the testsuite quits at core/test_topologyattrs.py:TestResids.test_set_atoms without any errors

[rathann]

Expected behaviour

All tests pass and testsuite completes.

Actual behaviour

Test execution dies when running core/test_topologyattrs.py:TestResids.test_set_atoms, but only when testing at least the whole file.

Code to reproduce the behaviour

./mda_nosetests --exe -v core/test_topologyattrs.py
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_get_atoms ... ok
Unless overriden by child class, this should yield values for all ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_get_atoms ... ok
Unless overriden by child class, this should yield values for all ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_get_atoms ... ok
Unless overriden by child class, this should yield values for all ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestAttr.test_align_principal_axes_with_self ... ok
MDAnalysisTests.core.test_topologyattrs.TestAttr.test_align_principal_axes_with_x ... ok
MDAnalysisTests.core.test_topologyattrs.TestAttr.test_principal_axes ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_residues ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_segment ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_segments ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<AtomGroup with 10 atoms>, 'resids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<Atom 1: AAA resid 1 and segid SegA>, 'resid') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<AtomGroup with 10 atoms>, 'segids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<Atom 1: AAA resid 1 and segid SegA>, 'segid') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<ResidueGroup with 5 residues>, 'names') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<ResidueGroup with 5 residues>, 'segids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<Residue 1>, 'segid') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<SegmentGroup with 2 segments>, 'names') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<SegmentGroup with 2 segments>, 'resids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_atom_indices ... ok
MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_residue_indices ... ok
MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_segment_indices ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_residues ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_segment ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_segments ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_residues ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_len ... ok
Setting the resids of atoms changes their residue membership. ... -bash-4.4$

Strangely enough, it passes if I limit the execution to the single class:

./mda_nosetests --exe -v core/test_topologyattrs.py:TestResids
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_residues ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_len ... ok
Setting the resids of atoms changes their residue membership. ... KNOWNFAIL: Test skipped due to expected failure
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residue_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_singular ... ok

Cleanup: deleting offset files in /builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/data


By the end of the tests, there are 0 open handles for 0 files:
----------------------------------------------------------------------
Ran 10 tests in 0.006s

OK (KNOWNFAIL=1)

Currently version of MDAnalysis:

0.16.0

This is on Fedora rawhide (27).

[kain88-de]

They all work for me on Fedora 25. Is there a docker/vagrant file to test this in a VM?

[rathann]

@kain88-de Thanks for taking a look. You can use the fedora:rawhide Docker image from official Fedora repository on Docker Hub: https://hub.docker.com/_/fedora/

Note that this doesn't happen when running plain nosetests.

[kain88-de]

I'm able to run all of these tests on a rawhide from the docker image

[rathann]

I cannot reproduce it any more, either. Sorry for the noise.

[richardjgowers]

No worries, thanks for packaging up our work for other users!

…

On Thu, 8 Jun 2017, 5:59 p.m. rathann, ***@***.***> wrote: I cannot reproduce it any more, either. Sorry for the noise. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1360 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI0jB0Z6jAQUmX1Fc2bVIYHC9CWKXv1sks5sCBpSgaJpZM4Ni6mq> .

[rathann]

Actually, scratch that. It's still reproducible:

[mockbuild@e23ca514884f4fbb804e72d129fd445f MDAnalysisTests]$ pwd
/builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests
[mockbuild@e23ca514884f4fbb804e72d129fd445f MDAnalysisTests]$ PYTHONPATH=/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.x86_64/usr/lib/python2.7/site-packages:/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.x86_64/usr/lib64/python2.7/site-packages ./mda_nosetests --exe -v core/test_topologyattrs.py
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_get_atoms ... ok
Unless overriden by child class, this should yield values for all ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_get_atoms ... ok
Unless overriden by child class, this should yield values for all ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_get_atoms ... ok
Unless overriden by child class, this should yield values for all ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestAttr.test_align_principal_axes_with_self ... ok
MDAnalysisTests.core.test_topologyattrs.TestAttr.test_align_principal_axes_with_x ... ok
MDAnalysisTests.core.test_topologyattrs.TestAttr.test_principal_axes ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_residues ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_segment ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_segments ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<AtomGroup with 10 atoms>, 'resids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<Atom 1: AAA resid 1 and segid SegA>, 'resid') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<AtomGroup with 10 atoms>, 'segids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<Atom 1: AAA resid 1 and segid SegA>, 'segid') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<ResidueGroup with 5 residues>, 'names') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<ResidueGroup with 5 residues>, 'segids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<Residue 1>, 'segid') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<SegmentGroup with 2 segments>, 'names') ... ok
MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(<SegmentGroup with 2 segments>, 'resids') ... ok
MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_atom_indices ... ok
MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_residue_indices ... ok
MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_segment_indices ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_residues ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_segment ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_segments ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_len ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atom_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_singular ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_residues ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_len ... ok
Setting the resids of atoms changes their residue membership. ... [mockbuild@e23ca514884f4fbb804e72d129fd445f MDAnalysisTests]$ 

Strangely enough, if I try running just the dying test, it passes (as KNOWNFAIL):

[mockbuild@e23ca514884f4fbb804e72d129fd445f MDAnalysisTests]$ PYTHONPATH=/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.x86_64/usr/lib/python2.7/site-packages:/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.x86_64/usr/lib64/python2.7/site-packages ./mda_nosetests --exe -v core/test_topologyattrs.py:TestResids.test_set_atoms
Setting the resids of atoms changes their residue membership. ... KNOWNFAIL: Test skipped due to expected failure

Cleanup: deleting offset files in /builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/data


By the end of the tests, there are 0 open handles for 0 files:
----------------------------------------------------------------------
Ran 1 test in 0.001s

OK (KNOWNFAIL=1)

Testing the whole class works, too:

[mockbuild@e23ca514884f4fbb804e72d129fd445f MDAnalysisTests]$ PYTHONPATH=/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.x86_64/usr/lib/python2.7/site-packages:/builddir/build/BUILDROOT/python-MDAnalysis-0.16.0-1.fc27.x86_64/usr/lib64/python2.7/site-packages ./mda_nosetests --exe -v core/test_topologyattrs.py:TestResids               
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_atoms ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_residues ... ok
Unless overriden by child class, this should yield values for all ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_len ... ok
Setting the resids of atoms changes their residue membership. ... KNOWNFAIL: Test skipped due to expected failure
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residue_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_VE ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_plural ... ok
MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_singular ... ok

Cleanup: deleting offset files in /builddir/build/BUILD/MDAnalysis-0.16.0/MDAnalysisTests-0.16.0/MDAnalysisTests/data


By the end of the tests, there are 0 open handles for 0 files:
----------------------------------------------------------------------
Ran 10 tests in 0.005s

OK (KNOWNFAIL=1)

Running the same under nosetests-2.7 doesn't die. I'm at a loss on how to debug this.

[orbeckst]

If it's in any way related to nose then it will (hopefully) go away when we have transitioned to pytest #884 .

[kain88-de]

@rathann yeah I also observe these random dying of nosetests currently on fedora 25. A way to fix them is to insert print statements in the test where the process dies. For a reason that is unknown to me this keeps the process alive.