[gmx-users] gromacs parallel doesn't work

[David van der Spoel]

Arneh Babakhani wrote:
> grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o 
> ResMD1 ;
you need -np 4 for grompp

> mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 -g 
> ResMD1 > & ResMD1.job &
> 
> 
> 
> Mark Abraham wrote:
>> Arneh Babakhani wrote:
>>> Hello, I'm having a similar problem, although my OS sees all 4 of my 
>>> processors just fine.
>>>
>>> When I run mpirun -c 4 mdrun . . .
>>>
>>> all 4 of my processors are running, but only at 50% each.  
>>> Furthermore, in present working directory, I see several backed up 
>>> files:
>>>
>>> [ababakha at chemcca50 TEMP]$ ls
>>> AfterResMD1.gro      #mdout.mdp.1#   ResMD1.job      ResMD1.trr
>>> #AfterResMD1.gro.1#  NoBadWater.top  ResMD1.log      #ResMD1.trr.1#
>>> #AfterResMD1.gro.2#  posre.itp       #ResMD1.log.1#  #ResMD1.trr.2#
>>> dmpc.itp             ResMD1.edr      #ResMD1.log.2#  #ResMD1.trr.3#
>>> lipid.itp            #ResMD1.edr.1#  #ResMD1.log.3#
>>> lipid_posre.itp      #ResMD1.edr.2#  ResMD1.mdp
>>> mdout.mdp            #ResMD1.edr.3#  ResMD1.tpr
>>>
>>> It's almost as if I'm running 4 identical jobs (one on each 
>>> processor) , instead of one job in parallel using 4 processors.
>>>
>>> Any thoughts?
>>
>> You probably are. What are your full grompp and mdrun commands?
>>
>> Mark
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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://folding.bmc.uu.se
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