[CIG-SHORT] a new question on PyLith

Brad Aagaard baagaard at usgs.gov
Fri Feb 17 08:15:40 PST 2017 

Yasemin,

First, you need to make corrections so that you do not get errors 
generating the mesh. Depending on which version of Trelis you have, you 
may need to make some updates to the journal files, so that the ids of 
the entities are correct for your version. If you do not understand what 
I mean by entity ids, then please make use of the tutorials provided by 
Trelis.

The error you get when running PyLith indicates that your mesh is not 
correct.

RuntimeError: Mesh missing group of vertices 'fault' for fault interface 
condition.

For help in debugging, please see the debugging sessions from recent 
tutorials posted on https://wiki.geodynamics.org/software:pylith:start.

Regards,
Brad



On 02/17/2017 04:26 AM, yasemin korkusuz wrote:
> Dear Prof. Aagard,
>
> Regarding your previous suggestions, I have selected the best SCEC
> example (TPV205, dynamic rupture) for my study. Thanks a lot again for
> your help.
> Actually, I am not familiar with Python now, but I will learn it (I have
> been using C programming language).
>
> I have installed Trelis and MPI (from the terminal) on my Ubuntu 16.04.
> Pylith also looks like working when I checked from the installation
> section from the manual.
>
> On the other hand, when I directly run "pylith pylithapp.cfg" or
> "pylith" command, I get the following error.  (By the way, I defined
> "cubit=trelis" in my .bashrc file, so both trelis and cubit commands are
> working)
>
> Could you please give me some suggestions to solve this problem? I think
> the code should be working properly and I might do something wrong.
>
> Best Regards
> Yasemin Korkusuz Öztürk
> KOERI, Turkey
>
> ///////////////////////////////////////////////////////////////////////////////////////////////
> *fearless# cubit tet4_200m.jou &
> fearless# cp tet4_200m.exo mesh.exo
> fearless# pylith*
>  >>
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
>  -- petsc(info)
>  -- Initialized PETSc.
>  >>
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:100:main
>  -- pylithapp(info)
>  -- Running on 1 process(es).
>  >>
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
>  -- meshiocubit(info)
>  -- Reading finite-element mesh
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:158:<unknown>
>  -- meshiocubit(info)
>  -- Reading 25875 vertices.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:217:<unknown>
>  -- meshiocubit(info)
>  -- Reading 119557 cells in 1 blocks.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:281:<unknown>
>  -- meshiocubit(info)
>  -- Found 7 node sets.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_xpos' with id 10 containing 1377 nodes.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_xneg' with id 11 containing 1376 nodes.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_ypos' with id 12 containing 2329 nodes.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_yneg' with id 13 containing 2362 nodes.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_zneg' with id 15 containing 2379 nodes.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_zpos' with id 16 containing 2376 nodes.
>  >> ../../../pylith-2.1.4/libsrc/pylith/meshio/MeshIOCubit.cc:309:<unknown>
>  -- meshiocubit(info)
>  -- Reading node set 'face_zpos_subset' with id 17 containing 528 nodes.
>  >>
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshImporter.py:110:create
>  -- meshimporter(info)
>  -- Reordering cells and vertices.
>  >>
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshImporter.py:119:create
>  -- meshimporter(info)
>  -- Adjusting topology.
>  >>
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:115:_adjustTopology
>  -- meshimporter(info)
>  -- Counting vertices for fault 'fault'.
> Fatal error. Calling MPI_Abort() to abort PyLith application.
> Traceback (most recent call last):
>   File
> "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
> line 74, in onComputeNodes
>     self.main(*args, **kwds)
>   File
> "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
> line 112, in main
>     mesh = self.mesher.create(self.problem.normalizer, interfaces)
>   File
> "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshImporter.py",
> line 120, in create
>     self._adjustTopology(mesh, faults)
>   File
> "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py",
> line 116, in _adjustTopology
>     nvertices = interface.numVerticesNoMesh(mesh)
>   File
> "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/lib/python2.7/site-packages/pylith/faults/faults.py",
> line 343, in numVerticesNoMesh
>     def numVerticesNoMesh(self, *args): return
> _faults.FaultCohesive_numVerticesNoMesh(self, *args)
> RuntimeError: Mesh missing group of vertices 'fault' for fault interface
> condition.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/nemesis:
> mpirun: exit 255
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/pylith:
> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/nemesis: exit 1
> ////////////////////////////////////////////////////////////////////////////////////////////
>
> ***************************************************************************************
>
> /////////////////////////////////////////////////////////////////////////////////////////////
> Error Messages within Trelis as a result of the following command are below:
> *fearless# cubit tet4_200m.jou *
>
> geometry.jou (67)
>
> Command: playback 'geometry.jou'
>
> ERROR: geometry.jou (67)
>
> In AcisModifyEngine::make_Curve
>
> Cannot make Curve object.
>
>
>
> geometry.jou (68)
>
> Command: playback 'geometry.jou'
>
> ERROR: geometry.jou (68)
>
> No entity with ID 21 was found
>
> ERROR: geometry.jou (68)
>
> Syntax error.
>
> Surface list not entered correctly.
>
> Type 'help split' for correct syntax.
>
>
>
> geometry.jou (69)
>
> Command: playback 'geometry.jou'
>
> ERROR: geometry.jou (69)
>
> No entity with ID 22 was found
>
>
>
> geometry.jou (75)
>
> Command: playback 'geometry.jou'
>
> ERROR: geometry.jou (75)
>
> Missing keyword in command.
>
> Command can not begin with a number
>
> ERROR: geometry.jou (75)
>
> syntax error (geometry.jou, line 88)
>
> ERROR: geometry.jou (75)
>
> Missing keyword in command.
>
> Command can not begin with a number
>
> ERROR: geometry.jou (75)
>
> syntax error (geometry.jou, line 89)
>
>
>
> gradient.jou (13)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (13)
>
> Curve 40 does not exist.
>
>
>
> gradient.jou (16)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (16)
>
> Curve 46 does not exist.
>
>
>
> gradient.jou (19)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (19)
>
> Curve 39 does not exist.
>
>
>
> gradient.jou (32)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (32)
>
> Unrecognized Identifier: 'fault_surface'
>
> ERROR: gradient.jou (32)
>
> syntax error (gradient.jou, line 32)
>
> ERROR: gradient.jou (32)
>
> Unrecognized Identifier: 'fault_surface'
>
> ERROR: gradient.jou (32)
>
> syntax error (gradient.jou, line 33)
>
>
>
> gradient.jou (33)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (33)
>
> No entity with ID 41 was found
>
> ERROR: gradient.jou (33)
>
> No valid start curves were specified for the Bias Sizing Function.
>
> ERROR: gradient.jou (33)
>
> Defaulting to no sizing function.
>
>
>
> gradient.jou (34)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (34)
>
> No entity with ID 19 was found
>
>
>
> gradient.jou (35)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (35)
>
> No entity with ID 20 was found
>
>
>
> gradient.jou (36)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (36)
>
> No entity with ID 23 was found
>
>
>
> gradient.jou (40)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (40)
>
> No entity with ID 40 was found
>
>
>
> gradient.jou (43)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (43)
>
> No entity with ID 46 was found
>
>
>
> gradient.jou (44)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (44)
>
> No entity with ID 47 was found
>
>
>
> gradient.jou (48)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (48)
>
> No entity with ID 42 was found
>
>
>
> gradient.jou (62)
>
> Command: playback 'gradient.jou'
>
> ERROR: gradient.jou (62)
>
> No entity with ID 39 was found
>
>
>
> createbc.jou (10)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (10)
>
> Unrecognized Identifier: 'fault_surface'
>
> ERROR: createbc.jou (10)
>
> syntax error (createbc.jou, line 10)
>
>
>
> createbc.jou (11)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (11)
>
> Unrecognized Identifier: 'fault_surface at a'
>
> ERROR: createbc.jou (11)
>
> syntax error (createbc.jou, line 11)
>
>
>
> createbc.jou (12)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (12)
>
> Unrecognized Identifier: 'fault_surface at b'
>
> ERROR: createbc.jou (12)
>
> syntax error (createbc.jou, line 12)
>
>
>
> createbc.jou (13)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (13)
>
> Unrecognized Identifier: 'fault_surface at c'
>
> ERROR: createbc.jou (13)
>
> syntax error (createbc.jou, line 13)
>
>
>
> createbc.jou (14)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (14)
>
> Unrecognized Identifier: 'fault'
>
> ERROR: createbc.jou (14)
>
> syntax error (createbc.jou, line 14)
>
>
>
> createbc.jou (15)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (15)
>
> No entity with ID 20 was found
>
> ERROR: createbc.jou (15)
>
> No entities specified.
>
>
>
> createbc.jou (20)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (20)
>
> No entity with ID 43 was found
>
>
>
> createbc.jou (21)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (21)
>
> No entity with ID 44 was found
>
>
>
> createbc.jou (22)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (22)
>
> No entity with ID 45 was found
>
>
>
> createbc.jou (23)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (23)
>
> Attempted to create empty nodeset; removing nodeset 21
>
>
>
> createbc.jou (24)
>
> Command: playback 'createbc.jou'
>
> ERROR: createbc.jou (24)
>
> No entity with ID 21 was found
>
> ERROR: createbc.jou (24)
>
> No entities specified.
>
> ////////////////////////////////////////////////////////////////
>
>
>
>
> _*/
> /*_
> _*/Your Previous reply:/*_
>
> Please see our responses to your questions on Jan 26:
>
> http://lists.geodynamics.org/pipermail/cig-short/2017-January/002706.html <http://lists.geodynamics.org/pipermail/cig-short/2017-January/002706.html>
>
> http://lists.geodynamics.org/pipermail/cig-short/2017-January/002707.html <http://lists.geodynamics.org/pipermail/cig-short/2017-January/002707.html>
>
> Regards,
> Brad

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