[gmx-users] Re: multi cpu problem (Anton Feenstra)

[David]

On Wed, 2004-01-28 at 21:44, Wei Fu wrote:
> Hi, Anton,
> 
>     As you stated in the "Subject: Re: [gmx-users] errors depending on (lack of) solvent",  the limitation is in solving (distance) constraints (e.g., for constant bondlengths). That means that I can run SD with muilt processors when setting the "constraints = none"?
> 
> I have done some SD tests on my protein by "constraints = none", the results are:
> it runs when submitting job directly (interactive) with 2 cpu
> but it can not run when submitting job to background (by nohup) with 2 cpu.
> 
> when set parameter to "constraints = hbonds"
> it can't run SD simulation on my protein with 2 cpu on both interactive and background mode, but SD can run with 1 cpu.
> 
>    So, whether this means I only can run SD with 1 cpu?  My proteins consist of 423 residues, 3431 atoms. How long it will take to do a simulation of 500 ns with 1 cpu? 
> 
>    By the way, whether there is some way to run SD on multiple cpu?
> 
> Thanks!!!
>            
> Fu, Wei


you have to use mpirun, and put the stuff in the background
mpirun -c 2 mdrun >& logfile &

for  LAM and cshell.

You can also use constraints = h-bonds

> 
> 2004-01-28
> ************************************************************
>   Wei Fu (Linda)
>   Postdoctoral Research Associate
>   Department of Biology and Biochemistry 
>   University of Houston
>   4800 Calhoun Rd. HSC #402C
>   Houston, TX 77204-5001   USA
>   Phone:713-743-8355(o)  713-795-9270(h) 
>   Fax:713-743-8351 
>   Email: fuwei at adrik.bchs.uh.edu
>   http://adrik.bchs.uh.edu/~fuwei/
> **************************************************************
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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
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