NAMD Wiki: Namd28Release
Issues with the 2.8 release of NAMD.
Please see the release notes at http://www.ks.uiuc.edu/Research/namd/2.8/notes.html
For bugs fixed since the 2.8b3 release see Namd28b3Release and for all changes see http://www.ks.uiuc.edu/Research/namd/cvs2html/chronological.html
Coulomb switching for MARTINI force field is incorrect. Fixed 9/22/2011.
Tabulated nonbonded potential only works if PME is enabled. Fixed 3/9/2012.
The experimental memory-optimized build option with parallel I/O is documented at NamdMemoryReduction.
Compilation note: If using the tcl libraries available on the namd site, be sure to download the correct version. These have moved a bit since the 2.8 release notes were written. On OS X 10.5 I had to use the following tcl library to get compilation to work: http://www.ks.uiuc.edu/Research/namd/libraries/old_2010/tcl-macosx-x86.tar.gz This is tcl version 8.4. The version in the current libraries directory on the namd site is 8.5 - with this version, and following the compilation instructions in the release notes, the final make step failed.
On Lincoln at NCSA:
runs on GPU-accelerated Lincoln nodes. See the CUDA section of the release notes for details.
On the Ember Altix UV at NCSA:
On Ranger at TACC:
can use 1way, 2way, or 4way processes per node with 15, 7, or 3 compute threads per process, and is again progressively slower because more cores are used for communication.
On Lonestar at TACC:
On Kraken at NICS:
still uses MPI but the binary is built with g++ for better performance.
will use 11 compute threads per process.
On KID (Keeneland Initial Delivery) GPU-accelerated cluster at NICS:
(Note that the KID filesystem is shared with Kraken, hence the KID_scripts directory.)