obspy.taup import fails (gfortran underscoring issue?)

[jkmacc]

Hi, everyone. I installed obspy.taup into the Enthought Python Distro 32 bit, and don't recall having any problems with the install. When I call taup, however, I get the following error (below). I don't have any problems using taup in the EPD 64 bit distribution. I'm using OS X 10.6.8. In looking at seteup.py, there seems to be a "-fno-underscoring" flag that should be passed along. Perhaps this isn't being passed? I apologize if this has been covered already; it didn't look like the previous issue with gfortran.

Thanks in advance!

Best, Jon

In [5]: from obspy.taup import taup
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/Volumes/jkmacc/projects/TienShan/db/<ipython-input-5-faae2965f0ae> in <module>()
----> 1 from obspy.taup import taup

/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/obspy.taup-0.0.3-py2.7-macosx-10.5-i386.egg/obspy/taup/taup.py in <module>()
      2 
      3 from obspy.taup import __path__
----> 4 from util import flibtaup as lib
      5 import ctypes as C
      6 import math

/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/obspy.taup-0.0.3-py2.7-macosx-10.5-i386.egg/obspy/taup/util.py in <module>()
     31 if not flibtaup:
     32     msg = 'Could not load shared library for obspy.taup.\n\n %s' % (e)
---> 33     raise ImportError(msg)

ImportError: Could not load shared library for obspy.taup.

 dlopen(/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/obspy.taup-0.0.3-py2.7-macosx-10.5-i386.egg/obspy/taup/lib/libtaup.so, 6): Symbol not found: __gfortran_compare_string
  Referenced from: /Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/obspy.taup-0.0.3-py2.7-macosx-10.5-i386.egg/obspy/taup/lib/libtaup.so
  Expected in: flat namespace
 in /Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/obspy.taup-0.0.3-py2.7-macosx-10.5-i386.egg/obspy/taup/lib/libtaup.so

[megies]

In [3005/obspy]:

taup: not sure if this is related to the bug but this import seems odd to me.. (see #308)

[megies]

I'm not sure if this was the problem but you could try to install obspy.taup again and try it. If not it might help to post the install log here (any compiler messages/errors..?).

EDIT: Ah no, that's definitely not what was going wrong here. So could you post the install/compiler log?

best, Tobias

[jkmacc]

Tobias, thanks for thinking about it. I rebuilt taup and below is my screen output. After installing, I can import taup now, but I get a different error when I try to use it (see end)...

jkmacc% python setup.py build
running build
running build_py
creating build/lib.macosx-10.5-i386-2.7
creating build/lib.macosx-10.5-i386-2.7/obspy
copying obspy/__init__.py -> build/lib.macosx-10.5-i386-2.7/obspy
creating build/lib.macosx-10.5-i386-2.7/obspy/taup
copying obspy/taup/__init__.py -> build/lib.macosx-10.5-i386-2.7/obspy/taup
copying obspy/taup/taup.py -> build/lib.macosx-10.5-i386-2.7/obspy/taup
copying obspy/taup/util.py -> build/lib.macosx-10.5-i386-2.7/obspy/taup
creating build/lib.macosx-10.5-i386-2.7/obspy/taup/tests
copying obspy/taup/tests/__init__.py -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tests
copying obspy/taup/tests/test_taup.py -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tests
running egg_info
writing requirements to obspy.taup.egg-info/requires.txt
writing obspy.taup.egg-info/PKG-INFO
writing namespace_packages to obspy.taup.egg-info/namespace_packages.txt
writing top-level names to obspy.taup.egg-info/top_level.txt
writing dependency_links to obspy.taup.egg-info/dependency_links.txt
reading manifest file 'obspy.taup.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'docs/api/*'
writing manifest file 'obspy.taup.egg-info/SOURCES.txt'
copying obspy/taup/LICENSE.txt -> build/lib.macosx-10.5-i386-2.7/obspy/taup
copying obspy/taup/README.txt -> build/lib.macosx-10.5-i386-2.7/obspy/taup
copying obspy/taup/VERSION.txt -> build/lib.macosx-10.5-i386-2.7/obspy/taup
creating build/lib.macosx-10.5-i386-2.7/obspy/taup/src
copying obspy/taup/src/emdlv.f -> build/lib.macosx-10.5-i386-2.7/obspy/taup/src
copying obspy/taup/src/iaspei-tau.tgz -> build/lib.macosx-10.5-i386-2.7/obspy/taup/src
copying obspy/taup/src/libtau.f -> build/lib.macosx-10.5-i386-2.7/obspy/taup/src
copying obspy/taup/src/ttimes_subrout.f -> build/lib.macosx-10.5-i386-2.7/obspy/taup/src
copying obspy/taup/src/ttlim.inc -> build/lib.macosx-10.5-i386-2.7/obspy/taup/src
creating build/lib.macosx-10.5-i386-2.7/obspy/taup/tables
copying obspy/taup/tables/ak135.hed -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tables
copying obspy/taup/tables/ak135.tbl -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tables
copying obspy/taup/tables/iasp91.hed -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tables
copying obspy/taup/tables/iasp91.tbl -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tables
creating build/lib.macosx-10.5-i386-2.7/obspy/taup/tests/data
copying obspy/taup/tests/data/sample_ttimes_ak135.lst -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tests/data
copying obspy/taup/tests/data/sample_ttimes_iasp91.lst -> build/lib.macosx-10.5-i386-2.7/obspy/taup/tests/data
running build_ext
building 'libtaup' extension
creating build/temp.macosx-10.5-i386-2.7
creating build/temp.macosx-10.5-i386-2.7/obspy
creating build/temp.macosx-10.5-i386-2.7/obspy/taup
creating build/temp.macosx-10.5-i386-2.7/obspy/taup/src
gfortran obspy/taup/src/emdlv.f -o build/temp.macosx-10.5-i386-2.7/obspy/taup/src/emdlv.o -c -fno-underscoring
gfortran obspy/taup/src/libtau.f -o build/temp.macosx-10.5-i386-2.7/obspy/taup/src/libtau.o -c -fno-underscoring
gfortran obspy/taup/src/ttimes_subrout.f -o build/temp.macosx-10.5-i386-2.7/obspy/taup/src/ttimes_subrout.o -c -fno-underscoring
creating build/lib.macosx-10.5-i386-2.7/obspy/taup/lib
gcc -bundle -undefined dynamic_lookup -g -arch i386 build/temp.macosx-10.5-i386-2.7/obspy/taup/src/emdlv.o build/temp.macosx-10.5-i386-2.7/obspy/taup/src/libtau.o build/temp.macosx-10.5-i386-2.7/obspy/taup/src/ttimes_subrout.o -lgfortran -o build/lib.macosx-10.5-i386-2.7/obspy/taup/lib/libtaup.so
ld: warning: in build/temp.macosx-10.5-i386-2.7/obspy/taup/src/emdlv.o, file was built for unsupported file format which is not the architecture being linked (i386)
ld: warning: in build/temp.macosx-10.5-i386-2.7/obspy/taup/src/libtau.o, file was built for unsupported file format which is not the architecture being linked (i386)
ld: warning: in build/temp.macosx-10.5-i386-2.7/obspy/taup/src/ttimes_subrout.o, file was built for unsupported file format which is not the architecture being linked (i386)

In [1]: from obspy.taup import taup

In [2]: taup.getTravelTimes(78.8, 100, model='ak135')
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/Users/jkmacc/<ipython-input-2-c3db94c548c5> in <module>()
----> 1 taup.getTravelTimes(78.8, 100, model='ak135')

/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/site-packages/obspy.taup-0.0.3-py2.7-macosx-10.5-i386.egg/obspy/taup/taup.pyc in getTravelTimes(delta, depth, model)
     70     flags = ['F_CONTIGUOUS', 'ALIGNED', 'WRITEABLE']
     71 
---> 72     lib.ttimes(C.byref(delta), C.byref(depth), modnam,
     73                phase_names,
     74                tt.ctypes.data_as(C.POINTER(C.c_float)),

/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/ctypes/__init__.pyc in __getattr__(self, name)
    364         if name.startswith('__') and name.endswith('__'):
    365             raise AttributeError(name)
--> 366         func = self.__getitem__(name)
    367         setattr(self, name, func)
    368         return func

/Library/Frameworks/Python.framework/Versions/7.1/lib/python2.7/ctypes/__init__.pyc in __getitem__(self, name_or_ordinal)
    369 
    370     def __getitem__(self, name_or_ordinal):
--> 371         func = self._FuncPtr((name_or_ordinal, self))
    372         if not isinstance(name_or_ordinal, (int, long)):
    373             func.__name__ = name_or_ordinal

AttributeError: dlsym(0x5100d60, ttimes): symbol not found

I get see ttimes in build/temp.macosx-10.5-i386-2.7/obspy/taup/src/ttimes_subrout.o (build/lib.macosx-10.5-i386-2.7/obspy/taup/lib/libtaup.so has almost no symbols in it). It looks like the final gcc build call failed.

jkmacc% nm temp.macosx-10.5-i386-2.7/obspy/taup/src/ttimes_subrout.o | grep ttimes
0000000000000000 T _ttimes
00000000000010a0 S _ttimes.eh

[krischer]

Hi Jon,

all symbols need to be in libtaup.so because that is the file actually called by ctypes.

Can you try to execute the following command in the src subdirectory?

gfortran -fno-underscoring -arch i386 -dynamiclib -lgfortran emdlv.f libtau.f ttimes_subrout.f -o libtaup.so

This will create a 32bit shared library which should contain all necessary symbols. Copying this to the lib subdirectory and replacing its libtaup.so should also work fine.

If this works than its either a issue with your compiler setup or with obspy.taup's setup.py.

Thanks for your help!

Lion

[jkmacc]

That did it!

Didn't work:

gcc -bundle -undefined dynamic_lookup -g -arch i386 emdlv.o libtau.o ttimes_subrout.o -lgfortran -o libtaup.so

Worked:

gfortran -fno-underscoring -arch i386 -dynamiclib -lgfortran emdlv.f libtau.f ttimes_subrout.f -o libtaup.so

I don't know why gcc instead of gfortran was called in my initial install, but it seems that the latter did the trick. Thanks again!

[krischer]

Hey.

Glad it worked. Unfortunately that does not really solve the problem because setup.py should also be able to correctly compile it. Not sure how to solve this. Your command should, in theory, also work. In your case setup.py uses gfortran to compile the source code to object files and then simply uses gcc to link them together. I'll look into it and maybe I can force setup.py into using a specific command to link the files.

Best wishes.

Lion