Compiling numpy with OpenBLAS integration
Solution 1
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 https://github.com/xianyi/OpenBLAS $ cd OpenBLAS && make FC=gfortran $ sudo make PREFIX=/opt/OpenBLAS install
If you don't have admin rights you could set
PREFIX=
to a directory where you have write privileges (just modify the corresponding steps below accordingly). -
Make sure that the directory containing
libopenblas.so
is in your shared library search path.-
To do this locally, you could edit your
~/.bashrc
file to contain the lineexport LD_LIBRARY_PATH=/opt/OpenBLAS/lib:$LD_LIBRARY_PATH
The
LD_LIBRARY_PATH
environment variable will be updated when you start a new terminal session (use$ source ~/.bashrc
to force an update within the same session). -
Another option that will work for multiple users is to create a
.conf
file in/etc/ld.so.conf.d/
containing the line/opt/OpenBLAS/lib
, e.g.:$ sudo sh -c "echo '/opt/OpenBLAS/lib' > /etc/ld.so.conf.d/openblas.conf"
Once you are done with either option, run
$ sudo ldconfig
-
-
Grab the
numpy
source code:$ git clone https://github.com/numpy/numpy $ cd numpy
-
Copy
site.cfg.example
tosite.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 inside a
virtualenv
)$ python setup.py config
The output should look something like this:
... openblas_info: FOUND: libraries = ['openblas', 'openblas'] library_dirs = ['/opt/OpenBLAS/lib'] language = c define_macros = [('HAVE_CBLAS', None)] FOUND: libraries = ['openblas', 'openblas'] library_dirs = ['/opt/OpenBLAS/lib'] language = c define_macros = [('HAVE_CBLAS', None)] ...
Installing with
pip
is preferable to usingpython setup.py install
, sincepip
will keep track of the package metadata and allow you to easily uninstall or upgrade numpy in the future.$ pip install .
-
Optional: you can use this script to test performance for different thread counts.
$ OMP_NUM_THREADS=1 python build/test_numpy.py version: 1.10.0.dev0+8e026a2 maxint: 9223372036854775807 BLAS info: * libraries ['openblas', 'openblas'] * library_dirs ['/opt/OpenBLAS/lib'] * define_macros [('HAVE_CBLAS', None)] * language c dot: 0.099796795845 sec $ OMP_NUM_THREADS=8 python build/test_numpy.py version: 1.10.0.dev0+8e026a2 maxint: 9223372036854775807 BLAS info: * libraries ['openblas', 'openblas'] * library_dirs ['/opt/OpenBLAS/lib'] * define_macros [('HAVE_CBLAS', None)] * language c dot: 0.0439578056335 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.
Solution 2
Just in case you are using ubuntu or mint, you can easily have openblas linked numpy by installing both numpy and openblas via apt-get as
sudo apt-get install numpy libopenblas-dev
On a fresh docker ubuntu, I tested the following script copied from the blog post "Installing Numpy and OpenBLAS"
import numpy as np
import numpy.random as npr
import time
# --- Test 1
N = 1
n = 1000
A = npr.randn(n,n)
B = npr.randn(n,n)
t = time.time()
for i in range(N):
C = np.dot(A, B)
td = time.time() - t
print("dotted two (%d,%d) matrices in %0.1f ms" % (n, n, 1e3*td/N))
# --- Test 2
N = 100
n = 4000
A = npr.randn(n)
B = npr.randn(n)
t = time.time()
for i in range(N):
C = np.dot(A, B)
td = time.time() - t
print("dotted two (%d) vectors in %0.2f us" % (n, 1e6*td/N))
# --- Test 3
m,n = (2000,1000)
A = npr.randn(m,n)
t = time.time()
[U,s,V] = np.linalg.svd(A, full_matrices=False)
td = time.time() - t
print("SVD of (%d,%d) matrix in %0.3f s" % (m, n, td))
# --- Test 4
n = 1500
A = npr.randn(n,n)
t = time.time()
w, v = np.linalg.eig(A)
td = time.time() - t
print("Eigendecomp of (%d,%d) matrix in %0.3f s" % (n, n, td))
Without openblas the result is:
dotted two (1000,1000) matrices in 563.8 ms
dotted two (4000) vectors in 5.16 us
SVD of (2000,1000) matrix in 6.084 s
Eigendecomp of (1500,1500) matrix in 14.605 s
After I installed openblas with apt install openblas-dev
, I checked the numpy linkage with
import numpy as np
np.__config__.show()
and the information is
atlas_threads_info:
NOT AVAILABLE
openblas_info:
NOT AVAILABLE
atlas_blas_info:
NOT AVAILABLE
atlas_3_10_threads_info:
NOT AVAILABLE
blas_info:
library_dirs = ['/usr/lib']
libraries = ['blas', 'blas']
language = c
define_macros = [('HAVE_CBLAS', None)]
mkl_info:
NOT AVAILABLE
atlas_3_10_blas_threads_info:
NOT AVAILABLE
atlas_3_10_blas_info:
NOT AVAILABLE
openblas_lapack_info:
NOT AVAILABLE
lapack_opt_info:
library_dirs = ['/usr/lib']
libraries = ['lapack', 'lapack', 'blas', 'blas']
language = c
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
blas_opt_info:
library_dirs = ['/usr/lib']
libraries = ['blas', 'blas']
language = c
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
atlas_info:
NOT AVAILABLE
blas_mkl_info:
NOT AVAILABLE
lapack_mkl_info:
NOT AVAILABLE
atlas_3_10_info:
NOT AVAILABLE
lapack_info:
library_dirs = ['/usr/lib']
libraries = ['lapack', 'lapack']
language = f77
atlas_blas_threads_info:
NOT AVAILABLE
It doesn't show linkage to openblas. However, the new result of the script shows that numpy must have used openblas:
dotted two (1000,1000) matrices in 15.2 ms
dotted two (4000) vectors in 2.64 us
SVD of (2000,1000) matrix in 0.469 s
Eigendecomp of (1500,1500) matrix in 2.794 s
Solution 3
Here's a simpler approach than @ali_m's answer and it works on macOS.
-
Install a gfortran compiler if you don't have one. E.g. using homebrew on macOS:
$ brew install gcc
-
Compile
OpenBLAS
from source [or use a package manager], either getting the source repo or downloading a release:$ git clone https://github.com/xianyi/OpenBLAS $ cd OpenBLAS && make FC=gfortran $ sudo make PREFIX=/opt/OpenBLAS install
If you don't/can't sudo, set
PREFIX=
to another directory and modify the path in the next step.OpenBLAS does not need to be on the compiler include path or the linker library path.
-
Create a
~/.numpy-site.cfg
file containing the PREFIX path you used in step 2:[openblas] libraries = openblas library_dirs = /opt/OpenBLAS/lib runtime_library_dirs = /opt/OpenBLAS/lib include_dirs = /opt/OpenBLAS/include
include_dirs
is for the compiler.library_dirs
is for the linker.runtime_library_dirs
is for the loader, and might not be needed. -
pip-install numpy and scipy from source (preferably into a virtualenv) without manually downloading them [you can also specify the release versions]:
pip install numpy scipy --no-binary numpy,scipy
-
In my experience, this
OPENBLAS_NUM_THREADS
setting at runtime makes OpenBLAS faster, not slower, esp. when multiple CPU processes are using it at the same time:export OPENBLAS_NUM_THREADS=1
(Alternatively, you can compile OpenBLAS with
make FC=gfortran USE_THREAD=0
.)
See the other answers for ways to test it.
Vijay
Updated on July 09, 2022Comments
-
Vijay almost 2 years
I am trying to install
numpy
withOpenBLAS
, however I am at loss as to how thesite.cfg
file needs to be written.When the installation procedure was followed the installation completed without errors, however there is performance degradation on increasing the number of threads used by OpenBLAS from 1 (controlled by the environment variable OMP_NUM_THREADS).
I am not sure if the OpenBLAS integration has been perfect. Could any one provide a
site.cfg
file to achieve the same.P.S.: OpenBLAS integration in other toolkits like Theano, which is based on Python, provides substantial performance boost on increasing the number of threads, on the same machine.
-
erogol over 10 yearsI apply what you did bu tending with foollowing error at your test script /linalg/lapack_lite.so: undefined symbol: zgelsd_
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erogol over 10 yearsI have following line even I do strictly what you typed above answer. libopenblas.so.0 => /usr/lib/libopenblas.so.0 (0x00007f77e08fc000)
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erogol over 10 yearsOne more question. Is openBlas depended to OpenMPI or using it increases the performance?
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Maddy.Shik over 9 yearsworked for me on mac except for additional installation of fortrang
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Felipe almost 9 yearsIn 2015, I had a few problems with the suggested steps here. I found this to work better.
-
Felipe almost 9 years@ali_m I had the same problem as @Erogol (undefined symbol: zgelsd_) and I checked that I saw the line you expected in the output from
ldd
, I uninstalled numpy, ran clean and build and install again but nothing worked. The other link I've provided suggests a few more edits tosite.cfg
in addition to what you suggested so I guess that's what you answer lacks (maybe it's due to my using a newer ubuntu version (14.04)). But your answer pointed me to the right path so I voted it up. -
Ash about 7 yearsWhat if not sudoer in step sudo ldconfig?
-
n1k31t4 about 7 years@Afshin - If not a
sudo
user, best thing it to alter the first stepsudo make PREFIX=/opt/OpenBLAS install
to use a prefix with a location in your own home directory (e.g.make PREFIX=/home/your_username/my_software/
), which then should allow you to run theldconfig
command for your own files. -
Jonno_FTW about 6 yearsThat test_numpy.py script doesn't exist anymore, got an alternative?
-
Jonno_FTW about 6 years@ali_m my bad, i was thinking it came with numpy
-
Savrige about 4 yearsfirst and foremost install
sudo apt install gfortran
-
Sadderdaze over 3 yearsWorked for me on macOS 11, python 3.9. You can install
openblas
with brew, and find the PREFIX withbrew info openblas
. For me it was/usr/local/Cellar/openblas/0.3.10_1/
-
digolira2 over 3 yearsI have macOs11 and installed
openblas
with brew, my prefix is:/usr/local/Cellar/openblas/0.3.12_1
, but I don't know what to do next, where should I put the ~/.numpy-site.cfg file??? The only content inside of the file should be the [openblas] bit ? or there must be something else? -
Jerry101 over 3 years@digolira2
~/
is an absolute path to your home directory, the same as$HOME
. Yes, it only needs the[openblas]
section. -
digolira2 over 3 yearswowww thank you @Jerry101, it worked perfectly!!! =))). Just one rookie question, how the numpy installer knew that it have to look over the ~/.numpy-site.cfg file? Because I haven't made any links, just created it in the root folder.
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Jerry101 over 3 years@digolira2 that path must be built into the numpy and scipy installers.
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Dave over 2 years
python setup.py config
returnsRuntimeError: Unrecognized setuptools command: ['config']
for me, is this deprecated?