[gmx-users] gromacs parallel doesn't work

[Mark Abraham]

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