[gmx-users] REMD problem

[Justin A. Lemkul]

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

========================================