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(JspServletWrapper.java:137)
...at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java: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(ApplicationFilterChain.java:269)
...at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
...at 
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
...at 
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
...at 
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
...at 
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
...at 
org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:686)
...at 
org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:656)
...at 
org.apache.jsp.views.hybridizations.index_jsp._jspService(index_jsp.java: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.java: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(ApplicationFilterChain.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]

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