commit 09f387f0958c5dcd46b64aa8d46b35a5d465d385
parent af574775374f8852224b0d036ce9eb9eb7e3bbc5
Author: Anders Damsgaard <anders@adamsgaard.dk>
Date: Tue, 5 May 2020 09:21:18 +0200
Add startspm.sh script with unix lineendings
Diffstat:
1 file changed, 71 insertions(+), 0 deletions(-)
diff --git a/code/spm/spm-3.4.8/startspm.sh b/code/spm/spm-3.4.8/startspm.sh
@@ -0,0 +1,71 @@
+#!/bin/bash
+
+if [ $# -eq 0 ]; then
+ echo "usage: $0 <SPMFOLDER> <MODELFOLDER> <QUEUE>"
+ echo "No arguments supplied. Example:"
+ echo " $0 ~/spm-3.1.3 ~/a1 q4"
+else
+
+EMAIL=david@geo.au.dk
+
+MODELFOLDER=$2
+
+#QUEUE=q4
+QUEUE=$3
+CORES=12
+
+HOURS=48
+
+#SPMFOLDER=~/spm-3.1.3
+SPMFOLDER=$1
+BIN=spm
+
+echo "Removing old files from the model output directory"
+rm -rf $MODELFOLDER/output/*
+
+echo "#!/bin/bash
+# These commands set up the Grid Environment for your job:
+
+# Job name and folder. Edit both this entry and MODELFOLDER!!
+#PBS -N `basename $MODELFOLDER`
+
+# Specify job requirements.
+# How many nodes (nodes) to use, no. of cores (ppn)?
+# The process walltime (hh:mm:ss)?
+#PBS -l nodes=1:ppn=$CORES,walltime=$HOURS:00:00
+
+# Specify queue
+# q4, q8, qfat, q12, q12fat
+#PBS -q $QUEUE
+
+# Your e-mail address
+#PBS -M $EMAIL
+
+# Mail options:
+# a: Mail is sent when the job is aborted by the batch system
+# b: Mail is sent when the job begins execution
+# e: Mail is sent when the job terminates
+#PBS -m abe
+
+MODELFOLDER=$MODELFOLDER
+
+# Print the user@hostname, the time and the date
+echo '\`whoami\`@\`hostname\`'
+echo 'Start at \`date\`'
+
+# Compile the program
+cd $SPMFOLDER/source && make
+
+# Run the model
+$SPMFOLDER/$BIN $MODELFOLDER
+
+# Print the time and date again
+echo 'End at \`date\`'
+" > $MODELFOLDER/job-script.sh
+
+echo "Job script written as $MODELFOLDER/job-script.sh"
+echo "cd $MODELFOLDER && qsub job-script.sh"
+cd $MODELFOLDER && qsub job-script.sh
+echo "Submitted with Torque. See status of your jobs with 'mj'"
+
+fi
