add help, usage, default values, and more robust option handling

src/submit-pol-job

 #!/bin/bash
 
-# schedule a policy run on gpfs
-
-outdir=$1
-policy=$2
-nodes=$3
-cores=$4
-ram=$5
-partition=$6
-filesystem=${7:-scratch}
-time=${8:-60}
-outfile=${9}
-
-DIR=$outdir POLICYFILE=$policy FILESYSTEM=${filesystem} OUTFILE=${outfile} && \
+set -euxo pipefail
+
+############################################################
+# Default Values                                           #
+############################################################
+
+nodes=1
+ntasks=16
+mem_per_cpu="8G"
+time="24:00:00"
+partition="amd-hdr100,medium"
+outdir="/data/rc/gpfs-policy/data"
+policy="./policy/list-path-external"
+
+############################################################
+# Help                                                     #
+############################################################
+usage()
+{
+>&2 cat << EOF
+Usage: $0 [ -h ] [ -o | --outdir ] [ -f | --outfile ] [ --with-dirs ] 
+          [ -N | --nodes ] [ -n | --ntasks ] [ -p | --partition] 
+          [ -t | --time ] [ -m | --mem-per-cpu ]
+          device
+EOF
+exit 1
+}
+
+help()
+{
+>&2 cat << EOF
+Wraps the  run-mmpol.sh script for applying a policy file. Must be run directly 
+as root or via the run-submit-pol-job.py script. The default policy file is
+./policy/list-path-external
+
+Usage: $0 [ -h ] [ -o | --outdir ] [ -f | --outfile ] [ --with-dirs ] 
+          [ -N | --nodes ] [ -n | --ntasks ] [ -p | --partition ] 
+          [ -t | --time ] [ -m | --mem ]
+          device
+
+options:
+    -h|--help       Print this Help.
+
+Required:
+    device              GPFS fileset/directory apply the policy to. Can be 
+                            specified as either the name of the fileset or the 
+                            full path to the directory 
+                            (Examples: scratch, /data/user/[username])
+
+Path:   
+    -o|--outdir         Parent directory to save policy output to 
+                            (default: /data/rc/gpfs-policy/data)
+    -f|--outfile        Name of the policy output file
+                            (default: "")
+
+Policy Options:
+    --with-dirs         Change to ./policy/list-path-dirplus (default: False)
+
+sbatch options:
+    -N|--nodes          Number of nodes to run the job on (default: 1)
+    -n|--ntasks         Number of tasks (default: 16)
+    -p|--partition      Partition to submit tasks to 
+                            (default: amd-hdr100,medium)
+    -t|--time           Max walltime (default: 24:00:00)
+    -m|--mem-per-cpu    RAM per task (default: 8G)
+EOF
+exit 0
+}
+
+args=$(getopt -a -o ho:f:N:n:p:t:m: --long help,outdir:,outfile:,with-dirs,nodes:,ntasks:,partition:,time:,mem: -- "$@")
+
+if [[ $? -gt 0 ]]; then
+  usage
+fi
+
+eval set -- ${args}
+
+while :
+do
+  case $1 in
+    -h | --help)        help                                ;;
+    -o | --outdir)      outdir=$2                           ; shift 2 ;;
+    -f | --outfile)     outfile=$2                          ; shift 2 ;;
+    --with-dirs)        policy="./policy/list-path-dirplus" ; shift 1 ;;
+    -N | --nodes)       nodes=$2                            ; shift 2 ;;
+    -n | --ntasks)      ntasks=$2                           ; shift 2 ;;
+    -p | --partition)   partition=$2                        ; shift 2 ;;
+    -t | --time)        time=$2                             ; shift 2 ;;
+    -m | --mem-per-cpu) mem_per_cpu=$2                      ; shift 2 ;;
+    --) shift; break ;;
+    *) >&2 echo Unsupported option: $1
+       usage ;;
+  esac
+done
+
+if [[ $# -eq 0 ]]; then
+  usage
+fi
+
+device="$1"
+
+# Ensure gpfs_logdir is set
+if [[ -z "$device" ]]; then
+    echo "Error: Specify either the name of a fileset or a directory path"
+    usage
+fi
+
+DIR=$outdir POLICYFILE=$policy FILESYSTEM=${device} OUTFILE=${outfile} && \
 DIR=$DIR POLICYFILE=$POLICYFILE FILESYSTEM=${FILESYSTEM} OUTFILE=${OUTFILE} \
 sbatch \
    -N $nodes \
-   -c $cores \
+   -n $ntasks \
    -t $time \
-   --mem-per-cpu=$ram \
+   --mem-per-cpu=$mem_per_cpu \
    -p $partition \
    ./run-mmpol.sh