[MacPorts] #43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing.
#43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing. -----------------------------+-------------------------------- Reporter: Peter.Danecek@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: py-scipy atlas -----------------------------+-------------------------------- I built py-scipy against ATLAS. This version of scipy crashes during testing with a Segmentation fault. The details below are for `py27-scipy +atlas`, but it was observed before (version @0.13.3) with other python subports as well. There seem to be some //real failures// before the crash as well. {{{ In [2]: import scipy In [3]: scipy.test() Running unit tests for scipy NumPy version 1.8.0 NumPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy SciPy version 0.13.3 SciPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy Python version 2.7.6 (default, Nov 22 2013, 13:39:24) [GCC 4.2.1 Compatible Apple Clang 4.1 ((tags/Apple/clang-421.11.66))] nose version 1.3.1 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/lib/utils.py:134: DeprecationWarning: `scipy.lib.blas` is deprecated, use `scipy.linalg.blas` instead! warnings.warn(depdoc, DeprecationWarning) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/lib/utils.py:134: DeprecationWarning: `scipy.lib.lapack` is deprecated, use `scipy.linalg.lapack` instead! warnings.warn(depdoc, DeprecationWarning) ..............................................................................................................................................................................................................................K..................................................................................................................K.......................................................................................K..K...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F..FF......................................................................................................................................SSSSSS......SSSSSS......SSSS..............................FFF.....................................................0-th dimension must be fixed to 3 but got 15 ..0-th dimension must be fixed to 3 but got 5 ...F.Segmentation fault }}} ATLAS is installed as: {{{ atlas @3.10.1_5+mpclang33 (active) }}} I also attach a crash report in the hope that it might help. Not sure if this could be due to compiler mismatch. I CC Vince as atlas maintainer as well. -- Ticket URL: <https://trac.macports.org/ticket/43321> MacPorts <http://www.macports.org/> Ports system for OS X
#43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing. ------------------------------+---------------------- Reporter: Peter.Danecek@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: Port: py-scipy atlas | ------------------------------+---------------------- Changes (by sean@…): * status: new => assigned * owner: macports-tickets@… => sean@… Comment: Thanks for the report. I see the failure for me is from `test_nonlin.TestJacobianDotSolve.test_broyden1` (ran with scipy.test(verbose=10)). Searching around on the internet makes it seem that this is a known problem with ATLAS: http://mail.scipy.org/pipermail/scipy-dev/2011-September/016582.html and that the workaround is just not to use ATLAS. -- Ticket URL: <https://trac.macports.org/ticket/43321#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing. ------------------------------+---------------------- Reporter: Peter.Danecek@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: Port: py-scipy atlas | ------------------------------+---------------------- Comment (by sean@…): In other words, I am stuck. -- Ticket URL: <https://trac.macports.org/ticket/43321#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing. ------------------------------+---------------------- Reporter: Peter.Danecek@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: Port: py-scipy atlas | ------------------------------+---------------------- Comment (by vince@…): If you deem it useful to you, I can ask Atlas maintainer (Clint) to know if this is fixed in the latest unstable version. -- Ticket URL: <https://trac.macports.org/ticket/43321#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing. ------------------------------+---------------------- Reporter: Peter.Danecek@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: Port: py-scipy atlas | ------------------------------+---------------------- Comment (by sean@…): Replying to [comment:3 vince@…]:
If you deem it useful to you, I can ask Atlas developer (Clint) to know if this is fixed in the latest unstable version.
Sure, but I suspect this is something in the fortran compiler (maybe misaligning the arrays?). The bug report from scipy is from 2011 and they basically just say, "If this is a problem, then use another lapack package." I'll try to point them to this bug report and see if that gains any traction. -- Ticket URL: <https://trac.macports.org/ticket/43321#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#43321: py-scipy @0.13.3_1: builds agains ATLAS (variant +atlas) Seg. fault during testing. ------------------------------+---------------------- Reporter: Peter.Danecek@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: Port: py-scipy atlas | ------------------------------+---------------------- Comment (by sean@…): Replying to [comment:4 sean@…]:
Replying to [comment:3 vince@…]:
If you deem it useful to you, I can ask Atlas developer (Clint) to know if this is fixed in the latest unstable version.
Sure, but I suspect this is something in the fortran compiler (maybe misaligning the arrays?). The bug report from scipy is from 2011 and they basically just say, "If this is a problem, then use another lapack package." I'll try to point them to this bug report and see if that gains any traction.
I found the issue on their github tracker here: https://github.com/scipy/scipy/issues/3193 -- Ticket URL: <https://trac.macports.org/ticket/43321#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
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