#!/bin/bash

set -o errexit
set -o nounset

print_help()
{
    echo "Usage: $prog [OPTION] ... -- COMMAND ... %INPUT% ..."
    echo ""
    echo "Run ..."
    echo ""
    echo "  --help, -h              display this help message"
    echo "  --jobs, -j  num         number of jobs (default: $jobs)"
    echo "  --input, -i file        file with input data"
    echo "  --prefix, -p prefix     prefix path for job directory (default: $prefix)"
    echo "  --jobname, -n name      job name (default: $name)"
    echo "  --wrapper, -w wrapper   exec wrapper (default: $wrapper)"
    echo "  --copy-from, -f         copy command from direcotry (default: src)" 
    echo "  --max-memory, -m mem    max mem (default: $mem)"
    echo "  --max-time, -t          timelimit (default: $timelimit)"
    echo "  --host, -s              remote host (default: $host)"
    echo "  --srcdir, -d            src for copying binary (default: $srcdir)"
    echo "                          assumed to be remote, if it starts with a \":\""
    echo ""
    echo " COMMAND is the command that should be executed on the HPC cluster, where"
    echo " %INPUT% will be replaced with a file containing the job-specific input data."
}



mk_jobdir(){
    echo "Creating temporary job directory in $workdir."
    mkdir -p "$workdir"/bin
    mkdir -p "$workdir"/cfg
    mkdir -p "$workdir"/input
    mkdir -p "$workdir"/output
    mkdir -p "$workdir"/tmp
}


clean_jobdir(){
   rm -rf "$workdir"
}

split_input(){
    echo "Splitting input."
    split -d -a 8 -e -n l/$jobs "$input" "$workdir/input/"
}

mk_hpc_script(){
    local HOSTNAME=`hostname -f`
    echo "Creating HPC script."
    cat <<EOF > $workdir/job.sge

#!/bin/bash
## This script was generated by $prog (version: $version) 
## on $timestamp 
## by $USER@$HOSTNAME 
## in $PWD 
## using the following command:
##   $invokation
## 
## SGE configuration:
#$ -V
#$ -t 1-$jobs
#$ -l rmem=$mem
#$ -l h_rt=$timelimit
#$ -j yes
#$ -o "$prefix"/"$name"/output

export JOBINPUT="$prefix"/"$name"/input/\`printf %08d \$SGE_TASK_ID\`

set -o nounset
set -x

/usr/bin/time -v $wrapper "$prefix"/"$name"/"bin"/$cmd
echo "Execution successful."
EOF
}


mk_remote_jobdir(){
    echo "Create remote working directory ($host:$prefix)."
    ssh $host mkdir -p $prefix
}

install_hpc_script(){
    echo "Installing HPC Script"
    scp -q -r "$workdir" "$host":"$prefix"/"$name"

    if [[ $srcdir == ":"* ]]; then
        echo "  Copying cmd from remote src."
        ssh $host cp "${srcdir:1}"/"$srccmd" "$prefix"/"$name"/bin;
    else
        echo "  Copying cmd from local src."
        scp $srccmd "$srcdir"/"$srccmd" "$host":"$prefix"/"$name"/bin;
    fi
}

submit_job(){
    echo "Submitting job."
    ssh $host qsub "$prefix"/"$name"/job.sge
}

## global configuration
version="0.0"
prog=`echo $0 | sed 's|.*/||'`;
invokation="$prog $(printf "%q " "$@")"
timestamp=`date --utc --iso-8601=ns | sed -e 's/:/_/g' -e 's/,/./'`
host=`hostname`
workdir=`mktemp -d`
echo $workdir

## default values
prefix="~/hpc/"
jobs=1
name="$host-$USER-$timestamp"
input=""
wrapper="singularity exec -B \$TMPDIR:$prefix/$name/tmp"
cmd=""
mem="2G"
timelimit="01:00:00"
local="false";
host="sharc.shef.ac.uk"
srcdir="."

while [ $# -gt 0 ]
do
    case "$1" in
	--jobs|-j)
	    jobs="$2";
            shift;;
	--input|-i)
	    input="$2";
            shift;;
	--jobname|-n)
	    name="$2";
            shift;;
        --max-memory|-m)
	    mem="$2";
            shift;;
        --max-time|-t)
	    timelimit="$2";
            shift;;
        --host|-s)
	    host="$2";
            shift;;
        --srcdir|-d)
	    srcdir="$2";
            shift;;
        --wrapper|-w)
	    wrapper="$2";
            shift;;
       --prefix|-p)
	    prefix="$2";
            shift;;
	--help|-h)
	    print_help
	    exit 0;;
        --) shift; break;;
	*)  print_help
            exit 1;;
    esac
    shift
done
cmd=`echo $(printf "%q " "$@") | sed -e 's/%INPUT%/\$JOBINPUT/'`
cmdarray=("$@")
srccmd=${cmdarray[0]}

mk_jobdir;

if [ -n "$input" ]; then
    if [ ! -f "$input" ]; then
        echo "Input file \"$input\" not found!"
        exit 1
    fi
    split_input;
fi

mk_hpc_script;

mk_remote_jobdir;

install_hpc_script;

clean_jobdir;

submit_job;