[gmx-developers] Gromacs trying to use OpenMP instead of thread-mpi despite trying to convince it?
roland at utk.edu
Mon Dec 3 05:12:31 CET 2012
On Sun, Dec 2, 2012 at 12:58 PM, Shirts, Michael (mrs5pt) <
mrs5pt at eservices.virginia.edu> wrote:
> So, more progress, but no simulations running yet.
> mdrun -nt 8 -ntmpi 8 gives the same error as before (I actually tried that
> before, and forgot to include it in my error report)
> mdrun -ntmpi 8 -ntomp 1 gives the error
> Fatal error:
> OMP_NUM_THREADS (8) and the number of threads requested on the command line
> (1) have different values
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
We probably should print a notice that OMP_NUM_THREADS is set. Otherwise
this is really confusing if OMP_NUM_THREADS isn't set by the user but by
> Fatal error:
> OMP_NUM_THREADS is invalid: '0'
This is also for ntomp. Also there you wand to use 1 not 0 to disable
OpenMP (1 because it is total number of threads and thus 1 means serial).
> /var/spool/PBS/mom_priv/jobs/2053253.lc5.itc.virginia.edu.SC: line 22:
> Illegal instruction /h3/n1/shirtsgroup/gromac
> s_46/install/bin/mdrun_d -ntomp 1 -ntmpi -8 -deffnm
I suppose the CPU on the compute node is different from the build host. You
need to change GMX_CPU_ACCELERATION to the one correct for the compute
node. It could also help to set GMX_DISTRIBUTABLE_BUILD (both are cmake
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> > From: Berk Hess <hess at kth.se>
> > Date: Sun, 2 Dec 2012 09:34:11 +0100
> > To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>,
> > list for GROMACS development <gmx-developers at gromacs.org>
> > Subject: Re: [gmx-developers] Gromacs trying to use OpenMP instead of
> > thread-mpi despite trying to convince it?
> > 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
> >> 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
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