[gmx-users] GROMACS on Bluegene

[Suman Chakrabarty]

I am interested in this as well, since I am planning to compile
version 4.0.2 in Blue Gene within a few days (once I get hold of my
account!).


--
Suman Chakrabarty.


On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby <mhanby at uab.edu> wrote:
> 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
>
> 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
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