[gmx-users] blue gene running error

[Albert]

hello:
   I am running NPT on a blue gene cluster, but the jobs always failed 
with following messages. However, everything goes well if I run it on my 
local cluster:


---------------log-----------------------------------
ol 0.66! imb F  6% pme/F 0.45 step 900, will finish Mon Apr 30 04:46:31 2012
vol 0.66! imb F  6% pme/F 0.46 step 1000, will finish Mon Apr 30 
04:41:19 2012

Step 1053, time 2.106 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000303, max 0.005164 (between atoms 18949 and 18948)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   18949  18948   42.3    0.1112   0.1117      0.1111

Step 1054, time 2.108 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.732914, max 37.515310 (between atoms 18947 and 18945)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   18948  18949   90.0    0.1117   4.2691      0.1111
   18947  18945   90.0    0.1110   4.2791      0.1111

Step 1054, time 2.108 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.580342, max 37.414397 (between atoms 18949 and 18948)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   18949  18948   90.0    0.1117   4.2678      0.1111
   18945  18947   89.9    0.1110   4.2789      0.1111
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 1055:

Step 1055:
The charge group starting at atom 18949 moved than the distance allowed 
by the domain decomposition (0.920188) in direction Z
The charge group starting at atom 18947 moved than the distance allowed 
by the domain decomposition (0.920188) in direction Z
distance out of cell -2.676795
distance out of cell 1.235327
Old coordinates:    5.667    0.005    7.374
Old coordinates:    5.792    6.019    7.474
New coordinates:    3.633    6.161    3.620
New coordinates:    8.203   -0.016   10.910
Old cell boundaries in direction Z:    6.295    7.449
Old cell boundaries in direction Z:    7.351    9.673
New cell boundaries in direction Z:    6.297    7.450
New cell boundaries in direction Z:    7.357    9.674


Program mdrun_mpi_bg, VERSION 4.5.5
Source code file: ../../../src/mdlib/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
-------------------------------------------------------

"They Were So Quiet About It" (Pixies)

Error on node 53, will try to stop all the nodes
Halting parallel program mdrun_mpi_bg on CPU 53 out of 64

-------------------------------------------------------
Program mdrun_mpi_bg, VERSION 4.5.5
Source code file: ../../../src/mdlib/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
-------------------------------------------------------

"They Were So Quiet About It" (Pixies)

Error on node 62, will try to stop all the nodes
Halting parallel program mdrun_mpi_bg on CPU 62 out of 64

gcq#37: "They Were So Quiet About It" (Pixies)

Abort(-1) on node 53 (rank 53 in comm 1140850688): application called 
MPI_Abort(MPI_COMM_WORLD, -1) - process 53

gcq#37: "They Were So Quiet About It" (Pixies)

Abort(-1) on node 62 (rank 62 in comm 1140850688): application called 
MPI_Abort(MPI_COMM_WORLD, -1) - process 62


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