How to use NAMD¶
|
Software
|
Version
|
Cluster
|
|---|---|---|
|
NAMD
|
3.06b
|
Dardel
|
Running on Dardel¶
Example job script for regular NAMD run on 2 nodes:
#!/bin/bash -l
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=128
# load the NAMD module
ml PDC/23.03
ml namd/3.0b6-cpeGNU-23.03
# Run namd
srun namd3 input.namd > output_file
Example job script for a 2-node shared-memory NAMD run with one MPI process per node:
#!/bin/bash -l
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=1
# load the NAMD module
ml PDC/23.03
ml namd/3.0b6-cpeGNU-23.03
# Run namd
srun -n 2 namd3 +ppn 31 input.namd > output_file
Example job script for a 2-node shared-memory NAMD run with 4 MPI processes per node and explicit mapping of communication and processing cores:
#!/bin/bash -l
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=4
# load the NAMD module
ml PDC/23.03
ml namd/3.0b6-cpeGNU-23.03
# Run namd
srun -n 8 namd3 +ppn 7 +pemap 1-7,9-15,17-23,25-31 +commap 0,8,16,24 input.namd > output_file
Disclaimer¶
PDC takes no responsibility for the correctness of results produced with the binaries. Always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.