[gmx-users] question about parallel runing of gromacs

[Xiang Mao]

I got something like this in log file

Host:XXX  pid:5504  nodeid :0  nnodes:1

and I think I compiled mdrun_mpi using --enable-mpi. I am wondeirng if I
should use lam_mpi instead of MPICH2?

thanks.

On Mon, Mar 9, 2009 at 11:03 PM, Diego Enry Gomes <diego.enry at gmail.com>wrote:

>  On Mar 9, 2009, at 5:12 PM, Mark Abraham wrote:
>
>  Xiang Mao wrote:
>
> My PC has a intel core2 cpu. I compiled gromacs under cygwin, and using
> MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi .... to run EM, MD.
>
>
> OK that might be working right. Now you need to look in the log file for an
> indication of whether the run has two component processes or one - right at
> the top, usually.
>
> Mark
>
>
> Hi Xiang, maybe the solution is simple and you just didn't use the
> "--enable-mpi" flag in the ./configure step.
> That explains the duplicate steps.
>
> Try a quick "ldd" test to check if MPI compilation worked.
>
> % which mdrun_mpi     (find where mdrun was installed, mine is at
> /usr/local/gmx4/bin/)
> % ldd /usr/local/gmx4/bin/mdrun_mpi
>
> You should see "libmpi.so.0" in the list of libraries, if not, go back to
> the ./configure step.
>
>
> Diego
>
> --
> =========================================
> Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
> /tmp/home/@ Pacific Northwest National Laboratory
>  Richland, WA.  +1 (509) 372.6363
> diegoenry.gomes at pnl.gov
> =========================================
>
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