Thanks for your help very much. <br><br>Best,<br><br>Ocean<br><br><div><span class="gmail_quote">On 12/21/06, <b class="gmail_sendername">Yang Ye</b> <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com
</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;">normally we use following commands when compiling gromacs<br>./configure ... --program_suffix=_mpi --enable-mpi ...
<br><br>So we will have mdrun_mpi in the end.<br><br>The usage of mdrun_mpi is the same as mdrun but -np, -replex and other<br>switches are activated.<br><br>That statement on the user manual is to clarify that you don't need
<br>MPI-enabled mdrun to run on a multiprocessor machine. But if you want to<br>tap the capability of the multiprocessor machine, you need to use MPI<br>and use mdrun_mpi<br><br>Regards,<br>Yang Ye<br><br>On 12/21/2006 4:20 PM, Seaclear Theory wrote:
<br>><br>><br>> On 12/20/06, *Mark Abraham* <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>> wrote:
<br>><br>> Seaclear Theory wrote:<br>> ><br>> ><br>> > On 12/20/06, *Mark Abraham* <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">
Mark.Abraham@anu.edu.au</a>><br>> > <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>>> wrote:
<br>> ><br>> > Seaclear Theory wrote:<br>> > > Hi! All,<br>> > ><br>> > > I have a linux server with 4 CPUs. How can I run gromacs<br>> on all CPUs?
<br>> > > The gromacs manual has very limit information. And it<br>> does not works.<br>> ><br>> > So which part of the manual section entitled "Running GROMACS in<br>
> > parallel" doesn't work?<br>> ><br>> ><br>> > What I want is to run gromacs on a signle machine with multiple<br>> > processors.<br>> ><br>> > In "
A.5 Running GROMACS in parallel"<br>> > "If you have a single machine with multiple processors you don't<br>> have to<br>> > use the mpirun command,<br>> > but you can do with an extra option to mdrun:
<br>> > % mdrun -np 8 -s topol -v -N 8<br>> > In this example MPI reads the first option from the command<br>> line. Since<br>> > mdrun also wants to<br>> > know the number of processes you have to type it twice."
<br>><br>> So what does it say? Should you be using mdrun_mpi? How about using a<br>> mpirun command anyway...<br>><br>> If you want meaningful feedback you need to describe your setup<br>> thoroughly, say what you've tried and why that didn't work and why
<br>> the<br>> error messages didn't help you. Otherwise, you need to pay someone<br>> for a<br>> support contract :-) I'll help solve problems, but I won't help if you<br>> don't give the impression you're helping yourself too!
<br>><br>> Mark<br>><br>><br>> I do not understand why you are so upset. Are you the author of the<br>> user manual :-) Any way, let's go back for the issue, not person.<br>><br>> The user manual said that "you don't have to use the mpirun command"
<br>> if you want to run gromacs on a single machine with multiple<br>> processors. How should I understand this? By the way, the manual (<br>> v.3.3) and the reference does not have information about "mdrun_mpi".
<br>> Thanks.<br>><br>> Ocean<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:
<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>> <<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a>><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>> <mailto:<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>> ------------------------------------------------------------------------<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 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>_______________________________________________<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 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></blockquote></div><br>