update local folder to match files acctually used

local/bin/suspend.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/ksh
-# $Id: suspend.sh 365 2013-11-18 09:58:17Z kasper $
+
 # This script should be added as the SUSPEND_METHOD in the
 # queue definition with a $job_pid, $job_id, and $job_owner arguments.
 # e.g. script.sh $job_pid $job_id $job_owner

local/bin/term.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/ksh
-# $Id: term.sh 364 2013-11-18 09:55:05Z kasper $
+
 # This script should be added as the TERMINATE_METHOD in the
 # queue definition with $job_pid, $job_id, $job_owner, and interval arguments.
 # e.g.  script.sh $job_pid $job_id $job_owner 90
@@ -10,16 +10,16 @@ then
     exit 1
 fi
 
-#echo "Term script Running on: $USER $1 $2 $3 $4" >> ~$3/qdel_log.log
-#echo `pgrep -g $1` >> ~$3/qdel_log.log
+#echo "Term script Running on $(hostname): $USER $1 $2 $3 $4" >> ~$3/qdel_log.log
+#echo $(pgrep -g $1) >> ~$3/qdel_log.log
 
-for sig in 2 15 9
+for sig in INT TERM KILL
 do
-    stat=`pgrep -g $1 -u $3`
-    if [ ! -z "$stat" ]
+    stat=$(pgrep -g $1 -u $3)
+    if [ ! -z "${stat}" ]
     then
-        #echo "Sending $sig to $1" >> ~$3/qdel_log.log
-        /usr/bin/pkill --signal $sig -g $1
+        #echo "Sending SIG${sig} to $1" >> ~$3/qdel_log.log
+        /usr/bin/pkill --signal ${sig} -g $1
         sleep $4
     else
         break

local/examples/jobs/periodic_sleeper.sh

@@ -47,7 +47,7 @@ esac
 
 # set other variables
 next=$(date -d "${T} minutes" +%Y%m%d%H%M)
-script=/opt/SGE/examples/jobs/periodic_sleeper.sh
+script=$0
 
 # output some informations
 if [ ${debug} -eq 1 ]; then
@@ -58,7 +58,7 @@ if [ ${debug} -eq 1 ]; then
 fi
 
 # commands to run in Grid Engine
-/opt/SGE/examples/jobs/sleeper.sh ${nap} ${do_echo}
+${script} ${nap} ${do_echo}
 
 # re-submit script to execute in T minutes
 jobid=$(qsub ${terse} -a ${next} ${script} ${debug_flag} ${T} ${nap})

local/examples/jobs/simple_conda_test.sh

@@ -16,6 +16,14 @@
 # Name the job 'Conda-Test'
 #$ -N Conda-Test
 
+# send e-mail after job has finished
+# use the -M option to define your e-mail address
+# #$ -M my-email@example.org
+#$ -m e
+
+# join stdout and stderr in one file
+#$ -j y
+
 #############################################################
 # initialize conda                                          #
 #############################################################

local/patch/fix_euid_set_bug.patch

@@ -1,33 +0,0 @@
-diff --git a/source/daemons/shepherd/shepherd.c b/source/daemons/shepherd/shepherd.c
-index 5af1463..e7b2831 100644
---- a/source/daemons/shepherd/shepherd.c
-+++ b/source/daemons/shepherd/shepherd.c
-@@ -299,17 +299,24 @@ static int handle_io_file(const char* file, const char* owner, bool rw) {
-       }
-    }
- 
--   /* reset egid and euid to the stored values */
--   if (sge_seteuid(old_euid) != 0) {
--      shepherd_trace("Cannot reset euid %s due to %s", owner, strerror(errno));
--      SGE_CLOSE(fd);
-+   /* set effective user-id to root again, because only root is allowed to change
-+    * the euid to any other than the current user-id.   */
-+   if (sge_seteuid(SGE_SUPERUSER_UID) != 0) {
-+      shepherd_trace("Cannot become root due to %s", strerror(errno));
-       return -1;
-    }
-+
-+   /* reset egid and euid to the stored values (e.g. those of the sgeadmin user) */
-    if (sge_setegid(old_egid) != 0) {
-       shepherd_trace("Cannot reset egid %s due to %s", owner, strerror(errno));
-       SGE_CLOSE(fd);
-       return -1;
-    }
-+   if (sge_seteuid(old_euid) != 0) {
-+      shepherd_trace("Cannot reset euid %s due to %s", owner, strerror(errno));
-+      SGE_CLOSE(fd);
-+      return -1;
-+   }
- 
-    return fd;
- }

local/pe_epilog.d/00_bin-true

@@ -0,0 +1 @@
+/bin/true

local/pe_prolog.d/00_bin-true

@@ -0,0 +1 @@
+/bin/true

local/prolog.d/00_bin-true

@@ -0,0 +1 @@
+/bin/true

local/scripts/SGESuspend.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/ksh
+# $Id: SGESuspend.sh 365 2013-11-18 09:58:17Z kasper $
+# This script should be added as the SUSPEND_METHOD in the
+# queue definition with a $job_pid, $job_id, and $job_owner arguments.
+# e.g. script.sh $job_pid $job_id $job_owner
+
+if [ -z "$3" ]
+then
+    echo "Usage: $0 \$job_pid \$job_id \$job_owner"
+    exit 1
+fi
+
+stat=`pgrep -g $1`
+if [ ! -z "$stat" ]
+then
+    #echo "Sending $sig to $1" >> ~$3/qdel_log.log
+    /usr/bin/pkill --signal SIGTSTP -g $1
+else
+    echo "Process $1 not found for job $2" >> ~$3/qdel_log.log
+    echo "Unable to suspend." >> ~$3/qdel_log.log
+    exit 1
+fi
+
+#uncomment the following for debugging
+#echo "Suspending Job $2 " >> ~$3/qdel_log.log

local/scripts/SGETerm.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/ksh
+# $Id: SGETerm.sh 364 2013-11-18 09:55:05Z kasper $
+# This script should be added as the TERMINATE_METHOD in the
+# queue definition with $job_pid, $job_id, $job_owner, and interval arguments.
+# e.g.  script.sh $job_pid $job_id $job_owner 90
+
+if [ -z "$4" ]
+then
+    echo "Usage: $0 \$job_pid \$job_id \$job_owner interval" 
+    exit 1
+fi
+
+#echo "Term script Running on: $USER $1 $2 $3 $4" >> ~$3/qdel_log.log
+#echo `pgrep -g $1` >> ~$3/qdel_log.log
+
+for sig in 2 15 9
+do
+    stat=`pgrep -g $1 -u $3`
+    if [ ! -z "$stat" ]
+    then
+        #echo "Sending $sig to $1" >> ~$3/qdel_log.log
+        /usr/bin/pkill --signal $sig -g $1
+        sleep $4
+    else
+        break
+    fi
+done
+
+#uncomment the following for debugging
+#echo "Job $2 killed." >> ~$3/qdel_log.log

local/scripts/epilog

@@ -0,0 +1,11 @@
+#! /bin/bash
+# $Id: epilog 181 2010-09-17 15:55:28Z kasper $
+
+## Delete the STDOUT and STDERR files (.o and .e) if they are empty
+##  ( we do not want to delete non-empty files, they may contain useful
+##    troubleshooting or debug information ... )
+##
+[ -r $SGE_STDOUT_PATH -a -f $SGE_STDOUT_PATH ] && [ ! -s $SGE_STDOUT_PATH ] && rm -f $SGE_STDOUT_PATH
+[ -r $SGE_STDERR_PATH -a -f $SGE_STDERR_PATH ] && [ ! -s $SGE_STDERR_PATH ] && rm -f $SGE_STDERR_PATH
+
+exit 0

local/scripts/pe_epilog

@@ -0,0 +1 @@
+/bin/true

local/scripts/pe_prolog

@@ -0,0 +1 @@
+/bin/true

local/scripts/prolog

@@ -0,0 +1 @@
+/bin/true

local/scripts/qlogin_wrapper

@@ -0,0 +1,5 @@
+#!/bin/sh
+# $Id: qlogin_wrapper 175 2010-09-15 15:34:28Z kasper $
+HOST=$1
+PORT=$2
+/usr/bin/ssh -XAq -p $PORT $USER@$HOST