I am not sure that mdrun_mpi or for that matter mdrun with options -np 2 -multi 1 (I have a core 2 duo machine) is actually running the process parallely, as the estimated time for completion for a simulation is the same as without.<br>
<br>I have built open-mpi library, so do I have to make some changes at its configuration level(even if I am using single machine with multiple core processor)? Like adding localhost and the no. of nodes. If yes, then can anybody help me with that.<br>
<br>Also, for the information, mdrum_mpi or mdrun with relevant options shows NNODES=1. why?<br><br>Thanks,<br>Manik<br><br><div class="gmail_quote">On Thu, Dec 18, 2008 at 1:24 PM, Jussi Lehtola <span dir="ltr"><<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">On Thu, 2008-12-18 at 01:03 +0530, Chitrita Dutta Roy wrote:<br>
> Can anyone give me a detailed notes on how to install gromacs 4 with<br>
> mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as<br>
> i am new to using gromacs plz give me as detailed note as possible..<br>
<br>
</div>Just install using yum:<br>
<br>
# yum -y install gromacs gromacs-mpi<br>
<br>
Due to some clashing names, all binaries have been renamed to start with<br>
g_, i.e. mdrun is g_mdrun and so on. Everything is compiled both in<br>
single and double precision, and MPI binaries are available of mdrun<br>
(and once the Makefiles are updated I'll put in also the MPI enabled<br>
analysis tools).<br>
<br>
Example:<br>
g_mdrun single precision<br>
g_mdrun_d double precision<br>
g_mdrun_mpi single precision MPI<br>
g_mdrun_mpi_d double precision MPI<br>
--<br>
------------------------------------------------------<br>
Jussi Lehtola, FM, Tohtorikoulutettava<br>
Fysiikan laitos, Helsingin Yliopisto<br>
<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>, p. 191 50632<br>
------------------------------------------------------<br>
Mr. Jussi Lehtola, M. Sc., Doctoral Student<br>
Department of Physics, University of Helsinki, Finland<br>
<font color="#888888"><a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a><br>
------------------------------------------------------<br>
</font><div><div></div><div class="Wj3C7c"><br>
<br>
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