[gmx-developers] Gromacs trying to use OpenMP instead of thread-mpi despite trying to convince it?

[Berk Hess]

Hi,

You queuing system probably doesn't set OMP_NUM_THREADS then
and I assume this machine has at least 16 (HT) cores.
mdrun -ntmpi 8 -ntomp 1
will do what you want, or:
mdrun -nt 8 -ntmpi 8

Cheers,

Berk

On 12/02/2012 08:28 AM, Shirts, Michael (mrs5pt) wrote:
> Quick question:
>
> Compiling the most recent code in release-4-6, I compile without OpenMP
> (because using group rather than verlet cutoffs), and using any of the
> below:
>
> mdrun_d -ntmpi 8 -deffnm ethrun
> or
> mdrun_d -nt 8 -deffnm ethrun
> or
> mdrun_d -deffnm ethrun
> or
> mdrun_d -ntomp 0 -deffnm ethrun
> or
> mdrun_d -ntomp 0 -ntmpi8 -deffnm ethrun
>
> I get:
> Fatal error:
> OpenMP threads are requested, but Gromacs was compiled without OpenMP
> support
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Even though I'm presumably requesting thread-mpi.  Worked fine with -nt
> previously (before the new -nt options introduced a few months back).
>
> Any suggestions or something I'm doing wrong?  Perhaps gromacs is
> interpreting the cluster environment as requesting OpenMP somehow? FWIW, the
> PBS script request line is "#PBS -l select=1:mpiprocs=8:ncpus=8".
>
> Apologies if I missed this answers somewhere out there already.
>
> Thanks,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>