[gmx-users] cannot do constraint force run in parallel?

[David van der Spoel]

Nickle Fan wrote:
> gmx-ers:
>  
> A while ago Beniamino posted a question regarding the difficulty in 
> doing constraint force in parallel. I am having the same problem now. 
> Specifically, when attemping to run on several nodes using mpirun, the 
> code says:
>  
> Fatal error: 
> Can not do constraint force calculation in parallel!
> 
> Is this a problem with the way I am using gromacs or it is a known 
> limitation (unlikely, I feel).

gromacs 4 will be the first and only program (so far) to allow parallel 
constraints, see announcement on the website. Until then you can use 
constraint = h-bonds, or use fewer cpus.

>  
> Nick
> ---------- Forwarded message ----------
> From: *Nickle Fan* <nicklefan at gmail.com <mailto:nicklefan at gmail.com>>
> Date: Wed, Feb 27, 2008 at 9:36 PM
> Subject: inquiry on constraint force run
> To: superbenji83 at gmail.com <mailto:superbenji83 at gmail.com>
> 
> 
> Hi, Beniamino:
> 
> I am attemping to do some constraint force calculation myself, but had 
> similar problems you mentioned earlier, i.e., mdrun shot back an error 
> saying "Can not do constraint force calculation in parallel!".
> 
> Did you resolved this issue at that time. I am not sending it to the 
> Gromacs list in case this has already been resolved.
> 
> Thanks.
> 
> Nick
> 
> On Sun, Jun 4, 2006 at 2:12 PM, Beniamino Sciacca 
> <superbenji83 at gmail.com <mailto:superbenji83 at gmail.com>> wrote:
>  >
>  >
>  > 2006/6/4, Beniamino Sciacca <superbenji83 at gmail.com 
> <mailto:superbenji83 at gmail.com>>:
>  > >
>  > > Ops... I've another new problem, that there wasn't before....
>  > >
>  > > ---------------------------------------------------------------
>  > >
>  > >
>  > > Program mdrun_d, VERSION 3.3.1
>  > >
>  > > Source code file: pullinit.c, line: 244
>  > >
>  > > Fatal error:
>  > > Can not do constraint force calculation in parallel!
>  > >
>  > > -------------------------------------------------------
>  > >
>  > > "Exactly" (Pulp Fiction)
>  > >
>  > > Error on node 0, will try to stop all the nodes
>  > > Halting parallel program mdrun_d on CPU 0 out of 2
>  > >
>  > > gcq#96: "Exactly" (Pulp Fiction)
>  > >
>  > >
>  > 
> -----------------------------------------------------------------------------
>  > > One of the processes started by mpirun has exited with a nonzero exit
>  > > code.  This typically indicates that the process finished in error.
>  > > If your process did not finish in error, be sure to include a "return
>  > > 0" or "exit(0)" in your C code before exiting the application.
>  > >
>  > > PID 7593 failed on node n0 ( 127.0.0.1 <http://127.0.0.1/>) with 
> exit status 32767.
>  > >
>  > 
> -------------------------------------------------------------------------------
>  > >
>  > > now i use mpirun -c 2, otherwise it uses only one processor. It 
> seems that
>  > with constraint forces it's impossible to work on two processes 
> together.
>  > > Before to have all these problem I didn't use mpirun, I didn't use 
> grompp
>  > -np 2.....
>  > > Before infact I had only one process on two processors.....
>  > > what can I do?
>  > > Thanks one more time
>  > > Beniamino
>  > >
>  > >
>  >
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> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se