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 - 02:00:03 PDT
