Xiang Mao wrote:
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?
It is better to *know* than to *think.* Did you try what was suggested to you
with ldd? If so, what did it show? Based on the log file, you probably did not
--enable-mpi.
MPICH2 is fine, no need to use LAM.
-Justin
thanks.
On Mon, Mar 9, 2009 at 11:03 PM, Diego Enry Gomes <diego.e...@gmail.com
<mailto:diego.e...@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
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========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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