Hi Niel
Thanks for bringing this up to our attention. I didn't have problems on my
testings of the code but it is always good to have more eyes looking. I'll
check what you say and I'll get back to you.
Romelia
> Hi,
>
> I'm not sure how much the Accelerated MD code has been tested ...
> I noticed that the amd.log file indicates that vastly different things
> are being done depending on whether using sander, pmemd, or
> pmemd.cuda.
>
> It looks like sander(.MPI) and pmemd.cuda are producing consistent,
> reasonable results. The serial pmemd produces incorrect potential
> energies in the amd.log file but seems to continue running. pmemd.MPI
> also does not report correct potential energies in the amd.log file and it
> crashes after a few thousand steps with a vlimit error.
>
> Hopefully someone more familiar with the code can diagnose this (see
> below).
>
> --Niel
>
> My computer:
> - Dual-Hex Intel Xeon Westmere X5660
> - Tesla M2090 GPU
> - Amber12 (bugfixed) compiled with Intel 12.1.3.293
> - Mvapich2-1.7
>
> Here is a snippet of the first 5 lines of the amd.log files for
> sander/pmemd (using identical input files):
>
> ----- sander -------
> 500 500 1 -25007.690267452886
> 97.756503548357 0.266050454349 0.034187216512
> 1169.152755500260 16.981277998957
> 500 500 2 -24690.817807373063
> 101.405382803730 0.332930689536 0.059337198428
> 797.638153040664 11.100091477062
> 500 500 3 -24267.077501445114
> 106.304598903008 0.470460860738 0.180232720594
> 369.977314168554 3.686330625345
> 500 500 4 -23833.546422042167
> 111.879880892760 0.724433898035 1.000000000000
> 66.969995258098 0.000000000000
> 500 500 5 -23529.988269129277
> 114.735166671938 1.000000000000 1.000000000000
> 0.000000000000 0.000000000000
>
> ----- pmemd -------
> 500 500 1 -4035.710352328125
> 97.739078899237 1.000000000000 0.034108678022
> 0.000000000000 17.009682999221
> 500 500 2 -4025.014279470225
> 101.728766328767 1.000000000000 0.062822293925
> 0.000000000000 10.587609924899
> 500 500 3 -4015.623017369073
> 106.687902362526 1.000000000000 0.203160613944
> 0.000000000000 3.163186263034
> 500 500 4 -4011.763895364519
> 111.525231242301 1.000000000000 1.000000000000
> 0.000000000000 0.000000000000
> 500 500 5 -4014.053067456131
> 112.584555024514 1.000000000000 1.000000000000
> 0.000000000000 0.000000000000
>
> ------ pmemd.MPI ------
> 500 500 1 -165212.893483722641
> 0.000000000000 0.000113479697 0.000615075147
> 236343.455471183988 181.217792148042
> 500 500 2 -165212.898910553078
> 0.000000000000 0.000113479689 0.000615075147
> 236343.464629531227 181.217792148042
> 500 500 3 -165212.903962433076
> 0.000000000000 0.000113479681 0.000615075147
> 236343.473155110085 181.217792148042
> 500 500 4 -165212.908289464307
> 0.000000000000 0.000113479674 0.000615075147
> 236343.480457430473 181.217792148042
> 500 500 5 -165212.911536836124
> 0.000000000000 0.000113479668 0.000615075147
> 236343.485937711986 181.217792148042
>
> ------ pmemd.cuda ------
> 500 500 1 -25006.887412592856
> 97.708975324000 0.266203374530 0.033973627781
> 1168.228358557432 17.060615439141
> 500 500 2 -24687.746908077854
> 101.242530671000 0.333745012483 0.057690924655
> 794.096550679039 11.360105169050
> 500 500 3 -24262.692940347857
> 105.747059168000 0.472521234810 0.153231057002
> 365.691248044969 4.471448308627
> 500 500 4 -23829.510644879862
> 110.686258329000 0.727710627560 1.000000000000
> 65.111177388485 0.000000000000
> 500 500 5 -23533.890157990856
> 113.611192760000 1.000000000000 1.000000000000
> 0.000000000000 0.000000000000
>
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>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Thu Jul 26 2012 - 17:30:03 PDT
