NetLogo HPC 内存错误

Question

#!/bin/bash
#$ -N para_three
#$ -q all.q
#$ -pe mpi 30
/home/abhishekb/netlogo/netlogo-5.2.0/netlogo-headless.sh \
    --model /home/abhishekb/models/try4.nlogo \
    --experiment experiment1 \
    --table /home/abhishekb/csvresults/24.04_Results.csv

错误：

Exception in thread "JobThread" 
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "JobThread"
Exception in thread "JobThread" 
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "JobThread"
Exception in thread "JobThread" 
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "JobThread"

为什么，我不明白？我在运行 NetLogo with 64bit java 上找到了建议。但是link[1][2]已经过期了，求助

令人惊讶的是，早些时候我在 NetLogo 5.1 上运行它并没有遇到这个错误。

脚本更改：我尝试在最后添加线程：

#!/bin/bash
#$ -N para_three
#$ -q all.q
#$ -pe mpi 30
/home/abhishekb/netlogo/netlogo-5.2.0/netlogo-headless.sh \
    --model /home/abhishekb/models/try4.nlogo \
    --experiment experiment1 \
    --table /home/abhishekb/csvresults/24.04_Results.csv \
    --threads 30

新错误：

Exception in thread "main" java.lang.OutOfMemoryError: PermGen space
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
    at org.nlogo.generator.CustomClassLoader.loadClass(CustomClassLoader.scala:27)
    at org.nlogo.generator.CustomClassLoader.loadBytecodeClass(CustomClassLoader.scala:32)
    at org.nlogo.generator.Generator$InstructionGenerator.finish(Generator.scala:241)

编辑 3：

#!/bin/sh
cd "`dirname "[=14=]"`"             # the copious quoting is for handling paths with spaces
#-Xmx3000m                     use up to 1GB RAM (edit to increase)
# -Dfile.encoding=UTF-8         ensure Unicode characters in model files are compatible cross-platform
# -classpath NetLogo.jar        specify main jar
# org.nlogo.headless.Main       specify we want headless, not GUI
# "$@"                          pass along any command line arguments
-XX:MaxPermSize=3200m          avoid OutOfMemory errors for large models
java -Xmx1024m -Dfile.encoding=UTF-8 -classpath NetLogo.jar org.nlogo.headless.Main "$@"

错误：

/home/abhishekb/netlogo/netlogo-5.2.0/netlogo-headless.sh: line 8: -XX:MaxPermSize=3200m: command not found Exception in thread "main" java.lang.OutOfMemoryError: PermGen space at java.lang.ClassLoader.defineClass(ClassLoader.java:800) at java.lang.ClassLoader.defineClass(ClassLoader.java:643) at org.nlogo.generator.CustomClassLoader.loadClass(CustomClassLoader.scala:27) at org.nlogo.generator.CustomClassLoader.loadBytecodeClass(CustomClassLoader.scala:32) at org.nlogo.generator.Generator$InstructionGenerator.finish(Generator.scala:241) at org.nlogo.generator.Generator$InstructionGenerator.generate(Generator.scala:93) at org.nlogo.generator.Generator.org$nlogo$generator$Generator$$recurse(Generator.scala:28) at org.nlogo.generator.Generator$InstructionGenerator$$anonfun$generateOldStyleCall.apply(Generator.scala:208) at org.nlogo.generator.Generator$InstructionGenerator$$anonfun$generateOldStyleCall.apply(Generator.scala:208) at scala.collection.TraversableLike$$anonfun$map.apply(TraversableLike.scala:233) at scala.collection.TraversableLike$$anonfun$map.apply(TraversableLike.scala:233) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:34) at scala.collection.mutable.ArrayOps.foreach(ArrayOps.scala:38) at scala.collection.TraversableLike$class.map(TraversableLike.scala:233) at scala.collection.mutable.ArrayOps.map(ArrayOps.scala:38) at org.nlogo.generator.Generator$InstructionGenerator.generateOldStyleCall(Generator.scala:208) at org.nlogo.generator.Generator$InstructionGenerator.generateInstruction(Generator.scala:146) at org.nlogo.generator.Generator$InstructionGenerator$$anonfun$generateInstruction.apply$mcVI$sp(Generator.scala:167) at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:78) at org.nlogo.generator.Generator$InstructionGenerator.generateInstruction(Generator.scala:159) at org.nlogo.generator.Generator$InstructionGenerator$$anonfun$generateInstruction.apply$mcVI$sp(Generator.scala:167) at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:78) at org.nlogo.generator.Generator$InstructionGenerator.generateInstruction(Generator.scala:159) at org.nlogo.generator.Generator$InstructionGenerator$$anonfun$generateInstruction.apply$mcVI$sp(Generator.scala:167) at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:81) at org.nlogo.generator.Generator$InstructionGenerator.generateInstruction(Generator.scala:159) at org.nlogo.generator.Generator$InstructionGenerator$$anonfun$generateInstruction.apply$mcVI$sp(Generator.scala:167) at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:78) at org.nlogo.generator.Generator$InstructionGenerator.generateInstruction(Generator.scala:159) at org.nlogo.generator.Generator$InstructionGenerator.generateBodyMethod(Generator.scala:115) at org.nlogo.generator.Generator$InstructionGenerator.generate(Generator.scala:90) at org.nlogo.generator.Generator.org$nlogo$generator$Generator$$recurse(Generator.scala:28)

Answer 1

错误消息指的是 PermGen，所以这意味着问题不是堆的总大小，而是具体的 PermGen 上限。您需要使用更高的 PermGen 设置启动 Java，例如-XX:MaxPermSize=512m。您的 netlogo-headless.sh 文件中可能已经有这样的设置；如果是这样，请增加它。如果那里没有这样的设置，请添加一个。

我大约 98% 确定这与 NetLogo 5.1 和 5.2 之间的任何差异无关。您现在使用 5.2 所做的事情与您当时使用 5.1 所做的事情可能存在其他不同之处（可能是 threads= 设置的大小）。

这里是 NetLogo 5.2 的默认 netlogo.sh 和 netlogo-headless.sh 文件的工作链接：https://github.com/NetLogo/NetLogo/blob/5.2.0/dist/netlogo.sh, https://github.com/NetLogo/NetLogo/blob/5.2.0/dist/netlogo-headless.sh

运行 64 位 JVM 与解决 PermGen 问题并不特别相关，但对于运行非常大的堆可能是必需的。

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