Hi Matthew, 2gb seems an awful lot of memory to allocate, and I had a case some time ago when I was getting OutOfMemoryErrors that wouldn't go away when I allocated more and more. I then found some references on the web that suggested that in fact allocating too much memory itself can lead to OutOfMemoryErrors, paradoxically.
Check out for example this one: http://confluence.atlassian.com/display/DOC/Fix+'Out+of+Memory'+errors+b y+increasing+available+memory There are more out there on Google, you need to dig a bit. Try reducing your heap size to a gig or perhaps half a gig and see what happens. Check in the tomcat manager interface that it's actually picking up the values you are feeding it. 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 Matthew Lange > Sent: 03 December 2007 22:16 > To: basedb-users@lists.sourceforge.net > Cc: 'Joseph Fass'; [EMAIL PROTECTED] > Subject: [base] Java memory error > > I am using the latest Base, and trying to load an initial data set. My > initial effort was to modify the reporter importer to load some affy > probes from a csv file. This worked fine for a small list, but as the > list approached >500 individuals, I started receiving out of memory > errors from the Java Heap...and even brought Tomcat to its knees on a > couple of occassions. As a workaround, I uploaded the an 80ish MB CDF > file from Affy, which contains the array design. This went in fine. > Then I tried to use the feature that allows me to import reporters from > the CDF file--again Java OOM errors, and tomcat whining. > > We have given Tomcat 2GB to play with, and this seems like it should be > more than enough. Are there known issues with this utility that I > should be aware of, or is there a rule-of-thumb to follow when > allocating memory to tomcat, based on the size of files that need to be > parsed? Or maybe another memory setting somewhere that I must have > overlooked? > > I will be happy to post more specific error messages if that will help > the troubleshooting process. > > Thanks in advance for any suggestions. > > Kind Regards, > > matthew _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
