<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
You should read the manual, look in the index for domain decomposition.<br>For domain decomposition the unit-cell is divided into n sub-cells n=nx*ny*nz.<br>If n is a prime, you can only decompose in one dimension and 57 cells in one<br>dimension is often not possible due to certain restrictions.<br>Also 57 is inconvenient for PME, whether you use separate PME nodes or not.<br><br>Berk<br><br><hr id="stopSpelling">Date: Fri, 25 Sep 2009 15:16:40 +0530<br>Subject: Re: [gmx-users] Error while scaling mdrun for more number of nodes.<br>From: viveksharma.iitb@gmail.com<br>To: gmx-users@gromacs.org<br><br>Hi Berk, <br>Thanks for your suggestion, It is working well now, Can you explain Why it didn't worked for prime number?<br><br><br>Thanks & Regards,<br>Vivek<br><div class="ecxgmail_quote">2009/9/25 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span><br>
<blockquote class="ecxgmail_quote" style="padding-left: 1ex;">
<div>
Hi,<br><br>Why do you want to run on exactly 57 nodes?<br>That is a nasty prime number.<br>I guess 56 or 60 nodes would work fine.<br><br>Berk<br><br><hr>Date: Fri, 25 Sep 2009 14:39:27 +0530<br>From: <a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] Error while scaling mdrun for more number of nodes.<div><div></div><div class="h5"><br><br>Hi There,<br>I was trying to rum mdrun on large number of nodes. When I tried the run on 57 nodes, I got an error which is pasted below.<br>
-------------------------------------------------------<br>Program mpi_mdrun_d, VERSION 4.0.3<br>
Source code file: domdec_setup.c, line: 147<br><br>Fatal error:<br>Could not find an appropriate number of separate PME nodes. i.e. >= 0.409991*#nodes (44) and <= #nodes/2 (57) and reasonable performance wise (grid_x=63, grid_y=63). <br>
Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the manual for details.<br>-------------------------------------------------------<br>then I tried with -npme option as "-npme 20", this time it failed with the following error.<br>
-------------------------------------------------------<br>Program mpi_mdrun_d, VERSION 4.0.3<br>Source code file: domdec.c, line: 5858<br><br>Fatal error:<br>There is no domain decomposition for 94 nodes that is compatible with the given box and a minimum cell size of 1.025 nm<br>
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings<br>Look in the log file for details on the domain decomposition<br>-------------------------------------------------------<br>Same system was running fine when I tried it on 4 nodes.<br>
I havn't used gromacs4.0 very well, so i don't understand these errors.<br>Please suggest me a way to get out of these errors, It will be really helpful if anybody can explain me these errors.<br><br>With thanks in advance.<br>
<br>Thanks & Regards,<br>Vivek<br> <br></div></div><hr>What can you do with the new Windows Live? <a href="http://www.microsoft.com/windows/windowslive/default.aspx">Find out</a></div>
<br>_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><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>
</html>