submit.yml.erb

<%
  groups = OodSupport::User.new.groups.map(&:name).drop(1)

  # your image location will differ
  ppn = num_cores.blank? ? 1 : num_cores.to_i
  walltime = (bc_num_hours.to_i * 60)
  memory_per_cpu = ((memory_per_node.to_f / ppn.to_f) * 1024).floor
%>
---
batch_connect:
  template: vnc
  websockify_cmd: '/usr/bin/websockify'
  script_wrapper: |
    module purge
    module load singularity
    cat << "CTRSCRIPT" > container.sh
    export PATH="$PATH:/opt/TurboVNC/bin"
    %s
    CTRSCRIPT

    # What is the OS *of the host*
    HOST_OS=`uname -r`
    # Where is this container
    if [[ $HOST_OS =~ "el8" ]]; then
        export container_image=/software/rhel8/quest_ondemand/desktops/xfce/quest-ood-xfce-desktop.sif
    elif [[ $HOST_OS =~ "el7" ]]; then
        export container_image=/software/openondemand/matlab/matlab-ood.sif
    else
        echo "Host OS not recognized, no container found"
    fi

    # All our software in /software so have to bind that
    export SING_BINDS="--bind /software:/software --bind /hpc/software:/hpc/software --bind /opt/intel:/opt/intel"

    ## bind some extra stuff to be able to talk to slurm from within the container
    export SING_BINDS="$SING_BINDS -B /etc/passwd -B /etc/slurm -B `which sbatch ` -B `which srun ` -B `which sacct ` -B `which scontrol ` -B `which salloc ` -B `which scancel ` -B `which squeue ` -B /usr/lib64/slurm/ -B /usr/lib64/libmunge.so.2 -B /usr/lib64/libmunge.so.2.0.0 -B /usr/lib64/libpmi2.so -B /usr/lib64/libpmi2.so.0 -B /usr/lib64/libpmi2.so.0.0.0 -B /usr/lib64/libpmi.so -B /usr/lib64/libpmi.so.0 -B /usr/lib64/libpmi.so.0.0.0 -B /run"

    ## bind some extra stuff to be able to talk to slurm from within the container
    if [[ $HOST_OS =~ "el7" ]]; then
        ## For the RHEL7 nodes
        export SING_BINDS="$SING_BINDS -B /usr/local/pmix -B /usr/local/hwloc -B /usr/local/ucx-1.13.0 -B /usr/local/ucx-1.10.0 -B /usr/local/ucx-1.8.1 -B /usr/local/spack -B /usr/local/spack_v20d1 -B /usr/local/libevent/ " 
    elif [[ $HOST_OS =~ "el8" ]]; then
        ## For the RHEL8 nodes
        export SING_BINDS="$SING_BINDS -B /usr/local/pmix -B /usr/local/hwloc -B /usr/local/libevent -B /usr/local/spack_v20d1 -B /usr/local/ucx/ " 
    fi

    # only bind /kellogg is individual is part of kellogg group
    export SING_BINDS="$SING_BINDS <%= groups.include?('kellogg') ? "--bind /kellogg/:/kellogg/" : "" %>"

    # only bind /scratch/<netid> if individual has a scratch space
    export SING_BINDS="$SING_BINDS <%= File.directory?("/scratch/#{User.new.name}") ? "--bind /scratch/#{User.new.name}:/scratch/#{User.new.name}" : "" %>"

    # Only bind projects directories that the user would have access to based on their unix groups
    <%- groups.each do |group| %>
    export SING_BINDS="$SING_BINDS <%= File.directory?("/projects/#{group}") ? "--bind /projects/#{group}:/projects/#{group}" : "" %>"
    <%- end %>

    # Need to add the --nv flag if we are running on a GPU
    <%- if gres_value != "" %>
    export SING_GPU="--nv"
    <%- else %>
    export SING_GPU=""
    <%- end %>

    singularity exec $SING_GPU $SING_BINDS "${container_image}" /bin/bash container.sh

  header: | 
    #!/bin/bash
        . ~/.bashrc

script:
   <%- if user_email != "" %>
   email_on_started: true
   <%- end %>
   native:
     # What partition is the user submitting to
     - "--partition"
     - "<%= slurm_partition %>"
     # Under what account is the user submitting this job
     - "--account"
     - "<%= slurm_account %>"
     # How much time (in hours)
     - "--time"
     - "<%= walltime %>"
     # How many nodes (always 1)
     <%- if number_of_nodes != "" %>
     - "--nodes"
     - "<%= number_of_nodes %>"
     <%- else %>
     - "--nodes"
     - "1"
     <%- end %>
     # How many CPUs
     - "--ntasks-per-node"
     - "<%= ppn %>"
     # How much memory
     - "--mem-per-cpu"
     - "<%= memory_per_cpu %>M"
     # Job Name
     - "--job-name"
     - "<%= job_name %>"
     # If the user supplies an e-mail, then they will get an e-mail when the job begins
     <%- if user_email != "" %>
     - "--mail-user"
     - "<%= user_email %>"
     <%- end %>
     # If the user requested a GPU, then we need to add this argument to our job submit command
     <%- if gres_value != "" %>
     - "--gres"
     - "<%= gres_value %>"
     <%- end %>
     # If the user requested some kind of constraint, the apply that
     <%- if constraint != "" %>
     - "--constraint"
     - "<%= constraint %>"
     <%- end %>