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On 26/01/2011 8:50 AM, Justin Kat wrote:
<blockquote
cite="mid:AANLkTinQR9Uman4Ciu4RmSprcrLOg9X+NWXBa7THVxX0@mail.gmail.com"
type="cite">Alright. So meaning I should have instead issued:<br>
<br>
<pre style="font-family: arial,helvetica,sans-serif;"><font size="2">./configure --enable-mpi --program-suffix=_mpi <code></code></font></pre>
<pre style="font-family: arial,helvetica,sans-serif;">
<font size="2">make mdrun</font></pre>
<pre style="font-family: arial,helvetica,sans-serif;"><font size="2">make install-mdrun</font></pre>
<pre><font style="font-family: arial,helvetica,sans-serif;" size="2">make links</font></pre>
<br>
to have installed an MPI-enabled executable called mdrun_mpi apart
from the existing mdrun executable? (Would I also need to append
the _mpi suffix when issuing the first two make and make install
commands above?<br>
</blockquote>
<br>
No. See <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Downloads/Installation_Instructions">http://www.gromacs.org/Downloads/Installation_Instructions</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinQR9Uman4Ciu4RmSprcrLOg9X+NWXBa7THVxX0@mail.gmail.com"
type="cite">
<br>
Thanks,<br>
Justin<br>
<br>
<div class="gmail_quote">On Mon, Jan 24, 2011 at 8:08 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
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 class="im"><br>
<br>
Justin Kat wrote:<br>
> Thank you for the reply!<br>
><br>
> hmm mdrun_mpi does not appear in the list of
executables in<br>
> /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<br>
> mdrun_mpi executable? And how should I go about getting
the mdrun_mpi<br>
> executable at this point?<br>
><br>
<br>
</div>
I see it now. When you configured with --enable-mpi, you
didn't specify<br>
--program-suffix=_mpi, so the installation procedure
over-wrote your existing<br>
(serial) mdrun with an MPI-enabled one simply called "mdrun."
The configure<br>
output should have warned you about this. You could, in
theory, simply re-name<br>
your existing executable "mdrun_mpi" and then re-install a
serial mdrun, if you<br>
need it.<br>
<font color="#888888"><br>
-Justin<br>
</font>
<div>
<div class="h5"><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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
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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