[gmx-users] run parallel

[Carsten Kutzner]

Hi Salem,

what are the very first few lines of your output (on screen)?
You should see something like

NODES=4, MYRANK=0, HOSTNAME=myhostname
NNODES=4, MYRANK=3, HOSTNAME=myhostname
NNODES=4, MYRANK=1, HOSTNAME=myhostname
NNODES=4, MYRANK=2, HOSTNAME=myhostname

Also, take care with the switches you pass to mdrun - as far as
I know the -f flag is not doing anything. That means, in all
cases mdrun will load "topol.tpr" as input file - since you do
not provide the -s <filename.tpr> flag. Maybe this is the
problem?

Check in the screen output if mdrun reads in the file you
think:

Option     Filename  Type         Description
------------------------------------------------------------
   -s       test.tpr  Input        Generic run input: tpr tpb tpa xml
            ^^^^^^^^

Carsten


ha salem wrote:
> dear user
> my molecule is HSA it has about 120000 atoms its not small I run the 
> calculation
> with
>  mpirun -np 4 /usr/local/share/gromacs_331/bin/mdrun -f topol.tpr  o 
> md.trr -c md_out.gro -e md.edr -g md.log &
> then I run top and I see 4 cores are working but the time of calculation 
> is the same without
> -np 4 option
> can you help me
> 
> 
> 
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-- 
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne