Thank you for the reply! hmm mdrun_mpi does not appear in the list of executables in /usr/local/gromacs/bin (and well therefore not in /usr/local/bin).
Which set of installation commands that I used should have compiled the mdrun_mpi executable? And how should I go about getting the mdrun_mpi executable at this point? Justin On Mon, Jan 24, 2011 at 6:57 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Justin Kat wrote: > > Dear gmx users, > > > > > > I have installed the parallel version 4.0.7 of gromacs on one of the > > nodes of my cluster. Here is the steps I've done through root: > > > > > > first, the normal installation: > > > > ./configure > > > > make > > > > > > make install > > > > make links > > > > > > > > then issued commands below for the mpi build: > > > > ./configure |--enable-mpi| > > > > make mdrun > > > > make install-mdrun > > > > make links > > > > > > I dont see any errors and everything seems to install fine. > > > > > > > > I then switch to a normal user to do my work and then after issuing the > grompp_md command as usual, I entered the command below: > > > > > > mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v >& > output.mdrun_md > > > > > > > > however, output.mdrun_md gives: > > > > > > > > mpirun was unable to launch the specified application as it could not > find an executable: > > > > > > > > > > Executable: mdrun_mpi > > Node: node3.reyclus.loc > > > > > > > > > > while attempting to start process rank 0. > > > > > > Was the installation procedure incorrect? Or do I need to go through a > > separate installation for the mdrun_mpi executable? Please guide me on > > what is wrong. > > > > No, the commands you gave should have built mdrun_mpi, as long as they > finished > successfully. Were there errors in the installation? > > With "make links" you should have links to all the Gromacs executables in > /usr/local/bin - are they there? You don't need to make links, instead you > can > follow the steps here: > > > http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation > > -Justin > > > Thanks, > > Justin > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists