[Camino-users] simulations

[Birkan Tunc]

Maybe these links can help 

http://blogs.opcodesolutions.com/roller/java/entry/solve_java_lang_outofmemoryerror_java

http://javarevisited.blogspot.com/2011/09/javalangoutofmemoryerror-permgen-space.html

http://stackoverflow.com/questions/37335/how-to-deal-with-java-lang-outofmemoryerror-java-heap-space-error-64mb-heap




________________________________
 From: ClaireMarie Barnes <cmbarnes at live.co.uk>
To: camino-users at www.nitrc.org 
Sent: Tuesday, December 4, 2012 10:57 AM
Subject: [Camino-users] simulations
 

 
Hi there,

I am trying to simulate data using the following command;

datasynth -walkers 100000 -tmax 1000 -voxels 1 -p 0.0 -schemefile 17x17x17new.scheme -initial uniform -substrate cylinder -packing hex -cylinderrad 1E-6 -cylindersep 2.1E-6 > regcylinderfornewscheme.bfloat


The simulation works fine if I do it for 10000 walkers but reading the literature it is better to do such a simulation with 100000 walkers however, I get the following error on my PC when I attempt this;

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at simulation.dynamics.Walker.<init>(Walker.java:98)
    at simulation.dynamics.WalkerFactory.getWalker(WalkerFactory.java:51)
    at simulation.DiffusionSimulation.initialiseWalkers(DiffusionSimulation.java:298)
    at simulation.DiffusionSimulation.nextVoxel(DiffusionSimulation.java:578)
    at apps.SyntheticData.execute(SyntheticData.java:74)
    at apps.EntryPoint.main(EntryPoint.java:266)
I understand you may not be able to help me but I do not know much about java and was wondering if you could shed some light on my problem

Many thanks in advance 
Claire

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