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<body class='hmmessage'><hr id="stopSpelling">> Date: Wed, 13 Aug 2008 17:06:34 +0200<br>> From: ckutzne@gwdg.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] invalid number of nodes<br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> > <br>> > In the CVS version the fourier grid is no longer required to be <br>> > divisible by the number of processors.<br>> > But in the other mail you had fourier_nz set to zero, which is complete <br>> > nonsens.<br>> grompp (at least 3.3.x) will use fourierspacing for each direction that<br>> has a fourier_n* value of 0, so why not set fourier_nz = 0?<br><br>Oops, I forgot that.<br>It got a bit late last night, I get I am still not fully recovered.<br><br>But the 1024 grid dimension is not required.<br>Separate PME nodes should be used, which means that one can probably<br>use the same fourier grid as for smaller numbers of processors.<br>Although the pme code still runs slightly faster when the grid dimensions<br>are a multiple of the number of pme nodes. But increases the grid dimensions<br>will often be more costly than just using the normal optimal grid dimensions.<br><br>Berk.<br><br><br>> <br>> > From: regafan@hotmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: RE: [gmx-users] invalid number of nodes<br>> > Date: Wed, 13 Aug 2008 14:12:04 +0000<br>> > Anyway, in the new version of Gromacs, the -np option of grompp does not <br>> > work, does it?<br>> The -np flag does not work any more in CVS since it is no longer needed.<br>> The atoms are now divided over the nodes in mdrun, in 3.3. this was done<br>> by grompp.<br>> <br>> Carsten<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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