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I'm having some difficulty getting the supercomputer to run my netlogo model. I'm attempting to follow the advice given here and here. But no luck. I think it's not finding some of the needed jars? The entirety of the v5.3.1 folder is located at:

/users/PAS1038/xxmyusernamexx/netlogo/netlogo-5.3.1/ and I've added the rnd extension in the app/ folder.

This is my submission script: 

#PBS -N testjob
#PBS -l walltime=00:30:00
#PBS -l nodes=1:ppn=1
#PBS -j oe
cd /users/PAS1038/xxmyusernamexx/netlogo/netlogo-5.3.1/
java -Xmx1024m -Dfile.encoding=UTF-8 -cp /users/PAS1038/xxmyusernamexx/netlogo/netlogo-5.3.1/app/NetLogo.jar \
org.nlogo.headless.Main \
--model /users/PAS1038/xxmyusername/netlogo/netlogo-5.3.1/MyModel.nlogo \
--experiment test \
--table  testoutput.csv \
--threads 8

but it is giving me the following error: 

java.lang.IllegalStateException: Can't find extension: profiler/profiler.jar
    at org.nlogo.workspace.ExtensionManager.resolvePathAsURL(ExtensionManager.java:315)
    at org.nlogo.workspace.ExtensionManager.importExtension(ExtensionManager.java:153)
    at org.nlogo.compiler.StructureParser.parseImport(StructureParser.scala:459)
    at org.nlogo.compiler.StructureParser.parse(StructureParser.scala:196)
    at org.nlogo.compiler.CompilerMain$.compile(CompilerMain.scala:25)
    at org.nlogo.compiler.Compiler$.compileProgram(Compiler.scala:28)
    at org.nlogo.headless.HeadlessModelOpener.openFromMap(HeadlessModelOpener.scala:53)
    at org.nlogo.headless.HeadlessWorkspace.openString(HeadlessWorkspace.scala:531)
    at org.nlogo.headless.HeadlessWorkspace.open(HeadlessWorkspace.scala:513)
    at org.nlogo.headless.Main$.newWorkspace$1(Main.scala:19)
    at org.nlogo.headless.Main$$anonfun$runExperiment$1.apply(Main.scala:24)
    at org.nlogo.headless.Main$$anonfun$runExperiment$1.apply(Main.scala:24)
    at org.nlogo.lab.Lab$$anonfun$1.apply(Lab.scala:33)
    at org.nlogo.lab.Lab$$anonfun$1.apply(Lab.scala:33)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:233)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:233)
    at scala.collection.immutable.Range.foreach(Range.scala:78)
    at scala.collection.TraversableLike$class.map(TraversableLike.scala:233)
    at scala.collection.immutable.Range.map(Range.scala:46)
    at org.nlogo.lab.Lab.run(Lab.scala:33)
    at org.nlogo.headless.Main$.runExperiment(Main.scala:24)
    at org.nlogo.headless.Main$$anonfun$main$1.apply(Main.scala:14)
    at org.nlogo.headless.Main$$anonfun$main$1.apply(Main.scala:14)
    at scala.Option.foreach(Option.scala:197)
    at org.nlogo.headless.Main$.main(Main.scala:14)
    at org.nlogo.headless.Main.main(Main.scala)
Exception in thread "main" Can't find extension: profiler at position 165 in 
    at org.nlogo.api.ErrorSource.signalError(ErrorSource.scala:12)
    at org.nlogo.workspace.ExtensionManager.importExtension(ExtensionManager.java:162)
    at org.nlogo.compiler.StructureParser.parseImport(StructureParser.scala:459)
    at org.nlogo.compiler.StructureParser.parse(StructureParser.scala:196)
    at org.nlogo.compiler.CompilerMain$.compile(CompilerMain.scala:25)
    at org.nlogo.compiler.Compiler$.compileProgram(Compiler.scala:28)
    at org.nlogo.headless.HeadlessModelOpener.openFromMap(HeadlessModelOpener.scala:53)
    at org.nlogo.headless.HeadlessWorkspace.openString(HeadlessWorkspace.scala:531)
    at org.nlogo.headless.HeadlessWorkspace.open(HeadlessWorkspace.scala:513)
    at org.nlogo.headless.Main$.newWorkspace$1(Main.scala:19)
    at org.nlogo.headless.Main$$anonfun$runExperiment$1.apply(Main.scala:24)
    at org.nlogo.headless.Main$$anonfun$runExperiment$1.apply(Main.scala:24)
    at org.nlogo.lab.Lab$$anonfun$1.apply(Lab.scala:33)
    at org.nlogo.lab.Lab$$anonfun$1.apply(Lab.scala:33)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:233)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:233)
    at scala.collection.immutable.Range.foreach(Range.scala:78)
    at scala.collection.TraversableLike$class.map(TraversableLike.scala:233)
    at scala.collection.immutable.Range.map(Range.scala:46)
    at org.nlogo.lab.Lab.run(Lab.scala:33)
    at org.nlogo.headless.Main$.runExperiment(Main.scala:24)
    at org.nlogo.headless.Main$$anonfun$main$1.apply(Main.scala:14)
    at org.nlogo.headless.Main$$anonfun$main$1.apply(Main.scala:14)
    at scala.Option.foreach(Option.scala:197)
    at org.nlogo.headless.Main$.main(Main.scala:14)
    at org.nlogo.headless.Main.main(Main.scala)
=>> PBS: job killed: walltime 1841 exceeded limit 1800
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1 回答 1

1

我已经完成了这个问题的答案。我需要在 App 文件夹中有所有输入文件、.nlogo 文件和 headless.sh。在这种情况下，使用以下代码：

#PBS -N runone
#PBS -l walltime=12:00:00
#PBS -l nodes=1:ppn=8
module load java/1.8.0_60
cd /users/PAS1038/myusername/netlogo/netlogo-5.3.1/app
./netlogo-headless.sh --model modelname.nlogo --experiment g --table output.csv --threads 8

注意： ppn=X 和 --threads x 需要更改为每个节点的处理器数量。

于 2016-09-25T13:44:34.613 回答