[gmx-developers] Install and run Gromacs

[Li Dawei]

Hi,

I think you mean MPI mdrun need a differect input file, compared with
non-mpi mdrun. If this is the case, the answer is yes.

Do you think this is a bug or something of MPICH? 

Thanks.

Li Dawei

-----Original Message-----
From: gmx-developers-bounces at gromacs.org
[mailto:gmx-developers-bounces at gromacs.org] On Behalf Of David
Sent: Saturday, May 15, 2004 4:38 PM
To: Discussion list for GROMACS development
Subject: RE: [gmx-developers] Install and run Gromacs


On Sat, 2004-05-15 at 02:36, Li Dawei wrote:
> Hi, Dear Erik:
>  
> The cluster is maintained by our computer center. Other mpi programs 
> run OK, including MOIL, CFD. I have also succeed in running a non-mpi 
> Gromacs.
>  
> This is the reason that confused me. The guys in computer center have 
> no idea, neighter. I have found one same report in this user list, 
> which receive no answer.

have you run grompp with the same number of processors?
>  
> Any suggest?
>  
> Thanks.
>  
> Dawei
>         -----Original Message-----
>         From: gmx-developers-bounces at gromacs.org
>         [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Erik
>         Lindahl
>         Sent: Friday, May 14, 2004 5:01 PM
>         To: Discussion list for GROMACS development
>         Subject: Re: [gmx-developers] Install and run Gromacs
>         
>         
>         Hi, 
>         On May 14, 2004, at 9:53 AM, Li Dawei wrote: 
>
------------------------------------------------------------------------
----- 
>                 It seems that at least one rank invoked some MPI
>                 function before 
>                 invoking MPI_INIT. The only information that I can
>                 give is that it 
>                 was PID 3257 on host atlas11.nus.edu.sg. 
>
------------------------------------------------------------------------
----- 
>                 It is very hard for me to understand this, since
>                 Gromacs surely will not do this. I have searched the
>                 achive of Gromacs and MPICH and found no answer.
>         No, I'm pretty sure this isn't a bug in Gromacs. Try and test
>         some trivial example MPI program (there is for instance one to
>         calculate PI in the MPICH distribution) and see if that works
>         first, and make sure that the non-parallel version of Gromacs
>         works too. 
>         Cheers, 
>         Erik
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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