run_sepia_stitching_remote.sh

#!/bin/bash -l
set -e

code_dir=$(dirname "$0")

# Parse command line args
rerun=false
for i in "$@"
do
    case $i in
        --mpicmd=*)
            mpicmd="${i#*=}"
            shift
            ;;
        --partition=*)
            partition="${i#*=}"
            shift
            ;;
        --stitching-slurm=*)
            stitching_slurm="${i#*=}"
            shift
            ;;
        --stitching-args=*)
            stitching_args="${i#*=}"
            shift
            ;;
        --rerun)
            rerun=true
            shift
            ;;
        *)
            sepia="$i"
            shift
            ;;
    esac
done

if [[ $debug = true ]]; then
    set -x
fi

sepia_dirs=($(ls -d "$sepia"*"/"))
queenframes=()
for sepia_dir in "${sepia_dirs[@]}"; do
    basename=$(basename "$sepia_dir")
    queenframe="$sepia_dir/${basename#*-}".queenframe
    queenframes+=("$queenframe")
done
stitching="$sepia.stitching"
stitching_log="$sepia.stitching.log"
dirname=$(dirname "$sepia")

check_stitching_jobid=$(sbatch \
    $(if [[ ! -z ${partition+x} ]]; then
        echo --partition="$partition"
    fi) \
    --kill-on-invalid-dep=yes \
    --job-name=check-stitching \
    -o"$dirname/%j.out" \
    $code_dir/check_filedeps.sh \
    --optional \
    "${queenframes[@]}" \
    --output="$stitching" \
    $(if [[ $rerun_stitching = true ]]; then
        echo "--skip-mtime"
    fi) \
    | awk '{print $4}'; 
    if [[ "${PIPESTATUS[0]}" -eq "0" ]]; then true; else false; fi)
stitching_jobid=$(sbatch \
    $(if [[ ! -z ${partition+x} ]]; then
        echo --partition="$partition"
    fi) \
    $stitching_slurm \
    --dependency=afterok:$check_stitching_jobid \
    --kill-on-invalid-dep=yes \
    --job-name=stitching \
    -o"$stitching_log" \
    $code_dir/run_stitching.sh \
    --mpicmd="$mpicmd" \
    --code-dir="$code_dir" \
    --chunks="${queenframes[*]}" \
    --stitching="$stitching" \
    --stitching-args="$stitching_args" \
    | awk '{print $4}'; 
    if [[ "${PIPESTATUS[0]}" -eq "0" ]]; then true; else false; fi)
echo "STITCHING_JOBID=$stitching_jobid"