submit.yml.erb

<%-

  base_slurm_args = ["--nodes", "1", "--ntasks-per-node", "#{num_cores.to_i}"]

  slurm_args = case node_type
              when "gpu-40core"
                base_slurm_args += ["--constraint", "40core"]
              when "gpu-48core"
                base_slurm_args += ["--constraint", "48core"]
              when "any-40core"
                base_slurm_args += ["--constraint", "40core"]
              when "any-48core"
                base_slurm_args += ["--constraint", "48core"]
              when "hugemem"
                base_slurm_args += ["--partition", "hugemem"]
              when "largemem"
                base_slurm_args += ["--partition", "largemem"]
              when "debug"
                base_slurm_args += ["--partition", "debug"]
              else
                base_slurm_args
              end

-%>

---
batch_connect:
  template: "basic"
  conn_params:
    - csrf_token
<% if cluster !~ /kubernetes/ -%>
script:
<% if node_type =~ /gpu/ -%>
  gpus_per_node: 1
<% end -%>
  native:
    <%- slurm_args.each do |arg| %>
    - "<%= arg %>"
    <%- end %>
<% elsif cluster =~ /kubernetes/
   if node_type =~ /pitzer/
     compute_cluster = "pitzer"
     apps_path = "/apps"
     # Memory per core with hyperthreading enabled
     memory_mb = num_cores.to_i * 4000
   end
   mounts = {
     'home'    => OodSupport::User.new.home,
     'support' => OodSupport::User.new('support').home,
     'project' => '/fs/project',
     'scratch' => '/fs/scratch',
     'ess'     => '/fs/ess',
   }
-%>
script:
  wall_time: "<%= bc_num_hours.to_i * 3600 %>"
  <%- if node_type =~ /gpu/ -%>
  gpus_per_node: 1
  <%- end -%>
  native:
    container:
      name: "rstudio-server"
      image: "docker-registry.osc.edu/ondemand/ondemand-base-rhel7:0.11.1"
      image_pull_policy: "IfNotPresent"
      command: ["/bin/bash","-l","<%= staged_root %>/job_script_content.sh"]
      restart_policy: 'OnFailure'
      env:
        CLUSTER: "<%= compute_cluster %>"
        KUBECONFIG: "/dev/null"
        TMPDIR: "/tmp"
      labels:
        osc.edu/cluster: "<%= compute_cluster %>"
      port: "8080"
      cpu: "<%= num_cores %>"
      memory: "<%= memory_mb %>Mi"
    configmap:
      files:
        - filename: "logging.conf"
          data: |
            [*]
            log-level=debug
            logger-type=file
            log-dir=<%= Pathname.new(staged_root).join('logs') %>
          mount_path: '/etc/rstudio/logging.conf'
          sub_path: 'logging.conf'
        - filename: "database.conf"
          data: |
            directory=/tmp/lib/rstudio-server
          mount_path: '/etc/rstudio/database.conf'
          sub_path: 'database.conf'
        - 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'
    mounts:
    <%- mounts.each_pair do |name, mount| -%>
      - type: host
        name: <%= name %>
        host_type: Directory
        path: <%= mount %>
        destination_path: <%= mount %>
    <%- end -%>
      - 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
        host_type: Directory
        path: /etc/slurm
        destination_path: /etc/slurm
      - type: host
        name: sssd-pipes
        host_type: Directory
        path: /var/lib/sss/pipes
        destination_path: /var/lib/sss/pipes
      - type: host
        name: sssd-conf
        host_type: Directory
        path: /etc/sssd
        destination_path: /etc/sssd
      - type: host
        name: nsswitch
        host_type: File
        path: /etc/nsswitch.conf
        destination_path: /etc/nsswitch.conf
      - type: host
        name: lmod-init
        host_type: File
        path: /apps/<%= compute_cluster %>/lmod/lmod.sh
        destination_path: /etc/profile.d/lmod.sh
      - type: host
        name: intel
        host_type: Directory
        path: /nfsroot/<%= compute_cluster %>/opt/intel
        destination_path: /opt/intel
      - type: host
        name: apps
        host_type: Directory
        path: /apps/<%= compute_cluster %>
        destination_path: <%= apps_path %>
    node_selector:
      node-role.kubernetes.io/ondemand: ''
<% end -%>