Re: compiling 1.3.4 against python 2.6? -- August 17, 2009 - 19:09

Hi,

I don't think this is an issue, as the include directories should only
contain *.h C header files.  Can you find any *.h python files which
are not in /sw/include/python2.6?  The second include directory is
just for the numpy *.h files.

Cheers,

Edward


2009/8/17 Jack Howarth <howarth@xxxxxxxxxxxxxxxx>:
> Edward,
>   I'll try these tonight as I don't have my laptop with me
> today. I do notice that if I compare the linkage of the two
> pythons....
>
> [prrg4:~] howarth% otool -L /sw/bin/python2.5
> /sw/bin/python2.5:
>        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 111.1.3)
>        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current 
> version 1.0.0)
> [prrg4:~] howarth% otool -L /sw/bin/python2.6
> /sw/bin/python2.6:
>        /sw/lib/python2.6/config/libpython2.6.dylib (compatibility version 
> 2.6.0, current version 2.6.0)
>        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 111.1.4)
>        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current 
> version 1.0.0)
>
> It would appear that...
>
> gcc -o maths_fns/relax_fit.so -bundle -bundle_loader /sw/bin/python2.6 
> -dynamic maths_fns/c_chi2.os maths_fns/exponential.os maths_fns/relax_fit.os
>
> ...isn't picking up /sw/lib/python2.6/config/libpython2.6.dylib for linkage.
>                    Jack
>
>
> On Mon, Aug 17, 2009 at 06:34:33PM +0200, Edward d'Auvergne wrote:
> > Hi,
> >
> > Does one of the following commands compile the module (with the
> > test-suite passing as well)?
> >
> > $ gcc -o maths_fns/relax_fit.so /sw/bin/python2.6 maths_fns/c_chi2.os
> > maths_fns/exponential.os maths_fns/relax_fit.os
> > $ gcc -o maths_fns/relax_fit.so /sw/bin/python2.6 -dynamic
> > maths_fns/c_chi2.os maths_fns/exponential.os maths_fns/relax_fit.os
> > $ gcc -o maths_fns/relax_fit.so -bundle_loader /sw/bin/python2.6
> > -dynamic maths_fns/c_chi2.os maths_fns/exponential.os
> > maths_fns/relax_fit.os
> > $ gcc -o maths_fns/relax_fit.so -bundle /sw/bin/python2.6 -dynamic
> > maths_fns/c_chi2.os maths_fns/exponential.os maths_fns/relax_fit.os
> > $ gcc -o maths_fns/relax_fit.so -module -bundle -bundle_loader
> > /sw/bin/python2.6 maths_fns/c_chi2.os maths_fns/exponential.os
> > maths_fns/relax_fit.os
> > $ gcc -o maths_fns/relax_fit.so -module -bundle -bundle_loader
> > /sw/bin/python2.6 -dynamic maths_fns/c_chi2.os
> > maths_fns/exponential.os maths_fns/relax_fit.os
> >
> > Cheers,
> >
> > Edward
> >
> >
> > 2009/8/17 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > Hi,
> > >
> > > The way we can solve this issue is to first type the gcc linking
> > > command by hand, rather than using scons.  Then once all is
> > > functional, I can fix the Scons script.  Here is what Douglas Kojetin
> > > did to make this work
> > > (https://mail.gna.org/public/relax-devel/2006-11/msg00092.html), and
> > > then I tailored the scons script to match.  If you cut an past this
> > > gcc command, can you compile the modules and run the system test
> > > without failures?  Also, once this is all functional, I would like to
> > > get your changes (well, modified to be compatible with all other
> > > operating systems) into the repository so that it is easier for you
> > > next time.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >
> > > 2009/8/17 Jack Howarth <howarth@xxxxxxxxxxxxxxxx>:
> > > > Edward,
> > > >   I'll have to look into that as I'm not very familar with scons.
> > > > Currently for 1.3.3, it is sufficient to use...
> > > >
> > > > --- relax-1.3.0.orig/relax      2007-02-19 00:36:06.000000000 -0500
> > > > +++ relax-1.3.0/relax   2008-08-11 02:13:30.000000000 -0400
> > > > @@ -1,4 +1,4 @@
> > > > -#! /usr/bin/env python
> > > > +#! /usr/bin/env python2.X
> > > >
> > > >  ###############################################################################
> > > >  #                                                                      
> > > >        #
> > > > --- relax-1.3.0/scons/install.py.sav    2008-08-10 15:31:01.000000000 
> > > > -0400
> > > > +++ relax-1.3.0/scons/install.py        2008-08-10 16:01:22.000000000 
> > > > -0400
> > > > @@ -112,8 +112,8 @@
> > > >     ###############
> > > >
> > > >     # Run relax to create the *.pyc files.
> > > > -    print "\nRunning relax to create the byte-compiled *.pyc files."
> > > > -    system(env['SYMLINK'] + " --test")
> > > > +    # print "\nRunning relax to create the byte-compiled *.pyc files."
> > > > +    # system(env['SYMLINK'] + " --test")
> > > >
> > > >     # Final print out.
> > > >     print "\n\n\n"
> > > > --- relax-1.3.0.orig/sconstruct 2007-02-19 00:36:06.000000000 -0500
> > > > +++ relax-1.3.0/sconstruct      2008-08-11 02:02:56.000000000 -0400
> > > > @@ -94,7 +94,7 @@
> > > >     SYS = SYSTEM
> > > >
> > > >     # Mac OS X installation path.
> > > > -    INSTALL_PATH = sys.prefix + sep + 'local'
> > > > +    INSTALL_PATH = 'FINK_INSTALL_DIR' + sep + 'lib'
> > > >
> > > >
> > > >  # All other operating systems.
> > > > @@ -111,16 +111,15 @@
> > > >  ###############
> > > >
> > > >  # Relax installation directory.
> > > > -RELAX_PATH = INSTALL_PATH + sep + 'relax'
> > > > +RELAX_PATH = INSTALL_PATH + sep + 'relax-py2X'
> > > >
> > > >  # Installation path for binaries.
> > > > -BIN_PATH = INSTALL_PATH + sep + 'bin'
> > > > +BIN_PATH = 'FINK_INSTALL_DIR' + sep + 'bin'
> > > >
> > > >  # Symbolic link installation path.
> > > >  SYMLINK = BIN_PATH + sep + 'relax'
> > > >
> > > >
> > > > -
> > > >  # The distribution files.
> > > >  #########################
> > > >
> > > > @@ -486,7 +485,7 @@
> > > >
> > > >         # Catch Mac OS X and send the correct command line options to 
> > > > the linker (these may become redundant as SCons improves).
> > > >         if env['PLATFORM'] == 'darwin':
> > > > -            env.Append(LINKFLAGS = ['-bundle', '-bundle_loader', 
> > > > sys.prefix + path.sep + 'bin' + path.sep + 'python', '-dynamic'])
> > > > +            env.Append(LINKFLAGS = ['-bundle', '-bundle_loader', 
> > > > sys.prefix + path.sep + 'bin' + path.sep + 'python2.X', '-dynamic'])
> > > >             env['SHLINKFLAGS'] = SCons.Util.CLVar('$LINKFLAGS')
> > > >             env['SHLIBSUFFIX'] = '.so'
> > > >
> > > >
> > > > to build against the fink python24 and python25 packages.
> > > >                 Jack
> > > >
> > > > On Mon, Aug 17, 2009 at 03:55:06PM +0200, Edward d'Auvergne wrote:
> > > > > Hi,
> > > > >
> > > > > It could be, that Python 2.6 dynamically linked libraries are now
> > > > > compiled differently to earlier Python versions.  I'll have to look
> > > > > that up as well.  Would you know the linker options now required?
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > > 2009/8/17 Jack Howarth <howarth@xxxxxxxxxxxxxxxx>:
> > > > > > Edward,
> > > > > >   I think I see the problem. The link line is missing a linkage on 
> > > > > > either
> > > > > > /sw/lib/python2.6/config/libpython2.6.a or 
> > > > > > /sw/lib/python2.6/config/libpython2.6,dylib.
> > > > > > What do you have for the linkage of maths_fns/relax_fit.so on linux? 
> > > > > > Does
> > > > > > that build explicitly link in the python library?
> > > > > >                  Jack
> > > > > >
> > > > > >
> > > > > > On Mon, Aug 17, 2009 at 11:50:10AM +0200, Edward d'Auvergne wrote:
> > > > > > > Hi,
> > > > > > >
> > > > > > > Thank you for building these packages (or at least attempting for 
> > > > > > > now
> > > > > > > ;).  I'm still looking into the problem, but it's looking like the
> > > > > > > Python header files are missing or are from an old version.  Do you
> > > > > > > know if this could be the issue, that the Python development 
> > > > > > > packages
> > > > > > > are out of date or are missing?
> > > > > > >
> > > > > > > Cheers,
> > > > > > >
> > > > > > > Edward
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Sun, Aug 16, 2009 at 4:08 AM, Jack 
> > > > > > > Howarth<howarth@xxxxxxxxxxxxxxxx> wrote:
> > > > > > > > Edward,
> > > > > > > >   I am trying to build updated relax-py packaging
> > > > > > > > for fink using the 1.3.4 release on x86_64 fink
> > > > > > > > with python2.6. Although your web page indicates
> > > > > > > > that the binaries available are built against
> > > > > > > > python 2.5 and 2.6, I am seeing build failures
> > > > > > > > when I try here with scons 1.2.0...
> > > > > > > >
> > > > > > > > /sw/bin/python2.6 /sw/bin/scons
> > > > > > > > scons: Reading SConscript files ...
> > > > > > > > scons: done reading SConscript files.
> > > > > > > > scons: Building targets ...
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > ###########################
> > > > > > > > # Compiling the C modules #
> > > > > > > > ###########################
> > > > > > > >
> > > > > > > >
> > > > > > > > Building the relaxation curve fitting module 
> > > > > > > > 'maths_fns/relax_fit.so'
> > > > > > > >
> > > > > > > > gcc -o maths_fns/c_chi2.os -c -I/sw/include/python2.6 
> > > > > > > > -I/sw/lib/python2.6/site-packages/numpy/core/include -fPIC 
> > > > > > > > maths_fns/c_chi2.c
> > > > > > > > gcc -o maths_fns/exponential.os -c -I/sw/include/python2.6 
> > > > > > > > -I/sw/lib/python2.6/site-packages/numpy/core/include -fPIC 
> > > > > > > > maths_fns/exponential.c
> > > > > > > > gcc -o maths_fns/relax_fit.os -c -I/sw/include/python2.6 
> > > > > > > > -I/sw/lib/python2.6/site-packages/numpy/core/include -fPIC 
> > > > > > > > maths_fns/relax_fit.c
> > > > > > > > gcc -o maths_fns/relax_fit.so -bundle -bundle_loader 
> > > > > > > > /sw/bin/python2.6 -dynamic maths_fns/c_chi2.os 
> > > > > > > > maths_fns/exponential.os maths_fns/relax_fit.os
> > > > > > > > Undefined symbols:
> > > > > > > >  "_PyArg_ParseTupleAndKeywords", referenced from:
> > > > > > > >      _setup in relax_fit.os
> > > > > > > >  "_PyErr_Print", referenced from:
> > > > > > > >      _initrelax_fit in relax_fit.os
> > > > > > > >  "_Py_InitModule4_64", referenced from:
> > > > > > > >      _initrelax_fit in relax_fit.os
> > > > > > > >  "_PyArg_ParseTuple", referenced from:
> > > > > > > >      _func in relax_fit.os
> > > > > > > >      _dfunc in relax_fit.os
> > > > > > > >  "_PyExc_RuntimeError", referenced from:
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >  "_PyList_New", referenced from:
> > > > > > > >      _back_calc_I in relax_fit.os
> > > > > > > >  "__Py_NoneStruct", referenced from:
> > > > > > > >      _setup in relax_fit.os
> > > > > > > >      _setup in relax_fit.os
> > > > > > > >      _setup in relax_fit.os
> > > > > > > >  "_PyExc_ImportError", referenced from:
> > > > > > > >      _initrelax_fit in relax_fit.os
> > > > > > > >  "_PyCObject_AsVoidPtr", referenced from:
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >  "_PyCObject_Type", referenced from:
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >  "_PyImport_ImportModule", referenced from:
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >  "_PyErr_SetString", referenced from:
> > > > > > > >      _initrelax_fit in relax_fit.os
> > > > > > > >  "_PyErr_Format", referenced from:
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >  "_PyList_SetItem", referenced from:
> > > > > > > >      _back_calc_I in relax_fit.os
> > > > > > > >  "_PyObject_GetAttrString", referenced from:
> > > > > > > >      __import_array in exponential.os
> > > > > > > >      __import_array in relax_fit.os
> > > > > > > >  "_Py_BuildValue", referenced from:
> > > > > > > >      _func in relax_fit.os
> > > > > > > >      _d2func in relax_fit.os
> > > > > > > >      _back_calc_I in relax_fit.os
> > > > > > > > ld: symbol(s) not found
> > > > > > > >
> > > > > > > > Is the 1.3.4 release really python2.6 compatible or do I need 
> > > > > > > > additional
> > > > > > > > patches? Thanks in advance for any information.
> > > > > > > >              Jack
> > > > > > > > ps I am updating the minfx-py package to the newer 1.0.2 release 
> > > > > > > > of
> > > > > > > > course for the python 2.6 compatibility changes.
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > relax (http://nmr-relax.com)
> > > > > > > >
> > > > > > > > This is the relax-users mailing list
> > > > > > > > relax-users@xxxxxxx
> > > > > > > >
> > > > > > > > To unsubscribe from this list, get a password
> > > > > > > > reminder, or change your subscription options,
> > > > > > > > visit the list information page at
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