[gmx-users] Installation of 4.0.5 on Cray XD1- gmxtest
Dean Cuebas
deancuebas at missouristate.edu
Wed Sep 2 17:17:50 CEST 2009
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.)
Thanks very much for your help.
Dean
--
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas at missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
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