[CIG-SEISMO] "3D Jacobian undefined" Error detected

[Dimitri Komatitsch]

Hi,

Usually this means that the mesh you created has very distorted elements 
with tiny or very big angles (less that 10 degrees or more than 170), 
i.e. that the quality of the mesh is not good enough.
Try to display a mesh quality histogram in your mesher to check if you 
have anomalous elements.

Best wishes,
Dimitri.

On 12/16/2013 01:50 PM, s.khan-1 at utwente.nl wrote:
> Dear All,
>
> I have been doing tests using SPECFEM3D. With some (not all) of the
> meshes I am receiving errors when generating databases (please see
> below). Everything goes well till mesh decomposing but when reaches
> database generation this problem starts. I am using version 2.0, not the
> development version.
>
> Thanks in advance
>
> Best regards,
> Saad Khan
>
> ===========================================================================================================
> * decomposing mesh...*
>
>   total number of nodes:
>     nnodes =         1575
>   total number of spectral elements:
>     nspec =         1176
>   materials:
>     num_mat =            1
>     defined =            1 undefined =            0
>   absorbing boundaries:
>     nspec2D_xmin =           84
>     nspec2D_xmax =           84
>     nspec2D_ymin =           84
>     nspec2D_ymax =           84
>     nspec2D_bottom =          196
>     nspec2D_top =          196
>   nodes valence:
>     min =            1 max =            8
>     nsize =            8 sup_neighbour =           38
>   mesh2dual:
>     max_neighbour =           26
>     moho elements =            0
>   partitions:
>     num =            4
>
>   Databases files in directory: in_out_files/DATABASES_MPI/
>   finished successfully
>
>
> *running database generation...*
>
>   3D Jacobian undefined
>   Error detected, aborting MPI... proc            1
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 30.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>   3D Jacobian undefined
>   Error detected, aborting MPI... proc            0
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 12093 on
> node svr exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [svr:12091] 1 more process has sent help message help-mpi-api.txt /
> mpi-a
>                                            bort
> [svr:12091] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
>
>                                       help / error messages
>
> *  running solver...*
>
>   error: could not open database
>   path: ../in_out_files/DATABASES_MPI/proc000002_external_mesh.bin
>   error opening database
>   Error detected, aborting MPI... proc            2
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
> with errorcode 30.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>   error: could not open database
>   path: ../in_out_files/DATABASES_MPI/proc000000_external_mesh.bin
>   error opening database
>   Error detected, aborting MPI... proc            0
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 2 with PID 12099 on
> node utsvr10491 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [svr:12096] 1 more process has sent help message help-mpi-api.txt /
> mpi-a
>                                            bort
> [svr:12096] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
>
>                                       help / error messages
>
> see results in directory: in_out_files/OUTPUT_FILES/
>
> done
> =================================================================================================================================================
>
>
>
>
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>

-- 
Dimitri Komatitsch
CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics,
UPR 7051, Marseille, France    http://komatitsch.free.fr