Re: [igraph] installing igraph 0.7.0 python version into Canopy on OSX - _igraph.so

[Blair Conn]

Hi Tamas,

So here is how it went. I did all three, although I'm not sure if you 
meant to try one at a time.


On 5/2/15 1:35 PM, Tamas Nepusz wrote:
> Hi,
>
> I think I have an idea but I'm not 100% sure. It seems that igraph is compiled
> with thread-local storage support by default (meaning that global variables are
> declared as thread-local, so in theory it should be safe to use igraph from
> multiple threads at the same time -- although it's highly experimental and not
> tested thoroughly at all, so we do not officially support this). This seems to
> be an error in the configure script because that was definitely not our
> intention at all. I will have to follow up on this later.
>
> Now, this means that when you install the C core, you get a copy of the igraph
> library somewhere in your library path where thread-local variables are
> enabled. On OS X, thread-local storage is actually emulated, and the
> ___emutls_get_address function is needed for this.
>
> The problem is then that later on you compile the Python interface, and the
> setup script of the Python interface is not able to find the installed C core
> (as you mentioned this), so it *downloads* the C core again and compiles it --
> but this time the installer explicitly passes the --disable-tls argument to the
> configure script. Then you end up with a Python interface which is expected to
> link to a C core *without* thread-local support, while the actual igraph
> library that you have on your system is compiled *with* thread-local support.
>
> I see three possible solutions if this is really the case:
>
> 1) Get rid of the existing C core installation of igraph. If you installed it
>     in /usr/local (which is what igraph does by default), you can simply remove
>     /usr/local/lib/libigraph* and /usr/local/include/igraph*
I removed both of these
> 2) Try to make the setup.py script of the Python interface find where the
>     C core was installed instead of downloading it again. By default the setup
>     script uses pkg-config to figure out where the C core is, so first try
>     typing "pkg-config --cflags --libs igraph" into a terminal and check whether
>     it is working. (It should print a bunch of compiler flags).

I had to add PKG_CONFIG_PATH to the PATH to get this to work.

-I/usr/local/include/igraph -L/usr/local/lib -ligraph


> 3) Recompile the C core with "./configure --disable-tls && make && make
>     install", then recompile the Python interface as well (just to be on the
>     safe side).

the c code ran ok with some warnings but nothing fatal.

then I re-ran the python, but I'm getting this error in Canopy, so I'm 
not sure if I properly did what you suggested in Step 1.

import igraph
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-8e950eb5d8d8> in <module>()
----> 1 import igraph

/Users/bconn/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/python_igraph-0.7.0-py2.7-macosx-10.6-x86_64.egg/igraph/__init__.py 
in <module>()
     32 # pylint: disable-msg=W0401
     33 # W0401: wildcard import
---> 34 from igraph._igraph import *
     35 from igraph._igraph import __version__, __build_date__
     36 from igraph.clustering import *

ImportError: 
dlopen(/Users/bconn/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/python_igraph-0.7.0-py2.7-macosx-10.6-x86_64.egg/igraph/_igraph.so, 
2): Symbol not found: ___emutls_get_address
  Referenced from: 
/Users/bconn/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/python_igraph-0.7.0-py2.7-macosx-10.6-x86_64.egg/igraph/_igraph.so
  Expected in: flat namespace
in 
/Users/bconn/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/python_igraph-0.7.0-py2.7-macosx-10.6-x86_64.egg/igraph/_igraph.so 


> Let me know if it didn't work so we can continue investigating.
>
> All the best,
> Tamas
Cheers,
Blair

--
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Blair Conn
Assistant Scientist
Queue Coordinator
Gemini Observatory, Chile
Ph: +56 512 205 793
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