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<br><br>> Date: Thu, 27 Nov 2008 02:49:10 +0000<br>> From: ijstokes@crystal.harvard.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] SMP/Parallel mdrun<br>> <br>> Hi Mark,<br>> <br>> Mark Abraham wrote:<br>> > Terminology - GROMACS is not threaded, but uses MPI processes for <br>> > parallelism.<br>> <br>> Yes, I gathered that.<br>> >> I have an MPI-compiled version of gromacs v4.0 and am attempting to <br>> >> get parallel execution on a 2x2 core AMD Opteron system via:<br>> >><br>> >> $ lamboot<br>> >> $ mdrun -np 4 -s ../1WOM.tpr -v -N 4<br>> ><br>> > -N does nothing, and -np is no longer accepted - as you'd know from <br>> > reading mdrun -h, right?<br>> That is a bit of a condecending way of putting it. If I knew -N did <br>> nothing and -np was no longer accepted, then of course I would not have <br>> used them. In fact, I was reading the documentation from a file called <br>> "manual-4.0.pdf" which stated:<br>> <br>> "<br>> If you have a single machine with multiple processors you don’t have to <br>> use the mpirun com-<br>> mand, but you can do with an extra option to mdrun:<br>> % mdrun -np 8 -s topol -v -N 8<br>> "<br>> <br>> so that is where I took the example from. I think this PDF was linked <br>> from the gromacs "documentation" section of the website.<br>> <br><br>Ah, I was not aware of this small section in the manual.<br>This information was already outdated about a decade ago.<br>I will remove it.<br><br>Note that mdrun also does not have the option -N.<br>(for some reason, which I still do not know, mdrun does<br>not check it command line options, unlike all other Gromacs<br>programs)<br><br>Berk<br><br>> > Like most MPI parallel codes, you need to use mpirun. If your lam <br>> > environment is correctly configured, then I think you will not need <br>> > -np 4 as an argument to mpirun.<br>> ><br>> > Also, probably you are actually running a non-MPI gromacs, since by <br>> > default, using --enable-mpi will suffix mdrun to be mdrun_mpi.<br>> Doesn't look like it:<br>> <br>> $ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi<br>> $ make<br>> $ make install<br>> $ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun<br>> mdrun<br>> <br>> Anyway, thanks for your suggestions because I now have it working via:<br>> <br>> $ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4<br>> <br>> and I see 4 processes running at 100% and an estimated run time 25% of <br>> the serial version.<br>> <br>> Ian.<br>> <br>> -- <br>> Ian Stokes-Rees, Research Associate<br>> SBGrid, Harvard Medical School<br>> http://sbgrid.org<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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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