[gmx-users] Gromacs 5.1.2 and OMP_NUM_THREADS

[Susan Chacko]

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