Hi Bob, I seem to remember having the same problem with another webapp under Tomcat some time ago. Have a look at http://wiki.apache.org/tomcat/OutOfMemory. There it says:
"A webapp that uses lots of libraries with many dependencies, or a server maintaining lots of webapps could exhauste the JVM PermGen space. This space is where the VM stores the classes and methods data. In those cases, the fix is to increase this size. The Sun VM has the flag -XX:MaxPermSize that allows to set its size (the default value is 64M)" >From what I remember I added that flag into the Tomcat startup script and that sorted it. Give it a try. Setting the max heap size with -Xmax is not enough anyway. Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer ================================== > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Bob MacCallum > Sent: 16 April 2008 14:17 > To: BASE ML > Subject: [base] PermGen space error > > > Hello, > > Is anyone else getting "PermGen space" memory errors after doing a lot > of GUI > clicking (e.g. creating biomaterials)? I've seen this a few times now > (no > particular click causes it as far as I can tell). Once it happens I > have to > restart tomcat. > > Any ideas how I can help track down the problem (the stack trace > doesn't look > very useful)? > > Note that I built the binary package on a different machine (see 2. > below). > It looks like upgrading Java on the dev/build machine is a good idea > (it is a few minor versions behind the production server). > I don't think I've had this memory problem on the dev server, but I > have also > clicked around on it much less. > > cheers, > Bob. > > > 1. Copy-paste of error message: > > > Version BASE 2.6.2pre (build #4204; schema #52) > Web server Apache Tomcat/5.5.26 > Database Server MySQL 5.0.51a > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect > JDBC Driver com.mysql.jdbc.Driver (version 5.0) > Java runtime Java(TM) SE Runtime Environment (1.6.0_04-b12), Sun > Microsystems Inc. > Operating system Linux amd64 2.6.18-53.1.4.el5 > Memory Total: 751.4 MB > Free: 670.5 MB > Max: 910.3 MB > Browser Mozilla/5.0 (Macintosh; U; Intel Mac OS X; en-US; > rv:1.8.1.13) Gecko/20080311 Firefox/2.0.0.13 > Error message PermGen space > Stack trace > > java.lang.OutOfMemoryError > ...at java.lang.ClassLoader.defineClass1(Native Method) > ...at java.lang.ClassLoader.defineClass(ClassLoader.java:620) > ...at > java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124) > ...at java.net.URLClassLoader.defineClass(URLClassLoader.java:260) > ...at java.net.URLClassLoader.access$000(URLClassLoader.java:56) > ...at java.net.URLClassLoader$1.run(URLClassLoader.java:195) > ...at java.security.AccessController.doPrivileged(Native Method) > ...at java.net.URLClassLoader.findClass(URLClassLoader.java:188) > > ...at > org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:131) > ...at > org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:63) > ...at > org.apache.jasper.JspCompilationContext.load(JspCompilationContext.java > :597) > ...at > org.apache.jasper.servlet.JspServletWrapper.getServlet(JspServletWrappe > r.java:137) > ...at > org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.j > ava:314) > ...at > org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329 > ) > ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) > ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) > ...at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic > ationFilterChain.java:269) > ...at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil > terChain.java:188) > ...at > org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispat > cher.java:679) > ...at > org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicati > onDispatcher.java:461) > ...at > org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDis > patcher.java:399) > ...at > org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispa > tcher.java:301) > ...at > org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.jav > a:686) > ...at > org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java: > 656) > ...at > org.apache.jsp.views.hybridizations.index_jsp._jspService(index_jsp.jav > a:375) > ...at > org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) > ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) > ...at > org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.j > ava:331) > ...at > org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329 > ) > ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) > ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) > ...at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic > ationFilterChain.java:269) > > > > 2. system config of dev server (on which binary package was built) > > > Version BASE 2.6.2pre (build #4204; schema #52) > Web server Apache Tomcat/5.5.20 > Database Server MySQL 5.0.21-max-log > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect > JDBC Driver com.mysql.jdbc.Driver (version 5.0) > Java runtime Java(TM) SE Runtime Environment (1.6.0-b105), Sun > Microsystems Inc. > Operating system Linux amd64 2.6.16.54-0.2.5-smp > Memory Total: 108.4 MB > Free: 22.6 MB > Max: 910.3 MB > > > > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > ----------------------------------------------------------------------- > -- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. 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