Re: [AMBER] running simulation using increased number of cores

From: onetwo <>
Date: 15 Sep 2013 05:21:18 -0000

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.


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.



Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Sep 14 2013 - 22:30:02 PDT
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