GSEA: java.lang.OutOfMemoryError: Java heap space

Question

[huwenhuo]

I am running GSEA in HPC. After run with qsub script.sh It gives me this memory error as shown in the title. Here are the most likely relevant parameters when I run it:

#$ -l  h_vmem=125G,virtual_free=2G
#$ -pe smp 3

 java -jar gsea2-2.2.0.jar xtools.gsea.GseaPreranked -nperm 1000000  other_parameters_not_shown

the parameters works as this:

#$ -l  h_vmem=5,virtual_free=2G
#$ -pe smp 5

 java -jar gsea2-2.2.0.jar xtools.gsea.GseaPreranked -nperm 1000  other_parameters_not_shown

But I really want to get the nice p values to plot a figure. Is this normal that memory error rise from the top setting?

[GenoMax]

You are trying to assign 125x3 = 375G RAM for this job in the top example. Is your account allowed to use that much memory (likely not)?

Number you assign to h_vmem will be used for each core you specify in smp "n". Does GSEA have any recommendation about how much memory you should use?

[huwenhuo]

Yes, you are right. That is also I am so supprised I got this error.

below is the whole script

/home/huw/program/jdk7/bin/java -Xmx10g -cp /home/huw/program/gsea2-2.2.0.jar xtools.gsea.GseaPreranked -gmx /home/huw/program/c1.all.v5.0.symbols.gmt -rnk nhd.symbol.rnk -rpt_label gsea.nhd.symbol.rnk.c1.all.v5.0.symbols.gmt -out gsea -collapse false -mode Max_probe -norm meandiv -nperm 100000 -scoring_scheme classic -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 2500 -set_min 10 -zip_report false -gui false

here is what I got at one moment by qstat -j jobid

  usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
   usage    2:                 cpu=00:00:01, mem=6.68676 GBs, io=0.00511, vmem=12.837G, maxvmem=12.837G
   usage    3:                 cpu=00:00:00, mem=5.85894 GBs, io=0.00465, vmem=12.837G, maxvmem=12.837G
   usage    5:                 cpu=00:00:10, mem=125.54828 GBs, io=0.01445, vmem=12.910G, maxvmem=12.910G

[GenoMax]

Based on this FAQ page, GSEA should not need a lot of memory so I would start with 8G or so to check. Here is some additional help for the command line.