Hello<br>You'll need FFTW (<a href="http://fftw.org">fftw.org</a>) LAM/MPI (<a href="http://lam-mpi.org">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">gondo@ibb.unesp.br</a><br>+55 (14) 3811-6254<br>
<br style="color: rgb(0, 0, 0);"><a href="http://www.gromacs.org/documentation/reference/online/grompp.html"></a><font color="#b80047"><span style="color: rgb(0, 0, 0);"></span><br></font>On Thu, Mar 6, 2008 at 5:35 PM, Ricardo Soares <<a href="mailto:rsoares@fcfrp.usp.br">rsoares@fcfrp.usp.br</a>> wrote:<br>
> Hi everybody,<br>> <br>> I think this may sound rather trivial for most users, but I intend to<br>> install gromacs 3.3.1 on a dual core machine and I want to be sure what<br>> to do. Could anyone indicate me some online tutorial to do so (as well<br>
> some simulation examples)? Is this considered parallelization (within<br>> one computer)? Simply compiling mdrun with MPI works?<br>> <br>> Thanks in advance.<br>> <br>> --<br>> ___________________________________________________________<br>
> <br>> Ricardo Oliveira dos Santos Soares<br>> Post-graduation Student in Biological Physics<br>> University of Sao Paulo - USP<br>> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP<br>> Phone: 55 (16) 3602-4840<br>
> Curriculum Lattes - <a href="http://lattes.cnpq.br/0777038258459931">http://lattes.cnpq.br/0777038258459931</a><br>> ___________________________________________________________<br>> <br>> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> <br><br>