[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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