[gmx-users] Error in BlueGene
Cintia C. Vequi-Suplicy
cintia at if.usp.br
Wed Jan 30 15:41:39 CET 2013
Hello,
I am having some problems to run my system in a bluegene cluster.
I am running a bilayer simulation. The simulation runs very well in my
local cluster.
After 50ns of simulation on my local cluster with 8 nodes, I got the
configurations and tried to run it in a bluegene with 512 nodes.
But I always get the same error (the whole output error is below as also
the md.mdp file):
"
-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"
Can anyone help me?
Thank you,
Cíntia
-------------------------------------------------------
md.mdp file
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 5000000
nstcomm = 5
comm-grps = Other SOL
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
xtc-grps =
energygrps = Other SOL
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = reaction-field
rcoulomb = 1.4
epsilon_rf = 66
vdw_type = cut-off
rvdw = 1.4
DispCorr = No
tcoupl = v-rescale
tc-grps = Other SOL
tau_t = 0.4 0.4
ref_t = 296 296
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 0.2 0.2
compressibility = 4.51e-5 4.51e-5
ref_p = 1.0 1.0
constraints = hbonds
constraint_algorithm = lincs
-------------------------------------------------------
error.log
vol 0.73 imb F 1% vol 0.71 imb F 1% vol 0.74 imb F 1% vol 0.74
vol 0.74 imb F 1% vol 0.74 imb F 1% imb F 1% vol 0.75 imb F 1% vol
0.74 imb F 1% step 3600, will finish Sat Feb 2 08:06:01 2013
Warning: 1-4 interaction between 7552 and 7556 at distance 6.386 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 3616 Warning: pressure scaling more than 1%, mu: 1.38174 1.38174
1.4951
...
Step 3616 Warning: pressure scaling more than 1%, mu: 1.38219 1.38219
1.49568
Warning: 1-4 interaction between 7556 and 7559 at distance 13.605 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
step 3618: Water molecule starting at atom 92582 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 3618: Water molecule starting at atom 81278 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 3618: Water molecule starting at atom 72206 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 3618: Water molecule starting at atom 58769 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 7757 and 7762 at distance 591.859 which
is larger than the 1-4 table size 2.400 nm
Warning: 1-4 interaction between 1301 and 1306 at distance 34172.198
which is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
step 3619: Water molecule starting at atom 70238 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 3619: Water molecule starting at atom 63254 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
...
Wrote pdb files with previous and current coordinates
Step 3620:
The charge group starting at atom 28175 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
Step 3620:
The charge group starting at atom 55220 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 33278 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 48080 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 46685 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 87410 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 58310 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 43016 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 97613 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 99203 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 44714 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 106400 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 39074 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 60470 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 31037 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 17771 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 18644 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 17700 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 108356 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 19900 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 3096 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 20612 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 10048 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 12592 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 22286 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 15112 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 29171 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
distance out of cell 647.486084
The charge group starting at atom 31865 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 21300 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 79919 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 63833 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 5440 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 26762 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 24551 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 59543 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 3100 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 18521 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 87722 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 4656 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 48941 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 31421 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 86456 moved than the distance allowed
by the domain decomposition (1.400000) in direction Y
The charge group starting at atom 108017 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 60608 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 75209 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 72839 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 59309 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 99512 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 106058 moved than the distance allowed
by the domain decomposition (1.400000) in direction X
The charge group starting at atom 36416 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 41018 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 107174 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 42809 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 78581 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 93632 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 41972 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
The charge group starting at atom 83948 moved than the distance allowed
by the domain decomposition (1.400000) in direction Z
distance out of cell 0.002726
distance out of cell 26.839146
distance out of cell 0.003713
distance out of cell 0.004078
distance out of cell 0.001312
distance out of cell 0.011308
distance out of cell 0.011100
distance out of cell 0.006741
distance out of cell 0.012880
distance out of cell 0.015096
distance out of cell -604.567810
distance out of cell 26.013380
distance out of cell -6.789657
distance out of cell nan
distance out of cell 0.007708
distance out of cell 0.016693
distance out of cell 0.003300
distance out of cell 0.006145
distance out of cell 0.020048
distance out of cell 0.005238
distance out of cell 0.046735
distance out of cell 0.000764
distance out of cell 0.011696
distance out of cell 0.000366
distance out of cell 0.001053
distance out of cell 423.841644
Old coordinates: 0.496 0.047 3.334
distance out of cell 0.016848
distance out of cell 0.005390
distance out of cell 0.011173
distance out of cell 0.011580
distance out of cell 0.052531
distance out of cell 0.001625
distance out of cell 0.012276
distance out of cell 0.004806
distance out of cell 0.026918
distance out of cell 0.022120
distance out of cell 0.021118
distance out of cell 0.010945
distance out of cell 0.001119
distance out of cell 0.020117
distance out of cell 0.006871
distance out of cell 0.009083
distance out of cell 0.006525
distance out of cell 0.007912
distance out of cell 0.008915
distance out of cell 0.002422
distance out of cell 0.012934
distance out of cell 0.001291
distance out of cell 0.008022
distance out of cell 0.000938
distance out of cell 0.011490
distance out of cell 0.002773
distance out of cell 0.001575
distance out of cell 0.006670
distance out of cell 0.003216
distance out of cell 0.005468
Old coordinates: 0.147 10.312 1.766
Old coordinates: 2.868 8.727 2.455
Old coordinates: 10.278 2.721 1.006
Old coordinates: 7.651 5.185 1.402
Old coordinates: 10.281 0.438 1.228
Old coordinates: 5.186 7.750 0.412
Old coordinates: 7.797 7.755 0.635
Old coordinates: 6.603 10.310 1.396
Old coordinates: 9.294 10.315 1.256
Old coordinates: 3.239 7.757 2.599
Old coordinates: 2.865 0.216 2.007
Old coordinates: 0.932 0.108 2.305
Old coordinates: 0.759 8.349 2.831
Old coordinates: 3.089 8.045 2.626
Old coordinates: 9.265 2.891 7.638
Old coordinates: 5.972 4.140 7.616
Old coordinates: 8.567 1.951 7.171
Old coordinates: 7.721 5.829 3.081
Old coordinates: 7.983 7.777 6.460
Old coordinates: 5.662 10.342 6.102
Old coordinates: 8.559 10.349 4.640
Old coordinates: 2.965 6.354 7.404
Old coordinates: 0.673 5.781 7.633
Old coordinates: 0.568 5.117 4.481
Old coordinates: 5.139 3.498 4.596
Old coordinates: 2.896 0.729 3.105
New coordinates: -103.165 77.950 659.372
Old coordinates: 0.643 8.696 11.000
Old coordinates: 5.159 7.846 6.832
Old coordinates: 9.355 5.212 10.628
Old coordinates: 5.382 4.046 10.856
Old coordinates: 10.377 0.212 7.958
Old coordinates: 7.478 1.826 10.834
Old coordinates: 5.491 7.760 9.156
Old coordinates: 9.456 7.765 10.605
Old coordinates: 5.893 10.327 6.469
Old coordinates: 7.766 10.346 8.428
Old coordinates: 4.161 7.760 10.317
Old coordinates: 1.386 5.099 9.041
Old coordinates: 3.082 5.154 9.647
Old coordinates: 3.081 0.570 10.773
Old coordinates: 1.431 10.311 12.006
Old coordinates: 3.955 8.652 13.479
Old coordinates: 9.973 3.087 13.477
Old coordinates: 6.016 4.080 13.475
Old coordinates: 8.444 0.069 13.476
Old coordinates: 5.258 1.576 13.477
Old coordinates: 6.849 6.141 13.479
Old coordinates: 10.278 6.122 12.066
Old coordinates: 6.648 9.189 13.477
Old coordinates: 9.989 8.732 13.476
Old coordinates: 3.229 5.572 13.471
Old coordinates: 2.147 5.393 13.467
Old coordinates: 2.117 3.543 13.468
Old coordinates: 3.239 3.325 13.473
Old coordinates: 2.664 2.142 13.478
Old coordinates: 0.203 1.340 13.473
New coordinates: 0.217 14.260 2.622
New coordinates: -39.278 132.575 30.660
New coordinates: 14.222 3.767 1.506
New coordinates: 10.558 7.173 2.116
New coordinates: 14.219 0.611 1.822
New coordinates: 7.180 10.724 0.624
New coordinates: 10.769 10.738 0.959
New coordinates: 9.142 14.263 2.083
New coordinates: 12.813 14.270 1.869
New coordinates: 4.486 10.726 3.874
New coordinates: 29.579 327.585 -604.568
New coordinates: -1.742 28.343 29.956
New coordinates: 4.270 3.448 -2.826
New coordinates: nan nan nan
New coordinates: 12.773 3.996 11.400
New coordinates: 8.239 5.705 11.372
New coordinates: 11.846 2.690 10.744
New coordinates: 10.663 8.053 4.600
New coordinates: 11.028 10.765 9.624
New coordinates: 7.810 14.281 9.096
New coordinates: 11.824 14.328 6.953
New coordinates: 4.094 8.775 11.064
New coordinates: 0.922 7.982 11.393
New coordinates: 0.746 7.081 6.690
New coordinates: 7.133 4.798 6.849
New coordinates: -658.323 1368.492 434.832
Old cell boundaries in direction Z: 2.653 7.985
New coordinates: 0.872 12.021 16.444
New coordinates: 7.131 10.819 10.167
New coordinates: 12.925 7.211 15.893
New coordinates: 7.433 5.593 16.253
New coordinates: 14.291 0.296 11.866
New coordinates: 10.336 2.526 16.215
New coordinates: 7.588 10.728 13.683
New coordinates: 13.054 10.737 15.857
New coordinates: 8.105 14.292 9.601
New coordinates: 10.722 14.285 12.600
New coordinates: 5.735 10.737 15.410
New coordinates: 1.925 7.081 13.551
New coordinates: 4.275 7.125 14.440
New coordinates: 4.263 0.792 16.127
New coordinates: 1.962 14.264 17.947
New coordinates: 5.474 11.973 20.173
New coordinates: 13.808 4.269 20.171
New coordinates: 8.326 5.616 20.168
New coordinates: 11.676 0.100 20.170
New coordinates: 7.276 2.199 20.165
New coordinates: 9.449 8.489 20.176
New coordinates: 14.219 8.462 18.036
New coordinates: 9.189 12.718 20.170
New coordinates: 13.818 12.055 20.167
New coordinates: 4.475 7.705 20.174
New coordinates: 2.974 7.465 20.165
New coordinates: 2.931 4.903 20.163
New coordinates: 4.461 4.593 20.168
New coordinates: 3.672 2.953 20.166
New coordinates: 0.293 1.842 20.168
Old cell boundaries in direction Y: 7.712 10.315
Old cell boundaries in direction Z: 0.000 2.553
Old cell boundaries in direction X: 7.697 10.287
Old cell boundaries in direction Y: 2.539 5.187
Old cell boundaries in direction X: 7.696 10.286
Old cell boundaries in direction Y: 5.186 7.750
Old cell boundaries in direction Y: 5.207 7.760
Old cell boundaries in direction Y: 7.750 10.314
Old cell boundaries in direction Y: 7.761 10.315
Old cell boundaries in direction Y: 5.153 7.751
Old cell boundaries in direction Z: 0.000 2.616
Old cell boundaries in direction Z: 0.000 2.653
Old cell boundaries in direction Z: 2.664 7.672
Old cell boundaries in direction Z: 2.553 6.382
Old cell boundaries in direction Z: 2.606 7.639
Old cell boundaries in direction Z: 2.642 7.619
Old cell boundaries in direction Z: 2.564 7.201
Old cell boundaries in direction X: 5.173 7.727
Old cell boundaries in direction Y: 5.227 7.789
Old cell boundaries in direction Y: 7.773 10.345
Old cell boundaries in direction Y: 7.789 10.352
Old cell boundaries in direction Z: 2.651 7.417
Old cell boundaries in direction Z: 2.591 7.633
Old cell boundaries in direction Y: 2.588 5.130
Old cell boundaries in direction X: 2.585 5.170
Old cell boundaries in direction Z: 2.615 7.378
New cell boundaries in direction Z: 3.919 11.886
Old cell boundaries in direction Z: 7.672 11.001
Old cell boundaries in direction X: 2.580 5.160
Old cell boundaries in direction Y: 2.598 5.210
Old cell boundaries in direction Z: 7.620 10.868
Old cell boundaries in direction X: 7.721 10.319
Old cell boundaries in direction Z: 7.576 10.847
Old cell boundaries in direction Y: 5.190 7.756
Old cell boundaries in direction Y: 5.213 7.768
Old cell boundaries in direction Y: 7.760 10.328
Old cell boundaries in direction Y: 7.768 10.324
Old cell boundaries in direction Y: 5.158 7.759
Old cell boundaries in direction Y: 2.580 5.114
Old cell boundaries in direction Y: 2.589 5.156
Old cell boundaries in direction Z: 7.379 10.776
Old cell boundaries in direction Y: 7.711 10.314
Old cell boundaries in direction Z: 10.801 13.480
Old cell boundaries in direction Z: 10.909 13.480
Old cell boundaries in direction Z: 10.868 13.480
Old cell boundaries in direction Z: 10.898 13.480
Old cell boundaries in direction Z: 10.847 13.480
Old cell boundaries in direction Z: 10.910 13.480
Old cell boundaries in direction X: 7.696 10.286
Old cell boundaries in direction Z: 10.741 13.480
Old cell boundaries in direction Z: 10.844 13.480
Old cell boundaries in direction Z: 10.879 13.480
Old cell boundaries in direction Z: 10.881 13.480
Old cell boundaries in direction Z: 10.872 13.480
New cell boundaries in direction Y: 10.665 14.257
New cell boundaries in direction Z: 0.000 3.820
Old cell boundaries in direction Z: 10.850 13.480
Old cell boundaries in direction Z: 10.777 13.480
Old cell boundaries in direction Z: 10.917 13.480
New cell boundaries in direction X: 10.637 14.218
New cell boundaries in direction Y: 3.513 7.169
New cell boundaries in direction X: 10.637 14.218
New cell boundaries in direction Y: 7.168 10.713
New cell boundaries in direction Y: 7.199 10.727
New cell boundaries in direction Y: 10.712 14.256
New cell boundaries in direction Y: 10.727 14.257
New cell boundaries in direction Y: 7.122 10.710
New cell boundaries in direction Z: 0.000 3.913
New cell boundaries in direction Z: 0.000 3.943
New cell boundaries in direction Z: 3.963 11.420
New cell boundaries in direction Z: 3.812 9.516
New cell boundaries in direction Z: 3.893 11.392
New cell boundaries in direction Z: 3.953 11.355
New cell boundaries in direction Z: 3.840 10.741
New cell boundaries in direction X: 7.134 10.657
New cell boundaries in direction Y: 7.211 10.745
New cell boundaries in direction Y: 10.727 14.276
New cell boundaries in direction Y: 10.745 14.281
New cell boundaries in direction Z: 3.960 11.063
New cell boundaries in direction Z: 3.887 11.382
New cell boundaries in direction Y: 3.578 7.081
New cell boundaries in direction X: 3.564 7.132
New cell boundaries in direction Z: 3.902 10.990
New cell boundaries in direction Z: 11.441 16.427
New cell boundaries in direction X: 3.561 7.126
New cell boundaries in direction Y: 3.589 7.200
New cell boundaries in direction Z: 11.380 16.241
New cell boundaries in direction X: 10.652 14.239
New cell boundaries in direction Z: 11.330 16.214
New cell boundaries in direction Y: 7.171 10.716
New cell boundaries in direction Y: 7.202 10.732
New cell boundaries in direction Y: 10.719 14.265
New cell boundaries in direction Y: 10.731 14.263
New cell boundaries in direction Y: 7.125 10.715
New cell boundaries in direction Y: 3.573 7.070
New cell boundaries in direction Y: 3.576 7.124
New cell boundaries in direction Z: 11.015 16.107
New cell boundaries in direction Y: 10.665 14.257
New cell boundaries in direction Z: 16.158 20.164
New cell boundaries in direction Z: 16.306 20.165
New cell boundaries in direction Z: 16.246 20.160
New cell boundaries in direction Z: 16.305 20.161
New cell boundaries in direction Z: 16.222 20.162
New cell boundaries in direction Z: 16.329 20.163
New cell boundaries in direction X: 10.637 14.218
New cell boundaries in direction Z: 16.073 20.162
New cell boundaries in direction Z: 16.236 20.166
New cell boundaries in direction Z: 16.275 20.162
New cell boundaries in direction Z: 16.284 20.162
New cell boundaries in direction Z: 16.255 20.161
New cell boundaries in direction Z: 16.234 20.161
New cell boundaries in direction Z: 16.116 20.163
New cell boundaries in direction Z: 16.342 20.163
-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"
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