[gmx-users] Thread affinity setting failed

[Reid Van Lehn]

Hello users,

I ran into a bug I do not understand today upon upgrading from v. 4.5.5 to
v 4.6. I'm using older 8 core Intel Xeon E5430 machines, and when I
submitted a job for 8 cores to one of the nodes I received the following
error:

NOTE: In thread-MPI thread #3: Affinity setting failed.
      This can cause performance degradation!

NOTE: In thread-MPI thread #2: Affinity setting failed.
      This can cause performance degradation!

NOTE: In thread-MPI thread #1: Affinity setting failed.
      This can cause performance degradation!

I ran mdrun simply with the flags:

mdrun -v -ntmpi 8 -deffnm em

Using the top command, I confirmed that no other programs were running and
that mdrun was in fact only using 5 cores. Reducing -ntmpi to 7, however,
resulted in no error (only a warning about not using all of the logical
cores) and mdrun used 7 cores correctly. Since it warned about thread
affinity settings, I tried setting -pin on -pinoffset 0 even though I was
using all the cores on the machine. This resulted in the same error.
However, turning pinning off explicitly with -pin off (rather than -pin
auto) did correctly give me the all 8 cores again.

While I figured out a solution in this particular instance, my question is
whether I should be have known from my hardware/settings that pinning
should be turned off (for future reference), or if this is a bug?

Thanks!
Reid