[gmx-users] Gromacs 5.1.2 and OMP_NUM_THREADS

[Mark Abraham]

Hi,

OpenMPI 1.10.0 has six months worth of bugs now fixed in 1.10.3, some of
which seem plausible to explain this behaviour. There's been no GROMACS
issue that seems similar. Please try another OpenMPI and let us know how
you go!

Mark

On Tue, 5 Jul 2016 15:55 Susan Chacko <susanc at helix.nih.gov> wrote:

>
> Hi all,
>
> One of our users is having problems with Gromacs 5.1.2. hanging at the
> start of an mdrun using OMP_NUM_THREADS=2. When run with OMP_NUM_THREADS=1,
> the job runs fine.
>
> The stalling command is:
> mpirun -np 128 mdrun_mpi -nb cpu -v -deffnm em
>
> The same command and job work fine in Gromacs 5.0.4 with OMP_NUM_THREADS=2
>
> Gromacs 5.0.4 and 5.1.2 were built on our system with Intel compiler
> 2015.1.133:
>
> cmake ../gromacs-5.1.2  \
> -DGMX_BUILD_OWN_FFTW=ON \
> -DREGRESSIONTEST_DOWNLOAD=ON \
> -DGMX_MPI=on \
> -DGMX_BUILD_MDRUN_ONLY=on  \
> -DBUILD_SHARED_LIBS=off
>
> One difference I can see is that Gromacs 5.0.4 was built with OpenMPI
> 1.8.4, and Gromacs 5.1.2 was built with OpenMPI 1.10.0. Is that likely to
> be the cause of the problem? If so, I could rebuilt Gromacs 5.1.2 with
> OpenMPI 1.8.4
>
> Any ideas what might be causing the stall? Any other flags we should use
> to compile?
>
> All suggestions appreciated,
> Susan.
>
>
> Susan Chacko, PhD
> HPC @ NIH staff
>
>
>
>
>
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