AMBER Archive (2008)

Subject: RE: AMBER: cluster for running amber10

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Sep 30 2008 - 10:25:09 CDT

Hi Guillermo,

I haven't used this specific cluster but a couple of comments.

> my laboratory is planning to buy a cluster. We have a proposal of a
> Dell PowerEdge 1950 III quadri-core (1 master and 3 units), 8Gb per
> machine
> and many Gb of disk space.
> Does anyone have expirience with this kind of cluster with amber10?
> Which will be the compiler to use?

For compiler you should probably use ifort - I assume this is an Intel box.
Is this 2xquad core or 1xquad core? Also what do you have for the
interconnect? If it is gigabit ethernet then you will be limited to 1 node
per run, so if they are 1xquad core nodes your limit will be 4 cores per MD
run. For pure MD, things like REMD should work with up to 4 cores per
replica assuming you can get the machinefile map such that it distributes
the jobs correctly. If they are dualx4core then you can run 8 threads per MD
run - although performance increases for PMEMD beyond 6 threads per machine
is limited - sander.MPI does well up to the 8 cores, although ultimate
throughput will be less than PMEMD.

If the machine is hooked up with infiniband then you are fine and should be
able to run jobs fine across the whole machine, just make sure you use a
decent MPI like MVAPICH/MVAPICH2/INTEL MPI (I'd avoid openMPI since the
performance is aweful.)

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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