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Run instructions for NAMD.
ntell@iasa.gr
After build of NAMD you have an executable called namd2.
The best performance and scaling of namd is achieved using
hybrid MPI/MT version. On a system with nodes of NC cores per node
use 1 MPI task per node and NC threads per task,
for example on a 32 cores/node system use 1 MPI process,
set OMP_NUM_THREADS or any batch system related variable to 32.
Set a variable, for example MYPPN to NC-1,
for example to 31 for a 32 cores/node system.
You can also try other combinations of TASKSPERNODE/THREADSPERTASK to check.
The control file is stmv.8M.memopt.namd for tier-1 and stmv.28M.memopt.namd
for tier-0 systems.
The general way to run is :
WRAPPER WRAPPER_OPTIONS PATH_TO_namd2 +ppn $MYPPN stmv.8M.memopt.namd > logfile
WRAPPER and WRAPPER_OPTIONS depend on system, batch system etc.
Few common pairs are :
CRAY : aprun -n TASKS -N NODES -d THREADSPERTASK
Curie : ccc_mrun with no options - obtained from batch system
Juqueen : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS
Slurm : srun with no options, obtained from slurm if the variables below are set.
#SBATCH --nodes=NODES
#SBATCH --ntasks-per-node=TASKSPERNODE
#SBATCH --cpus-per-task=THREADSPERTASK
The run walltime is reported at the end of logfile : grep WallClock: logfile | awk -F ' ' '{print $2}'