From da0e60c1731cd5c76737cf58fa831c5366f6ec85 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 4 Sep 2020 14:43:03 -0400 Subject: [PATCH] Apply changes to remaining containers --- .../singularity/ubuntu18.04_intel_opencl.def | 67 ++++++++++++++++-- tools/singularity/ubuntu18.04_nvidia.def | 66 ++++++++++++++++-- tools/singularity/ubuntu20.04_nvidia.def | 68 +++++++++++++++++-- 3 files changed, 189 insertions(+), 12 deletions(-) diff --git a/tools/singularity/ubuntu18.04_intel_opencl.def b/tools/singularity/ubuntu18.04_intel_opencl.def index b60da61b91..ef521be19e 100644 --- a/tools/singularity/ubuntu18.04_intel_opencl.def +++ b/tools/singularity/ubuntu18.04_intel_opencl.def @@ -4,8 +4,10 @@ From: ubuntu:18.04 %post export DEBIAN_FRONTEND=noninteractive apt-get update - apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y software-properties-common + add-apt-repository ppa:openkim/latest + apt-get update + apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ bc \ build-essential \ @@ -38,6 +40,8 @@ From: ubuntu:18.04 libpng-dev \ libproj-dev \ libvtk6-dev \ + libyaml-dev \ + libzstd-dev \ make \ mpi-default-bin \ mpi-default-dev \ @@ -61,14 +65,62 @@ From: ubuntu:18.04 wget \ xxd \ valgrind \ - gdb + gdb \ + zstd \ + libkim-api-dev \ + openkim-models + + ########################################################################### + # Intel OpenCL + ########################################################################### add-apt-repository ppa:intel-opencl/intel-opencl apt-get update apt-get install -y intel-opencl-icd - # clean cache - rm -rf /var/lib/apt/lists/* + ########################################################################### + # KIM-API + ########################################################################### + + # workaround for installing files in /usr/share/doc inside of a container + sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes + apt-get install -y libkim-api-doc + sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes + + # install KIM models + KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples + gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz + gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz + + kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003 + kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003 + kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu + + + ########################################################################### + # Plumed + ########################################################################### + + export PLUMED_PKG_VERSION=2.6.1 + + mkdir plumed + cd plumed + curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz + tar -xzf plumed.tar.gz + cd plumed-${PLUMED_PKG_VERSION} + ./configure --disable-doc --prefix=/usr + make + make install + cd ../../ + rm -rvf plumed + + + ########################################################################### + # Customizations + ########################################################################### # set custom prompt indicating the container name CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh @@ -79,6 +131,13 @@ EOF chmod 755 $CUSTOM_PROMPT_ENV + ########################################################################### + # Cleanup + ########################################################################### + # clean cache + rm -rf /var/lib/apt/lists/* + + %environment LC_ALL=C export LC_ALL diff --git a/tools/singularity/ubuntu18.04_nvidia.def b/tools/singularity/ubuntu18.04_nvidia.def index 74476562c8..68d2a9166e 100644 --- a/tools/singularity/ubuntu18.04_nvidia.def +++ b/tools/singularity/ubuntu18.04_nvidia.def @@ -4,8 +4,10 @@ From: nvidia/cuda:11.0-devel-ubuntu18.04 %post export DEBIAN_FRONTEND=noninteractive apt-get update - apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y software-properties-common + add-apt-repository ppa:openkim/latest + apt-get update + apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ bc \ build-essential \ @@ -38,6 +40,8 @@ From: nvidia/cuda:11.0-devel-ubuntu18.04 libpng-dev \ libproj-dev \ libvtk6-dev \ + libyaml-dev \ + libzstd-dev \ make \ mpi-default-bin \ mpi-default-dev \ @@ -61,13 +65,61 @@ From: nvidia/cuda:11.0-devel-ubuntu18.04 wget \ xxd \ valgrind \ - gdb + gdb \ + zstd \ + libkim-api-dev \ + openkim-models + + ########################################################################### + # NVIDIA OpenCL + ########################################################################### mkdir -p /etc/OpenCL/vendors echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd - # clean cache - rm -rf /var/lib/apt/lists/* + ########################################################################### + # KIM-API + ########################################################################### + + # workaround for installing files in /usr/share/doc inside of a container + sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes + apt-get install -y libkim-api-doc + sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes + + # install KIM models + KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples + gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz + gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz + + kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003 + kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003 + kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu + + + ########################################################################### + # Plumed + ########################################################################### + + export PLUMED_PKG_VERSION=2.6.1 + + mkdir plumed + cd plumed + curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz + tar -xzf plumed.tar.gz + cd plumed-${PLUMED_PKG_VERSION} + ./configure --disable-doc --prefix=/usr + make + make install + cd ../../ + rm -rvf plumed + + + ########################################################################### + # Customizations + ########################################################################### # set custom prompt indicating the container name CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh @@ -78,6 +130,12 @@ EOF chmod 755 $CUSTOM_PROMPT_ENV + ########################################################################### + # Cleanup + ########################################################################### + # clean cache + rm -rf /var/lib/apt/lists/* + %environment LC_ALL=C export LC_ALL diff --git a/tools/singularity/ubuntu20.04_nvidia.def b/tools/singularity/ubuntu20.04_nvidia.def index affd6597ea..06fccc52d1 100644 --- a/tools/singularity/ubuntu20.04_nvidia.def +++ b/tools/singularity/ubuntu20.04_nvidia.def @@ -4,8 +4,10 @@ From: nvidia/cuda:11.0-devel-ubuntu20.04 %post export DEBIAN_FRONTEND=noninteractive apt-get update - apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y software-properties-common + add-apt-repository ppa:openkim/latest + apt-get update + apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ bc \ build-essential \ @@ -38,6 +40,8 @@ From: nvidia/cuda:11.0-devel-ubuntu20.04 libpng-dev \ libproj-dev \ libvtk6-dev \ + libyaml-dev \ + libzstd-dev \ make \ mpi-default-bin \ mpi-default-dev \ @@ -57,13 +61,63 @@ From: nvidia/cuda:11.0-devel-ubuntu20.04 wget \ xxd \ valgrind \ - gdb + gdb \ + zstd \ + libkim-api-dev \ + openkim-models + + + ########################################################################### + # NVIDIA OpenCL + ########################################################################### mkdir -p /etc/OpenCL/vendors echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd - # clean cache - rm -rf /var/lib/apt/lists/* + + ########################################################################### + # KIM-API + ########################################################################### + + # workaround for installing files in /usr/share/doc inside of a container + sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes + apt-get install -y libkim-api-doc + sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes + + # install KIM models + KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples + gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz + gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz + + kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003 + kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ + kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003 + kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu + + + ########################################################################### + # Plumed + ########################################################################### + + export PLUMED_PKG_VERSION=2.6.1 + + mkdir plumed + cd plumed + curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz + tar -xzf plumed.tar.gz + cd plumed-${PLUMED_PKG_VERSION} + ./configure --disable-doc --prefix=/usr + make + make install + cd ../../ + rm -rvf plumed + + + ########################################################################### + # Customizations + ########################################################################### # set custom prompt indicating the container name CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh @@ -74,6 +128,12 @@ EOF chmod 755 $CUSTOM_PROMPT_ENV + ########################################################################### + # Cleanup + ########################################################################### + # clean cache + rm -rf /var/lib/apt/lists/* + %environment LC_ALL=C export LC_ALL