GC overhead limit exceeded, during mzmatch.ipeak.sort.RelatedPeaks

[Vincent Bonifay]

Hi,

I got this error message during one the latest step when doing the alignment with mzmatch. It looks like it is an error with the heap space from java. I was trying to fix it by using this command at the beginning: options(java.parameters = "-Xmx4g"). But without success. Do you know how to fix this problem? 

> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=3,rtwindow=6)

 ------------------------------------------------------

| Copyright 2007-2009

| Groningen Bioinformatics Centre

| University of Groningen

|

| RelatedPeaks 1.0.0

|

| libraries:

|  - jfreechart    1.0.13

|  - itext         2.1.7

|  - jama          1.0.2

|  - lma           1.4.0

|  - cmdline       2.0.0

|  - domsax        1.1.0

|  - peakml        1.0.0

|  - mzmatch       1.0.2

 ------------------------------------------------------

Options {

  v:         true

  minrt:     -1.0

  rtwindow:  6.0

  ppm:       3.0

  basepeaks: mzMatch_basepeaks.peakml

  o:         mzMatch_output.peakml

  h:         false

  i:         highintensity_gapfilled.peakml

}

loading data

Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

        at java.lang.AbstractStringBuilder.<init>(Unknown Source)

        at java.lang.StringBuilder.<init>(Unknown Source)

        at domsax.SpecialToken.dereference(SpecialToken.java:83)

        at domsax.XmlParser.characters(XmlParser.java:222)

        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.characters(Unknown Source)

        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)

        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)

        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)

        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)

        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)

        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)

        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(Unknown Source)

        at javax.xml.parsers.SAXParser.parse(Unknown Source)

        at domsax.XmlParser.parse(XmlParser.java:104)

        at peakml.io.peakml.PeakMLParser.run(PeakMLParser.java:402)

        at peakml.io.peakml.PeakMLParser.parseIPeakSet(PeakMLParser.java:384)

        at mzmatch.ipeak.sort.RelatedPeaks.main(RelatedPeaks.java:257)

Warning message:

running command 'java -da -dsa -Xmn1g -Xss160k -XX:+UseParallelGC -XX:ParallelGCThreads=10 -Xms1425m -Xmx1425m -cp C:/R-2.15.1/library/mzmatch.R/java/mzmatch.jar mzmatch.ipeak.sort.RelatedPeaks -i highintensity_gapfilled.peakml -o mzMatch_output.peakml -basepeaks mzMatch_basepeaks.peakml -ppm 3 -rtwindow 6 -v' had status 1 

I also found this in a few forum and website, but I could not find how to enter this type of command in the R script:

The parallel collector will throw an OutOfMemoryError if too much time is being spent in garbage collection: if more than 98% of the total time is spent in garbage collection and less than 2% of the heap is recovered, an OutOfMemoryError will be thrown. This feature is designed to prevent applications from running for an extended period of time while making little or no progress because the heap is too small. If necessary, this feature can be disabled by adding the option -XX:-UseGCOverheadLimit to the command line

Thank you

Kind Regards

[Darren Creek]

Hi Vincent,

Apologies for this error. The default memory allocation for the 'ipeak' commands is only about 1425 Mb, so if you have a large data set you'll need to add a parameter to each 'ipeak'  function: JHeapSize=4000  

(replace 4000 with the amount of memory you wish to allocate to this task). 

http://mzmatch.sourceforge.net/mzmatch.R/mzmatch.ipeak.sort.RelatedPeaks.html 

Please adjust the R script and you should be fine (In future versions of IDEOM this memory value will be taken from the value provided on the IDEOM settings page. 

e.g. 

> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=3,rtwindow=6, JHeapSize=4000) 

cheers,

Darren

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--
Dr Darren Creek

NHMRC Training Fellow
Department of Biochemistry and Molecular Biology, Bio21 Institute

University of Melbourne

dcr...@unimelb.edu.au

darre...@gmail.com

(+61) 3 83442351

[Vincent Bonifay]

Thank you Darren, It worked perfectly. I had to do the same for the mzmatch.ipeak.convert.ConvertToText. But then everything went well and the output text file was created with success

Regards