Add SLURM batch script for single CPU/GPU job

The flag `-u` can be passed to `savu_launcher.sh` to run a single
CPU/GPU cluster job with SLURM.

system_files/dls/mpi/savu_launcher.sh

@@ -3,12 +3,17 @@
 all_args=$*
 original_command="savu_mpi $all_args"
 
+# Define var for holding whether the job should be multi-process (regular case)
+# or single-process (edge case)
+single_proc_job=0
+
 # input optional arguments
 keep=false
-while getopts ":t:i:s:z:ck::" opt; do
+while getopts ":t:i:s:z:uck::" opt; do
 	case ${opt} in
 		s ) version=$OPTARG ;;
         k ) keep=$OPTARG ;;
+        u ) single_proc_job=1 ;;
 		\? ) echo "Invalid option: $OPTARG" 1>&2 ;;
 		: ) echo "Invalid option: $OPTARG requires an argument" 1>&2 ;;
 	esac
@@ -91,6 +96,14 @@ function create_folder()
 # get the Savu path
 DIR="$(cd "$(dirname "$0")" && pwd)"
 filepath=$DIR'/savu_mpijob.sh'
+filepath_single=$DIR'/savu_mpijob_single.sh'
+# Check if the flag for denoting a single process job (1 CPU, 1 GPU) has been
+# passed
+if [ $single_proc_job -eq 1 ] ; then
+	filepath=$filepath_single
+else
+	filepath=$filepath
+fi
 savupath=$(python -c "import savu, os; print (savu.__path__[0])")
 savupath=${savupath%/savu}
 

system_files/dls/mpi/savu_mpijob_single.sh

@@ -0,0 +1,60 @@
+#!/bin/sh
+#SBATCH --job-name=savu
+#SBATCH --partition=cs05r
+#SBATCH --account=test05r
+#SBATCH --nodes=1
+#SBATCH --gpus-per-node=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+
+version=$1
+shift 1
+module load savu/$version
+
+savupath=$1
+datafile=$2
+processfile=$3
+outfile=$4
+delete=$5
+shift 5
+
+# These should match the values for `--ntasks-per-node` and `--gpus-per-node`
+# respectively
+nCPUs=1
+nGPUs=1
+
+export PYTHONPATH=$savupath:$PYTHONPATH
+filename=$savupath/savu/tomo_recon.py
+
+UNIQHOSTS=${TMPDIR}/machines-u
+#echo $HOSTNAME
+awk '{print $1 }' ${PE_HOSTFILE} | uniq > ${UNIQHOSTS}
+uniqslots=$(wc -l <${UNIQHOSTS})
+echo "number of unique hosts: ${uniqslots}"
+echo "running on these hosts:"
+cat ${UNIQHOSTS}
+
+processes=`bc <<< "$((uniqslots*nCPUs))"`
+
+for i in $(seq 0 $((nGPUs-1))); do GPUs+="GPU$i " ; done
+for i in $(seq 0 $((nCPUs-1-nGPUs))); do CPUs+="CPU$i " ; done
+CPUs=$(echo $GPUs$CPUs | tr ' ' ,)
+echo $CPUs
+
+echo "Processes running are : ${processes}"
+
+if [ ! $delete == false ]; then
+  delete=`readlink -f $delete`
+  echo "***Deleting the intermediate folder" $delete "at the end of this run"
+fi
+       #-mca btl sm,self,openib \
+
+# Run Savu processes
+srun python $filename $datafile $processfile $outfile -n $CPUs $@
+
+if [ ! $delete == false ]; then
+  cd /dls/tmp/savu
+  cp $delete/savu.o* $delete/../
+  rm -rf $delete
+fi
+