Special Linux-KNL-icc and CRAY-XC-KNL-intel builds enable vectorizable mixed-precision kernels while preserving full alchemical and other functionality. Multi-host runs require multiple smp processes per host (as many as 13 for Intel Omni-Path, 6 for Cray Aries) in order to drive the network. Careful attention to CPU affinity settings (see below) is required, as is 1 or 2 (but not 3 or 4) hyperthreads per PE core (but only 1 per communication thread core).
There appears to be a bug in the Intel 17.0 compiler that breaks the non-KNL-optimized NAMD kernels (used for alchemical free energy, etc.) on KNL. Therefore the Intel 16.0 compilers are recommended on KNL.