[gpaw-users] MPI-Scalapack library for Python

[marc]

 From my experience, scipy has a good parallelization through Blas 
routines if build against the right library (e.g. mkl). But this is only 
for shared memory parallelization and it can not be use with MPI. Scipy 
therefore is missing MPI capabilities that it could be nice to add.

On 09/21/2017 04:25 PM, Ask Hjorth Larsen wrote:
> It is worth noting that scipy calls a lot of BLAS functions, but I
> don't know how it works (maybe they actually have a complete
> interface?).
>
> 2017-09-21 16:16 GMT+02:00 Peter Koval via gpaw-users
> <gpaw-users at listserv.fysik.dtu.dk>:
>> Yes, I agree. Ultimately the lib or similar should be a pary of scipy.
>>
>> El 21 sept. 2017 2:50 PM, "marc" <marc.barbry at mailoo.org> escribió:
>>> Hi Mikael,
>>>
>>> nice to see that you are interested in writing a Scalapack wrapper. I
>>> think it is really missing in python.
>>> I found one, name scalapy. But it is not maintained anymore and the
>>> installation failed. We could try to write something similar using the code
>>> from GPAW.
>>>
>>> Best regards,
>>> Marc
>>>
>>> On 09/21/2017 01:42 PM, Kuisma, Mikael wrote:
>>>
>>> Hi!
>>>
>>> I added some Scalapack/blacs routines while implementing the LCAO-TDDFT
>>> for GPAW and it was somewhat cumbersome. Also, the API we have in GPAW is
>>> somewhat tedious to use at the moment: we have a lot of code to handle
>>> ScaLAPACK and LAPACK calls as different cases. So I would vote for writing a
>>> general Python-Scalapack library (instead that you take code from GPAW to
>>> your Python/C code).  We could make this library transparent, so it would
>>> work also without ScaLAPACK performing serial linear algebra..
>>>
>>> ScaPACK does not parallize as well as I would like it to parallelize.
>>> With a library wrapper, one could also try other libraries (for
>>> eigensolvers, there are at least more parallel solvers than ScaLAPACK).
>>>
>>> One more remark regarding GPAW: I always resist adding external libraries
>>> to GPAW, so if one does a python with c-bindings library, I think it would
>>> make sense to embed that Python and C-code directly to GPAW repository. The
>>> end users do not like install new dependencies every time the version number
>>> increases by 0.1. (I wish that we should also provide basic working
>>> installation of libxc and libvdwxc as well in our repository, with option to
>>> link to external libraries).
>>>
>>> I do not know about licencing issues that well, but as far as I think, it
>>> should be ok to take code from GPAW (GPL), if your code is also GPL and make
>>> your code available.
>>>
>>> BR,
>>> Mikael Kuisma
>>>
>>> Academy of Finland Post Doc
>>>
>>> Nanoscience Center
>>> Department of Chemistry
>>> University of Jyväskylä
>>> P.O. Box 35
>>> FIN-40014 University of Jyväskylä
>>> Finland
>>>
>>> E-mail: mikael.j.kuisma (at) jyu.fi
>>> Phone: +358 40 077 4114
>>>
>>> https://scholar.google.se/citations?user=w0eP9esAAAAJ
>>>
>>> Visiting address: NSC, 3rd floor, YN320
>>>
>>> ________________________________________
>>> Lähettäjä: gpaw-users-bounces at listserv.fysik.dtu.dk
>>> [gpaw-users-bounces at listserv.fysik.dtu.dk] k&#228;ytt&#228;j&#228;n marc via
>>> gpaw-users [gpaw-users at listserv.fysik.dtu.dk] puolesta
>>> Lähetetty: 21. syyskuuta 2017 14:10
>>> Vastaanottaja: gpaw-users at listserv.fysik.dtu.dk
>>> Kopio: Peter Koval
>>> Aihe: [gpaw-users] MPI-Scalapack library for Python
>>>
>>> Dear Gpaw developers,
>>>
>>> We are actually developing a python code to perform efficient TDDFT
>>> calculation with LCAO. Our program can read DFT data from different code
>>> such as Siesta, OpenMX, Pyscf and GPAW (with some limitations for the
>>> moment).
>>> We would like to parallelize our code using MPI and Scalapack but we
>>> could not find any library in python that wrap both MPI and Scalapack.
>>> Looking to the GPAW code, we have seen that you wrote your own wrapper
>>> for MPI-Saclapack. My question is the following, would it be difficult
>>> to modify your MPI wrapper to use it in our code? Is it feasible from a
>>> license point of view?
>>> Do you think it could be feasible to write a general python wrapper for
>>> MPI and Scalapack in an other library using your implementation?
>>>
>>> Best regards,
>>> Marc Barbry
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
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