[Swift-devel] Falkon and Coaster support for MPI

[Michael Wilde]

Ben,

On 6/29/08 2:19 PM, Ben Clifford wrote:
> On Sun, 29 Jun 2008, Michael Wilde wrote:
> 
>> The app that accelerated this discussion is CHARMM for molecular 
>> dynamics. CHARMM on BGP with the parameters needed in the use case in 
>> question has a long runtime on 1 CPU (24-36 hours), and seems to peak in 
>> performance using MPI at 32 CPUS. Runs >6 hours are also not runnable 
>> today on the Argonne BGP without a reservation. So the most effective 
>> way to use the BGP for some specific CHARMM runs needed by Benoit Roux's 
>> group is to run large numbers of multi-hour 32-rank MPI jobs.
> 
> OK.
> 
> This seems like an interesting application.
> 
> I can spend some time working on this in the next few weeks, as long as 
> you provide me with the following:
> 
>  i) someone who knows how the charmm applications work (eg from Benoit's 
> group)

Wei Jiang from Benoit's group spent several hours with me Friday 
explaining how they run CHARMM.

The approach uses scripts that Yuqing Deng, who recently left the group, 
developed.  These are on the Argonne "KBT" cluster. You should get on 
the Argonne accounts web and request access to that cluster, 
kbt.mcs.anl.gov.

One there, you can run perl scripts that generate either shell scripts 
or pbs jobs to do a CHARMM run. It was fairly complex, and I need to 
transcribe some notes on this.

Benoit was going to try to locate slides and/or docs from a talk that 
Yuqing gave before he left, on how to run his tools.

Ray Loy of the ALCF team is working on compiling a non-MPI CHARMM 
runnable under ZeptoOS on the BGP, and he also wanted to try HTC mode.

Nika's latest workflows running CHARMM are also a good reference point.

Wei can provide info on how to do a sample run from Yuquing's scripts.

>  ii) someone who knows how MPI works on the BG/P (maybe Kamil?)

MPI on BGP under ZeptoOS is still several weeks away from friendly-user 
testing capability. Kamil and Kaz (and Pete Beckman) are the Argonne 
ZeptoOS team. Kaz is working on ZeptoOS MPI and just reached hello-world 
about a week ago.

- Mike