[mpich-discuss] Using MPICH for gromacs

[bharat gupta]

Actually I am trying to do REMD(Replica Exchange Molecular Dynamics) on my
system , which needs MPI for parallel calculation. But I want to know how
can I enable MPI for all the 4 processors in my CPU for parallel
calculation. Also, what does this error means :-
Fatal error:
> The number of nodes (1) is not a multiple of the number of simulations (4)



On Sat, Feb 11, 2012 at 7:32 AM, Reuti <reuti at staff.uni-marburg.de> wrote:

> Hi,
>
> Am 10.02.2012 um 05:51 schrieb bharat gupta:
>
> > I have installed MPICH as per the instruction mentioned in README file
> for using it in gromacs. After executing the command :
> >
> > mdrun_mpi mdrun -np 4 -s prefix_.tpr -multi 4 -replex 1000
> >
> > I am getting the following error  :-
> >
> > Fatal error:
> > The number of nodes (1) is not a multiple of the number of simulations
> (4)
> >
> >
> > I asked the for help in gromacs user list and they replied that :
> >
> > If mdrun is reporting the number of nodes is 1, then you have not
> configured your MPI environment correctly so that it knows how many
> processors you have available. You will need to solve this by reading your
> MPI documentation.
> >
> > I have also checked my installation by running the following command on
> MPICH :-
> >
> > [root at BHARATPC mpich2-1.4.1p1]# mpiexec -n 4 ./examples/cpi
> > Process 0 of 4 is on BHARATPC
> > Process 1 of 4 is on BHARATPC
> >
> > Process 2 of 4 is on BHARATPC
> >
> > Process 3 of 4 is on BHARATPC
> > pi is approximately 3.1415926544231239, Error is 0.0000000008333307
> > wall clock time = 0.000447
> >
> > I am having 4 processors in my PC. I want to know how to configure MPI
> to recognize these 4 processors, so that I can use it in gromacs . Please
> help in this regard
>
> Although it should work with MPI: if you use only one machine you don't
> need MPI any longer as they implemented to use threads in Gromacs. Please
> have a look at the option -nt to mdrun in their man page.
>
> -- Reuti
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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