xios.def

Bootstrap: localimage
From: base_container/baseOS.sif

####
##
## Authors:      Michael Wathen, Plymouth Marine Laboratory <miwa@pml.ac.uk>
##
## Definition file for building XIOS Singularity Containers
##
#####

%files
    input_files/arch/xios-arch/arch-singularity.fcm input_files/arch/xios-arch/arch-singularity.fcm
    input_files/arch/xios-arch/arch-singularity.env input_files/arch/xios-arch/arch-singularity.env
    input_files/arch/xios-arch/arch-singularity.path input_files/arch/xios-arch/arch-singularity.path

%post
    apt-get install subversion
    svn checkout http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 xios
    
    PATH=$PATH:/opt/mpi/install/bin:/opt/hdf5/install/bin
    LD_LIBRARY_PATH=/opt/hdf5/install/lib:$LD_LIBRARY_PATH

    cd xios
    cp /input_files/arch/xios-arch/arch* ./arch

    echo "Compiling xios"
    ./make_xios --full --prod --arch singularity --netcdf_lib netcdf4_par -j 8
    
    mkdir /opt/xios
    mv /xios/bin/xios_server.exe /opt/xios

%environment
    
    export XIOS_DIR=xios
    export XIOS_HOME=$XIOS_DIR

%runscript
    #!/bin/bash

    # This runscript will take 2 arguments: program to run (NEMO or XIOS), and an 
    # output directory. By default, the output directory will be the job id 
    # (passed using $SLURM_JOB_ID).    

    if ! [[ $1 == "xios" ]]    
    then
      echo "The program argument should be either 'nemo' or 'xios'"
      exit 1
    fi
    
    /opt/xios/xios_server.exe

%labels
    Author miwa@pml.ac.uk

%help
    The definition file used to build XIOS:

    To build the container, run

        singularity build xios.sif xios.def