<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>if you run without PME, there will be no all-to-all communication anyway, </div><div>so in this sense the paper is (mostly) irrelevant here. Since you mention this</div><div>paper I assume that your network is gigabit ethernet. If you run on recent</div><div>processors then I would say that for a 10000 atom system on 8 cores the</div><div>ethernet is clearly the limiting factor, even if it runs optimal (the chance for</div><div>congestion problems on two nodes only is also very limited - these are</div><div>likely to appear on 3 or more nodes). </div><div><br></div><div>What is your performance on a single node (4 CPUs)? You could compare </div><div>that to the performance of 4 CPUs on 2 nodes to determine the network</div><div>impact.</div><div><br></div><div>Carsten</div><div><br></div><div><br><div><div>On Sep 24, 2009, at 5:08 PM, FLOR MARTINI wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><table cellspacing="0" cellpadding="0" border="0" style="position: static; z-index: auto; "><tbody><tr><td valign="top" style="font: inherit; ">Thanks for your question.<br>We are running a lipid bilayer of 128 DPPC and 3655 water molecules and the nstep of the mdp is a total for 10 ns. I don´t think really that our system is a small one...<br><br>Dra.M.Florencia Martini<br>Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas<br>Cátedra de Química General e Inorgánica<br>Facultad de Farmacia y Bioquímica<br>Universidad de Buenos Aires<br>Junín 956 2º (1113)<br>TE: 54 011 4964-8249 int 24<br><br>--- El<span class="Apple-converted-space"> </span><b>jue 24-sep-09, Berk Hess<span class="Apple-converted-space"> </span><i><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></i></b><span class="Apple-converted-space"> </span>escribió:<br><blockquote style="border-left-width: 2px; border-left-style: solid; border-left-color: rgb(16, 16, 255); margin-left: 5px; padding-left: 5px; "><br>De: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>Asunto: RE: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4<br>Para: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Fecha: jueves, 24 de septiembre de 2009, 11:22 am<br><br><div id="yiv477980010" style="font-size: 10pt; font-family: Verdana; ">Hi,<br><br>You don't mention what kind of benchmark system tou are using for these tests.<br>A too small system could explain these results.<br><br>Berk<br><br><br><hr id="stopSpelling">Date: Thu, 24 Sep 2009 07:01:04 -0700<br>From:<span class="Apple-converted-space"> </span><a href="mailto:flormartini@yahoo.com.ar">flormartini@yahoo.com.ar</a><br>To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td valign="top" style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-stretch: inherit; ">hi,<br><br> We are about to start running GROMACS 4.0.4 with OpenMPI, in 8<br>nodes, quad core Rocks cluster. We made some tests, without PME and<br>found two notable things:<br><br>* We are getting the best speedup (6) with 2 nodes ( == 8 cores ). I read<br>the "Speeding Up Parallel GROMACS in High Latency networks" paper, and<br>thought that the culprit was the switch, but ifconfig shows no retransmits<br>(neither does ethtool -s or netstat -s). Does version 4 includes the<br>alltoall patch? Is the paper irrelevant with GROMACS 4?<br><br>* When running with the whole cluster ( 8 nodes, 32 cores ), top reports<br>in any node a 50% system CPU usage. Is that normal? Can it be accounted to<br>the use of the network? The sys usage gets a bit up when we configured the<br>Intel NICs with Interrupt Coalescense Off, so I'm tempted to think it is<br>just OpenMPI hammering the tcp stack, polling for packages.<br><br>Thanks in advance,<br><br>Dra.M.Florencia Martini<br>Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas<br>Cátedra de Química General e Inorgánica<br>Facultad de Farmacia y Bioquímica<br>Universidad de Buenos Aires<br>Junín 956 2º (1113)<br>TE: 54 011 4964-8249 int 24</td></tr></tbody></table><br><hr size="1"><br><font size="-2" face="Verdana">Encontra las mejores recetas con Yahoo! 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Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-interchange-newline">--</div><div>Dr. Carsten Kutzner</div><div>Max Planck Institute for Biophysical Chemistry</div><div>Theoretical and Computational Biophysics</div><div>Am Fassberg 11, 37077 Goettingen, Germany</div><div>Tel. +49-551-2012313, Fax: +49-551-2012302</div><div><a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a></div><div><br></div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span> </div><br></div></body></html>