[gmx-users] mdrun_mpi executable not found

[Justin Kat]

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 <jalemkul at 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
>
> ========================================
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