[Biopython-dev] Benchmarking PDBParser

[Peter Cock]

On Fri, May 6, 2011 at 8:45 AM, João Rodrigues <anaryin at gmail.com> wrote:
> Hello all,
>
> I'd love to come with results but I ran into some problems. The parser is
> consuming too much memory after a while (>2GB) and I can't get reliable
> timings then because of swapping.. Therefore, I'll just take a random sample
> of 8000 structures and use it as a benchmark.

Memory bloat is bad - it sounds like a garbage collection problem.
Are you recreating the parser object each time?

> I'll post the results today, shall I put it up on the wiki? This could be an
> interesting thing to post for both users and future developments.

I'd like to see the script and the results, so maybe the wiki is better.

Peter