HPC/Applications/namd: Difference between revisions
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[[HPC/Getting_started]] | [[HPC/Getting_started]] | ||
=== Modules === | === Modules === | ||
* Versions | |||
:<pre> | |||
:$ module avail namd | |||
:------------------------------- /opt/soft/modulefiles ------------------------------- | |||
:namd/2.6.2009-02-11-Linux-x86_64-MPI-icc-1(default) | |||
:namd/2.7b1-MPI-icc-1 | |||
:</pre> | |||
: Version 2.6 is the CVS development version, and [http://www.ks.uiuc.edu/Research/namd/2.7b1/announce.html NAMD 2.7b1] the subsequently released official version. | |||
* Add the following to the end of your <code>~/.bashrc</code> file: | * Add the following to the end of your <code>~/.bashrc</code> file: | ||
:<pre>module load namd</pre> | :<pre> | ||
:module switch openmpi openmpi/1.3-intel10-4 | |||
:module load namd | |||
:</pre> | |||
: and ''also'' issue it on the command line (or simply re-login). The program will be available under the name <code>namd2</code>. | : and ''also'' issue it on the command line (or simply re-login). The program will be available under the name <code>namd2</code>. | ||
* Verify availability | * Verify availability | ||
:<pre>$ type -p namd2 | :<pre> | ||
:$ type -p namd2 | |||
:/opt/soft/namd-2.6.2009-02-11-Linux-x86_64-MPI-icc-1/bin/namd2</pre> | :/opt/soft/namd-2.6.2009-02-11-Linux-x86_64-MPI-icc-1/bin/namd2</pre> | ||
: Note: This step is solely meant to verify that the binary is reachable simply by its name. As with other applications, do not call it directly, as the paths are version dependent. Use the <code>module</code> command to select appropriate versions. | : Note: This step is solely meant to verify that the binary is reachable simply by its name. As with other applications, do not call it directly, as the paths are version dependent. Use the <code>module</code> command to select appropriate versions. | ||
Revision as of 19:51, April 3, 2009
Introduction
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
Subject to Univ. of Illinois Non-Exclusive, Non-Commercial Use License.
The NAMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969).
NAMD on Carbon
Required reading
Modules
- Versions
- $ module avail namd
- ------------------------------- /opt/soft/modulefiles -------------------------------
- namd/2.6.2009-02-11-Linux-x86_64-MPI-icc-1(default)
- namd/2.7b1-MPI-icc-1
- Version 2.6 is the CVS development version, and NAMD 2.7b1 the subsequently released official version.
- Add the following to the end of your
~/.bashrcfile:
- module switch openmpi openmpi/1.3-intel10-4
- module load namd
- and also issue it on the command line (or simply re-login). The program will be available under the name
namd2.
- Verify availability
- $ type -p namd2
- /opt/soft/namd-2.6.2009-02-11-Linux-x86_64-MPI-icc-1/bin/namd2
- Note: This step is solely meant to verify that the binary is reachable simply by its name. As with other applications, do not call it directly, as the paths are version dependent. Use the
modulecommand to select appropriate versions.
Special instructions
- NAMD uses its own MPI wrapper, called Charm++. Instead of "mpirun" in the PBS example job use:
- ...
- charmrun +p $NPROCS namd2 ...
Documentation
- See Documentation on the NAMD home page – contains official User guide
- Local documentation:
$ ls $NAMD_HOME/share/doc
- README.txt announce.txt license.txt notes.txt ug.pdf