www.neuron.yale.edu

Posted: **Mon Feb 22, 2010 12:09 pm**

Hello,

I'm trying to upgrade to the latest version of Neuron.
Compilation of Interview and Neuron works fine but I can't build the nrnpython.

It seems the setup.py coming with the package is somehow broken (or it's not well formed in my systems)

This is the error

Code: Select all

mattioni@pogo:nrnpython$ python setup.py install --prefix=~/local/
  File "setup.py", line 64
    = [ epre+libdirs[0],epre+libdirs[1] ],
    ^
SyntaxError: invalid syntax

and this is the part which cause trouble:

Code: Select all

hoc_module = Extension(
      "neuron.hoc",
      ["inithoc.cpp"],
      library_dirs=libdirs,
       = [ epre+libdirs[0],epre+libdirs[1] ],
      #extra_objects = [],
      libraries = [
	"nrnpython",
        "nrnoc", "oc", "nrniv", "ivoc",
        "memacs", "meschach", "neuron_gnu", "nrnmpi",
        "scopmath", "sparse13", "sundials", "IVhines",
	"readline"
      ],
      include_dirs = include_dirs,
      define_macros=defines
    )

Follows the whole file.

Code: Select all

#setup.py
from distutils.core import setup, Extension

import sys

# NRNPYTHON_DEFINES which were enabled at configure time
extern_defines = ""
nrnpython_exec = ""
nrn_srcdir = "."
if nrn_srcdir[0] != '/' :
    nrn_srcdir = '../../' + nrn_srcdir

if nrnpython_exec!=sys.executable:
    print "Error:"
    print "NEURON configure time python: "+nrnpython_exec
    print "Python presently executing setup.py: "+sys.executable
    print "These do not match, and the should!"
    sys.exit(1)


ldefs = extern_defines.split('-D')

# if using MPI then at least for linking need special paths and libraries
mpicc_bin = "gcc"
mpicxx_bin = "g++"
import os
os.environ["CC"]=mpicc_bin
os.environ["CXX"]=mpicxx_bin

# apparently we do not need the following
#################################
## following http://code.google.com/p/maroonmpi/wiki/Installation
## hack into distutils to replace the compiler in "linker_so" with mpicxx_bin
#
#import distutils
#import distutils.unixccompiler
#
#class MPI_UnixCCompiler(distutils.unixccompiler.UnixCCompiler):
#    __set_executable = distutils.unixccompiler.UnixCCompiler.set_executable
#
#    def set_executable(self,key,value):
#	print "MPI_UnixCCompiler ", key, " | ", value
#        if key == 'linker_so' and type(value) == str:
#            value = mpicxx_bin + ' ' + ' '.join(value.split()[1:])
#
#        return self.__set_executable(key,value)
#    
#distutils.unixccompiler.UnixCCompiler = MPI_UnixCCompiler
#################################

include_dirs = [nrn_srcdir+'/src/oc', '../oc']
defines = []

libdirs = ["/homes/mattioni/local/x86_64/lib",
  "/homes/mattioni/local/x86_64/lib"
]
epre='-Wl,-R'


hoc_module = Extension(
      "neuron.hoc",
      ["inithoc.cpp"],
      library_dirs=libdirs,
       = [ epre+libdirs[0],epre+libdirs[1] ],
      #extra_objects = [],
      libraries = [
	"nrnpython",
        "nrnoc", "oc", "nrniv", "ivoc",
        "memacs", "meschach", "neuron_gnu", "nrnmpi",
        "scopmath", "sparse13", "sundials", "IVhines",
	"readline"
      ],
      include_dirs = include_dirs,
      define_macros=defines
    )



setup(name="NEURON", version="7.0",
      description = "NEURON bindings for python",
      package_dir = {'':nrn_srcdir+'/share/lib/python'},
      packages=['neuron','neuron.tests'],
      ext_modules=[hoc_module]
)

Posted: **Mon Feb 22, 2010 2:04 pm**

On a max os x that line is supposed to read
#extra_link_args = [ epre+libdirs[0],epre+libdirs[1] ],
and on all other machines it is supposed to read
extra_link_args = [ epre+libdirs[0],epre+libdirs[1] ],

I looked at the precursor file, setup.py.in which reads:
@setup_extra_link_args@ = [ epre+libdirs[0],epre+libdirs[1] ],
where configure decides what to put in place of the @...@ token.
In looking at nrn/m4/nrnpython.m4 I see that the only way this fails to
be set is if you configure with the '--with-nrnpython=dynamic' argument.
Is that how you are configuring?
Anyway, you can fix the setup.py file manually by putting in the correct
line above.

Posted: **Tue Feb 23, 2010 6:58 am**

Hi!

Actually I figured out that I was not giving the --with-nrnpython option.
that fix my setup and the installation work properly.

I misread somewhere that the python interpreter was built by default. Anyway happy ending. thanks.

www.neuron.yale.edu

Troubles in building the nrnpython for Neuron 7.1

Troubles in building the nrnpython for Neuron 7.1

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