So after your last post, I was still having plenty of trouble. So I decided to start fresh. I wiped my hard drive and installed OS 10.10.5. (Hence my disappearance from the forums for a few days). I've installed openmpi and anaconda-3, and today I'm trying to install neuron.
I was able to configure, make, and install inter-views with no issues.
I configured neuron with the following line:
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./configure --prefix=`pwd` --with-iv=/Applications/Neuron-7.4/iv --with-nrnpython=/Applications/Anaconda-3/bin/python --with-paranrn
I decided to not set paranrn=dynamic since I only have one mip installation now. I also committed --disable-rx3d and --with-readline=yes. I wanted to troubleshoot with a simpler ./configure before adding more options.
I did set python to point to my anaconda installation. I was able to configure, make, and make install without throwing errors. However, I did see this in the ./configure output, which may be the source of the problem I'll describe below.
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RefactoringTool: Refactored src/nrnpython/setup.py
--- src/nrnpython/setup.py (original)
+++ src/nrnpython/setup.py (refactored)
@@ -25,8 +25,8 @@
if nrnpython_pyver!=get_python_version():
print("Error:")
- print("NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver)
- print("Python presently executing setup.py: "+sys.executable+" "+ get_python_version())
+ print(("NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver))
+ print(("Python presently executing setup.py: "+sys.executable+" "+ get_python_version()))
print("These do not match, and they should!")
sys.exit(1)
RefactoringTool: Files that were modified:
RefactoringTool: src/nrnpython/setup.py
After installation, this is the result of running nrniv (I already added the nrn/x86_64/bin to my path):
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~ » nrniv ~ [12:11:49]
dyld: Library not loaded: libpython3.4m.dylib
Referenced from: /Applications/Neuron-7.4/nrn/x86_64/bin/nrniv
Reason: image not found
[1] 3572 trace trap nrniv
Having seen this before, I added the following to my .profile.
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export DYLD_LIBRARY_PATH=/Applications/Anaconda-3/lib:$DYLD_LIBRARY_PATH
Now, running nrniv yields:
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~ » nrniv ~ [12:12:43]
NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Fatal Python error: Py_Initialize: unable to load the file system codec
ImportError: No module named 'encodings'
[1] 5096 abort nrniv
In digging through the internet, I was able to find a few posts that suggested this resulted from an error in my PYTHONHOME environment variable. So I added the following to my .profile:
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export PYTHONHOME=/Applications/Anaconda-3/bin
The results of running nrniv are now:
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~ » nrniv ~ [12:13:43]
NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits
Fatal Python error: Py_Initialize: unable to load the file system codec
ImportError: No module named 'encodings'
[1] 6736 abort nrniv
From what I understand with this, there seems to be a problem with the python interpreter finding the NEURON-7.4-py3.4.egg-info file. I already ran python setup.py install in nrn/src/nrnpython, and it said the file was copied into /Applications/Anaconda-3/lib. I tried to add /Applications/Anaconda-3/lib to my PYTHONPATH, and nothing changed. I've also tried adding /Applications/Neuron-7.4/nrn/lib (as well as /Applications/Neuron-7.4/nrn/lib/python) to my PYTHONPATH, and again no change. So now that's where I am. Any insight?