[gmx-users] help about "Inconsistent DD boundary staggering limits"

Desheng Zheng dzheng at bgsu.edu
Thu Apr 26 20:52:59 CEST 2012


Hi Guys,

I have done the simulation. The total steps is 5000000. At around 900000 steps, the error information appear like the followings.

Please give me some suggestions to fix it.

Best wishes,

Desheng 

------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 102, will try to stop all the nodes
Halting parallel program mdrun on CPU 102 out of 120
Error on node 105, will try to stop all the nodes
Halting parallel program mdrun on CPU 105 out of 120
Error on node 51, will try to stop all the nodes
Halting parallel program mdrun on CPU 51 out of 120

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 81, will try to stop all the nodes
Halting parallel program mdrun on CPU 81 out of 120

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 63, will try to stop all the nodes
Halting parallel program mdrun on CPU 63 out of 120

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 33, will try to stop all the nodes
Halting parallel program mdrun on CPU 33 out of 120

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 54, will try to stop all the nodes
Halting parallel program mdrun on CPU 54 out of 120
Error on node 24, will try to stop all the nodes
Halting parallel program mdrun on CPU 24 out of 120

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 84, will try to stop all the nodes
Halting parallel program mdrun on CPU 84 out of 120

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 42

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 36, will try to stop all the nodes
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 21
Halting parallel program mdrun on CPU 36 out of 120

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 114

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 66

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


-------------------------------------------------------

-------------------------------------------------------

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 45

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 39, will try to stop all the nodes
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 18

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Halting parallel program mdrun on CPU 39 out of 120
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 93

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 117

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 69

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 90

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 75

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 108

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 30
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 72

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 15

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 99

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 87
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 78

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 57
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 96

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 27
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 48
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 60

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 81

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 24
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 102
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 33

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 51
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 36
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 84

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 54

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 39

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 9

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 12

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 105

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 111

gcq#359: "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 63
srun: error: cu08n87: tasks 0,3,6: Exited with exit code 255
srun: error: cu08n124: tasks 18,21: Exited with exit code 255
srun: error: cu09n191: tasks 66,69: Exited with exit code 255
srun: error: cu11n188: tasks 114,117: Exited with exit code 255
srun: error: cu11n185: tasks 90,93: Exited with exit code 255
srun: error: cu09n141: tasks 42,45: Exited with exit code 255
srun: error: cu09n192: tasks 72,75,78: Exited with exit code 255
srun: error: cu11n187: tasks 105,108,111: Exited with exit code 255
srun: error: cu11n186: tasks 96,99,102: Exited with exit code 255
srun: error: cu08n125: tasks 24,27,30: Exited with exit code 255
srun: error: cu08n110: tasks 9,12,15: Exited with exit code 255
srun: error: cu08n126: tasks 33,36,39: Exited with exit code 255
srun: error: cu09n142: tasks 48,51,54: Exited with exit code 255
srun: error: cu11n184: tasks 81,84,87: Exited with exit code 255
srun: error: cu09n164: tasks 57,60,63: Exited with exit code 255
                                                              10946,1       



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