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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>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).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Roland Schulz<br>
<b>Sent:</b> Wednesday, November 12, 2008 12:55 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] GROMACS on Bluegene<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>Mathias has updated the wiki:<br>
<a href="http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene">http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene</a><br>
<br>
<o:p></o:p></p>
<div>
<p class=MsoNormal>On Wed, Nov 12, 2008 at 11:57 AM, Suman Chakrabarty <<a
href="mailto:suman@sscu.iisc.ernet.in">suman@sscu.iisc.ernet.in</a>> wrote:<o:p></o:p></p>
<p class=MsoNormal>I am interested in this as well, since I am planning to
compile<br>
version 4.0.2 in Blue Gene within a few days (once I get hold of my<br>
account!).<br>
<br>
<br>
--<br>
Suman Chakrabarty.<o:p></o:p></p>
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<p class=MsoNormal><br>
<br>
On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby <<a href="mailto:mhanby@uab.edu">mhanby@uab.edu</a>>
wrote:<br>
> Has there been any further discussion about fixing the issues discussed<br>
> below regarding Blue Gene?<br>
><br>
> -----Original Message-----<br>
> From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a><br>
> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]
On Behalf Of Mark Abraham<br>
> Sent: Thursday, October 16, 2008 10:43 PM<br>
> To: Gromacs Users<br>
> Subject: [gmx-users] GROMACS on Bluegene<br>
><br>
> Hi,<br>
><br>
> I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene,<br>
><br>
> however the distribution is incomplete. At least the files<br>
><br>
> interaction.h<br>
> nb_kernel_w3_bluegene.h<br>
> nb_kernel_w3w3_bluegene.h<br>
> nb_kernel_w4_bluegene.h<br>
> nb_kernel_w4w4_bluegene.h<br>
> nb_kernel_gen_bluegene.h<br>
><br>
> are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official<br>
><br>
> distribution.<br>
><br>
> Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h<br>
> contains the contents of file<br>
> src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which<br>
> obviously won't work.<br>
><br>
> Further, GROMACS configure won't work out-of-the-box on this platform<br>
> (see also<br>
> <a
href="http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html"
target="_blank">http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html</a>
and<br>
> discussions on this list months back). Since I can see in the source<br>
> code that Mathias Puetz at IBM has done (at least some of) the<br>
> development work here, then I suggest that IBM may like to provide some<br>
> official build instructions. I have my own black magic that makes<br>
> configure work on my machine, and I'm prepared to make that available<br>
> off-list to interested parties, but I don't know how portable it will be<br>
><br>
> between Bluegene installations. A better solution should be available if<br>
><br>
> one of the GROMACS developers can approach the IBM people for us,<br>
> please.<br>
><br>
> Mark<br>
> _______________________________________________<br>
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><o:p></o:p></p>
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<br>
-- <br>
ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><o:p></o:p></p>
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