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Dockerfile.intel-impi-app
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Dockerfile.intel-impi-app
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FROM ubuntu:20.04 AS build
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends -o=Dpkg::Use-Pty=0 build-essential pkg-config ca-certificates gnupg apt-utils && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
autoconf \
bc \
bison \
clang-tidy \
csh \
curl \
emacs \
file \
flex \
git \
ksh \
less \
libboost-thread-dev \
libcurl4-openssl-dev \
libexpat1-dev \
libgmp-dev \
libmpfr-dev \
libncurses-dev \
libssl-dev \
libx11-dev \
libxml2-dev \
lsb-release \
man-db \
nano \
openssh-server \
pkg-config \
screen \
swig \
tar \
tcl \
tcsh \
time \
tk \
unzip \
vim \
wget \
wish && \
rm -rf /var/lib/apt/lists/*
# CMake version 3.19.2
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
make \
wget && \
rm -rf /var/lib/apt/lists/*
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.19/cmake-3.19.2-Linux-x86_64.sh && \
mkdir -p /usr/local && \
/bin/sh /var/tmp/cmake-3.19.2-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
rm -rf /var/tmp/cmake-3.19.2-Linux-x86_64.sh
ENV PATH=/usr/local/bin:$PATH
RUN rm -f /usr/bin/gmake && \
ln -s /usr/bin/make /usr/bin/gmake
RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends git-lfs && \
git lfs install --skip-repo
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
python3-dev \
python3-pip \
python3-scipy \
python3-yaml && \
rm -rf /var/lib/apt/lists/*
RUN ln -s /usr/bin/python3 /usr/bin/python
# Mellanox OFED version 5.2-1.0.4.0
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
ca-certificates \
gnupg \
wget && \
rm -rf /var/lib/apt/lists/*
RUN wget -qO - https://www.mellanox.com/downloads/ofed/RPM-GPG-KEY-Mellanox | apt-key add - && \
mkdir -p /etc/apt/sources.list.d && wget -q -nc --no-check-certificate -P /etc/apt/sources.list.d https://linux.mellanox.com/public/repo/mlnx_ofed/5.2-1.0.4.0/ubuntu18.04/mellanox_mlnx_ofed.list && \
apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
ibverbs-providers \
ibverbs-utils \
libibmad-dev \
libibmad5 \
libibumad-dev \
libibumad3 \
libibverbs-dev \
libibverbs1 \
librdmacm-dev \
librdmacm1 && \
rm -rf /var/lib/apt/lists/*
# Mellanox HPC-X version 2.8.0
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
bzip2 \
openssh-client \
tar \
wget && \
rm -rf /var/lib/apt/lists/*
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp http://www.mellanox.com/downloads/hpc/hpc-x/v2.8/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64.tbz && \
mkdir -p /var/tmp && tar -x -f /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64.tbz -C /var/tmp -j && \
cp -a /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64 /usr/local/hpcx && \
echo "source /usr/local/hpcx/hpcx-mt-init-ompi.sh" >> /etc/bash.bashrc && \
echo "hpcx_load" >> /etc/bash.bashrc && \
rm -rf /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64.tbz /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64
# KNEM version 1.1.4
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
ca-certificates \
git && \
rm -rf /var/lib/apt/lists/*
RUN mkdir -p /var/tmp && cd /var/tmp && git clone --depth=1 --branch knem-1.1.4 https://gitlab.inria.fr/knem/knem.git knem && cd - && \
mkdir -p /usr/local/knem && \
cd /var/tmp/knem && \
mkdir -p /usr/local/knem/include && \
cp common/*.h /usr/local/knem/include && \
rm -rf /var/tmp/knem
ENV CPATH=/usr/local/knem/include:$CPATH
# XPMEM branch master
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
autoconf \
automake \
ca-certificates \
file \
git \
libtool \
make && \
rm -rf /var/lib/apt/lists/*
RUN mkdir -p /var/tmp && cd /var/tmp && git clone --depth=1 --branch master https://gitlab.com/hjelmn/xpmem.git xpmem && cd - && \
cd /var/tmp/xpmem && \
autoreconf --install && \
cd /var/tmp/xpmem && ./configure --prefix=/usr/local/xpmem --disable-kernel-module && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/xpmem
ENV CPATH=/usr/local/xpmem/include:$CPATH \
LD_LIBRARY_PATH=/usr/local/xpmem/lib:$LD_LIBRARY_PATH \
LIBRARY_PATH=/usr/local/xpmem/lib:$LIBRARY_PATH
# UCX version 1.9.0
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
binutils-dev \
file \
libnuma-dev \
make \
wget && \
rm -rf /var/lib/apt/lists/*
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://github.com/openucx/ucx/releases/download/v1.9.0/ucx-1.9.0.tar.gz && \
mkdir -p /var/tmp && tar -x -f /var/tmp/ucx-1.9.0.tar.gz -C /var/tmp -z && \
cd /var/tmp/ucx-1.9.0 && ./configure --prefix=/usr/local/ucx --disable-assertions --disable-debug --disable-doxygen-doc --disable-logging --disable-params-check --enable-optimizations --with-knem --with-rdmacm --with-verbs --with-xpmem --without-cuda && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/ucx-1.9.0 /var/tmp/ucx-1.9.0.tar.gz
ENV CPATH=/usr/local/ucx/include:$CPATH \
LD_LIBRARY_PATH=/usr/local/ucx/lib:$LD_LIBRARY_PATH \
LIBRARY_PATH=/usr/local/ucx/lib:$LIBRARY_PATH \
PATH=/usr/local/ucx/bin:$PATH
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
default-libmysqlclient-dev \
file \
freeipmi-tools \
hwloc \
libevent-dev \
libfreeipmi-dev \
libglib2.0-0 \
libglib2.0-dev \
libgtk-3-0 \
libgtk-3-dev \
libhwloc-dev \
libjson-c-dev \
liblua5.2-0 \
liblua5.2-dev \
libmunge-dev \
libmunge2 \
libpam0g-dev \
libyaml-dev && \
rm -rf /var/lib/apt/lists/*
ENV APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1
RUN wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB && \
apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB && \
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB && \
echo "deb https://apt.repos.intel.com/oneapi all main" > /etc/apt/sources.list.d/oneAPI.list
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends -o=Dpkg::Use-Pty=0 intel-hpckit-getting-started intel-oneapi-clck intel-oneapi-common-licensing intel-oneapi-common-vars intel-oneapi-dev-utilities intel-oneapi-dpcpp-cpp-compiler-pro intel-oneapi-ifort intel-oneapi-inspector intel-oneapi-itac intel-oneapi-mpi-devel intel-oneapi-mkl-devel && \
rm -rf /var/lib/apt/lists/*
RUN echo "if [ -z $INTEL_SH_GUARD ]; then" > /etc/profile.d/intel.sh && \
echo " source /opt/intel/oneapi/setvars.sh -i_mpi_library_kind=release_mt" >> /etc/profile.d/intel.sh && \
echo "fi" >> /etc/profile.d/intel.sh && \
echo "export INTEL_SH_GUARD=1" >> /etc/profile.d/intel.sh && \
chmod a+x /etc/profile.d/intel.sh
SHELL ["/bin/bash", "-c"]
ENV BOOST_ROOT=/opt/jedistack \
CC=mpiicc \
CMAKE_CXX_COMPILER=mpiicpc \
CMAKE_C_COMPILER=mpiicc \
CMAKE_Fortran_COMPILER=mpiifort \
CMAKE_PREFIX_PATH=/opt/jedistack \
CMAKE_Platform=linux.intel \
CPATH=/opt/jedistack/include:/usr/local/include:/usr/include:/usr/local/pmix/include:$CPATH \
CXX=mpiicpc \
EIGEN3_INCLUDE_DIR=/opt/jedistack \
FC=mpiifort \
HDF5_ROOT=/opt/jedistack \
I_MPI_LIBRARY_KIND=release_mt \
I_MPI_THREAD_SPLIT=1 \
LD_LIBRARY_PATH=/opt/jedistack/lib:/usr/local/lib:/usr/lib:/usr/lib/x86_64-linux-gnu:/opt/intel/oneapi/compiler/2021.2.0/linux/compiler/lib/intel64_lin//usr/local/pmix/lib:$LD_LIBRARY_PATH \
LIBRARY_PATH=/opt/jedistack/lib:/usr/local/lib:/usr/lib:/usr/lib/x86_64-linux-gnu:$LIBRARY_PATH \
MPI_CC=mpiicc \
MPI_CXX=mpiicpc \
MPI_FC=mpiifort \
NETCDF=/opt/jedistack \
PATH=/opt/jedistack/bin:/usr/local/bin:/usr/local/pmix/bin:$PATH \
PIO=/opt/jedistack \
PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig \
PNETCDF=/opt/jedistack \
PYTHONPATH=/opt/jedistack/lib:/usr/local/lib:$PYTHONPATH \
SERIAL_CC=icc \
SERIAL_CXX=icpc \
SERIAL_FC=ifort
RUN source /etc/profile && \
cd /root && \
git clone https://github.com/jcsda/jedi-stack.git && \
cd jedi-stack/buildscripts && \
git checkout develop && \
./build_stack.sh "container-intel-impi-app" && \
mv ../jedi-stack-contents.log /etc && \
chmod a+r /etc/jedi-stack-contents.log && \
cd /root/jedi-stack/pkg/NCEPLIBS-bufr/build/python && \
python3 setup.py build && \
python3 setup.py install --prefix=/opt/jedistack --install-lib=/opt/jedistack/lib/python3.8/site-packages && \
rm -rf /root/jedi-stack && \
mkdir /worktmp
COPY hello_world_mpi.c /root/hello_world_mpi.c
RUN source /etc/profile && \
mkdir -p /opt/jedi && \
cd /opt/jedi && \
git clone https://github.com/jcsda/fv3-bundle.git && \
cd /opt/jedi/fv3-bundle && \
git checkout develop && \
git clone https://github.com/jcsda/crtm.git -b v2.3-jedi && \
mkdir -p /opt/jedi/build && \
cd /opt/jedi/build && \
ecbuild --build=Release ../fv3-bundle && \
make -j4 && \
ctest -R get_ && \
cd /opt/jedi/build/test_data && \
find . -type f -name "*.tar.gz" -delete && \
chmod -R 777 /opt/jedi/fv3-bundle && \
cd /root && \
mpiicc /root/hello_world_mpi.c -o /opt/jedistack/bin/hello_world_mpi -lstdc++
RUN source /etc/profile && \
mkdir -p /var/tmp && \
wget -q -nc --no-check-certificate -P /var/tmp https://github.com/openpmix/openpmix/releases/download/v3.1.5/pmix-3.1.5.tar.gz && \
tar -x -f /var/tmp/pmix-3.1.5.tar.gz -C /var/tmp -z && \
cd /var/tmp/pmix-3.1.5 && \
./configure --prefix=/opt/jedistack/pmix && \
make -j$(nproc) && \
make -j$(nproc) install && \
rm -rf /var/tmp/pmix-3.1.5 /var/tmp/pmix-3.1.5.tar.gz
RUN source /etc/profile && \
mkdir -p /var/tmp && \
wget -q -nc --no-check-certificate -P /var/tmp https://download.schedmd.com/slurm/slurm-19.05.4.tar.bz2 && \
tar -x -f /var/tmp/slurm-19.05.4.tar.bz2 -C /var/tmp -j && \
cd /var/tmp/slurm-19.05.4 && \
./configure --prefix=/opt/jedistack/slurm-pmi2 --with-hdf5=/opt/jedistack/bin && \
cd /var/tmp/slurm-19.05.4 && \
make -C contribs/pmi2 install && \
rm -rf /var/tmp/slurm-19.05.4 /var/tmp/slurm-19.05.4.tar.bz2
FROM ubuntu:20.04 AS runtime
COPY --from=build /opt/jedistack /opt/jedi/jedistack
COPY --from=build /opt/jedi /opt/jedi
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends -o=Dpkg::Use-Pty=0 build-essential pkg-config ca-certificates gnupg apt-utils && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
autoconf \
bc \
bison \
clang-tidy \
csh \
curl \
emacs \
file \
flex \
git \
ksh \
less \
libboost-thread-dev \
libcurl4-openssl-dev \
libexpat1-dev \
libgmp-dev \
libmpfr-dev \
libncurses-dev \
libssl-dev \
libx11-dev \
libxml2-dev \
lsb-release \
man-db \
nano \
openssh-server \
pkg-config \
screen \
swig \
tar \
tcl \
tcsh \
time \
tk \
unzip \
vim \
wget \
wish && \
rm -rf /var/lib/apt/lists/*
RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends git-lfs && \
git lfs install --skip-repo
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
python3-dev \
python3-pip \
python3-scipy \
python3-yaml && \
rm -rf /var/lib/apt/lists/*
RUN ln -s /usr/bin/python3 /usr/bin/python
# Mellanox OFED version 5.2-1.0.4.0
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
ca-certificates \
gnupg \
wget && \
rm -rf /var/lib/apt/lists/*
RUN wget -qO - https://www.mellanox.com/downloads/ofed/RPM-GPG-KEY-Mellanox | apt-key add - && \
mkdir -p /etc/apt/sources.list.d && wget -q -nc --no-check-certificate -P /etc/apt/sources.list.d https://linux.mellanox.com/public/repo/mlnx_ofed/5.2-1.0.4.0/ubuntu18.04/mellanox_mlnx_ofed.list && \
apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
ibverbs-providers \
ibverbs-utils \
libibmad-dev \
libibmad5 \
libibumad-dev \
libibumad3 \
libibverbs-dev \
libibverbs1 \
librdmacm-dev \
librdmacm1 && \
rm -rf /var/lib/apt/lists/*
# Mellanox HPC-X version 2.8.0
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
bzip2 \
openssh-client \
tar \
wget && \
rm -rf /var/lib/apt/lists/*
RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp http://www.mellanox.com/downloads/hpc/hpc-x/v2.8/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64.tbz && \
mkdir -p /var/tmp && tar -x -f /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64.tbz -C /var/tmp -j && \
cp -a /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64 /usr/local/hpcx && \
echo "source /usr/local/hpcx/hpcx-mt-init-ompi.sh" >> /etc/bash.bashrc && \
echo "hpcx_load" >> /etc/bash.bashrc && \
rm -rf /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64.tbz /var/tmp/hpcx-v2.8.0-gcc-MLNX_OFED_LINUX-5.2-1.0.4.0-ubuntu20.04-x86_64
# KNEM
COPY --from=0 /usr/local/knem /usr/local/knem
ENV CPATH=/usr/local/knem/include:$CPATH
# XPMEM
COPY --from=0 /usr/local/xpmem /usr/local/xpmem
ENV CPATH=/usr/local/xpmem/include:$CPATH \
LD_LIBRARY_PATH=/usr/local/xpmem/lib:$LD_LIBRARY_PATH \
LIBRARY_PATH=/usr/local/xpmem/lib:$LIBRARY_PATH
# UCX
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
libbinutils && \
rm -rf /var/lib/apt/lists/*
COPY --from=0 /usr/local/ucx /usr/local/ucx
ENV CPATH=/usr/local/ucx/include:$CPATH \
LD_LIBRARY_PATH=/usr/local/ucx/lib:$LD_LIBRARY_PATH \
LIBRARY_PATH=/usr/local/ucx/lib:$LIBRARY_PATH \
PATH=/usr/local/ucx/bin:$PATH
ENV APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1
RUN wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB && \
apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB && \
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB && \
echo "deb https://apt.repos.intel.com/oneapi all main" > /etc/apt/sources.list.d/oneAPI.list
SHELL ["/bin/bash", "-c"]
RUN source /etc/profile && \
apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends -o=Dpkg::Use-Pty=0 kmod linux-headers-5.4.0-1041-aws libnuma-dev && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update -y && \
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends -o=Dpkg::Use-Pty=0 intel-oneapi-runtime-ccl intel-oneapi-runtime-compilers intel-oneapi-runtime-dnnl intel-oneapi-runtime-dpcpp-cpp intel-oneapi-runtime-dpcpp-library intel-oneapi-runtime-fortran intel-oneapi-runtime-libs intel-oneapi-runtime-mkl intel-oneapi-runtime-mpi intel-oneapi-runtime-opencl intel-oneapi-runtime-openmp intel-oneapi-runtime-tbb intel-oneapi-runtime-vpl intel-hpckit-runtime && \
rm -rf /var/lib/apt/lists/*
ENV BOOST_ROOT=/opt/jedistack \
CC=mpiicc \
CMAKE_CXX_COMPILER=mpiicpc \
CMAKE_C_COMPILER=mpiicc \
CMAKE_Fortran_COMPILER=mpiifort \
CMAKE_PREFIX_PATH=/opt/jedistack \
CMAKE_Platform=linux.intel \
CPATH=/opt/jedistack/include:/usr/local/include:/usr/include:/usr/local/pmix/include:$CPATH \
CXX=mpiicpc \
EIGEN3_INCLUDE_DIR=/opt/jedistack \
FC=mpiifort \
HDF5_ROOT=/opt/jedistack \
I_MPI_LIBRARY_KIND=release_mt \
I_MPI_THREAD_SPLIT=1 \
LD_LIBRARY_PATH=/opt/jedistack/lib:/usr/local/lib:/usr/lib:/usr/lib/x86_64-linux-gnu:/opt/intel/oneapi/compiler/2021.2.0/linux/compiler/lib/intel64_lin//usr/local/pmix/lib:$LD_LIBRARY_PATH \
LIBRARY_PATH=/opt/jedistack/lib:/usr/local/lib:/usr/lib:/usr/lib/x86_64-linux-gnu:$LIBRARY_PATH \
MPI_CC=mpiicc \
MPI_CXX=mpiicpc \
MPI_FC=mpiifort \
NETCDF=/opt/jedistack \
PATH=/opt/jedistack/bin:/usr/local/bin:/usr/local/pmix/bin:$PATH \
PIO=/opt/jedistack \
PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig \
PNETCDF=/opt/jedistack \
PYTHONPATH=/opt/jedistack/lib:/usr/local/lib:$PYTHONPATH \
SERIAL_CC=icc \
SERIAL_CXX=icpc \
SERIAL_FC=ifort
RUN echo "if [ -z $INTEL_SH_GUARD ]; then" > /etc/profile.d/intel.sh && \
echo " source /opt/intel/oneapi/setvars.sh -i_mpi_library_kind=release_mt" >> /etc/profile.d/intel.sh && \
echo "fi" >> /etc/profile.d/intel.sh && \
echo "export INTEL_SH_GUARD=1" >> /etc/profile.d/intel.sh && \
chmod a+x /etc/profile.d/intel.sh