segfault running /pipeline/engine/tests/test_utils.py

[djarecka]

Summary

Segfault when running tests from /pipeline/engine/tests/test_utils.py

Actual behavior

See e.g. https://travis-ci.org/nipy/nipype/builds/195258843
appears randomly, but never seen outside py2.7
It's probably the same problem as described in #1757, but the temporary @satra solution doesn't always work(?).

Not sure, if my recent failure in different tests might be related: https://travis-ci.org/djarecka/nipype/jobs/189379626

How to replicate the behavior

From my experience, it might appear more often on some systems than on the others. It should be python2.7 (other travis setting are not important IMO). You can use the docker container nipype/nipype_test:py27 and run pytest -v nipype/pipeline/engine/tests/test_utils.py (after installing pytest) multiple times, 10 should be enough.

It usually returns segfault when running test_mapnode_crash2 or test_mapnode_crash2, but running any of these tests separately do not give segfault (at least not as often).

[satra]

and those particular tests will pass if unicode_literals is turned off. so it's some interaction between the traits and unicode literals

[oesteban]

traits has C "fast" checking on some types. It looks to me that could be the source of the segfault

[djarecka]

looks better after updating traits to 4.6, but have to test more.

[djarecka]

Traits 4.6 either solves the problem or hides it pretty well so the segfault occurs very rare (having problem with getting one). Since I don't understand this segfault, can't really say which one is true.

btw. I've just found that this is not the first time you have problems with traits&unicode_literals errors that are not reported by Travis (at least not in every run) #1621

[satra]

@djarecka - the change you made in interfaces.base in dynamic traits was based on traits 4.6. perhaps we should set that as the minimum version.

[djarecka]

yes, all test should pass with traits 4.6. I've created a PR, but would keep the issue open

[djarecka]

it looks like travis with traits4.6 still have sagfault

[mgxd]

@djarecka @satra how do we progress with this? Will moving from traits to traitlets help this?

[djarecka]

@mgxd - I will check traitlets as @satra suggested.

[oesteban]

The most prominent issue I can foresee switching to traitlets right now is the different use of metadata (https://traitlets.readthedocs.io/en/stable/migration.html#separation-of-metadata-and-keyword-arguments-in-traittype-contructors).

Other than that, I guess migration will be less painful than it could seem.

[satra]

@djarecka - let's do migration after api change. for now let's figure out a fix for segfault (will require python in debug mode and gdb) and the new api.