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)
%>
---
batch_connect:
  template: basic
  websockify_cmd: '/usr/bin/websockify'
  conn_params:
    - ssh_tunnel
    - connection_string
    - staged_root
    - cs_email
    - cs_password
  script_wrapper: |
    module purge
    module load singularity
    cat << "CTRSCRIPT" > container.sh
    export PATH="$PATH:/opt/TurboVNC/bin"
    %s
    CTRSCRIPT

    # What container are we using
    export container_image="<%= version %>"

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

    if grep -q $USER /etc/passwd; then
        export SING_BINDS="$SING_BINDS -B /etc/passwd "
    fi

    # What is the OS *of the host*
    HOST_OS=`uname -r`
    # Where is this container
    if [[ $HOST_OS =~ "el8" ]]; then
        ## bind some extra stuff to be able to talk to slurm from within the container
        export SING_BINDS="$SING_BINDS -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/liblua-5.3.so:/usr/lib/x86_64-linux-gnu/liblua-5.3.so -B /usr/lib64/liblua-5.3.so:/usr/lib/x86_64-linux-gnu/liblua.so -B /usr/lib64/libjson-c.so.4:/usr/lib/x86_64-linux-gnu/libjson-c.so.4 -B /usr/lib64/libjson-c.so.4.0.0:/usr/lib/x86_64-linux-gnu/libjson-c.so.4.0.0 -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"
    elif [[ $HOST_OS =~ "el7" ]]; then
        ## bind some extra stuff to be able to talk to slurm from within the container
        export SING_BINDS="$SING_BINDS -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/liblua-5.1.so:/usr/lib/x86_64-linux-gnu/liblua-5.1.so -B /usr/lib64/liblua-5.1.so:/usr/lib/x86_64-linux-gnu/liblua.so -B /usr/lib64/libjson-c.so.2:/usr/lib/x86_64-linux-gnu/libjson-c.so.2 -B /usr/lib64/libjson-c.so.2.0.1:/usr/lib/x86_64-linux-gnu/libjson-c.so.2.0.1 -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"
    else
        echo "Host OS not recognized, no container found"
    fi

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

    ######################################################
    ### ensure we have a cryosparc directory under home ##
    ######################################################
    export CRYOSPARC_DATADIR=<%= cryosparc_database_directory == "" ? "${HOME}" : cryosparc_database_directory %>/cryosparc

    if [ ! -d "$CRYOSPARC_DATADIR" ]; then
        touch <%= staged_root %>/.first_run
        echo "Creating cryosparc datadir ${CRYOSPARC_DATADIR}..."
        mkdir -p ${CRYOSPARC_DATADIR}/run
        mkdir -p ${CRYOSPARC_DATADIR}/cryosparc_database
    fi

    ######################################################
    ### Create the place holder config_master.sh file ####
    ######################################################
    cat ><%= staged_root %>/config_master.sh <<END
    # Instance Configuration
    export CRYOSPARC_DB_PATH="/app/cryosparc_database"
    export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000

    # Security
    export CRYOSPARC_INSECURE=false
    export CRYOSPARC_DB_ENABLE_AUTH=true

    # Cluster Integration
    export CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=20
    export CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000

    # Project Configuration
    export CRYOSPARC_PROJECT_DIR_PREFIX='CS-'

    # Development
    export CRYOSPARC_DEVELOP=false

    # Other
    export CRYOSPARC_FORCE_USER=true
    export CRYOSPARC_CLICK_WRAP=true
    END

    ######################################################
    ### Create the place holder config_master.sh file ####
    ######################################################
    cat ><%= staged_root %>/config_worker.sh <<END
    <%- if gres_value != "" %>
    export CRYOSPARC_USE_GPU=true
    <%- end %>
    END

    singularity exec -B ${CRYOSPARC_DATADIR}/run:/app/cryosparc_master/run -B ${CRYOSPARC_DATADIR}/cryosparc_database:/app/cryosparc_database -B <%= staged_root %>/config_master.sh:/app/cryosparc_master/config.sh -B <%= staged_root %>/config_worker.sh:/app/cryosparc_worker/config.sh $SING_GPU $SLURM_BINDS $SING_BINDS "${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"
     - "<%= memory_per_node %>G"
     # 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 %>