[gmx-developers] Possible regression in gromacs 4.6

[Alexey Shvetsov]

Hi!

Ghmmm. There were no warning at all =)

build log http://omrb.pnpi.spb.ru/~alexxy/gromacs-4.6-git.log


David van der Spoel писал 2012-06-21 20:32:
> On 2012-06-21 18:22, Alexey Shvetsov wrote:
>> Hi all!
>>
>> After merging commit
>> commit 5ba7125c5972f2aafde2310eaa4a345cbac55da5
>> Author: Erik Lindahl <erik at kth.se>
>> Date: Mon May 28 20:54:17 2012 +0200
>>
>> New CPU detection & AVX/SSE code, removed raw assembly files.
>
> If you checked the installation output, you would have been warned 
> :).
> Don't worry in a couple of days it will be fixed.
>
>>
>> I noticed regression in gromacs speed. I used two systems for tests 
>> one
>> 7bna and second speptide froma examples
>>
>> For 7bna system old 4.6 version 4.6-dev-20120418-3759a-dirty-unknown 
>> gives
>> 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
>>
>> Computing: Nodes Number G-Cycles Seconds %
>> 
>> -----------------------------------------------------------------------
>> Domain decomp. 16 5000 502.025 335.5 1.5
>> DD comm. load 16 5000 4.309 2.9 0.0
>> DD comm. bounds 16 5000 13.941 9.3 0.0
>> Comm. coord. 16 50001 497.769 332.7 1.5
>> Neighbor search 16 5001 1630.241 1089.6 4.8
>> Force 16 50001 23079.690 15425.1 67.3
>> Wait + Comm. F 16 50001 618.862 413.6 1.8
>> PME mesh 16 50001 6564.978 4387.7 19.1
>> Write traj. 16 101 16.666 11.1 0.0
>> Update 16 50001 384.280 256.8 1.1
>> Constraints 16 50001 592.154 395.8 1.7
>> Comm. energies 16 5001 125.537 83.9 0.4
>> Rest 16 256.227 171.2 0.7
>> 
>> -----------------------------------------------------------------------
>> Total 16 34286.680 22915.3 100.0
>> 
>> -----------------------------------------------------------------------
>> 
>> -----------------------------------------------------------------------
>> PME redist. X/F 16 100002 1176.273 786.2 3.4
>> PME spread/gather 16 100002 2119.858 1416.8 6.2
>> PME 3D-FFT 16 100002 1041.014 695.8 3.0
>> PME 3D-FFT Comm. 16 200004 1905.967 1273.8 5.6
>> PME solve 16 50001 316.714 211.7 0.9
>> 
>> -----------------------------------------------------------------------
>>
>> Parallel run - timing based on wallclock.
>>
>> NODE (s) Real (s) (%)
>> Time: 716.102 716.102 100.0
>> 11:56
>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>> Performance: 1482.789 73.686 12.066 1.989
>>
>> New version 4.6-dev-20120618-283a0e5-dirty-unknown with sse4.1
>> acceleration enabled gives only
>> 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
>>
>> Computing: Nodes Number G-Cycles Seconds %
>> 
>> -----------------------------------------------------------------------
>> Domain decomp. 16 5000 503.648 336.6 0.5
>> DD comm. load 16 5000 5.666 3.8 0.0
>> DD comm. bounds 16 5000 11.637 7.8 0.0
>> Comm. coord. 16 50001 480.473 321.1 0.4
>> Neighbor search 16 5001 1665.565 1113.2 1.5
>> Force 16 50001 98860.466 66073.0 89.0
>> Wait + Comm. F 16 50001 608.138 406.4 0.5
>> PME mesh 16 50001 7605.687 5083.2 6.8
>> Write traj. 16 103 17.010 11.4 0.0
>> Update 16 50001 383.590 256.4 0.3
>> Constraints 16 50001 582.954 389.6 0.5
>> Comm. energies 16 5001 132.665 88.7 0.1
>> Rest 16 257.063 171.8 0.2
>> 
>> -----------------------------------------------------------------------
>> Total 16 111114.560 74263.0 100.0
>> 
>> -----------------------------------------------------------------------
>> 
>> -----------------------------------------------------------------------
>> PME redist. X/F 16 100002 2258.309 1509.3 2.0
>> PME spread/gather 16 100002 2111.979 1411.5 1.9
>> PME 3D-FFT 16 100002 1046.271 699.3 0.9
>> PME 3D-FFT Comm. 16 200004 1854.221 1239.3 1.7
>> PME solve 16 50001 329.985 220.5 0.3
>> 
>> -----------------------------------------------------------------------
>>
>> Parallel run - timing based on wallclock.
>>
>> NODE (s) Real (s) (%)
>> Time: 2320.719 2320.719 100.0
>> 38:40
>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>> Performance: 457.569 22.739 3.723 6.446
>>
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru