[gpaw-users] MPI-Scalapack library for Python

Thu Sep 21 18:32:43 CEST 2017

Yes, I agree. I share Marc 's view.

El 21 sept. 2017 18:00, "marc" <marc.barbry at mailoo.org> escribió:

> I think for starting we should implement an external library for
> Scalapack. But ultimately, I believe that it would be nice for the
> community if this functions are available directly through Scipy, as the
> BLAS and LAPACK wrapper are already implemented there. Then, since they are
> already implemented, I don't think it is useful to pack BLAS and LAPACK.
>
> I'm not a GPAW developer, but you could replace the call to BLAS and
> LAPACK in GPAW by the scipy wrapper instead of your one. We are doing it in
> our own code and the functions are as fast than C/Fortran implementation
> (almost all blas routine are implemented, not so sure for lapack),
>
> Simple code like this one can be use,
>
> import scipy.linalg.blas as blas
>
> C = blas.gemm(1.0, A, B)
>
> Concerning the MPI wrapper, as Ask already commented, we should use the
> mpi4py library, then only Scalapack routines need to be implemented.
>
> Marc
>
> On 09/21/2017 05:42 PM, Kuisma, Mikael wrote:
>
> Hi!
>
> There is one question which needs to be figured out. As Ask, I believe that
> "It would be very useful to have a well-designed stack of Python binding
> for BLAS, LAPACK, MPI, and ScaLAPACK." It could even allow new novel
> parallelization methods and algorithms as they become available (say for
> efficient diagonalization). Such a library would in general be quite good
> to the community even outside DFT.
>
> The question is, however, how hard would it be to restructure GPAW to use
> that library? Although, the general library would be nice, writing it
> should make a useful contribution to GPAW implementation too. What do other
> GPAW developers think on the tediousness compared to usefullness of
> packaking BLAS, LAPACK, MPI, and ScaLAPACK to one independent package?
>
> Regarding scipy. Why scipy, why not just an external Python library with
> c-bindings?
>
> Mikael
>
> ------------------------------
> *Lähettäjä:* gpaw-users-bounces at listserv.fysik.dtu.dk [
> gpaw-users-bounces at listserv.fysik.dtu.dk] käyttäjän Peter Koval via
> gpaw-users [gpaw-users at listserv.fysik.dtu.dk] puolesta
> *Lähetetty:* 21. syyskuuta 2017 17:51
> *Vastaanottaja:* marc Barbry
> *Kopio:* gpaw-users at listserv.fysik.dtu.dk
> *Aihe:* Re: [gpaw-users] MPI-Scalapack library for Python
>
> 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
>>>>> _______________________________________________
>>>>> gpaw-users mailing list
>>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>>
>>>>>
>>>>> _______________________________________________
>>>> gpaw-users mailing list
>>>> gpaw-users at listserv.fysik.dtu.dk
>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20170921/f3f557c4/attachment.html>