Intermittent error in pysph.parallel.tests.test_parallel.MPIReduceArrayTestCase.test_parallel_reduce
avalentino opened this issue · 5 comments
avalentino commented
The test pysph.parallel.tests.test_parallel.MPIReduceArrayTestCase.test_parallel_reduce fails form time to time in the debian-ci infrastructure.
The error does not happen at every run so it is quite hard to track down.
Please find below the test output:
============================= test session starts ==============================
platform linux -- Python 3.9.9, pytest-6.2.5, py-1.10.0, pluggy-0.13.0
rootdir: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd, configfile: tox.ini
collected 889 items / 90 deselected / 799 selected
pysph/base/tests/test_device_helper.py .ss.ss.ss.ss.ss.ss.ss.ss.ss.ss.ss [ 4%]
.ss.ss.ss.ss.ss.ss.sss [ 6%]
pysph/base/tests/test_domain_manager.py sss......... [ 8%]
pysph/base/tests/test_kernel.py ........................................ [ 13%]
................................................................. [ 21%]
pysph/base/tests/test_linalg3.py ....... [ 22%]
pysph/base/tests/test_neighbor_cache.py .... [ 22%]
pysph/base/tests/test_nnps.py .......ssssssssss......................... [ 28%]
....................................................ssssssssssssssssssss [ 37%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss........ [ 46%]
......................................... [ 51%]
pysph/base/tests/test_octree.py .....s...s...s...s...s...s...s...s. [ 55%]
pysph/base/tests/test_particle_array.py ................................ [ 59%]
...ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 67%]
pysph/base/tests/test_periodic_nnps.py ............ [ 69%]
pysph/base/tests/test_reduce_array.py ...... [ 70%]
pysph/base/tests/test_utils.py .. [ 70%]
pysph/examples/tests/test_riemann_solver.py s........ [ 71%]
pysph/parallel/tests/test_openmp.py . [ 71%]
pysph/parallel/tests/test_parallel.py .ss.F. [ 72%]
pysph/parallel/tests/test_parallel_run.py . [ 72%]
pysph/solver/tests/test_application.py ... [ 72%]
pysph/solver/tests/test_solver.py .. [ 73%]
pysph/solver/tests/test_solver_utils.py ............ [ 74%]
pysph/sph/bc/tests/test_simple_inlet_outlet.py ....... [ 75%]
pysph/sph/tests/test_acceleration_eval.py ....................ssssssssss [ 79%]
ssssssssssssssssssssssssssssssssssssssssssssss [ 84%]
pysph/sph/tests/test_acceleration_eval_cython_helper.py ... [ 85%]
pysph/sph/tests/test_equations.py ............... [ 87%]
pysph/sph/tests/test_integrator.py ...............ssssssss [ 90%]
pysph/sph/tests/test_integrator_cython_helper.py . [ 90%]
pysph/sph/tests/test_integrator_step.py .. [ 90%]
pysph/sph/tests/test_kernel_corrections.py ................ [ 92%]
pysph/sph/tests/test_linalg.py ............. [ 94%]
pysph/sph/tests/test_multi_group_integrator.py .s [ 94%]
pysph/sph/tests/test_riemann_solver.py ............. [ 95%]
pysph/sph/tests/test_scheme.py . [ 96%]
pysph/tools/tests/test_geometry.py .............s... [ 98%]
pysph/tools/tests/test_geometry_stl.py ........... [ 99%]
pysph/tools/tests/test_interpolator.py ... [100%]
=================================== FAILURES ===================================
_________________ MPIReduceArrayTestCase.test_parallel_reduce __________________
self = <pysph.parallel.tests.test_parallel.MPIReduceArrayTestCase testMethod=test_parallel_reduce>
@mark.parallel
def test_parallel_reduce(self):
args = ['--directory=%s' % self.root]
> run_parallel_script.run(
filename='simple_reduction.py', args=args, nprocs=nprocs, path=path
)
pysph/parallel/tests/test_parallel.py:101:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = 'simple_reduction.py', args = ['--directory=/tmp/tmpag842xi0']
nprocs = 2, timeout = 30.0
path = '/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests'
def run(filename, args=None, nprocs=2, timeout=30.0, path=None):
"""Run a python script with MPI or in serial (if nprocs=1). Kill process
if it takes longer than the specified timeout.
Parameters:
-----------
filename - filename of python script to run under mpi.
args - List of arguments to pass to script.
nprocs - number of processes to run (1 => serial non-mpi run).
timeout - time in seconds to wait for the script to finish running,
else raise a RuntimeError exception.
path - the path under which the script is located
Defaults to the location of this file (__file__), not curdir.
"""
if args is None:
args = []
file_path = abspath(join(path, filename))
cmd = [sys.executable, file_path] + args
if nprocs > 1:
cmd = ['mpiexec', '-n', str(nprocs)] + cmd
print('running test:', cmd)
process = Popen(cmd, stdout=PIPE, stderr=PIPE)
timer = Timer(timeout, kill_process, [process])
timer.start()
out, err = process.communicate()
timer.cancel()
retcode = process.returncode
if retcode:
msg = 'test ' + filename + ' failed with returncode ' + str(retcode)
print(out.decode('utf-8'))
print(err.decode('utf-8'))
print('#'*80)
print(msg)
print('#'*80)
> raise RuntimeError(msg)
E RuntimeError: test simple_reduction.py failed with returncode -9
pysph/tools/run_parallel_script.py:54: RuntimeError
----------------------------- Captured stdout call -----------------------------
running test: ['mpiexec', '-n', '2', '/usr/bin/python3.9', '/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/simple_reduction.py', '--directory=/tmp/tmpag842xi0']
KILLING PROCESS ON TIMEOUT
Rank 0: Generating output in /tmp/tmpag842xi0
Rank 1: Generating output in /tmp/tmpag842xi0
ValueError: Dimension 1 invalid for PyZoltan!
Exception ignored in: 'pyzoltan.core.zoltan.get_geometry_list'
Traceback (most recent call last):
File "/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/solver/application.py", line 1353, in _setup_parallel_manager_and_initial_load_balance
pm.update()
ValueError: Dimension 1 invalid for PyZoltan!
################################################################################
test simple_reduction.py failed with returncode -9
################################################################################
=============================== warnings summary ===============================
../../../../../../../usr/lib/python3/dist-packages/compyle/types.py:164
/usr/lib/python3/dist-packages/compyle/types.py:164: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.dtype(np.bool): 'char',
../../../../../../../usr/lib/python3/dist-packages/compyle/types.py:173
/usr/lib/python3/dist-packages/compyle/types.py:173: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
'bool': np.bool,
../../../../../../../usr/lib/python3/dist-packages/pyximport/pyximport.py:51
/usr/lib/python3/dist-packages/pyximport/pyximport.py:51: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
../../../../../../../usr/lib/python3/dist-packages/_pytest/mark/structures.py:337
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:337: PytestCollectionWarning: cannot collect 'test_all_backends' because it is not a function.
def __call__(self, *args: object, **kwargs: object):
pysph/base/nnps.py:1
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/base/nnps.py:1: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
from pysph.base.nnps_base import get_number_of_threads, py_flatten, \
pysph/examples/tests/test_examples.py:84
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/examples/tests/test_examples.py:84: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.slow
pysph/parallel/tests/test_openmp.py:17
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_openmp.py:17: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.slow
pysph/parallel/tests/test_openmp.py:33
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_openmp.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.slow
pysph/parallel/tests/test_parallel.py:55
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:55: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel.py:59
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:59: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel.py:72
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:72: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.slow
pysph/parallel/tests/test_parallel.py:73
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:73: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel.py:92
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:92: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel.py:98
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:98: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel.py:112
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel.py:112: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel_run.py:25
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel_run.py:25: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.slow
pysph/parallel/tests/test_parallel_run.py:26
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel_run.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel_run.py:39
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel_run.py:39: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.slow
pysph/parallel/tests/test_parallel_run.py:40
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel_run.py:40: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
pysph/parallel/tests/test_parallel_run.py:50
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/parallel/tests/test_parallel_run.py:50: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
@mark.parallel
<frozen importlib._bootstrap>:228
<frozen importlib._bootstrap>:228: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
pysph/tools/tests/test_geometry_stl.py:7
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry_stl.py:7: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
import pysph.tools.geometry_stl as G
.pybuild/cpython3_3.9/build/pysph/sph/bc/tests/test_simple_inlet_outlet.py::TestSimpleInlet1D::test_inlet_calls_callback
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_d4d2f4620a7b2524086275ccd7e1980a.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/bc/tests/test_simple_inlet_outlet.py::TestSimpleOutlet1D::test_outlet_absorbs_particles_from_source
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_e33701e75932aa50c325a9da5905e046.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_call_initialize_pair
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_23a3818adde45352a04c1b7364f8beb8.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_call_pre_post_functions_in_group
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_6bd24ef6276cfb0a627c4a76f48d9905.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_call_py_initialize
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_2050fc7c6320c48dbe6a33538cf05088.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_handle_repeated_helper_functions
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_766c702abd060b362383b083d9c03275.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_iterate_iterated_group
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_33b81f4dba430aaf42210931044b04c0.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_iterate_nested_groups
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_7717c1442a4d826d0e187f434ef96cbc.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_not_iterate_normal_group
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_cfe2eb093a39e8e702efa0cf780bf4e3.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_run_reduce
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_678795442fd61741ccc5ce5dd5c5c753.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_support_constants
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_7bb1bab96b93bbdaafc45e03d4993835.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_support_loop_all_and_loop
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_e7e9ab313fa06d6ac295a713d6d20ed0.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_support_loop_all_and_loop
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_536b4600578e21ae33f7deb8aa1f71fe.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_work_with_non_double_arrays
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_f9827192da77f6672a3575a967f33ba7.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestIntegratorAdaptiveTimestep::test_compute_timestep_with_dt_adapt
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_76734bae3a461753975fbf791fdbb19b.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestIntegratorAdaptiveTimestep::test_compute_timestep_with_dt_adapt_trumps_dt_cfl
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_3eef2402041a6d8884be144e1ea8a11f.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestIntegratorAdaptiveTimestep::test_compute_timestep_with_dt_cfl
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_14fdd08882c92b4eca96b8e5525a5e26.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestIntegratorAdaptiveTimestep::test_compute_timestep_without_adaptive
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_a0271db338b0a591d39b669652df021c.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_helper_can_be_used_with_stepper
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_afce861c4d3d616622e5e739877d460b.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_integrator_calls_only_py_when_no_stage
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_a8dbf3b89f1f24e1514c5a05249db577.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_integrator_calls_py_stage1
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_5d94160891ab9d7b65d483394d53f090.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_integrator_calls_py_stage1_stage2
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_91ff9b09094d9dbbd640f4b6119df413.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_leapfrog
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_17141a5fd5c62030e087718d7d2cd89f.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_integrator.py::TestPEFRLIntegrator::test_pefrl
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_28bc252d0d0bd9e4d053fe4ec8d0ebc8.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_crksph
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_03fdf2f0a8238e4859e602e5100a8ae8.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_crksph_symmetric
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_3879b817675749e849fa14f03c2f577e.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_gradient_correction
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_c2abdc8087fe603ffd109cd9e5859cec.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_mixed_gradient_correction
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_d286287fc29a88343393d0c2866d769c.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection3D::test_gradient_correction
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_aa0363728d382da65870dd91f24707af.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection3D::test_mixed_gradient_correction
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_102aa4de9cd8d5ff37ffec30e2e1c5a5.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_band_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:92: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
mat = np.matrix(mat)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_band_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:93: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
new_b = mat * np.transpose(np.matrix(result))
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_band_matrix
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_dense_matrix
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_general_matrix
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_matrix
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_positivedefinite_Matrix
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_tridiagonal_matrix
.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
/usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:69: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
return matrix(data, dtype=dtype, copy=False)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_dense_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:103: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
mat = np.matrix(mat)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_dense_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:104: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
new_b = mat * np.transpose(np.matrix(result))
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_general_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:81: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
mat = np.matrix(mat)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_general_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:82: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
new_b = mat * np.transpose(np.matrix(result))
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:126: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
mat = np.matrix(mat)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:127: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
new_b = mat * np.transpose(np.matrix(result))
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_positivedefinite_Matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:138: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
mat = np.matrix(mat)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_positivedefinite_Matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:139: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
new_b = mat * np.transpose(np.matrix(result))
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_tridiagonal_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:115: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
mat = np.matrix(mat)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_tridiagonal_matrix
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/sph/tests/test_linalg.py:116: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
new_b = mat * np.transpose(np.matrix(result))
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_multi_group_integrator.py::TestMultiGroupIntegrator::test_different_accels_per_integrator
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_03d2f3c8840eaa38e2d13edb3a0927a1.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/sph/tests/test_multi_group_integrator.py::TestMultiGroupIntegrator::test_different_accels_per_integrator
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/.pysph/source/py3.9-linux-x86_64/m_f16a981c222b02ffbc9a137fd99ac24b.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/tools/geometry.py:176: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
rotation_matrix = matrix_exp(np.matrix(matrix))
.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
/build/2/pysph-1.0~b0~20191115.gite3d5e10/2nd/.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry.py:76: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
rotation_matrix = G.matrix_exp(np.matrix(mat))
.pybuild/cpython3_3.9/build/pysph/tools/tests/test_geometry_stl.py::TestGeometry::test_get_points_from_mgrid
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:1970: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
result = asarray(a).shape
-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
FAILED pysph/parallel/tests/test_parallel.py::MPIReduceArrayTestCase::test_parallel_reduce
= 1 failed, 525 passed, 273 skipped, 90 deselected, 77 warnings in 2228.24s (0:37:08) =prabhuramachandran commented
Is the test machine a bit resource strapped as this launches 4 MPI processes. The error raised is also that the program did not complete in 30 seconds, is it fixed if you double that to 60 seconds?
avalentino commented
Actually I reduced the number of processes to 2, not sure if this can be an issue.
Right now I'm not on my Debian box, I will make a test with timeout at 60 seconds ASAP.
avalentino commented
@prabhuramachandran yes, increasing the timeout seems to work.
Thanks
Feel free to close.
prabhuramachandran commented
@avalentino -- Great, thank you for checking! Should I bump up the timeout in our code also? The tests on GH do not need it. Please let me know. I am about to cut a release, and could squeeze this in if it will be convenient.
avalentino commented
@prabhuramachandran if increasing a little bit the timeout is not an issue, it would be nice to have it in the next delivery.
Thanks again