What is the easiest way to install BLAS and LAPACK for scipy?
PythonNumpyPython Problem Overview
I would like to run a programme that someone else has prepared and it includes scipy. I have tried to install scipy with
pip install scipy
but it gives me a long error. I know there are ways with Anaconda and Canopy but I think these are long ways. I would like to have a short way. I have also tried
G:\determinator_Oskar>pip install scipy
Collecting scipy
Using cached scipy-0.16.1.tar.gz
Building wheels for collected packages: scipy
Running setup.py bdist_wheel for scipy
Complete output from command g:\myve\scripts\python.exe -c "import setuptools;
__file__='e:\\temp_n~1\\pip-build-1xigxu\\scipy\\setup.py';exec(compile(open(__f
ile__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d e:\temp_
n~1\tmp07__zrpip-wheel-:
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['g:\\myve\\lib', 'C:\\']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['g:\\myve\\lib', 'C:\\']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries tatlas,tatlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries satlas,satlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries ptf77blas,ptcblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries f77blas,cblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
libraries lapack not found in ['g:\\myve\\lib', 'C:\\']
NOT AVAILABLE
lapack_src_info:
NOT AVAILABLE
NOT AVAILABLE
g:\myve\lib\site-packages\numpy\distutils\system_info.py:1552: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
g:\myve\lib\site-packages\numpy\distutils\system_info.py:1563: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
g:\myve\lib\site-packages\numpy\distutils\system_info.py:1566: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "e:\temp_n~1\pip-build-1xigxu\scipy\setup.py", line 253, in <module>
setup_package()
File "e:\temp_n~1\pip-build-1xigxu\scipy\setup.py", line 250, in setup_packa
ge
setup(**metadata)
File "g:\myve\lib\site-packages\numpy\distutils\core.py", line 135, in setup
config = configuration()
File "e:\temp_n~1\pip-build-1xigxu\scipy\setup.py", line 175, in configurati
on
config.add_subpackage('scipy')
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in
add_subpackage
caller_level = 2)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 970, in
get_subpackage
caller_level = caller_level + 1)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 907, in
_get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in
add_subpackage
caller_level = 2)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 970, in
get_subpackage
caller_level = caller_level + 1)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 907, in
_get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\linalg\setup.py", line 20, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Failed building wheel for scipy
Failed to build scipy
Installing collected packages: scipy
Running setup.py install for scipy
Complete output from command g:\myve\scripts\python.exe -c "import setuptool
s, tokenize;__file__='e:\\temp_n~1\\pip-build-1xigxu\\scipy\\setup.py';exec(comp
ile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __fi
le__, 'exec'))" install --record e:\temp_n~1\pip-3hncqr-record\install-record.tx
t --single-version-externally-managed --compile --install-headers g:\myve\includ
e\site\python2.7\scipy:
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['g:\\myve\\lib', 'C:\\']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['g:\\myve\\lib', 'C:\\']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries tatlas,tatlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries satlas,satlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries ptf77blas,ptcblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in g:\myve\lib
libraries lapack_atlas not found in g:\myve\lib
libraries f77blas,cblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
libraries lapack not found in ['g:\\myve\\lib', 'C:\\']
NOT AVAILABLE
lapack_src_info:
NOT AVAILABLE
NOT AVAILABLE
g:\myve\lib\site-packages\numpy\distutils\system_info.py:1552: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
g:\myve\lib\site-packages\numpy\distutils\system_info.py:1563: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
g:\myve\lib\site-packages\numpy\distutils\system_info.py:1566: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "e:\temp_n~1\pip-build-1xigxu\scipy\setup.py", line 253, in <module>
setup_package()
File "e:\temp_n~1\pip-build-1xigxu\scipy\setup.py", line 250, in setup_pac
kage
setup(**metadata)
File "g:\myve\lib\site-packages\numpy\distutils\core.py", line 135, in set
up
config = configuration()
File "e:\temp_n~1\pip-build-1xigxu\scipy\setup.py", line 175, in configura
tion
config.add_subpackage('scipy')
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 1001,
in add_subpackage
caller_level = 2)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 970, i
n get_subpackage
caller_level = caller_level + 1)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 907, i
n _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 1001,
in add_subpackage
caller_level = 2)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 970, i
n get_subpackage
caller_level = caller_level + 1)
File "g:\myve\lib\site-packages\numpy\distutils\misc_util.py", line 907, i
n _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\linalg\setup.py", line 20, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Command "g:\myve\scripts\python.exe -c "import setuptools, tokenize;__file__='e:
\\temp_n~1\\pip-build-1xigxu\\scipy\\setup.py';exec(compile(getattr(tokenize, 'o
pen', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install
--record e:\temp_n~1\pip-3hncqr-record\install-record.txt --single-version-exter
nally-managed --compile --install-headers g:\myve\include\site\python2.7\scipy"
failed with error code 1 in e:\temp_n~1\pip-build-1xigxu\scipy
I have also tried
pip install lapack
with this result
Collecting lapack
Could not find a version that satisfies the requirement lapack (from versions
)
No matching distribution found for lapack
I have also tried
pip install blas
with similar results
G:\determinator_Oskar>pip install blas
Collecting blas
Could not find a version that satisfies the requirement blas (from versions: )
No matching distribution found for blas
Why does a scipy get so complicated ?
Python Solutions
Solution 1 - Python
For Debian Jessie and Stretch installing the following packages resolves the issue:
sudo apt install libblas3 liblapack3 liblapack-dev libblas-dev
Your next issue is very likely going to be a missing Fortran compiler, resolve this by installing it like this:
sudo apt install gfortran
If you want an optimized scipy, you can also install the optional libatlas-base-dev package:
sudo apt install libatlas-base-dev
If you have any issue with a missing Python.h file like this:
> Python.h: No such file or directory
Then have a look at this post: https://stackoverflow.com/a/21530768/209532
Solution 2 - Python
The SciPy installation page already recommends several ways of installing python with SciPy already included, such as WinPython.
Another way is to use wheels (a built-package format):
pip install SomePackage-1.0-py2.py3-none-any.whl
The wheel packages you can find on: http://www.lfd.uci.edu/~gohlke/pythonlibs/
For SciPy you need:
- the NumPy wheel packages
- and the SciPy wheel packages
Solution 3 - Python
> "Why does a scipy get so complicated?
It gets so complicated because Python's package management system is built to track Python package dependencies, and SciPy and other scientific tools have dependencies beyond Python. Wheels fix part of the problem, but my experience is that tools like pip/virtualenv are just not sufficient for installing and managing a scientific Python stack.
If you want an easy way to get up and running with SciPy, I would highly suggest the Anaconda distribution. It will give you everything you need for scientific computing in Python.
If you want a "short way" of doing this (I'm interpreting that as "I don't want to install a huge distribution"), you might try miniconda and then run conda install scipy.
Solution 4 - Python
Always for Ubuntu/Debian, chjortlund's answer it's very good but not perfect, since this way you get an unoptimized BLAS library. You have simply to do:
sudo apt install libatlas-base-dev
and voila'!
Solution 5 - Python
Using conda install scipy instead of pip solved the problem for me!
Solution 6 - Python
For windows: Best is to use pre-compiled package available from this site: http://www.lfd.uci.edu/%7Egohlke/pythonlibs/#scipy
Solution 7 - Python
For completeness, though this probably would not work well given your particular setup (external program + Windows), one can also acquire Scipy hassle-free as part of the (large) SageMath download.
Solution 8 - Python
Either use SciPy whl, download the appropriate one and run pip install <whl_file>
OR
Read through SciPy Windows issue and run one of the methods.
OR
Use Miniconda.
Additionally, install Visual C++ compiler for python2.7 in-case it asks for it.
Solution 9 - Python
I got this problem on freeBSD. It seems lapack packages are missing, I solved it installing them (as root) with:
pkg install lapack
pkg install atlas-devel #not sure this is needed, but just in case
I imagine it could work on other system too using the appropriate package installer (e.g. apt-get)
Solution 10 - Python
pip install Cython
before
pip install sklearn
did the trick for me.
Solution 11 - Python
conda install liblapack
this worked for me