Sorry, the numpy compilation should be download http://sourceforge.net/projects/numpy/files/NumPy/1.7.1/numpy-1.7.1.tar.gz/download and open it up on your Mac. Then:
$ cd ~/Downloads/numpy-1.7.1 $ /usr/local/bin/python setup.py install For scipy, download http://sourceforge.net/projects/scipy/files/scipy/0.12.0/scipy-0.12.0.tar.gz/download and open it. Then: $ cd ~/Downloads/scipy-0.12.0 $ PATH=/usr/local/bin/:$PATH C_INCLUDE_PATH=/sw/include/ suitesparse/ /usr/local/bin/python2.7 setup.py install The instructions in the last mail were for my Framework Python build, so are not useful for you. Regards, Edward On 9 August 2013 11:14, Edward d'Auvergne <[email protected]> wrote: > Hi, > > >>> % locate python | grep '\/python$\|\/python...$' | grep bin | xargs -I >>> % echo % -c "\"import numpy; print(numpy.__version__)\"" >> >> >> I am not sure what these two commands were supposed to return; I assume a >> list of numpy versions. Something in the syntax goes wrong there. I tried a >> number of different variations of brackets and quotes, but nothing >> conclusive came out. > > Sorry, I keep forgetting you use the C shell rather than bash. The > syntax is annoyingly different between the two. Instead try: > > $ locate python | grep '\/python$\|\/python...$' | grep bin | xargs -I > % echo % -c '"import numpy ; print ( numpy.__version__ )"' > > That should work better. I'm just glad you didn't decide to use the Korn > shell! > > >> Anyways. >> Importing numpy and scipy into the python version (/usr/local/bin/python) is >> indeed a problem. Here is certainly the reason why relax does not find >> numpy. See below the ImportErrors. >> >> (If I use my standard python, I have numpy... >> >> [gre:~] paul% which python >> python: aliased to >> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python >> [gre:~] paul% python >> >> Python 2.7.5 (default, Jun 27 2013, 19:56:45) >> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >> Type "help", "copyright", "credits" or "license" for more information. > > This date is recent, but it cannot be the new official version you > installed in the last day. That one should have a date just before > the 15th of May, when it was released. Is this one self compiled? If > so, we might be able to set up that one to work with relax, if all > else fails. > > > >> [gre:~] paul% /usr/local/bin/python >> >> Python 2.7.5 (v2.7.5:ab05e7dd2788, May 13 2013, 13:18:45) > > Better :) > > >>>>> import numpy;print(numpy.__version__) >> >> >> Traceback (most recent call last): >> >> File "<stdin>", line 1, in <module> > [snip] >> ImportError: >> dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so, >> 2): no suitable image found. Did find: >> >> >> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so: >> no matching architecture in universal wrapper > > This is quite a bizarre error. This is a clear architecture mismatch! > I'm reinstalling as I go here, and on my system I've tried both: > > numpy-1.7.1-py2.7-python.org- > macosx10.6.dmg > (http://sourceforge.net/projects/numpy/files/NumPy/1.7.1/numpy-1.7.1-py2.7-python.org-macosx10.6.dmg/download) > numpy-1.7.1-py2.7-python.org-macosx10.3.dmg > (http://sourceforge.net/projects/numpy/files/NumPy/1.7.1/numpy-1.7.1-py2.7-python.org-macosx10.3.dmg/download) > > This is Mac OS X 10.6.8. It boots into 32-bit mode. But I have > 64-bit Python running. Both test numpy versions import fine on my > system. Maybe you need to try the other numpy version? And if that > doesn't work, then it will have to be compiled to get the correct > architecture! > > >>>>> import wx; print(wx.__version__) >> >> >> 2.9.4.0 > > This looks good! wxPython is the most difficult part to set up, normally. > > >> Now I could either use a different version of python for relax (I guess you >> would not recommend), or place numpy into the right path. I should rather >> try the latter. > > For this Python version, numpy is horribly broken. Try the other > numpy DMG version and, if that fails, we compile > http://sourceforge.net/projects/numpy/files/NumPy/1.7.1/numpy-1.7.1.tar.gz/download > with: > > $ cd numpy-1.7.1.tar.gz > $ /usr/local/bin/python setup.py install > > The same with scipy. > > >>> Hopefully one of these will work. Oh, also make sue that the Python >>> version printed out matches the DMG file you recently downloaded >>> exactly, just in case /usr/local/bin/python is a symbolic link to a >>> different Python version :S Maybe also type: >>> >>> % ls -alh /usr/local/bin/python >>> >>> and make sure that the date on that symlink is less than a day old, >>> and that it points to >>> /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7. >> >> This seems to be ok: >> >> [gre026248:~] paul% ls -alh /usr/local/bin/python >> lrwxr-xr-x 1 root wheel 68B 8 Aug 22:52 /usr/local/bin/python -> >> ../../../Library/Frameworks/Python.framework/Versions/2.7/bin/python > > That date looks good. The date that Python gives also looks good. > > >> However, the fact that the owner is root may be a problem. >> Unfortunately, a chown does not solve the issue: > > No, that should be the case. Changing to a user is a security > problem. It is world executable, so the owner being root is > reasonable. > > >> [gre:/Users/paul] root# chown paul /usr/local/bin/python >> >> [gre:/Users/paul] root# ls -alh /usr/local/bin/python >> >> lrwxr-xr-x 1 root wheel 68B 8 Aug 22:52 /usr/local/bin/python -> >> ../../../Library/Frameworks/Python.framework/Versions/2.7/bin/python > > Hehe, your Mac stopped you from doing that :P > > >> I still hesitate to compile numpy from source. >> I might do so, though, especially if nothing else works. > > Like I said above, try the other numpy DMG file, and if not, compile. > Numpy is straight forward. Scipy is more difficult and may require: > > $ PATH=/usr/local/bin/:$PATH C_INCLUDE_PATH=/sw/include/suitesparse/ > ~/bin/python2.7 setup.py install > > You'll have to find where suitesparse is installed on your system and > then point to the correct directory. > > Regards, > > Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
