<table cellspacing="0" cellpadding="0" border="0" ><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 <b>jue 24-sep-09, Berk Hess <i><gmx3@hotmail.com></i></b> escribió:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>De: Berk Hess <gmx3@hotmail.com><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" <gmx-users@gromacs.org><br>Fecha: jueves, 24 de septiembre de 2009, 11:22 am<br><br><div id="yiv477980010">
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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: flormartini@yahoo.com.ar<br>To: gmx-users@gromacs.org<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 style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">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>
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