NAMD is a parallel, object-oriented, molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Versions and Availability
Module Names for namd on smic
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Depending on which cluster it is installed, NAMD may or may not need MPI to run.
On SuperMIC, use "charmrun" to run NAMD. Below is a sample script which runs NAMD with 4 nodes (80 CPU cores and 8 Xeon Phi co-processors):
#!/bin/bash #PBS -A hpc_smictest3 #PBS -l walltime=2:00:00 #PBS -l nodes=4:ppn=20 #PBS -q checkpt cd $PBS_O_WORKDIR module add namd/2.10/INTEL-14.0.2-ibverbs-mic for node in `cat $PBS_NODEFILE | uniq`; do echo host $node; done > hostfile charmrun ++p 80 ++nodelist ./hostfile ++remote-shell ssh `which namd2` apoa1.namd
Use "mpirun" to run NAMD (e.g. on QB2). Below is a sample script which runs NAMD with 4 nodes (80 CPU cores):
#!/bin/bash #PBS -A your_allocation_name #PBS -l walltime=2:00:00 #PBS -l nodes=4:ppn=20 #PBS -q checkpt cd $PBS_O_WORKDIR module add namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0 mpirun -n 80 -f $PBS_NODEFILE `which namd2` apoa1.namd
On Super Mike 2, first make sure that the proper keys are loaded in .soft file:
Then run NAMD using scripts similar to this one:
#!/bin/bash #PBS -A hpc_your_allocation #PBS -l walltime=2:00:00 #PBS -l nodes=4:ppn=16 #PBS -q checkpt cd $PBS_O_WORKDIR mpirun -n 64 -hostfile $PBS_NODEFILE `which namd2` apoa1.namd
To run NAMD with GPU support (e.g. on QB2), please use the below script as a reference, the example data and detailed instructions can be downloaded from the namd tutorial titled "GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis" from here.
#PBS -A your_allocation_name #PBS -l walltime=2:00:00 #PBS -l nodes=1:ppn=20 #PBS -q checkpt cd $PBS_O_WORKDIR module add namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0 namd2 +idlepoll benchmark_gpu.conf > benchmark_gpu.log
Last modified: August 17 2015 16:16:39.