On Fri, Jul 1, 2016 at 1:03 AM, bharat gupta <bharat.85.monu.gmail.com>
wrote:
> Hello Amber Users,
>
> I have already asked this question previously , but nobody has responded.
>
Gustavo replied to you in the same day you asked your question. Please
check your spam folder.
You're using sander.MPI and it does not scale very well with large number
of cores.
You can check the benchmark here: http://ambermd.org/amber10.bench1.html
Getting 5 ns/day for 76K atom system is not that bad.
You should do your own benchmark by varying the number of core (as Gustavo
suggested)
Hai
> So, I am posting the question again. 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 that 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 Thu Jun 30 2016 - 23:00:03 PDT
