What kind of calculation is it? Have you benchmarked your calculations with 1,2,4,8… processors, to see how well they parallelize?
—
Gustavo Seabra.
> Em 29 de jun de 2016, à(s) 05:56, bharat gupta <bharat.85.monu.gmail.com> escreveu:
>
> Hello Amber Users,
>
> I am running my simulations on a cluster with six 16 processors nodes and I
> am running a total of 96 processes with -npernode 16. My system contains
> 76441 atoms including protein+ligand+water. For completing 5 ns simulation,
> it took around more than 1 day.
>
> Sample command which I use for running:
>
> $]mpirun -np 96 -machinefile machinefile sander.MPI ...
>
> This is the information for one of the nodes:
>
> ===== Processor composition =====
> Processor name : Intel(R) Xeon(R) E5-2650 v2
> Packages(sockets) : 2
> Cores : 16
> Processors(CPUs) : 16
> Cores per package : 8
> Threads per core : 1
>
> Memory info:
> [sandia.node06 ~]$ free -m
> total used free shared buffers cached
> Mem: 64454 2777 61676 95 154 265
>
>
>
> Here's the output from the run file:
>
> | Final Performance Info:
> | -----------------------------------------------------
> | Average timings for all steps:
> | Elapsed(s) = 118385.53 Per Step(ms) = 47.35
> | ns/day = 3.65 seconds/ns = 23677.11
> | -----------------------------------------------------
>
> | Job began at 10:31:31.193 on 06/27/2016
> | Setup done at 10:31:32.150 on 06/27/2016
> | Run done at 19:24:37.680 on 06/28/2016
> | wallclock() was called******** times
>
>
> I feel the simulation is running at a very slow speed. What could be the
> reason for this or is this normal or my settings for the parallel run might
> be wrong??
>
> Thanks in advance for your suggestions.
> --
> *Best Regards*
> BM
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Received on Wed Jun 29 2016 - 07:00:03 PDT
