Affinity setting not supported on Cray XK7
The Cray programming environment (xt-asyncpe) somewhere between the version 5.17(5.18?) and 5.20 versions broke
mdrun-s affinity setting capabilities - at least that's what the warning message appearing in the stderr and log suggests.
The behavior was observed on Toedi, the Cray XK7 at CSCS.
Note that by default aprun sets thread affinites (the default is
-cc cpu), but this results in poor performance. Previously, the
-cc none setting has been used to disable the aprun-set affinities and rely on the affinity set by mdrun.
#1 Updated by Szilárd Páll about 7 years ago
Note that based on performance observed earlier, I suspect that already Cray runtimes preceding xt-asyncpe 5.17 were perhaps silnetly ignoring affinity settings. I'm not entirely sure, I'll have to dig up some old log files and redo the runs with affinities set through aprun which seems to work; e.g. for a Cray XK7 with a single Interlagos CPU per rank, running 4 ranks with 4 threads each getting the otherwise default mdrun affinity requires
aprun -cc 0,1,2,3:4,5,6,7:8,9,10,11:12,13,14,15.