gdk-code

gdk_code.sh

#!/usr/bin/env bash

usage=$(cat <<-END

Use like this:

    gdk-code -m <memory> -t <walltime> -a <account> ~/some/dir/on/genomedk

The following needs to be part of your .ssh/config file:

Host gdk
    HostName    login.genome.au.dk
    User        your_user_name_on_genomedk

Host cn-* gn-* s21n* s22n*
    HostName    %h
    ProxyJump   gdk
    User        your_user_name_on_genomedk
END
)

while getopts ":m:t:a:k:j" opt; do
  case $opt in
    k) jobname="$OPTARG"
    ssh gdk "scancel --name=wrap"
    exit 0;;  
    j) ssh gdk 'sacct -X --state=PENDING,RUNNING --format="jobid,jobname%30,partition,ReqMem,ReqCPUS,time,elapsed,state"'
    exit 0;;  
    m) mem="$OPTARG"
    ;;
    t) walltime="$OPTARG"
    ;;
    a) account="$OPTARG"
    ;;
    h) usage
    exit 0;;
    *) usage
    exit 1;;
  esac
done

shift $((OPTIND - 1))

open_dir=$1

if [ -z "$mem" ]; then mem="8g"; fi
if [ -z "$walltime" ]; then walltime="08:00:00"; fi

if [ "$1" = "-h" ] || [ -z "$1" ]; then
    echo "$USAGE"
    exit
fi

if [ "$HOSTNAME" = "fe-ipsych-01" ]; then
    jobid=$(sbatch --mem-per-cpu=${mem} --cores=1 --time=${walltime} --account=${account} --wrap='sleep 6d' | awk '{print $4}')
    echo "Submitted job with id: ${jobid}"
    while [ -z "${is_running}" ]; do
        sleep 5
        is_running=$(jobinfo ${jobid} | grep RUNNING)
    done
    node=$(jobinfo $jobid | grep Nodes | awk '{print $3}')
    echo "Job allocated core on node ${node}"
    # conda run -n $environment ~/ChrXh2/VSCode-linux-x64/bin/code --folder-uri "vscode-remote://ssh-remote+${node}${open_dir}"
    conda run -n $environment code --folder-uri "vscode-remote://ssh-remote+${node}${open_dir}"
else
    jobid=$(ssh gdk "sbatch --mem-per-cpu=${mem} --cores=1 --time=${walltime} --account=${account}  --wrap='sleep 6d'" | awk '{print $4}')
    echo "Submitted job with id: ${jobid}"
    while [ -z "${is_running}" ]; do
        sleep 5
        is_running=$(ssh gdk "jobinfo ${jobid}" | grep RUNNING)
    done
    node=$(ssh gdk "jobinfo $jobid" | grep Nodes | awk '{print $3}')
    echo "Job allocated core on node ${node}"
    code --folder-uri "vscode-remote://ssh-remote+${node}${open_dir}" 
fi