[Biojava-l] performance problems with BJX

[Mark Schreiber]

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 <gabrielle_doan at gmx.net> 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
>
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