[Numpy-discussion] performance matrix multiplication vs. matlab

[Chris Colbert]

since there is demand, and someone already emailed me, I'll put what I
did in this post. It pretty much follows whats on the scipy website,
with a couple other things I gleaned from reading the ATLAS install
guide:

and here it goes, this is valid for Ubuntu 9.04 64-bit  (# starts a
comment when working in the terminal)


download lapack 3.2.1 http://www.netlib.org/lapack/lapack.tgz
download atlas 3.8.3
http://sourceforge.net/project/downloading.php?group_id=23725&filename=atlas3.8.3.tar.bz2&a=65663372

create folder  /home/your-user-name/build/atlas   #this is where we build
create folder /home/your-user-name/build/lapack #atlas and lapack

extract the folder lapack-3.2.1 to /home/your-user-name/build/lapack
extract the contents of atlas to /home/your-user-name/build/atlas



now in the terminal:

# remove g77 and get stuff we need
sudo apt-get remove g77
sudo apt-get install gfortran
sudo apt-get install build-essential
sudo apt-get install python-dev
sudo apt-get install python-setuptools
sudo easy_install nose


# build lapack
cd /home/your-user-name/build/lapack/lapack-3.2.1
cp INSTALL/make.inc.gfortran make.inc

gedit make.inc
#################
#in the make.inc file make sure the line   OPTS = -O2 -fPIC -m64
#and    NOOPTS = -O0 -fPIC -m64
#the -m64 flags build 64-bit code, if you want 32-bit, simply leave
#the -m64 flags out
#################

cd SRC

#this should build lapack without error
make



# build atlas

cd /home/your-user-name/build/atlas

#this is simply where we will build the atlas
#libs, you can name it what you want
mkdir Linux_X64SSE2

cd Linux_X64SSE2

#need to turn off cpu-throttling
sudo cpufreq-selector -g performance

#if you don't want 64bit code remove the -b 64 flag. replace the
#number 2400 with your CPU frequency in MHZ
#i.e. my cpu is 2.53 GHZ so i put 2530
../configure -b 64 -D c -DPentiumCPS=2400 -Fa  -alg -fPIC
--with-netlib-lapack=/home/your-user-name/build/lapack/lapack-3.2.1/Lapack_LINUX.a

#the configure step takes a bit, and should end without errors

 #this takes a long time, go get some coffee, it should end without error
make build

#this will verify the build, also long running
make check

#this will test the performance of your build and give you feedback on
#it. your numbers should be close to the test numbers at the end
make time

cd lib

#builds single threaded .so's
make shared

#builds multithreaded .so's
make ptshared

#copies all of the atlas libs (and the lapack lib built with atlas)
#to our lib dir
sudo  cp  *.so  /usr/local/lib/



#now we need to get and build numpy

download numpy 1.3.0
http://sourceforge.net/project/downloading.php?group_id=1369&filename=numpy-1.3.0.tar.gz&a=93506515

extract the folder numpy-1.3.0 to /home/your-user-name/build

#in the terminal

cd /home/your-user-name/build/numpy-1.3.0
cp site.cfg.example site.cfg

gedit site.cfg
###############################################
# in site.cfg uncomment the following lines and make them look like these
[DEFAULT]
library_dirs = /usr/local/lib
include_dirs = /usr/local/include

[blas_opt]
libraries = ptf77blas, ptcblas, atlas

[lapack_opt]
libraries = lapack, ptf77blas, ptcblas, atlas
###################################################
#if you want single threaded libs, uncomment those lines instead


#build numpy- should end without error
python setup.py build

#install numpy
python setup.py install

cd /home

sudo ldconfig

python
>>import numpy
>>numpy.test()   #this should run with no errors (skipped tests and known-fails are ok)
>>a = numpy.random.randn(6000, 6000)
>>numpy.dot(a, a)     # look at your cpu monitor and verify all cpu cores are at 100% if you built with threads


Celebrate with a beer!


Cheers!

Chris





On Sat, Jun 6, 2009 at 10:42 AM, Keith Goodman<kwgoodman at gmail.com> wrote:
> On Fri, Jun 5, 2009 at 2:37 PM, Chris Colbert <sccolbert at gmail.com> wrote:
>> I'll caution anyone from using Atlas from the repos in Ubuntu 9.04  as the
>> package is broken:
>>
>> https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/363510
>>
>>
>> just build Atlas yourself, you get better performance AND threading.
>> Building it is not the nightmare it sounds like. I think i've done it a
>> total of four times now, both 32-bit and 64-bit builds.
>>
>> If you need help with it,  just email me off list.
>
> That's a nice offer. I tried building ATLAS on Debian a year or two
> ago and got stuck.
>
> Clear out your inbox!
> _______________________________________________
> Numpy-discussion mailing list
> Numpy-discussion at scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>