[cctbxbb] Azure pipelines Linux builds failing with segmentation fault

[Billy Poon]

I just checked in a fix, so the linux test step should not crash with a
segmentation fault. The issue was that an extra copy of Boost was being
installed by conda.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Wed, Jul 31, 2019 at 9:38 AM Billy Poon <BKPoon at lbl.gov> wrote:

> Hi Richard,
>
> I'm seeing this on some forks as well, and this only started a few days
> ago, so I'll try to debug this week or next.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
>
> On Wed, Jul 31, 2019 at 8:10 AM richard.gildea at diamond.ac.uk <
> richard.gildea at diamond.ac.uk> wrote:
>
>> Recent Azure builds are failing for the Linux builds with the following
>> error:
>>
>>
>> ##[section]Starting: Test
>>
>> ==============================================================================
>> Task : Command line
>> Description : Run a command line script using Bash on Linux and macOS and
>> cmd.exe on Windows
>> Version : 2.151.2
>> Author : Microsoft Corporation
>> Help :
>> https://docs.microsoft.com/azure/devops/pipelines/tasks/utility/command-line
>>
>> ==============================================================================
>> Generating script.
>> ========================== Starting Command Output
>> ===========================
>> [command]/bin/bash --noprofile --norc
>> /__w/_temp/823d09b8-e953-4f93-a9a8-0d863a25f1ce.sh
>> /__w/_temp/823d09b8-e953-4f93-a9a8-0d863a25f1ce.sh: line 11: 6307
>> Segmentation fault (core dumped) libtbx.run_tests_parallel
>> module=boost_adaptbx module=cctbx module=cma_es module=fable module=gltbx
>> module=iotbx module=libtbx module=rstbx module=scitbx module=simtbx
>> module=smtbx module=spotfinder module=annlib_adaptbx module=cbflib_adaptbx
>> nproc=4
>> ##[error]Bash exited with code '139'.
>> ##[section]Finishing: Test
>>
>>
>> https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=256
>>
>>
>> The last successful Linux Python 2.7 master build was
>> https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=240
>>
>>
>> The first failing Linux Python 2.7 master build was
>> https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=245
>>
>>
>> Mac builds appear to be fine. Does anyone have any idea what is the issue?
>>
>>
>> Cheers,
>>
>>
>> Richard
>>
>>
>> Dr Richard Gildea
>> Data Analysis Scientist
>> Tel: +441235 77 8078
>>
>> Diamond Light Source Ltd.
>> Diamond House
>> Harwell Science & Innovation Campus
>> Didcot
>> Oxfordshire
>> OX11 0DE
>>
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