On Feb 22, 2010, at 5:37 PM, Kenny Daily wrote:
> from pygr import worldbase
> all_resources = worldbase.dir("Bio.Test.Annotation")
> dbs = filter(lambda x: x.endswith("db"), all_resources)
>
> for x in dbs:
> resource = worldbase(x)
> resource.close()
>
> This uses ~50-100MB per resource loaded, and it accumulates. In my
> case, the AnnotationDB's sliceDB is a MySQL table. Any ideas about
> where the memory could be going?
Our XMLRPC server loads all the AnnotationDB that it serves (must be at least
100 - 200) with little memory usage, so this horrible memory usage should
absolutely not be happening to you. If you tested this with beta1 code, please
re-run your example with an official release i.e. 0.8.0 or 0.8.1. I suspect
that this may solve your problem -- as I recall we discovered a nasty bug in
MySQLdb that uses up massive amounts of memory when you simply ask for an
iterator. Starting with 0.8.0 we included a workaround to avoid that problem.
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