New versions of NAMD and GROMACS on Biowulf (Biowulf)

New versions of NAMD and GROMACS offering significant increases
in performance are now available on the NIH Biowulf Cluster.
In particular, high scalability can be achieved on the Biowulf
Infiniband network.


NAMD

An Infiniband version of NAMD has been built directly from the CVS
sources of the NAMD project.  This version has some profound performance
advantages over the available 2.6 version and is frequently preferred
over the release version for this reason (it should be noted however
that it is considered a "development" source tree so some bugs may  
exist).
If you'd like fewer days per nanosecond in your NAMD runs, please feel
free to give it a try.  If you decide to use the CVS version please let
us know if it works for you, or more importantly, if it does not. (Note
that the standard 2.6 version of NAMD remains available).  See
http://biowulf.nih.gov/apps/namd.html#ib_cvs for details.


GROMACS

Gromacs v4.0.3 has been built for Infiniband, Infinipath, and Gigabit
ethernet, and this version is now the default on the Biowulf cluster.
There are many changes from the previous default version 3.3.3,
so your scripts may need to be modified.  Gromacs v4.0.3 scales
significantly better than v3.3.3, especially on Infiniband where the
standard d.dppc benchmark scales to 128 processors at 80% efficiency.
Please see  http://biowulf.nih.gov/apps/gromacs.html for details.


PERFORMANCE

As usual, benchmark you should your runs to optimize the use of  
resources.
A good rule of thumb is >= 70% efficiency (see
http://biowulf.nih.gov/apps/namd.html#benchmarks for calculating the
efficiency of your job).  PLEASE NOTE: when running on Infiniband the
cpu load (e.g., "jobload" or the user monitor) will always be 100%,
so this should not be used as a measure of efficiency.