Molecular dynamics is a good area to look at. Something like a
particle in cell (PIC) code is easy to implement and allows you to
play around with load balancing. If you want something a fair bit
harder but extremely educational, try a 2D adaptive mesh code solving
a fluid flow problem - you'll learn a real lot about MPI and parallel
processing.
I wrote a PIC code to use in MPI courses to demonstrate the effect of
different load balances and how it effects the time to solve the
system. You can find it online at
https://nf.apac.edu.au/training/MPIAppOpt/
It is the last example of the course. Its not a great code, it was
meant to be simple and easy to modify and to demonstrate load
balance, but all the ideas are there.
Stu.
On 21/02/2006, at 21:52, Joe Landman wrote:
Hi Timo:
Timo Mechler wrote:
Hello all,
Over the past couple years I have done research one Beowulf
clusters and
also implemented the first one at my school. Now that I'm getting
closer
to graduating, I'm looking of turning all this work into a senior
project.
The only part that's missing though, is a good physics problem
that I
could code up a numerical solution for and run in parallel. I
have done
some of this, but it's mostly been simple stuff, such as a simple
numerical integration via the Monte Carlo method in parallel. I
know some
of you on this list are professors and professionals that have
extensive
physics knowledge. What sorts of physics problems would you
suggest I
might be able to code up that would take a some time run on a Beowulf
cluster? I'm going to be using Fortran 77 with MPI libraries as
my base
for coding. Thanks in advance for your help on this, I appreciate
it.
A problem I coded up for a class I teach on HPC applications is an
ideal gas in a 2D box, with correct (momentum conserving, energy
conserving) dynamics. It was done in C though. I might suggest
something like this. Then you can measure pressure (number of
impacts on perimeter wall per time step), temperature, and volume,
and do experiments where you suddenly double the volume, or have
one of the wall boundaries start creeping downwards to decrease the
volume, or chill the walls, so that upon collisions with the walls
the atoms get slower/faster (lose/gain KE to/from the reserviour).
I did this as an example that I wanted them to add in how to move
atoms between processors (no periodic BCs, just "partitions" that
atoms can cross. And if they cross it, you need to move them to
the adjacent processor.
I have done up to about 1 million "atoms" on a 32 way run, and it
works pretty nicely. Somewhat hard to visualize the output, so I
had it write stuff out in ".xyz" format, and used VMD to generate a
movie. You can see it (about 100 atoms, tiny interaction radius,
and a few thousand steps) here at http://
www.scalableinformatics.com/public/idealgas.mpg .
Joe
--
Dr Stuart Midgley
Industry Uptake Program Leader
iVEC, 'The hub of advanced computing in Western Australia'
26 Dick Perry Avenue, Technology Park
Kensington WA 6151
Australia
Phone: +61 8 6436 8545
Fax: +61 8 6436 8555
Email: [EMAIL PROTECTED]
WWW: http://www.ivec.org
--
Dr Stuart Midgley
[EMAIL PROTECTED]
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