Subject: Summary: Software on mpi or pvm.

From: "Iraj Daizadeh" <[email-masked]>
Date: Thu, 16 Jul 1998 10:45:09 -0700

Hello.

The contents of this summary are as follows:

	1. Initial question concerning the use of MPI or PVM within the
					Chemistry community.

	2. Replies.

	3. I have asked Dr. W. Gropp, who is the Senior Computer Scientist at
		 the Mathematics and and Computer Science Division of Argonne
		 National Laboratory, to contribute to this discussion.  Dr.
		 Gropp has been with the MPI project at ANL since its genesis
		 and is one of the authors of the very popular MPICH
		 implementation of MPI.  His comments have been appended to
		 the end of this list.

I should mention that the commonly used G94 program utilizes Linda instead of
the standardized MPI or PVM systems.

Those of you who would like to gain a greater understanding of MPI or PVM,
please see the following URL sites:

	MPI:	http://www-c.mcs.anl.gov/mpi/
	PVM:	http://www.netlib.org/pvm3/faq_html/faq.html
		http://www.epm.ornl.gov/pvm/

I would like to thank Dr. Gropp as well as those who replied to this query.  It
is my hope that this summary will be of use to others in the future.

Iraj.
--
Iraj Daizadeh
Department of Chemistry
University of California
One Shields Ave.
Davis, CA  95616-5295
Phone:  530.754.8695
Fax:    530.752.8995
email:  [email-masked]

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1.

Hello.

We have a couple of dec 500 au's (DEC unix 4.0c) and a sgi r10000 (6.2 irix)
machine that we are considering parallelizing via mpi or pvm.

I would like to know what chemistry software can utilize mpi or pvm.  For
example, it would be nice if there were dynamics packages such as Amber or
Gromos that could use these tools; thus, one could run two classical
trajectories simultaneously.

If there is enough interest in this question, then I will post a summary of all
results as is traditionally done on the CCL.

Thank you in advance.

Iraj.

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2.

Dear Iraj,
AMBER is fully parallel using MPI or other native
communications schemes (such as on Cray t3e where shmem is faster
than MPI). PVM is no longer supported in AMBER.
However, it is not parallel in the sense that one would run two classical
traj. at once. That is called an "embarassingly parallel" application
by the computer science people. To do that one would most likely write a shell
script that would start up several instances of AMBER on separate
processors.
Rather, AMBER spreads the work of single traj. over many processors
getting the work done that much faster.
If you want more detail, please ask.
Sincerely,
Mike Crowley

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Dear Iraj Daizadeh,

daizad>I would like to know what chemistry software can utilize mpi or pvm.

I know of a few chemistry software packages that use PVM and MPI.
The MD programs Gromacs and DLpoly can use both, and the ab inition
package GAMESS uses PVM. I have successfully compiled and runned all three
on IBM SP computers, ordinary IBM RS/6k and Linux boxes.

Best regards,
  Kenneth

-----------------------------------------------------------
Kenneth Geisshirt, M.Sc., Ph.D.     Computational Scientist
Structural Bioinformatics               Tel:  +45 4516 2804
Advanced Technologies                   Fax:  +45 4516 2802
http://www.strubix.com                     [email-masked]

                 LOAD "http://www.sslug.dk",8,1
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Hello,

  The ADF (Amsterdam Density Functional) code uses
PVM. I have installed it Origin 200 SGI computers
(Irix 6.4).

Nathalie

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| Nathalie Godbout                           |
| University of Illinois at Urbana-Champaign |
| 600 S. Goodwin Av. Box 23.6                |
| Urbana, IL 61801                           |
 --------------------------------------------
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My MD simulation code Moldy will run in parallel using MPI.  If you
take a look at my web page http://www.earth.ox.ac.uk/~keith/moldy.html
it contains links to other parallel MD codes including AMBER and
GROMOS and DL_POLY.

One piece of advice though.  If your machines are connected to an
unswitched ethernet shared by others in your department, forget it.
You will at least need a switched network to get good parallel
performance. This does depend on the parallelization strategy, but
even a replicated-data approach as used in Moldy won't give much of a
gain unless you have an essentially dedicated (ie switched) network.

Keith Refson

--
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Email: Keith.Refson@  | Tel: +44 1865 272026 | Dr Keith Refson,              |
       earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences        |
Spam:            [email-masked]         | Parks Road, Oxford OX1 3PR, UK|
------------------------------------------------------------------------------
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See http://rugmd4.chem.rug.nl/~gmx/index.html
Good luck.

Dayong

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We're using CHARMM built over PVM, and it (claims it:) can just as
easily be configured to use MPI instead.

dan
--
Daniel Macks
[email-masked]
[email-masked]
http://www.netspace.org/~dmacks

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Hi,

check out the GROMACS package for MD and trajectory analysis. It runs with
either PVM or MPI on (homogeneous) cluster of workstations.

http://rugmd0.chem.rug.nl/~gmx

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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3.

At 02:36 PM 7/14/98 -0700, Iraj Daizadeh wrote:
>Hello Dr. Gropp.
>
>I have another question I would like to raise if you have time.
>
>I have recently submitted a query to the Computational Chemistry List (CCL)
>concerning the topic of MPI and PVM (see below) and its use in Chemistry
>software.  I will submit to them a summary of all responses that I receive
>concerning the question.  Since you are an authority in this field, I would
>like to append onto this summary any information that you could kindly supply
>to me concerning MPI.
>
MPI (particularly MPI-1) is most suited to massively parallel applications
that run with a fixed number of processes; it is particular good for
applications requiring good communications performance for both
point-to-point and collective operations.  It isn't appropriate for most
task-farm approaches.  PVM is more appropriate for applications that use
changing numbers of processes.

MPI-2 adds a number of features, such as dynamic processes and parallel
I/O.  To date, only the parallel I/O is widely available.

Bill

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At 02:25 PM 7/14/98 -0700, Iraj Daizadeh wrote:
>Hello.
>
>We are considering parallizing two DEC 500 a.u.'s (DEC UNIX 4.0c) and an sgi
>r10000 (irix 6.2), and were wondering if this was a worth while venture when
>these machines are on an ethernet connection that is used by others.
>
It really depends on your application, but my guess would be that it is not
worthwhile.  Because of load balancing and the low bandwidth/high latency
of Ethernet, any application that would work would be easily written with
rsh or ssh directly.

Bill

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