[gmx-users] Hyper-threading Gromacs 5.0.1

[Johnny Lu]

Ah. Thanks a lot.
As suggested by (
https://www.ibm.com/developerworks/community/blogs/brian/entry/linux_show_the_number_of_cpu_cores_on_your_system17?lang=en),

$ cat /proc/cpuinfo | grep "physical id" | sort | uniq | wc -l
2
$ cat /proc/cpuinfo | egrep "core id|physical id" | tr -d "\n" | sed
s/physical/\\nphysical/g | grep -v ^$ | sort | uniq | wc -l
12

There are 12 real cores.
Type "top" and then press 1 sometimes give double the number of real cores,
but sometimes doesn't double the number (tested on different machines).

How to run "an MPI  rank per core" ? By this way? "OMP_NUM_THREADS=12
mdrun" on a 12 core machine?

I tried openmp threads instead of mpi thread because gromacs wiki says
openmp threads are faster than mpi based parallelization.

from the gromacs wiki (
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI_and_OpenMP
):

In GROMACS 4.6 compiled with thread-MPI, OpenMP-only parallelization is the
default with Verlet scheme when using up to 8 cores on AMD platforms and up
to 12 and 16 cores on Intel Nehalem and Sandy Bridge, respectively. Note
that even running across two CPUs (in different sockets) on Intel platforms
OpenMP mutithreading is, in the majority of the cases, significantly faster
than MPI-based parallelization.

...

Assuming that there are N cores available, the following commands are
equivalent:

mdrun -ntomp N -ntmpi 1
OMP_NUM_THREADS=N mdrun
mdrun #assuming that N <= 8 on AMD or N <= 12/16 on Intel Nehalem/Sandy Bridge