numpy delete

I just compiled numpy inside a virtualenv with OpenBLAS integration, and it seems to be working ok. This was my process:

Compile OpenBlas:

git clone git://github.com/xianyi/OpenBLAS
cd OpenBLAS && make FC=gfortran
sudo make PREFIX=/opt/OpenBLAS install
sudo ldconfig

Grab the numpy source code:

git clone https://github.com/numpy/numpy
cd numpy

Copy site.cfg.example to site.cfg and edit the copy:

cp site.cfg.example site.cfg
nano site.cfg

Uncomment these lines:

....
[openblas]
libraries = openblas
library_dirs = /opt/OpenBLAS/lib
include_dirs = /opt/OpenBLAS/include
....

Check configuration, build, install (optionally in a virutalenv)

python setup.py config

The output should look something like this:

...
openblas_info:
  FOUND:
    libraries = [‘openblas‘, ‘openblas‘]
    library_dirs = [‘/opt/OpenBLAS/lib‘]
    language = f77

  FOUND:
    libraries = [‘openblas‘, ‘openblas‘]
    library_dirs = [‘/opt/OpenBLAS/lib‘]
    language = f77
...

Then just build and install:

python setup.py build && python setup.py install

Optional: you can use this script to test performance for different thread counts.

OMP_NUM_THREADS=1 python build/test_numpy.py

FAST BLAS
version: 1.8.0.dev-27690e3
maxint: 9223372036854775807

dot: 0.100896406174 sec


OMP_NUM_THREADS=8 python test_numpy.py

FAST BLAS
version: 1.8.0.dev-27690e3
maxint: 9223372036854775807

dot: 0.0660264015198 sec

There seems to be a noticeable improvement in performance for higher thread counts. However, I haven‘t tested this very systematically, and it‘s likely that for smaller matrices the additional overhead would outweigh the performance benefit from a higher thread count.

I apply what you did bu tending with foollowing error at your test script /linalg/lapack_lite.so: undefined symbol: zgelsd_ – Erogol Jan 30 at 17:47

@Erogol Could you check that lapack_lite.so is correctly linked against the libopenblas.so you just built? You can call ldd /<path-to-site-packages>/numpy/linalg/lapack_lite.so - if you installed OpenBLAS with PREFIX=/usr/local you should see something like libopenblas.so.0 => /usr/local/lib/libopenblas.so.0 in the output. – ali_m Jan 30 at 18:01

I have following line even I do strictly what you typed above answer. libopenblas.so.0 => /usr/lib/libopenblas.so.0 (0x00007f77e08fc000) – Erogol Jan 30 at 18:06

It sounds like numpy has not been built correctly. I would suggest you uninstall the broken copy of numpy, do a python setup.py clean and python setup.py build and look for any error messages during the compilation. – ali_m Jan 30 at 18:14

Also, you should probably call sudo ldconfig after installing OpenBLAS if you haven‘t already (I‘ve added this line to my answer) – ali_m Jan 30 at 18:21