-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 24/07/13 03:00, Tim Wickberg wrote:
> I'm assuming the jobs are running across multiple nodes, using MPI > for communication? That's correct, 70 nodes each running 16 ranks per node. > I'm guessing that srun is resulting in communication going across a > GigE fabric rather than IB, where mpirun directly is using the IB. > A ~20% performance penalty would make sense in that context. Sadly I don't believe that's the case. I've checked and the NAMD processes have the IB verbs devices open in the same way they do with mpirun, plus I believe that NAMD2 is quite closely coupled as in the past we've run it over gigE as a test and found it performs really poorly. That was quite a few years ago now though since last time we tried it. All the best, Chris - -- Christopher Samuel Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.org.au/ http://twitter.com/vlsci -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlHvEikACgkQO2KABBYQAh/hHQCeLmZBX0YOYgVso+/P+lSkt8eZ 8noAn1NBHOiJF0Eww6+TX32na0CDVHVk =mkb0 -----END PGP SIGNATURE-----