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:
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> *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 - 05:30:03 PST
