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:
[EMAIL PROTECTED] 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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