Neuron on Ubuntu Natty 11.04

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mattions
Posts: 65
Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Neuron on Ubuntu Natty 11.04

Post by mattions » Mon May 16, 2011 12:06 pm

Dear all,
I'm trying to install NEURON on the latest ubuntu (11.04) but I run into trouble.

This is the error:

Code: Select all

make[3]: Leaving directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn/src/oc'
Making all in nrnoc
make[3]: Entering directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn/src/nrnoc'
(MODLUNIT=../../share/lib/nrnunits.lib ; \
		export MODLUNIT ; ../nmodl/nocmodl ./hh )
Can't create C file: ./hh.c at line 0 in file ./hh.mod
^
make[3]: *** [hh.c] Error 1
make[3]: Leaving directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn/src/nrnoc'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn'
make: *** [all] Error 2
Any idea why this is happening?

I just running the classic ./configure make routine.

mattions
Posts: 65
Joined: Tue Jul 15, 2008 11:21 am
Location: EMBL-EBI Cambridge UK

Re: Neuron on Ubuntu Natty 11.04

Post by mattions » Tue May 17, 2011 8:42 am

Actually I found out that the problem was a folder with root permission. Deleting the repo and clining again fixed the compilation.

Installing the python instead was a bit more tricky.

I have no idea why, but using the classic ./configure (no prefix) the python module is installed in two different location with two different folder, with different modules inside.

Code: Select all

/usr/local/nrn/share/nrn/lib/python
/usr/local/lib/python2.7/dist-packages
Remarkably, the hoc library is present only in one directory, and the rdxml module in the other one. Pickiing up and copying all the content in one and exporting that directory seems ok to solve the problem.

wwlytton
Posts: 65
Joined: Wed May 18, 2005 10:37 pm
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Re: Neuron on Ubuntu Natty 11.04 --- readline problem

Post by wwlytton » Mon May 30, 2011 9:45 am

An unrelated problem with install on Natty: slow processing of input lines due to some kind of readline incompatibility.

This manifested in an xterm by extremely slow cut and paste of commands into neuron with either the hoc or python prompt (slow line parsing)

The solution was to use the NEURON native readline instead of the system readline: configure with '--with-readline=no'

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