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

[Brent Pedersen]

On Sat, Jan 16, 2010 at 7:07 AM, Gordon Gremme <gremme at gmail.com> wrote:
> Hi Brent,
>
> libgenometools is not thread-safe yet.
> So, currently you shouldn't do such things.
>
> Gordon
>


ok. thanks.
obviously (now), this is why i have intermittent trouble running code
using gtpython.
-brent


>
> 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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