[gmx-users] Gromacs 5.0.2 no parallei run

[Jernej Zidar]

Hi all,
  Lately I noticed I have a rather weird problem with Gromacs on my
workstation and I'm unable to pinpoint whether it's a hardware or a
software problem.

  The problem is that none of the jobs are using all the CPUs or
threads. I compiled Gromacs with support for OpenMP and without
support for MPI and GPU as instructed on the documentation page. FFTW
was pulled of the internet during the make stage.

  After building Gromacs I load up the environment and start a job:
mdrun -v -deffnm system1-npt-prod -maxh 0.1 -nsteps -1

Until recently, the job would start with 1 MPI thread and 12 OpenMP
threads and use all the available CPUs (the machine is a dual Xeon
X5650 machine with hyperthreading disabled) as evidenced by the usage
in utilities like 'top'/'htop'. The end result is relatively decent
performance of ~20 ns/day for the system1.

What happens now is that I get this message from Gromacs:
Non-default thread affinity set, disabling internal thread affinity
Using 1 MPI thread
Using 12 OpenMP threads

On another machine that is similar in terms of hardware, the job
starts without any complaints:
Overriding nsteps with value passed on the command line: -1 steps, -0.002 ps
Using 1 MPI thread
Using 12 OpenMP threads

I can't find any error in the log file. It appears the CPUs are
somewhat off-limits for me. Running the job as root or rebooting
doesn't help.

I'm running Debian stable (Wheezy) with nothing much installed.

Any advice will be appreciated!

Thanks in advance,
Jernej Zidar