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

Thu Apr 26 21:05:43 CEST 2012

On 4/26/12 2:52 PM, Desheng Zheng wrote:
> 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.
>

Based on the comment that precedes the error call in the code:

/* Make sure that the grid is not shifted too much */

I would assume that this means your system has simply become unstable and is 
blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> 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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================