Illegal value for physical properties returned from spatial database

PyLith
1

Hi,

I am running a quasi-static simulation using a power-law rheology and imposing slip on the fault. I am running into an error that says “Spatial database returned illegal value for physical properties.” I am using the same spatialdb files as in the set of hex8 samples. I attach the script I am using and the error log output is copy-pasted below:

thanks,

Alba

powerlaw_62.cfg (9.7 KB)

eduroam-169-233-246-98:Rheology_models absrp$ pylith powerlaw_62.cfg

./pylithapp.cfg:55:

– pyre.inventory(warning)

– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename ← ‘spatialdb/mat_elastic.spatialdb’

– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’

./pylithapp.cfg:55:

– pyre.inventory(warning)

– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename ← ‘spatialdb/mat_elastic.spatialdb’

– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’

./pylithapp.cfg:55:

– pyre.inventory(warning)

– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename ← ‘spatialdb/mat_elastic.spatialdb’

– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize

– petsc(info)

– Initialized PETSc.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:103:main

– pylithapp(info)

– Running on 1 process(es).

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read

– meshiocubit(info)

– Reading finite-element mesh

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:158:void pylith::meshio::MeshIOCubit::_readVertices(pylith::meshio::ExodusII &, scalar_array *, int *, int *) const

– meshiocubit(info)

– Reading 49919 vertices.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:217:void pylith::meshio::MeshIOCubit::_readCells(pylith::meshio::ExodusII &, int_array *, int_array *, int *, int *) const

– meshiocubit(info)

– Reading 255484 cells in 1 blocks.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:281:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Found 8 node sets.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_zpos’ with id 1 containing 11660 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_zneg’ with id 2 containing 1199 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_xpos’ with id 3 containing 493 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_xneg’ with id 4 containing 477 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_ypos’ with id 5 containing 577 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_yneg’ with id 6 containing 567 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘fault’ with id 7 containing 482 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘fault_edges’ with id 8 containing 43 nodes.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:93:preinitialize

– timedependent(info)

– Pre-initializing problem.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:360:_setupMaterials

– implicit(info)

– Pre-initializing materials.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:373:_setupMaterials

– implicit(info)

– Added elasticity integrator for material ‘Upper crust material’.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:389:_setupBC

– implicit(info)

– Pre-initializing boundary conditions.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC

– implicit(info)

– Added boundary condition ‘face_xpos’ as a constraint.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC

– implicit(info)

– Added boundary condition ‘face_xneg’ as a constraint.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC

– implicit(info)

– Added boundary condition ‘face_zneg’ as a constraint.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:425:_setupInterfaces

– implicit(info)

– Pre-initializing interior interfaces.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py:108:preinitialize

– faultcohesivekin(info)

– Pre-initializing fault ‘fault’.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:434:_setupInterfaces

– implicit(info)

– Added interface condition ‘fault’ as an integrator.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:162:preinitialize

– implicit(info)

– Pre-initializing output.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration

– timedependent(info)

– Verifying compatibility of problem configuration.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:118:initialize

– timedependent(info)

– Initializing problem.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:466:_initialize

– implicit(info)

– Initializing integrators.

Fatal error. Calling MPI_Abort() to abort PyLith application.

Traceback (most recent call last):

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PetscApplication.py”, line 74, in onComputeNodes

self.main(*args, **kwds)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py”, line 128, in main

self.problem.initialize()

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py”, line 120, in initialize

self.formulation.initialize(self.dimension, self.normalizer)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Implicit.py”, line 121, in initialize

self._initialize(dimension, normalizer)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py”, line 470, in _initialize

integrator.initialize(totalTime, numTimeSteps, normalizer)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/ElasticityImplicit.py”, line 56, in initialize

ModuleElasticityImplicit.initialize(self, self.mesh())

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/feassemble.py”, line 359, in initialize

def initialize(self, *args): return _feassemble.IntegratorElasticity_initialize(self, *args)

RuntimeError: Spatial database returned illegal value for physical properties.

density: 2500

vp: 5291.5

vs: 3000

referenceStrainRate: 0

referenceStress: 0

powerLawExponent: 0

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: mpirun: exit 255

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/pylith: /Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: exit 1Hi,

I am running a quasistatic simulation using a power-law rheology and imposing slip on the fault. I am running into an error that says “Spatial database returned illegal value for physical properties.” I am using the same spatialdb files as in the set of hex8 samples. I attach the script I am using and the error log outputed is copy pasted below:

thanks,

Alba

eduroam-169-233-246-98:Rheology_models absrp$ pylith powerlaw_62.cfg

./pylithapp.cfg:55:

– pyre.inventory(warning)

– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename ← ‘spatialdb/mat_elastic.spatialdb’

– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’

./pylithapp.cfg:55:

– pyre.inventory(warning)

– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename ← ‘spatialdb/mat_elastic.spatialdb’

– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’

./pylithapp.cfg:55:

– pyre.inventory(warning)

– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename ← ‘spatialdb/mat_elastic.spatialdb’

– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize

– petsc(info)

– Initialized PETSc.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:103:main

– pylithapp(info)

– Running on 1 process(es).

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read

– meshiocubit(info)

– Reading finite-element mesh

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:158:void pylith::meshio::MeshIOCubit::_readVertices(pylith::meshio::ExodusII &, scalar_array *, int *, int *) const

– meshiocubit(info)

– Reading 49919 vertices.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:217:void pylith::meshio::MeshIOCubit::_readCells(pylith::meshio::ExodusII &, int_array *, int_array *, int *, int *) const

– meshiocubit(info)

– Reading 255484 cells in 1 blocks.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:281:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Found 8 node sets.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_zpos’ with id 1 containing 11660 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_zneg’ with id 2 containing 1199 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_xpos’ with id 3 containing 493 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_xneg’ with id 4 containing 477 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_ypos’ with id 5 containing 577 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘face_yneg’ with id 6 containing 567 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘fault’ with id 7 containing 482 nodes.

…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)

– meshiocubit(info)

– Reading node set ‘fault_edges’ with id 8 containing 43 nodes.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:93:preinitialize

– timedependent(info)

– Pre-initializing problem.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:360:_setupMaterials

– implicit(info)

– Pre-initializing materials.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:373:_setupMaterials

– implicit(info)

– Added elasticity integrator for material ‘Upper crust material’.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:389:_setupBC

– implicit(info)

– Pre-initializing boundary conditions.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC

– implicit(info)

– Added boundary condition ‘face_xpos’ as a constraint.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC

– implicit(info)

– Added boundary condition ‘face_xneg’ as a constraint.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC

– implicit(info)

– Added boundary condition ‘face_zneg’ as a constraint.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:425:_setupInterfaces

– implicit(info)

– Pre-initializing interior interfaces.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py:108:preinitialize

– faultcohesivekin(info)

– Pre-initializing fault ‘fault’.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:434:_setupInterfaces

– implicit(info)

– Added interface condition ‘fault’ as an integrator.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:162:preinitialize

– implicit(info)

– Pre-initializing output.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration

– timedependent(info)

– Verifying compatibility of problem configuration.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:118:initialize

– timedependent(info)

– Initializing problem.

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:466:_initialize

– implicit(info)

– Initializing integrators.

Fatal error. Calling MPI_Abort() to abort PyLith application.

Traceback (most recent call last):

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PetscApplication.py”, line 74, in onComputeNodes

self.main(*args, **kwds)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py”, line 128, in main

self.problem.initialize()

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py”, line 120, in initialize

self.formulation.initialize(self.dimension, self.normalizer)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Implicit.py”, line 121, in initialize

self._initialize(dimension, normalizer)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py”, line 470, in _initialize

integrator.initialize(totalTime, numTimeSteps, normalizer)

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/ElasticityImplicit.py”, line 56, in initialize

ModuleElasticityImplicit.initialize(self, self.mesh())

File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/feassemble.py”, line 359, in initialize

def initialize(self, *args): return _feassemble.IntegratorElasticity_initialize(self, *args)

RuntimeError: Spatial database returned illegal value for physical properties.

density: 2500

vp: 5291.5

vs: 3000

referenceStrainRate: 0

referenceStress: 0

powerLawExponent: 0

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: mpirun: exit 255

/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/pylith: /Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: exit 1

2

The error message shows that the values from the mat_powerlaw.spatialdb are all zero. This appears to be triggering the error. Are these zero values consistent with the values listed in the spatial database? The file examples/3d/hex8/spatialdb/mat_powerlaw.spatialdb does not have zero values. You should also check to make sure the spatial database spans your domain.

3

Hi Brad,

Thanks for getting back to me so fast. The mat_powerlaw.spatialdb file I am using is the exact same as in hex8, so there are no zero values. By “You should also check to make sure the spatial database spans your domain.” do you mean verifying whether I am actually assigning the spatialdb properties to the appropriate section of the mesh? I am calling the spatialdb file the same way as in hex8 step8 except for assigning it to the upper crust instead of the lower crust. I copy-pasted the spatialdb folder from hex8 to my working domain so the same databases should be accessible.

Thanks,

Alba

4

I fixed this. The issue was an extra line of code that specified the query to linear when assigning the power-law parameters.

Alba