[gmx-users] SMP/Parallel mdrun

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 27 04:10:38 CET 2008

Ian Stokes-Rees wrote:
> Hi Mark,
> Mark Abraham wrote:
>> Terminology - GROMACS is not threaded, but uses MPI processes for 
>> parallelism.
> Yes, I gathered that.
>>> I have an MPI-compiled version of gromacs v4.0 and am attempting to 
>>> get parallel execution on a 2x2 core AMD Opteron system via:
>>> $ lamboot
>>> $ mdrun -np 4 -s ../1WOM.tpr -v -N 4
>> -N does nothing, and -np is no longer accepted - as you'd know from 
>> reading mdrun -h, right?
> That is a bit of a condecending way of putting it. If I knew -N did 
> nothing and -np was no longer accepted, then of course I would not have 
> used them. In fact, I was reading the documentation from a file called 
> "manual-4.0.pdf" which stated:
> "
> If you have a single machine with multiple processors you don’t have to 
> use the mpirun com-
> mand, but you can do with an extra option to mdrun:
> % mdrun -np 8 -s topol -v -N 8
> "
> so that is where I took the example from. I think this PDF was linked 
> from the gromacs "documentation" section of the website.

Hmmm that's been in the documentation since v3.3 and I've never seen 
code that might make it work. That looks like a documentation error.


More information about the gromacs.org_gmx-users mailing list