[Swift-devel] Falkon and Coaster support for MPI

[Benoit Roux]

On Jun 29, 2008, at 4:07 PM, Michael Wilde wrote:

> 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.

Note that a non-MPI CHARMM job on BG would be not super fast, and MPI  
capability would be desirable.

>
> 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

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