Dear Jason,
Thanks a lot for the reply.
I am using SANDER program for MD simulation. Regarding pmemd.mpi, i have never used it.
If sander and pmemd works the same way ?
Also if all the nodes have been interconnected, i will ask the vendor about it. Or if u have
can suggest how to find it out, it will be very helpful.
Thanks again.
Regards
On Sat, 14 Sep 2013 19:25:47 +0530 wrote
>On Sat, Sep 14, 2013 at 12:13 AM, onetwo wrote:
> Dear All,
>
>
>
> We have just installed RACK server in our lab, in which we have installed
> AMBER software in
>
> parallel. Server shows that it has 160 cores. When I run simulation job, I
> give np 160,
>
> equilibration job crashed. Then I tried using np 8, then it worked, then
> again I increased np to
>
> 32, it is running fine, but for 4ns production run for 321 amino acid, it
> is taking 72 hours to
>
> finish. When I used to run it on 8 cores on our previous workstation, it
> used to take same time.
>
> I tried on server np 80 also, still it shows more than 70 hours to finish.
>
A couple comments here. First, 'Amber' is a suite of programs, not a
single one. You need to tell us _which_ program you were using.
Typically, pmemd.MPI gives better parallel scaling than sander.MPI (and it
gives better single-processor performance, as well). If you are not
using pmemd.MPI, you should start using that program instead.
Second, the interconnect between the nodes is very important -- unless you
have very fast infiniband, you will not be able to use multiple nodes (as
you've seen in the lack of speed-up).
>
>
> Please suggest, if I am missing something. and how to utilize all the
> cores for faster simulation
>
You may not be able to use all cores to speed up your simulation. This
will be true of all MD codes.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Sep 14 2013 - 22:30:02 PDT
