[gmx-users] REMD problem
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 28 23:08:56 CEST 2011
Liu, Liang wrote:
> Thanks. currently what I see is the program runs very slowly, but get
> .log file for all the 50 replicas, does this mean all of them are running?
>
Are the log files being updated, or do they all simply contain a fatal error
message that there are insufficient nodes? I cannot think of a reason why 50
simulations could possibly run on 2 processors.
-Justin
> On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Liu, Liang wrote:
>
> Well, although this makes sense, why all the 50 replicas are
> running when I run "mpirun
> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own
> computer with only 2 cores?
>
>
> I can offer no explanation for this behavior, but I expect that
> either not all of them are actually running, or at the very least
> you will get horribly slow performance.
>
>
> By the way, would you please show me where I can find the
> reasonable replex number information in the literature? I did
> not find it in the link you posted and the manual either.
>
>
> A few minutes of real literature searching will be far more valuable
> than some random person on the Internet giving you a value that you
> blindly use ;)
>
> -Justin
>
> Thanks.
>
>
> --
> Best,
> Liang Liu
>
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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>
> --
> Best,
> Liang Liu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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