[gmx-users] Installation of 4.0.5 on Cray XD1- gmxtest
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Sep 3 00:47:02 CEST 2009
Dean Cuebas wrote:
> Dear colleagues,
>
> After installation of 4.0.5 on my MacBook, all is fine after testing with
> gmxtest 4.0.4
> (except for the [0-4]2[0-4] kernel errors that are noted in
> http://oldwiki.gromacs.org/index.php/Test-set)
>
> But after install on Cray XD1, all is well except the kernel errors, AND
> bad virial errors in these:
>
> FAILED. Check files in aminoacids
> FAILED. Check files in field
> FAILED. Check files in tip4p
> FAILED. Check files in tip4pflex
> FAILED. Check files in water
>
> I know that the oldwiki says " It is normal for GROMACS 4.0-4.0.5 to fail
> gmxtest-4.0.4 on tip4p, tip4pflex, perhaps some others,..."
>
> but I just wanted to check for sure that these errors are in the gmxtest,
> and not my installation.
>
> the energies are fine, but the checkvir.out for the water test results in
> the following:
>
> Vir-ZY step 23: -132.302, step 23: -130.526
> Vir-YZ step 24: -46.1021, step 24: -45.3469
> Vir-XZ step 30: -3955.79, step 30: -3909.04
> Vir-ZX step 30: -3953.66, step 30: -3908.28
> Vir-ZZ step 30: -4260.19, step 30: -4381.16
> Vir-XZ step 31: -3754.27, step 31: -3700.21
> Vir-ZX step 31: -3752.9, step 31: -3701.78
> Vir-ZZ step 31: -3976.42, step 31: -4100.35
> Vir-XZ step 32: -3234.1, step 32: -3170.21
> Vir-ZX step 32: -3232.99, step 32: -3170.8
> Vir-ZY step 32: -522.406, step 32: -528.714
> Vir-ZZ step 32: -3343.25, step 32: -3476.03
> Vir-XY step 33: 190.88, step 33: 193.219
> Vir-XZ step 33: -2207.41, step 33: -2132.02
> Vir-YZ step 33: -296.469, step 33: -308.25
> Vir-ZX step 33: -2207.1, step 33: -2130.68
> Vir-ZY step 33: -297.242, step 33: -308.24
> Vir-ZZ step 33: -3395.03, step 33: -3528.7
> Vir-XZ step 34: -1261.6, step 34: -1169.32
> Vir-YZ step 34: 253.726, step 34: 241.23
> Vir-ZX step 34: -1260.16, step 34: -1171.26
> Vir-ZY step 34: 255.451, step 34: 240.019
> Vir-ZZ step 34: -4326.35, step 34: -4443.42
> Vir-XZ step 35: -733.406, step 35: -628.372
> Vir-YZ step 35: 984.893, step 35: 970.402
> Vir-ZX step 35: -734.102, step 35: -629.179
> Vir-ZY step 35: 984.288, step 35: 970.839
> Vir-ZZ step 35: -5252.03, step 35: -5375.68
> Vir-XZ step 36: -563.935, step 36: -447.161
> Vir-ZX step 36: -562.932, step 36: -445.203
> Vir-ZZ step 36: -5485.69, step 36: -5641.42
> Vir-XY step 37: 1808.55, step 37: 1779.78
> Vir-XZ step 37: -518.982, step 37: -412.322
> Vir-YX step 37: 1808.47, step 37: 1780.3
> Vir-YZ step 37: 1023.48, step 37: 1050.7
> Vir-ZX step 37: -518.936, step 37: -412.305
> Vir-ZY step 37: 1023.99, step 37: 1051.44
> Vir-ZZ step 37: -5184.18, step 37: -5410.04
> Vir-XY step 38: 1039.88, step 38: 1024
> Vir-XZ step 38: -276.865, step 38: -193.253
> Vir-YX step 38: 1039.43, step 38: 1023.67
> Vir-YZ step 38: 535.852, step 38: 632.737
> Vir-ZX step 38: -277.38, step 38: -192.959
> Vir-ZY step 38: 535.738, step 38: 632.855
> Vir-ZZ step 38: -4845.03, step 38: -5123.82
> Pressure (bar) step 39: 77135.4, step 39: 78214.5
> Vir-XY step 39: 272.697, step 39: 300.437
> Vir-XZ step 39: 113.03, step 39: 134.648
> Vir-YX step 39: 273.549, step 39: 300.282
> Vir-YY step 39: -12353.4, step 39: -12634.1
> Vir-YZ step 39: -86.8086, step 39: 96.9297
> Vir-ZX step 39: 114.745, step 39: 135.612
> Vir-ZY step 39: -86.5166, step 39: 98.2657
> Vir-ZZ step 39: -4626.46, step 39: -4880.27
> Pressure (bar) step 40: 76118.8, step 40: 76922.9
> Vir-XY step 40: 28.5289, step 40: 90.0801
> Vir-XZ step 40: -1032.5, step 40: -1186.33
> Vir-YX step 40: 27.8441, step 40: 89.0082
> Vir-YY step 40: -11921.6, step 40: -12276.8
> Vir-YZ step 40: -354.577, step 40: -80.0877
> Vir-ZX step 40: -1031.82, step 40: -1185.84
> Vir-ZY step 40: -355.184, step 40: -79.8926
> Vir-XY step 41: -256.858, step 41: -58.3765
> Vir-XZ step 41: -157.337, step 41: -333.937
> Vir-YX step 41: -256.052, step 41: -57.9436
> Vir-YY step 41: -11814.6, step 41: -12075.3
> Vir-YZ step 41: -393.582, step 41: -123.112
> Vir-ZX step 41: -157.198, step 41: -334.432
> Vir-ZY step 41: -393.264, step 41: -124.242
> Vir-ZZ step 41: -2190.59, step 41: -2163.87
> Vir-XX step 42: -12342.2, step 42: -12485.4
> Vir-XY step 42: -529.83, step 42: -230.243
> Vir-XZ step 42: 1382.87, step 42: 1254.87
> Vir-YX step 42: -531.684, step 42: -229.925
> Vir-YZ step 42: -782.548, step 42: -609.416
> Vir-ZX step 42: 1381.31, step 42: 1254.65
> Vir-ZY step 42: -783.091, step 42: -609.663
> Vir-ZZ step 42: -601.758, step 42: -679.94
> Pressure (bar) step 43: 59922.1, step 43: 60705.1
> Vir-XX step 43: -10707.8, step 43: -10946.3
> Vir-XY step 43: -1138.7, step 43: -896.666
> Vir-XZ step 43: 2385.12, step 43: 2301.16
> Vir-YX step 43: -1139.06, step 43: -898.088
> Vir-YZ step 43: -1426.5, step 43: -1367
> Vir-ZX step 43: 2383.65, step 43: 2301.23
> Vir-ZY step 43: -1426.9, step 43: -1366.28
> Vir-ZZ step 43: 955.955, step 43: 697.018
> Pressure (bar) step 44: 51604.7, step 44: 52918.7
> Vir-XX step 44: -8958.9, step 44: -9270.15
> Vir-XY step 44: -1737.15, step 44: -1670.68
> Vir-XZ step 44: 2492.2, step 44: 2361.59
> Vir-YX step 44: -1737.38, step 44: -1671.91
> Vir-YY step 44: -4254.76, step 44: -4337.05
> Vir-ZX step 44: 2492.09, step 44: 2360.84
> Vir-ZZ step 44: 1750.38, step 44: 1380.74
> Pressure (bar) step 45: 45928.5, step 45: 47411.2
> Vir-XX step 45: -7311.26, step 45: -7518.85
> Vir-XY step 45: -1878.87, step 45: -1964.91
> Vir-XZ step 45: 1869, step 45: 1760.99
> Vir-YX step 45: -1878.59, step 45: -1964.57
> Vir-YY step 45: -2732.33, step 45: -3002.29
> Vir-YZ step 45: -1477.76, step 45: -1554.38
> Vir-ZX step 45: 1867.51, step 45: 1762.29
> Vir-ZY step 45: -1479.22, step 45: -1554
> Vir-ZZ step 45: 1713.96, step 45: 1330.91
> Pressure (bar) step 46: 42430.9, step 46: 43616.7
> Vir-XY step 46: -2107.65, step 46: -2271.88
> Vir-XZ step 46: 798.872, step 46: 727.563
> Vir-YX step 46: -2109.74, step 46: -2272.1
> Vir-YY step 46: -1768.94, step 46: -2089.67
> Vir-YZ step 46: -1332.56, step 46: -1408.74
> Vir-ZX step 46: 800.354, step 46: 724.807
> Vir-ZY step 46: -1330.64, step 46: -1409.12
> Vir-ZZ step 46: 1143.19, step 46: 852.741
> Vir-XX step 47: -5618.44, step 47: -5536.34
> Vir-XY step 47: -2469.99, step 47: -2566.83
> Vir-XZ step 47: -326.209, step 47: -432.586
> Vir-YX step 47: -2470.87, step 47: -2567.3
> Vir-YY step 47: -1102.94, step 47: -1312.51
> Vir-ZX step 47: -328.885, step 47: -434.294
> Vir-ZZ step 47: -20.5518, step 47: -72.1807
> Pressure (bar) step 48: 43223.2, step 48: 42524.7
> Vir-XX step 48: -5354.39, step 48: -5143.36
> Vir-XY step 48: -2809.38, step 48: -2736.35
> Vir-XZ step 48: -651.573, step 48: -817.92
> Vir-YX step 48: -2810.75, step 48: -2734.92
> Vir-YY step 48: -1143.24, step 48: -1095.92
> Vir-YZ step 48: -1053.42, step 48: -930.663
> Vir-ZX step 48: -651.381, step 48: -817.185
> Vir-ZY step 48: -1054.32, step 48: -931.654
> Vir-ZZ step 48: -1973.21, step 48: -1774.21
> Pressure (bar) step 49: 46073.2, step 49: 44880.8
> Vir-XX step 49: -6020.39, step 49: -5770.05
> Vir-XY step 49: -2904.9, step 49: -2625.09
> Vir-XZ step 49: -77.2606, step 49: -351.229
> Vir-YX step 49: -2903.51, step 49: -2623.71
> Vir-YY step 49: -1061.57, step 49: -957.809
> Vir-YZ step 49: -1163.56, step 49: -917.527
> Vir-ZX step 49: -76.4861, step 49: -350.882
> Vir-ZY step 49: -1163.53, step 49: -918.895
> Vir-ZZ step 49: -3378.99, step 49: -3031.39
> Pressure (bar) step 50: 46893.3, step 50: 44950.2
> Vir-XX step 50: -6211.69, step 50: -6027.86
> Vir-XY step 50: -2423.21, step 50: -1865.56
> Vir-XZ step 50: 667.327, step 50: 480.726
> Vir-YX step 50: -2422.22, step 50: -1865.69
> Vir-YY step 50: -3194.86, step 50: -2817.2
> Vir-YZ step 50: -2208.7, step 50: -2647.63
> Vir-ZX step 50: 667.878, step 50: 481.076
> Vir-ZY step 50: -2207.77, step 50: -2648.09
> Vir-ZZ step 50: -1482.41, step 50: -967.051
>
> I just wanted to be sure that these diverging errors are actually errors in
> the test, (especially since I got NO such errors on the MacBook install of
> the exact same source files.)
Yes, that does look normal. These tests fail because MD is intrinsically
irreproducible across architectures, and the virial components are about
the most sensitive parts. A difference that is large enough to exceed
the tolerances in gmxtest is inevitable, and once such a difference is
observed, others will snowball.
Testing with double-precision (./configure --enable-double and
./gmxtest.pl -double) can reduce the incidence of such reported
failures, which might ease your mind somewhat.
Mark
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