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 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 [email protected] < [email protected]> 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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