When I run nrniv -python it uses python 2.3 instead of the 2.4 where I have numpy installed. I've been working on getting neuron and python working together for a while now on mac osx 10.4 ppc.
I build with:
./configure --prefix=`pwd` --with-iv=$N/iv-17 --with-nrnpython=/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/python --enable-carbon --enable-numpy PYLIB=-lpython PYLIBLINK=-lpython
Everything builds and installs fine. I had a silly problem with one of the dylibs being looked for in the wrong place and I fixed that with a symbolic link (probably a better way but it worked.)
When I run python it runs the 2.4 version, and all the output in the /.configure seems to be indicating that the 2.4 version would be used, but when I run nrniv -python it can't find numpy and when I import sys and check sys.version it is the 2.3 version.
Any help would be greatly appreciated,
David Morton
nrniv -python (uses wrong python version)
Moderator: hines
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The goal is to have --with-nrnpython=... figure out everything needed (by asking python) for all versions of linux, mswin, mac, and python. I haven't been able to meet it yet... You can work around the problem by being explicit for everything just like I do for the BlueGene. e.g on that machine I use the options
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'--with-nrnpython' 'PYLIBDIR=/home/hines/python/pyobj' 'PYINCDIR=/home/hines/python/python/include/python2.5' 'PYVER=python2.5.1' 'EXTRAPYLIBS=-lm -lc -lnss_files -lnss_dns -lresolv' 'PYLIB=-L/home/hines/python/pyobj -lpython2.5 -lm -lc -lnss_files -lnss_dns -lresolv'
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I don't understand all the options
I'm not terribly familiar with these configure options and I couldn't figure out what -L</some/path> and -l<something> were supposed to be doing. I've tried a number of feeble combinations with no success. Here is what I've tried:
./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy 'PYLIB=-L/Library/Frameworks/Python.framework/Versions/2.4/lib -lpython2.4 -lm -lc -lnss_files -lnss_dns -lresolv' 'EXTRAPYLIBS=-lm -lc -lnss_files -lnss_dns -lresolv'
./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=-lpython2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy 'PYLIB=-lpython2.4'
./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy 'PYLIB=/Library/Frameworks/Python.framework/Versions/2.4/lib'
Always with the result:
Python binary found (/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/python)
checking nrnpython configuration... checking if python include files and libraries work... configure: error: could not run a test that used the python library.
Examine config.log to see error details. Something wrong with
PYLIB=-L/Library/Frameworks/Python.framework/Versions/2.4/lib
or
PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4
./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy 'PYLIB=-L/Library/Frameworks/Python.framework/Versions/2.4/lib -lpython2.4 -lm -lc -lnss_files -lnss_dns -lresolv' 'EXTRAPYLIBS=-lm -lc -lnss_files -lnss_dns -lresolv'
./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=-lpython2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy 'PYLIB=-lpython2.4'
./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy 'PYLIB=/Library/Frameworks/Python.framework/Versions/2.4/lib'
Always with the result:
Python binary found (/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/python)
checking nrnpython configuration... checking if python include files and libraries work... configure: error: could not run a test that used the python library.
Examine config.log to see error details. Something wrong with
PYLIB=-L/Library/Frameworks/Python.framework/Versions/2.4/lib
or
PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4
Your first case was close except for
the bluegene specific libraries. Try
If you continue to have problems, let me know how you installed python2.4 and I'll do the same and figure out a configuration that links against it. In fact, let me know anyway and I'll see if I can figure out an improvement to the nrn/m4/nrnpython.m4 macros so that --with-nrnpython=<working python> does everything automatically.[/quote]
the bluegene specific libraries. Try
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./configure --prefix=`pwd` --with-iv=$N/iv-17 '--with-nrnpython' 'PYLIBDIR=/Library/Frameworks/Python.framework/Versions/2.4/lib' 'PYINCDIR=/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4' 'PYVER=python2.4.4' --enable-carbon --enable-numpy PYLIB='-L/Library/Frameworks/Python.framework/Versions/2.4/lib -lpython2.4'
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- Posts: 10
- Joined: Fri Apr 11, 2008 11:07 pm
Same ole
I tried the configure as you stated last and no luck. I installed python from python.org following these links. I used 2.4 because it had precompiled binaries for numpy, scipy and matplotlib which I want to use.
http://www.pythonmac.org/packages/py24-fat/index.html
After installing I ran:
"/Applications/MacPython 2.4/Update Shell Profile.command"
to add the directory to the beginning of my path. Other than that I've got the latest svn copy of nrnpy (revision 45) and I've got iv-17 as you can see.
Thanks a bunch for helping me out,
David
http://www.pythonmac.org/packages/py24-fat/index.html
After installing I ran:
"/Applications/MacPython 2.4/Update Shell Profile.command"
to add the directory to the beginning of my path. Other than that I've got the latest svn copy of nrnpy (revision 45) and I've got iv-17 as you can see.
Thanks a bunch for helping me out,
David
I experienced the same problem you did. The following configuration
built with 2.4.4
After I installed python, 2.4.2 was the default version that runs from
a terminal.
built with 2.4.4
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"/Users/hines/neuron/nrn/configure" '--prefix=/Applications/NEURON-6.2/nrn' '--srcdir=/Users/hines/neuron/nrn' '--with-iv=/Applications/NEURON-6.2/iv' '--enable-carbon' '--with-nrnpython' '--enable-UniversalMacBinary' PYLIBLINK='-framework Python' PYLIB='-framework Python'
a terminal.
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- Joined: Fri Apr 11, 2008 11:07 pm
Thanks
Beautiful, thanks. Built and runs okay as far as I can tell.
David
David