[gmx-users] GROMACS on Bluegene

[Mike Hanby]

If I could make a request, it would be helpful to have the FFTW 3.1.x
configure statements for both the frontend node version and the Blue
Gene version to ensure that FFTW is being compiled using the same
options from blue gene to blue gene (or if not the user could state how
their configure differed from the wiki).

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Roland Schulz
Sent: Wednesday, November 12, 2008 12:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] GROMACS on Bluegene

 

Mathias has updated the wiki:
http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene



On Wed, Nov 12, 2008 at 11:57 AM, Suman Chakrabarty
<suman at sscu.iisc.ernet.in> wrote:

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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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov

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