Issues with the 2.8b2 release of NAMD.

Please see the release notes at http://www.ks.uiuc.edu/Research/namd/2.8b2/notes.html

For bugs fixed since the 2.8b1 release see Namd28b1Release and for all changes see http://www.ks.uiuc.edu/Research/namd/cvs2html/chronological.html

Pencil PME may hang on large processor counts when all patches on a processor are empty. Fixed in May 18 nightly build.

Colvars may report very high energies (9999999999.9999 in the MISC energy column). Fixed in May 14 nightly build.

Martini switching is silently broken (switch distance is set to cutoff). Fixed in May 13 nightly build.

The experimental memory-optimized build option with parallel I/O is documented at NamdMemoryReduction.

On Lincoln at NCSA:

/u/ac/jphillip/NAMD_scripts/runbatch_2.8b2_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_2.8b2

On Ranger at TACC:

/share/home/00288/tg455591/NAMD_scripts/runbatch_2.8b2

uses ibverbs.

/share/home/00288/tg455591/NAMD_scripts/runbatch_2.8b2_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_2.8b2

and

/home1/00288/tg455591/NAMD_scripts/runbatch_2.8b2_smp
  

On Kraken at NICS:

/nics/b/home/jphillip/NAMD_scripts/runbatch_2.8b2

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

/nics/b/home/jphillip/NAMD_scripts/runbatch_2.8b2_smp

will use 11 compute threads per process.