Thank you for the reply! <br><br>hmm mdrun_mpi does not appear in the list of executables in /usr/local/gromacs/bin (and well therefore not in /usr/local/bin).<br><br>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?<br>
<br>Justin<br><br><br><div class="gmail_quote">On Mon, Jan 24, 2011 at 6:57 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Justin Kat wrote:<br>
> Dear gmx users,<br>
><br>
><br>
> I have installed the parallel version 4.0.7 of gromacs on one of the<br>
> nodes of my cluster. Here is the steps I've done through root:<br>
><br>
><br>
> first, the normal installation:<br>
><br>
> ./configure<br>
><br>
> make<br>
><br>
><br>
> make install<br>
><br>
> make links<br>
><br>
><br>
><br>
> then issued commands below for the mpi build:<br>
><br>
> ./configure |--enable-mpi|<br>
><br>
> make mdrun<br>
><br>
> make install-mdrun<br>
><br>
> make links<br>
><br>
><br>
> I dont see any errors and everything seems to install fine.<br>
><br>
><br>
><br>
> 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:<br>
><br>
><br>
> mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v >& output.mdrun_md<br>
><br>
><br>
><br>
> however, output.mdrun_md gives:<br>
><br>
><br>
><br>
> mpirun was unable to launch the specified application as it could not find an executable:<br>
><br>
><br>
><br>
><br>
> Executable: mdrun_mpi<br>
> Node: node3.reyclus.loc<br>
><br>
><br>
><br>
><br>
> while attempting to start process rank 0.<br>
><br>
><br>
> Was the installation procedure incorrect? Or do I need to go through a<br>
> separate installation for the mdrun_mpi executable? Please guide me on<br>
> what is wrong.<br>
><br>
<br>
</div></div>No, the commands you gave should have built mdrun_mpi, as long as they finished<br>
successfully. Were there errors in the installation?<br>
<br>
With "make links" you should have links to all the Gromacs executables in<br>
/usr/local/bin - are they there? You don't need to make links, instead you can<br>
follow the steps here:<br>
<br>
<a href="http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation</a><br>
<br>
-Justin<br>
<br>
> Thanks,<br>
> Justin<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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