[gmx-users] Re: multi cpu problem

[Wei Fu]

Hi, David, 

Thanks for your reply. You mean I can do SD with multi processors only in
linux with cshell. Am I right? Anyway, I do a test on sgi workstation, it
turns out: MPI: bad process count. 

In addition, I did some extra tests. Here is my summary:

For SD, it can run with 1 cpu, can't run with multi cpu on several
proteins I tested (I tested several proteins).

For MD on only protein, as Santarossa said, it can run with 2 cpu, but
can't run with more than 2 cpus, is it strange?

Cheers,

Fu, Wei

************************************************************
  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/
**************************************************************

>     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