Issues with the 2.7b4 release of NAMD.

Please see the release notes at http://www.ks.uiuc.edu/Research/namd/2.7b4/notes.html

For bugs fixed since the 2.7b3 release see Namd27b3Release and for all changes see http://www.ks.uiuc.edu/Research/namd/cvs2html/chronological.html

The charm-6.2.2 included with NAMD 2.7b4 is a pre-release (charm-6.2.2-pre3).

The Linux-x86_64 binary was actually a multicore (shared memory only) build. Replaced 6-Oct-2010.

The memory-optimized build of NAMD is broken in 2.7b3 and 2.7b4. The current implementation will be replaced with full parallel I/O in 2.8b1. It will not be incorporated before 2.7 final because of the risk of introducing new bugs.

On Abe at NCSA:

/u/ac/jphillip/NAMD_scripts/runbatch_2.7b4

now uses the ibverbs build.

/u/ac/jphillip/NAMD_scripts/runbatch_2.7b4_smp

uses one process per node for increased maximum available memory, but is slightly slower since one core per node is reserved for the communication thread.

On Ranger at TACC:

/share/home/00288/tg455591/NAMD_scripts/runbatch_27b4

uses ibverbs.

/share/home/00288/tg455591/NAMD_scripts/runbatch_27b4_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 Kraken at NICS:

/nics/b/home/jphillip/NAMD_scripts/runbatch_27b4

still uses MPI but the binary is built with g++ now so it should be noticably faster.

/nics/b/home/jphillip/NAMD_scripts/runbatch_27b4_smp

will use 11 compute threads per process.

The memory optimized build is broken, so you'll want to stick with the builds from April for those projects. As an alternative, the SMP builds share molecular data within a node, allowing larger simulations to run on a given machine.