[gmx-users] GROMACS on Bluegene

[Mark Abraham]

Hi,

I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, 
however the distribution is incomplete. At least the files

interaction.h
nb_kernel_w3_bluegene.h
nb_kernel_w3w3_bluegene.h
nb_kernel_w4_bluegene.h
nb_kernel_w4w4_bluegene.h
nb_kernel_gen_bluegene.h

are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official 
distribution.

Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h 
contains the contents of file 
src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which 
obviously won't work.

Further, GROMACS configure won't work out-of-the-box on this platform 
(see also 
http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and 
discussions on this list months back). Since I can see in the source 
code that Mathias Puetz at IBM has done (at least some of) the 
development work here, then I suggest that IBM may like to provide some 
official build instructions. I have my own black magic that makes 
configure work on my machine, and I'm prepared to make that available 
off-list to interested parties, but I don't know how portable it will be 
between Bluegene installations. A better solution should be available if 
one of the GROMACS developers can approach the IBM people for us, please.

Mark