[Camino-users] simulations

[Philip A Cook]

It sounds like in Claire's case the simulation is going to be too big to be done entirely in memory, but in general, you can give Camino more memory by setting a shell variable to the number of megabytes you want to allow.

  export CAMINO_HEAP_SIZE=2000

for example. The maximum value needs to be slightly less than the RAM on your machine or Java will fail to allocate it.



On Dec 4, 2012, at 8:13 PM, Birkan Tunc wrote:

> 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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> 
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