Slow as Hecks on OSX
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- numpy, python
- Domain
- machine-learning, performance
Research direction
Start by reproducing the reported diagnostics on OSX: run the numpy.distutils atlas check and np.config.show() in the project environment. The issue provides no file or test entry point; done would mean determining how the missing ATLAS/BLAS support affects knnimpute and defining a verified resolution for the reported slowdown.
Written by the indexing model from the issue text.
Description
knnimpute is slow on OSX because of missing ATLAS/BLAS. Confirm with:
import numpy.distutils.system_info as sysinfo
sysinfo.get_info('atlas')
np.__config__.show()
-> import numpy.distutils.system_info as sysinfo
(Pdb) import numpy.distutils.system_info as sysinfo
(Pdb) sysinfo.get_info('atlas')
{}
(Pdb) np.__config__.show()
lapack_opt_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
blas_opt_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
openblas_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
blis_info:
NOT AVAILABLE
openblas_lapack_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
lapack_mkl_info:
NOT AVAILABLE
blas_mkl_info:
NOT AVAILABLE
Related:
https://github.com/CellCognition/cecog/wiki/Build-build-accelerated-numpy-using-ATLAS-on-Mac-OSX
https://joernhees.de/blog/2013/06/08/mac-os-x-10-8-scientific-python-with-homebrew/
- Dominant language
- Python
- Stars
- 2
- Forks
- 0
- PR merge metrics
- No merged PRs in 30d
Getting set up
- Ships a Dockerfile or Docker Compose file
- No pull request template
- No contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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