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kumiori / irrevolutions

Computing Irreversible Evolutions
GNU General Public License v3.0
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Tests and test structure #56

Closed jorgensd closed 2 months ago

jorgensd commented 3 months ago

Ref: https://github.com/openjournals/joss-reviews/issues/6897

I cannot get several of the tests to run locally, as i get:

root@e29591a5575e:/home/numerix/irrevolutions/src/irrevolutions/test# pytest -xvs .
======================================= test session starts ========================================
platform linux -- Python 3.10.12, pytest-7.4.2, pluggy-1.3.0 -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /home/numerix/irrevolutions
configfile: pytest.ini
plugins: anyio-4.3.0, xdist-3.3.1
collecting ... GITHUB_REF environment variable not found.
GITHUB_SHA environment variable not found.
collecting 1 item                                                                                  Info    : Meshing 1D...
Info    : [  0%] Meshing curve 0 (Line)
Info    : [ 30%] Meshing curve 1 (Line)
Info    : [ 50%] Meshing curve 2 (Line)
Info    : [ 80%] Meshing curve 3 (Line)
Info    : Done meshing 1D (Wall 0.000182015s, CPU 0.000167s)
Info    : Meshing 2D...
Info    : Meshing surface 1 (Plane, Frontal-Delaunay)
Info    : Done meshing 2D (Wall 0.00397538s, CPU 0.003975s)
Info    : 360 nodes 722 elements
  0 SNES Function norm 0.000000000000e+00 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    14  0.000037  0.000517
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |     5  0.000233  0.001167
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     1  0.000144  0.000144
~First Order: AltMin-Elastic solver                                         |     1  0.000303  0.000303
~Second Order: Bifurcation                                                  |     1  0.943233  0.943233
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 3.341981445294e-16 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    26  0.000035  0.000911
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |     8  0.000268  0.002142
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     2  0.000115  0.000229
~First Order: AltMin-Elastic solver                                         |     2  0.001830  0.003660
~Second Order: Bifurcation                                                  |     2  0.488039  0.976078
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 3.984105306175e-16 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    38  0.000036  0.001362
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    11  0.000279  0.003069
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     3  0.000106  0.000317
~First Order: AltMin-Elastic solver                                         |     3  0.002202  0.006607
~Second Order: Bifurcation                                                  |     3  0.336151  1.008454
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 5.624130914496e-16 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    50  0.000036  0.001784
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    14  0.000286  0.004011
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     4  0.000101  0.000405
~First Order: AltMin-Elastic solver                                         |     4  0.002403  0.009611
~Second Order: Bifurcation                                                  |     4  0.260236  1.040944
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 6.294411955572e-16 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    62  0.000036  0.002217
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    17  0.000292  0.004967
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     5  0.000099  0.000497
~First Order: AltMin-Elastic solver                                         |     5  0.002545  0.012723
~Second Order: Bifurcation                                                  |     5  0.214719  1.073597
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 8.560821404371e-16 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    74  0.000036  0.002657
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    20  0.000295  0.005894
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     6  0.000097  0.000579
~First Order: AltMin-Elastic solver                                         |     6  0.002596  0.015577
~Second Order: Bifurcation                                                  |     6  0.184332  1.105992
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 9.779611323703e-16 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    86  0.000036  0.003094
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    23  0.000297  0.006824
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     7  0.000095  0.000668
~First Order: AltMin-Elastic solver                                         |     7  0.002638  0.018465
~Second Order: Bifurcation                                                  |     7  0.162586  1.138104
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 1.115587072823e-15 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |    98  0.000036  0.003522
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    26  0.000298  0.007760
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     8  0.000093  0.000748
~First Order: AltMin-Elastic solver                                         |     8  0.002671  0.021365
~Second Order: Bifurcation                                                  |     8  0.146360  1.170884
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 1.131980350140e-15 
  0 SNES Function norm 0.000000000000e+00 
ALTMIN - Iterations:   1,            Error: 0.0000e+00, alpha_H1,            alpha_max: 0.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: True
State's inertia: (0, 0, 720)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |   110  0.000036  0.003970
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    29  0.000301  0.008718
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |     9  0.000094  0.000847
~First Order: AltMin-Elastic solver                                         |     9  0.002702  0.024320
~Second Order: Bifurcation                                                  |     9  0.133704  1.203337
  0 SNES Function norm 3.909186116588e-01 
  1 SNES Function norm 3.271666527291e-01 
  2 SNES Function norm 1.996627348698e-01 
  3 SNES Function norm 1.226086218954e-15 
  0 SNES Function norm 1.089304571943e-05 
  1 SNES Function norm 3.322428842213e-19 
  0 SNES Function norm 5.358578430492e-05 
  1 SNES Function norm 1.182768905252e-15 
  0 SNES Function norm 1.013363261942e-05 
  1 SNES Function norm 2.707814482344e-19 
  0 SNES Function norm 4.759446033309e-05 
  1 SNES Function norm 1.207023264356e-15 
  0 SNES Function norm 1.305298794686e-05 
  1 SNES Function norm 7.546362353926e-06 
  2 SNES Function norm 6.167691931957e-06 
  3 SNES Function norm 3.583761241963e-06 
  4 SNES Function norm 6.425197475000e-07 
  5 SNES Function norm 2.524581150812e-19 
  0 SNES Function norm 7.174297546167e-05 
  1 SNES Function norm 1.175302510552e-15 
  0 SNES Function norm 1.888734562434e-05 
  1 SNES Function norm 1.022107436353e-05 
  2 SNES Function norm 7.479349527952e-06 
  3 SNES Function norm 3.171802840302e-06 
  4 SNES Function norm 3.761088473362e-19 
  0 SNES Function norm 1.041632663390e-04 
  1 SNES Function norm 1.143517519875e-15 
  0 SNES Function norm 2.605387921938e-05 
  1 SNES Function norm 1.159599314971e-05 
  2 SNES Function norm 5.438577221150e-06 
  3 SNES Function norm 4.160134572086e-19 
  0 SNES Function norm 1.476791397044e-04 
  1 SNES Function norm 1.082451515859e-15 
  0 SNES Function norm 3.577081547663e-05 
  1 SNES Function norm 7.013709399226e-06 
  2 SNES Function norm 7.076551706576e-19 
  0 SNES Function norm 2.063552954961e-04 
  1 SNES Function norm 1.213324035949e-15 
  0 SNES Function norm 4.933925836775e-05 
  1 SNES Function norm 1.646942340439e-06 
  2 SNES Function norm 7.529161002598e-19 
  0 SNES Function norm 2.868870954830e-04 
  1 SNES Function norm 1.184106763246e-15 
  0 SNES Function norm 6.887198486846e-05 
  1 SNES Function norm 1.865474430969e-18 
  0 SNES Function norm 3.996414671710e-04 
  1 SNES Function norm 1.149680698376e-15 
  0 SNES Function norm 9.754272558343e-05 
  1 SNES Function norm 8.212133539871e-06 
  2 SNES Function norm 1.624706336643e-18 
  0 SNES Function norm 5.574590342408e-04 
  1 SNES Function norm 1.073476426976e-15 
  0 SNES Function norm 1.378485729254e-04 
  1 SNES Function norm 4.137223011601e-18 
  0 SNES Function norm 7.807088874892e-04 
  1 SNES Function norm 1.052229388285e-15 
  0 SNES Function norm 1.991926410160e-04 
  1 SNES Function norm 6.128404046182e-06 
  2 SNES Function norm 2.891306138040e-18 
  0 SNES Function norm 1.095614446470e-03 
  1 SNES Function norm 1.023047729255e-15 
  0 SNES Function norm 2.903853676585e-04 
  1 SNES Function norm 7.374361826004e-18 
  0 SNES Function norm 1.540253523084e-03 
  1 SNES Function norm 1.064552418166e-15 
  0 SNES Function norm 4.360707380390e-04 
  1 SNES Function norm 9.511957205781e-18 
  0 SNES Function norm 2.170201751514e-03 
  1 SNES Function norm 9.608662605885e-16 
  0 SNES Function norm 6.762610320127e-04 
  1 SNES Function norm 4.224831598760e-05 
  2 SNES Function norm 1.012558036813e-17 
  0 SNES Function norm 3.044289962645e-03 
  1 SNES Function norm 8.700326224202e-04 
  2 SNES Function norm 1.017158524177e-15 
  0 SNES Function norm 1.091884630665e-03 
  1 SNES Function norm 1.773781224521e-05 
  2 SNES Function norm 1.086518252842e-17 
  0 SNES Function norm 4.216694451348e-03 
  1 SNES Function norm 2.299196510528e-03 
  2 SNES Function norm 8.814958062534e-16 
  0 SNES Function norm 1.881733037220e-03 
  1 SNES Function norm 4.307283893607e-05 
  2 SNES Function norm 1.666225170920e-17 
  0 SNES Function norm 5.604893158835e-03 
  1 SNES Function norm 4.007270735740e-03 
  2 SNES Function norm 8.120258895513e-04 
  3 SNES Function norm 8.984161153711e-16 
  0 SNES Function norm 3.496252802230e-03 
  1 SNES Function norm 2.195518169275e-04 
  2 SNES Function norm 5.764165244059e-05 
  3 SNES Function norm 1.842896448901e-17 
  0 SNES Function norm 6.775370510465e-03 
  1 SNES Function norm 5.509141235356e-03 
  2 SNES Function norm 2.976682685137e-03 
  3 SNES Function norm 8.816832529737e-16 
  0 SNES Function norm 6.809717776631e-03 
  1 SNES Function norm 9.424326523047e-04 
  2 SNES Function norm 4.159328557021e-04 
  3 SNES Function norm 2.022315213615e-17 
  0 SNES Function norm 6.822290614115e-03 
  1 SNES Function norm 5.777878422625e-03 
  2 SNES Function norm 3.689054039645e-03 
  3 SNES Function norm 7.935076784163e-16 
  0 SNES Function norm 1.180195082578e-02 
  1 SNES Function norm 6.288665428240e-04 
  2 SNES Function norm 1.271789336095e-04 
  3 SNES Function norm 1.951758365434e-17 
  0 SNES Function norm 5.208339636826e-03 
  1 SNES Function norm 4.194037424264e-03 
  2 SNES Function norm 2.165432999140e-03 
  3 SNES Function norm 9.544902181134e-16 
  0 SNES Function norm 1.306273172649e-02 
  1 SNES Function norm 4.239966443943e-04 
  2 SNES Function norm 2.947537881791e-17 
  0 SNES Function norm 2.219783047898e-03 
  1 SNES Function norm 9.664399201563e-04 
  2 SNES Function norm 1.046704888874e-15 
  0 SNES Function norm 3.321942945808e-03 
  1 SNES Function norm 2.548029729217e-17 
  0 SNES Function norm 1.885485706141e-04 
  1 SNES Function norm 1.114963437411e-15 
  0 SNES Function norm 5.541364455081e-04 
  1 SNES Function norm 3.823562071498e-17 
  0 SNES Function norm 9.202901684355e-05 
  1 SNES Function norm 1.081122726466e-15 
  0 SNES Function norm 8.238826808631e-04 
  1 SNES Function norm 4.638652515272e-17 
  0 SNES Function norm 1.534573722881e-04 
  1 SNES Function norm 1.177400938534e-15 
  0 SNES Function norm 1.353997850173e-03 
  1 SNES Function norm 2.995682435887e-17 
  0 SNES Function norm 2.485446593770e-04 
  1 SNES Function norm 1.199528921819e-15 
  0 SNES Function norm 2.032203643011e-03 
  1 SNES Function norm 4.156317036449e-17 
  0 SNES Function norm 3.477704691700e-04 
  1 SNES Function norm 1.281257658624e-05 
  2 SNES Function norm 1.257881702928e-15 
  0 SNES Function norm 2.394553248615e-03 
  1 SNES Function norm 7.788508892339e-05 
  2 SNES Function norm 4.135704828547e-17 
  0 SNES Function norm 3.397621492595e-04 
  1 SNES Function norm 1.396456546803e-15 
  0 SNES Function norm 1.856394884080e-03 
  1 SNES Function norm 9.601071313796e-05 
  2 SNES Function norm 3.104287330819e-17 
  0 SNES Function norm 2.159724650051e-04 
  1 SNES Function norm 1.268340206875e-15 
  0 SNES Function norm 9.970412915543e-04 
  1 SNES Function norm 3.223432330786e-17 
  0 SNES Function norm 1.003873002548e-04 
  1 SNES Function norm 1.210736674134e-15 
  0 SNES Function norm 4.261985264308e-04 
  1 SNES Function norm 4.488353312055e-17 
  0 SNES Function norm 3.683677717487e-05 
  1 SNES Function norm 1.365720219622e-15 
  0 SNES Function norm 1.499112350574e-04 
  1 SNES Function norm 4.472778092727e-17 
  0 SNES Function norm 1.203013372276e-05 
  1 SNES Function norm 1.476532226976e-15 
  0 SNES Function norm 4.815515576119e-05 
  1 SNES Function norm 5.124888278464e-17 
  0 SNES Function norm 3.774576070804e-06 
  1 SNES Function norm 1.656186837705e-15 
  0 SNES Function norm 1.499794042835e-05 
  1 SNES Function norm 4.533931067893e-17 
  0 SNES Function norm 1.173426965475e-06 
  1 SNES Function norm 1.363744822387e-15 
  0 SNES Function norm 4.639978321124e-06 
  1 SNES Function norm 5.981559358992e-17 
ALTMIN - Iterations:  33,            Error: 4.9094e-05, alpha_H1,            alpha_max: 1.0000e+00
Saving the eigenvectors for the following eigenvalues
[]
State is elastic: False
State's inertia: (0, 0, 858)
Path is unique: True

[MPI_MAX] Summary of timings                                                |  reps  wall avg  wall tot
-------------------------------------------------------------------------------------------------------
Build dofmap data                                                           |     4  0.000158  0.000633
Build sparsity                                                              |   122  0.000036  0.004413
Compute connectivity 1-2                                                    |     1  0.000004  0.000004
Compute dof reordering map                                                  |     4  0.000004  0.000018
Compute entities of dim = 1                                                 |     1  0.000249  0.000249
Compute local part of mesh dual graph                                       |     1  0.000173  0.000173
Compute local-to-local map                                                  |     1  0.000018  0.000018
Compute-local-to-global links for global/local adjacency list               |     1  0.000004  0.000004
Distribute row-wise data (scalable)                                         |     1  0.000019  0.000019
GPS: create_level_structure                                                 |     4  0.000006  0.000023
Gibbs-Poole-Stockmeyer ordering                                             |     1  0.000058  0.000058
Init dofmap from element dofmap                                             |     4  0.000014  0.000057
SparsityPattern::finalize                                                   |    32  0.000302  0.009657
Topology: create                                                            |     1  0.000258  0.000258
Topology: determine shared index ownership                                  |     1  0.000071  0.000071
Topology: determine vertex ownership groups (owned, undetermined, unowned)  |     1  0.000013  0.000013
~First Order: AltMin-Damage solver                                          |    42  0.001102  0.046293
~First Order: AltMin-Elastic solver                                         |    42  0.001702  0.071491
~Second Order: Bifurcation                                                  |    10  0.123713  1.237134
       load  elastic_energy  ...                                          eigs-ball  unique
0  0.000000        0.000000  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
1  0.111222        0.000619  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
2  0.222444        0.002474  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
3  0.333667        0.005567  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
4  0.444889        0.009896  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
5  0.556111        0.015463  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
6  0.667333        0.022267  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
7  0.778556        0.030307  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
8  0.889778        0.039585  ...  [0.0001142434866611133, 0.0007643769234243502,...    True
9  1.001000        0.000386  ...  [4.6249234943830826e-05, 7.083627005366033e-05...    True

[10 rows x 7 columns]
collected 1 item / 1 error                                                                         

============================================== ERRORS ==============================================
_________________ ERROR collecting src/irrevolutions/test/test_cone_convergence.py _________________
/usr/local/lib/python3.10/dist-packages/_pytest/runner.py:341: in from_call
    result: Optional[TResult] = func()
/usr/local/lib/python3.10/dist-packages/_pytest/runner.py:372: in <lambda>
    call = CallInfo.from_call(lambda: list(collector.collect()), "collect")
/usr/local/lib/python3.10/dist-packages/_pytest/python.py:531: in collect
    self._inject_setup_module_fixture()
/usr/local/lib/python3.10/dist-packages/_pytest/python.py:545: in _inject_setup_module_fixture
    self.obj, ("setUpModule", "setup_module")
/usr/local/lib/python3.10/dist-packages/_pytest/python.py:310: in obj
    self._obj = obj = self._getobj()
/usr/local/lib/python3.10/dist-packages/_pytest/python.py:528: in _getobj
    return self._importtestmodule()
/usr/local/lib/python3.10/dist-packages/_pytest/python.py:617: in _importtestmodule
    mod = import_path(self.path, mode=importmode, root=self.config.rootpath)
/usr/local/lib/python3.10/dist-packages/_pytest/pathlib.py:567: in import_path
    importlib.import_module(module_name)
/usr/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1050: in _gcd_import
    ???
<frozen importlib._bootstrap>:1027: in _find_and_load
    ???
<frozen importlib._bootstrap>:1006: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:688: in _load_unlocked
    ???
/usr/local/lib/python3.10/dist-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
test_cone_convergence.py:62: in <module>
    with XDMFFile(
E   RuntimeError: Unable to open HDF5 file. File /home/numerix/irrevolutions/src/irrevolutions/test/data/input_data.h5 does not exist.
========================================= warnings summary =========================================
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
../../../../../../usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56
  /usr/local/lib/python3.10/dist-packages/ufl/core/ufl_type.py:56: DeprecationWarning: attach_operators_from_hash_data deprecated, please use UFLObject instead.
    warnings.warn("attach_operators_from_hash_data deprecated, please use UFLObject instead.", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
===================================== short test summary info ======================================
ERROR test_cone_convergence.py - RuntimeError: Unable to open HDF5 file. File /home/numerix/irrevolutions/src/irrevolutions/test...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=================================== 8 warnings, 1 error in 4.67s ===================================
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
There are 2 unused database options. They are:
Option left: name:-inertia_ksp_type value: preonly source: code
Option left: name:-mat_mumps_icntl_24 value: 1 source: code

when running the following:

docker run --rm -ti -v "$(pwd)":/home/numerix -w /home/numerix  kumiori3/numerix:stable-amd64
cd irrevolutions/
python3 -m pip install -e .
cd src/irrevolutions/test/
pytest -xvs .
cd ..
pytest -xvs .

The CI does not yield any outputs of success or not: https://github.com/kumiori/irrevolutions/actions/runs/9664048492/workflow and I would strongly suggest rewriting this to something along the lines of https://github.com/jorgensd/irrevolutions/actions/runs/9879045838/workflow which produces the following trace: https://github.com/jorgensd/irrevolutions/actions/runs/9879045838/job/27284368533

jorgensd commented 3 months ago

I also see no good motivation to put all the tests inside src/irrevolutions, as I would rather have them at the root of the repository.

jorgensd commented 3 months ago

Additionally, I would advice isolating tests inside functions with the prefix test_* within each test file as several test does not adhere to this principle

kumiori commented 2 months ago

Thank you very much for the comments and suggestions.

Tests have been moved to the root, cleaned, isolated within test_* prefixed functions, and the workflow simplified as suggested. All (10) tests pass albeit with several warnings, currently under investigation.