Sorry, I sent this earlier and then I read that attaching a file can cause spam problems. So here is my netbeans.conf file inline showing 1024 Mg ram to be used for heap size: # ${HOME} will be replaced by JVM user.home system property # netbeans_default_userdir="${HOME}/.netbeans/6.5" # Options used by NetBeans launcher by default, can be overridden by explicit # command line switches: netbeans_default_options="-J-Dorg.glassfish.v3.installRoot=\"C:\Program Files\glassfish-v3-prelude\" -J-Dcom.sun.aas.installRoot=\"C:\Program Files\glassfish-v2ur2\" -J-client -J-Xverify:none -J-Xss2m -J-Xms32m -J-XX:PermSize=32m -J-XX:MaxPermSize=200m -J-Dapple.laf.useScreenMenuBar=true -J-Dsun.java2d.noddraw=true" # Note that a default -Xmx is selected for you automatically. # You can find this value in var/log/messages.log file in your userdir. # The automatically selected value can be overridden by specifying -J-Xmx here # or on the command line. # command line switches netbeans_default_options="-J-Xms32m -J-Xmx1024m -J-XX:PermSize=32m -J-XX:MaxPermSize=96m -J-Xverify:none -J-Dapple.laf.useScreenMenuBar=true -J-XX:+UseConcMarkSweepGC -J-XX:+CMSClassUnloadingEnabled -J-XX:+CMSPermGenSweepingEnabled -J-XX:+UseParNewGC" # If you specify the heap size (-Xmx) explicitely, you may also want to enable # Concurrent Mark & Sweep garbage collector. In such case add the following # options to the netbeans_default_options: # -J-XX:+UseConcMarkSweepGC -J-XX:+CMSClassUnloadingEnabled -J-XX:+CMSPermGenSweepingEnabled # -J-XX:+UseParNewGC # (see http://wiki.netbeans.org/wiki/view/FaqGCPauses) # Default location of JDK, can be overridden by using --jdkhome <dir>: netbeans_jdkhome="C:\Program Files\Java\jdk1.6.0_06" # Additional module clusters, using ${path.separator} (';' on Windows or ':' on Unix): #netbeans_extraclusters="/absolute/path/to/cluster1:/absolute/path/to/cluster2" # If you have some problems with detect of proxy settings, you may want to enable # detect the proxy settings provided by JDK5 or higher. # In such case add -J-Djava.net.useSystemProxies=true to the netbeans_default_options.
--- On Wed, 3/11/09, Paul B <tallpaulin...@yahoo.com> wrote: From: Paul B <tallpaulin...@yahoo.com> Subject: Out of heap space during structure parsing. To: biojav...@biojava.org Date: Wednesday, March 11, 2009, 8:51 AM Hi, I am using BioJava 1.6.1 to parse PDB files. My machine has 2GB of RAM. I am using Netbeans 6.5 as my development environment with Java 1.6. My user-specific netbeans.conf file is attached, with a heap space of 1GB. The relevant BioJava code is below: try { pdbreader = new PDBFileReader(); pdbreader.setPath(localFilePath); pdbreader.setAutoFetch(true); struc = pdbreader.getStructureById(pdbCode); ... Using this code, I had successfully parsed smaller PDB files like 2BEG and 1Q80. Then I tried to parse a slightly larger file 1FFK and received this message on the 'struc =' line: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at org.biojava.bio.alignment.NeedlemanWunsch.pairwiseAlignment(NeedlemanWunsch.java:411) at org.biojava.bio.alignment.NeedlemanWunsch.getAlignment(NeedlemanWunsch.java:315) at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:220) at org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:140) at org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2249) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2155) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2013) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:439) at biojavatest.PdbDemo.grabPdbFileStruc(PdbDemo.java:105) at biojavatest.PdbDemo.runTest(PdbDemo.java:67) at biojavatest.PdbDemo.main(PdbDemo.java:58) Any suggestions? Is the problem specific to some deviation in 1FFK, or in BioJava's parser implementation? By the way, I am using BioJava simply as a parser, and I am then dumping the data into class objects of my own design and persisting them to a SQL Server database. As such, I don't need all the ATOM information held in memory. Perhaps there is a way to lazy load that information upon request? Is there a development version of BioJava that's downloadable and offers a more memory efficient way of grabbing data? Thanks, Paul _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l