NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Versions installées
- MPI version
- GPU version
$module avail namd namd/2.12 namd/2.11b2(default) namd/gpu/2.9b3
Using NAMD with MPI
SGE Example Script
- NAMD_mpi.sge
#!/bin/bash -l #----------------CHANGE-ONLY-HERE--------------------- #$ -pe mpi 32 #--------------^ (CPUs NUMBER) #------------^ (EXEC. TIME) #$ -q parallel.q #-------^(queue to use) #$ -N ABFhB #-------^ (JOB NAME) NAMD_SCRIPT=scriptname_without_extention #-----------------^ (SCRIPT NAME) #----------------------------------------------------- #$ -o compute.$JOB_ID.out -j y module load namd/2.12 echo " ## DEBUG ## This NAMD program got $NSLOTS slots across $NHOSTS machines..." echo "" echo "Calculated script is $NAMD_SCRIPT.namd" echo "" echo "Starting NAMD run at" `date` mpirun -np $NSLOTS namd2 $NAMD_SCRIPT.namd > $NAMD_SCRIPT.out echo "Finished NAMD run at" `date` exit 0
Using NAMD with OpenMP + GPU
For better performances please use one therad by GPu card. for example -pe openmp 2 and -l gpu=2
SGE script
- namd_gpu.sge
#!/bin/bash -l #----------------CHANGE-ONLY-HERE--------------------- #$ -pe openmp 2 #--------------^ (CPUs NUMBER) #------------^ (EXEC. TIME) #$ -q tesla.q #$ -l gpu=2 #-------^(QUEUE TO USE) #$ -N DR4_PBS_1 #-------^ (JOB NAME) NAMD_SCRIPT1=DR4_PBS.01b #----------------^ (SCRIPT NAME) #----------------------------------------------------- #$ -l h_vmem=800M module load namd/gpu/2.9b3 echo " ## DEBUG ## This NAMD program got $NSLOTS slots across $NHOSTS machines..." echo "" echo "Calculated script is $NAMD_SCRIPT1.namd" echo "" echo "Starting NAMD run at" `date` namd2 +p$NSLOTS +idlepoll $NAMD_SCRIPT1.namd > $NAMD_SCRIPT1.out echo "Finished NAMD run at" `date`
