[mpich-discuss] Using MPICH for gromacs

[bharat gupta]

Hi,

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






-- 
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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