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Trouble installing NumPy in virtualenv on Ubuntu 14.04

May 5, 2014 10.3k views
Yesterday was my first day using DigitalOcean. I set up Ubuntu v. 14.04, cloned the repository my colleague and I are working on, and tried to install all the required Python modules and non-Python dependencies, but there were problems with NumPy that I could not resolve. I have not used Ubuntu in some months, but I normally use pip for almost all Python installations, within a virtualenv virtual environment, and install the many dependencies using apt-get. I remember that NumPy often presents problems. This time it seemed impossible to make NumPy compile. Installing with root privileges succeeded, but then NumPy was not available within the virtualenv environment. I have now installed the Anaconda distribution, instead, so that I can move forward, but I'd be glad to hear of suggestions for effective NumPy installation using pip within a virtual environment.
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2 Answers
asb MOD May 5, 2014
Without seeing the error, it's hard to say exactly what went wrong. Though one thing to remember is that installing numpy with pip requires compiling
C code, so you need gcc and Python's developmental headers around:

apt-get install python-dev build-essential

Also, if you want your virtualenv to be able to access packages installed through apt, create it using:

virtualenv --system-site-packages your_enev
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  • wmattgardner July 1, 2015

    (My droplet: 1GB Ram 30GB SSD Disk New York 3 Ubuntu 14.04 x64).

    I am having the same issue. When I try to install scipy, I get a LOT of output. I'm not sure where to post it because it's probably a few thousand lines of output, but it begins and ends in this (I'm not sure what's relevant but here's a gist of my entire console output):

    Collecting scipy (from seaborn==0.5.1->-r requirements.txt (line 25))
  Using cached scipy-0.15.1.tar.gz
Building wheels for collected packages: scipy
  Running setup.py bdist_wheel for scipy
^@^@^@^@^@^@  Complete output from command /home/matt/.virtualenvs/airbnb/bin/python3 -c "import setuptools;__file__='/tmp/pip-build-556p2ube/scipy/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpp7nc_u95pip-wheel-:
  lapack_opt_info:
  openblas_lapack_info:
    libraries openblas not found in ['/home/matt/.virtualenvs/airbnb/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
    NOT AVAILABLE

  lapack_mkl_info:
  mkl_info:
    libraries mkl,vml,guide not found in ['/home/matt/.virtualenvs/airbnb/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
    NOT AVAILABLE

    NOT AVAILABLE

  atlas_3_10_threads_info:
  Setting PTATLAS=ATLAS
    libraries tatlas,tatlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries lapack_atlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries tatlas,tatlas not found in /usr/local/lib
    libraries lapack_atlas not found in /usr/local/lib
    libraries tatlas,tatlas not found in /usr/lib/atlas-base
    libraries tatlas,tatlas not found in /usr/lib
    libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
    libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
  <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
    NOT AVAILABLE

  atlas_3_10_info:
    libraries satlas,satlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries lapack_atlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries satlas,satlas not found in /usr/local/lib
    libraries lapack_atlas not found in /usr/local/lib
    libraries satlas,satlas not found in /usr/lib/atlas-base
    libraries satlas,satlas not found in /usr/lib
    libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
    libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
  <class 'numpy.distutils.system_info.atlas_3_10_info'>
    NOT AVAILABLE

  atlas_threads_info:
  Setting PTATLAS=ATLAS
    libraries ptf77blas,ptcblas,atlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries lapack_atlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
    libraries lapack_atlas not found in /usr/local/lib
    libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas-base
    libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
    libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
  <class 'numpy.distutils.system_info.atlas_threads_info'>
    NOT AVAILABLE

  atlas_info:
    libraries f77blas,cblas,atlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries lapack_atlas not found in /home/matt/.virtualenvs/airbnb/lib
    libraries f77blas,cblas,atlas not found in /usr/local/lib
    libraries lapack_atlas not found in /usr/local/lib
  <class 'numpy.distutils.system_info.atlas_info'>
  customize Gnu95FCompiler
  Found executable /usr/bin/gfortran
  customize Gnu95FCompiler
  customize Gnu95FCompiler using config
  compiling '_configtest.c':
...
    customize Gnu95FCompiler
    customize Gnu95FCompiler
    customize Gnu95FCompiler using build_ext
    building 'scipy.sparse._sparsetools' extension
    compiling C++ sources
    C compiler: x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC

    compile options: '-D__STDC_FORMAT_MACROS=1 -Iscipy/sparse/sparsetools -I/home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include -I/usr/include/python3.4m -I/home/matt/.virtualenvs/airbnb/include/python3.4m -c'
    x86_64-linux-gnu-g++: scipy/sparse/sparsetools/bsr.cxx
    In file included from /home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                     from /home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                     from scipy/sparse/sparsetools/sparsetools.h:5,
                     from scipy/sparse/sparsetools/bsr.cxx:4:
    /home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    virtual memory exhausted: Cannot allocate memory
    Running from scipy source directory.
    error: Command "x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D__STDC_FORMAT_MACROS=1 -Iscipy/sparse/sparsetools -I/home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include -I/usr/include/python3.4m -I/home/matt/.virtualenvs/airbnb/include/python3.4m -c scipy/sparse/sparsetools/bsr.cxx -o build/temp.linux-x86_64-3.4/scipy/sparse/sparsetools/bsr.o" failed with exit status 1
    In file included from /home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                     from /home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                     from scipy/sparse/sparsetools/sparsetools.h:5,
                     from scipy/sparse/sparsetools/bsr.cxx:4:
    /home/matt/.virtualenvs/airbnb/lib/python3.4/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    virtual memory exhausted: Cannot allocate memory

    ----------------------------------------
Command "/home/matt/.virtualenvs/airbnb/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip-build-556p2ube/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-sjzugg9m-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/matt/.virtualenvs/airbnb/include/site/python3.4/scipy" failed with error code 1 in /tmp/pip-build-556p2ube/scipy
  • caoliu1994 January 28, 2016

    thanks a lot , that solves my problems just right.
    After installing the c packages , i have the right result

wmattgardner July 1, 2015
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