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:

/u/ac/jphillip/NAMD_scripts/runbatch_2.8_cuda

runs on GPU-accelerated Lincoln nodes. See the CUDA section of the release notes for details.

On the Ember Altix UV at NCSA:

/gpfs1/u/ac/jphillip/NAMD_scripts/runbatch_2.8

On Ranger at TACC:

/share/home/00288/tg455591/NAMD_scripts/runbatch_2.8

uses ibverbs.

/share/home/00288/tg455591/NAMD_scripts/runbatch_2.8_smp

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:

/home1/00288/tg455591/NAMD_scripts/runbatch_2.8

and

/home1/00288/tg455591/NAMD_scripts/runbatch_2.8_smp
  

On Kraken at NICS:

/nics/b/home/jphillip/NAMD_scripts/runbatch_2.8

still uses MPI but the binary is built with g++ for better performance.

/nics/b/home/jphillip/NAMD_scripts/runbatch_2.8_smp

will use 11 compute threads per process.

On KID (Keeneland Initial Delivery) GPU-accelerated cluster at NICS:

/nics/b/home/jphillip/KID_scripts/runbatch_2.8_cuda

(Note that the KID filesystem is shared with Kraken, hence the KID_scripts directory.)