[gt-users] gt python with (multi)processing

[Gordon Gremme]

Hi Brent,

libgenometools is not thread-safe yet.
So, currently you shouldn't do such things.

Gordon


On Fri, Jan 15, 2010 at 10:07 PM, Brent Pedersen <bpederse at gmail.com> wrote:
> hi, multiprocessing is in the python stdlib as of 2.6:
> http://docs.python.org/dev/library/multiprocessing.html
>
> i am unable to use it to parallelize stuff when working with gt python
> because i see segfaults when using multiprocessing
> with FeatureIndexMemory.
> the script below segfaults on my machine. i add the gff3 file twice as
> sometimes the segfault does not occur for that file (which
> is included with genome tools).
>
> so, i guess this is a bug report, unless it's known that i shouldn't
> do such things.
> -brent
>
> =========================
>
> #import multiprocessing as processing
> import processing
> import gt
> p = processing.Pool(4)
>
> f = gt.FeatureIndexMemory()
> f.add_gff3file('./testdata/encode_known_genes_Mar07.gff3')
> f.add_gff3file('./testdata/encode_known_genes_Mar07.gff3')
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