Hello Ricardo<br><br>Did you install with the sources ? (make install) ?<br>Go to the folder where you ran this command and run "make uninstall"<br><br>
Matheus Fazian Ige Gondo<br>
Departamento de Física e Biofísica<br>
Instituto de Biociências<br>
Unesp - Botucatu - SP<br>
<a href="mailto:gondo@ibb.unesp.br" target="_blank">gondo@ibb.unesp.br</a><br>
+55 (14) 3811-6254<br><br><div class="gmail_quote">On Tue, Mar 11, 2008 at 1:55 PM, Ricardo Soares <<a href="mailto:rsoares@fcfrp.usp.br">rsoares@fcfrp.usp.br</a>> 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 bgcolor="#ffffff" text="#000000"><div class="Ih2E3d">
Kpiwara De X-nelo wrote:
<blockquote cite="http://mid3087adce0803101902x5cd40634w104db7a7b10c76aa@mail.gmail.com" type="cite">Hello<br>
You'll need FFTW (<a href="http://fftw.org" target="_blank">fftw.org</a>) LAM/MPI (<a href="http://lam-mpi.org" target="_blank">lam-mpi.org</a>) and gromacs sources<br>
Download the 3 packages<br>
start with the Lam/MPI (configure , make , make install)<br>
Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is
still unstable) (configure --enable-mpi, make, make install)<br>
Then, finally, the GROMACS (configure --with-fft=fftw2 --enable-mpi ,
make , make install)<br>
<br>
It should be running<br>
as a non root user type lamboot<br>
It should start the lam/mpi<br>
<br>
run your simulations as usual just changing these<br>
grompp -v -f xx -o xx -c xx -p xx -<span style="color: rgb(255, 0, 0);">np
#<br>
<br>
<font color="#000000">the -np </font></span>generate statusfile for
# nodes<span style="color: rgb(255, 0, 0);"><br>
</span><br>
then<br>
<br style="color: rgb(0, 0, 0);">
<font color="#b80047"><span style="color: rgb(0, 0, 0);">mpirun c0 C
mdrun
-v -s xx -o xx -e xx -c xx -g x <span style="color: rgb(255, 0, 0);">-np
#</span> log >& xx<br>
<br>
</span></font> Number of nodes (#) , must be the same as used for
grompp<br>
<br>
the mpirun c0 C tells it to run on the maximun available nodes.<br>
<br>
Hope I helped.<br>
<br>
Matheus Fazian Ige Gondo<br>
Departamento de Física e Biofísica<br>
Instituto de Biociências<br>
Unesp - Botucatu - SP<br>
<a href="mailto:gondo@ibb.unesp.br" target="_blank">gondo@ibb.unesp.br</a><br>
+55 (14) 3811-6254<br>
</blockquote></div>
Hello Matheus, you sure did help!<br>
But that way I'd need to uninstall gromacs and reinstall. Is there a
way to include the LAM/MPI package in an already installed instance of
Gromacs? If not, how do I uninstal it?<br>
<br>
Thanks again!<br>
<pre cols="72">--
___________________________________________________________
Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - <a href="http://lattes.cnpq.br/0777038258459931" target="_blank">http://lattes.cnpq.br/0777038258459931</a>
___________________________________________________________</pre>
</div>
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