[mvapich-discuss] MVAPICH2 2.2, GROMACS 2016.x, and MV2_ENABLE_AFFINITY

[Ryan Novosielski]

Hi all,

I had reported to me some time ago users seeing an error like the following when running GROMACS with MVAPICH2 2.2 (using PMI2 with SLURM 16.05.10):

[novosirj at perceval2 build]$ module load intel/17.0.1  mvapich2/2.2 gromacs
[novosirj at perceval2 build]$ srun --pty -p main -t 20:00 bash -i
[novosirj at node073 build]$ gmx_mpi
Warning! : Core id 32525 does not exist on this architecture!
CPU Affinity is undefined
Error parsing CPU mapping string
INTERNAL ERROR: invalid error code ffffffff (Ring Index out of range) in MPIDI_CH3I_set_affinity:2391

I recently discovered that I can get around this by setting MV2_ENABLE_AFFINITY=0. I’m told by one of my users that they don’t see this on MVAPICH2 2.1 or 2.3a. Does anyone know what the deal is with this and whether there’s something wrong that causes it?

I see someone else asked about this right around the time of SC16, but there doesn’t seem to have been a resolution:

http://mailman.cse.ohio-state.edu/pipermail/mvapich-discuss/2016-November/006253.html

Thanks!

--
____
|| \\UTGERS,  	 |---------------------------*O*---------------------------
||_// the State	 |         Ryan Novosielski - novosirj at rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
||  \\    of NJ	 | Office of Advanced Research Computing - MSB C630, Newark
     `'

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