[gmx-users] problem with cluster

[David van der Spoel]

On Wed, 2005-04-13 at 15:09 +0200, Nguyen Hoang Phuong wrote:
> Dear All,
> 
> we have a new cluster consists of 11 Intel cpus with hyperthreading. I
> have some problems with running gromacs on this cluster:
> 
> a) When I submit a job, it is distributed at random on 2 cpus (I asked for
> 2 cpus). How can I run the job on specific cpus?
That depends on you queueing system and/or MPI, not gromacs.
> 
> b) The cpus which run the mdrun program alway work with about 40% of
> power. How can I increase the power of the cpus?
This could be due to Linux throttling back the clock speed and not
setting it back to highest clock. I have the same problem on some
desktop machines and not found a solution yet.

> 
> Thank you very much in advance for any hint.
> 
> Phuong
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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