HPC/Applications/namd: Difference between revisions

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[[HPC/Getting_started]]
[[HPC/Getting_started]]
=== Modules ===
=== Modules ===
* Versions
* For versions, see
:<pre>
module avail namd
:$ 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:
:<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>.
* Verify  availability
:<pre>
:$ type -p namd2
:/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.


=== Special instructions ===
=== Special instructions ===
* NAMD uses its own MPI wrapper, called [http://charm.cs.uiuc.edu/ Charm++]. Instead of "mpirun" in the [[HPC/Getting_started#Example job file|PBS example job]] use:
* NAMD uses its own MPI wrapper, called [http://charm.cs.uiuc.edu/ Charm++], but the default <code>mpirun</code> from OpenMPI works just fine.
:<pre>
* Use the [[HPC/Getting_started#Example job file|Generic job template]]
:...
<syntaxhighlight lang="bash">
:charmrun +p $NPROCS namd2 ...</pre>
#!/bin/bash
…
 
cd $PBS_O_WORKDIR
mpirun -machinefile $PBS_NODEFILE -np $PBS_NP \
        namd2 inputfile.namd
</syntaxhighlight>


== Documentation ==
== Documentation ==
* See ''Documentation'' on the [http://www.ks.uiuc.edu/Research/namd/ NAMD home page] – contains official [http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/ User guide]  
* See ''Documentation'' on the [http://www.ks.uiuc.edu/Research/namd/ NAMD home page] – contains official [http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/ User guide]  
* Local documentation:
* Local documentation:
:<pre>
<pre>
:$ ls $NAMD_HOME/share/doc
$ ls $NAMD_HOME/share/doc
:README.txt  announce.txt  license.txt  notes.txt  ug.pdf</pre>
README.txt  announce.txt  license.txt  notes.txt  ug.pdf
</pre>
 
== Benchmarks ==
* Using ApoA1 example from http://www.ks.uiuc.edu/Research/namd/performance.html
grep Benchm *2.7*/*.o* | sort -k4,4n | _ -w
namd-2.7b1-gen2-1/namd-gen2-1.o248034:Info: Benchmark time: 1 CPUs 1.81607 s/step 21.0193 days/ns 241.219 MB memory
namd-2.7b1-gen2-1/namd-gen2-1.o248034:Info: Benchmark time: 1 CPUs 1.8238 s/step 21.1088 days/ns 240.773 MB memory
namd-2.7b1-gen2-4/namd-gen2-4.o248032:Info: Benchmark time: 4 CPUs 0.428028 s/step 4.95403 days/ns 90.7305 MB memory
namd-2.7b1-gen2-4/namd-gen2-4.o248032:Info: Benchmark time: 4 CPUs 0.430383 s/step 4.98129 days/ns 90.25 MB memory
<font color="grey">namd-2.7b1-gen2-8/namd-gen2-8.o248035:Info: Benchmark time: 8 CPUs 0.568039 s/step 6.57453 days/ns 65.707 MB memory
namd-2.7b1-gen2-8/namd-gen2-8.o248035:Info: Benchmark time: 8 CPUs 0.887236 s/step 10.2689 days/ns 65.3945 MB memory</font>
namd-2.7b1-gen2-8/namd-gen2-8.o248036:Info: Benchmark time: 8 CPUs 0.227086 s/step 2.62831 days/ns 64.2656 MB memory
namd-2.7b1-gen2-8/namd-gen2-8.o248036:Info: Benchmark time: 8 CPUs 0.229058 s/step 2.65113 days/ns 64.5469 MB memory
namd-2.7b1-gen2-16/namd-gen2-16.o248033:Info: Benchmark time: 16 CPUs 0.105355 s/step 1.21938 days/ns 50.6367 MB memory
namd-2.7b1-gen2-16/namd-gen2-16.o248033:Info: Benchmark time: 16 CPUs 0.105658 s/step 1.2229 days/ns 50.3477 MB memory
grep Benchm *2.9*/*.o* | sort -k4,4n | _ -w
namd-2.9-gen2-1/namd-gen2-1.o248004:Info: Benchmark time: 1 CPUs 1.58065 s/step 18.2946 days/ns 398.93 MB memory
namd-2.9-gen2-1/namd-gen2-1.o248004:Info: Benchmark time: 1 CPUs 1.58666 s/step 18.3641 days/ns 398.695 MB memory
namd-2.9-gen2-1/namd-gen2-1.o248011:Info: Benchmark time: 1 CPUs 1.79167 s/step 20.737 days/ns 398.926 MB memory
namd-2.9-gen2-1/namd-gen2-1.o248011:Info: Benchmark time: 1 CPUs 1.79819 s/step 20.8124 days/ns 398.695 MB memory
<font color="grey">namd-2.9-gen2-4/namd-gen2-4.o248003:Info: Benchmark time: 4 CPUs 1.05068 s/step 12.1606 days/ns 254.582 MB memory
namd-2.9-gen2-4/namd-gen2-4.o248003:Info: Benchmark time: 4 CPUs 1.17972 s/step 13.6542 days/ns 254.582 MB memory</font>
namd-2.9-gen2-4/namd-gen2-4.o248006:Info: Benchmark time: 4 CPUs 0.424272 s/step 4.91055 days/ns 269.023 MB memory
namd-2.9-gen2-4/namd-gen2-4.o248006:Info: Benchmark time: 4 CPUs 0.42632 s/step 4.93426 days/ns 269.023 MB memory
namd-2.9-gen2-8/namd-gen2-8.o247983:Info: Benchmark time: 8 CPUs 0.211136 s/step 2.4437 days/ns 242.109 MB memory
namd-2.9-gen2-8/namd-gen2-8.o247983:Info: Benchmark time: 8 CPUs 0.219128 s/step 2.53621 days/ns 242.109 MB memory
namd-2.9-gen2-16/namd-gen2-1.o248005:Info: Benchmark time: 16 CPUs 0.103843 s/step 1.20188 days/ns 226.25 MB memory
namd-2.9-gen2-16/namd-gen2-1.o248005:Info: Benchmark time: 16 CPUs 0.103924 s/step 1.20282 days/ns 225.961 MB memory


[[Category:HPC|Applications]]
[[Category:HPC|Applications]]

Revision as of 20:54, July 31, 2012

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

HPC/Getting_started

Modules

  • For versions, see
module avail namd

Special instructions

#!/bin/bash
…

cd $PBS_O_WORKDIR
mpirun -machinefile $PBS_NODEFILE -np $PBS_NP \
        namd2 inputfile.namd

Documentation

$ ls $NAMD_HOME/share/doc
README.txt  announce.txt  license.txt  notes.txt  ug.pdf

Benchmarks

grep Benchm *2.7*/*.o* | sort -k4,4n | _ -w
namd-2.7b1-gen2-1/namd-gen2-1.o248034:Info: Benchmark time: 1 CPUs 1.81607 s/step 21.0193 days/ns 241.219 MB memory
namd-2.7b1-gen2-1/namd-gen2-1.o248034:Info: Benchmark time: 1 CPUs 1.8238 s/step 21.1088 days/ns 240.773 MB memory
namd-2.7b1-gen2-4/namd-gen2-4.o248032:Info: Benchmark time: 4 CPUs 0.428028 s/step 4.95403 days/ns 90.7305 MB memory
namd-2.7b1-gen2-4/namd-gen2-4.o248032:Info: Benchmark time: 4 CPUs 0.430383 s/step 4.98129 days/ns 90.25 MB memory
namd-2.7b1-gen2-8/namd-gen2-8.o248035:Info: Benchmark time: 8 CPUs 0.568039 s/step 6.57453 days/ns 65.707 MB memory
namd-2.7b1-gen2-8/namd-gen2-8.o248035:Info: Benchmark time: 8 CPUs 0.887236 s/step 10.2689 days/ns 65.3945 MB memory
namd-2.7b1-gen2-8/namd-gen2-8.o248036:Info: Benchmark time: 8 CPUs 0.227086 s/step 2.62831 days/ns 64.2656 MB memory
namd-2.7b1-gen2-8/namd-gen2-8.o248036:Info: Benchmark time: 8 CPUs 0.229058 s/step 2.65113 days/ns 64.5469 MB memory
namd-2.7b1-gen2-16/namd-gen2-16.o248033:Info: Benchmark time: 16 CPUs 0.105355 s/step 1.21938 days/ns 50.6367 MB memory
namd-2.7b1-gen2-16/namd-gen2-16.o248033:Info: Benchmark time: 16 CPUs 0.105658 s/step 1.2229 days/ns 50.3477 MB memory

grep Benchm *2.9*/*.o* | sort -k4,4n | _ -w
namd-2.9-gen2-1/namd-gen2-1.o248004:Info: Benchmark time: 1 CPUs 1.58065 s/step 18.2946 days/ns 398.93 MB memory
namd-2.9-gen2-1/namd-gen2-1.o248004:Info: Benchmark time: 1 CPUs 1.58666 s/step 18.3641 days/ns 398.695 MB memory
namd-2.9-gen2-1/namd-gen2-1.o248011:Info: Benchmark time: 1 CPUs 1.79167 s/step 20.737 days/ns 398.926 MB memory
namd-2.9-gen2-1/namd-gen2-1.o248011:Info: Benchmark time: 1 CPUs 1.79819 s/step 20.8124 days/ns 398.695 MB memory
namd-2.9-gen2-4/namd-gen2-4.o248003:Info: Benchmark time: 4 CPUs 1.05068 s/step 12.1606 days/ns 254.582 MB memory
namd-2.9-gen2-4/namd-gen2-4.o248003:Info: Benchmark time: 4 CPUs 1.17972 s/step 13.6542 days/ns 254.582 MB memory
namd-2.9-gen2-4/namd-gen2-4.o248006:Info: Benchmark time: 4 CPUs 0.424272 s/step 4.91055 days/ns 269.023 MB memory
namd-2.9-gen2-4/namd-gen2-4.o248006:Info: Benchmark time: 4 CPUs 0.42632 s/step 4.93426 days/ns 269.023 MB memory
namd-2.9-gen2-8/namd-gen2-8.o247983:Info: Benchmark time: 8 CPUs 0.211136 s/step 2.4437 days/ns 242.109 MB memory
namd-2.9-gen2-8/namd-gen2-8.o247983:Info: Benchmark time: 8 CPUs 0.219128 s/step 2.53621 days/ns 242.109 MB memory
namd-2.9-gen2-16/namd-gen2-1.o248005:Info: Benchmark time: 16 CPUs 0.103843 s/step 1.20188 days/ns 226.25 MB memory
namd-2.9-gen2-16/namd-gen2-1.o248005:Info: Benchmark time: 16 CPUs 0.103924 s/step 1.20282 days/ns 225.961 MB memory
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