[gmx-users] run gromacs on a single machine with mutiple CPUs

[Yang Ye]

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* <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     Seaclear Theory wrote:
>     >
>     >
>     > On 12/20/06, *Mark Abraham* <Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>
>     > <mailto:Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>>> 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
>
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