<br><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 2:39 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5">On 2011-02-08 23.07, Roland Schulz wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
Hi,<br>
<br>
for benchmarking purposes I require a minimal MD compute kernel with a<br>
fast serial PME implementation (in C and Open Source). Does someone<br>
happen to have a GROMACS version laying around, which is just the<br>
computer kernel plus the minimal required to run (e.g. reading input)?<br>
If I need to strip it down myself, what version do you recommend to<br>
start from? Thus at what version did the neighbor-list and PME achieved<br>
roughly todays performance? My thinking is if I start with an older<br>
version I have to remove less to obtain a minimal version.<br>
<br>
Thanks<br>
Roland<br>
<br>
--<br></div></div>
ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a> <<a href="http://cmb.ornl.gov" target="_blank">http://cmb.ornl.gov</a>><div class="im"><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>
<br>
</div></blockquote>
How about running the spec benchmark? That has a minimal gromacs, but maybe not PME.<br></blockquote><div><br></div><div>Where can I get the SPEC benchmark version (besides from SPEC)? Is this minimal version also available under GPL?</div>
<div><br></div><div>Roland</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><font color="#888888">
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>