The warning is in the mdrun output.<br><br><div class="gmail_quote">On Thu, Jun 21, 2012 at 12:55 PM, Alexey Shvetsov <span dir="ltr"><<a href="mailto:alexxy@omrb.pnpi.spb.ru" target="_blank">alexxy@omrb.pnpi.spb.ru</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi!<br>
<br>
Ghmmm. There were no warning at all =)<br>
<br>
build log <a href="http://omrb.pnpi.spb.ru/~alexxy/gromacs-4.6-git.log" target="_blank">http://omrb.pnpi.spb.ru/~alexxy/gromacs-4.6-git.log</a><br>
<br>
<br>
David van der Spoel ΠΙΣΑΜ 2012-06-21 20:32:<br>
<div class="im HOEnZb">> On 2012-06-21 18:22, Alexey Shvetsov wrote:<br>
>> Hi all!<br>
>><br>
>> After merging commit<br>
>> commit 5ba7125c5972f2aafde2310eaa4a345cbac55da5<br>
>> Author: Erik Lindahl <<a href="mailto:erik@kth.se">erik@kth.se</a>><br>
>> Date: Mon May 28 20:54:17 2012 +0200<br>
>><br>
>> New CPU detection & AVX/SSE code, removed raw assembly files.<br>
><br>
</div><div class="im HOEnZb">> If you checked the installation output, you would have been warned<br>
> :).<br>
> Don't worry in a couple of days it will be fixed.<br>
><br>
>><br>
</div><div class="HOEnZb"><div class="h5">>> I noticed regression in gromacs speed. I used two systems for tests<br>
>> one<br>
>> 7bna and second speptide froma examples<br>
>><br>
>> For 7bna system old 4.6 version 4.6-dev-20120418-3759a-dirty-unknown<br>
>> gives<br>
>> R E A L C Y C L E A N D T I M E A C C O U N T I N G<br>
>><br>
>> Computing: Nodes Number G-Cycles Seconds %<br>
>><br>
>> -----------------------------------------------------------------------<br>
>> Domain decomp. 16 5000 502.025 335.5 1.5<br>
>> DD comm. load 16 5000 4.309 2.9 0.0<br>
>> DD comm. bounds 16 5000 13.941 9.3 0.0<br>
>> Comm. coord. 16 50001 497.769 332.7 1.5<br>
>> Neighbor search 16 5001 1630.241 1089.6 4.8<br>
>> Force 16 50001 23079.690 15425.1 67.3<br>
>> Wait + Comm. F 16 50001 618.862 413.6 1.8<br>
>> PME mesh 16 50001 6564.978 4387.7 19.1<br>
>> Write traj. 16 101 16.666 11.1 0.0<br>
>> Update 16 50001 384.280 256.8 1.1<br>
>> Constraints 16 50001 592.154 395.8 1.7<br>
>> Comm. energies 16 5001 125.537 83.9 0.4<br>
>> Rest 16 256.227 171.2 0.7<br>
>><br>
>> -----------------------------------------------------------------------<br>
>> Total 16 34286.680 22915.3 100.0<br>
>><br>
>> -----------------------------------------------------------------------<br>
>><br>
>> -----------------------------------------------------------------------<br>
>> PME redist. X/F 16 100002 1176.273 786.2 3.4<br>
>> PME spread/gather 16 100002 2119.858 1416.8 6.2<br>
>> PME 3D-FFT 16 100002 1041.014 695.8 3.0<br>
>> PME 3D-FFT Comm. 16 200004 1905.967 1273.8 5.6<br>
>> PME solve 16 50001 316.714 211.7 0.9<br>
>><br>
>> -----------------------------------------------------------------------<br>
>><br>
>> Parallel run - timing based on wallclock.<br>
>><br>
>> NODE (s) Real (s) (%)<br>
>> Time: 716.102 716.102 100.0<br>
>> 11:56<br>
>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)<br>
>> Performance: 1482.789 73.686 12.066 1.989<br>
>><br>
>> New version 4.6-dev-20120618-283a0e5-dirty-unknown with sse4.1<br>
>> acceleration enabled gives only<br>
>> R E A L C Y C L E A N D T I M E A C C O U N T I N G<br>
>><br>
>> Computing: Nodes Number G-Cycles Seconds %<br>
>><br>
>> -----------------------------------------------------------------------<br>
>> Domain decomp. 16 5000 503.648 336.6 0.5<br>
>> DD comm. load 16 5000 5.666 3.8 0.0<br>
>> DD comm. bounds 16 5000 11.637 7.8 0.0<br>
>> Comm. coord. 16 50001 480.473 321.1 0.4<br>
>> Neighbor search 16 5001 1665.565 1113.2 1.5<br>
>> Force 16 50001 98860.466 66073.0 89.0<br>
>> Wait + Comm. F 16 50001 608.138 406.4 0.5<br>
>> PME mesh 16 50001 7605.687 5083.2 6.8<br>
>> Write traj. 16 103 17.010 11.4 0.0<br>
>> Update 16 50001 383.590 256.4 0.3<br>
>> Constraints 16 50001 582.954 389.6 0.5<br>
>> Comm. energies 16 5001 132.665 88.7 0.1<br>
>> Rest 16 257.063 171.8 0.2<br>
>><br>
>> -----------------------------------------------------------------------<br>
>> Total 16 111114.560 74263.0 100.0<br>
>><br>
>> -----------------------------------------------------------------------<br>
>><br>
>> -----------------------------------------------------------------------<br>
>> PME redist. X/F 16 100002 2258.309 1509.3 2.0<br>
>> PME spread/gather 16 100002 2111.979 1411.5 1.9<br>
>> PME 3D-FFT 16 100002 1046.271 699.3 0.9<br>
>> PME 3D-FFT Comm. 16 200004 1854.221 1239.3 1.7<br>
>> PME solve 16 50001 329.985 220.5 0.3<br>
>><br>
>> -----------------------------------------------------------------------<br>
>><br>
>> Parallel run - timing based on wallclock.<br>
>><br>
>> NODE (s) Real (s) (%)<br>
>> Time: 2320.719 2320.719 100.0<br>
>> 38:40<br>
>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)<br>
>> Performance: 457.569 22.739 3.723 6.446<br>
>><br>
>><br>
><br>
><br>
> --<br>
</div></div><div class="im HOEnZb">> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205">+46184714205</a>.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
<br>
</div><div class="HOEnZb"><div class="h5">--<br>
Best Regards,<br>
Alexey 'Alexxy' Shvetsov<br>
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,<br>
Gatchina, Russia<br>
Department of Molecular and Radiation Biophysics<br>
Gentoo Team Ru<br>
Gentoo Linux Dev<br>
mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
mailto:<a href="mailto:alexxy@gentoo.org">alexxy@gentoo.org</a><br>
mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
--<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <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>