Out of memory error

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Out of memory error

Ed Johnson
Out of memory error

I can get Apollo to load a 14mb fasta file with GFF annotation on Win XP Pro, but it dies when I try to load a 23mb fasta file.  The error log shows ;

Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space

        at java.util.Arrays.copyOf(Unknown Source)

        at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)

        at java.lang.AbstractStringBuilder.append(Unknown Source)

        at java.lang.StringBuffer.append(Unknown Source)

        at apollo.seq.io.FastaFile.parse(FastaFile.java:180)

        at apollo.seq.io.FastaFile.processReader(FastaFile.java:60)

        at apollo.seq.io.FastaFile.<init>(FastaFile.java:71)

        at apollo.dataadapter.gff3.GFF3Adapter.parseSeq(GFF3Adapter.java:408)

        at apollo.dataadapter.gff3.GFF3Adapter.parseSeq(GFF3Adapter.java:422)

        at apollo.dataadapter.gff3.GFF3Adapter.getCurationSet(GFF3Adapter.java:143)

        at apollo.dataadapter.gff3.GFF3AdapterGUI.doOperation(GFF3AdapterGUI.java:198)

        at org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:361)

        at apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:750)

        at org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)

        at java.lang.Thread.run(Unknown Source)

Apollo will not start if the Apollo.vmoptions file is in the root directory, so I cant try to adjust the Java memory size.  Changing the memory size in the Apollo.conf file seems to have no effect.  The same thing happens on my Win 7 64 machine.  The XP machine has 4gb (3.25gb usable) and the Win 7 machine has 16gb so I dont think its actually running out of memory.  Is this standard behavior? Wed love to use Apollo in our labs annotation effort but the most of our reference sequences are at least 15mb.  Any suggestions?

Thanks,

Ed

Virgil Ed Johnson

Scientific Computing Professional Principle

Tsai Laboratory

Warnell School of Forestry

University of Georgia

706-542-4743

 

__________ Information from ESET NOD32 Antivirus, version of virus signature database 5324 (20100729) __________

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Re: Out of memory error

Ed Lee
Hi Ed,

Windows always end up being the tricky OS to get cross platform
applications running.  Perhaps you can edit the apollo.vmoptions
file but make the following modifications:

1) Merge both lines into one.  So instead of having something like:

-Xms80m
  -Xmx1000m

you can try:

-Xms80m -Xmx1000m

2) Change the -Xmx value to something sensible for your machine
(usually half of the available memory is a good start).  The installer
tries to set a reasonable value for the memory but it sometimes
seems to mess up in Windows.

If those two suggestions don't work, we'll have to setup a batch file
for Windows to launch Apollo (so that it can make use of the
memory configuration option),

Cheers,
Ed

On Thu, 29 Jul 2010, Ed Johnson wrote:

>
> I can get Apollo to load a 14mb fasta file with GFF annotation on Win XP
> Pro, but it dies when I try to load a 23mb fasta file.  The error log shows
> ;
>
> Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space
>
>         at java.util.Arrays.copyOf(Unknown Source)
>
>         at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
>
>         at java.lang.AbstractStringBuilder.append(Unknown Source)
>
>         at java.lang.StringBuffer.append(Unknown Source)
>
>         at apollo.seq.io.FastaFile.parse(FastaFile.java:180)
>
>         at apollo.seq.io.FastaFile.processReader(FastaFile.java:60)
>
>         at apollo.seq.io.FastaFile.<init>(FastaFile.java:71)
>
>         at
> apollo.dataadapter.gff3.GFF3Adapter.parseSeq(GFF3Adapter.java:408)
>
>         at
> apollo.dataadapter.gff3.GFF3Adapter.parseSeq(GFF3Adapter.java:422)
>
>         at
> apollo.dataadapter.gff3.GFF3Adapter.getCurationSet(GFF3Adapter.java:143)
>
>         atapollo.dataadapter.gff3.GFF3AdapterGUI.doOperation(GFF3AdapterGUI.java:198)
>
>         atorg.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapter
> Chooser.java:361)
>
>         at
> apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:750)
>
>         atorg.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChoo
> ser.java:136)
>
>         at java.lang.Thread.run(Unknown Source)
>
> Apollo will not start if the Apollo.vmoptions file is in the root directory,
> so I can’t try to adjust the Java memory size.  Changing the memory size in
> the Apollo.conf file seems to have no effect.  The same thing happens on my
> Win 7 64 machine.  The XP machine has 4gb (3.25gb usable) and the Win 7
> machine has 16gb so I don’t think its actually running out of memory.  Is
> this standard behavior? We’d love to use Apollo in our lab’s annotation
> effort but the most of our reference sequences are at least 15mb.  Any
> suggestions?
>
> Thanks,
>
> Ed
>
> Virgil Ed Johnson
>
> Scientific Computing Professional Principle
>
> Tsai Laboratory
>
> Warnell School of Forestry
>
> University of Georgia
>
> 706-542-4743
>
>  
>
> __________ Information from ESET NOD32 Antivirus, version of virus signature
> database 5324 (20100729) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>  
>
>
>
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