Index of /Research/namd/utilities/stmv_sc14

      Name                    Last modified       Size  Description

[DIR] Parent Directory 30-Oct-2016 14:33 - [TXT] 1stmv2fs.namd 23-Aug-2016 20:41 2k [TXT] 20stmv2fs.namd 23-Aug-2016 20:41 2k [TXT] 210stmv2fs.namd 23-Aug-2016 20:41 2k [TXT] compress_1stmv.namd 23-Aug-2016 20:42 2k [TXT] compress_20stmv.namd 23-Aug-2016 20:42 2k [TXT] compress_210stmv.namd 23-Aug-2016 20:42 2k [   ] make_210stmv.pgn 23-Aug-2016 20:41 1k [   ] make_5x2x2stmv.pgn 23-Aug-2016 20:41 1k [   ] make_stmv.pgn 23-Aug-2016 20:41 1k

NAMD benchmarks from Phillips et al., SC14

You need two versions of NAMD: a regular multicore build (can be downloaded)
with the included psfgen standalone binary, and a memopt build for your
parallel machine (./config ... --with-memopt).

tar xzf stmv.tar.gz
mv stmv/* .
rmdir stmv

The following commands generate multiple copies of the STMV structure.

psfgen make_stmv.pgn
psfgen make_5x2x2stmv.pgn
psfgen make_210stmv.pgn

The following commands use a regular NAMD binary to compress the STMV
structure and should be run on a machine with at least 128GB of memory.

namd2 compress_1stmv.namd
namd2 compress_20stmv.namd
namd2 compress_210stmv.namd

The folowing NAMD config files require a memopt binary.  Even if memory
usage isn't an issue the memopt version greatly reduces startup time.