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