[chimera-dev] Chimera python

[Wolfgang Lugmayr]

hi xbl,

i've a running version of chimera built from the chimera svn source with 
scipy 0.13.1 included in ../foreign/scipy.

unfortunatly this build only runs on scientific linux 6.4 because of (my 
builds?) library incompabilities with ubuntu.

e.g. when starting my distribution version on ubuntu (i cannot install 
development stuff on this server)
       from numpy.linalg import lapack_lite
       ImportError: liblapack.so.3: cannot open shared object file: No 
such file
       or directory

this is the main problem since scipy depends on numpy and numpy can be 
compiled with various different optimizing libraries e.g. blas, atlas, 
... (.numpy-site.cfg?).
in addition scipy has a lot of native code (e.g. fortran). i'm not aware 
how this will be handled by the chimera python installer as in the 
previous message.


so if you have a sl6.4, i can build you an installable version with scipy.

or if you have a developer at hand, i can give you the source patches to 
the current chimera svn version to build your own chimera distribution.

fyi:
the following files have to be patched
mk/foreign.make
foreign/GNUmakefile

new files:
foreign/scipy/GNUmakefile
foreign/scipy/scipy-0.13.1.tar.gz (original download from the scipy website)

cheers,
wolfgang



On 12/04/2013 03:57 AM, Tom Goddard wrote:
> Here is how to install a Python package for use with Chimera is described in mailing list message
>
> 	http://www.cgl.ucsf.edu/pipermail/chimera-dev/2013/000914.html
>
> Since Chimera includes its own Python to ensure version compatibility with the dozens of compiled Python modules it uses, you need to install Scipy into the Chimera Python.  This means you can't install a binary distribution with "sudo apt-get …".  Instead you need to get the Scipy source code and build it specifically for the Chimera version of Python.  This is a pain.  I have not tried installing Scipy in Chimera so I don't know how many problems you will encounter.
>
> 	Tom
>
>
> On Dec 3, 2013, at 8:08 AM, Xiao-Bo Li <x22li at cs.uwaterloo.ca> wrote:
>
>> Hello,
>>
>> I want to use scipy with Chimera because the QR factorization in numpy does not give a square Q matrix.
>>
>> However, Chimera does not allow scipy to be imported.  The only discussion of scipy I see is a post where you talk about prebuilding Scipy.   These instructions are not helpful as I do not know where to set these variables.  Can you provide me some more detailed instructions on how to use scipy with Chimera.
>>
>> I am using Ubuntu linux.
>>
>> Best,
>>
>> XBL
>> _______________________________________________
>> Chimera-dev mailing list
>> Chimera-dev at cgl.ucsf.edu
>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>
>
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