[CIG-SHORT] a new question on PyLith
yasemin korkusuz
fairlesysmn at gmail.com
Fri Feb 17 04:26:43 PST 2017
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.exofearless# 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/002707.html
Regards,
Brad
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