Install nrnpython when Python is in home

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

Moderator: hines

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arb
Posts: 19
Joined: Mon Jul 02, 2007 6:18 am
Location: Humboldt-University, Berlin

Install nrnpython when Python is in home

Post by arb » Sat Sep 06, 2008 9:45 am

Hi,

I am using a server where python is not installed and I cannot install python as root.
So I have installed python locally in my home directory and it works without any problems.

When I want to install neuron, it finds my python version, but it seems to have problems with other standard libraries that
neuron does not find any more...

./configure -with-iv=/home/bahl --with-nrnpython=/home/bahl/bin/python

.......
....

Python binary found (/home/bahl/bin/python)
checking nrnpython configuration... get_python_version() '2.5'
get_python_inc(1) '/home/bahl/include/python2.5'
get_config_var('LIBS') '-lpthread -ldl -lutil'
get_config_var('LINKFORSHARED') '-Xlinker -export-dynamic'
get_config_var('LIBDIR') '/home/bahl/lib'
checking numpy availability... 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/home/bahl/lib -lpython2.5 -lpthread -ldl -lutil -Xlinker -export-dynamic -R/home/bahl/lib
or
PYLIBDIR=/home/bahl/lib
or
PYLIBLINK=-L/home/bahl/lib -lpython2.5 -lpthread -ldl -lutil
or
PYINCDIR=/home/bahl/include/python2.5



Neuron does not seem to find the stardard libraries like pthread or dl (which exist in the global library)...

Does anyone has an idea, how to tell neuron, that python libraries are in my home directory but all the other libraries in some standard global directory??

Thank very much,
Armin

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Install nrnpython when Python is in home

Post by hines » Sat Sep 06, 2008 4:16 pm

Examine config.log to see error details. Something wrong with
PYLIB=-L/home/bahl/lib -lpython2.5 -lpthread -ldl -lutil -Xlinker -export-dynamic -R/home/bahl/lib
In config.log , search for lpy5hon2.5 and somwhere around there should be more precise information
about what went wrong. With that, you can specify your own strings for PYLIB
PYLIBDIR,PYLIBLINK,and PYINCDIR. For example, on a BlueGene/L I use

Code: Select all

../multicore4/configure --prefix=`pwd` --srcdir=../multicore4 \
 --enable-bluegene \
 --with-paranrn --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'
However, I am a bit disturbed that all my efforts in checking the python configuration went for naught.
I, myself, have used a private version of Python2.5 compiled without optimization and my configure was
../nrn/configure '--prefix=/home/hines/neuron/valgrind' '--srcdir=../nrn' '--with-nrnpython=/home/hines/python/python_valgrind/bin/python'

arb
Posts: 19
Joined: Mon Jul 02, 2007 6:18 am
Location: Humboldt-University, Berlin

Re: Install nrnpython when Python is in home

Post by arb » Sat Sep 06, 2008 6:33 pm

Hi Michael,

Unfortunately, all combination of pylib and pyinc, etc... yield the same effect when I try to configure python.

I am trying to install neuron on a beowulf cluster -- and on a single 64bit machine..
Beowulf has Suse Linux 10 installed and the single 64bit machine debian,
the messages are the same...

How did you install python?

I just did this
./configure --prefix=/home/me
make
make install

this creates my binaries and the python libraries in in /home/me/bin and /home/me/lib ... and python works.

then I install neuron:
./configure --prefix=/home/me --with-nrnpython=/home/me/bin/python
... + many different combination of pylib, etc.

Thank you,
Armin

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