<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
<br><br>> From: zhao0139@ntu.edu.sg<br>> To: gmx-users@gromacs.org<br>> Date: Tue, 6 Apr 2010 21:05:32 +0800<br>> Subject: [gmx-users] Re: Re: loab imbalance<br>> <br>> <br>> lina wrote:<br>> >> On 6/04/2010 5:39 PM, lina wrote:<br>> >>> Hi everyone,<br>> >>><br>> >>> Here is the result of the mdrun which was performed on 16cpus. I am<br>> not<br>> >>> clear about it, was it due to using MPI reason? or some other<br>> reasons.<br>> >>><br>> >>> Writing final coordinates.<br>> >>><br>> >>> Average load imbalance: 1500.0 %<br>> >>> Part of the total run time spent waiting due to load imbalance:<br>> 187.5 %<br>> >>> Steps where the load balancing was limited by -rdd, -rcon and/or<br>> -dds:<br>> >>> X 0 % Y 0 %<br>> >>><br>> >>> NOTE: 187.5 % performance was lost due to load imbalance<br>> >>> in the domain decomposition.<br>> >> You ran an inefficient but otherwise valid computation. Check out<br>> the <br>> >> manual section on domain decomposition to learn why it was<br>> inefficient, <br>> >> and whether you can do better.<br>> >><br>> >> Mark<br>> > <br>> > I search the "decomposition" keyword on Gromacs manual, no match<br>> found.<br>> > Are you positive about that? Thanks any way, but can you make it more<br>> <br>> The title of section 3.17 is "Domain Decomposition" and discusses the<br>> algorithm <br>> and mdrun parameters relevant to controlling performance.<br>> <br>> -Justin<br>> <br>> Sorry, the acroread is really not sensitive in searching "domain" or<br>> "decomposition" on version 3.3. I did the same search on version 3.2 and<br>> I found it. I am not so familiar with this manual. Thanks again.<br>> <br>> lina <br><br>Since you performance roughly doubles when going from 8 to 16 cores,<br>I think there is no significant load imbalance and there is a bug in the routine<br>that calculates the total load imbalance.<br><br>In my previous mail I asked which Gromacs version you are using.<br>Could you please tell me this?<br><br>Berk<br><br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
</html>