Click Start Over at the left bottom to start Back to Content
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
setenv HUGETLB_DEFAULT_PAGE_SIZE 8M
setenv HUGETLB_MORECORE no
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.
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.