next up previous contents index
Next: SGI Altix UV Up: Running NAMD Previous: Shared-Memory and Network-Based Parallelism   Contents   Index

Cray XT

You will need to load the GNU compiler module, build Charm++ for mpi-crayxt and NAMD for CRAY-XT-g++, use the following command in your batch script:

  aprun -n $PBS_NNODES -cc cpu namd2

To reduce memory usage, build Charm++ mpi-crayxt-smp instead and use (assuming you have 12 cores per node on your machine):

setenv MPICH_PTL_UNEX_EVENTS 100000
@ NPROC = $PBS_NNODES / 12
aprun -n $NPROC -N 1 -d 12 namd2 +ppn 11 +setcpuaffinity +pemap 1-11 +commap 0

For two processes per node (for possibly better scaling) use:

setenv MPICH_PTL_UNEX_EVENTS 100000
@ NPROC = $PBS_NNODES / 6
aprun -n $NPROC -N 2 -d 6 namd2 +ppn 5 +setcpuaffinity \
                                +pemap 1-8,10,11 +commap 0,9 ...

For three processes per node use:

setenv MPICH_PTL_UNEX_EVENTS 100000
@ NPROC = $PBS_NNODES / 4
aprun -n $NPROC -N 3 -d 4 namd2 +ppn 3 +setcpuaffinity \
                                +pemap 1-5,7,8,10,11 +commap 0,6,9 ...

The strange +pemap and +commap settings place the communication threads on cores that have been observed to have higher operating system loads.



http://www.ks.uiuc.edu/Research/namd/