diff --git a/cleanup.sh b/cleanup.sh new file mode 100755 index 0000000..11e3962 --- /dev/null +++ b/cleanup.sh @@ -0,0 +1,3 @@ +rm *.in +rm *.out +rm *.sbatch diff --git a/process_vast_epoch.sh b/process_vast_epoch.sh new file mode 100755 index 0000000..e21ae92 --- /dev/null +++ b/process_vast_epoch.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +epoch=$1 +in_dir=$SCRATCHDIR/data/vast/epoch_$1 +out_dir=$SCRATCHDIR/stokesv_processing/finished/epoch_$1 + +echo python run_selavy.py $in_dir --out-dir=$out_dir diff --git a/run_selavy.py b/run_selavy.py index c01a88a..5747456 100644 --- a/run_selavy.py +++ b/run_selavy.py @@ -51,6 +51,11 @@ def parse_args(): default='21', help='Number of tasks per node for each slurm job' ) + parser.add_argument('--project-code', + type=str, + default='ja3', + help='Number of tasks per node for each slurm job' + ) parser.add_argument('--submit-jobs', action='store_true', help='Submit the jobs' @@ -85,6 +90,7 @@ def generate_files(filename, jobname, args, invert=False, outdir="."): ntasks=args.ntasks, ntasks_per_node=args.ntasks_per_node, memory=args.mem_request, + project_code=args.project_code ) return diff --git a/selavybatch.sh b/selavybatch.sh new file mode 100755 index 0000000..9aa81e2 --- /dev/null +++ b/selavybatch.sh @@ -0,0 +1 @@ +sbatch selavy.nimage.v.VAST_0530-68.SB50408.cont.taylor.0.restored.conv.sbatch diff --git a/setonix_selavy.py b/setonix_selavy.py index a8ea782..585914c 100644 --- a/setonix_selavy.py +++ b/setonix_selavy.py @@ -158,7 +158,8 @@ def _write_sbatch(job_name, walltime, ntasks, ntasks_per_node, - memory + memory, + project_code ): '''write sbatch files''' logger = logging.getLogger('makeparset.sbatch') @@ -181,10 +182,11 @@ def _write_sbatch(job_name, #SBATCH --ntasks={ntasks} #SBATCH --ntasks-per-node={ntasks_per_node} #SBATCH --mem={memory} +#SBATCH --account={project_code} -module use /software/projects/ja3/modulefiles -module load singularity/3.8.6 -module load askapsoft/1.10.0.a +module use /software/projects/askaprt/modulefiles +module load singularity/4.1.0-mpi +module load askapsoft/1.15.0 srun selavy -c {parset_name} ''') @@ -198,6 +200,7 @@ def writebatch(job_name, ntasks = '21', ntasks_per_node = '21', memory = '110G', + project_code='ja3' ): '''write the final .sh file for submission''' logger = logging.getLogger('writebatch') @@ -215,6 +218,7 @@ def writebatch(job_name, ntasks, ntasks_per_node, memory, + project_code ) sbatch_names.append(sbatch_name) logger.info(f"Written {sbatch_name}") diff --git a/stage_data.sh b/stage_data.sh old mode 100644 new mode 100755 index 9a9b3a9..3de9552 --- a/stage_data.sh +++ b/stage_data.sh @@ -1,6 +1,8 @@ indir=$1 outdir=$2 +mkdir $outdir + mv $indir/selavy-*.xml $outdir/ mv $indir/noiseMap.image.*.fits $outdir/ mv $indir/meanMap.image*.fits $outdir/ diff --git a/stage_vast_epoch.sh b/stage_vast_epoch.sh new file mode 100755 index 0000000..0cfd8a9 --- /dev/null +++ b/stage_vast_epoch.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +epoch=$1 + +finished_dir=$SCRATCHDIR/stokesv_processing/finished/epoch_$1 +staging_dir=$SCRATCHDIR/stokesv_processing/staging/epoch_$1 + +./stage_data.sh $finished_dir $staging_dir diff --git a/unstage_data.sh b/unstage_data.sh new file mode 100755 index 0000000..9a9b3a9 --- /dev/null +++ b/unstage_data.sh @@ -0,0 +1,6 @@ +indir=$1 +outdir=$2 + +mv $indir/selavy-*.xml $outdir/ +mv $indir/noiseMap.image.*.fits $outdir/ +mv $indir/meanMap.image*.fits $outdir/ diff --git a/unstage_vast_epoch.sh b/unstage_vast_epoch.sh new file mode 100755 index 0000000..1d1dccd --- /dev/null +++ b/unstage_vast_epoch.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +epoch=$1 + +finished_dir=$SCRATCHDIR/stokesv_processing/finished/epoch_$1 +staging_dir=$SCRATCHDIR/stokesv_processing/staging/epoch_$1 + +mv $staging_dir/* $finished_dir