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Hi,<br><br>I am using openmpi 1.2.8 and it works fine.<br>You get 15% performance increase when going from 4 to 8 processes.<br>Note that with 4 processes you have to use:<br>mpirun -np 4 taskset 0xf mdrun ...<br>to avoid two processes running on the same physical core.<br><br>The only problem I can think of is that your system is so small<br>that it will anyhow not scale to more than 4 processes.<br><br>Berk<br><br>> From: x.periole@rug.nl<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] link gromacs i7<br>> Date: Wed, 7 Apr 2010 10:10:26 +0200<br>> <br>> <br>> We have been using gromacs-4.0.7 on I7 with up to 8 CPUs. The<br>> scaling is pretty good.<br>> Note that upgrading to openmpi-1.4.1 was necessary to be able<br>> to scale to up to 8 CPUs, if not the jobs where hanging ...<br>> Since you have it already, I do not see where the problem can<br>> come from. Are you sure you are using openmpi-1.4.1?<br>> <br>> On Apr 7, 2010, at 12:50 AM, Mark Abraham wrote:<br>> <br>> > On 7/04/2010 5:32 AM, Maurício Menegatti Rigo wrote:<br>> >><br>> >> We are using an i7 920 processor to run Gromacs-4.0.7 with<br>> >> openmpi-1.4.1. The simulations run well using 4 threads (using <br>> >> "mpirun<br>> >> -np 4 mdrun...") but the performance is worse when we use 6 or 8<br>> >> threads.<br>> ><br>> > Sure. You have four physical cores. If you're trying to get more <br>> > across a network, unless it is Infiniband you will take a big <br>> > performance hit. Intel's hyperthreading may work (it did 5 years ago <br>> > on different technology), but only if it is turned on, the MPI <br>> > processes are all on the same piece of processor, and you compile <br>> > with MPI and use mpirun -np x for x=1-8.<br>> ><br>> > Even then, 8 virtual cores might over-saturate cache bandwidth, or <br>> > something. You'll need to provide a lot more information for more <br>> > help there.<br>> ><br>> >> Looking for some way to improve our performance we found out<br>> >> this forum and then started to try use threads without openmpi. We<br>> >> compiled gromacs again and used the command line as described here<br>> >> ("mdrun -nt 8..."), but the following error appears:<br>> >><br>> >> ------<br>> >> Program mdrun, VERSION 4.0.7<br>> >> Source code file: mdrun.c, line: 410<br>> >><br>> >> Fatal error:<br>> >> GROMACS compiled without threads support - can only use one thread<br>> >> ------<br>> >><br>> >> But in gromacs-4.0.7 threads are not supposed to be ON by default?<br>> ><br>> > No post to this list has implied that threads work, because they <br>> > will not before GROMACS 4.1. The fact that the installation guides <br>> > on the website don't suggest using threads would also have guided <br>> > you here.<br>> ><br>> > Mark<br>> > -- <br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www <br>> > interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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