Fix tests that don't work in parallel #550

guyer · 2018-01-18T02:39:31Z

A few tests don't look like they ever worked in parallel. This pull requests ensures the run in serial or on processor 0 only.

This mesh is too small to parallelize and periodic meshes don't work in parallel (usnistgov#518)

Other tests are on serial meshes, but it seems like these got missed

wd15 · 2018-01-19T16:23:54Z

@guyer, get the same 3 Gmsh related errors in serial and parallel FiPy segfaults for me when I try and run the tests.

$ mpirun -np python setup.py test
[mpiexec@barrow] HYD_pmcd_pmi_alloc_pg_scratch (pm/pmiserv/pmiserv_utils.c:527): assert (pg->pg_process_count * sizeof(struct HYD_pmcd_pmi_ecount)) failed
[mpiexec@barrow] HYD_pmci_launch_procs (pm/pmiserv/pmiserv_pmci.c:108): error allocating pg scratch space
Segmentation fault (core dumped)

but `mpirun -np 2 python examples/parallel.py" works.

guyer · 2018-01-19T17:57:21Z

@wd15 Did you literally write mpirun -np python setup.py test or mpirun -np 2 python setup.py test?

wd15 · 2018-01-19T18:26:48Z

@guyer, I literally did! 3 errors when I run using -np 2.

======================================================================
FAIL: _test (fipy.meshes.gmshMesh.GmshGrid2D)
Doctest: fipy.meshes.gmshMesh.GmshGrid2D._test======================================================================
FAIL: _test (fipy.meshes.gmshMesh.GmshGrid2D)
Doctest: fipy.meshes.gmshMesh.GmshGrid2D._test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for fipy.meshes.gmshMesh.GmshGrid2D._test
  File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2189, in _test

----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2200, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    numerix.allclose(yogmsh._faceAreas, yogrid._faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2203, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    yogmsh.cellCenters.value.size == yogrid.cellCenters.value.size # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2208, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    mesh.numberOfCells == 4 # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2211, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    len(mesh.faceCenters[0]) == 12 # doctest: +GMSH
Expected:
    True
Got:
    False


======================================================================
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for fipy.meshes.gmshMesh.GmshGrid2D._test
  File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2189, in _test

----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2200, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    numerix.allclose(yogmsh._faceAreas, yogrid._faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2203, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    yogmsh.cellCenters.value.size == yogrid.cellCenters.value.size # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2208, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    mesh.numberOfCells == 4 # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2211, in fipy.meshes.gmshMesh.GmshGrid2D._test
Failed example:
    len(mesh.faceCenters[0]) == 12 # doctest: +GMSH
Expected:
    True
Got:
    False


======================================================================

FAIL: _test (fipy.meshes.gmshMesh.GmshGrid3D)
Doctest: fipy.meshes.gmshMesh.GmshGrid3D._test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for fipy.meshes.gmshMesh.GmshGrid3D._test
  File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2263, in _test

----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2277, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    yogmsh.cellCenters.value.size == yogrid.cellCenters.value.size # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2280, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    numerix.allclose(yogmsh._faceAreas, yogrid._faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2283, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    numerix.allclose(yogmsh._faceAreas, yogrid._faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2292, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    len(mesh.cellCenters.value[0]) == 8 # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2299, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    nx.allclose(mesh._faceAreas, faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2309, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    nx.allclose(mesh._cellAreas, cellAreas) # doctest: +GMSH
Expected:
    True
Got:
    False


======================================================================FAIL: _test (fipy.meshes.gmshMesh.GmshGrid3D)
Doctest: fipy.meshes.gmshMesh.GmshGrid3D._test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for fipy.meshes.gmshMesh.GmshGrid3D._test
  File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2263, in _test

----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2277, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    yogmsh.cellCenters.value.size == yogrid.cellCenters.value.size # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2280, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    numerix.allclose(yogmsh._faceAreas, yogrid._faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2283, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    numerix.allclose(yogmsh._faceAreas, yogrid._faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2292, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    len(mesh.cellCenters.value[0]) == 8 # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2299, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    nx.allclose(mesh._faceAreas, faceAreas) # doctest: +GMSH
Expected:
    True
Got:
    False
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/fipy/meshes/gmshMesh.py", line 2309, in fipy.meshes.gmshMesh.GmshGrid3D._test
Failed example:
    nx.allclose(mesh._cellAreas, cellAreas) # doctest: +GMSH
Expected:
    True
Got:
    False


======================================================================

FAIL: anisotropy (examples.diffusion)
Doctest: examples.diffusion.anisotropy
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for examples.diffusion.anisotropy
  File "/home/wd15/git/fipy-project/fipy/examples/diffusion/anisotropy.py", line 6, in anisotropy

----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/examples/diffusion/anisotropy.py", line 87, in examples.diffusion.anisotropy
Failed example:
    for i in range(20):
        var.updateOld() # doctest: +GMSH
        res = 1.

        while res > 1e-2:
            res = eqn.sweep(var, dt=dt) # doctest: +GMSH

        if __name__ == '__main__':
            viewer.plot()
        time += dt
Exception raised:
    Traceback (most recent call last):
      File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest examples.diffusion.anisotropy[17]>", line 6, in <module>
        res = eqn.sweep(var, dt=dt) # doctest: +GMSH
      File "/home/wd15/git/fipy-project/fipy/fipy/terms/term.py", line 225, in sweep
        residual = solver._calcResidual(residualFn=residualFn)
      File "/home/wd15/git/fipy-project/fipy/fipy/solvers/trilinos/trilinosSolver.py", line 165, in _calcResidual
        return comm.Norm2(residual)
      File "/home/wd15/git/fipy-project/fipy/fipy/tools/comms/serialCommWrapper.py", line 52, in Norm2
        return numerix.L2norm(vec)
      File "/home/wd15/git/fipy-project/fipy/fipy/tools/numerix.py", line 940, in L2norm
        return sqrt(add.reduce(arr**2))
    TypeError: unsupported operand type(s) for ** or pow(): 'Vector' and 'int'
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/examples/diffusion/anisotropy.py", line 102, in examples.diffusion.anisotropy
Failed example:
    print max(abs((var - solution) / max(solution))) < 0.08 # doctest: +GMSH
Expected:
    True
Got:
    False


FAIL: anisotropy (examples.diffusion)
Doctest: examples.diffusion.anisotropy
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for examples.diffusion.anisotropy
  File "/home/wd15/git/fipy-project/fipy/examples/diffusion/anisotropy.py", line 6, in anisotropy

----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/examples/diffusion/anisotropy.py", line 87, in examples.diffusion.anisotropy
Failed example:
    for i in range(20):
        var.updateOld() # doctest: +GMSH
        res = 1.

        while res > 1e-2:
            res = eqn.sweep(var, dt=dt) # doctest: +GMSH

        if __name__ == '__main__':
            viewer.plot()
        time += dt
Exception raised:
    Traceback (most recent call last):
      File "/home/wd15/miniconda/envs/fipy/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest examples.diffusion.anisotropy[17]>", line 6, in <module>
        res = eqn.sweep(var, dt=dt) # doctest: +GMSH
      File "/home/wd15/git/fipy-project/fipy/fipy/terms/term.py", line 225, in sweep
        residual = solver._calcResidual(residualFn=residualFn)
      File "/home/wd15/git/fipy-project/fipy/fipy/solvers/trilinos/trilinosSolver.py", line 165, in _calcResidual
        return comm.Norm2(residual)
      File "/home/wd15/git/fipy-project/fipy/fipy/tools/comms/serialCommWrapper.py", line 52, in Norm2
        return numerix.L2norm(vec)
      File "/home/wd15/git/fipy-project/fipy/fipy/tools/numerix.py", line 940, in L2norm
        return sqrt(add.reduce(arr**2))
    TypeError: unsupported operand type(s) for ** or pow(): 'Vector' and 'int'
----------------------------------------------------------------------
File "/home/wd15/git/fipy-project/fipy/examples/diffusion/anisotropy.py", line 102, in examples.diffusion.anisotropy
Failed example:
    print max(abs((var - solution) / max(solution))) < 0.08 # doctest: +GMSH
Expected:
    True
Got:
    False


----------------------------------------------------------------------
Ran 555 tests in 311.640s

----------------------------------------------------------------------
Ran 555 tests in 311.641s

FAILED (failures=3)
FAILED (failures=3)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Skipped 2 doctest examples because `lsmlib` must be used to run some tests
Skipped 2 doctest examples because the PySparse solvers are not being used.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Skipped 2 doctest examples because `lsmlib` must be used to run some tests
Skipped 2 doctest examples because the PySparse solvers are not being used.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

guyer added 2 commits January 17, 2018 21:18

Only index variable on PROCESSOR_0

09ca5b9

This mesh is too small to parallelize and periodic meshes don't work in parallel (usnistgov#518)

Make meshes serial

71eac77

Other tests are on serial meshes, but it seems like these got missed

guyer requested review from wd15 and tkphd January 18, 2018 02:39

Merge branch 'develop' into fix_tests_that_dont_work_in_parallel

13a1382

wd15 approved these changes Jan 19, 2018

View reviewed changes

guyer merged commit 9f81cbd into usnistgov:develop Jan 19, 2018

guyer deleted the fix_tests_that_dont_work_in_parallel branch January 19, 2018 17:57

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Fix tests that don't work in parallel #550

Fix tests that don't work in parallel #550

guyer commented Jan 18, 2018

wd15 commented Jan 19, 2018

guyer commented Jan 19, 2018

wd15 commented Jan 19, 2018

Fix tests that don't work in parallel #550

Fix tests that don't work in parallel #550

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guyer commented Jan 18, 2018

wd15 commented Jan 19, 2018

guyer commented Jan 19, 2018

wd15 commented Jan 19, 2018