Thanks for your help very much. Best,
Ocean On 12/21/06, Yang Ye <[EMAIL PROTECTED]> wrote:
normally we use following commands when compiling gromacs ./configure ... --program_suffix=_mpi --enable-mpi ... So we will have mdrun_mpi in the end. The usage of mdrun_mpi is the same as mdrun but -np, -replex and other switches are activated. That statement on the user manual is to clarify that you don't need MPI-enabled mdrun to run on a multiprocessor machine. But if you want to tap the capability of the multiprocessor machine, you need to use MPI and use mdrun_mpi Regards, Yang Ye On 12/21/2006 4:20 PM, Seaclear Theory wrote: > > > On 12/20/06, *Mark Abraham* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Seaclear Theory wrote: > > > > > > On 12/20/06, *Mark Abraham* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > > <mailto:[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>> wrote: > > > > Seaclear Theory wrote: > > > Hi! All, > > > > > > I have a linux server with 4 CPUs. How can I run gromacs > on all CPUs? > > > The gromacs manual has very limit information. And it > does not works. > > > > So which part of the manual section entitled "Running GROMACS in > > parallel" doesn't work? > > > > > > What I want is to run gromacs on a signle machine with multiple > > processors. > > > > In "A.5 Running GROMACS in parallel" > > "If you have a single machine with multiple processors you don't > have to > > use the mpirun command, > > but you can do with an extra option to mdrun: > > % mdrun -np 8 -s topol -v -N 8 > > In this example MPI reads the first option from the command > line. Since > > mdrun also wants to > > know the number of processes you have to type it twice." > > So what does it say? Should you be using mdrun_mpi? How about using a > mpirun command anyway... > > If you want meaningful feedback you need to describe your setup > thoroughly, say what you've tried and why that didn't work and why > the > error messages didn't help you. Otherwise, you need to pay someone > for a > support contract :-) I'll help solve problems, but I won't help if you > don't give the impression you're helping yourself too! > > Mark > > > I do not understand why you are so upset. Are you the author of the > user manual :-) Any way, let's go back for the issue, not person. > > The user manual said that "you don't have to use the mpirun command" > if you want to run gromacs on a single machine with multiple > processors. How should I understand this? By the way, the manual ( > v.3.3) and the reference does not have information about "mdrun_mpi". > Thanks. > > Ocean > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users > <http://www.gromacs.org/mailman/listinfo/gmx-users> > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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