ ; do
for i in $SCRIPTS ; do
set +e #disable error trapping
if [[ `head -n1 $i` =~ "python3" && "$PYTHON" != "python3" ]]; then
if [[ $(head -n1 "$i") =~ "python3" && "$PYTHON" != "python3" ]]; then
echo "Skipping $i - it's Python3 only."
continue
fi
echo "Selftesting" $i
cd $(dirname $i)
$PYTHON -B ./$(basename $i) --selftest
if [ $? -ne 0 ]; then
echo "Selftesting $i"
cd "$(dirname "$i")"
SCRIPT=$(basename "$i")
if ! $PYTHON -B "./${SCRIPT}" --selftest ; then
echo "Selftest of $i failed"
ERRORS=$((ERRORS+1))
fi
set -e #re-enable error trapping
cd $BASEDIR
cd "$BASEDIR"
done
}
#===============================================================================
echo -e "\n========== Copying Changed Files =========="
mkdir /opt/cp2k-local-rw/
cp -r /opt/cp2k-local/tools /opt/cp2k-local-rw/tools
cp -r /opt/cp2k-local/src /opt/cp2k-local-rw/src
cd /opt/cp2k-local-rw/
ERRORS=0
cd /workspace/cp2k
# find executable python scripts
ALL_SCRIPTS=`find ./src/ ./tools/ -name "*.py" -executable`
ESSENTIAL_SCRIPTS=`find ./tools/build_utils -name "*.py" -executable`
ALL_SCRIPTS=$(find ./src/ ./tools/ -name "*.py" -executable)
ESSENTIAL_SCRIPTS=$(find ./tools/build_utils -name "*.py" -executable)
ESSENTIAL_SCRIPTS="$ESSENTIAL_SCRIPTS ./src/dbcsr/libsmm_acc/libcusmm/generate.py"
# python 2.6
run_selftests python2.6 $ESSENTIAL_SCRIPTS
run_selftests python2.6 "${ESSENTIAL_SCRIPTS}"
# python 2.7
run_selftests python2.7 $ALL_SCRIPTS
run_selftests python2.7 "${ALL_SCRIPTS}"
# python 3.x
run_selftests python3 $ALL_SCRIPTS
run_selftests python3 "${ALL_SCRIPTS}"
# print report
NUM_SCRIPTS=`echo $ALL_SCRIPTS | wc -w`
NUM_SCRIPTS=$(echo "${ALL_SCRIPTS}" | wc -w)
echo ""
echo "Summary: Checked ${NUM_SCRIPTS} Python scripts, found ${ERRORS} errors."
if [ $ERRORS == 0 ]; then

20
tools/docker/scripts/test_regtest.sh Executable file
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@ -0,0 +1,20 @@
#!/bin/bash -e
# author: Ole Schuett
if (( $# != 2 )) ; then
echo "Usage: test_regtest.sh <ARCH> <VERSION>"
exit 1
fi
ARCH=$1
VERSION=$2
# shellcheck disable=SC1091
source /opt/cp2k-toolchain/install/setup
echo -e "\n========== Running Regtests =========="
cd /workspace/cp2k
make ARCH="${ARCH}" VERSION="${VERSION}" TESTOPTS="${TESTOPTS}" test
#EOF

49
tools/docker/test_aiida/Dockerfile
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@ -1,49 +0,0 @@
FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
RUN ls -l cp2k-master/
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
WORKDIR /opt/cp2k-master
RUN source /opt/cp2k-toolchain/install/setup && \
make -j VERSION=pdbg && \
rm -rf lib exe
# install Debian packages
RUN export DEBIAN_FRONTEND=noninteractive DEBCONF_NONINTERACTIVE_SEEN=true && \
apt-get update && apt-get install -y --no-install-recommends \
build-essential \
python-setuptools \
python-wheel \
python-pip \
python-dev \
postgresql \
less \
nano \
sudo \
ssh \
git \
rsync \
&& rm -rf /var/lib/apt/lists/*
# install python packages
RUN pip install flake8 aiida ase
# create ubuntu user with sudo powers
RUN adduser --disabled-password --gecos "" ubuntu && \
echo "ubuntu ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
WORKDIR /opt/cp2k_test_aiida
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

83
tools/docker/test_aiida/cmd.sh
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@ -1,83 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
echo -e "\n========== Compiling CP2K =========="
source /opt/cp2k-toolchain/install/setup
cd /opt/cp2k-master
make -j VERSION=pdbg cp2k
echo -e "\n========== Installing CP2K =========="
cat > /usr/bin/cp2k << EndOfMessage
#!/bin/bash -e
source /opt/cp2k-toolchain/install/setup
/opt/cp2k-master/exe/local/cp2k.pdbg "\$@"
EndOfMessage
chmod +x /usr/bin/cp2k
echo -e "\n========== Installing AiiDA-CP2K plugin =========="
cd /opt/
git clone https://github.com/cp2k/aiida-cp2k.git
pip install ./aiida-cp2k/
echo -e "\n========== Configuring AiiDA =========="
for i in $(dirname $(which mpirun))/* ; do ln -sf $i /usr/bin/; done
SUDO="sudo -u ubuntu -H"
cd /opt/aiida-cp2k/test/
$SUDO ./configure_aiida.sh
echo -e "\n========== Running AiiDA-CP2K Tests =========="
cd /opt/aiida-cp2k/test/
set +e # disable error trapping for remainder of script
(
set -e # abort on error
$SUDO ./run_tests.sh
)
EXIT_CODE=$?
echo ""
AIIDA_COMMIT=`git rev-parse --short HEAD`
if (( $EXIT_CODE )); then
echo "Summary: Something is wrong with aiida-cp2k commit ${AIIDA_COMMIT}."
echo "Status: FAILED"
else
echo "Summary: aiida-cp2k commit ${AIIDA_COMMIT} works fine."
echo "Status: OK"
fi
#EOF

42
tools/docker/test_ase/Dockerfile
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@ -1,42 +0,0 @@
FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
WORKDIR /opt/cp2k-master
RUN source /opt/cp2k-toolchain/install/setup && \
make -j VERSION=pdbg && \
rm -rf lib exe
# install Debian packages
RUN apt-get update && apt-get install -y --no-install-recommends \
python3 \
python3-dev \
python3-pip \
python3-wheel \
python3-setuptools \
build-essential \
rsync \
git \
&& rm -rf /var/lib/apt/lists/*
# install python packages
RUN pip3 install numpy scipy matplotlib flask
# clone ase reprository
WORKDIR /opt/
RUN git clone https://gitlab.com/ase/ase.git
WORKDIR /opt/cp2k_test_ase
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

74
tools/docker/test_ase/cmd.sh
View file

@ -1,74 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
echo -e "\n========== Compiling CP2K =========="
source /opt/cp2k-toolchain/install/setup
cd /opt/cp2k-master
make -j VERSION=pdbg cp2k_shell
echo -e "\n========== Installing ASE =========="
cd /opt/ase/
git pull
pip3 install .
echo -e "\n========== Running ASE Tests =========="
cd /opt/ase/
export ASE_CP2K_COMMAND="mpiexec -np 2 /opt/cp2k-master/exe/local/cp2k_shell.pdbg"
set +e # disable error trapping for remainder of script
(
set -e # abort if error is encountered
for i in ./ase/test/cp2k/cp2k_*.py
do
echo "Running $i ..."
python3 $i
done
)
EXIT_CODE=$?
echo ""
ASE_REVISION=`git rev-parse --short HEAD`
if (( $EXIT_CODE )); then
echo "Summary: Something is wrong with ASE commit ${ASE_REVISION}."
echo "Status: FAILED"
else
echo "Summary: ASE commit ${ASE_REVISION} works fine."
echo "Status: OK"
fi
#EOF

28
tools/docker/test_conventions/Dockerfile
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@ -1,28 +0,0 @@
FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
WORKDIR /opt/cp2k-master/tools/conventions/
RUN source /opt/cp2k-toolchain/install/setup && \
./test_conventions.sh && \
rm -rf ../lib/ ../exe/
# install Debian packages
RUN apt-get update && apt-get install -y --no-install-recommends \
rsync \
&& rm -rf /var/lib/apt/lists/*
WORKDIR /opt/cp2k_test_conventions
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

43
tools/docker/test_conventions/cmd.sh
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@ -1,43 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
echo -e "\n========== Running Conventions Test =========="
source /opt/cp2k-toolchain/install/setup
cd /opt/cp2k-master/tools/conventions/
#TODO port to Python3
./test_conventions.sh
#EOF

1
tools/docker/test_coverage-pdbg
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regtest

1
tools/docker/test_coverage-sdbg
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regtest

1
tools/docker/test_farming
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regtest/

28
tools/docker/test_formatting/Dockerfile
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@ -1,28 +0,0 @@
FROM ubuntu:rolling
# author: Ole Schuett
RUN apt-get update && apt-get install -y --no-install-recommends \
python \
ca-certificates \
wget \
unzip \
less \
make \
rsync \
libfindbin-libs-perl \
&& rm -rf /var/lib/apt/lists/*
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master
RUN ./tools/formatting/test_formatting.sh
WORKDIR /opt/cp2k_test_formatting
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

26
tools/docker/test_formatting/cmd.sh
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@ -1,26 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
echo -e "\n========== Running Formatting Test =========="
cd /opt/cp2k-master
./tools/formatting/test_formatting.sh
#EOF

41
tools/docker/test_i-pi/Dockerfile
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@ -1,41 +0,0 @@
FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
WORKDIR /opt/cp2k-master
RUN source /opt/cp2k-toolchain/install/setup && \
make -j VERSION=pdbg && \
rm -rf lib exe
# install Debian packages
RUN apt-get update && apt-get install -y --no-install-recommends \
python \
python-pip \
python-wheel \
python-setuptools \
rsync \
git \
&& rm -rf /var/lib/apt/lists/*
# install python packages
RUN pip install numpy
# clone i-pi repository (200MB!)
WORKDIR /opt/
RUN git clone https://github.com/i-pi/i-pi.git
WORKDIR /opt/cp2k_test_i-pi
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

84
tools/docker/test_i-pi/cmd.sh
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@ -1,84 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
echo -e "\n========== Compiling CP2K =========="
source /opt/cp2k-toolchain/install/setup
cd /opt/cp2k-master
make -j VERSION=pdbg cp2k
echo -e "\n========== Installing i-Pi =========="
cd /opt/i-pi
git pull
pip install .
echo -e "\n========== Running i-Pi Tests =========="
cd /opt/i-pi/examples/cp2k/nvt-cl
set +e # disable error trapping for remainder of script
# launch cp2k
(
mkdir -p run_1
cd run_1
echo 42 > cp2k_exit_code
sleep 2 # give i-pi some time to startup
mpiexec -np 2 /opt/cp2k-master/exe/local/cp2k.pdbg ../in.cp2k
echo $? > cp2k_exit_code
) &
# launch i-pi
sed -i "s/total_steps>1000/total_steps>10/" input.xml
/usr/local/bin/i-pi input.xml
IPI_EXIT_CODE=$?
wait # for cp2k to shutdown
CP2K_EXIT_CODE=`cat ./run_1/cp2k_exit_code`
echo ""
echo "CP2K exit code: " $CP2K_EXIT_CODE
echo "i-Pi exit code: " $IPI_EXIT_CODE
IPI_REVISION=`git rev-parse --short HEAD`
if (( $IPI_EXIT_CODE || $CP2K_EXIT_CODE )); then
echo "Summary: Something is wrong with i-Pi commit ${IPI_REVISION}."
echo "Status: FAILED"
else
echo "Summary: i-Pi commit ${IPI_REVISION} works fine."
echo "Status: OK"
fi
#EOF

30
tools/docker/test_manual/Dockerfile
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@ -1,30 +0,0 @@
FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
WORKDIR /opt/cp2k-master
RUN source /opt/cp2k-toolchain/install/setup && \
make -j VERSION="sopt" cp2k && \
rm -rf lib exe
# install Debian packages
RUN apt-get update && apt-get install -y --no-install-recommends \
default-jre-headless \
libsaxonhe-java \
rsync \
&& rm -rf /var/lib/apt/lists/*
WORKDIR /opt/cp2k_test_manual
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

74
tools/docker/test_manual/cmd.sh
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@ -1,74 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
source ./install/setup
echo -e "\n========== Compiling CP2K =========="
cd /opt/cp2k-master
echo ${CP2K_REVISION} > REVISION
touch src/cp2k_info.F # ensure latest REVISION is picked up.
make -j VERSION="sopt" cp2k
echo -e "\n========== Generating Manual =========="
mkdir -p /opt/cp2k_test_artifacts/manual
cd /opt/cp2k_test_artifacts/manual
/opt/cp2k-master/exe/local/cp2k.sopt --version
/opt/cp2k-master/exe/local/cp2k.sopt --xml
TOOLS=/opt/cp2k-master/tools
cp ${TOOLS}/manual/favicon.png .
cp ${TOOLS}/manual/toggle_folding.js .
set +e # disable error trapping for remainder of script
(
set -e # abort if error is encountered
SAXON="java -jar /usr/share/java/Saxon-HE.jar"
$SAXON -o:index.html ./cp2k_input.xml ${TOOLS}/manual/cp2k_input.xsl add_edit_links=yes
$SAXON -o:cp2k.vim ./cp2k_input.xml ${TOOLS}/input_editing/vim/vim.xsl
)
EXIT_CODE=$?
echo ""
if (( $EXIT_CODE )); then
echo "Summary: Something is wrong."
echo "Status: FAILED"
else
echo "Summary: Manual generation works fine."
echo "Status: OK"
fi
#EOF

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tools/docker/test_minimal
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regtest/

1
tools/docker/test_pdbg
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regtest/

1
tools/docker/test_popt
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regtest/

1
tools/docker/test_psmp
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regtest/

41
tools/docker/test_python/Dockerfile
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@ -1,41 +0,0 @@
FROM ubuntu:rolling
# author: Ole Schuett
# TODO: maybe use conda instead?
RUN apt-get update && apt-get install -y --no-install-recommends \
python \
python3 \
python-pip \
python3-pip \
python-wheel \
python3-wheel \
python-setuptools \
python3-setuptools \
python-dev \
python3-dev \
build-essential \
ca-certificates \
wget \
&& rm -rf /var/lib/apt/lists/*
RUN pip install numpy matplotlib requests
RUN pip3 install numpy matplotlib requests
# install python2.6
WORKDIR /opt/
RUN wget -q https://www.python.org/ftp/python/2.6.9/Python-2.6.9.tgz && \
tar -xzf Python-2.6.9.tgz && \
cd Python-2.6.9 && \
./configure && \
make -j && \
make install && \
cd .. && \
rm -rf Python-2.6.9*
WORKDIR /opt/cp2k_test_python
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

29
tools/docker/test_scaling/Dockerfile
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@ -1,29 +0,0 @@
FROM cp2k/toolchain:latest
# author: Ole Schuett
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
WORKDIR /opt/cp2k-master/arch
RUN ln -vs /opt/cp2k-toolchain/install/arch/local* .
WORKDIR /opt/cp2k-master
RUN source /opt/cp2k-toolchain/install/setup && \
make -j VERSION="popt psmp ssmp" cp2k && \
rm -rf lib exe
# install Debian packages
RUN apt-get update && apt-get install -y --no-install-recommends \
python3-numpy \
rsync \
&& rm -rf /var/lib/apt/lists/*
WORKDIR /opt/cp2k_test_scaling
COPY cmd.sh .
CMD ["./cmd.sh"]
#EOF

46
tools/docker/test_scaling/cmd.sh
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@ -1,46 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/tools/toolchain/ /opt/cp2k-toolchain/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-toolchain/
./install_cp2k_toolchain.sh --install-all --with-make=no
echo -e "\n========== Compiling CP2K =========="
source /opt/cp2k-toolchain/install/setup
cd /opt/cp2k-master
make -j VERSION="popt psmp ssmp" cp2k
echo -e "\n========== Running Scaling Test =========="
cd tests/QS/benchmark
python3 ../../../tools/regtesting/test_scaling.py 30.0 ../../../exe/local/ H2O-32.inp -550.50556087853511
#EOF

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tools/docker/test_sdbg
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regtest/

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tools/docker/test_sopt
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regtest/

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tools/docker/test_ssmp
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60
tools/docker/test_ubuntu/Dockerfile
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@ -1,60 +0,0 @@
FROM ubuntu:rolling
# author: Ole Schuett
# install Ubuntu packages
RUN apt-get update && apt-get install -y \
build-essential \
ca-certificates \
gfortran \
python \
git \
wget \
less \
unzip \
fftw3-dev \
libopenblas-dev \
liblapack-dev \
libint-dev \
rsync \
--no-install-recommends \
&& rm -rf /var/lib/apt/lists/*
RUN ln -sf bash /bin/sh
# download and compile cp2k snapshot
WORKDIR /opt/
RUN wget -q -O cp2k-master.zip https://github.com/cp2k/cp2k/archive/master.zip && \
unzip -q cp2k-master.zip && \
rm cp2k-master.zip
# build toolchain relying mostly on ubuntu packages
WORKDIR /opt/cp2k-master/tools/toolchain
RUN ./install_cp2k_toolchain.sh \
--mpi-mode=no \
--with-gcc=system \
--with-binutils=system \
--with-make=system \
--with-fftw=system \
--with-openblas=system \
--with-reflapack=system \
--with-libint=system \
--with-libxc=install \
--with-libxsmm=install \
&& rm -rf ./build
WORKDIR /opt/cp2k-master/arch
RUN ln -vs ../tools/toolchain/install/arch/local* .
# run regtests which lack fixed reference value
WORKDIR /opt/cp2k-master
RUN source ./tools/toolchain/install/setup && \
make -j VERSION=ssmp && \
make test VERSION=ssmp TESTOPTS="-restrictdir QS/regtest-almo-md -restrictdir QS/regtest-almo-1 -restrictdir SE/regtest-3-4 -restrictdir QS/regtest-ot-1-vib -restrictdir Fist/regtest-5-vib -restrictdir QS/regtest-optbas -restrictdir TMC/regtest_ana_post_proc" && \
rm -rf lib exe regtesting/local/ssmp/TEST-*
WORKDIR /opt/cp2k_test_ubuntu
COPY ./cmd.sh .
CMD ["./cmd.sh"]
#EOF

40
tools/docker/test_ubuntu/cmd.sh
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@ -1,40 +0,0 @@
#!/bin/bash
# author: Ole Schuett
set -e
echo -e "\n========== Copying Changed Files =========="
rsync --exclude="*~" \
--exclude=".*/" \
--exclude="*.pyc" \
--exclude=/obj/ \
--exclude=/lib/ \
--exclude=/exe/ \
--executability \
--ignore-times \
--update \
--verbose \
--recursive \
--checksum \
/opt/cp2k-local/ /opt/cp2k-master/
echo -e "\n========== Updating Toolchain =========="
cd /opt/cp2k-master/tools/toolchain
./install_cp2k_toolchain.sh \
--mpi-mode=no \
--with-gcc=system \
--with-binutils=system \
--with-make=system \
--with-fftw=system \
--with-openblas=system \
--with-reflapack=system \
--with-libint=system \
--with-libxc=install \
--with-libxsmm=install
echo -e "\n========== Running Regtests =========="
source /opt/cp2k-master/tools/toolchain/install/setup
cd /opt/cp2k-master
make VERSION=ssmp test TESTOPTS="${TESTOPTS}"
#EOF

1
tools/docker/test_valgrind-pdbg
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regtest/

1
tools/docker/test_valgrind-sdbg
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regtest/