Re: [base] Illumina Bead Summary importer
Thanks again Nicklas! About Configuration was only showing 128 available. I checked and apparently the default Tomcat service startup script that was installed by my Ubuntu distro wasn't reading CATALINA_OPTS and only reading the JAVA_OPTS variable which I hadn't set. Fixed and all good. Thanks again Thomas From: Nicklas Nordborg [nick...@thep.lu.se] Sent: Monday, February 14, 2011 1:37 AM To: BASE ML Subject: Re: [base] Illumina Bead Summary importer On 2011-02-11 23:23, Thomas Person wrote: Howdy all, I'm still having issues with the Illumina Plug in, When running the job the summary window gives: Bead Summary importer Executing: New raw bioassay -parsed 93094 lines in 2 files Preparing database for import... Then eventually crashes with OutOfMemoryErrror: Java heap space. I've tried upping Xmx up to 2gb under CATALINA_OPTS. and setting the Illumina Bead Summary importer plugin max memory to 1gb, but still no luck. Thanks in advance for your help, This seems strange. 2Gb should be more than enough. The memory setting on the plug-in is only used when running on a a job agent but even 1Gb should be enough. Our test data set is about the same size as your data set and when I made a test today the memory usage peeked at 300Mb. Please check the information in Help - About - Configuration to verify your memory settings. /Nicklas -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net UT Southwestern Medical Center The future of medicine, today. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Illumina Bead Summary importer
On 2011-02-11 23:23, Thomas Person wrote: Howdy all, I'm still having issues with the Illumina Plug in, When running the job the summary window gives: Bead Summary importer Executing: New raw bioassay -parsed 93094 lines in 2 files Preparing database for import... Then eventually crashes with OutOfMemoryErrror: Java heap space. I've tried upping Xmx up to 2gb under CATALINA_OPTS. and setting the Illumina Bead Summary importer plugin max memory to 1gb, but still no luck. Thanks in advance for your help, This seems strange. 2Gb should be more than enough. The memory setting on the plug-in is only used when running on a a job agent but even 1Gb should be enough. Our test data set is about the same size as your data set and when I made a test today the memory usage peeked at 300Mb. Please check the information in Help - About - Configuration to verify your memory settings. /Nicklas -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] Illumina Bead Summary importer
Howdy all, I'm still having issues with the Illumina Plug in, When running the job the summary window gives: Bead Summary importer Executing: New raw bioassay -parsed 93094 lines in 2 files Preparing database for import... Then eventually crashes with OutOfMemoryErrror: Java heap space. I've tried upping Xmx up to 2gb under CATALINA_OPTS. and setting the Illumina Bead Summary importer plugin max memory to 1gb, but still no luck. Thanks in advance for your help, Thomas The stack trace from catalina.out is: 12:40:20,315 ERROR jobqueue:366 - Exception while starting jobs java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:2734) at java.util.ArrayList.toArray(ArrayList.java:275) at java.util.ArrayList.addAll(ArrayList.java:472) at org.jaxen.expr.DefaultStep.evaluate(DefaultStep.java:164) at org.jaxen.expr.DefaultLocationPath.evaluate(DefaultLocationPath.java:140) at org.jaxen.expr.DefaultAbsoluteLocationPath.evaluate(DefaultAbsoluteLocationPath.java:113) at org.jaxen.expr.DefaultXPathExpr.asList(DefaultXPathExpr.java:102) at org.jaxen.BaseXPath.selectNodesForContext(BaseXPath.java:674) at org.jaxen.BaseXPath.selectNodes(BaseXPath.java:213) at org.jaxen.BaseXPath.selectSingleNode(BaseXPath.java:234) at org.jdom.xpath.JaxenXPath.selectSingleNode(JaxenXPath.java:153) at net.sf.basedb.core.PredefinedQuery.getQueryString(PredefinedQuery.java:150) at net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1660) at net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1646) at net.sf.basedb.core.InternalJobQueue.run(InternalJobQueue.java:309) at net.sf.basedb.util.timer.ThreadTimerTask$1.run(ThreadTimerTask.java:85) at java.lang.Thread.run(Thread.java:662) Exception in thread Timer-1 Feb 11, 2011 12:40:56 PM unknown unknown SEVERE: Exception invoking periodic operation: java.lang.OutOfMemoryError: Java heap space at java.lang.StringCoding$StringEncoder.encode(StringCoding.java:232) at java.lang.StringCoding.encode(StringCoding.java:272) at java.lang.String.getBytes(String.java:946) at java.io.UnixFileSystem.getBooleanAttributes0(Native Method) at java.io.UnixFileSystem.getBooleanAttributes(UnixFileSystem.java:228) at java.io.File.exists(File.java:733) at org.apache.catalina.startup.HostConfig.checkResources(HostConfig.java:1113) at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1342) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:303) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119) at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1337) at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1601) at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1610) at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1590) at java.lang.Thread.run(Thread.java:662) 12:41:22,716 WARN DbControl:1147 - Found unclosed DbControl during finalize; isLoggedIn = true; clientId = 5; userId = 1 java.lang.Throwable: Please check the code to make sure that DbControl.close() is always called. Stacktrace of code that created this DbControl: at net.sf.basedb.core.DbControl.init(DbControl.java:156) at net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:320) at org.apache.jsp.views.jobs.ajax_jsp._jspService(ajax_jsp.java:75) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:377) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at
