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Merge pull request #71 from edoapra/master
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hadolint fixes
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@edoapra
edoapra authored Nov 1, 2022
2 parents 4b9e5f7 + 25869d3 commit 309e287
Showing 1 changed file with 38 additions and 38 deletions.
76 changes: 38 additions & 38 deletions nwchem-dev/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ ARG FC
ARG NWCHEM_BRANCH
ARG GITHUB_REPOSITORY_OWNER
ENV NWCHEM_TOP="/opt/nwchem"
ENV FC=$FC
ENV NWCHEM_BRANCH=$NWCHEM_BRANCH
ENV GITHUB_REPOSITORY_OWNER=$GITHUB_REPOSITORY_OWNER
ENV FC=${FC}
ENV NWCHEM_BRANCH=${NWCHEM_BRANCH}
ENV GITHUB_REPOSITORY_OWNER=${GITHUB_REPOSITORY_OWNER}
ARG NWCHEM_MODULES="all python " \
ARMCI_NETWORK=MPI-PT \
USE_OPENMP=1 \
Expand All @@ -54,54 +54,54 @@ ENV FFIELD=amber \
OMPI_MCA_btl_vader_single_copy_mechanism=none \
OMP_NUM_THREADS=1 \
COMEX_MAX_NB_OUTSTANDING=16 \
PATH=$PATH:/opt/nwchem/bin
PATH=${PATH}:/opt/nwchem/bin
#get NWCHEM_TARGET
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
RUN arch=$(uname -m) ; if [[ $arch == "x86_64" ]] || [[ $arch == "aarch64" ]] || [[ $arch == "riscv64" ]] || [[ $arch == "ppc64le" ]]; then echo "export NWCHEM_TARGET=LINUX64" > /tmpfile ; fi
RUN arch=$(uname -m) ; arch_123=$(uname -m|cut -c 1-3); if [[ $arch == "i686" ]] || [[ $arch == "i386" ]] || [[ $arch_123 == "arm" ]] ; then echo "export NWCHEM_TARGET=LINUX" > /tmpfile ; fi
RUN . /tmpfile; echo "NWCHEM_TARGET is " $NWCHEM_TARGET
RUN arch=$(uname -m) ; if [[ "$arch" == "x86_64" ]] || [[ "$arch" == "aarch64" ]] || [[ "$arch" == "riscv64" ]] || [[ "$arch" == "ppc64le" ]]; then echo "export NWCHEM_TARGET=LINUX64" > /tmpfile ; fi
RUN arch=$(uname -m) ; arch_123=$(uname -m|cut -c 1-3); if [[ "$arch" == "i686" ]] || [[ "$arch" == "i386" ]] || [[ "$arch_123" == "arm" ]] ; then echo "export NWCHEM_TARGET=LINUX" > /tmpfile ; fi
RUN . /tmpfile; echo "NWCHEM_TARGET is " ${NWCHEM_TARGET}

#one single ugly command to reduce docker size
RUN apt-get update \
&& apt-get -y upgrade \
&& apt-get install -y rsync python3-dev gfortran libopenmpi-dev openmpi-bin make curl unzip cmake git file wget tar bzip2 bc \
&& echo FCFCFC is $FC \
&& echo NWCHEM_BRANCH is $NWCHEM_BRANCH \
&& echo GITHUB_REPOSITORY_OWNER is $GITHUB_REPOSITORY_OWNER \
&& apt-get install -y --no-install-recommends rsync python3-dev gfortran libopenmpi-dev openmpi-bin make curl unzip cmake git file wget tar bzip2 bc ca-certificates \
&& echo FCFCFC is ${FC} \
&& echo NWCHEM_BRANCH is ${NWCHEM_BRANCH} \
&& echo GITHUB_REPOSITORY_OWNER is ${GITHUB_REPOSITORY_OWNER} \
&& arch=$(uname -m) \
&& echo arch is $arch \
&& echo arch is "$arch" \
&& arch_dpkg=$(dpkg --print-architecture) \
&& if [[ $arch == "aarch64" ]]; then arch_dpkg="arm64"; fi \
&& if [[ $arch == "x86_64" ]]; then arch_dpkg="amd64"; fi \
&& if [[ "$arch" == "aarch64" ]]; then arch_dpkg="arm64"; fi \
&& if [[ "$arch" == "x86_64" ]]; then arch_dpkg="amd64"; fi \
&& nv_year=2022 && nv_major=22 && nv_minor=7 && nverdot="$nv_major"."$nv_minor" && nverdash="$nv_major"-"$nv_minor" \
&& if [[ $FC == "nvfortran" ]]; then apt-get install -y g++ libtinfo5 libncursesw5 mpich libmpich-dev; wget https://developer.download.nvidia.com/hpc-sdk/ubuntu/$arch_dpkg/nvhpc-"$nverdash"_"$nverdot"_$arch_dpkg.deb >& log1 ; wget https://developer.download.nvidia.com/hpc-sdk/ubuntu/$arch_dpkg/nvhpc-"$nv_year"_"$nverdot"_$arch_dpkg.deb >& log2 ; tail -n 2 log1 log2; ls -lrt nv*deb; dpkg -i nvhpc*deb ; /opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/bin/makelocalrc -x ; export MPICH_FC=$FC ; MPIF90=mpif90.mpich ; MPIRUN_PATH=/usr/bin/mpirun.mpich ; update-alternatives --set mpi /usr/bin/mpicc.mpich; update-alternatives --set mpirun /usr/bin/mpirun.mpich; update-alternatives --list mpi ; mpif90 -show; export ARMCI_NETWORK=MPI-TS; rm -f nvhpc*deb ; mkdir -p /opt/lib || true; rsync -av /opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/lib/*.so* /opt/lib/.; unset SCALAPACK_SIZE; unset BUILD_SCALAPACK; fi \
&& export PATH=/opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/bin:$PATH \
&& export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/lib:$LD_LIBRARY_PATH \
&& if [[ "$FC" == "nvfortran" ]]; then apt-get install -y --no-install-recommends g++ libtinfo5 libncursesw5 mpich libmpich-dev; wget https://developer.download.nvidia.com/hpc-sdk/ubuntu/"$arch_dpkg/"nvhpc-"$nverdash"_"$nverdot"_$arch_dpkg.deb >& log1 ; wget https://developer.download.nvidia.com/hpc-sdk/ubuntu/$arch_dpkg/nvhpc-"$nv_year"_"$nverdot"_"$arch_dpkg".deb >& log2 ; tail -n 2 log1 log2; ls -lrt nv*deb; dpkg -i nvhpc*deb ; /opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/bin/makelocalrc -x ; export MPICH_FC="$FC" ; MPIF90=mpif90.mpich ; MPIRUN_PATH=/usr/bin/mpirun.mpich ; update-alternatives --set mpi /usr/bin/mpicc.mpich; update-alternatives --set mpirun /usr/bin/mpirun.mpich; update-alternatives --list mpi ; mpif90 -show; export ARMCI_NETWORK=MPI-TS; rm -f nvhpc*deb ; mkdir -p /opt/lib || true; rsync -av /opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/lib/*.so* /opt/lib/.; unset SCALAPACK_SIZE; unset BUILD_SCALAPACK; fi \
&& export PATH=/opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/bin:"$PATH" \
&& export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_"$arch"/"$nverdot"/compilers/lib:"$LD_LIBRARY_PATH" \
&& echo "URL for cloning" https://github.com/${GITHUB_REPOSITORY_OWNER}/nwchem.git \
&& cd /opt; rm -rf nwchem || true; git clone -b $NWCHEM_BRANCH --depth 1 https://github.com/$GITHUB_REPOSITORY_OWNER/nwchem.git \
&& cd /opt; rm -rf nwchem || true; git clone -b "$NWCHEM_BRANCH" --depth 1 https://github.com/"$GITHUB_REPOSITORY_OWNER"/nwchem.git \
&& cd nwchem/src \
#set NWCHEM_TARGET
&& . /tmpfile; echo "NWCHEM_TARGET is " $NWCHEM_TARGET \
&& . /tmpfile; echo "NWCHEM_TARGET is " ${NWCHEM_TARGET} \
#fix openblas cross-compilation
&& arch=$(uname -m) \
&& arch3=$(uname -m|cut -c 1-3) \
&& arch5=$(uname -m|cut -c 1-5) \
&& if [[ $FC == "nvfortran" ]] && [[ $arch == "aarch64" ]]; then cd /tmp ; wget https://raw.githubusercontent.com/edoapra/nwchem-dockerfiles/master/patches/nv_arm64.patch; cd / ; patch -p0 < /tmp/nv_arm64.patch; cd /opt/nwchem/src; fi \
&& if [[ $arch == "aarch64" ]]; then export FORCETARGET=" TARGET=ARMV8 "; fi \
&& if [[ $arch == "ppc64le" ]]; then export FORCETARGET=" TARGET=POWER8 "; fi \
&& if [[ $arch == "riscv64" ]]; then export FORCETARGET=" TARGET=RISCV64_GENERIC "; export ARMCI_NETWORK=MPI-TS; unset USE_OPENMP; fi \
&& if [[ $arch5 == "armv6" ]]; then export FORCETARGET=" TARGET=ARMV6 "; fi \
&& if [[ $arch5 == "armv7" ]]; then export FORCETARGET=" TARGET=ARMV7 "; export ARMCI_NETWORK=MPI-TS; fi \
&& if [[ "$FC" == "nvfortran" ]] && [[ "$arch" == "aarch64" ]]; then cd /tmp ; wget https://raw.githubusercontent.com/edoapra/nwchem-dockerfiles/master/patches/nv_arm64.patch; cd / ; patch -p0 < /tmp/nv_arm64.patch; cd /opt/nwchem/src; fi \
&& if [[ "$arch" == "aarch64" ]]; then export FORCETARGET=" TARGET=ARMV8 "; fi \
&& if [[ "$arch" == "ppc64le" ]]; then export FORCETARGET=" TARGET=POWER8 "; fi \
&& if [[ "$arch" == "riscv64" ]]; then export FORCETARGET=" TARGET=RISCV64_GENERIC "; export ARMCI_NETWORK=MPI-TS; unset USE_OPENMP; fi \
&& if [[ "$arch5" == "armv6" ]]; then export FORCETARGET=" TARGET=ARMV6 "; fi \
&& if [[ "$arch5" == "armv7" ]]; then export FORCETARGET=" TARGET=ARMV7 "; export ARMCI_NETWORK=MPI-TS; fi \
# _SIZE=4 and openblas pkg for 32bit archs
&& if [[ $NWCHEM_TARGET == "LINUX" ]]; then export BLAS_SIZE=4; unset SCALAPACK_SIZE; unset BUILD_SCALAPACK; unset BUILD_OPENBLAS; export BLASOPT=-lopenblas ; export LAPACK_LIB=-lopenblas; apt-get install -y openmpi-bin libopenblas-dev; fi \
&& if [[ ${NWCHEM_TARGET} == "LINUX" ]]; then export BLAS_SIZE=4; unset SCALAPACK_SIZE; unset BUILD_SCALAPACK; unset BUILD_OPENBLAS; export BLASOPT=-lopenblas ; export LAPACK_LIB=-lopenblas; apt-get install -y --no-install-recommends openmpi-bin libopenblas-dev; fi \
# smaller build on qemu emulated archs
&& if [[ $arch != "x86_64" ]]; then export NWCHEM_MODULES="nwdft driver solvation python"; fi \
&& if [[ "$arch" != "x86_64" ]]; then export NWCHEM_MODULES="nwdft driver solvation python"; fi \
# compile libxc for amd64
&& if [[ $arch == "x86_64" ]]; then export USE_LIBXC=1; fi \
&& if [[ "$arch" == "x86_64" ]]; then export USE_LIBXC=1; fi \
&& if [[ -f /tmp/libext.tar.bz2 ]]; then cd libext ; tar xjvf /tmp/libext.tar.bz2; rm -rf /tmp/libext.tar.bz2 ; cd .. ; fi \
&& df -h /dev/shm \
&& mkdir -p ../bin/$NWCHEM_TARGET \
&& gcc -o ../bin/$NWCHEM_TARGET/depend.x config/depend.c \
&& mkdir -p ../bin/${NWCHEM_TARGET} \
&& gcc -o ../bin/"$NWCHEM_TARGET/depend.x" config/depend.c \
&& make nwchem_config \
&& cd libext && make V=-1 && cd .. \
&& cd tools && make V=-1 && cd .. \
Expand All @@ -111,26 +111,26 @@ RUN apt-get update \
&& tail -10 deps.log \
&& echo done tail deps.log '@@@' \
&& make V=1 || true \
&& if [[ -f ../bin/$NWCHEM_TARGET/nwchem ]]; then echo 'NWChem binary created' ; else echo 'compilation error1'; exit 1; fi \
&& if [[ -f ../bin/${NWCHEM_TARGET}/nwchem ]]; then echo 'NWChem binary created' ; else echo 'compilation error1'; exit 1; fi \
&& ../contrib/getmem.nwchem 1000 || true \
&& if [[ -f ../bin/$NWCHEM_TARGET/nwchem ]]; then echo 'NWChem binary created' ; else echo 'compilation error2'; exit 1; fi \
&& if [[ -f ../bin/${NWCHEM_TARGET}/nwchem ]]; then echo 'NWChem binary created' ; else echo 'compilation error2'; exit 1; fi \
# QA tests
&& cd .. \
&& if [[ $NWCHEM_TARGET == "LINUX64" && $FC != "nvfortran" ]]; then SKIP_CACHE=1 OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
NWCHEM_EXECUTABLE=$(pwd)/bin/$NWCHEM_TARGET/nwchem ./travis/run_qas.sh ; fi \
&& if [[ ${NWCHEM_TARGET} == "LINUX64" && "$FC" != "nvfortran" ]]; then SKIP_CACHE=1 OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
NWCHEM_EXECUTABLE=$(pwd)/bin/${NWCHEM_TARGET}/nwchem ./travis/run_qas.sh ; fi \
&& cd src \
#clean unnecessary source to reduce docker size
&& rm -rf tce tools nwdft NWints geom symmetry util nwxc ddscf lapack blas rism argos peigs rmdft gradients symmetry property smd lucia dplot propery hessian ccsd mp2_grad moints cafe analyz dimqm /opt/nwchem/lib libext/scalapack libext/openblas develop ../QA ../contrib ../examples ../.git ../travis ../web nwpw/nwpwlib/nwpwxc rdmft ../doc libext/libxc/libxc* libext/mpich /tmp/libext || true \
&& ls -lrt libext/libxc || true \
&& ls -lrt libext/lib || true \
&& strip ../bin/$NWCHEM_TARGET/nwchem \
&& strip ../bin/${NWCHEM_TARGET}/nwchem \
&& rm libext/libxc/install/bin/xc* || true \
&& cd libext ; tar cjvf libext.tar.bz2 lib/* libxc/install/lib/* libxc/install/include/* ||true \
&& rm -rf lib/* libxc/install/lib/* ||true \
&& cd .. \
&& ln -sf ../bin/$NWCHEM_TARGET/nwchem ../bin/nwchem \
&& ln -sf ../bin/${NWCHEM_TARGET}/nwchem ../bin/nwchem \
#clean unnecessary packages
&& DEBIAN_FRONTEND=noninteractive apt-get -y install localepurge \
&& DEBIAN_FRONTEND=noninteractive apt-get -y install --no-install-recommends localepurge \
&& echo MANDELETE > /etc/locale.nopurge \
&& echo DONTBOTHERNEWLOCALE >> /etc/locale.nopurge \
&& echo en_US.UTF-8 >> /etc/locale.nopurge \
Expand All @@ -140,7 +140,7 @@ RUN apt-get update \
# && apt-get -y purge wget git make curl unzip cmake cmake-data libhwloc-plugins libicu66 manpages manpages-dev iproute2 libelf1 libmnl0 libxtables12 libxau6 libxcb1 libxdmcp6 libx11-6 libx11-data libxext6 libxmuu1 xauth xz-utils localepurge g++-8 g++ libstdc++-9-dev libmpich-dev && apt-get -y autoremove \
&& apt-get -y purge cpp-9 gfortran-9 gcc-9 libnl-3-dev libnl-route-3-dev libnuma-dev libibverbs-dev libgcc-9-dev autotools-dev libevent-dev libpython3.8-dev libc6-dev linux-libc-dev libexpat1-dev zlib1g-dev libcrypt-dev perl-modules-5.30 libperl5.30 || true \
&& apt-get clean \
&& if [[ $NWCHEM_TARGET == "LINUX" ]]; then apt-get -y purge libopenblas-dev; fi \
&& if [[ ${NWCHEM_TARGET} == "LINUX" ]]; then apt-get -y purge libopenblas-dev; fi \
&& chown -R nwchem /opt/nwchem && chgrp -R nwchem /opt/nwchem \
&& du -sh /opt/nwchem \
&& du -sh /opt/nwchem/src/libext/lib || true \
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