BLAS/LAPACK not installed: How to install it?

Question

I am trying to run pip install tsnefor python2.7 and I keep on getting the same error. I followed the instructions on http://bickson.blogspot.com/2011/02/installing-blaslapackitpp-on-amaon-ec2.html and installed LAPACK/BLAS which I thought should have solved the problem. Nothing helped. What am I doing wrong? I am less familiar with bash.

running build_ext

cythoning tsne/bh_sne.pyx to tsne/bh_sne.cpp

building 'bh_sne' extension

creating build/temp.linux-x86_64-2.7

creating build/temp.linux-x86_64-2.7/tsne

creating build/temp.linux-x86_64-2.7/tsne/bh_sne_src

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/home/ubuntu/env/work/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include -Itsne/bh_sne_src/ -I/usr/include/python2.7 -c tsne/bh_sne_src/quadtree.cpp -o build/temp.linux-x86_64-2.7/tsne/bh_sne_src/quadtree.o -msse2 -O3 -fPIC -w

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/home/ubuntu/env/work/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include -Itsne/bh_sne_src/ -I/usr/include/python2.7 -c tsne/bh_sne_src/tsne.cpp -o build/temp.linux-x86_64-2.7/tsne/bh_sne_src/tsne.o -msse2 -O3 -fPIC -w

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/home/ubuntu/env/work/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include -Itsne/bh_sne_src/ -I/usr/include/python2.7 -c tsne/bh_sne.cpp -o build/temp.linux-x86_64-2.7/tsne/bh_sne.o -msse2 -O3 -fPIC -w

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]

c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/tsne/bh_sne_src/quadtree.o build/temp.linux-x86_64-2.7/tsne/bh_sne_src/tsne.o build/temp.linux-x86_64-2.7/tsne/bh_sne.o -L/usr/local/lib -o build/lib.linux-x86_64-2.7/bh_sne.so -lcblas

/usr/bin/ld: cannot find -lcblas

collect2: error: ld returned 1 exit status

error: command 'c++' failed with exit status 1

----------------------------------------
Cleaning up...
Command /home/ubuntu/env/work/bin/python -c "import setuptools, tokenize;__file__='/home/ubuntu/env/work/build/tsne/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-3X17dU-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/ubuntu/env/work/include/site/python2.7 failed with error code 1 in /home/ubuntu/env/work/build/tsne
Traceback (most recent call last):
  File "/home/ubuntu/env/work/bin/pip", line 11, in 
    sys.exit(main())
  File "/home/ubuntu/env/work/local/lib/python2.7/site-packages/pip/__init__.py", line 185, in main
    return command.main(cmd_args)
  File "/home/ubuntu/env/work/local/lib/python2.7/site-packages/pip/basecommand.py", line 161, in main
    text = '\n'.join(complete_log)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 42: ordinal not in range(128)

Answer 1

Ubuntu doesn't have a binary distribution of either cblas or openblas, which are required for tsne according to their github. However, ATLAS, which is available on Ubuntu, comes with precompiled cblas.

In Ubuntu, debian, that should work with:

apt-get install libatlas-base-dev 

https://launchpad.net/ubuntu/+source/atlas

If you need to have different compiler options, you'll have to build openblas yourself.

And check that you get libcblas.a in /usr/lib

Edited: Corrected package name.

Answer 2

Use this:

sudo apt-get install libblas-dev liblapack-dev

Answer 3

Download a copy of OpenBLAS and compile it yourself. Install it into /usr/local using make install. There are OpenBLAS and ATLAS packages and whatever else in the official repositories, but their performance is suspect.