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SciLifeLab / facs

Fast and Accurate Classification of Sequences using Bloom filters
http://facs.scilifelab.se/
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Memory benchmarking #105

Closed guillermo-carrasco closed 10 years ago

guillermo-carrasco commented 10 years ago

Would be nice to have also some numbers on memory usage.

brainstorm commented 10 years ago

http://fa.bianp.net/blog/2013/different-ways-to-get-memory-consumption-or-lessons-learned-from-memory_profiler/

guillermo-carrasco commented 10 years ago

Great post @brainstorm , thank you :-)

guillermo-carrasco commented 10 years ago

It is quite difficult to perform memory benchmarks for processes that create threads or that call subprocesses that create threads, which would be our case, with the test function calling FACS/fastq_screen.

I've been trying out memory_profiler and others, but they all have the same problem with subprocesses. I sent an email to Fabian Pedregosa, author of memory_profiler, and he is willing to help. I'll keep you posted.

guillermo-carrasco commented 10 years ago

I was mailing with Fabian, but I though that is better to make this discussion public, other people may be interested on this. You can follow-up the public issue that I just created here.

guillermo-carrasco commented 10 years ago

We have a fix guys, let's benchmark!