超级计算机提交脚本运行NetLogo的问题

Question

我在使用超级计算机运行我的netlogo模型时遇到了一些困难。 我试图按照给出的建议here和here。但没有运气。我认为这不是找到一些需要的罐子？在V5.3.1文件夹的全部位于：

/users/PAS1038/xxmyusernamexx/netlogo/netlogo-5.3.1/ ，我已经添加了rnd扩展在app/文件夹中。

这是我提交的脚本：

#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$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 

Answer 1

我跑下来的问题的答案。我需要在App文件夹中包含所有输入文件，.nlogo文件和headless.sh。当是这种情况，使用这个代码：

#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：PPN = X和--threads x将需要改变到任何每个节点处理器的数量是。