Jonathan, What does "ldd /home/jtaylor/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so" say ?
You need to make sure that it's using the libraries in /usr/local/lib. You can remove the ones in /usr/lib or "export LD_LIBRARY_PATH=/usr/local/lib/:$LD_LIBRARY_PATH". Hope it helps. Best, N On Fri, Jul 17, 2009 at 3:57 PM, Jonathan Taylor<jonathan.tay...@utoronto.ca> wrote: > 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<sccolb...@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<kwgood...@gmail.com> wrote: >>> On Fri, Jun 5, 2009 at 2:37 PM, Chris Colbert <sccolb...@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 >>> >> _______________________________________________ >> Numpy-discussion mailing list >> Numpy-discussion@scipy.org >> http://mail.scipy.org/mailman/listinfo/numpy-discussion >> > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > -- Nicolas Pinto Ph.D. Candidate, Brain & Computer Sciences Massachusetts Institute of Technology, USA http://web.mit.edu/pinto _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion