combine sync_output_to_gdata.sh, sync_restarts_to_gdata.sh, RM_SYNCHE…

…D_OUTPUT.sh into sync_to_gdata.sh and also copy git history. Closes COSIMA/access-om2#171

config.yaml

@@ -54,4 +54,4 @@ platform:
 
 # DANGER! Do not uncomment this without checking the script is synching 
 # to the correct location!
-# postscript: sync_output_to_gdata.sh
+# postscript: sync_to_gdata.sh

sync_to_gdata.sh

@@ -0,0 +1,101 @@
+#!/bin/bash
+#PBS -q copyq
+#PBS -l ncpus=1
+#PBS -l wd
+#PBS -l walltime=4:00:00,mem=4GB
+#PBS -P v45
+#PBS -l storage=gdata/hh5+scratch/v45
+#PBS -N sync
+
+# Set this directory to something in /g/data3/hh5/tmp/cosima/
+# Make a unique path for your set of runs. Must be an absolute path.
+# DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT!
+GDATADIR=/ERROR/SET/GDATADIR/IN/sync_to_gdata.sh
+
+exitcode=0
+help=false
+restarts=false
+rmlocal=false
+
+# parse argument list
+while [ $# -ge 1 ]; do
+    case $1 in
+        -h)
+            help=true
+            ;;
+        -r)
+            echo "syncing restarts instead of output directories"
+            restarts=true
+            ;;
+        -D)
+        # --remove-source-files tells rsync to remove from the sending side the files (meaning non-directories) 
+        # that are a part of the transfer and have been successfully duplicated on the receiving side.
+        # This option should only be used on source files that are quiescent.
+        # Require interaction here to avoid syncing and removing partially-written files.
+            echo "DELETING LOCAL COPIES OF SYNCED FILES!"
+            echo "WARNING: to avoid losing data, do not proceed if there are any running jobs or collations underway."
+            read -p "Proceed? (y/n) " yesno
+            case $yesno in
+                [Yy] ) rmlocal=true;;
+                * ) echo "Cancelled. Wait until all jobs are finished before trying again."; exit 0;;
+            esac
+            ;;
+        -*)
+            echo $1": invalid option"
+            help=true
+            exitcode=1
+            ;;
+        *)
+            echo $1": invalid argument"
+            help=true
+            exitcode=1
+            ;;
+    esac
+    shift
+done
+
+if [ $exitcode != "0" -o $help == true ]; then
+    echo $0": rsync model run outputs (and optionally restarts) to /g/data"
+    echo "  Must be invoked from a control directory."
+    echo "  "$0" should be edited to set GDATADIR."
+    echo "  Default will rsync all output directories, leaving local copies intact."
+    echo "  Also rsyncs error_logs and pbs_logs."
+    echo "  Also updates git-runlog, a git clone of the control directory (whose git history documents all changes in the run)."
+    echo "usage: "$0" [-h] [-r] [-D]"
+    echo "  -h: show this help message and exit"
+    echo "  -r: sync all restart directories (default syncs output directories)"
+    echo "  -D: delete local copies of synced files in all but the most recent synced directories (outputs or restarts, depending on -r). Must be done interactively. (Default leaves local copies intact.)"
+    exit $exitcode
+fi
+
+sourcepath="$PWD"
+mkdir -p ${GDATADIR} || exit 1
+cd archive || exit 1
+
+if [ $restarts == true ]; then
+    # only sync/remove restarts
+    rsync -vrltoD --safe-links restart* ${GDATADIR}
+    if [ $rmlocal == true ]; then
+        # Now do removals. Don't remove final local copy, so we can continue run.
+        rsync --remove-source-files --exclude `\ls -1d restart[0-9][0-9][0-9] | tail -1` -vrltoD --safe-links restart* ${GDATADIR}
+    fi
+else
+    # default - only sync/remove outputs
+    rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR}
+    if [ $rmlocal == true ]; then
+        # Now do removals. Don't remove final local copy, so we can continue run.
+        rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR}
+    fi
+fi
+
+# Also sync error and PBS logs
+rsync -vrltoD --safe-links error_logs ${GDATADIR}
+rsync -vrltoD --safe-links pbs_logs ${GDATADIR}
+
+# create/update a clone of the run history in ${GDATADIR}/git-runlog
+cd ${GDATADIR} || exit 1
+ls git-runlog || git clone $sourcepath git-runlog
+cd git-runlog
+git pull
+
+echo $0" completed successfully"