submit.yml.erb

<%
   user = OodSupport::User.new

   weka_nfs_server = Resolv.getaddress("weka-nfs")

   # Initialize nesi_gid to nil
   nesi_gid = nil

   # Fetch the GID for the account group only if the account is present
   if account.present?
     nesi_group = Etc.getgrnam(account)  # Fetching the group based on the account
     nesi_gid = nesi_group ? nesi_group.gid : nil  # Get the GID, or nil if not found
   end
   
   # Get ALL groups the user belongs to that match the project pattern
   # Same approach as used in form.yml
   all_user_groups = OodSupport::User.new.groups.sort_by(&:id).tap { |groups|
     groups.unshift(groups.delete(OodSupport::Process.group))
   }.map(&:name)
   
   # Collect GIDs for ALL user's projects (not just selected ones)
   additional_gids = []
   all_user_groups.each do |project|
     begin
       project_group = Etc.getgrnam(project)
       additional_gids << project_group.gid if project_group && project_group.gid != nesi_gid
     rescue ArgumentError
       # Handle case where group doesn't exist
       Rails.logger.warn "Group not found for project: #{project}"
     end
   end
   
   # Combine all supplemental groups
   all_supplemental_groups = [nesi_gid].compact + additional_gids
%>
---
<% if cluster == "my-k8s-cluster" -%>
batch_connect:
  template: "vnc"

script:
  accounting_id: "<%= account %>"
  wall_time: "<%= bc_num_hours.to_i * 3600 %>"
  native:
    container:
      name: "<%= account.present? ? "vmd-#{account}" : 'vmd' %>"
      image: "ghcr.io/nesi/nesi-ondemand-vnc:v0.9.0"
      command: ["/bin/bash","-l","<%= staged_root %>/custom_job_script.sh"]
      restart_policy: 'OnFailure'
      <% if all_supplemental_groups.any? %>
      supplemental_groups:
        <% all_supplemental_groups.each do |gid| %>
        - <%= gid %>
        <% end %>
      <% end %>
      env:
        TZ: "Pacific/Auckland"
        LMOD_CONFIG_DIR: "/opt/nesi/etc/lmod"
        MODULEPATH_ROOT: "/opt/nesi/lmod"
        MODULEPATH: "/opt/nesi/lmod/generic"
        BASH_ENV: "/usr/share/lmod/lmod/init/bash"
        WEBSOCKIFY_CMD: "/usr/local/bin/websockify"
        SESSION_DIR: "<%= staged_root %>"
        PRIMARY_PROJECT: "<%= account %>"
        OMP_NUM_THREADS: "<%= num_cores %>"
        <% if additional_projects.present? %>
        ADDITIONAL_PROJECTS: "<%= Array(additional_projects).join(':') %>"
        <% end %>
      port: "5901"
      cpu: "<%= num_cores %>"
      memory: "<%= num_mem %>Gi"
    mounts:
      - type: host
        name: home
        path: /home
        destination_path: /home
      - type: host
        name: wlghome
        path: /home
        destination_path: /scale_wlg_persistent/filesets/home
      - type: host
        name: project
        path: /nesi/project
        destination_path: /nesi/project
      - type: host
        name: wlgproject
        path: /nesi/project
        destination_path: /scale_wlg_persistent/filesets/project
      - type: host
        name: nobackup
        path: /nesi/nobackup
        destination_path: /nesi/nobackup
      - type: host
        name: software
        path: /opt/nesi
        destination_path: /opt/nesi
      - type: host
        name: nss-socket
        host_type: Socket
        path: /var/lib/sss/pipes/nss
        destination_path: /var/lib/sss/pipes/nss
      - type: host
        name: nsswitch-conf
        host_type: File
        path: /etc/nsswitch.conf
        destination_path: /etc/nsswitch.conf
        
      # Required mounts for SLURM
      - type: host
        name: munge-socket
        host_type: Socket
        path: /var/run/munge/munge.socket.2
        destination_path: /var/run/munge/munge.socket.2
      - type: host
        name: slurm-conf
        path: /run/slurm/conf
        destination_path: /etc/slurm/
    configmap:
      files:
        - filename: "logging.conf"
          data: |
            [*]
            log-level=debug
            logger-type=file
            log-dir=<%= staged_root %>/logs
          mount_path: '/etc/matlab'
        - filename: 'k8_helper'
          data: |
            #!/usr/bin/env bash

            set -x

            KEY=$1
            VALUE=$(echo -n $2 | base64)
            CFG="$(hostname)-secret"

            kubectl get secret ${CFG} -o json | jq --arg key $KEY --arg value $VALUE '.data[$key] = $value'  | kubectl apply -f -
          mount_path: '/opt/open_ondemand/helpers'

<%- else -%>
batch_connect:
  template: "vnc"
  websockify_cmd: '/usr/local/bin/websockify'
  header: |
    #!/bin/bash
    #. ~/.bashrc
  script_wrapper: |
    cat << "CTRSCRIPT" > container.sh
    export PATH="$PATH:/opt/TurboVNC/bin"
    export LMOD_CONFIG_DIR=/opt/nesi/etc/lmod
    export MODULEPATH_ROOT=/opt/nesi/lmod
    export MODULEPATH=/opt/nesi/lmod/generic
    export BASH_ENV=/usr/share/lmod/lmod/init/bash
    %s
    CTRSCRIPT

    export APPTAINER_BIND="$HOME,/nesi,/opt/nesi,/etc/passwd,/etc/group,/var/lib/sss/pipes,/etc/nsswitch.conf,/var/run/munge/munge.socket.2,/var/run/slurm/conf,/var/spool/slurmd/conf-cache"

    apptainer exec --writable-tmpfs /opt/nesi/containers/nesi-ood-base/nesi-ondemand-vnc-0.8.0.aimg /bin/bash container.sh

script:
  accounting_id: "<%= account %>"
  wall_time: "<%= bc_num_hours.to_i * 3600 %>"
  native:
    - "--ntasks"
    - "1"
    - "--cpus-per-task"
    - "<%= num_cores %>"
    - "--mem"
    - "<%= num_mem %>G"
<%- end -%>