[gmx-users] gromacs parallel doesn't work

[Arneh Babakhani]

grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o 
ResMD1 ;
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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