submit.yml.erb

#
# Configure the content of the job script for the batch job here
# @see http://www.rubydoc.info/gems/ood_core/OodCore/BatchConnect/Template
#
#
# Job submission configuration file
#
<%
  # 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 %>", 
    "-c", "<%= ha_cpus.blank?  ? 1 : ha_cpus.to_i %>",
     <%- if not ha_gpus.blank? -%>
        "--gres=gpu:<%= ha_gpus.to_i %>",
     <%- end -%>
     <%- if not ha_mem.blank? -%>
         "--mem=<%= ha_mem.to_i %>G",
     <%- end -%>
     <%- if not ha_qos.blank? -%>
         "--qos=<%= ha_qos.strip %>"
     <%- end -%>

     ]
  queue_name: <%= ha_partition.blank? ? "dev" : ha_partition.strip %>
  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

  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

    # your bindpath will differ
    mkdir -p /tmp/$USER
    export SINGULARITY_BINDPATH="/opt/slurm/22.05.8-1,/etc/ssh,/home,/nfshome,/scratch,/var,/run,/tmp/$USER:/run/user"
    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