[gpaw-users] MPI-Scalapack library for Python

[Peter Koval]

I think scipy could be more tolerant to mpi calls than numpy.

El 21 sept. 2017 4:28 PM, "marc" <marc.barbry at mailoo.org> escribió:

> 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
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>>>> gpaw-users at listserv.fysik.dtu.dk
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>>>>
>>>>
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>>
>
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