NAMD at TACC
Last update: September 9, 2024
NAMD Nanoscale Molecular Dynamics program, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD can perform geometry optimization, molecular dynamics simulations, chemical and conformational free energy calculations, enhanced sampling via replica exchange. It also supports Tcl based scripting and steering forces.
Installations
NAMD is currently installed on TACC's Frontera, Stampede3, and Lonestar6 compute resources. NAMD is managed under the module system on TACC resources. Read the following instructions carefully. NAMD performance is particularly sensitive to its configuration. Try running benchmarks with different configurations to find your optimal NAMD set up. You can initiate interactive idev debugging sessions on all systems.
NAMD on Frontera
The recommended and latest installed NAMD version is 3.0 on Frontera. Users are welcome to install different NAMD versions in their own directories.
login1$ module load namd/3.0Job Scripts
Tip
TACC staff recommends that users attempt runs with 4 tasks per node and 8 tasks per node (scales better at large number of nodes) and then pick the configuration that provides the best performance.
This job script demontstrate how to run NAMD on Frontera's Cascade Lake nodes.
4 Tasks per Node
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 2 # Total number of nodes
#SBATCH -n 8 # Total number of mpi tasks
#SBATCH -p normal # Queue (partition) name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 13 \
+pemap 2-26:2,30-54:2,3-27:2,31-55:2 \
+commap 0,28,1,29 input &> output8 Tasks per Node
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 12 # Total number of nodes
#SBATCH -n 96 # Total number of mpi tasks
#SBATCH -p normal # Queue (partition) name -- skx-normal, skx-dev, etc.
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 6 \
+pemap 2-12:2,16-26:2,30-40:2,44-54:2,3-13:2,17-27:2,31-41:2,45-55:2\
+commap 0,14,28,42,1,15,29,43 input &> outputNAMD on Stampede3
These job scripts demontstrate how to run NAMD on Stampede3's Sapphire Rapids nodes.
Sapphire Rapids
4 Tasks per Node
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 2 # Total number of nodes
#SBATCH -n 8 # Total number of mpi tasks
#SBATCH -p spr # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 27 \
+pemap 2-54:2,58-110:2,3-55:2,59-111:2 \
+commap 0,56,1,57 input &> output8 Tasks per Node
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 12 # Total number of nodes
#SBATCH -n 96 # Total number of mpi tasks
#SBATCH -p spr # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 13 \
+pemap 2-26:2,30-54:2,58-82:2,86-110:2,3-27:2,31-55:2,59-83:2,87-111:2 \
+commap 0,28,56,84,1,29,57,85 input &> outputIce Lake Nodes
These job scripts demontstrate how to run NAMD on Stampede's Ice Lake nodes.
4 Tasks per Node
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 2 # Total number of nodes
#SBATCH -n 8 # Total number of mpi tasks
#SBATCH -p icx # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 19 \
+pemap 2-38:2,42-78:2,3-39:2,43-79:2 \
+commap 0,40,1,41 input &> output8 Tasks per Node
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 12 # Total number of nodes
#SBATCH -n 96 # Total number of mpi tasks
#SBATCH -p icx # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 9 \
+pemap 2-18:2,22-38:2,42-58:2,62-78:2,3-19:2,23-39:2,43-59:2,63-79:2 \
+commap 0,20,40,60,1,21,41,61 input &> outputSky Lake Nodes
These job scripts demontstrate how to run NAMD on Stampede's Sky Lake nodes.
4 tasks per node
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 2 # Total number of nodes
#SBATCH -n 8 # Total number of mpi tasks
#SBATCH -p skx # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 11 \
+pemap 2-22:2,26-46:2,3-23:2,27-47:2 \
+commap 0,24,1,25 input &> output8 Tasks per Node
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 12 # Total number of nodes
#SBATCH -n 96 # Total number of mpi tasks
#SBATCH -p skx # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0b6
ibrun namd3 +ppn 5 \
+pemap 2-10:2,14-22:2,26-34:2,38-46:2,3-11:2,15-23:2,27-35:2,39-47:2 \
+commap 0,12,24,36,1,13,25,37 input &> outputNAMD on Lonestar6
NAMD ver3.0 is installed on Lonestar6 as this version provides best performance. Feel free to install your own newer version locally.
login1$ module load namd/3.0Job Script
TACC staff recommends assigning 4 tasks per node for NAMD jobs running on Lonestar6's compute nodes.
The following Lonestar6 job script requests 2 node and 8 MPI tasks. To run the same job on more nodes, vary the -N and -n Slurm directives, ensuring the value of n is four times the value of N.
#!/bin/bash
#SBATCH -J test # Job Name
#SBATCH -o test.o%j
#SBATCH -N 2 # Total number of nodes
#SBATCH -n 8 # Total number of mpi tasks
#SBATCH -p normal # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load namd/3.0
ibrun namd3 +ppn 31 \
+pemap 1-31,33-63,65-95,97-127 \
+commap 0,32,64,96 input &> outputReferences
- NAMD website
- NAMD 2.14 User Guide