Java Heap Space

[Adeyeye Haastrup]

Hello. I am having this error on the app :
<Error Details>

---- Full Error Message ----
Java heap space

---- Stack Trace ----
# of exceptions: 1
------Java heap space------
java.lang.OutOfMemoryError: Java heap space

how do I solve it please?

[Anthony Castanza]

Hi Adeyeye,

This would appear to be an issue with the amount of memory allocated to Java on your machine.

Is this a Mac or a PC and are you using the application bundle or the command line version of GSEA?

How much RAM is your machine configured with and what size is the expression dataset you're attempting to analyze?

If you have a severely memory constrained machine, or an extremely large dataset, one option would be to run GSEA through the free bioinformatics cloud platform at cloud.genepattern.org.

This offers GSEA with all the same features as the desktop application, but with the ability to request very large amounts of memory which will allow exceptionally large datasets to be analyzed.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[David Eby]

Hi Adeyeye,

I just wanted to let you know that we released a new version of GSEA (v4.4.0) over the weekend that gives another way to address this problem.  You can now add a special configuration file that GSEA will use when loading to set a custom memory specification.

The details are in this README.  As that document covers other material (and is a bit technical as well), here's a summary.  You can change the default memory specification by editing GSEA's java_arguments file, found here (create it if it doesn't exist):

• $HOME/.gsea/java_arguments           (Mac and Linux)
• %USERPROFILE%/.gsea/java_arguments   (Windows)

Within that file, adding the following on a single line will allow GSEA to use 8 GB on memory instead of the default of 4 GB:

-Xmx8g

You can change this accordingly for 16 GB, etc.  Note that you'll be limited by your computer's actual memory capacity.

Regards,

David

Thanks!
David

David Eby
www.gsea-msigdb.org

To view this discussion visit https://groups.google.com/d/msgid/gsea-help/CAGCeyZxpBhi8dz%3DuLM5-_70dcxh-F475oBPf0QaTEYBRsvVWSg%40mail.gmail.com.

[David Eby]

Just as a quick follow-up, it's worth mentioning that the java_arguments file should be created with a plain-text editor (like NotePad, TextEdit, or emacs) and should have no extension.  I should add that note to the README.

David Eby
www.gsea-msigdb.org