Dear Amber users,
Today, I decided to install Amber 16 on my servers, which are running ubuntu 14.04, and cuda 7.5. Each server is equipped with two K20 graphic cards.
serial and parallel CPU compilation worked very well, as did the serial cuda enabled one (meaning all the installation passed all tests with very minor differences). When it came to cuda parallel, things were a bit different though.
On test 4096wat the electric field values show very large differences (or at least they look large to me). I'd love to hear if anyone has any input on this, and how critical this test failures are to NPT or NVT simulations.
Thank you very much!
Manuel
P.S. I'm copy pasting the diff file here, just to help it along. Thanks again!
possible FAILURE: check mdout.pure_wat_efield.dif
/usr/local/xtal/amber16/test/cuda/4096wat
77c77
< NSTEP = 1 TIME(PS) = 1.001 TEMP(K) = 298.30 PRESS = 0.
> NSTEP = 1 TIME(PS) = 1.001 TEMP(K) = 298.33 PRESS = 0.
78c78
< Etot = -32104.0964 EKtot = 7283.2797 EPtot = -39387.3761
> Etot = -32148.0445 EKtot = 7283.9830 EPtot = -39432.0275
82c82
< ELECTRIC_FIELD = -44.6514
> ELECTRIC_FIELD = -89.3028
84c84
< NSTEP = 2 TIME(PS) = 1.002 TEMP(K) = 298.05 PRESS = 0.
> NSTEP = 2 TIME(PS) = 1.002 TEMP(K) = 298.23 PRESS = 0.
85c85
< Etot = -32104.1986 EKtot = 7277.1259 EPtot = -39381.3244
> Etot = -32148.1427 EKtot = 7281.4102 EPtot = -39429.5529
87c87
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6029.7294
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6029.7222
88c88
< EELEC = -45364.7143 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45364.7741 EHBOND = 0. RESTRAINT = 0.
89c89
< ELECTRIC_FIELD = -46.3394
> ELECTRIC_FIELD = -94.5010
91c91
< NSTEP = 3 TIME(PS) = 1.003 TEMP(K) = 297.92 PRESS = 0.
> NSTEP = 3 TIME(PS) = 1.003 TEMP(K) = 298.35 PRESS = 0.
92c92
< Etot = -32104.1463 EKtot = 7273.8678 EPtot = -39378.0140
> Etot = -32148.1242 EKtot = 7284.4690 EPtot = -39432.5932
94c94
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6030.3295
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6030.3194
95c95
< EELEC = -45359.3171 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45359.4164 EHBOND = 0. RESTRAINT = 0.
96c96
< ELECTRIC_FIELD = -49.0264
> ELECTRIC_FIELD = -103.4961
98c98
< NSTEP = 4 TIME(PS) = 1.004 TEMP(K) = 297.90 PRESS = 0.
> NSTEP = 4 TIME(PS) = 1.004 TEMP(K) = 298.69 PRESS = 0.
99c99
< Etot = -32104.1539 EKtot = 7273.3270 EPtot = -39377.4809
> Etot = -32148.1901 EKtot = 7292.6682 EPtot = -39440.8583
101c101
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6030.8500
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6030.8160
102c102
< EELEC = -45355.6508 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45355.4981 EHBOND = 0. RESTRAINT = 0.
103c103
< ELECTRIC_FIELD = -52.6801
> ELECTRIC_FIELD = -116.1763
105c105
< NSTEP = 5 TIME(PS) = 1.005 TEMP(K) = 297.97 PRESS = 0.
> NSTEP = 5 TIME(PS) = 1.005 TEMP(K) = 299.20 PRESS = 0.
106c106
< Etot = -32104.2660 EKtot = 7275.1598 EPtot = -39379.4258
> Etot = -32148.2881 EKtot = 7305.2339 EPtot = -39453.5220
108c108
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6031.2665
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6031.2143
109c109
< EELEC = -45353.4381 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45352.3579 EHBOND = 0. RESTRAINT = 0.
110c110
< ELECTRIC_FIELD = -57.2542
> ELECTRIC_FIELD = -132.3784
112c112
< NSTEP = 6 TIME(PS) = 1.006 TEMP(K) = 298.12 PRESS = 0.
> NSTEP = 6 TIME(PS) = 1.006 TEMP(K) = 299.86 PRESS = 0.
113c113
< Etot = -32104.2858 EKtot = 7278.9064 EPtot = -39383.1922
> Etot = -32148.3696 EKtot = 7321.1896 EPtot = -39469.5592
115c115
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6031.6963
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6031.6147
116c116
< EELEC = -45352.1996 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45349.2833 EHBOND = 0. RESTRAINT = 0.
117c117
< ELECTRIC_FIELD = -62.6888
> ELECTRIC_FIELD = -151.8905
119c119
< NSTEP = 7 TIME(PS) = 1.007 TEMP(K) = 298.34 PRESS = 0.
> NSTEP = 7 TIME(PS) = 1.007 TEMP(K) = 300.60 PRESS = 0.
120c120
< Etot = -32104.3846 EKtot = 7284.0507 EPtot = -39388.4353
> Etot = -32148.4966 EKtot = 7339.4489 EPtot = -39487.9455
122c122
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6032.1757
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6032.0648
123c123
< EELEC = -45351.6995 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45345.5547 EHBOND = 0. RESTRAINT = 0.
124c124
< ELECTRIC_FIELD = -68.9115
> ELECTRIC_FIELD = -174.4556
126c126
< NSTEP = 8 TIME(PS) = 1.008 TEMP(K) = 298.58 PRESS = 0.
> NSTEP = 8 TIME(PS) = 1.008 TEMP(K) = 301.40 PRESS = 0.
127c127
< Etot = -32104.3939 EKtot = 7290.0714 EPtot = -39394.4652
> Etot = -32148.5354 EKtot = 7358.9005 EPtot = -39507.4358
129c129
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6032.6307
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6032.4717
130c130
< EELEC = -45351.2574 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45340.1312 EHBOND = 0. RESTRAINT = 0.
131c131
< ELECTRIC_FIELD = -75.8386
> ELECTRIC_FIELD = -199.7763
133c133
< NSTEP = 9 TIME(PS) = 1.009 TEMP(K) = 298.84 PRESS = 0.
> NSTEP = 9 TIME(PS) = 1.009 TEMP(K) = 302.20 PRESS = 0.
134c134
< Etot = -32104.3639 EKtot = 7296.4826 EPtot = -39400.8465
> Etot = -32148.5934 EKtot = 7378.4864 EPtot = -39527.0798
136c136
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6033.1408
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6032.8946
137c137
< EELEC = -45350.6108 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45332.4531 EHBOND = 0. RESTRAINT = 0.
138c138
< ELECTRIC_FIELD = -83.3765
> ELECTRIC_FIELD = -227.5214
140c140
< NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 299.11 PRESS = 0.
> NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 302.97 PRESS = 0.
141c141
< Etot = -32104.3653 EKtot = 7302.8708 EPtot = -39407.2361
> Etot = -32148.6392 EKtot = 7397.2739 EPtot = -39545.9131
143c143
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6033.6681
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6033.3493
144c144
< EELEC = -45349.4798 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45321.9301 EHBOND = 0. RESTRAINT = 0.
145c145
< ELECTRIC_FIELD = -91.4244
> ELECTRIC_FIELD = -257.3323
148c148
< NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 298.31 PRESS = 0.
> NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 299.98 PRESS = 0.
149c149
< Etot = -32104.2655 EKtot = 7283.5142 EPtot = -39387.7797
> Etot = -32148.3424 EKtot = 7324.3064 EPtot = -39472.6487
151c151
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6031.4439
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6031.3419
152c152
< EELEC = -45356.0044 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45349.3075 EHBOND = 0. RESTRAINT = 0.
153c153
< ELECTRIC_FIELD = -63.2191
> ELECTRIC_FIELD = -154.6831
156c156
< NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 0.39 PRESS = 0.
> NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 1.64 PRESS = 0.
157c157
< Etot = 0.1051 EKtot = 9.5649 EPtot = 9.6360
> Etot = 0.2038 EKtot = 40.1414 EPtot = 40.3390
159c159
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 1.4357
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 1.3412
160c160
< EELEC = 6.8291 EHBOND = 0. RESTRAINT = 0.
> EELEC = 14.2172 EHBOND = 0. RESTRAINT = 0.
161c161
< ELECTRIC_FIELD = 15.3999
> ELECTRIC_FIELD = 55.4718
### Maximum absolute error in matching lines = 1.66e+02 at line 145 field 3
### Maximum relative error in matching lines = 3.21e+00 at line 156 field 9
---------------------------------------
possible FAILURE: check mdout.cellulose_nvt.dif
/usr/local/xtal/amber16/test/cuda/cellulose
212c212
< Etot = 5.8651 EKtot = 273.2191 EPtot = 276.4278
> Etot = 5.8650 EKtot = 273.2191 EPtot = 276.4278
### Maximum absolute error in matching lines = 1.00e-04 at line 212 field 3
### Maximum relative error in matching lines = 1.71e-05 at line 212 field 3
---------------------------------------
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Received on Sun Jun 05 2016 - 22:30:02 PDT
