chaste/develop failed running cmake on M1
fieldofnodes opened this issue · 13 comments
fieldofnodes commented
Hi,
I deleted all of my old chaste containers/images via the mac docker desktop app.
Then I ran
% docker run --init -it --rm -v chaste_data:/home/chaste chaste/develop
Unable to find image 'chaste/develop:latest' locally
latest: Pulling from chaste/develop
20274425734a: Already exists
b2d36b6d0bf6: Pull complete
f0bb237d4064: Pull complete
7e199c47e330: Pull complete
b042b4d73918: Pull complete
272e2a7676fc: Pull complete
0dedfe0998a9: Pull complete
c5a4343418eb: Pull complete
8501ce5d4ecb: Pull complete
c8dd44e601bb: Pull complete
028197a9da1c: Pull complete
da0146c5b973: Pull complete
4f4fb700ef54: Pull complete
0b7c919a8edd: Pull complete
20d352b0a0ae: Pull complete
f56d90b99b35: Pull complete
7bd43fbba0da: Pull complete
d1e309e1b203: Pull complete
7fef6ec28788: Pull complete
3e609ede5280: Pull complete
5cd7e5bcafe1: Pull complete
675e7f4e1664: Pull complete
9266254cdfea: Pull complete
Digest: sha256:1d7a74e9c1942cb68a62fdf3450151e5929f7238a77884726ba102b1c12f5458
Status: Downloaded newer image for chaste/develop:latest
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.
chaste@1be22132e813:~$ cd lib
chaste@1be22132e813:~/lib$ cmake ~/src
####################################
# Setting compilers and build type
####################################
-- CMake version: 3.22.1
Traceback (most recent call last):
File "/home/chaste/src/cmake/Modules/ChasteHostOperatingSystem.py", line 110, in <module>
print(main(), end='')
File "/home/chaste/src/cmake/Modules/ChasteHostOperatingSystem.py", line 52, in main
linux_ver = platform.linux_distribution()
AttributeError: module 'platform' has no attribute 'linux_distribution'
-- Operating system detected as...
-- ... : Linux-5.15.49-linuxkit
-- Adding build types...
-- Current build type is : Debug
-- Adding compiler flags...
-- ...for GNU compiler, version 11.3.0
####################################
# Finding libraries
####################################
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.10.12", minimum required is "3.5")
-- Updating pip setuptools and wheel
Traceback (most recent call last):
File "/home/chaste/lib/codegen_python3_venv/bin/pip", line 5, in <module>
from pip._internal.cli.main import main
ModuleNotFoundError: No module named 'pip'
-- Installing chaste_codegen
Traceback (most recent call last):
File "/home/chaste/lib/codegen_python3_venv/bin/pip", line 5, in <module>
from pip._internal.cli.main import main
ModuleNotFoundError: No module named 'pip'
-- The pair PETSC_DIR=/usr/lib/petscdir/petsc3.12 PETSC_ARCH=x86_64-linux-gnu-real does not specify a valid PETSc installation
-- Attempting to look in default locations instead...
CMake Error at cmake/Modules/FindPETSc.cmake:75 (message):
PETSC_DIR can not be used,
/usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscversion.h
does not exist
Call Stack (most recent call first):
cmake/Modules/FindPETSc.cmake:276 (petsc_get_version)
CMakeLists.txt:367 (find_package)
CMake Error at cmake/Modules/FindPETSc.cmake:297 (message):
The pair PETSC_DIR=/usr/lib/petscdir/petsc3.12
PETSC_ARCH=x86_64-linux-gnu-real do not specify a valid PETSc installation
Call Stack (most recent call first):
CMakeLists.txt:367 (find_package)
-- No HDF5 found in /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real: looking for alternative HDF5 instead
CMake Error in /home/chaste/lib/CMakeFiles/CMakeTmp/CMakeLists.txt:
Imported target "MPI::MPI_C" includes non-existent path
"/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
CMake Error in /home/chaste/lib/CMakeFiles/CMakeTmp/CMakeLists.txt:
Imported target "MPI::MPI_C" includes non-existent path
"/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
CMake Error at /usr/share/cmake-3.22/Modules/FindMPI.cmake:1264 (try_compile):
Failed to generate test project build system.
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/FindMPI.cmake:1315 (_MPI_try_staged_settings)
/usr/share/cmake-3.22/Modules/FindMPI.cmake:1638 (_MPI_check_lang_works)
CMakeLists.txt:428 (find_package)
-- Configuring incomplete, errors occurred!
See also "/home/chaste/lib/CMakeFiles/CMakeOutput.log".
See also "/home/chaste/lib/CMakeFiles/CMakeError.log".
chaste@1be22132e813:~/lib$
What am I missing?
bdevans commented
It looks like you haven't passed the paths that cmake needs. Have a look at the scripts e.g. https://github.com/Chaste/chaste-docker/blob/master/scripts/build_chaste.sh and either run those from the home directory or see how they call cmake etc. and adapt for your needs.
fieldofnodes commented
From the home director
% docker run -it --init --rm -v chaste_data:/home/chaste chaste/develop
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.
chaste@d339b72ff36c:~$ build_chaste.sh
Cloning Chaste from https://github.com/Chaste/Chaste.git#master into /home/chaste/src...
fatal: destination path '/home/chaste/src' already exists and is not an empty directory.
chaste@d339b72ff36c:~$
fieldofnodes commented
I use chaste docker on a linux machine and I can download the docker and immediately
cd lib
camke ~/src
and chaste will configure. I am not sure why it wont do that on mac.
fieldofnodes commented
I also run: chaste@d339b72ff36c:~/lib$ ctest -j$(nproc) -L Continuous as stated in the README.md from the ~/lib (I assume this is the build folder) and I get the following:
The following tests FAILED:
1 - TestArchivingHelperClasses (Failed)
2 - TestArchiving (Failed)
3 - TestCitations (Failed)
4 - TestCommandLineArguments (Failed)
5 - TestCellBasedEventHandler (Failed)
6 - TestChasteBuildInfo (Failed)
7 - TestModernCppFeatures (Failed)
8 - TestCwd (Failed)
9 - TestDebug (Failed)
10 - TestDistributedVector (Failed)
11 - TestException (Failed)
12 - TestExecutableSupport (Failed)
13 - TestFileFinder (Failed)
14 - TestFileComparison (Failed)
15 - TestGenericEventHandler (Failed)
16 - TestHeartEventHandler (Failed)
17 - TestHelloWorld (Failed)
18 - TestLogFile (Failed)
19 - TestMathsCustomFunctions (Failed)
20 - TestNumericFileComparison (Failed)
21 - TestObjectCommunicator (Failed)
22 - TestOutputDirectoryFifoQueue (Failed)
23 - TestOutputFileHandler (Failed)
24 - TestPetscEvents (Failed)
25 - TestPetscSetup (Failed)
26 - TestPetscTools (Failed)
27 - TestPetscTools2 (Failed)
28 - TestProgressReporter (Failed)
29 - TestRandomNumberGenerator (Failed)
30 - TestReplicatableVector (Failed)
31 - TestTimer (Failed)
32 - TestTimeStepper (Failed)
33 - TestWarnings (Failed)
34 - TestWritingTestsTutorial (Failed)
45 - TestColumnDataReaderWriter (Failed)
46 - TestHdf5DataReader (Failed)
47 - TestHdf5DataWriter (Failed)
48 - TestParallelColumnDataReaderWriter (Failed)
49 - TestParallelWriterPerformance (Failed)
50 - TestSimpleDataWriter (Failed)
53 - TestChebyshevIteration (Failed)
54 - TestFourthOrderTensor (Failed)
55 - TestLinearSystem (Failed)
56 - TestNonlinearSolvers (Failed)
57 - TestPetscMatTools (Failed)
58 - TestPetscVecTools (Failed)
59 - TestPCBlockDiagonal (Failed)
60 - TestPCLDUFactorisation (Failed)
61 - TestPCTwoLevelsBlockDiagonal (Failed)
62 - TestUblasCustomFunctions (Failed)
63 - TestChastePoint (Failed)
64 - TestChasteRegions (Failed)
65 - TestDistributedQuadraticMesh (Failed)
66 - TestDistributedTetrahedralMesh (Failed)
67 - TestElement (Failed)
68 - TestElementAttributes (Failed)
69 - TestMixedDimensionMesh (Failed)
70 - TestMutableMesh (Failed)
71 - TestMutableMeshRemesh (Failed)
72 - TestNode (Failed)
73 - TestNodeAttributes (Failed)
74 - TestNodesOnlyMesh (Failed)
75 - TestNonCachedTetrahedralMesh (Failed)
76 - TestQuadraticMesh (Failed)
77 - TestTetrahedralMesh (Failed)
78 - TestTransformations (Failed)
79 - TestCylindrical2dMesh (Failed)
80 - TestCylindrical2dNodesOnlyMesh (Failed)
81 - TestCylindricalHoneycombMeshGenerator (Failed)
82 - TestHoneycombMeshGenerator (Failed)
83 - TestPeriodicNodesOnlyMesh (Failed)
84 - TestFemlabMeshReader (Failed)
85 - TestGmshMeshReader (Failed)
86 - TestMemfemMeshReader (Failed)
87 - TestTrianglesMeshReader (Failed)
88 - TestVtkMeshReader (Failed)
89 - TestDistributedBoxCollection (Failed)
90 - TestDistanceMapCalculator (Failed)
91 - TestObsoleteBoxCollection (Failed)
92 - TestPerElementWriter (Failed)
93 - TestCylindrical2dVertexMesh (Failed)
94 - TestCylindricalHoneycombVertexMeshGenerator (Failed)
95 - TestHoneycombVertexMeshGenerator (Failed)
96 - TestMutableVertexMesh (Failed)
97 - TestMutableVertexMeshReMesh (Failed)
98 - TestMutableVertexMeshRosetteMethods (Failed)
99 - TestToroidal2dVertexMesh (Failed)
100 - TestToroidalHoneycombVertexMeshGenerator (Failed)
101 - TestVertexElement (Failed)
102 - TestVertexMesh (Failed)
103 - TestVertexMeshReader (Failed)
104 - TestVertexMeshWriter (Failed)
105 - TestVoronoiVertexMeshGenerator (Failed)
106 - TestMeshWriters (Failed)
107 - TestXmlMeshWriters (Failed)
119 - TestAbstractIvpOdeSolver (Failed)
120 - TestAbstractCvodeSystem (Failed)
121 - TestAbstractOdeSystem (Failed)
122 - TestAbstractAnalyticJacobian (Failed)
123 - TestBackwardEulerIvpOdeSolver (Failed)
124 - TestCombinedOdeSystem (Failed)
125 - TestCvodeAdaptor (Failed)
126 - TestGRL1IvpOdeSolver (Failed)
127 - TestGRL2IvpOdeSolver (Failed)
128 - TestMockEulerIvpOdeSolver (Failed)
129 - TestRKC21IvpOdeSolver (Failed)
130 - TestRungeKuttaFehlbergIvpOdeSolver (Failed)
131 - TestSolvingStiffOdeSystems (Failed)
132 - TestSolvingOdesTutorial (Failed)
133 - TestHeun2IvpOdeSolver (Failed)
135 - Test1D3DLinearEllipticSolver (Failed)
136 - TestCableTestProblem (Failed)
137 - TestCoupledCableTestProblem (Failed)
138 - TestLinearParabolicPdeSystemForCoupledOdeSystem (Failed)
139 - TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver (Failed)
140 - TestPdeTestClasses (Failed)
141 - TestSimpleLinearParabolicSolver (Failed)
142 - TestSimpleLinearEllipticSolver (Failed)
143 - TestSimpleNonlinearEllipticSolver (Failed)
144 - TestSolvingCoupledPdes (Failed)
145 - TestSolveLaplacianWithQuadratics (Failed)
146 - TestSolvingNonlinearPdesTutorial (Failed)
147 - TestWritingPdeSolversTutorial (Failed)
148 - TestWritingPdeSolversTwoTutorial (Failed)
149 - TestAbstractFeCableIntegralAssembler (Failed)
150 - TestAbstractFeSurfaceIntegralAssembler (Failed)
151 - TestAbstractFeVolumeIntegralAssembler (Failed)
152 - TestAbstractFunctionalCalculator (Failed)
153 - TestBoundaryConditionsContainer (Failed)
154 - TestConstBoundaryCondition (Failed)
155 - TestFineCoarseMeshPair (Failed)
156 - TestGaussianQuadratureRule (Failed)
157 - TestHdf5Converters (Failed)
158 - TestLinearBasisFunction (Failed)
159 - TestPdeSimulationTime (Failed)
160 - TestQuadraticBasisFunction (Failed)
161 - TestQuadraturePointsGroup (Failed)
162 - TestTimeAdaptivityController (Failed)
171 - TestAbstractContinuumMechanicsAssembler (Failed)
172 - TestCompressibleNonlinearElasticitySolver (Failed)
173 - TestContinuumMechanicsNeumannBcsAssembler (Failed)
174 - TestIncompressibleNonlinearElasticitySolver (Failed)
175 - TestMaterialLaws (Failed)
176 - TestMoreMechanics (Failed)
177 - TestNonlinearElasticityTools (Failed)
178 - TestProblemDefinitions (Failed)
179 - TestStokesFlowAssembler (Failed)
180 - TestStokesFlowSolver (Failed)
181 - TestVtkNonlinearElasticitySolutionWriter (Failed)
186 - TestArchiveCell (Failed)
187 - TestCell (Failed)
188 - TestCellSrn (Failed)
189 - TestCellBasedCellProperties (Failed)
190 - TestCellCycleModelOdeSolver (Failed)
191 - TestCellDataMaps (Failed)
192 - TestCellMutationStates (Failed)
193 - TestCellProliferativeTypes (Failed)
194 - TestCellPropertyCollection (Failed)
195 - TestCellPropertyRegistry (Failed)
196 - TestCellsGenerator (Failed)
197 - TestOdeBasedCellCycleModels (Failed)
198 - TestOdeBasedSrnModels (Failed)
199 - TestParallelCellsGenerator (Failed)
200 - TestSimpleCellCycleModels (Failed)
201 - TestCellBasedEllipticPdes (Failed)
202 - TestCellBasedEllipticPdeSolver (Failed)
203 - TestCellBasedParabolicPdes (Failed)
204 - TestEllipticBoxDomainPdeModifier (Failed)
205 - TestEllipticGrowingDomainPdeModifier (Failed)
206 - TestParabolicBoxDomainPdeModifier (Failed)
207 - TestParabolicGrowingDomainPdeModifier (Failed)
208 - TestSimulationsWithEllipticBoxDomainPdeModifier (Failed)
209 - TestSimulationsWithEllipticGrowingDomainPdeModifier (Failed)
210 - TestSimulationsWithParabolicBoxDomainPdeModifier (Failed)
211 - TestSimulationsWithParabolicGrowingDomainPdeModifier (Failed)
212 - TestOdeLinearSystemSolver (Failed)
213 - TestSimulationTime (Failed)
214 - TestPottsElement (Failed)
215 - TestPottsMesh (Failed)
216 - TestPottsMeshGenerator (Failed)
217 - TestPottsMeshReader (Failed)
218 - TestPottsMeshWriter (Failed)
219 - TestAlarcon2004OxygenBasedCellCycleOdeSystem (Failed)
220 - TestDeltaNotchOdeSystem (Failed)
221 - TestGoldbeter1991OdeSystem (Failed)
222 - TestTysonNovak2001OdeSystem (Failed)
223 - TestBuskeForces (Failed)
224 - TestCaBasedCellPopulation (Failed)
225 - TestCaBasedDivisionRules (Failed)
226 - TestCaUpdateRules (Failed)
227 - TestCellKillers (Failed)
228 - TestCellPopulationBoundaryConditions (Failed)
229 - TestCellPopulationCountWriters (Failed)
230 - TestCellPopulationWriters (Failed)
231 - TestCellwiseDataGradient (Failed)
232 - TestCellWriters (Failed)
233 - TestCentreBasedDivisionRules (Failed)
234 - TestDiscreteSystemForceCalculator (Failed)
235 - TestForces (Failed)
236 - TestMeshBasedCellPopulation (Failed)
237 - TestMeshBasedCellPopulationWithGhostNodes (Failed)
238 - TestNodeBasedCellPopulation (Failed)
239 - TestNodeBasedCellPopulationParallelMethods (Failed)
240 - TestNodeBasedCellPopulationWithBuskeUpdate (Failed)
241 - TestNodeBasedCellPopulationWithParticles (Failed)
242 - TestPeriodicNodeBasedCellPopulationParallelMethods (Failed)
243 - TestPottsBasedCellPopulation (Failed)
244 - TestPottsUpdateRules (Failed)
245 - TestT2SwapCellKiller (Failed)
246 - TestVertexBasedCellPopulation (Failed)
247 - TestVertexBasedDivisionRules (Failed)
248 - TestDeltaNotchModifier (Failed)
249 - TestNumericalMethods (Failed)
250 - TestOffLatticeSimulation (Failed)
251 - TestOffLatticeSimulation3d (Failed)
252 - TestOffLatticeSimulationWithBuskeForces (Failed)
253 - TestOffLatticeSimulationWithNodeBasedCellPopulation (Failed)
254 - TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d (Failed)
255 - TestOffLatticeSimulationWithPdes (Failed)
256 - TestOffLatticeSimulationWithVertexBasedCellPopulation (Failed)
257 - TestOnLatticeSimulationWithCaBasedCellPopulation (Failed)
258 - TestOnLatticeSimulationWithPdes (Failed)
259 - TestOnLatticeSimulationWithPottsBasedCellPopulation (Failed)
260 - TestSimpleTargetAreaModifier (Failed)
261 - TestTargetAreaLinearGrowthModifier (Failed)
262 - TestStepSizeException (Failed)
263 - TestVolumeTrackingModifier (Failed)
264 - TestCreatingAndUsingANewCellBasedSimulationModifierTutorial (Failed)
265 - TestCreatingAndUsingANewCellCycleModelTutorial (Failed)
266 - TestCreatingAndUsingANewCellKillerTutorial (Failed)
267 - TestCreatingAndUsingANewCellMutationStateTutorial (Failed)
268 - TestCreatingAndUsingANewCellPopulationBoundaryConditionTutorial (Failed)
269 - TestCreatingAndUsingANewCellPropertyTutorial (Failed)
270 - TestCreatingAndUsingANewForceTutorial (Failed)
271 - TestCreatingAndUsingANewSrnModelTutorial (Failed)
272 - TestCreatingAndUsingNewCellBasedWritersTutorial (Failed)
273 - TestRunningContactInhibitionSimulationsTutorial (Failed)
274 - TestRunningDeltaNotchSimulationsTutorial (Failed)
275 - TestRunningDifferentialAdhesionSimulationsTutorial (Failed)
276 - TestRunningMeshBasedSimulationsTutorial (Failed)
277 - TestRunningNodeBasedSimulationsTutorial (Failed)
278 - TestRunningPottsBasedSimulationsTutorial (Failed)
279 - TestRunningTumourSpheroidSimulationsTutorial (Failed)
280 - TestRunningVertexBasedSimulationsTutorial (Failed)
281 - TestVisualizingWithParaviewTutorial (Failed)
291 - TestCellForCrypt (Failed)
292 - TestCryptCellsGenerator (Failed)
293 - TestOdeBasedCellCycleModelsForCrypt (Failed)
294 - TestSimpleCellCycleModelsForCrypt (Failed)
295 - TestSingleOdeWntCellCycleModel (Failed)
296 - TestWntConcentration (Failed)
297 - TestCryptProjectionForce (Failed)
298 - TestLinearSpringWithVariableSpringConstantsForce (Failed)
299 - TestVertexCryptBoundaryForce (Failed)
300 - TestMirams2010WntOdeSystem (Failed)
301 - TestVanLeeuwen2009WntSwatCellCycleOdeSystem (Failed)
302 - TestWntCellCycleOdeSystem (Failed)
303 - TestCellBetaCateninWriter (Failed)
304 - TestCryptDivisionRules (Failed)
305 - TestCryptSimulationBoundaryCondition (Failed)
306 - TestShovingCaBasedDivisionRules (Failed)
307 - TestSloughingCellKillers (Failed)
308 - TestVertexBasedCellPopulationForCrypt (Failed)
309 - TestOffLatticeCryptProjectionSimulation (Failed)
310 - TestArchiveFormat (Failed)
311 - TestCryptSimulation1d (Failed)
312 - TestCryptSimulation2dWithMeshBasedCellPopulation (Failed)
313 - TestCryptSimulation2dWithVertexBasedCellPopulation (Failed)
314 - TestPottsBasedCryptSimulation (Failed)
315 - TestCryptProjectionStatistics (Failed)
316 - TestCryptStatistics (Failed)
317 - TestRunningCryptSimulationsWithMutationsTutorial (Failed)
318 - TestRunningMeshBasedCryptSimulationsTutorial (Failed)
319 - TestRunningVertexBasedCryptSimulationsTutorial (Failed)
326 - TestAirwayBranch (Failed)
327 - TestAirwayPropertiesCalculator (Failed)
328 - TestAirwayTreeWalker (Failed)
329 - TestImpedancePostProcessor (Failed)
330 - TestSimpleImpedanceProblem (Failed)
331 - TestLobePropertiesCalculator (Failed)
332 - TestAirwayGeneration (Failed)
333 - TestAirwayGenerator (Failed)
334 - TestAirwayRemesher (Failed)
335 - TestMajorAirwaysCentreLinesCleaner (Failed)
336 - TestMultiLobeAirwayGenerator (Failed)
337 - TestAcinarUnitModels (Failed)
338 - TestAirwayWallModels (Failed)
339 - TestDynamicVentilation (Failed)
340 - TestMatrixVentilationProblem (Failed)
341 - TestVentilationProblem (Failed)
347 - TestBenchmarkPreconditionersForMeshIndependence (Failed)
348 - TestBidomainDistributedMesh (Failed)
349 - TestBidomainTissue (Failed)
350 - TestBidomainProblem (Failed)
351 - TestBidomainWithBathProblem (Failed)
352 - TestBidomainWithSvi (Failed)
353 - TestArchivingExtendedBidomain (Failed)
354 - TestExtendedVsBidomainProblem (Failed)
355 - TestExtendedBidomainTissue (Failed)
356 - TestExtendedBidomainProblem (Failed)
357 - TestFibreReaderAbilityExtendedBidomainProblem (Failed)
358 - TestStimulusFactory (Failed)
359 - TestGIModifiedModels (Failed)
360 - TestConvergenceTester (Failed)
361 - TestFibreReader (Failed)
362 - TestFibreWriter (Failed)
363 - TestPapillaryFibreCalculator (Failed)
364 - TestStreeterFibreGenerator (Failed)
365 - TestCvodeCells (Failed)
366 - TestCvodeCellsWithDataClamp (Failed)
367 - TestCvodeWithJacobian (Failed)
368 - TestDynamicallyLoadedCellModels (Failed)
369 - TestGeneralizedRushLarsen (Failed)
370 - TestHodgkinHuxleySquidAxon1952OriginalOdeSystem (Failed)
371 - TestIonicModels (Failed)
372 - TestIonicModelsWithSacs (Failed)
373 - TestCodegenPresent (Failed)
374 - TestModifiers (Failed)
375 - TestCodegen (Failed)
376 - TestRushLarsen (Failed)
377 - TestSteadyStateRunner (Failed)
378 - TestCardiacElectroMechanicsProblem (Failed)
379 - TestCardiacElectroMechanicsFurtherFunctionality (Failed)
380 - TestContractionModels (Failed)
381 - TestElectroMechanicsProblemDefinition (Failed)
382 - TestElectroMechanicsExactSolution (Failed)
383 - TestImplicitCardiacMechanicsSolver (Failed)
384 - TestExplicitCardiacMechanicsSolver (Failed)
385 - TestNhsModelWithBackwardSolver (Failed)
386 - TestMonodomainStiffnessMatrixAssembler (Failed)
387 - TestMonodomainConductionVelocity (Failed)
388 - TestMonodomainProblem (Failed)
389 - TestMonodomainPurkinjeAssemblersAndSolver (Failed)
390 - TestMonodomainPurkinjeProblem (Failed)
391 - TestMonodomainFitzHughNagumo (Failed)
392 - TestMonodomainMassLumping (Failed)
393 - TestMonodomainTissue (Failed)
394 - TestMonodomainWithSvi (Failed)
395 - TestMonodomainWithTimeAdaptivity (Failed)
396 - TestOperatorSplittingMonodomainSolver (Failed)
397 - Test1dMonodomainShannonCvodeBenchmarks (Failed)
398 - TestCellProperties (Failed)
399 - TestHdf5ToVisualizerConverters (Failed)
400 - TestPostProcessingWriter (Failed)
401 - TestPropagationPropertiesCalculator (Failed)
402 - TestPseudoEcgCalculator (Failed)
403 - TestSpiralWaveAndPhase (Failed)
404 - TestVoltageInterpolaterOntoMechanicsMesh (Failed)
405 - TestNeumannStimulus (Failed)
406 - TestPlaneStimulusCellFactory (Failed)
407 - TestRestitutionStimuli (Failed)
408 - TestStimulus (Failed)
409 - TestStimulusBoundaryCondition (Failed)
410 - TestAbstractContractionCellFactory (Failed)
411 - TestAbstractPurkinjeCellFactory (Failed)
412 - TestCardiacSimulation (Failed)
413 - TestCardiacSimulationArchiver (Failed)
414 - TestCheckpointing (Failed)
415 - TestConductivityTensors (Failed)
416 - TestElectrodes (Failed)
417 - TestHeartConfig (Failed)
418 - TestHeartFileFinder (Failed)
419 - TestHeartGeometryInformation (Failed)
420 - TestHeartRegionCodes (Failed)
421 - TestHeterogeneousConductivities (Failed)
523 - TestDiskSpace (Failed)
524 - TestExample (Failed)
525 - TestInfraFunctionality (Failed)
526 - TestUtilsFunctionality (Failed)
527 - TestCapsuleBasedDivisionRules (Not Run)
528 - TestCapsuleForce (Not Run)
529 - TestCapsuleNodeAttributes (Not Run)
530 - TestNumericalMethodForCapsules (Not Run)
531 - TestCellLengthDifferentiatedCellType (Not Run)
532 - TestSingleDifferentiatedCellMachineStateAndPosition3D (Not Run)
533 - TestVisualizingCapsules (Not Run)
534 - TestSingleCapsuleSimulation2D (Not Run)
535 - TestCapsuleSimulation2d (Not Run)
536 - TestCapsuleSimulation3d (Not Run)
537 - TestTypeSixMachineModifier (Not Run)
538 - TestTypeSixMachineStateAndPositionModifier (Not Run)
539 - TestTypeSixMachineCellKiller (Not Run)
540 - TestTypeSixMachineProperty (Not Run)
541 - TestSingleCellPopulationGrowth3D (Not Run)
542 - TestSingleCellBaselineParametersMultipleRunsTestWaitingTimes (Not Run)
543 - TestSingleCellSingleMachineModel (Not Run)
544 - TestSingleCellSingleMachineK3AndNoise (Not Run)
545 - TestSinglePopulationGrowth3D (Not Run)
546 - TestCompetitionScorePartitionedPopulations (Not Run)
547 - TestTwoPopulationsK3AndNoise (Not Run)
548 - TestTwoCellPopulationsAttackerTargetBaselineParameters (Not Run)
549 - TestDifferentGrowthRates (Not Run)
550 - TestRemainingTargetPopulations (Not Run)
551 - TestCircularDomainSurroundedByAttackers (Not Run)
552 - TestWideVarianceCellCycle (Not Run)
553 - TestSampleManyTestForCriticalPopulation (Not Run)
554 - TestK1SteadyStateMachinesPerCell (Not Run)
555 - TestTwoCellsAttackerTargetDeathRates (Not Run)
556 - TestResidualTargetPopulationSuite (Failed)
557 - TestSingleCellAttacker (Not Run)
558 - TestTimeToDeathSingleAttacherTarget (Not Run)
559 - TestCircularTargetsSurroundedByAttackers (Failed)
560 - TestTwoCellBehaviourForValidation (Not Run)
561 - TestTemplateTwoPopulationsAttackersTargets (Not Run)
562 - TestCellLabellingWithTwoT6SSPopulations (Not Run)
563 - TestCellLabellingWithTwoT6SSPopulationsArchivingParameterSweep (Not Run)
564 - TestCellLabellingWithTwoT6SSPopulationsIn3D (Not Run)
565 - TestCellLabellingWithTwoT6SSPopulationsIn3DArchivingParameterSweep (Not Run)
566 - TestCellLabellingWithTwoT6SSPopulationsIn3DArchivingParameterSweepRealisations (Not Run)
567 - TestCellLabellingWithTwoT6SSPopulationsParameterSweep (Not Run)
568 - TestTwoCellPopulationsGrowth3D (Not Run)
Errors while running CTest
Output from these tests are in: /home/chaste/lib/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.
chaste@d339b72ff36c:~/lib$
bdevans commented
It looks like you have mounted your previous chaste_data volume over the new image. Backup any work in the volume then delete it with:
docker volume rm chaste_data
Then try rerunning the container.
fieldofnodes commented
% docker volume rm chaste_data
chaste_data
(base) jmille15@S47-6033N94T /Users/jmille15
% docker run --init -it --rm -v chaste_data:/home/chaste chaste/develop
Unable to find image 'chaste/develop:latest' locally
latest: Pulling from chaste/develop
bfbe77e41a78: Pull complete
2070411ef154: Pull complete
86bb25e9ea07: Pull complete
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Digest: sha256:56a7a1c03b397743b7e225f7a6789b1bfd1e24907e2bd37832f253f4b6c3e259
Status: Downloaded newer image for chaste/develop:latest
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.
chaste@bb212e33541f:~$ build_chaste.sh
Cloning Chaste from https://github.com/Chaste/Chaste.git#main into /home/chaste/src...
fatal: destination path '/home/chaste/src' already exists and is not an empty directory.
chaste@bb212e33541f:~$
fieldofnodes commented
I removed docker, pulled as seen above, then ran the build_chaste.sh in the home directory as seen above. Is that what is supposed to happen?
fieldofnodes commented
Deleted everything and re-pulled
Then did
chaste@ca7958331f30:~$ cd build
chaste@ca7958331f30:~/build$ cmake ~/src
...
...
...
...
Configuring Chaste app
Configuring MeshConvert app
Configuring tests for python
-- Configuring done
-- Generating done
-- Build files have been written to: /home/chaste/build
chaste@ca7958331f30:~/build$
fieldofnodes commented
I then
ctest -j$(nproc) -L Continuous
99% tests passed, 2 tests failed out of 380
Label Time Summary:
Continuous_cell_based = 235.89 sec*proc (102 tests)
Continuous_continuum_mechanics = 8.29 sec*proc (11 tests)
Continuous_crypt = 53.18 sec*proc (29 tests)
Continuous_global = 6.70 sec*proc (36 tests)
Continuous_heart = 277.97 sec*proc (75 tests)
Continuous_io = 0.68 sec*proc (6 tests)
Continuous_linalg = 1.21 sec*proc (10 tests)
Continuous_lung = 22.83 sec*proc (16 tests)
Continuous_mesh = 21.92 sec*proc (48 tests)
Continuous_ode = 1.62 sec*proc (15 tests)
Continuous_pde = 11.68 sec*proc (28 tests)
Continuous_python = 0.33 sec*proc (4 tests)
Total Test time (real) = 138.09 sec
The following tests FAILED:
401 - TestMonodomainPurkinjeProblem (Failed)
423 - TestCardiacSimulation (Failed)
Errors while running CTest
Output from these tests are in: /home/chaste/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.
chaste@ca7958331f30:~/build$
I use cell-based chaste, so I do not think this affects me. But wanted to share.
bdevans commented
I'm not sure why those tests failed but if you are in the home directory then running build_chaste.sh . should work (note the .).
fieldofnodes commented
Oh the . I did not do. I will try that.
bdevans commented
I'm closing this as no news is good news but feel free to reopen it if the . didn't do the trick.
fieldofnodes commented
Sorry,done. Works great