submit.yml.erb

<%
  # your image location will differa
  image="/apps/ondemand/containers/febio-studio_v1.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:${my_sport}
    if [ -n "$CUDA_VISIBLE_DEVICES" ]
    then
      GPU_BUS_ID=`nvidia-smi --query-gpu=gpu_bus_id --format=csv,noheader | head -n 1 |  tr '[:upper:]' '[:lower:]'`
      if [ -z ${GPU_BUS_ID} ]
      then
          DRI_DEVICE=`basename /sys/bus/pci/devices/${GPU_BUS_ID:4}/drm/card*`
          echo "print Slurm taskprolog: Setting VGL_DISPLAY=/dev/dri/$DRI_DEVICE"
          export VGL_DISPLAY="/dev/dri/$DRI_DEVICE"
      fi
    fi

  websockify_cmd: '/usr/bin/websockify'
  script_wrapper: |
    cat << "CTRSCRIPT" > container.sh
    export PATH="$PATH:/opt/TurboVNC/bin"
    %s
    CTRSCRIPT

    # your bindpath will differ
    mkdir -p /tmp/$USER
    export SINGULARITY_BINDPATH="/etc/ssh,/home,/nfshome,/scratch,/var,/run,/tmp/$USER:/run/user"
    module load singularity
    echo "INFO: About to run singularity"
    singularity exec --nv <%= image %> /bin/bash container.sh