Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed

From: Tru Huynh <tru.pasteur.fr>
Date: Wed, 3 Jul 2013 21:32:46 +0200

On Wed, Jul 03, 2013 at 07:35:56PM +0200, Tru Huynh wrote:
> On Wed, Jul 03, 2013 at 10:00:44AM -0700, Ross Walker wrote:
> > Be sure to update your version of AMBER to AmberTools 13 and the latest
> > bug fixes first though.
>
> I am doing it now, upgrading to amberools13 and applying the update to amber12.
> >
> > Plus it is the PME tests that really matter - cellulose NPT is the best
> > one to try.
> ok
> PME/Cellulose_production_NPT will be run ASAP.

And the results are not good :(

out of the 4 serial runs, 2 died and the 2 which finished
show energy divergence around steps 11000.

|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.3
|
| 04/24/2013
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------

[tru.margy Cellulose_production_NPT]$ diff mdout.1GTXTITAN.3 mdout.1GTXTITAN.2| less
355,360c355,360
< NSTEP = 11000 TIME(PS) = 42.020 TEMP(K) = 300.00 PRESS = -163.5
< Etot = -442287.6638 EKtot = 257793.9063 EPtot = -700081.5700
< BOND = 20360.0408 ANGLE = 53537.6960 DIHED = 23629.9853
< 1-4 NB = 21792.7460 1-4 EEL = 742524.7952 VDWAALS = 95955.2014
< EELEC = -1657882.0348 EHBOND = 0.0000 RESTRAINT = 0.0000
< EKCMT = 95434.5939 VIRIAL = 109598.9815 VOLUME = 4012261.4740 
---
>  NSTEP =    11000   TIME(PS) =      42.020  TEMP(K) =   300.01  PRESS =  -164.1
>  Etot   =   -442287.2335  EKtot   =    257801.7188  EPtot      =   -700088.9522
>  BOND   =     20360.6584  ANGLE   =     53537.8758  DIHED      =     23631.2159
>  1-4 NB =     21792.4622  1-4 EEL =    742526.0845  VDWAALS    =     95951.4649
>  EELEC  =  -1657888.7138  EHBOND  =         0.0000  RESTRAINT  =         0.0000
>  EKCMT  =     95440.4161  VIRIAL  =    109659.2366  VOLUME     =   4012261.8348
<snip>
1360,1365c1360,1365
<  NSTEP =   100000   TIME(PS) =     220.020  TEMP(K) =     0.36  PRESS =    80.5
<  Etot   =       570.0128  EKtot   =       307.0828  EPtot      =       572.1520
<  BOND   =       128.0521  ANGLE   =       228.4923  DIHED      =        72.9718
<  1-4 NB =        64.8977  1-4 EEL =       342.5954  VDWAALS    =       523.6439
<  EELEC  =       947.5848  EHBOND  =         0.0000  RESTRAINT  =         0.0000
<  EKCMT  =       275.2482  VIRIAL  =      6981.4558  VOLUME     =      5056.4070
---
>  NSTEP =   100000   TIME(PS) =     220.020  TEMP(K) =     0.39  PRESS =    86.4
>  Etot   =       643.9263  EKtot   =       337.3628  EPtot      =       645.6993
>  BOND   =       131.1889  ANGLE   =       236.0164  DIHED      =       108.3710
>  1-4 NB =        63.8634  1-4 EEL =       470.0020  VDWAALS    =       605.0091
>  EELEC  =      1022.6194  EHBOND  =         0.0000  RESTRAINT  =         0.0000
>  EKCMT  =       280.7610  VIRIAL  =      7544.5179  VOLUME     =      5198.6004
     
...
mdout.1GTXTITAN.3:
|  Final Performance Info:
|     -----------------------------------------------------
|     Average timings for last    2000 steps:
|         Elapsed(s) =      58.28 Per Step(ms) =      29.14
|             ns/day =       5.93   seconds/ns =   14570.60
| 
|     Average timings for all steps:
|         Elapsed(s) =    2808.12 Per Step(ms) =      28.08
|             ns/day =       6.15   seconds/ns =   14040.58
|     -----------------------------------------------------
...
mdout.1GTXTITAN.2:
|  Final Performance Info:
|     -----------------------------------------------------
|     Average timings for last       0 steps:
|         Elapsed(s) =       0.00 Per Step(ms) =  +Infinity
|             ns/day =       0.00   seconds/ns =  +Infinity
|
|     Average timings for all steps:
|         Elapsed(s) =    2954.11 Per Step(ms) =      29.54
|             ns/day =       5.85   seconds/ns =   14770.56
|     -----------------------------------------------------
I will now re-run the GB/nucleosome test with this version of pmemd.CUDA
to verify my initial claims!
Cheers,
Tru
-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru.pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  
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Received on Wed Jul 03 2013 - 13:00:02 PDT
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