Memory allocation for Java Webstart Application

I'm using a Java webstart application called BLAST2GO I'm running into problems with memory allocation. It needs to load a large data set into memory, so I've been trying to allocate 3-6GB to this application. However, no matter what I set as the max heap size, it always uses 455MB (as indicated by the message bar: 'Memory usage: xxMB of 455MB'). I've tried setting it to very reasonable levels (1024 MB), but still only 455MB are allocation.

Any ideas?

BTW, I'm using Ubuntu 10.04 32-bit with 24GB memory, 8 procs.

Update: Here is the JNLP they provide. I get the same result when I edit the values of the initial-heap-size and max-heap-size attributes.

<jnlp spec="1.0+" codebase="http://bioinfo.cipf.es/blast2go/webstart" href="http://bioinfo.cipf.es/blast2go/webstart/makeJnlp.php?mem=3072">
<information>
<title>Blast2GO 3072M</title>
<vendor>CIPF - UPV - IVIA</vendor>
<homepage href="http://www.blast2go.org"/>
<description>Blast2GO 3072M</description>
<description kind="short">Blast2GO 3072M</description>
<icon href="splash.gif"/>
<offline-allowed/>
</information>
<security>
<all-permissions/>
</security>
<resources>
<j2se version="1.5+" initial-heap-size="64m" max-heap-size="3072M"/>
<jar href="ext/blast2go.jar"/>
<jar href="ext/biojava-1.3.1.jar"/>
<jar href="ext/jfreechart-1.0.10.jar"/>
<jar href="ext/mysql-connector-java-3.0.11-stable-bin.jar"/>
<jar href="ext/zvtm.jar"/>
<jar href="ext/jakarta-regexp-1.4.jar"/>
<jar href="ext/jcommon-1.0.13.jar"/>
<jar href="ext/Simpat1.1.jar"/>
<jar href="ext/iText-2.1.1.jar"/>
<jar href="ext/jdom/activation.jar"/>
<jar href="ext/jdom/ant.jar"/>
<jar href="ext/jdom/jaxen-core.jar"/>
<jar href="ext/jdom/jaxen-jdom.jar"/>
<jar href="ext/jdom/jdom.jar"/>
<jar href="ext/jdom/mail.jar"/>
<jar href="ext/jdom/saxpath.jar"/>
<jar href="ext/jdom/xalan.jar"/>
<jar href="ext/jdom/xerces.jar"/>
<jar href="ext/jdom/xml-apis.jar"/>
<jar href="ext/interpro/commons-cli-1.0.jar"/>
<jar href="ext/interpro/commons-cli.jar"/>
<jar href="ext/interpro/freefluo.jar"/>
<jar href="ext/interpro/servlet.jar"/>
<jar href="ext/interpro/WSInterProScan.jar"/>
<jar href="ext/axis_1_4/axis-ant.开发者_运维百科jar"/>
<jar href="ext/axis_1_4/axis.jar"/>
<jar href="ext/axis_1_4/commons-discovery-0.2.jar"/>
<jar href="ext/axis_1_4/commons-logging-1.0.4.jar"/>
<jar href="ext/axis_1_4/jaxrpc.jar"/>
<jar href="ext/axis_1_4/keggapi.jar"/>
<jar href="ext/axis_1_4/log4j-1.2.8.jar"/>
<jar href="ext/axis_1_4/saaj.jar"/>
<jar href="ext/axis_1_4/wsdl4j-1.5.1.jar"/>
<jar href="ext/axis2/activation-1.1.jar"/>
<jar href="ext/axis2/annogen-0.1.0.jar"/>
<jar href="ext/axis2/axiom-api-1.2.2.jar"/>
<jar href="ext/axis2/axiom-dom-1.2.2.jar"/>
<jar href="ext/axis2/axiom-impl-1.2.2.jar"/>
<jar href="ext/axis2/axis2-adb-1.1.1.jar"/>
<jar href="ext/axis2/axis2-adb-codegen-1.1.1.jar"/>
<jar href="ext/axis2/axis2-codegen-1.1.1.jar"/>
<jar href="ext/axis2/axis2-java2wsdl-1.1.1.jar"/>
<jar href="ext/axis2/axis2-jaxbri-1.1.1.jar"/>
<jar href="ext/axis2/axis2-jibx-1.1.1.jar"/>
<jar href="ext/axis2/axis2-kernel-1.1.1.jar"/>
<jar href="ext/axis2/axis2-saaj-1.1.1.jar"/>
<jar href="ext/axis2/axis2-soapmonitor-1.1.1.jar"/>
<jar href="ext/axis2/axis2-spring-1.1.1.jar"/>
<jar href="ext/axis2/axis2-tools-1.1.1.jar"/>
<jar href="ext/axis2/axis2-xmlbeans-1.1.1.jar"/>
<jar href="ext/axis2/backport-util-concurrent-2.2.jar"/>
<jar href="ext/axis2/commons-codec-1.3.jar"/>
<jar href="ext/axis2/commons-fileupload-1.1.1.jar"/>
<jar href="ext/axis2/commons-httpclient-3.0.1.jar"/>
<jar href="ext/axis2/commons-io-1.2.jar"/>
<jar href="ext/axis2/commons-logging-1.1.jar"/>
<jar href="ext/axis2/geronimo-spec-jms-1.1-rc4.jar"/>
<jar href="ext/axis2/jakarta-httpcore-4.0-alpha2.jar"/>
<jar href="ext/axis2/jaxb-api-2.0.2.jar"/>
<jar href="ext/axis2/jaxb-impl-2.0.2.jar"/>
<jar href="ext/axis2/jaxb-xjc-2.0.2.jar"/>
<jar href="ext/axis2/jaxen-1.1-beta-10.jar"/>
<jar href="ext/axis2/jibx-bind-1.1.3.jar"/>
<jar href="ext/axis2/jibx-run-1.1.3.jar"/>
<jar href="ext/axis2/mail-1.4.jar"/>
<jar href="ext/axis2/neethi-2.0.jar"/>
<jar href="ext/axis2/servletapi-2.3.jar"/>
<jar href="ext/axis2/stax-api-1.0.1.jar"/>
<jar href="ext/axis2/woden-1.0.0M6.jar"/>
<jar href="ext/axis2/wsdl4j-1.6.2.jar"/>
<jar href="ext/axis2/wstx-asl-3.2.0.jar"/>
<jar href="ext/axis2/xalan-2.7.0.jar"/>
<jar href="ext/axis2/xbean-2.2.0.jar"/>
<jar href="ext/axis2/xercesImpl-2.8.1.jar"/>
<jar href="ext/axis2/xml-apis-1.3.03.jar"/>
<jar href="ext/axis2/XmlSchema-1.2.jar"/>
<jar href="ext/batik/batik-anim.jar"/>
<jar href="ext/batik/batik-awt-util.jar"/>
<jar href="ext/batik/batik-bridge.jar"/>
<jar href="ext/batik/batik-codec.jar"/>
<jar href="ext/batik/batik-css.jar"/>
<jar href="ext/batik/batik-dom.jar"/>
<jar href="ext/batik/batik-extension.jar"/>
<jar href="ext/batik/batik-ext.jar"/>
<jar href="ext/batik/batik-gui-util.jar"/>
<jar href="ext/batik/batik-gvt.jar"/>
<jar href="ext/batik/batik-parser.jar"/>
<jar href="ext/batik/batik-script.jar"/>
<jar href="ext/batik/batik-svg-dom.jar"/>
<jar href="ext/batik/batik-svggen.jar"/>
<jar href="ext/batik/batik-swing.jar"/>
<jar href="ext/batik/batik-transcoder.jar"/>
<jar href="ext/batik/batik-util.jar"/>
<jar href="ext/batik/batik-xml.jar"/>
<jar href="ext/batik/js.jar"/>
<jar href="ext/batik/pdf-transcoder.jar"/>
<jar href="ext/batik/xalan-2.6.0.jar"/>
<jar href="ext/batik/xerces_2_5_0.jar"/>
<jar href="ext/batik/xml-apis-ext.jar"/>
<jar href="ext/batik/xml-apis.jar"/>
</resources>
<application-desc main-class="es.blast2go.prog.MainProg"/>
</jnlp>

Update: I tried changing the href attribute in the root jnlp tag and I got a very strange message on the terminal. I wonder if Java is re-downloading the JNLP from this URL each time and ignoring my attempts to edit the JNLP. Is there a way I can prevent this?

> javaws blast2go3GB.jnlp 
Error occurred during initialization of VM
CCoouulldd  nnoott  crreesaetrev et heen oJuagvha  svpiarcteu aflo rm aocbhjiencet. 
heap

Final Update: Turns out this was a problem with the Java Version. I got the expected behavior when I downloaded and used Sun Java.

You can specify the heap size in the j2se tag like this:

    <resources>
    .........
            <j2se version="1.6.0+" href="" initial-heap-size="1024m" max-heap-size="3000m" />
            <j2se version="1.5.0_05" href="" initial-heap-size="1024m" max-heap-size="3000m" />
            <j2se version="1.4.2_04" href="" initial-heap-size="1024m" max-heap-size="3000m" />        
    .........
    </resources>

And specify every jre version you would use.

If you are running a 32-bit Linux, you can only run a 32-bit JVM which is limited to about 4 Gb memory per instance. I believe this is also the case even if you have more visible to the kernel.

If you really, really need a lot of memory in a single JVM you need to go 64-bit.

EDIT: Java WebStart was not open sourced for OpenJDK so an alternative implementation is used. Try to download and use Sun Java for this instead. It should be enough to download and unzip the JDK, and run bin/javaws foo.jnlp.

Try to set it by using a manual command line parameter. Something like this:

<j2se version="1.6+" java-vm-args="-Xms3072m"/>

You can change it simply via command line option, e.g.

javaws -J-Xmx16384m -J-Xms16384m <jnlp url>

Did you try the solution from the blast2go start page?

"Blast2GO needs more memory? Use the dynamic memory JNLP URL:"

http://bioinfo.cipf.es/blast2go/webstart/makeJnlp.php?mem=<put here the amount of memory you need>

It is not clear what is going on here, but I think it is likely that blast2go is doing some manual memory management tricks. (The fact that it claims to report how much memory is used is indicative of this.) If that is the case, then there may be application specific arguments or properties that need to be set if you tweak the JNLP file.

In the production, if the customer want to customize the java heap size in jnlp based on the system configuration available ( RAM size on the client machine)

Changes in the APPLICATION_TEMPLATE.JNLP: use * to accept the configurable values

Changes in the appliation.jnlp :

Pass the actual values to intial-heap-size and max-heap-size. jnlp file supports the scriptlets and expressions.

• Using scriptlet <% %> read the properties file for the configured values
• Pass the <%=> expression pointing the actual values to intial-heap-size and max-heap-size