BUGFIX: Change ownership to executing USER and group to atlab. Also automatically gzip the log output

This is a continuing revision for !17 (merged) and !18 (closed). Changes from !18 (closed) have been added here for convenience in resolving merge conflicts.

Major changes:

• Set user:group ownership to $USER:atlab.
• Set permissions to rws for the containing directory and r-- for the log itself
• Automatically gzip the log file
• Implements changes suggested in #17 (closed). run-mmpol now creates a single directory to store the raw policy output, the split gz files, and the parquet files plus anything else associated with the run. The directory name matches the name of the log file.

Minor changes:

• Full device path is used in the prefix, changing / to -. All metadata entries in the file/directory names are separated by _ for clarity
• Added dry-run option to all 3 scripts for testing. Dry runs submit no jobs and make no changes to any directory structure.
• Changed methods for finding the raw log once it's created and moving/renaming it
• Removed default device from run-mmpol.sh. Now the device must be specified regardless of which script is run.

Syntax Changes:

• Encased all called variables in "{}" for clarity in variable substitution.
• Replaced ```` syntax with $() when performing command substitution

Issues Fixed:

• Fixes #26 (closed)
• Fixes #17 (closed)

src/run-policy/run-mmpol.sh

@@ -102,7 +102,7 @@ tmpscratch="${outdir}/slurm-tmp-${SLURM_JOBID}"
 nodes=$(scontrol show hostnames "${SLURM_JOB_NODELIST}" | tr '\n' ',' | sed -e 's/,$//')
 cores="${SLURM_CPUS_PER_TASK}"
 
-DATESTR=$(date +'%Y%m%dT%H%M%S')
+DATESTR=$(date +'%Y-%m-%dT%H:%M:%S')
 
 policy=$(basename ${policy_file})
 filetag="${policy}_slurm-${SLURM_JOBID}_${DATESTR}"
@@ -124,17 +124,19 @@ if [[ ! ${dry_run} ]]; then
     ${cmd}
 
     log_name="${output_log_prefix}_${filetag}"
-    log_dir="${outdir}/${log_name}.d"
+    log_dir="${outdir}/${log_name}"
 
-    mkdir ${log_dir}
+    mkdir -p ${log_dir}/raw
     chmod 1770 ${log_dir}
 
     # tag output file with run metadata
     raw_log_file=$(find ${outdir} -maxdepth 1 -name "list-${SLURM_JOBID}*" -type f | head -1)
     if [[ "$raw_log_file" != "" ]]; then
-        mv -n ${raw_log_file} ${log_dir}/${log_name}
-        chmod 440 ${log_dir}/${log_name}
-        gzip ${log_dir}/${log_name}
+        mv -n ${raw_log_file} ${log_dir}/raw/${log_name}
+        gzip ${log_dir}/raw/${log_name}
+
+        chmod 440 ${log_dir}/raw/${log_name}.gz
+        chmod 550 ${log_dir}/raw
     fi
 
     chown -R ${USER}:atlab ${log_dir}