[Numpy-discussion] performance matrix multiplication vs. matlab

Jonathan Taylor jonathan.taylor@utoronto...
Fri Jul 17 14:57:08 CDT 2009


Following these instructions I have the following problem when I
import numpy.  Does anyone know why this might be?

Thanks,
Jonathan.

>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jtaylor/lib/python2.5/site-packages/numpy/__init__.py",
line 130, in <module>
    import add_newdocs
  File "/home/jtaylor/lib/python2.5/site-packages/numpy/add_newdocs.py",
line 9, in <module>
    from lib import add_newdoc
  File "/home/jtaylor/lib/python2.5/site-packages/numpy/lib/__init__.py",
line 13, in <module>
    from polynomial import *
  File "/home/jtaylor/lib/python2.5/site-packages/numpy/lib/polynomial.py",
line 18, in <module>
    from numpy.linalg import eigvals, lstsq
  File "/home/jtaylor/lib/python2.5/site-packages/numpy/linalg/__init__.py",
line 47, in <module>
    from linalg import *
  File "/home/jtaylor/lib/python2.5/site-packages/numpy/linalg/linalg.py",
line 22, in <module>
    from numpy.linalg import lapack_lite
ImportError: /usr/local/lib/libptcblas.so: undefined symbol: ATL_cpttrsm


On Sat, Jun 6, 2009 at 12:59 PM, Chris Colbert<sccolbert@gmail.com> wrote:
> 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@gmail.com> wrote:
>> On Fri, Jun 5, 2009 at 2:37 PM, Chris Colbert <sccolbert@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@scipy.org
>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
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