From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Aug 29 2012 - 23:19:27 CDT
Thomas Albers <talbers_at_binghamton.edu> writes:
> Date: Wed, 29 Aug 2012 22:38:20 -0400
> From: Thomas Albers <talbers_at_binghamton.edu>
> To: Jeff Wereszczynski <jmweresz_at_mccammon.ucsd.edu>, Namd Mailing List
> <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: Accelerated MD
>
> Dear Jeff,
>
> > Yes, something looks weird there.
>
> It seems there is something very wrong when CUDA acceleration is
> combined with a boost to the total potential:
>
> Here's the relevant output for aMDd mode with graphics card acceleration:
>
> Info: NAMD 2.9 for Linux-x86_64-ibverbs-CUDA
> ..
> Info: BOOSTING DIHEDRAL POTENTIAL
> Info: accelMDE: 6900 KCAL/MOL, accelMDalpha: 570 KCAL/MOL
> Info: accelMD WILL BE DONE FROM STEP 0 TO THE END OF THE SIMULATION
> Info: accelMD OUTPUT FREQUENCY 100
> ..
> ACCELERATED MD: STEP 20000 dV 253.844 dVAVG 275.381 BOND 1338.24 ANGLE 6925.25 D
> IHED 6372.08 IMPRP 69.7927 ELECT -7868.19 VDW -3003.61 POTENTIAL 3833.56
> ..
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 20000 1338.2441 6925.2481 6372.0787 69.7927
> -75197.2498 1439.0778 0.0000 0.0000
> 18897.7076 -40155.1008 300.7371 -59052.8084
> -40031.7866 300.6322 -612.8711 -603.8231
> 281748.7794 -7.7389 -7.5624
>
> and here the equivalent output with plain NAMD:
>
> Info: NAMD 2.9 for Linux-x86_64-ibverbs
> ..
> ACCELERATED MD: STEP 6000 dV 333.131 dVAVG 323.749 BOND 1253.58 ANGLE 7059.32 DI
> HED 6266.93 IMPRP 70.9914 ELECT -75591.7 VDW 1599.76 POTENTIAL -59341.2
> ..
> ENERGY: 6000 1253.5799 7059.3184 6266.9277
> 70.9914 -75591.7370 1599.7616 0.0000
> 0.0000 18788.4535 -40552.7046 298.9985
> -59341.1581 -40425.8879 299.9954 241.0034
> 256.3487 278915.3123 -8.1178 -8.3545
>
> The numbers are comparable.
>
> Here's output for aMDT mode with GPU acceleration:
> Info: NAMD 2.9 for Linux-x86_64-ibverbs-CUDA
> ..
> Info: ACCELERATED MD ACTIVE
> Info: BOOSTING TOTAL POTENTIAL
> Info: accelMDE: -56550 KCAL/MOL, accelMDalpha: 4690 KCAL/MOL
> ..
> ACCELERATED MD: STEP 500 dV 0 dVAVG 0 BOND 1325.53 ANGLE 6894.1 DIHED
> 4092.79 IMPRP 61.4494 ELECT -7851.73 VDW -2788.71 POTENTIAL 1733.43
> ..
> ENERGY: 500 1325.5256 6894.0969 4092.7913
> 61.4494 -75364.0230 1507.6438 0.0000
> 0.0000 19104.2109 -42378.3050 304.0234
> -61482.5159 -42247.3078 300.6413 -361.8518
> -328.5936 280609.2766 20.7882 21.6944
>
> And here is output for the same with vanilla NAMD:
> Info: NAMD 2.9 for Linux-x86_64-ibverbs
> ..
> Info: ACCELERATED MD ACTIVE
> Info: BOOSTING TOTAL POTENTIAL
> Info: accelMDE: -56550 KCAL/MOL, accelMDalpha: 4690 KCAL/MOL
> ..
> ACCELERATED MD: STEP 3000 dV 21.1076 dVAVG 17.9464 BOND 1476.16 ANGLE
> 7939.6 DIHED 4252.22 IMPRP 69.9781 ELECT -71794.8 VDW 1181.47
> POTENTIAL -56875.4
> ..
> ENERGY: 3000 1476.1563 7939.5996 4252.2218
> 69.9781 -71794.7873 1181.4665 0.0000
> 0.0000 19102.0412 -37773.3239 303.9889
> -56875.3651 -37660.1795 301.9512 -103.8260
> -80.9638 288694.1023 -11.3759 -11.3094
>
> It would seem that with the CUDA version, no boost is applied to the
> total energy.
>
> Thomas
>
Thomas,
Something does look odd here. Can you send me your inputs? Also, on
what model GPU card were you running?
Best,
Chris
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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