[BioPython] Is BioPython thread safe?

[Mike Cariaso]

I only use biopython occasionally, but have been
through similar issues with perl, and will share what
I can.

I think the lack of responses indicates that no one
can say authoritatively, since there are so many
developers. Presumably some parts of biopython are 
threadsafe, but that may be more a matter of luck than
of design. 

Doing threadsafe signals is considerably more complex
than non-threadsafe. If you don't see a lot of code
gymnastics and comments about threads, any library
using signals for is very unlikely to be threadsafe.

if you need biopython and threads, you'll probably
have to wrap all biopython code behind a single
semaphore, and prevent concurrent access. Depending on
what you're doing this may serialize all your code, or
only a portion. Manually inspect the most crucial
biopython components and see if you can use multiple
semaphors, perhaps one for pieces which use signals,
and another for components which read/write class
variables. Gradually keep decreasing the granularity
of the semaphors. Also look for places where signals
are used only as timeouts, and replace these with
another thread.

Its probably going to be real painful.



--- Brandon King <kingb at caltech.edu> wrote:

> Hello All,
>     Did I not give enough information about the
> problem? Any one have 
> any suggestions or ideas?
> 
> -Brandon King
> 
> Brandon King wrote:
> 
> > Hi All,
> >    I'm trying to use BioPython within a thread of
> my main program and 
> > I end up getting this error. Is BioPython intended
> to be thread safe?
> >
> > TraceBack:
> > <snip>
> >    from Bio.Blast import NCBIStandalone
> >  File
> "/usr/lib/python2.3/site-packages/Bio/__init__.py",
> line 106, in ?
> >    _load_registries()
> >  File
> "/usr/lib/python2.3/site-packages/Bio/__init__.py",
> line 98, in 
> > _load_registries
> >    module = __import__("Bio.config.%s" % module,
> {}, {}, 
> > ["Bio","config"])
> >  File
>
"/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py",
> 
> > line 26, in ?
> >    import _support
> >  File
>
"/usr/lib/python2.3/site-packages/Bio/config/_support.py",
> line 
> > 26, in ?
> >    from Bio.MultiProc.copen import copen_fn
> >  File
>
"/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py",
> line 
> > 322, in ?    signal.signal(signal.SIGTERM,
> _handle_sigterm)
> > ValueError: signal only works in main thread
> >
> > -Brandon King
> >
> > _______________________________________________
> > BioPython mailing list  -  BioPython at biopython.org
> > http://biopython.org/mailman/listinfo/biopython
> >
> >
> 
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> http://biopython.org/mailman/listinfo/biopython
> 


=====
Mike Cariaso