超级计算机向运行 NetLogo 提交脚本的问题

Question

我在将超级计算机连接到运行我的 netlogo 模型时遇到了一些困难。我正在尝试遵循 and 给出的建议。但没有运气。我认为它没有找到一些需要的罐子？整个 v5.3.1 文件夹位于：

/users/PAS1038/xxmyusernamexx/netlogo/netlogo-5.3.1/ 并且我在 app/ 文件夹中添加了 rnd 扩展名。

这是我的提交脚本：

#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

但它给我以下错误：

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(Main.scala:19)
    at org.nlogo.headless.Main$$anonfun$runExperiment.apply(Main.scala:24)
    at org.nlogo.headless.Main$$anonfun$runExperiment.apply(Main.scala:24)
    at org.nlogo.lab.Lab$$anonfun.apply(Lab.scala:33)
    at org.nlogo.lab.Lab$$anonfun.apply(Lab.scala:33)
    at scala.collection.TraversableLike$$anonfun$map.apply(TraversableLike.scala:233)
    at scala.collection.TraversableLike$$anonfun$map.apply(TraversableLike.scala:233)
    at scala.collection.immutable.Range.foreach(Range.scala:78)
    at scala.collection.TraversableLike$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$$anonfun$main.apply(Main.scala:14)
    at org.nlogo.headless.Main$$anonfun$main.apply(Main.scala:14)
    at scala.Option.foreach(Option.scala:197)
    at org.nlogo.headless.Main$.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(Main.scala:19)
    at org.nlogo.headless.Main$$anonfun$runExperiment.apply(Main.scala:24)
    at org.nlogo.headless.Main$$anonfun$runExperiment.apply(Main.scala:24)
    at org.nlogo.lab.Lab$$anonfun.apply(Lab.scala:33)
    at org.nlogo.lab.Lab$$anonfun.apply(Lab.scala:33)
    at scala.collection.TraversableLike$$anonfun$map.apply(TraversableLike.scala:233)
    at scala.collection.TraversableLike$$anonfun$map.apply(TraversableLike.scala:233)
    at scala.collection.immutable.Range.foreach(Range.scala:78)
    at scala.collection.TraversableLike$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$$anonfun$main.apply(Main.scala:14)
    at org.nlogo.headless.Main$$anonfun$main.apply(Main.scala:14)
    at scala.Option.foreach(Option.scala:197)
    at org.nlogo.headless.Main$.main(Main.scala:14)
    at org.nlogo.headless.Main.main(Main.scala)
=>> PBS: job killed: walltime 1841 exceeded limit 1800

Answer 1

我已经运行记下了问题的答案。我需要在 App 文件夹中包含所有输入文件、.nlogo 文件和 headless.sh。如果是这种情况，请使用此代码：

#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。

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