Thanks for the guideline. I installed the lam/mpi 7.0.6 and compile the gromance with "--enable-mpi" option. <br>When I run mdrun, I got message that lamboot is not start. Then I start the lamboot and try to run mdrun witn "-np 4 -v N 4" (gromacs user guide example). However, the gromacs still run on single CPU. It does not take the advantage of other three CPUs on the server. Do I miss anything? Or I misunderstand the parallel computing/MPI concept? Thanks.
<br><br>Best,<br><br>Ocean<br><br><div><span class="gmail_quote">On 12/20/06, <b class="gmail_sendername">Erik Lindahl</b> <<a href="mailto:lindahl@cbr.su.se">lindahl@cbr.su.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>On Dec 21, 2006, at 3:12 AM, Seaclear Theory wrote:<br><br>> Hi! All,<br>><br>> I have a linux server with 4 CPUs. How can I run gromacs on all CPUs?<br>> The gromacs manual has very limit information. And it does not works.
<br>> I installed Lam/mpi and compile gromacs with mpi. Thanks lot!<br>><br><br>The problem is that there is no standard for how you start MPI<br>programs - that is entirely up to the MPI implementation.<br><br>Essentially, add "-np 4" to grompp to get a parallel input file, boot
<br>your "virtual" parallel computer with "lamboot <hostfile>", and then<br>start a parallel run as "mpirun -np 4 mdrun <normal args>".<br><br>Most MPI libraries use mpirun is some form, but they differ in how
<br>you specify the machines to run on.<br><br>Cheers,<br><br>Erik<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">
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