specfem3d_globe/Dockerfile at main · SeisSCOPED/specfem3d_globe · GitHub

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FROM ghcr.io/seisscoped/container-base:ubuntu20.04

# install cmake3 and boost
RUN apt-get update && apt-get install -y \
    cmake \
    libboost-all-dev \
    git \
    gcc-9 g++-9 gfortran-9 \
    && apt-get clean

# use gnu v9 compilers
RUN ln -sf /usr/bin/gcc-9 /usr/bin/gcc \
    && ln -sf /usr/bin/g++-9 /usr/bin/g++ \
    && ln -sf /usr/bin/gfortran-9 /usr/bin/gfortran

# go to /home/scoped
WORKDIR /home/scoped

# install HDF5 with parallel option (this uses gcc+intelmpi)
RUN wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.3/src/hdf5-1.13.3.tar.gz \
    && source ${MPIVARS_SCRIPT} \
    && tar -xvf hdf5-1.13.3.tar.gz \
    && cd hdf5-1.13.3 \
    && CC=mpicc FC=mpif90 \
    && ./configure --enable-fortran --enable-parallel --prefix=/home/scoped/hdf5 --enable-shared --enable-static \
    && make -j12 && make install \
    && cd .. && rm -rf hdf5-*

ENV HDF5_DIR=/home/scoped/hdf5
# add hdf5 bin to PATH
ENV PATH=$PATH:/home/scoped/hdf5/bin
# add hdf5 lib to LD_LIBRARY_PATH
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/scoped/hdf5/lib

# install asdf-library
# workaround to use gfortran with intel mpi (not a good engineering practice)
RUN mv /opt/intel/compilers_and_libraries/linux/mpi/intel64/include/mpi.mod /opt/intel/compilers_and_libraries/linux/mpi/intel64/include/mpi.modbak \
   && ln -s /opt/intel/compilers_and_libraries/linux/mpi/intel64/include/gfortran/9.1.0/mpi.mod /opt/intel/compilers_and_libraries/linux/mpi/intel64/include

RUN git clone https://github.com/SeismicData/asdf-library.git \
    && cd asdf-library \
    && mkdir build && cd build \
    && cmake .. -DCMAKE_Fortran_COMPILER=h5pfc -DCMAKE_INSTALL_PREFIX=/home/scoped/asdf -DBUILD_DOCUMENTATION=False \
    && make && make install \
    && cd ../../ \
    && rm -rf asdf-library

# install ADIOS2
RUN git clone https://github.com/ornladios/ADIOS2.git && cd ADIOS2 \
    && mkdir build && cd build\
    && cmake .. -DCMAKE_INSTALL_PREFIX=/home/scoped/adios2 \
    && make -j4 && make install \
    && cd ../../ && rm -rf ADIOS2
ENV PATH=$PATH:/home/scoped/adios2/bin

# compile specfem3d_globe
RUN git clone --recursive --branch devel https://github.com/SPECFEM/specfem3d_globe.git \
    && cd specfem3d_globe \
    && ./configure --enable-vectorization \
        --with-adios2 ADIOS2_CONFIG=/home/scoped/adios2/bin/adios2-config \
        --with-asdf 'ASDF_LIBS=-L/home/scoped/asdf/lib -L/opt/intel/compilers_and_libraries/linux/mpi/intel64/lib/release/ -L/home/scoped/hdf5/lib' \
        MPIFC=mpif90 FC=gfortran CC=gcc \
        'FLAGS_CHECK=-O2 -mcmodel=medium -Wunused -Waliasing -Wampersand -Wcharacter-truncation -Wline-truncation -Wsurprising -Wno-tabs -Wunderflow' \
        CFLAGS="-std=c99" \
    && make all \
    && cd ../

# add specfem3d_globe/bin to PATH
ENV PATH=$PATH:/home/scoped/specfem3d_globe/bin

# install necessary python packages for pre/post processing
RUN conda config --prepend channels conda-forge \
    && conda install \
        obspy \
        pandas \
        cartopy \
    && pip install git+https://github.com/adjtomo/pyadjoint.git \
    && conda clean -afy \
    && docker-clean