<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>On Mar 9, 2009, at 5:12 PM, Mark Abraham wrote:</div><div><div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Xiang Mao wrote:<br><blockquote type="cite">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.<br></blockquote><br>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.<br><br>Mark<br></div></blockquote><div><div><br></div><div>Hi Xiang, maybe the solution is simple and you just didn't use the "--enable-mpi" flag in the ./configure step. </div><div>That explains the duplicate steps.</div><div><br></div><div>Try a quick "ldd" test to check if MPI compilation worked.</div><div><br></div><div>% which mdrun_mpi (find where mdrun was installed, mine is at /usr/local/gmx4/bin/)</div><div>% ldd /usr/local/gmx4/bin/mdrun_mpi </div><div><br></div><div>You should see "libmpi.so.0" in the list of libraries, if not, go back to the ./configure step.</div><div><br></div><div><br></div></div><div>Diego</div><div><br></div><div>--</div><div>=========================================</div><div>Diego Enry B Gomes | PhD Student @ UFRJ - Brazil</div><div>/tmp/home/@ Pacific Northwest National Laboratory</div><div><div>Richland, WA. +1 (509) 372.6363 </div><div><a href="mailto:diegoenry.gomes@pnl.gov">diegoenry.gomes@pnl.gov</a></div><div>=========================================</div></div></div></div></body></html>