I just installed relax on a Mac using fink.
relax-py26 1.3.4-2 Protein dynamics by NMR relax. data analysis
I also installed the dependencies using fink.
minfx-py26 1.0.2-1 The minfx optimisation library
numpy-py26 [virtual package]
python26 1:2.6.4-101 Interpreted, object-oriented language
scientificpython-py26 2.8-1 Python modules for scientific
computing
scons 0.98.3-1 Python-based build tool
I created a link in the relax directory pointing to the minfx directory:
minfx@ -> /sw/lib/python2.6/site-packages/minfx/
This should not be necessary. If there are any strange optimisation
issues, this should be the first place to look.
In fact, if the link is not present, relax complains about minfx not being
installed...
Ah, this is an indication that there are 2 python versions present!!!
I have just added a new command line option to relax to help work out
what is happening. I'm guessing you have a repository copy from the
1.3 line? If so, update this copy (for those who don't know, you
type):
$ svn up
and then run one of:
$ relax -i
$ relax --info
This should tell you all you need to know about versions, etc.! I can
add other useful info later on - i.e. modules installed or missing and
their versions.
After, I launched relax but got the following warning:
========
ImportError: dlopen(/sw/lib/relax-py26/maths_fns/relax_fit.so, 2): no
suitable image found. Did find:
/sw/lib/relax-py26/maths_fns/relax_fit.so: mach-o, but wrong
architecture
Relaxation curve fitting is unavailable, try compiling the C modules.
========
Try "scons clean_all" followed by "scons". Does the file
/sw/lib/relax-py26/maths_fns/relax_fit.so exist? This will be a
problem for curve-fitting!
"scons clean_all" works fine and then, "scons" creates the "relax_fit.so"
executable. The file type (obtained from the command "file") is as follows:
"Mach-O bundle i386".
Is it what it's supposed to be ?
(I am really new to Mac...)
I really have no idea either. Maybe someone else on this list knows
something? It could actually be a version issue again as maybe relax
is running with an old python version but scons build the module for
the 2.6 version?
Concerning the test-suite, there were nultiple errors:
System tests
4 failures + 20 errors
Unit tests
12 errors
The unit tests errors were all the same:
======
Traceback (most recent call last):
File
"/sw/lib/relax-py26/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py",
line 54, in setUp
self.data = Scientific_data()
File "/sw/lib/relax-py26/generic_fns/structure/scientific.py", line
60, in __init__
raise RelaxError, "The Scientific python PDB module
Scientific.IO.PDB could not be imported."
RelaxError: RelaxError: The Scientific python PDB module
Scientific.IO.PDB could not be imported.
======
...
I guess all these errors are not normal...
Any idea to help me debug this issue ?
Thank you !!!
This is normal as Scientific python is not installed. Maybe it would
be good to add a new section to the test suite listing the installed
and missing modules, and then disabling the relevant system and unit
tests (scientific-python, relax curve-fitting C modules, etc.) if
missing. This will be a bit of work though, hence why I haven't done
it yet! I would guess that all the failures are due to these 2
missing pieces, but it's hard to tell.
Scientific Python is installed...
scientificpython-py26 2.8-1 Python modules for scientific computing
Maybe, yes, it would be good to simply give a warning for missing
dependencies and avoid the tests to be performed...
Thanks for your insights !
This could be again related to Python versions, with Scientific Python
installed for Python 2.6 but relax running with Python 1.5 (Mac Unix
software versions are painfully old :P). I hope this helps.
Regards,
Edward
Re: relax on Mac with fink