Anuga-user Digest, Vol 72, Issue 5

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Today's Topics:

1. Re: Anuga-user Digest, Vol 71, Issue 3 (Jos? Galaz)


----------------------------------------------------------------------

Message: 1
Date: Thu, 27 Nov 2014 09:26:18 -0300
From: Jos? Galaz <jdg...@uc.cl>
Subject: Re: [Anuga-user] Anuga-user Digest, Vol 71, Issue 3
To: anuga...@lists.sourceforge.net
Message-ID:
<CALTyBRnZzWCmzgDQjBPwbPpm...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi all,
I googled and found on the mpi4py forum the discussion of the user who
wrote the wrapper you told me, here is the link
*https://groups.google.com/forum/#!topic/mpi4py/S0fG8YwFcGo
<https://groups.google.com/forum/#!topic/mpi4py/S0fG8YwFcGo>*. I tried to
contact him so maybe he could share his code with the anuga community, but
didn't succeed. Also I have never programmed C++ or C, so I can hardly read
the codes he posted there. I was wondering if you may have any better idea
on this respect.

On the other hand, I was reading some of the anuga_parallel codes, and
found something interesting. In the
anuga_core/source/anuga_parallel/parallel_abstraction.py file is a
exception handle for when the system does not have pypar installed. Will it
work if I just redefine the functions that there appear ( abort, finalize,
barrier, etc), with the mpi4py analogues?, Which arguments would it be
neccesary to ask for in each function then? I have some experience with
mpi4py and MPI in Fortran, so I think I can give it a try.


Thanks!

Jos?

2014-10-18 9:18 GMT-03:00 <anuga-use...@lists.sourceforge.net>:

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>
>
> Today's Topics:
>
> 1. Re: Anuga-user Digest, Vol 71, Issue 2 (Stephen Roberts)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 18 Oct 2014 09:46:23 +1100
> From: Stephen Roberts <stephen...@anu.edu.au>
> Subject: Re: [Anuga-user] Anuga-user Digest, Vol 71, Issue 2
> To: anuga...@lists.sourceforge.net
> Message-ID: <54419C3F...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Jos,
>
> I know of a user who wrote a wrapper around mpi4py to mimic pypar and so
> was able to run anuga parallel using mpi4py.
>
> I will try to obtain his code.
>
> But it was not too difficult.
>
> The only tricky part was realising that pypar checks for contiguous data
> (when sending numpy arrays) and mpi4py doesn't, so the wrapper needed to
> check for that and copy to contiguous data before sending.
>
> Cheers
> Steve
>
>
>
> On 17/10/2014 11:02 PM, anuga-use...@lists.sourceforge.net wrote:
> > Send Anuga-user mailing list submissions to
> > anuga...@lists.sourceforge.net
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://lists.sourceforge.net/lists/listinfo/anuga-user
> > or, via email, send a message with subject or body 'help' to
> > anuga-use...@lists.sourceforge.net
> >
> > You can reach the person managing the list at
> > anuga-us...@lists.sourceforge.net
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Anuga-user digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Anuga-Parallel not compatible with cluster configuration
> > (Jos? Galaz)
> > 2. Parallel anuga not compatible with cl?ster configuration
> > (Jos? Galaz)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 16 Oct 2014 18:23:28 -0300
> > From: Jos? Galaz <jdg...@uc.cl>
> > Subject: [Anuga-user] Anuga-Parallel not compatible with cluster
> > configuration
> > To: anuga...@lists.sourceforge.net
> > Message-ID:
> > <CALTyBR=vmqvKEFAUgtM_39Wz6FpJwc2cno=
> vTUvsJC...@mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear mailing-list,
> >
> > I am currently having some troubles trying to use AnuGA in a cluster
> > installed at my university. The administrator of the cluster tells me
> that
> > pypar handles the memory in a different way than it is currently being
> done
> > here, and hence, it is not compatible.
> >
> > One solution they suggested was to run my program using mpi4py, but I
> > assume that it is not an easy thing to do with AnuGA. Has anyone had
> faced
> > a problem like this before?
> >
> > I'm totally open to suggestions, and please, feel free to ask about any
> > other detail you may consider important.
> >
> > Best regards,
> >
> > Jos?
> > -------------- next part --------------
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> > Message: 2
> > Date: Thu, 16 Oct 2014 18:18:39 -0300
> > From: Jos? Galaz <jdga...@gmail.com>
> > Subject: [Anuga-user] Parallel anuga not compatible with cl?ster
> > configuration
> > To: anuga...@lists.sourceforge.net
> > Message-ID:
> > <CALTyBR=gxDB7-6Kemzp_+TwFHTLsoAgpe2Bot+=4+67xbzPy=
> w...@mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear mailing-list,
> >
> > I am currently having some troubles trying to use AnuGA in a cluster
> > installed at my university. The administrator of the cluster tells me
> that
> > pypar handles the memory in a different way than it is currently being
> done
> > here, and hence, it is not compatible.
> >
> > One solution they suggested was to run my program using mpi4py, but I
> > assume that it is not an easy thing to do with AnuGA. Has anyone had
> faced
> > a problem like this before?
> >
> > I'm totally open to suggestions, and please, feel free to ask about any
> > other detail you may consider important.
> >
> > Best regards,
> >
> > Jos?
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> >
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> --
> +--------------------------------------------------------------------+
> | Steve Roberts | My Office: (61)(2) 6125 4445 |
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> | Mathematical Sciences Institute| Fax: (61)(2) 6125 4984 |
> | John Dedman Building #27 | mailto:stephen...@anu.edu.au |
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[Stephen Roberts]

Hi Jos,

Roberto Vidmar has sent me his code which replaces pypar with mpi4py.

As you observed, Roberto adds the mpi4py wrapper via parallel_abstraction.py

There are a few other places that needed changes, but mostly just
picking up pypar calls and changing them to the parallel_abstraction calls.

It should not take too long to include the changes, so if I get a free
day in the next week or so I will incorporate the changes.

If you are in a desperate hurry I can send you Roberto's code

Cheers
steve