From 6d1a2e9759325c8fe9aaf4bf41efdf44aa7aa5ef Mon Sep 17 00:00:00 2001
From: "Kasper D. Fischer" <kasper.fischer@rub.de>
Date: Fri, 28 Jan 2022 16:30:39 +0100
Subject: [PATCH] Add example periodic_sleeper.sh

This can be used as an template to create jobs which run periodically. Users should use this instead of cronjobs on the servers.
---
 examples/jobs/periodic_sleeper.sh | 75 +++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100755 examples/jobs/periodic_sleeper.sh

diff --git a/examples/jobs/periodic_sleeper.sh b/examples/jobs/periodic_sleeper.sh
new file mode 100755
index 0000000..3a86e1c
--- /dev/null
+++ b/examples/jobs/periodic_sleeper.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+# This job script takes a nap for 10 seconds (or paramter $2) every 30 minutes (or paramter $1)
+
+# SGE options
+#$ -N PSleeper
+#$ -l scf=1M,mem=100M,h_vmem=100M
+#$ -q normal.q
+#$ -cwd
+
+# process args
+case "$1" in
+    -h)
+        echo "usage: $0 [-h | [-d] [T] [nap]]"
+        echo "periodically take a nap"
+        echo ""
+        echo "-h   print this help and exit"
+        echo "-d   print debug info"
+        echo "T    take a nap every T minutes (default: 30)"
+        echo "nap  take a nap for nap seconds (default: 10)"
+        exit 1
+        ;;
+    *)
+        debug=0
+        terse="-terse"
+        debug_flag=""
+        do_echo=0
+        T=30
+        nap=10
+        while (( "$#" )); do
+            case "$1" in
+                -d)
+                    debug=1
+                    terse=""
+                    debug_flag="-d"
+                    do_echo=1
+                    ;;
+                *)
+                    T=${1:-30}
+                    nap=${2:-10}
+                    break
+                    ;;
+            esac
+            shift
+        done
+        ;;
+esac
+
+# set other variables
+next=$(date -d "${T} minutes" +%Y%m%d%H%M)
+script=/opt/SGE/examples/jobs/periodic_sleeper.sh
+
+# output some informations
+if [ ${debug} -eq 1 ]; then
+    echo "T = ${T}, nap=${nap}"
+    echo "next run at ${next} (YYYYMMDDhhmm)"
+    echo "debug_flag = ${debug_flag}, do_echo = ${do_echo}"
+    echo ""
+fi
+
+# commands to run in Grid Engine
+/opt/SGE/examples/jobs/sleeper.sh ${nap} ${do_echo}
+
+# re-submit script to execute in T minutes
+jobid=$(qsub ${terse} -a ${next} ${script} ${debug_flag} ${T} ${nap})
+exit_code=$?
+if [ ${debug} -eq 1 ]; then
+    echo "${jobid}"
+fi
+if [ ${exit_code} -ne 0 ]; then
+    if [ ${debug} -eq 1 ]; then
+        echo "${jobid}"
+        echo "Ups, something went wrong, check output!"
+    fi
+    exit ${exit_code}
+fi