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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>The fftw used during compilation was FFTW 3.1.2 compiled using
the GNU compilers.<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>Yawar JQ<br>
<b>Sent:</b> Sunday, November 09, 2008 3:31 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Gromacs 4 Scaling Benchmarks...<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>I was
wondering if anyone could comment on these benchmark results for the d.dppc benchmark?</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width=239
style='width:179.0pt;border-collapse:collapse'>
<tr style='height:15.0pt'>
<td width=47 style='width:35.0pt;padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>Nodes</span><o:p></o:p></p>
</td>
<td width=103 style='width:77.0pt;padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>Cutoff
(ns/day)</span><o:p></o:p></p>
</td>
<td width=89 style='width:67.0pt;padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>PME
(ns/day)</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>4</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>1.331</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>0.797</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>8</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>2.564</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>1.497</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>16</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>4.5</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>1.92</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>32</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>8.308</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>0.575</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>64</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>13.5</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>0.275</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>128</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>20.093</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>-</span><o:p></o:p></p>
</td>
</tr>
<tr style='height:15.0pt'>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>192</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>21.6</span><o:p></o:p></p>
</td>
<td style='padding:0in 0in 0in 0in;height:15.0pt'>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'>-</span><o:p></o:p></p>
</td>
</tr>
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</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>It seems to
scale relatively well up to 32-64 nodes without PME. This seems slightly better
than the benchmark results for Gromacs 3 on <a href="http://www.gromacs.org/">www.gromacs.org</a>. </span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>Can someone
comment on the magnitude of the performance hit and lack of scaling with PME is
worrying me. </span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>For the PME
runs, I set rlist,rvdw,rouloumb=1.2 and the rest set to the defaults. I can try
it with some other settings, larger spacing for the grid, but I'm not sure how
much more that would help. Is there a more standardized system I should use for
testing PME scaling?</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>This is with
GNU compilers and parallelization with OpenMPI 1.2. I'm not sure what we're
using for the FFTW The compute nodes are Dell m600 blades w/ 16GB of RAM
and dual quad core Intel Xeon 3GHz processors. I believe it's all ethernet
interconnects.</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>Thanks,</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif"'>YQ</span><o:p></o:p></p>
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