submit.yml.erb

<%
  # your image location will differa
  image="/apps/ondemand/containers/mate_v11a.sif"
%>
---
script:
  native: [
    "-n", "<%= ha_tasks.blank? ? 1 : ha_tasks.to_i %>",
    "--ntasks-per-node=<%= [ha_tasks.blank? ? 1 : ha_tasks.to_i, 40 ].min %>",
     <%- if not ha_gpus.blank? -%>
        "--gres=gpu:<%= ha_gpus.to_i %>",
     <%- end -%>
     <%- if not ha_cpus.blank? -%>
        "--cpus-per-task=<%= ha_cpus.to_i %>",
     <%- end -%>
     <%- if not ha_mem.blank? -%>
        "--mem=<%= ha_mem.to_i %>G"
     <%- end -%>

     ]
  reservation_id: <%= ha_reservation.blank? ? "" : ha_reservation.strip %>
  <% unless email.blank? %>
  email: <%= email %>
  <% end %> 
batch_connect:
  template: "vnc"
  before_script: |
    # Export the module function if it exists
    [[ $(type -t module) == "function"  ]] && export -f module
    #export my_sport=$(find_port ${host})
    #ssh -f -N -D${my_sport} cl1 
    # Running these here to be included inside the container.
    #echo "DEBUG: SOCKS port is ${my_sport}"
    #DISPLAY=:${display} gsettings set org.gnome.system.proxy mode manual
    #DISPLAY=:${display} gsettings set org.gnome.system.proxy.socks host localhost
    #DISPLAY=:${display} gsettings set org.gnome.system.proxy.socks port ${my_sport}
    #export https_proxy=socks5h://localhost:${my_sport}
    #export http_proxy=socks5h://localhost:${my_sport}

  websockify_cmd: '/usr/bin/websockify'
  script_wrapper: |
    cat << "CTRSCRIPT" > container.sh
    export PATH="$PATH:/opt/TurboVNC/bin"
    [ -e /usr/local/cuda-11.2 ] && export CUDA_HOME=/usr/local/cuda-11.2
    %s
    CTRSCRIPT
    random_number () {
      shuf -i ${1}-${2} -n 1
    }
    find_port () {
      local host="${1:-localhost}"
      local port=$(random_number "${2:-2000}" "${3:-65535}")
      while port_used "${host}:${port}"; do
        port=$(random_number "${2:-2000}" "${3:-65535}")
      done
      echo "${port}"
    }
    export mumax_port=$(find_port ${host})
    module load mumax3/3.10
    <%- if not mumax_wdpath.blank? -%>
    MUMAX_WDPATH=<%= mumax_wdpath %>
    [ -d $MUMAX_WDPATH ] && cd $MUMAX_WDPATH
    [ ! -d $MUMAX_WDPATH ] && echo "ERROR: $MUMAX_WDPATH not found."
    <%- end -%>
    mumax3-server -l 127.0.0.1:$mumax_port -scan 127.0.0.1 -ports $mumax_port  &
    <%- if not mumax_wdpath.blank? -%>
    cd -
    <%- end -%>
    
    # your bindpath will differ
    mkdir -p /tmp/$USER
    export SINGULARITY_BINDPATH="/etc/ssh,/home,/nfshome,/scratch,/var,/run,/tmp/$USER:/run/user,/usr/share/glvnd"
    if [ -e /usr/local/cuda ]
    then
      export SINGULARITY_BINDPATH="$SINGULARITY_BINDPATH,/usr/local/cuda"
    fi
    module load singularity
    echo "INFO: About to run singularity"
    singularity exec --nv <%= image %> /bin/bash container.sh