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Add swan src code and docker files
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‎docker/.env

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SWAN_VERSION=4141
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MPICH_VERSION=3.3.1
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HDF5_MAJOR_VERSION=1.13
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HDF5_MINOR_VERSION=3
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NETCDF_C_VERSION=4.9.0
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NETCDF_FORTRAN_VERSION=4.6.0

‎docker/compose.yaml

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services:
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swansrc:
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image: oceanum/swan:${SWAN_VERSION}
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build:
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context: ./swan
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dockerfile: Dockerfile
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tags:
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- oceanum/swan:latest
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args:
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SWAN_VERSION: $SWAN_VERSION
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MPICH_VERSION: $MPICH_VERSION
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HDF5_MAJOR_VERSION: $HDF5_MAJOR_VERSION
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HDF5_MINOR_VERSION: $HDF5_MINOR_VERSION
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NETCDF_C_VERSION: $NETCDF_C_VERSION
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NETCDF_FORTRAN_VERSION: $NETCDF_FORTRAN_VERSION

‎docker/swan/Dockerfile

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FROM ubuntu:20.04
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LABEL maintainer "CSIRO <[email protected]>"
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ARG MPICH_VERSION
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ARG HDF5_MAJOR_VERSION
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ARG HDF5_MINOR_VERSION
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ARG NETCDF_C_VERSION
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ARG NETCDF_FORTRAN_VERSION
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ARG SWAN_VERSION
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ENV SWAN_VERSION=$SWAN_VERSION
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ENV HDF5_VERSION=$HDF5_MAJOR_VERSION.$HDF5_MINOR_VERSION
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ENV BUILD_DIR=/tmp/build
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ENV INSTALL_DIR=/usr/local
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ENV DEBIAN_FRONTEND noninteractive
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RUN echo "-------------------- Install system libraries --------------------" & \
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apt update && apt install -y --no-install-recommends \
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autoconf \
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automake \
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ca-certificates \
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cmake \
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make \
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gcc \
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gfortran \
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git \
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g++ \
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ninja-build \
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patch \
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wget \
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zlib1g-dev && \
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apt clean && \
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rm -rf /var/lib/apt/lists/*
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#==========================================
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# Model build dependencies
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#==========================================
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WORKDIR $BUILD_DIR
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RUN echo "-------------------- Build MPICH --------------------" && \
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wget http://www.mpich.org/static/downloads/$MPICH_VERSION/mpich-$MPICH_VERSION.tar.gz && \
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tar zxvf mpich-$MPICH_VERSION.tar.gz && \
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cd $BUILD_DIR/mpich-$MPICH_VERSION && \
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./configure --prefix=$INSTALL_DIR --enable-shared=no --enable-static=yes && \
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make && \
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make install && \
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ldconfig $INSTALL_DIR/lib && \
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cd .. && \
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rm -rf $BUILD_DIR/mpich-$MPICH_VERSION
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WORKDIR $BUILD_DIR
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RUN echo "-------------------- Build HDF5 --------------------" && \
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wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$HDF5_MAJOR_VERSION/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.gz && \
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tar zxvf hdf5-$HDF5_VERSION.tar.gz && \
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cd $BUILD_DIR/hdf5-$HDF5_VERSION && \
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./configure --prefix=$INSTALL_DIR --enable-fortran --enable-cxx --enable-hl && \
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make && \
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make install && \
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ldconfig $INSTALL_DIR/lib && \
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cd .. && \
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rm -rf $BUILD_DIR/hdf5-$HDF5_VERSION
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WORKDIR $BUILD_DIR
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RUN echo "-------------------- Build NETCDF4-C --------------------" && \
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wget https://downloads.unidata.ucar.edu/netcdf-c/$NETCDF_C_VERSION/netcdf-c-$NETCDF_C_VERSION.tar.gz && \
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tar zxvf netcdf-c-$NETCDF_C_VERSION.tar.gz && \
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cd $BUILD_DIR/netcdf-c-$NETCDF_C_VERSION && \
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./configure --prefix=$INSTALL_DIR --disable-dap --enable-shared --enable-static --disable-v2 && \
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make && \
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make install && \
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nc-config --all && \
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ldconfig $INSTALL_DIR/lib && \
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cd .. && \
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rm -rf $BUILD_DIR/netcdf-c-$NETCDF_C_VERSION
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WORKDIR $BUILD_DIR
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RUN echo "-------------------- Build NETCDF4-FORTRAN --------------------" && \
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wget https://downloads.unidata.ucar.edu/netcdf-fortran/$NETCDF_FORTRAN_VERSION/netcdf-fortran-$NETCDF_FORTRAN_VERSION.tar.gz && \
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tar zxvf netcdf-fortran-$NETCDF_FORTRAN_VERSION.tar.gz && \
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cd $BUILD_DIR/netcdf-fortran-$NETCDF_FORTRAN_VERSION && \
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./configure --prefix=$INSTALL_DIR --enable-shared --enable-static && \
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make && \
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make install && \
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nf-config --all && \
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ldconfig $INSTALL_DIR/lib && \
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cd .. && \
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rm -rf $BUILD_DIR/netcdf-fortran-$NETCDF_FORTRAN_VERSION
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#==========================================
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# Model build
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#==========================================
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# cmake configuration files are provided in the new swan gitlab but tags / releases
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# are currently not available in that repo. Previous releases of the model are also
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# not available in sourceforge. Hense this will use the cmake configs from gitlab to
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# define the build environment but wil use tagged versions of the source code copied
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# from sourceforge and stored in rompy so versions can be tracked.
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WORKDIR $BUILD_DIR
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ADD src-$SWAN_VERSION/swan$SWAN_VERSION.tar.gz .
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RUN echo "-------------------- Build SWAN --------------------" && \
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git clone --depth 1 https://gitlab.tudelft.nl/citg/wavemodels/swan.git && \
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cd swan && \
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mv src src-git && \
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mv ../swan$SWAN_VERSION src && \
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cp -r src-git/hcat src-git/CMakeLists.txt src-git/*.cmake src/ && \
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mkdir build && \
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cd build && \
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cmake .. -GNinja -DNETCDF=ON -DMPI=ON && \
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cmake --build . && \
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cmake --install . --prefix $INSTALL_DIR && \
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cd ../../ && \
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rm -rf $BUILD_DIR/swan
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#==========================================
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# Test model with mpi and netcdf output
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#==========================================
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ADD tests/refrac.tar.gz $BUILD_DIR
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WORKDIR $BUILD_DIR/refrac
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RUN ln -s a11refr.swn INPUT && \
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sed -i 's/a11ref01.spc/a11ref01.nc/g' INPUT && \
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mpiexec -n 2 swan.exe && \
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ncdump -h a11ref01.nc && \
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cd .. && \
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rm -rf $BUILD_DIR/refrac
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WORKDIR /home
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RUN rm -rf $BUILD_DIR

‎docker/swan/README.md

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# SWAN model docker
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This image builds the [SWAN wave model](https://swanmodel.sourceforge.io/) with netcdf and mpich support using gfortran. The image uses the cmake configuration files available in the new [gitlab repository](https://gitlab.tudelft.nl/citg/wavemodels/swan) but installs a local copy of the source code given previous releases are currently not available in either sourceforge or gitlab swan repositories.
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The following structure is expected in order to build an specific version of SWAN, for instance version 4141:
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src-4141
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├── `swan4141.tar.gz`
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├── `patch41.41.A`
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├── `patch41.41.B`
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└── ...
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where `swan4141.tar.gz` is the tarball for this release downloaded from sourceforge and the patch files `A`, `B`, etc are the patch files to apply (patching is currently not implemented in the docker build).
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SWAN is instaled inside the docker at */usr/local/bin/swan.exe*.
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Versions for SWAN and some other building tools are specified in the *.env* file next to *compose.yaml*.

‎docker/swan/src-4141/README.md

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# Source code and patch files for SWAN version 41.41

‎docker/swan/src-4141/swan4141.tar.gz

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‎docker/swan/tests/refrac.tar.gz

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