qsbatch

#!/bin/bash

#echo "in function interactive"

inital_command="$@"

cpus=""
mem=""
exanode=""
sbatch_options=""
sbatch_body=""
execute=true
conda_env=""

#echo "starting to parse args $@"

OPTIND=
OPTARG=
opt=
sbatch_body="#!/bin/bash

### --------  SLURM  ----------- ###"

while getopts ":m:c:n:t:e:Edvh" opt; do
    #echo "parsing arg $opt"
    
    case "$opt" in
        h)
            echo "\
            usage:
            ------
            qsbatch [ -h ] [ -c CUPS ] [ -m MEMORY ] [ -t TIME ] [ -n NODE ] [ -e CONDAENV ] 
                      [ -E ] [ -d ] [ -v ]
            
            description:
            ------------
            Submits the command as a batch job by creating a dummy batch file with the specified
            options. This allows you to have error and log files using slurm environment variables.
            
            An added feature is being able to activate a conda environment to run the command in.

            To Do:
            - Creating work directory and log files directories.
            - Better at capturing provenance.            

            optional arguments:
            -------------------
            -h          Print this help message and exit.
            -c CPUS     Request CPUS number of cores.
            -m MEMORY   Request MEMORY amount of RAM. The
                        default units are megabyts. However
                        The following suffixes can be used:
                        [K|M|G|T]
             -t TIME     Request connection time. Acceptable time formats:
                            minutes
                            minutes:seconds
                            hours:minutes:seconds
                            days-hours
                            days-hours:minutes
                            days-hours:minutes:seconds

            -n NODE     Request a particular child exanode, e.g. 2-5
            -E          Run the job in the users login environment
            -e CONDAENV Activate the conda environment CONDAENV
            -d          Don't execute. Just display command.
            -v          Print command. Use with dry run to verify command.
            "
            execute=false
            #exit 2
            ;;
        c)
            cpus="$OPTARG"
            sbatch_options="$sbatch_options --mincpus $cpus"
            sbatch_body="$sbatch_body
#SBATCH --mincpus=$cpus" 
            #echo "cpus=$cpus"
            ;;
        m)
            mem="$OPTARG"
            sbatch_options="$sbatch_options --mem ${mem}"
            sbatch_body="$sbatch_body
#SBATCH --mem=${mem}" 
            #echo "mem=$mem"
            ;;
        n)
            exanode="$OPTARG"
            sbatch_options="$sbatch_options --exanodelist \"exaexanode-${exanode}\""
            sbatch_body="$sbatch_body
#SBATCH --exanodelist \"exaexanode-${exanode}\""
            #echo "exanode=$exanode"
            ;;
        t)
            time="$OPTARG"
            sbatch_options="$sbatch_options --time ${time}"
            sbatch_body="$sbatch_body
#SBATCH --time=${time}"
            #echo "time=$time"
            ;;                      
        e)
            conda_env="$OPTARG"
            ;;   
        E)
            sbatch_body="$sbatch_body
#SBATCH --get-user-env"
            ;;
        d)
            execute=false
            ;;
        v)
            verbose=true
            ;;
        ?)
            echo "Error: did not recognize option, ${OPTARG}."
            echo "Please try -h for help."
            execute=false
            #exit 1
            ;;
    esac

done

shift $(($OPTIND - 1))
executable=$1
actual_command=$@
#echo "actual command: $actual_command"   
 
out="${executable}_%A_%a_%j.out"
sbatch_options="$sbatch_options --output=$out"
sbatch_body="$sbatch_body
#SBATCH --output=$out"

err="${executable}_%A_%a_%j.err"
sbatch_body="$sbatch_body
#SBATCH --error=$err"
sbatch_options="$sbatch_options --error=$err"

sbatch_body="$sbatch_body
### -------------------------- ###

echo "$initial_command"
"

if [[ $conda_env != "" ]]; then
    sbatch_body="$sbatch_body
source /home/exacloud/tempwork/teamMicrobiome/conda/etc/profile.d/conda.sh
conda activate $conda_env"
fi

if [[ $verbose ]]; then
    echo "batch file:"

    cat<<sbatch_file
$sbatch_body
srun $actual_command
sbatch_file

fi



if [[ $execute == true ]]; then

    sbatch<<sbatch_file
$sbatch_body
srun $actual_command
sbatch_file

fi

exit 0