NAMD is a parallel, object-oriented, molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Versions and Availability
Softenv Keys for namd on philip
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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.
SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.
System Default Path
When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.
SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.
Viewing Available Packages
The command softenv will provide a list of available packages. The listing will look something like:
$ softenv These are the macros available: * @default These are the keywords explicitly available: +amber-8 Applications: 'Amber', version: 8 Amber is a +apache-ant-1.6.5 Ant, Java based XML make system version: 1.6. +charm-5.9 Applications: 'Charm++', version: 5.9 Charm++ +default this is the default environment...nukes /etc/ +essl-4.2 Libraries: 'ESSL', version: 4.2 ESSL is a sta +gaussian-03 Applications: 'Gaussian', version: 03 Gaussia ... some stuff deleted ...
The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:
To update the environment after modifying this file, one simply uses the resoft command:
The command soft can be used to manipulate the environment from the command line. It takes the form:
$ soft add/delete +keyword
Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.
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
On QB2, use "mpirun" to run NAMD. Below is a sample script which runs NAMD with 4 nodes (80 CPU cores and 8 Nvidia K20X GPUs):
#!/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/2.10b1/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
Last modified: July 06 2015 14:34:42.