<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Looks like you are using MPICH2 as "mpi" software. </div><div>Try including "mpirun" before mdrun_mpi.</div><div><br></div><div>mpirun -n 4 mdun_mpi -v -s topol.tpr</div><div><br></div><div><br></div><div>If that doesn't work you shoud run start the MPI DAEMON ( MPD ) before mpirun:</div><div><br></div><div>mpdboot </div><div><div>mpirun -n 2 mdun_mpi -v -s topol.tpr</div><div><br></div><div>after you job finishes you might want to stop the mpi daemon by running:</div><div>mpdallexit </div></div><div><br></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><br></div></div><div><br></div><div><div>On Mar 6, 2009, at 5:13 AM, ANINDITA GAYEN wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0" style="position: static; z-index: auto; "><tbody><tr><td valign="top" style="font: inherit;"><p style="MARGIN-BOTTOM: 0in">Dear all, </p><p style="MARGIN-BOTTOM: 0in"> Sorry for the former post without any subject.<br> I want to install <span>gromacs</span> in parallel version. I already have the normal version of gromacs and i want an MPI version of mdrun. The commands i have used are as followed.........<br><b>make distclean</b><br><b>./configure --enable-float --enable-mpi --prefix=/home/x --program-suffix=_mpi</b><br><b>make mdrun -j 4</b><br><b>make install-mdrun</b><br>[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include .......<br> export CPPFLAGS=-I/home/x/fftw-3.2.1/include<br> export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]<br>grmmacs installation run successfully.<br>But when i run <br>mdrun_mpi ..................i got the message "Can't read MPIRUN_MPD" and the mdrun_mpi program does not run.<br>Any suggestion regarding this problem will be highly acceptable.<br>thanks in advance,<br><br>Ms. Anindita Gayen<br>C/O Dr. Chaitali Mukhopadhyay<br>Senior Research Fellow<br>Department of Chemistry<br>University of Calcutta<br>92, A. P. C. Road<br>Kolkata-700 009<br>India</p></td></tr></tbody></table><br> <!--6--><hr size="1"> Add more friends to your messenger and enjoy! <a href="http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/"> Invite them now.</a>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></body></html>