[gmx-users] question about parallel runing of gromacs
swallowswift at gmail.com
Tue Mar 10 16:32:08 CET 2009
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?
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.
> 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
> % 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 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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