Thank you Mark.
Sorry, I forgot to mention that I already installed MPI library. I used following .rpm files to install MPI. openmpi-1.2.3-4.fc8.i386.rpm openmpi-devel-1.2.3-4.fc8.i386.rpm openmpi-libs-1.2.3-4.fc8.i386.rpm The details of the installation: Step 1: FFTW (fftw-3.0.1.tar.gz) Step 2. MPI (all the above openmpi rpms) Step 3. GROMACS (gromacs-3.3.1.tar.gz) The output of "which mpirun" is ==================================== [EMAIL PROTECTED] ~]$ which mpirun /usr/bin/mpirun [EMAIL PROTECTED] ~]$ ==================================== I was thinking MPI and LAM are to be installed separately. That's what confused me. But, now it is clear. Thank you again. Regards, sunita > ----- Original Message ----- > From: [EMAIL PROTECTED] > Date: Wednesday, February 13, 2008 10:20 pm > Subject: Re: [gmx-users] "Lam" is not required for running parallel job > To: Discussion list for GROMACS users <[email protected]> > >> > >> > >> > ----- Original Message ----- >> > From: [EMAIL PROTECTED] >> > Date: Wednesday, February 13, 2008 5:40 pm >> > Subject: [gmx-users] "Lam" is not required for running >> parallel job >> > To: [email protected] >> > >> >> Dear Users, >> >> >> >> Lam doesn't seem to be essential for running parallel job. >> > >> > An MPI library is essential. >> > >> >> Because in one of our Xeon machine with quardcore 1.6 Ghz >> >> processor and >> >> with 6 nodes we installed parallel version of gromacs (version >> >> 3.3.1) and >> >> its running without any problem. Lam is not installed in this >> machine>> still it is running the parallel job. >> > >> > How are you running grompp and mdrun, and what makes you think the >> > calculation is running in parallel? >> > >> I used the following command to run parallel job and tested it by >> generating .tpr file for 2 nodes, 4 nodes and 6 nodes. With 6 >> nodes it >> took least time to finish the mdjob. >> >> grompp -np 6 -f ...... >> mpirun -np 6 mdrun_mpi -v -s ..... >> >> It seems correct to me. >> What do you say? > > You have an MPI library installed, else mpirun would not exist. Said > library doesn't have to be called LAM, however. It also existed when > someone compiled mdrun_mpi, unless they actually did it single-processor > and your above snippets don't reflect what you're actually doing. > > It's a good idea when seeking feedback to give full information, e.g. > copying and pasting your actual commands. If the contents of your head > were always right, you would probably already have solved your own > problem. Accordingly, we'd much prefer know what you actually did, rather > than something that's been filtered through your head. :-) > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
