From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Tue Dec 25 2012 - 17:56:16 CST
Did you use the same seed value in every case? I would expect to see some
small differences between the GPU and CPU version (NAMD-CUDA does not run
in full double precision as far as I know).
Thomas
On 26 December 2012 01:29, Jacqueline Schmidt <
jacqueline_schmidt_1983_at_yahoo.com> wrote:
> Dear Namd users,
> I have cam across a weird discrepancy in namd results on different
> machines:
> I have run a test system on tree clusters and I got different results as
> below
>
> 1-red hat 64 bit (used 12 cpus)
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 2000 6281.3116 3470.8004 36.9492
> 2.4299 -205400.7859 1323.2906 0.0000 0.0000
> 5776.4835 -188509.5208 273.2524 -188466.2680
> -188470.2608 267.9630 1183.8851 490.4254
> 78989.2992 36.6953 31.7657
>
> 2-red hat 64 bit (used 12 cpus) - another cluster than above
> ENERGY: 2000 6231.8194 3307.1326 40.0257
> 2.9600 -205430.4443 1463.4158 0.0000 0.0000
> 5632.5355 -188752.5553 266.4430 -188710.4544
> -188711.2469 264.3466 168.5647 69.4911
> 78739.9095 -63.1504 -57.8641
>
> 3-red hat 64 bit (machine is accessorized with gpu, here I used the same
> executable file as I did on the other machines for initial test)
> ENERGY: 2000 6238.3632 3279.5853 38.7594
> 6.3686 -205074.7611 1388.3075 0.0000 0.0000
> 5733.3590 -188390.0181 271.2124 -188345.6856 -188346.5149
> 271.4772 -409.1661 -111.6605 78769.2246
> 3.6113 3.6517
>
>
> The differences are very large (at 2 ps simulation); specially for
> pressure(the differences are really dramatic)
>
> Is this something than others have observed? I have been using the
> available executable file, shouldn't I? I assumed it should work fine!!!
>
> I would appreciate any comment on this please
>
> Thanks and merry Christmas!
> jackie
>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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