execution on OSX 10.12.2

[jtlz2]

@darafferty After a successful build and root install on a Mac, python -c 'import bdsf' throws the following:

Traceback (most recent call last):
File "", line 1, in
File "bdsf/init.py", line 19, in
from collapse import Op_collapse
File "bdsf/collapse.py", line 10, in
import _cbdsm
ImportError: dlopen(bdsf/_cbdsm.so, 2): Symbol not found: __ZN5boost6python7objects15function_objectERKNS1_11py_functionERKSt4pairIPKNS0_6detail7keywordES9_E
Referenced from: /Users/myname/src/PyBDSF/build/lib.macosx-10.6-x86_64-2.7/bdsf/_cbdsm.so
Expected in: flat namespace
in /Users/jtlz2/src/PyBDSF/build/lib.macosx-10.6-x86_64-2.7/bdsf/_cbdsm.so

Is this just a name mangling issue? I can't see where to put a -stdlib=libstdc++ (if it is that).

Let me know if you need any more info. Thanks!

[tammojan]

You could alter setup.py by adding extra_link_args and extra_compile_args to the extensions.
I have not been able to install pybdsf on a mac yet, so if you have success please report back!

[jtlz2]

@tammojan -stdlib=libstdc++ didn't work via that route.

An issue with my boost compilation?

[jtlz2]

http://stackoverflow.com/questions/35006614/what-does-symbol-not-found-expected-in-flat-namespace-actually-mean ?

[tammojan]

When compiling boost, was libc++ or libstdc++ used?

[jtlz2]

Is there an easy way to find out? :\

[tammojan]

On my machine (10.12.3, where I installed boost-python with homebrew), it's using libc++:

/usr/local/lib$ otool -L /usr/local/lib/libboost_python.dylib
libboost_python.dylib:
	/usr/local/opt/boost-python/lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)

[jtlz2]

Ditto:

/usr/local/lib/libboost_python.dylib:
/usr/local/opt/boost-python/lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)

[jtlz2]

 extra_link_args=["-std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7"],
 extra_compile_args=["-std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7"]

fixes the boost error, but now there's a gfortran error:

Traceback (most recent call last):
File "", line 1, in
File "bdsf/init.py", line 19, in
from collapse import Op_collapse
File "bdsf/collapse.py", line 10, in
import _cbdsm
ImportError: dlopen(bdsf/_cbdsm.so, 2): Symbol not found: __gfortran_stop_numeric_f08
Referenced from: /Users/jtlz2/src/PyBDSF/build/lib.macosx-10.6-x86_64-2.7/bdsf/_cbdsm.so
Expected in: flat namespace
in /Users/jtlz2/src/PyBDSF/build/lib.macosx-10.6-x86_64-2.7/bdsf/_cbdsm.so

[darafferty]

I have it working on 10.12.3, but I didn't use homebrew (I used anaconda to install boost and got gfortran from https://gcc.gnu.org/wiki/GFortranBinaries). I also had to alter setup.py as follows:

--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@ def find_boost():
             boost_python = "boost_python"
     elif system == 'Darwin':
         if sys.version_info[0] == 2:
-            boost_python = "boost_python-mt"
+            boost_python = "boost_python"
         else:
             boost_python = "boost_python3-mt"
     return boost_python
@@ -65,8 +65,8 @@ extensions.append(Extension(
              "src/c++/stat.cc",
              "src/c++/num_util/num_util.cpp"],
      libraries=['minpack', 'port3', 'gfortran', boost_python],
-     include_dirs=["src/c++"],
-     library_dirs=[join(srcpath,"minpack"), join(srcpath,"port3")]
+     include_dirs=["src/c++", '/anaconda/include'],
+     library_dirs=[join(srcpath,"minpack"), join(srcpath,"port3"), '/anaconda/lib/', '/usr/local/gfortran/lib/']
      ))

[jtlz2]

@tammojan @darafferty You both beat me to it, but I also now have it working (ugly I know - sensitive to version of gfortran):

 boost_python = "boost_python"

...

 library_dirs=["/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6",join(srcpath,"minpack"), join(srcpath,"port3")],
 extra_link_args=["-std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7"],extra_compile_args=["-std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7"]

Thanks both

[mattia-vaccari]

I went through all of the above suggestions as closely as possible (modulo my using macports in /opt/local for my software) but still get the following missing symbol error at start-up.

ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/bdsf-1.8.9-py2.7-macosx-10.10-x86_64.egg/bdsf/_cbdsm.so, 2): Symbol not found: __ZNSt8ios_base4InitD1Ev
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/bdsf-1.8.9-py2.7-macosx-10.10-x86_64.egg/bdsf/_cbdsm.so
Expected in: flat namespace
in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/bdsf-1.8.9-py2.7-macosx-10.10-x86_64.egg/bdsf/_cbdsm.so

where the ios_base issue (upon some googling) seems to be related to libstdc++

any thoughts?

[tammojan]

On OSX, the best way seems to be to use libc++ instead of libstdc++. Could you check to which of those boost-python links?

[tammojan]

If necessary, you can build your own boost-python, casacore/casacore#596 (comment)