[gmx-users] PARALLEL PROBLEM

[David van der Spoel]

On Fri, 2003-03-21 at 15:25, Osmany Guirola Cruz wrote:
> Hi 
>  I have a problem with gromacs and my linux cluster  look at this.
> 
> system with ~4000atoms(200ps)           system with ~40000atoms(40ps)
> 1 machine  1 micro   12589s                 1 machine  1 micro   8312s
> 1 machine  2 micro     7410s                 1 machine  2 micro   5060s
> 2 machine  4 micro     7535s                 2 machine  4 micro   5765s
> 4 machine  8 micro     6272s                 4 machine  8 micro   3701s
> 8 machine 16 micro    8783s                 8 machine 16 micro  3629s 
> i am using coulomtype=cuttoff if i  use PME its worst
> 
> and this is not very funny, I did a test with NAMD and it works 
> perfectly(scalable) but i hate NAMD, it's a real pain. which is the 
> diference? I think that my problem is the MPI library . now i am using the 
> rpm of my distribution (SuSE 8.1).(I think that i have to compile it). If 
> this is the solution ,i need to know which are the options for do it. In the 
> site of gromacs there are a rpm , is this the correct to resolve this 
> problem? ,PLEASE tell me what to do
> I have a lot of work and run a simulaton in 1 machine with the posibility to 
> use 32 it is terrible
>  HELP ME 

Try running the same problem in NAMD: the sequential code is so much
slower that it isn't hurt so much by the communication. Having said
that, their parallellization is better than the one on GROMACS, we are
working on it.

You can improve the numbers a bit by using two grompp options 
grompp -shuffle -sort

this will mess up the order of the molecules though. You can unshuffle
but not unsort.

>             thanks
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++