SciPy/Python install on Ubuntu

Question

I'm currently following the tutorial Installing the SciPy Stack to install SciPy on Ubuntu 12.04 (Precise Pangolin) (I can't use apt-get install because I need a recent version).

However, I get errors when I do the following commands:

python setup.py build sudo python setup.py install --prefix=/usr/local   # Installs to /usr/local  python setup.py build  michael@michael-laptop-ubuntu:~/Downloads/scipy-0.11.0rc1$ python setup.py buildRunning from scipy source directory. blas_opt_info: blas_mkl_info:   libraries mkl,vml,guide not found in /usr/local/lib   libraries mkl,vml,guide not found in /usr/lib   libraries mkl,vml,guide not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  atlas_blas_threads_info: Setting PTATLAS=ATLAS   libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2   libraries ptf77blas,ptcblas,atlas not found in /usr/lib   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/i386-linux-gnu/sse2   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  atlas_blas_info:   libraries f77blas,cblas,atlas not found in /usr/local/lib   libraries f77blas,cblas,atlas not found in /usr/lib/sse2   libraries f77blas,cblas,atlas not found in /usr/lib   libraries f77blas,cblas,atlas not found in /usr/lib/i386-linux-gnu/sse2   libraries f77blas,cblas,atlas not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1423: 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__) blas_info:   libraries blas not found in /usr/local/lib   libraries blas not found in /usr/lib   libraries blas not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1432: UserWarning:      Blas (http://www.netlib.org/blas/) libraries not found.     Directories to search for the libraries can be specified in the     numpy/distutils/site.cfg file (section [blas]) or by setting     the BLAS environment variable.   warnings.warn(BlasNotFoundError.__doc__) blas_src_info:   NOT AVAILABLE  /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1435: UserWarning:      Blas (http://www.netlib.org/blas/) sources not found.     Directories to search for the sources can be specified in the     numpy/distutils/site.cfg file (section [blas_src]) or by setting     the BLAS_SRC environment variable.   warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last):   File "setup.py", line 208, in <module>     setup_package()   File "setup.py", line 199, in setup_package     configuration=configuration )   File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 152, in setup     config = configuration()   File "setup.py", line 136, in configuration     config.add_subpackage('scipy')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/setup.py", line 8, in configuration     config.add_subpackage('integrate')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/integrate/setup.py", line 10, in configuration     blas_opt = get_info('blas_opt',notfound_action=2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 320, in get_info     return cl().get_info(notfound_action)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 471, in get_info     raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError:      Blas (http://www.netlib.org/blas/) libraries not found.     Directories to search for the libraries can be specified in the     numpy/distutils/site.cfg file (section [blas]) or by setting     the BLAS environment variable. Error in sys.excepthook: Traceback (most recent call last):   File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 64, in apport_excepthook     from apport.fileutils import likely_packaged, get_recent_crashes   File "/usr/lib/python2.7/dist-packages/apport/__init__.py", line 1, in <module>     from apport.report import Report   File "/usr/lib/python2.7/dist-packages/apport/report.py", line 18, in <module>     import problem_report   File "/usr/lib/python2.7/dist-packages/problem_report.py", line 14, in <module>     import zlib, base64, time, sys, gzip, struct, os   File "/usr/lib/python2.7/gzip.py", line 10, in <module>     import io   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/__init__.py", line 83, in <module>     from matlab import loadmat, savemat, byteordercodes   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/matlab/__init__.py", line 11, in <module>     from mio import loadmat, savemat   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/matlab/mio.py", line 15, in <module>     from mio4 import MatFile4Reader, MatFile4Writer   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/matlab/mio4.py", line 9, in <module>     import scipy.sparse   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/__init__.py", line 180, in <module>     from csr import *   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/csr.py", line 12, in <module>     from sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/sparsetools/__init__.py", line 4, in <module>     from csr import *   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/sparsetools/csr.py", line 25, in <module>     _csr = swig_import_helper()   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/sparsetools/csr.py", line 17, in swig_import_helper     import _csr ImportError: No module named _csr  Original exception was: Traceback (most recent call last):   File "setup.py", line 208, in <module>     setup_package()   File "setup.py", line 199, in setup_package     configuration=configuration )   File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 152, in setup     config = configuration()   File "setup.py", line 136, in configuration     config.add_subpackage('scipy')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/setup.py", line 8, in configuration     config.add_subpackage('integrate')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/integrate/setup.py", line 10, in configuration     blas_opt = get_info('blas_opt',notfound_action=2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 320, in get_info     return cl().get_info(notfound_action)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 471, in get_info     raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError:      Blas (http://www.netlib.org/blas/) libraries not found.     Directories to search for the libraries can be specified in the     numpy/distutils/site.cfg file (section [blas]) or by setting     the BLAS environment variable. 

sudo python setup.py install --prefix=/usr/local # installs to /usr/local

michael@michael-laptop-ubuntu:~/Downloads/scipy-0.11.0rc1$ sudo python setup.py install --prefix=/usr/local [sudo] password for michael:  Running from scipy source directory. blas_opt_info: blas_mkl_info:   libraries mkl,vml,guide not found in /usr/local/lib   libraries mkl,vml,guide not found in /usr/lib   libraries mkl,vml,guide not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  atlas_blas_threads_info: Setting PTATLAS=ATLAS   libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2   libraries ptf77blas,ptcblas,atlas not found in /usr/lib   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/i386-linux-gnu/sse2   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  atlas_blas_info:   libraries f77blas,cblas,atlas not found in /usr/local/lib   libraries f77blas,cblas,atlas not found in /usr/lib/sse2   libraries f77blas,cblas,atlas not found in /usr/lib   libraries f77blas,cblas,atlas not found in /usr/lib/i386-linux-gnu/sse2   libraries f77blas,cblas,atlas not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1423: 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__) blas_info:   libraries blas not found in /usr/local/lib   libraries blas not found in /usr/lib   libraries blas not found in /usr/lib/i386-linux-gnu   NOT AVAILABLE  /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1432: UserWarning:      Blas (http://www.netlib.org/blas/) libraries not found.     Directories to search for the libraries can be specified in the     numpy/distutils/site.cfg file (section [blas]) or by setting     the BLAS environment variable.   warnings.warn(BlasNotFoundError.__doc__) blas_src_info:   NOT AVAILABLE  /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1435: UserWarning:      Blas (http://www.netlib.org/blas/) sources not found.     Directories to search for the sources can be specified in the     numpy/distutils/site.cfg file (section [blas_src]) or by setting     the BLAS_SRC environment variable.   warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last):   File "setup.py", line 208, in <module>     setup_package()   File "setup.py", line 199, in setup_package     configuration=configuration )   File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 152, in setup     config = configuration()   File "setup.py", line 136, in configuration     config.add_subpackage('scipy')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/setup.py", line 8, in configuration     config.add_subpackage('integrate')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/integrate/setup.py", line 10, in configuration     blas_opt = get_info('blas_opt',notfound_action=2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 320, in get_info     return cl().get_info(notfound_action)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 471, in get_info     raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError:      Blas (http://www.netlib.org/blas/) libraries not found.     Directories to search for the libraries can be specified in the     numpy/distutils/site.cfg file (section [blas]) or by setting     the BLAS environment variable. Error in sys.excepthook: Traceback (most recent call last):   File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 64, in apport_excepthook     from apport.fileutils import likely_packaged, get_recent_crashes   File "/usr/lib/python2.7/dist-packages/apport/__init__.py", line 1, in <module>     from apport.report import Report   File "/usr/lib/python2.7/dist-packages/apport/report.py", line 18, in <module>     import problem_report   File "/usr/lib/python2.7/dist-packages/problem_report.py", line 14, in <module>     import zlib, base64, time, sys, gzip, struct, os   File "/usr/lib/python2.7/gzip.py", line 10, in <module>     import io   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/__init__.py", line 83, in <module>     from matlab import loadmat, savemat, byteordercodes   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/matlab/__init__.py", line 11, in <module>     from mio import loadmat, savemat   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/matlab/mio.py", line 15, in <module>     from mio4 import MatFile4Reader, MatFile4Writer   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/io/matlab/mio4.py", line 9, in <module>     import scipy.sparse   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/__init__.py", line 180, in <module>     from csr import *   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/csr.py", line 12, in <module>     from sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/sparsetools/__init__.py", line 4, in <module>     from csr import *   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/sparsetools/csr.py", line 25, in <module>     _csr = swig_import_helper()   File "/home/michael/Downloads/scipy-0.11.0rc1/scipy/sparse/sparsetools/csr.py", line 17, in swig_import_helper     import _csr ImportError: No module named _csr  Original exception was: Traceback (most recent call last):   File "setup.py", line 208, in <module>     setup_package()   File "setup.py", line 199, in setup_package     configuration=configuration )   File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 152, in setup     config = configuration()   File "setup.py", line 136, in configuration     config.add_subpackage('scipy')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/setup.py", line 8, in configuration     config.add_subpackage('integrate')   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage     caller_level = 2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage     caller_level = caller_level + 1)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py     config = setup_module.configuration(*args)   File "scipy/integrate/setup.py", line 10, in configuration     blas_opt = get_info('blas_opt',notfound_action=2)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 320, in get_info     return cl().get_info(notfound_action)   File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 471, in get_info     raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError:      Blas (http://www.netlib.org/blas/) libraries not found.     Directories to search for the libraries can be specified in the     numpy/distutils/site.cfg file (section [blas]) or by setting     the BLAS environment variable. 

Moreover, how do I test if this module was installed correctly?

Answer 1

My usual work flow is to use a virtualenv to have a Python distribution with up-to-date packages.

Within this environment you can than install and update all packages you need with pip and without any sudo calls.

So if you only need SciPy (and NumPy) this would be:

$ sudo apt-get install python-virtualenv python-pip $ sudo apt-get build-dep python-numpy python-scipy $ # Create virtualenv in home $ virtualenv .myenv $ # Activate the virtualenv $ source .myenv/bin/activate (myenv)$ pip install -U numpy (myenv)$ pip install -U scipy 

(If you don't have root access, you can install virtualenv and pip as described here. However, you need the dependencies of NumPy and SciPy.)

You can include source .myenv/bin/activate in your .bash_profile and your shell will always start with that environment. If you use requirement files it is easy to install and maintain the same environments on all your machines.

Answer 2

Had the same problem. The following worked for me:

sudo apt-get install libblas-dev sudo apt-get install liblapack-dev sudo apt-get install gfortran