Unverified Commit 3bdfbdcf authored by Richard Berger's avatar Richard Berger
Browse files

Update Ubuntu 18.04 GPU container and add Ubuntu 20.04

parent 60d25c2e

tools/singularity/ubuntu18.04_gpu.def

+85 −23
Original line number Diff line number Diff line
@@ -2,11 +2,11 @@ BootStrap: docker 
From: ubuntu:18.04



%environment

    export PATH=/usr/lib/ccache:/usr/local/cuda-10.2/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64

    export CUDADIR=/usr/local/cuda-10.2

    export CUDA_PATH=/usr/local/cuda-10.2

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64

    export LIBRARY_PATH=/usr/local/cuda-10.2/lib64/stubs

    export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64

    export CUDADIR=/usr/local/cuda-11.0

    export CUDA_PATH=/usr/local/cuda-11.0

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.0/lib64

    export LIBRARY_PATH=/usr/local/cuda-11.0/lib64/stubs

%post

    export DEBIAN_FRONTEND=noninteractive

    apt-get update
@@ -28,6 +28,8 @@ From: ubuntu:18.04 
        build-essential



    apt-get install --no-install-recommends -y software-properties-common

    add-apt-repository ppa:openkim/latest

    apt-get update

    apt-get install --no-install-recommends -y \

        bc \

        build-essential \
@@ -36,30 +38,29 @@ From: ubuntu:18.04 
        cmake \

        cmake-curses-gui \

        curl \

        doxygen \

        enchant \

        g++ \

        gcc \

        gfortran \

        git \

        hdf5-tools \

        kmod \

        less \

        libblas-dev \

        libeigen3-dev \

        libenchant-dev \

        libfftw3-dev \

        libgsl-dev \

        libhdf5-serial-dev \

        libhwloc-dev \

        libjpeg-dev \

        liblapack-dev \

        libnetcdf-dev \

        libomp-dev \

        libopenblas-dev \

        libnuma-dev \

        libpng-dev \

        libproj-dev \

        libvtk6-dev \

        libyaml-dev \

        libzstd-dev \

        make \

        mpi-default-bin \

        mpi-default-dev \
@@ -81,7 +82,15 @@ From: ubuntu:18.04 
        wget \

        xxd \

        valgrind \

        gdb

        gdb \

        zstd \

        libkim-api-dev \

        openkim-models





    ###########################################################################

    # CUDA

    ###########################################################################



    wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin

    mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
@@ -89,7 +98,7 @@ From: ubuntu:18.04 
    add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"

    apt-get update



    export CUDA_PKG_VERSION=10.2

    export CUDA_PKG_VERSION=11.0



    apt-get install -y --no-install-recommends \

        cuda-libraries-$CUDA_PKG_VERSION \
@@ -97,37 +106,90 @@ From: ubuntu:18.04 
        cuda-libraries-dev-$CUDA_PKG_VERSION \

        cuda-minimal-build-$CUDA_PKG_VERSION \

        cuda-compat-$CUDA_PKG_VERSION \

        libcublas10 \

        libcublas-dev

        libcublas-11-0 \

        libcublas-dev-11-0



    echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf

    echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf



    # add missing symlink

    ln -s /usr/local/cuda-11.0 /usr/local/cuda

    ln -s /usr/local/cuda-11.0/lib64/stubs/libcuda.so /usr/local/cuda-11.0/lib64/stubs/libcuda.so.1





    ###########################################################################

    # ROCm hipCUB

    ###########################################################################



    export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64

    git clone -b master-rocm-3.5 https://github.com/ROCmSoftwarePlatform/hipCUB.git

    git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git

    mkdir hipCUB/build

    cd hipCUB/build

    CXX=hipcc cmake -D BUILD_TEST=off ..

    make -j4

    make -j 8

    make package

    make install



    echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf

    echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf



    # clean cache

    rm -rf /var/lib/apt/lists/*

    ###########################################################################

    # KIM-API

    ###########################################################################



    # add missing symlink

    ln -s /usr/local/cuda-10.2 /usr/local/cuda

    ln -s /usr/local/cuda-10.2/lib64/stubs/libcuda.so /usr/local/cuda-10.2/lib64/stubs/libcuda.so.1

    # 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 -j 8

    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

    cat >$CUSTOM_PROMPT_ENV <<EOF

#!/bin/bash

PS1="[ubuntu18/gpu:\u@\h] \W> "

PS1="[ubuntu18.04/gpu:\u@\h] \W> "

EOF

    chmod 755 $CUSTOM_PROMPT_ENV





    ###########################################################################

    # Cleanup

    ###########################################################################

    # clean cache

    rm -rf /var/lib/apt/lists/*



%environment

    LC_ALL=C

    export LC_ALL

tools/singularity/ubuntu20.04_gpu.def

0 → 100644
+200 −0
Original line number Diff line number Diff line 
BootStrap: docker

From: ubuntu:20.04



%environment

    export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64

    export CUDADIR=/usr/local/cuda-11.0

    export CUDA_PATH=/usr/local/cuda-11.0

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.0/lib64

    export LIBRARY_PATH=/usr/local/cuda-11.0/lib64/stubs

%post

    export DEBIAN_FRONTEND=noninteractive

    apt-get update

    apt-get upgrade --no-install-recommends -y



    apt-get install -y --no-install-recommends curl libnuma-dev gnupg



    curl -sL http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key | apt-key add -

    # AMD is using xenial folder also for focal

    printf "deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main" > /etc/apt/sources.list.d/rocm.list



    apt-get update

    apt-get install --no-install-recommends -y \

        kmod \

        file \

        sudo \

        libelf1 \

        rocm-dev \

        rocm-libs \

        build-essential



    apt-get install --no-install-recommends -y software-properties-common

    add-apt-repository ppa:openkim/latest

    apt-get update

    apt-get install --no-install-recommends -y \

        bc \

        build-essential \

        ccache \

        clang \

        cmake \

        cmake-curses-gui \

        curl \

        g++ \

        gcc \

        gfortran \

        git \

        hdf5-tools \

        less \

        libblas-dev \

        libeigen3-dev \

        libfftw3-dev \

        libgsl-dev \

        libhdf5-serial-dev \

        libhwloc-dev \

        libjpeg-dev \

        liblapack-dev \

        libnetcdf-dev \

        libomp-dev \

        libopenblas-dev \

        libnuma-dev \

        libpng-dev \

        libproj-dev \

        libvtk6-dev \

        libyaml-dev \

        libzstd-dev \

        make \

        mpi-default-bin \

        mpi-default-dev \

        ninja-build \

        python3-dev \

        python3-pip \

        python3-pkg-resources \

        python3-setuptools \

        python3-virtualenv \

        rsync \

        ssh \

        vim-nox \

        virtualenv \

        voro++-dev \

        wget \

        xxd \

        valgrind \

        gdb \

        zstd \

        libkim-api-dev \

        openkim-models





    ###########################################################################

    # CUDA

    ###########################################################################



    wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin

    mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600

    apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub

    add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"

    apt-get update



    export CUDA_PKG_VERSION=11.0



    apt-get install -y --no-install-recommends \

        cuda-libraries-$CUDA_PKG_VERSION \

        cuda-command-line-tools-$CUDA_PKG_VERSION \

        cuda-libraries-dev-$CUDA_PKG_VERSION \

        cuda-minimal-build-$CUDA_PKG_VERSION \

        cuda-compat-$CUDA_PKG_VERSION \

        libcublas-11-0 \

        libcublas-dev-11-0



    echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf

    echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf



    # add missing symlink

    ln -s /usr/local/cuda-11.0 /usr/local/cuda

    ln -s /usr/local/cuda-11.0/lib64/stubs/libcuda.so /usr/local/cuda-11.0/lib64/stubs/libcuda.so.1





    ###########################################################################

    # ROCm hipCUB

    ###########################################################################



    export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64

    git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git

    mkdir hipCUB/build

    cd hipCUB/build

    CXX=hipcc cmake -D BUILD_TEST=off ..

    make -j 8

    make package

    make install





    ###########################################################################

    # 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

    cat >$CUSTOM_PROMPT_ENV <<EOF

#!/bin/bash

PS1="[ubuntu20.04/gpu:\u@\h] \W> "

EOF

    chmod 755 $CUSTOM_PROMPT_ENV





    ###########################################################################

    # Cleanup

    ###########################################################################

    # clean cache

    rm -rf /var/lib/apt/lists/*



%environment

    LC_ALL=C

    export LC_ALL

    # tell OpenMPI to not try using Infiniband

    OMPI_MCA_btl="^openib"

    # do not warn about unused components as this messes up testing

    OMPI_MCA_btl_base_warn_component_unused="0"

    export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused



%labels

    Author rbberger, akohlmey

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