[gmx-users] gromacs parallel doesn't work

[Arneh Babakhani]

Ok, got it to work.  (I had to go back and reinstall the parallel 
version of mdrun).

question though: I notice that there's a log file created for each node 
(so in my case, there are 4 log files).  Why is this, is this typical?  
I guess what I'm asking is, how exactly does GROMACS divide the problem 
up amongst the processors?

Thanks,

Arneh

Beniamino Sciacca wrote:
> maybe you should type:
> "grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top 
> -o ResMD1 -np 4"
> and so
> "mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 
> -g ResMD1 > & ResMD1.job &"
>
> Beniamino
>
> Arneh Babakhani ha scritto:
>> 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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