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

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Sun Dec 2 08:28:07 CET 2012

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

mdrun_d -ntmpi 8 -deffnm ethrun
mdrun_d -nt 8 -deffnm ethrun
mdrun_d -deffnm ethrun
mdrun_d -ntomp 0 -deffnm ethrun
mdrun_d -ntomp 0 -ntmpi8 -deffnm ethrun

I get:
Fatal error:
OpenMP threads are requested, but Gromacs was compiled without OpenMP
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.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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