netlogo 6.0.1 example added

CADES/NETLOGO/netlogo_6_0_1_job.pbs

+#!/bin/bash
+#PBS -S /bin/bash
+#PBS -m be
+#PBS -M youremail@ornl.gov
+#PBS -N sample_job
+#PBS -q batch
+#PBS -l nodes=1:ppn=32:hw32
+#PBS -l walltime=0:10:00
+#PBS -l naccesspolicy=singlejob
+#PBS -W group_list=cades-cnms
+#PBS -l qos=std
+#PBS -A cnms
+
+export OMP_NUM_THREADS=1
+
+cd $PBS_O_WORKDIR
+
+#this can be useful to see from outside shells
+cat $PBS_NODEFILE >pbs_nodefile
+
+
+module load env/cades-cnms
+. $SOFTWARECNMS/spack/share/spack/setup-env.sh
+spack load jdk
+module load NetLogo/6.0.1
+
+#each of these () surrounded commands launches in a subshell
+(java -Xms8g -Xmx128g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath app/args4j-2.0.12.jar:$NETLOGOROOT/app/asm-5.0.3.jar:$NETLOGOROOT/app/asm-all-5.0.4.jar:$NETLOGOROOT/app/asm-analysis-5.0.3.jar:$NETLOGOROOT/app/asm-tree-5.0.3.jar:$NETLOGOROOT/app/asm-util-5.0.3.jar:$NETLOGOROOT/app/behaviorsearch.jar:$NETLOGOROOT/app/commons-codec-1.10.jar:$NETLOGOROOT/app/commons-logging-1.1.1.jar:$NETLOGOROOT/app/gluegen-rt-2.3.2.jar:$NETLOGOROOT/app/httpclient-4.2.jar:$NETLOGOROOT/app/httpcore-4.2.jar:$NETLOGOROOT/app/httpmime-4.2.jar:$NETLOGOROOT/app/jcommon-1.0.16.jar:$NETLOGOROOT/app/jfreechart-1.0.13.jar:$NETLOGOROOT/app/jhotdraw-6.0b1.jar:$NETLOGOROOT/app/jmf-2.1.1e.jar:$NETLOGOROOT/app/jogl-all-2.3.2.jar:$NETLOGOROOT/app/json-simple-1.1.1.jar:$NETLOGOROOT/app/log4j-1.2.16.jar:$NETLOGOROOT/app/macro-compat_2.12-1.1.1.jar:$NETLOGOROOT/app/netlogo-6.0.1.jar:$NETLOGOROOT/app/parboiled-core-1.1.7.jar:$NETLOGOROOT/app/parboiled-java-1.1.7.jar:$NETLOGOROOT/app/parboiled_2.12-2.1.3.jar:$NETLOGOROOT/app/pegdown-1.6.0.jar:$NETLOGOROOT/app/picocontainer-2.13.6.jar:$NETLOGOROOT/app/rsyntaxtextarea-2.6.0.jar:$NETLOGOROOT/app/scala-library-2.12.0.jar:$NETLOGOROOT/app/scala-library-2.12.1.jar:$NETLOGOROOT/app/scala-parser-combinators_2.12-1.0.5.jar:$NETLOGOROOT/app/shapeless_2.12-2.3.2.jar  org.nlogo.headless.Main --model ./predator-prey.nlogo --experiment experiment1 2>&1 >out1) &
+
+#wait for all subshells to complete
+wait
+

CADES/NETLOGO/netlogo_job.pbs

@@ -8,7 +8,8 @@
 #PBS -l walltime=0:10:00
 #PBS -l naccesspolicy=singlejob
 #PBS -W group_list=cades-cnms
-#PBS -l qos=condo
+#PBS -l qos=std
+#PBS -A cnms
 
 export OMP_NUM_THREADS=1