[gmx-users] GROMACS on Bluegene

Mike Hanby mhanby at uab.edu
Wed Nov 12 15:51:46 CET 2008

Has there been any further discussion about fixing the issues discussed
below regarding Blue Gene?

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Thursday, October 16, 2008 10:43 PM
To: Gromacs Users
Subject: [gmx-users] GROMACS on Bluegene


I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene,

however the distribution is incomplete. At least the files


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


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,

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