Edward d'Auvergne wrote:
On 3/20/07, Gary S. Thompson <garyt@xxxxxxxxxxxxxxx> wrote:
Edward d'Auvergne wrote:
> Hi,
>
> Just a quick point, it would be good to either start a new thread for
> these types of questions or changing the subject field (unless you use
> the Gmail web interface like I am at the moment). People may miss
> important discussions with such scary subject lines!
>
>
> On 3/20/07, Gary S. Thompson <garyt@xxxxxxxxxxxxxxx> wrote:
>
>> garyt@xxxxxxxxxxxxxxx wrote:
>>
>> Dear Ed
>> d this is a good enough point to tell you how to run things and
what to
>> install for the mpi version i am testing with
>>
>> I have installed mpipy and lam
>
>
> Are both, together with mpi4py, essential for MPI operation?
yes lam is an mpi implementation and mpi4py is the interface code
between the c world of mpi and the python world
Got it. I installed lam-runtime and mpi4py but I could not install
mpipy as that didn't exist as a package.
sorry typo there is a 4 missing there!
I have run the example you
gave in the parent of this thread but I used the command:
mpirun-lam -np 6 python relax --multi mpi4py test_multi1.py
The program 'mpirun' doesn't exist on my computer.
fine i think it is the same thing by a different name
The output was:
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
relax repository checkout
Protein dynamics by NMR relaxation data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
This is free software which you are welcome to modify and redistribute
under the conditions of the
GNU General Public License (GPL). This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'.
Assistance in using this program
can be accessed by typing 'help'.
script = 'test_multi1.py'
----------------------------------------------------------------------------------------------------
import multi
cmd = multi.mpi4py_processor.Get_name_command()
self.relax.processor.run_command(cmd)
----------------------------------------------------------------------------------------------------
1 pc172-31-2-63.biochem.unimelb.edu.au-29691
2 pc172-31-2-63.biochem.unimelb.edu.au-29692
3 pc172-31-2-63.biochem.unimelb.edu.au-29693
4 pc172-31-2-63.biochem.unimelb.edu.au-29694
5 pc172-31-2-63.biochem.unimelb.edu.au-29695
Should I have something else installed for the 'mpirun' program?
no that is all you need the results are correct
> As MPI
> is solely for those who are very serious and have access to clusters,
not true! mpi can run over ssh as well. For example lam has an ssh
backend and this is what i am using for testing on my computer!
MPI can be used for grid computing but that is not what it is designed
for and hence isn't optimal
why?
. If I get the grid computing code working
again then you should be able to run relax on you posix system and
then get all those idle Windows boxes to do all your calculations for
you! Anyway, I would hope that most people doing a model-free
analysis are very serious ;)
Of course I am very serious but in a playful way ;-)
> the user should be able handle installing these dependencies (or at
> least be able to get someone to install it for them).
>
>
lam or mpich is often available in a linux distributions software
repository e.g
http://rpmfind.net/linux/rpm2html/search.php?query=lam-devel lists rpms
for mandriva and a variety of other platforms. I chose lam to play with
because it is the best performing library on our cluster, but have also
used mpich. mpi4py has instructions on building and seetting up a
variety of configurations
Do you think the relax MPI implementation will have lam as a
dependency or would mpich work equally as well (i.e. the end user
could install one or the other)? It would be useful to define the
exact dependencies with links to their webpages.
any of the mpi backends that mpi4py lists should be fine (obviously
people would have to test it but hey thats what test suites are for ;-)
cf http://www.cimec.org.ar/python/mpi4py.html which lists
*
/MPICH 2/
*
/Open MPI/
*
/LAM/
*
/MPICH 1/
>> lam should be available in your linux distribution ??? ;-) run
>
>
> I'm using Mandriva so I would assume that it is within it's 'contrib'
> repositories. You are talking about http://www.lam-mpi.org/ aren't
> you? As OpenMPI (http://www.open-mpi.org/) seems to be the future of
> that project, wouldn't this be the better option? It's more likely to
> be supported in future linux distros.
>
see above it shouldn't matter which mpi distribution you choose they all
have almost identical apis and mpi4py deals with that
So we could list multiple MPI software packages in the relax manual as
dependencies and let the user choose?
yep
>> mpi4py came from http://www.python.org/pypi/mpi4py (there is an
mpi4py
>> website but it is out of date, however, mpi4py is under recent
>> development)
>
>
> Do you think mpi4py 0.4 or below will be stable enough? Are there
> alternatives?
I would use mpi4py 0.4.0rc4 from the cheese shop. This is that I have
developed with and it seems to work _well___
<http://cheeseshop.python.org/pypi/mpi4py/0.4.0rc4>
That's what I'm using. There should be a stable version out by the
time the MPI code is operation and incorporated back into the main
line.
Cheers,
Edward
P.S. I'll get to the rest in another post.
.
--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: garyt@xxxxxxxxxxxxxxx Fax +44-113-2331407
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Re: r3237 - in /branches/multi_processor: multi/mpi4py_processor.py relax