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2.1 Run NAMD at Cray-XC40

Your batch job will need to load modules and set environment variables:

module swap PrgEnv-cray PrgEnv-gnu

module load rca

module load craype-hugepages8M



To run an SMP build with one process per node on 16 32-core nodes:

aprun -n 16 -r 1 -N 1 -d 31 /path/to/namd2 +ppn 30 +pemap 1-30 +commap 0 <configfile>

or the same with 4 processes per node:

aprun -n 64 -N 4 -d 8 /path/to/namd2 +ppn 7 +pemap 1-7,9-15,17-23,25-31 +commap 0,8,16,24 <configfile>

or non-SMP, leaving one core free for the operating system:

aprun -n 496 -r 1 -N 31 -d 1 /path/to/namd2 +pemap 0-30 <configfile>

The explicit +pemap and +commap settings are necessary to avoid having multiple threads assigned to the same core (or potentially all threads assigned to the same core). If the performance of NAMD running on a single compute node is much worse than comparable non-Cray host then it is very likely that your CPU affinity settings need to be fixed.

2.2 Compile NAMD

Tried every option at NAMD_2.13_Source/charm-6.8.2/src/arch/gni-crayxc. Only gnu works. The following is the building process.

2 Install NAMD2.13 at Cray-XC40