Re: relax on Mac with fink -- February 24, 2010 - 15:31

Edward,   
     I'll try to find some time to look at these issues over the
weekend with the current 1.3 line code. As far as I recall,
1.3.4 still had some bogus testsuite failures on Darwin intel that
were fixed for the next release of relax 1.3.x.
              Jack


On Tue, Feb 23, 2010 at 02:57:23PM +0100, Edward d'Auvergne wrote:
> Hi,
>
> It might be worth talking with Jack Howarth (howarth att bromo dott
> med dott uc dott edu) as he is the maintainer of the relax fink
> packages.  You can see our previous discussions about fink at:
>
> http://www.google.com/search?q=fink&btnG=Google+Search&domains=http%3A%2F%2Fnmr-relax.com&sitesearch=https%3A%2F%2Fmail.gna.org%2Fpublic%2Frelax-users
>
> He modified the sconstruct script for this, but I don't think this was
> merged upstream (it's not in the 1.3 line).  Maybe all of these
> problems is because one of the other essential components of fink have
> been upgraded (numpy, python, etc.) causing a breakage in the relax C
> modules and in the Scientific python module.
>
> I you have the time and would like to try to get the 1.3 line test
> suite passing 100% and attempt to deposit the newest relax versions
> into fink, this would be appreciated.  relax should run without
> problems on Mac OS X, and it shouldn't be too hard to modify relax for
> 100% compatibility.  The only problem for me is that I don't have Mac
> hardware.
>
> Cheers,
>
> Edward
>
>
> On 22 February 2010 19:16, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> 
> wrote:
> > Hi Ed,
> >
> > Unfortunately, the problem here arises from the fink version of relax, 
> > i.e.
> > 1.3.4.
> > Hence, the '-i' option is unavailable.
> >
> > For python, I indeed have two versions installed...
> >    2.6: standard version
> >    2.5: for rdiff-backup...
> >
> > For the sconstruct file, it was modified by fink. Hence, it seems the fink
> > version of relax might be problematic...
> >
> > ...
> >
> > In order to see if the repository version is also having troubles, I
> > installed it (as well as the minfx repository version) and tested it.
> > The compilation with scons worked fine and relax does not complain anymore
> > about the relax_fit.so file...
> > However, there are still 12 errors from the unit tests and 1 failure and 
> > 16
> > errors from the system tests.
> >
> > It is better than with the fink version, although ScientificPython still 
> > not
> > works...
> > How should ScientificPython be installed ?
> > Presently, it is installed from fink...
> >
> > ...
> >
> > Here is the output from 'relax -i':
> >
> > ==========
> > Hardware information:
> >    Machine:                 i386
> >    Processor:               i386
> >
> > System information:
> >    System:                  Darwin
> >    Release:                 10.2.0
> >    Version:                 Darwin Kernel Version 10.2.0: Tue Nov  3
> > 10:37:10 PST 2009; root:xnu-1486.2.11~1/RELEASE_I386
> >    Mac version:             10.6.2 (, , ) i386
> >    Distribution:
> >    Full platform string:    Darwin-10.2.0-i386-64bit
> >
> > Software information:
> >    Architecture:            64bit
> >    Python version:          2.6.1
> >    Python branch:           tags/r261
> >    Python build:            r261:67515, Jul  7 2009 23:51:51
> >    Python compiler:         GCC 4.2.1 (Apple Inc. build 5646)
> >    Python implementation:   CPython
> >    Python revision:         67515
> >    Numpy version:           1.2.1
> >    Libc version:
> >    Network name:            dhcp-160-189.rsvs.ulaval.ca
> > ==========
> >
> > Any idea ?
> >
> >
> > Séb  :)
> >
> >
> >
> >
> > On 10-02-22 12:41 PM, Edward d'Auvergne wrote:
> > > Hi Seb,
> > >
> > > Could you paste the output of 'relax -i'?  This will help in working
> > > out what is happening and will be useful to have on record.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > > On 22 February 2010 18:30, Edward d'Auvergne<edward@xxxxxxxxxxxxx>  
> > > wrote:
> > >
> > > > > > > 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
> >
> > --
> > Sébastien Morin
> > PhD Student
> > S. Gagné NMR Laboratory
> > Université Laval&  PROTEO
> > Québec, Canada