#883 Can't compile with Eigen on Mac OS X

2.3.x
closed
nobody
None
1
2013-11-29
2013-06-11
Shyue Ping Ong
No

I am trying to get openbabel to compile on Mac OS X because I need the Python bindings. In general, I can get most of openbabel with python bindings working using the instructions I have written in this page: http://pythonhosted.org/pymatgen/installation.html#installation-tips-for-optional-libraries. Pls note that I have since upgraded to openbabel 2.3.2 and eigen3.

However, it seems that eigen3 is not detected at all. When I do

import openbabel as ob
ob.OBAlign

I get an AttributeError. Switching back to eigen2 did not work either.

Can someone advise on how to get openbabel with python working properly on a Mac? I would also suggest making those instructions available somewhere.

SP

Related

Bugs: #883

Discussion

  • Shyue Ping Ong
    Shyue Ping Ong
    2013-06-24

    Help anyone?

     
  • Noel O'Boyle
    Noel O'Boyle
    2013-06-27

    Please provide the cmake command you used and the output of running CMakeLists.txt.

     
  • Noel O'Boyle
    Noel O'Boyle
    2013-06-27

    Sorry - I meant please provide the cmake command you used and the output when you run it for the first time.

     
  • Shyue Ping Ong
    Shyue Ping Ong
    2013-06-27

    Thanks for helping.

    The cmake command I used was "cmake -DPYTHON_BINDINGS=ON -DEIGEN3_INCLUDE_DIR=../eigen3 ../ob-src 2>&1 | tee cmake.out". This is using openbabel src v 2.3.2 and eigen 3.1.3.

    The output I get is as follows:

    -- The C compiler identification is GNU 4.2.1
    -- The CXX compiler identification is Clang 4.2.0
    -- Checking whether C compiler has -isysroot
    -- Checking whether C compiler has -isysroot - yes
    -- Checking whether C compiler supports OSX deployment target flag
    -- Checking whether C compiler supports OSX deployment target flag - yes
    -- Check for working C compiler: /usr/bin/gcc
    -- Check for working C compiler: /usr/bin/gcc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Using included inchi library.
    -- Found LibXml2: /usr/lib/libxml2.dylib (found version "2.7.8")
    -- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5")
    -- Could NOT find wxWidgets (missing: wxWidgets_FOUND)
    -- Looking for conio.h
    -- Looking for conio.h - not found
    -- Looking for sys/time.h
    -- Looking for sys/time.h - found
    -- Looking for time.h
    -- Looking for time.h - found
    -- Looking for strings.h
    -- Looking for strings.h - found
    -- Looking for rpc/xdr.h
    -- Looking for rpc/xdr.h - not found
    -- Looking for regex.h
    -- Looking for regex.h - found
    -- Looking for C++ include sstream
    -- Looking for C++ include sstream - found
    -- Looking for rint
    -- Looking for rint - found
    -- Looking for snprintf
    -- Looking for snprintf - found
    -- Looking for sranddev
    -- Looking for sranddev - found
    -- Looking for strcasecmp
    -- Looking for strcasecmp - found
    -- Looking for strncasecmp
    -- Looking for strncasecmp - found
    -- Looking for dlopen in dl
    -- Looking for dlopen in dl - found
    -- Looking for sys/types.h
    -- Looking for sys/types.h - found
    -- Looking for stdint.h
    -- Looking for stdint.h - found
    -- Looking for stddef.h
    -- Looking for stddef.h - found
    -- Check size of clock_t
    -- Check size of clock_t - done
    -- Performing Test SCANDIR_NEEDS_CONST
    -- Performing Test SCANDIR_NEEDS_CONST - Failed
    -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.27.1")
    -- checking for module 'cairo'
    -- package 'cairo' not found
    -- Could NOT find Cairo. PNG output will NOT be supported.
    -- Looking for getopt
    -- Looking for getopt - found
    -- GUI will not be built
    -- Found PythonInterp: /Library/Frameworks/Python.framework/Versions/2.7/bin/python (found version "2.7.4")
    -- Found PythonLibs: /usr/lib/libpython2.7.dylib (found version "2.7.4")
    -- Python bindings will be compiled
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /Volumes/Macintosh HD2/Software/libraries/obabel/ob-build

     
  • Sorry for the long delay. For some reason, I'm not getting the bug postings by e-mail. Try installing pkg-config and see if that helps.

    http://www.freedesktop.org/wiki/Software/pkg-config/

    Supplying the path for EIGEN3 should be enough, but if things work with pkg-config, I'll be better able to find the problem. Thanks!

     
  • Shyue Ping Ong
    Shyue Ping Ong
    2013-09-26

    HI Geoff,

    We have managed to find a fix for this. It is rather tricky and we have posted the install instructions at

    http://pymatgen.org/installation.html#installation-tips-for-optional-libraries

    Maybe you could take a look and see if this is the right method. And perhaps you could modify open babel's install to better support Mac OS.

    Shyue Ping

    On Tuesday, September 24, 2013 at 8:29 AM, Geoff Hutchison wrote:

    Sorry for the long delay. For some reason, I'm not getting the bug postings by e-mail. Try installing pkg-config and see if that helps.
    http://www.freedesktop.org/wiki/Software/pkg-config/
    Supplying the path for EIGEN3 should be enough, but if things work with pkg-config, I'll be better able to find the problem. Thanks!
    [bugs:#883] (http://sourceforge.net/p/openbabel/bugs/883/) Can't compile with Eigen on Mac OS X
    Status: open
    Created: Tue Jun 11, 2013 05:07 PM UTC by Shyue Ping Ong
    Last Updated: Thu Jun 27, 2013 12:37 PM UTC
    Owner: nobody
    I am trying to get openbabel to compile on Mac OS X because I need the Python bindings. In general, I can get most of openbabel with python bindings working using the instructions I have written in this page: http://pythonhosted.org/pymatgen/installation.html#installation-tips-for-optional-libraries. Pls note that I have since upgraded to openbabel 2.3.2 and eigen3.
    However, it seems that eigen3 is not detected at all. When I do
    import openbabel as ob
    ob.OBAlign
    I get an AttributeError. Switching back to eigen2 did not work either.
    Can someone advise on how to get openbabel with python working properly on a Mac? I would also suggest making those instructions available somewhere.
    SP
    Sent from sourceforge.net (http://sourceforge.net) because you indicated interest in https://sourceforge.net/p/openbabel/bugs/883/
    To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

     

    Related

    Bugs: #883

  • Noel O'Boyle
    Noel O'Boyle
    2013-11-29

    • status: open --> closed