[gmx-users] invalid number of nodes

[Berk Hess]

Hi,

In the CVS version the fourier grid is no longer required to be divisible by the number of processors.
But in the other mail you had fourier_nz set to zero, which is complete nonsens.
I guess you should do some reading.

Berk.


From: regafan at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] invalid number of nodes
Date: Wed, 13 Aug 2008 14:12:04 +0000








Thanks a lot for your suggestion.

What I was refering was to this post:


http://www.gromacs.org/pipermail/gmx-developers/2008-February/002378.html

 

"OR use the 3.3 grompp to produce the mdp files since it will automatically set the fourier grid to fit the number of processors."

 

Sorry for not explaining it better. 

 

Anyway, in the new version of Gromacs, the -np option of grompp does not work, does it?

 

I am new in Gromacs, and I am using a version installed in a common cluster. I don´t know if I could install your modificated version myself.

 

If I use grompp from the my new version, and I only change fourier_nx and fourier_ny in the input .mdp file, would it be enough to create a correct mdp.out file that works.

 

Best wishes,

 

Rebeca García Fandiño

Parc Cientific de Barcelona

 


 





From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] invalid number of nodes
Date: Wed, 13 Aug 2008 14:52:30 +0200






Hi,

I don't understand your remark about the mdp file.
Where on the wiki does it say something like this?
The number of processors is never present in the mdp file.

Just use the new version of grompp.
A week ago I have committed large changes to the CVS
which make the tpr files much smaller and large simulations a bit more efficient.

Berk.



From: regafan at hotmail.com
To: gmx-users at gromacs.org
Date: Wed, 13 Aug 2008 11:51:56 +0000
Subject: [gmx-users] invalid number of nodes




Hello,
I want to simulate a membrane+proteína system  (more than 700.000 atoms) with Gromacs 4 and I would like to use 512 proc.
I am creating the mdp file with Gromacs 3, since I have read in the wiki that it was a good way to include the number or processors ins the mdp file for the new version.
 
For grompp with Gromacs 3.3 I amincluding this options in the input mdp file:
 

fourierspacing           = 0.12
fourier_nx               = 1024
fourier_ny               = 1024
fourier_nz               = 0
 

but when I execute:

 

grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o equilibrado2.tpr -n index.ndx -np 512
 
I receive this error:
 
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1021
 
Fatal error:
invalid number of nodes 512
 
-------------------------------------------------------
 

When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the correspondent error did not appear.
Is there a limit of processors in Gromacs for grompp or which could be the problem?
 
Thank you very much for your help in advance,
 
Rebeca García Fandiño
Parc Cientific of Barcelona


¿Todavía no conoces El Duelo? Descúbrelo y reta a tus contactos de Messenger El Duelo 


Express yourself instantly with MSN Messenger! MSN Messenger 
¿Todavía no conoces El Duelo? Descúbrelo y reta a tus contactos de Messenger El Duelo

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080813/127f2bc6/attachment.html>