[Cython] [psc.edu #16673] Fwd: [PETSC #19028] PETSc and Python

Mon Feb 16 16:55:22 CET 2009

Two separate issues here...

1) Regarding mpi4py, as it is based on the C API for MPI, it does not
have complex support natively. Of course, you could use

COMPLEX = MPI.DOUBLE.Create_contiguous(2)

and then the new 'COMPLEX' datatype will likely work for communicating
arrays with (double precision) complex entries.

1) Regarding petsc4py, the support for complex numbers is not ready
yet. The big issue is that Cython does not natively support them.
Rather than hacking petsc4py for complex support, I would prefer to
spend my time on hacking Cython to enable good complex support.
However, if there is a strong need for petsc4py+complex, I could work
on providing a patch to make it work.

Now a request to the Cython folks,

Could we create a branch 'cython-devel-complex' for start working on
good complex support?
This way I could push my preliminary work on this, all you can review
my progress, and other users can pull and build petsc4py with complex
support...

On Mon, Feb 16, 2009 at 1:17 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>
> Begin forwarded message:
>
> From: Wonseok Shin <wsshin at stanford.edu>
> Date: February 15, 2009 9:44:08 PM CST
> To: petsc-maint Maintenance <petsc-maint at mcs.anl.gov>
> Cc: petsc-maint at mcs.anl.gov
> Subject: Fwd: [psc.edu #16673] Fwd: [PETSC #19028] PETSc and Python
> Dear PETSc developers,
> I have received the following quoted email from the PETSc installer of
> BIgben, PSC.
> Is it true that mpi4py and petsc4py cannot be used with PETSc built for
> complex numbers?  Is there any workaround?
>
> Regards,
> Wonseok Shin
> Ph.D candidate
> Department of Electrical Engineering, Stanford University
> wsshin at stanford.edu
>
> Begin forwarded message:
>
> From: "Rick Costa via RT" <remarks at psc.edu>
> Date: February 15, 2009 8:22:21 AM PST
> To: wsshin at stanford.edu
> Subject: Re: [psc.edu #16673] Fwd: [PETSC #19028] PETSc and Python
> Reply-To: remarks at psc.edu
>
>
> ---------- Forwarded message ----------
> Date: Fri, 13 Feb 2009 01:50:27 -0500
> From: David O'Neal <oneal at psc.edu>
> To: R.F. Costa <costa at psc.edu>
> Subject: Re: PETsc additions
>
> Hi Rick.
>
> I've run into a problem with the build requested by the user. Support for
> Python
> features is incompatible with the complex data type...
>
> *********************************************************************************
>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
> details):
> -----------------------------------------------------------------------------------
> Cannot use mpi4py with complex numbers it is not coded for this capability
> *********************************************************************************
>
> At 08:21 AM 2/10/2009 -0500, you wrote:
>
> Dave
>
> Is it possible to make these additions to PETSc? Have you had a chance
>
> to install the bug fix to PETSc? Thanks.
>
> Rick
>
> ---------- Forwarded message ----------
>
> Date: Tue, 10 Feb 2009 07:58:55 -0500 (EST)
>
> From: Wonseok Shin via RT <remarks at psc.edu>
>
> Subject: [psc.edu #16673] Fwd: [PETSC #19028] PETSc and Python
>
> Tue Feb 10 07:58:55 2009: Request 16673 was acted upon.
>
> Transaction: Ticket created by wsshin at stanford.edu
>
>      Queue: Remarks
>
>    Subject: Fwd: [PETSC #19028] PETSc and Python
>
>      Owner: Nobody
>
> Requestors: wsshin at stanford.edu
>
>     Status: new
>
> Ticket <URL: https://tickets.psc.edu/Ticket/Display.html?id=16673 >
>
>
>
> Dear Rick,
>
> I am Wonseok Shin using bigben.
>
> I would like to distribute input data to my PETSc program using
>
> Python.  I asked PETSc developers how to do that, and they sent me the
>
> email quoted below.
>
> Basically, the Python packages called mpi4py and petsc4py should be
>
> installed, and they said that this can be done by configuring PETSc
>
> with the options written in the quoted email.
>
> Is it possible to install mpi4py and petsc4py?  Could you forward this
>
> email to the PETSc or Python installer of bigben?
>
>
> Best regards,
>
> Wonseok Shin
>
> Ph.D candidate
>
> Department of Electrical Engineering, Stanford University
>
> wsshin at stanford.edu
>
>
>
> Begin forwarded message:
>
> From: Matthew Knepley <petsc-maint at mcs.anl.gov>
>
> Date: February 10, 2009 4:39:57 AM PST
>
> To: Wonseok Shin <wsshin at stanford.edu>
>
> Cc: petsc-maint Maintenance <petsc-maint at mcs.anl.gov>
>
> Subject: Re: [PETSC #19028] PETSc and Python
>
> Reply-To: petsc-maint at mcs.anl.gov
>
> You can use mpi4py and petsc4py. They both can be automatically
>
> installed by configure:
>
> --download-petsc4py --download-mpi4py
>
> They have a lot of documentation associated with them and examples.
>
>  Matt
>
> On Tue, Feb 10, 2009 at 5:42 AM, Wonseok Shin <wsshin at stanford.edu>
>
> wrote:
>
> Dear PETSc developers,
>
> I am interested in the interaction of PETSc and Python.  Is it
>
> possible to
>
> distribute data from Python to PETSc and vice versa?  I know how to
>
> do this
>
> for a single process, but don't know for multiple processes.
>
> If I need some Python MPI module, could you recommend a specific
>
> one that
>
> works well with PETSc?
>
>
> Best regards,
>
> Wonseok Shin
>
> Ph.D candidate
>
> Department of Electrical Engineering, Stanford University
>
> wsshin at stanford.edu
>
>
>
>
>
>
>
> --
>
> What most experimenters take for granted before they begin their
>
> experiments is infinitely more interesting than any results to which
>
> their experiments lead.
>
> -- Norbert Wiener
>
>
>
> Dear Rick,
>
> I am Wonseok Shin using bigben.
>
> I would like to distribute input data to my PETSc program using Python.  I
> asked PETSc developers how to do that, and they sent me the email quoted
> below.
>
> Basically, the Python packages called mpi4py and petsc4py should be
> installed, and they said that this can be done by configuring PETSc with the
> options written in the quoted email.
>
> Is it possible to install mpi4py and petsc4py?  Could you forward this email
> to the PETSc or Python installer of bigben?
>
>
> Best regards,
>
> Wonseok Shin
>
> Ph.D candidate
>
> Department of Electrical Engineering, Stanford University
>
> <mailto:wsshin at stanford.edu>wsshin at stanford.edu
>
>
>
> Begin forwarded message:
>
> From: Matthew Knepley
> <<mailto:petsc-maint at mcs.anl.gov>petsc-maint at mcs.anl.gov>
>
> Date: February 10, 2009 4:39:57 AM PST
>
> To: Wonseok Shin <<mailto:wsshin at stanford.edu>wsshin at stanford.edu>
>
> Cc: petsc-maint Maintenance
> <<mailto:petsc-maint at mcs.anl.gov>petsc-maint at mcs.anl.gov>
>
> Subject: Re: [PETSC #19028] PETSc and Python
>
> Reply-To: <mailto:petsc-maint at mcs.anl.gov>petsc-maint at mcs.anl.gov
>
> You can use mpi4py and petsc4py. They both can be automatically
>
> installed by configure:
>
> --download-petsc4py --download-mpi4py
>
> They have a lot of documentation associated with them and examples.
>
>  Matt
>
> On Tue, Feb 10, 2009 at 5:42 AM, Wonseok Shin
> <<mailto:wsshin at stanford.edu>wsshin at stanford.edu> wrote:
>
> Dear PETSc developers,
>
> I am interested in the interaction of PETSc and Python.  Is it possible to
>
> distribute data from Python to PETSc and vice versa?  I know how to do this
>
> for a single process, but don't know for multiple processes.
>
> If I need some Python MPI module, could you recommend a specific one that
>
> works well with PETSc?
>
>
> Best regards,
>
> Wonseok Shin
>
> Ph.D candidate
>
> Department of Electrical Engineering, Stanford University
>
> <mailto:wsshin at stanford.edu>wsshin at stanford.edu
>
>
>
>
>
>
>
> --
>
> What most experimenters take for granted before they begin their
>
> experiments is infinitely more interesting than any results to which
>
> their experiments lead.
>
> -- Norbert Wiener
>
>
>
> Our PETSc installer has created a new version of PETSc. You can run it
> by issuing the command
>
>   module load petsc/3.0.0-p3.complex
>
> I am not sure what it includes. I do not think it includes the Python
> additions you requested, because they are incompatible with the complex
> data type. I have asked for clarification on what this new version
> includes.
>
> Rick Costa
> PSC User Services
>
>
>
>
>

-- 
Lisandro Dalcín
---------------
Centro Internacional de Métodos Computacionales en Ingeniería (CIMEC)
Instituto de Desarrollo Tecnológico para la Industria Química (INTEC)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
PTLC - Güemes 3450, (3000) Santa Fe, Argentina
Tel/Fax: +54-(0)342-451.1594