[gmx-users] how to optimize performance of IBM Power 775?

[Carsten Kutzner]

Hi Albert,

On Aug 25, 2012, at 7:37 AM, Albert <mailmd2011 at gmail.com> wrote:

> Dear:
> 
>  Our institute got a  IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme.
Are you shure that it is not supported? Maybe you just need the right syntax.

> I use the following script for job submission:
> 
> 
> 
> #@ job_name = gromacs_job
> #@ output = gromacs.out
> #@ error = gromacs.err
> #@ class = kdm
> #@ node = 4
> #@ tasks_per_node = 32
> #@ wall_clock_limit = 01:00:00
> #@ network.MPI = sn_all,not_shared,US,HIGH
> #@ notification = never
> #@ environment = COPY_ALL
> #@ job_type = parallel
> #@ queue
> mpiexec -n 128 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr
> 
> it is only 7 ns/day.
> 
> However, in another cluster with the same system, Core number and parameters, I can get up to 30 ns/day.
> 
> Does anybody have any advices for this issue?
On a Power6 machine, I have successfully used the following job file:

# @ shell=/bin/ksh
#
# Sample script for LoadLeveler
#
# @ error   = run_1.err.$(jobid)
# @ output  = run_1.out.$(jobid)
# @ job_type = parallel
# @ environment= COPY_ALL
# @ node_usage= not_shared
# @ node = 1
# @ tasks_per_node = 4
# @ resources = ConsumableCpus(1)
# @ network.MPI = sn_all,not_shared,us
# @ wall_clock_limit = 0:05:00
# @ notification = complete
# @ queue

#
# run the program
#
export MDRUN=/path/to/gromacs-4.5.1/bin/mdrun_mpi
export MPIRUN=poe

#no poe here!
/path/to/g_tune_pme -np 4 \
-npstring none -s ./ap.tpr -resetstep 1 -steps 10

Hope that helps,
  Carsten



> 
> thank you very much
> Albert
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne