Object relational mapping can be memory hungry but this does seem expensive. Probably the easiest way to track the problem is to run a memory profiler (such as the one in Netbeans) and see if there is either some very large object or a proliferation of thousands of small objects which would point to a memory leak.
Best regards, - Mark On Tue, Nov 4, 2008 at 4:29 PM, Gabrielle Doan <[EMAIL PROTECTED]> wrote: > > Dear all, > I have some perfomance problems with BioJavaX. > > I wanted to add the human chromosome 1 into my MySQL database with the build > in method addRichSequence from the > org.biojavax.bio.db.biosql.BioSQLRichSequenceDB and was wondered why this > method waste so much memory. I started my program with -Xmx8G but I got a > Java heap space messseage on my console. So I used -Xmx15G to insert the > chromsome (range between 8G and 15G not tested). > > I wonder why a genbank file of about 300 MB needs about 15G memory to be > added into the database. > > Does anybody has the same problem or can give me any advice? > > Cheers, Gabrielle > > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
