Re: Relax [relaxation dispersion] [2] -- July 25, 2013 - 17:33

Hi,

If you are totally stuck, as this is an nasty scons installation
issue, you can manually compile the C modules.  From the message which
missed the mailing list (visible below), I have modified the command
that scons normally runs for your Mac OS X system:

gcc -o target_functions/c_chi2.os -c
-I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7
-arch i386 -arch x86_64 -fPIC target_functions/c_chi2.c
gcc -o target_functions/exponential.os -c
-I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7
-arch i386 -arch x86_64 -fPIC target_functions/exponential.c
gcc -o target_functions/relax_fit.os -c
-I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7
-arch i386 -arch x86_64 -fPIC target_functions/relax_fit.c
gcc -o target_functions/relax_fit.so -bundle -bundle_loader
/Library/Frameworks/Python.framework/Versions/7.3/bin/python2.7
-dynamic -undefined dynamic_lookup -arch i386 -arch x86_64
target_functions/c_chi2.os target_functions/exponential.os
target_functions/relax_fit.os

This builds a 32 and 64-bit module for your specific Python Framework,
which should run fine.  I removed the ppc target that I use for the
released Mac OS X application.  These need to be run in the base relax
directory.  I hope this solves the problem.

Regards,

Edward



On 25 July 2013 17:05, Dominique Marion (IBS) <Dominique.Marion@xxxxxx> wrote:
> Hi,
>
> Here is the output of the command you suggested.  One module is not
> compiled... but I don't know how to solve it. On the other hand, the error
> message issued by scons is still there.
>
> Dominique
>
> ________________________________
>
> ImportError: relaxation curve fitting is unavailable, the corresponding C
> modules have not been compiled.
>
> Processor fabric:  Uni-processor.
>
>
> Hardware information:
>     Machine:                 x86_64
>     Processor:               i386
>     Endianness:              little
>     Total RAM size:          ? Mb
>     Total swap size:         ? Mb
>
> Operating system information:
>     System:                  Darwin
>     Release:                 12.4.0
>     Version:                 Darwin Kernel Version 12.4.0: Wed May  1
> 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64
>     Mac version:             10.8.4 (, , ) x86_64
>     Distribution:
>     Full platform string:    Darwin-12.4.0-x86_64-i386-32bit
>
> Python information:
>     Architecture:            32bit
>     Python version:          2.7.3
>     Python branch:
>     Python build:            default, Apr 12 2012 11:28:34
>     Python compiler:         GCC 4.0.1 (Apple Inc. build 5493)
>     Libc version:
>     Python implementation:   CPython
>     Python revision:
>     Python executable:
> /Library/Frameworks/Python.framework/Versions/7.3/Resources/Python.app/Contents/MacOS/Python
>     Python flags:            sys.flags(debug=0, py3k_warning=0,
> division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
> dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
> tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
>     Python float info:       sys.float_info(max=1.7976931348623157e+308,
> max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
> radix=2, rounds=1)
>     Python module path:
> ['/Volumes/Overhauser/Dominique/Documents/Documents_2013/Juillet_2013/relax_disp',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/setuptools-0.9.7-py2.7.egg',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python27.zip',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/plat-darwin',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/plat-mac',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/plat-mac/lib-scriptpackages',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/lib-tk',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/lib-old',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/lib-dynload',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages',
> '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/PIL',
> '/Library/Python/2.7/site-packages']
>
> Python packages and modules (most are optional):
>
> Name               Installed    Version                   Path
> minfx              True         1.0.5
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/minfx
> bmrblib            True         1.0.3
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/bmrblib
> numpy              True         1.6.1
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy
> scipy              True         0.10.1
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/scipy
> wxPython           True         2.8.10.1 (mac-unicode)
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/wx
> mpi4py             False
> epydoc             False
> optparse           True         1.5.3
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/optparse.pyc
> readline           True
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/lib-dynload/readline.so
> profile            True
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/profile.pyc
> bz2                True
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/lib-dynload/bz2.so
> gzip               True
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/gzip.pyc
> io                 True
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/io.pyc
> xml                True         0.8.4 (internal)
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/xml/__init__.pyc
> xml.dom.minidom    True
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/xml/dom/minidom.pyc
>
> relax information:
>     Version:                 repository checkout
>     Processor fabric:        Uni-processor.
>
> relax C modules:
>
> Module                        Compiled    File type    Path
> target_functions.relax_fit    False
>
>
> [DominiqueMacBook:Documents_2013/Juillet_2013/relax_disp] Dominique%
>
> On 25/7/13 14:25 , Edward d'Auvergne wrote:
>
> One useful trick for finding out what is missing it to run relax with:
>
> $ relax --info
>
> It will print out a status report of all the modules.  However this
> minimally requires Python, numpy, and minfx to be installed.
>
> Regards,
>
> Edward
>
>
>
> On 25 July 2013 14:22, Dominique Marion (IBS) <Dominique.Marion@xxxxxx>
> wrote:
>
> I have installed again minfx... but some dependency seems to be missing.
>
> Dominique
>
>  >> scons
> scons: Reading SConscript files ...
> The dependency 'minfx' has not been installed (see
> https://gna.org/projects/minfx/).
>
>
>
> On 25/7/13 14:15 , Edward d'Auvergne wrote:
>
> Ah, I have to add that to the wiki page
> (http://wiki.nmr-relax.com/Installation_linux).  To compile the C
> modules, if the instructions on that page have been followed and the
> python-headers and scons are installed, is simply a matter of typing:
>
> $ scons
>
> This needs to be in the relax_disp base directory.
>
> Regards,
>
> Edward