GSEA: java.lang.OutOfMemoryError: Java heap space
Entering edit mode
4.5 years ago
huwenhuo ▴ 40

I am running GSEA in HPC. After run with qsub 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?

next-gen sequencing software error • 4.0k views
Entering edit mode

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?

Entering edit mode

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
Entering edit mode

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.


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