<div dir="ltr"><div class="gmail_extra">Hi,<div><br></div><div>As Roland sugested, the automated thread affinity setting will end up locking multiple mdrun processes started on the same machine to the first N cores (N=#of threads mdrun is started with).</div>
<div><br></div><div>The thread pinning is really a must with OpenMP and NUMA platforms (without it you can loose up to 50% performance, perhaps even more depending on how dumb your kernel is) and it does a small advantage even without it (haven't seen more than 5%). Linux kernels by default spread out threads across NUMA regions which will maximize memory throughput of an application, but it's almost always the worst strategy when it comes to inter-thread communication. While for the sake of convenience we could disable affinity setting if not running with OpenMP, this would lead to an inconsistent mdrun behavior, one that depends on the command line options i a non-obvious manner.</div>
<div><br></div><div style>Sander suggested a way to detect the multiple mdrun/node case and avoid it in an elegant manner by implementing a small mdrun-mdrun communication interface (sockets would probably be the best). This would enable mdrun to do have an optional feature that enables an mdrun discovery phase of a few seconds during which all other running mdrun-s would communicate which cores are they pinned to and this would enable the newly starting mdrun to avoid clashes.</div>
<div style><br></div><div style>However, we will probably have no time to add this minor feature to mdrun before 4.6, unless somebody could help with the implementation.</div><div style><br></div><div style>Does anybody know any other way to detect that in general some other process is pinned to a certain CPU?</div>
<div class="gmail_extra"><br clear="all"><div style>Cheers,</div></div><div>--<br>Szilárd</div><br>
<br><br><div class="gmail_quote">On Wed, Dec 19, 2012 at 8:16 PM, Shirts, Michael (mrs5pt) <span dir="ltr"><<a href="mailto:mrs5pt@eservices.virginia.edu" target="_blank">mrs5pt@eservices.virginia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>
University of Virginia</blockquote></div><br></div></div>