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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Mon, 3 Nov 2008 10:33:41 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] gromacs-4: statring in parallel on solaris 8<br>> <br>> <br>> <br>> DimitryASuplatov wrote:<br>> > Hello,<br>> > I have installed gromacs-4 on Solaris 8 with mpi support.<br>> > I was very disappointed by the lack of -np option in grompp and mdrun.<br>> <br>> The -np option is absent in grompp, as it is no longer necessary. The -np flag <br>> is indeed present for mdrun, however.<br><br>The mdrun flag has been removed from mdrun a long time ago,<br>it was already gone in 3.3 (but mdrun does not check for incorrect<br>command line options).<br><br>> <br>> > After reading the manual and the site I came to a conclusion that now we<br>> > do not need to specify number of nodes via gromacs status file but<br>> > instead use mpirun option only.<br>> > Executing (for gromacs benchmarking set)<br>> > <br>> > grompp<br>> > mpirun c0-5 mdrun_mpi -v<br>> > <br>> > starts six threads on six processors though output speed is the same as<br>> > for a single-node run. No errors, no warnings.<br>> ><br>> <br>> I didn't think threading was supported yet, maybe I'm wrong. But you can <br>> definitely use -np 6 with mdrun_mpi.<br><br>The is no multi-threading in 4.0.<br><br>Berk<br><br><br>> <br>> -Justin<br>> <br>> <br>> > So, am I doing wrong with gromacs parallelization or is this the problem<br>> > of the Solaris MPI?<br>> > <br>> > Thank you.<br>> > <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>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <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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