Getting "django.core.exceptions.ImproperlyConfigured: GEOS is required and has not been detected." although GEOS is installed

Question

I'm running Django 1.8 and Python 3.4 on Ubuntu 14.04 LTS. Just recently, my Django app has been reporting that GEOS is not present. GEOS is installed and libgeos_c.so is where it's supposed to be (/usr/lib/). My code seems fine. It is the source of a docker image which still works. This seems to indicate an os/incompatibility issue. Any help would be much appreciated.

The full traceback is

Traceback (most recent call last):
  File "<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydevd.py", line 2358, in <module>
    globals = debugger.run(setup['file'], None, None, is_module)
  File "<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydevd.py", line 1778, in run
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc) 
  File "<path/to/my/pycharm/project>/manage.py", line 10, in <module>
    execute_from_command_line(sys.argv)
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/core/management/__init__.py", line 338, in execute_from_command_line
    utility.execute()
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/core/management/__init__.py", line 312, in execute
    django.setup()
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/__init__.py", line 18, in setup
    apps.populate(settings.INSTALLED_APPS)
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/apps/registry.py", line 108, in populate
    app_config.import_models(all_models)
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/apps/config.py", line 198, in import_models
    self.models_module = import_module(models_module_name)
  File "/usr/lib/python3.4/importlib/__init__.py", line 109, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 2231, in _gcd_import
  File "<frozen importlib._bootstrap>", line 2214, in _find_and_load
  File "<frozen importlib._bootstrap>", line 2203, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1129, in _exec
  File "<frozen importlib._bootstrap>", line 1448, in exec_module
  File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/auth/models.py", line 41, in <module>
    class Permission(models.Model):
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/db/models/base.py", line 139, in __new__
    new_class.add_to_class('_meta', Options(meta, **kwargs))
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/db/models/base.py", line 324, in add_to_class
    value.contribute_to_class(cls, name)
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/db/models/options.py", line 250, in contribute_to_class
    self.db_table = truncate_name(self.db_table, connection.ops.max_name_length())
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/db/__init__.py", line 36, in __getattr__
    return getattr(connections[DEFAULT_DB_ALIAS], item)
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/db/utils.py", line 240, in __getitem__
    backend = load_backend(db['ENGINE'])
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/db/utils.py", line 111, in load_backend
    return import_module('%s.base' % backend_name)
  File "/usr/lib/python3.4/importlib/__init__.py", line 109, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 2231, in _gcd_import
  File "<frozen importlib._bootstrap>", line 2214, in _find_and_load
  File "<frozen importlib._bootstrap>", line 2203, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1129, in _exec
  File "<frozen importlib._bootstrap>", line 1448, in exec_module
  File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/gis/db/backends/postgis/base.py", line 8, in <module>
    from .features import DatabaseFeatures
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/gis/db/backends/postgis/features.py", line 1, in <module>
    from django.contrib.gis.db.backends.base.features import BaseSpatialFeatures
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/gis/db/backends/base/features.py", line 3, in <module>
    from django.contrib.gis.db.models import aggregates
  File "<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/gis/db/models/__init__.py", line 12, in <module>
    "See also https://docs.djangoproject.com/en/%s/ref/contrib/gis/install/geolibs/" % get_docs_version())
django.core.exceptions.ImproperlyConfigured: GEOS is required and has not been detected. Are you sure it is installed? See also https://docs.djangoproject.com/en/1.8/ref/contrib/gis/install/geolibs/

I've tried reinstalling libgdal-dev. All relevant packages (GDAL, GEOS etc) are up to date.

I've tried working my way back through the Python code. it fails in djanjo/contrib/gis/geos/__init__.py on the following. As HAS_GEOS is set to false it reports that GEOS is not present.

try:
    from .libgeos import geos_version, geos_version_info  # NOQA: flake8 detects only the last __all__
    HAS_GEOS = True
    __all__ += ['geos_version', 'geos_version_info']
except ImportError:
    HAS_GEOS = False

I suspect that a recent OS upgrade/patch has broken GEOS or GDAL. The root cause seems to be something to do with ctypes, but I can't see what it could be.

The following might be useful.

>>> from _ctypes import Union, Structure, Array
Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
ImportError: /usr/lib/python3.4/lib-dynload/_ctypes.cpython-34m-x86_64-linux-gnu.so: undefined symbol: _PyTraceback_Add


>>> from django.contrib.gis import gdal
Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/gis/gdal/__init__.py", line 47, in <module>
    from django.contrib.gis.gdal.driver import Driver  # NOQA
  File "/<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/<path/to/my/virtualenv>/lib/python3.4/site-packages/django/contrib/gis/gdal/driver.py", line 1, in <module>
    from ctypes import c_void_p
  File "/<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/usr/lib/python3.4/ctypes/__init__.py", line 7, in <module>
    from _ctypes import Union, Structure, Array
  File "/<path/to/my/homedir>/pycharm-4.5.1/helpers/pydev/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
ImportError: /usr/lib/python3.4/lib-dynload/_ctypes.cpython-34m-x86_64-linux-gnu.so: undefined symbol: _PyTraceback_Add

Answer 1

I had the same problem today, though in an unrelated python project. This is is the line I also encountered and which led me here:

ImportError: /usr/lib/python3.4/lib-dynload/_ctypes.cpython-34m-x86_64-linux-gnu.so: undefined symbol: _PyTraceback_Add

It looks like Ubunut has pushed a Python 3.4 update which is not compatible with existing virtual environments. I'm able to fix the problem by recreating the virtualenv. Where this was impractical for the moment I simply replaced the virtualenv's python with the system one:

cd my-virtualenv
cp /usr/bin/python3.4 bin/python3.4

I can't say if this is a very sane thing to do, but it does seem to work in my case.

Answer 2

You should do

cp /usr/bin/python3 /path/to/my-virtualenv/bin/python3

instead, because that's the actual non-symlink file.