This is the command I'm using:
mpiexec -n 36 pmemd.MPI -O -i heat.mdin -c crys.min.rst7 -p crys.parm7
-cpin crys.cpin -o crys.heat.mdout -r crys.heat.rst7 -ref crys.min.rst7 -x
crys.heat.nc
(so I guess it's ok). I'm using 3 nodes, 12 cores each.
Elisa
On Thu, Feb 11, 2016 at 2:00 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>
> > Dear all,
> >
> > I'm heating my system, but the maximum walltime in my cluster is 1 week,
> > that won't probably be enough. This in my current input:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
> > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002,
> ntt=3,
> > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
> > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
> > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
> > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
> VALUE1=10.0,
> > VALUE2=300.0, / &wt TYPE='END' /*
> >
> > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores
> > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond,
> > so it will take more than two weeks to finish. Is it normal? Isn't it
> VERY
> > slow?
> >
>
> How exactly are you running in parallel? (i.e., what is the exact command
> that you are using?) There are a number of possible issues.
>
> A common mistake people make trying to run pmemd in parallel is to use a
> command that looks like
>
> mpirun -np 36 pmemd -O -i mdin ...
>
> The problem here is that pmemd (and sander) are serial executables that are
> incapable of parallelizing their calculation. The correct thing to do is
>
> mpirun -np 36 pmemd.MPI -O -i ...
>
> If you use pmemd instead of pmemd.MPI, then you will get the exact same
> performance as running on 1 CPU (perhaps worse if the CPUs are
> oversubscribed). It's also possible if you are asking for multiple nodes
> that all of the threads are running on a single node (which will slow down
> performance substantially). You'd have to ask your help staff to figure
> out if that's happening (and how to fix it), though.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Feb 11 2016 - 05:30:05 PST
