I tried installing Python after that, version 2.7.5 into the folder C:\Python27, but still got the same error. Do I need to reinstall NEURON after having installed Python? Why will it work in the rxvt shell but not the Cygwin shell? Ideally, I want to run a NEURON program using a system call from MATLAB, but right now that generates the same error as starting nrniv from the Cygwin shell.NEURON -- Release 7.3 (849:5be3d097b917) 2013-04-11
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
Traceback (most recent call last):
File "/cygdrive/c/cygwin/lib/python2.7/site.py", line 563, in <module>
main()
File "/cygdrive/c/cygwin/lib/python2.7/site.py", line 545, in main
known_paths = addusersitepackages(known_paths)
File "/cygdrive/c/cygwin/lib/python2.7/site.py", line 278, in addusersitepackages
user_site = getusersitepackages()
File "/cygdrive/c/cygwin/lib/python2.7/site.py", line 253, in getusersitepackages
user_base = getuserbase() # this will also set USER_BASE
File "/cygdrive/c/cygwin/lib/python2.7/site.py", line 243, in getuserbase
USER_BASE = get_config_var('userbase')
File "/cygdrive/c/cygwin/lib/python2.7/sysconfig.py", line 521, in get_config_var
return get_config_vars().get(name)
File "/cygdrive/c/cygwin/lib/python2.7/sysconfig.py", line 420, in get_config_vars
_init_posix(_CONFIG_VARS)
File "/cygdrive/c/cygwin/lib/python2.7/sysconfig.py", line 299, in _init_posix
raise IOError(msg)
IOError: invalid Python installation: unable to open /cygdrive/c/cygwin/include/python2.7/pyconfig.h (No such file or directory)
Here's the other info from NEURON:
Thanks,oc>nrnversion(1)
NEURON -- Release 7.3 (849:5be3d097b917) 2013-04-11
oc>nrnversion(2)
Release 7.3 (849:5be3d097b917)
oc>nrnversion(3)
5be3d097b917
oc>nrnversion(4)
2013-04-11
oc>nrnversion(5)
849
oc>nrnversion(6)
'--prefix=/home/hines/neuron/nrnrelsetup' '--with-nrnpython' '--srcdir=/home/hines/neuron/nrn' '--with-paranrn'
oc>nrnversion(7)
nrniv
oc>nrnversion(8)
i686-pc-cygwin
Marianne