Python: Running from cygwin works, while running f

I can successfully run a python script that uses

from sklearn.cluster import DBSCAN

from the 64 bit cygwin terminal prompt which uses a 64bit build of python 2.7.

When I run the same from both 64 bit and 32 bit pycharm with -vv interpreter options, I get (the first 2 lines are the verbose output):

import numpy.linalg.linalg # precompiled from /usr/lib/python2.7/site-packages/numpy/linalg/linalg.pyc
dlopen("/usr/lib/python2.7/site-packages/numpy/linalg/lapack_lite.dll", 2);
Traceback (most recent call last):
  File "C:/Users/mack0242/Dropbox/PhD/scripts/cluster.py", line 5, in <module>
    from sklearn.cluster import DBSCAN
  File "/usr/lib/python2.7/site-packages/sklearn/__init__.py", line 57, in <module>
    from .base import clone
  File "/usr/lib/python2.7/site-packages/sklearn/base.py", line 9, in <module>
    import numpy as np
  File "/usr/lib/python2.7/site-packages/numpy/__init__.py", line 170, in <module>
    from . import add_newdocs
  File "/usr/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in <module>
    from .polynomial import *
  File "/usr/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 19, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/usr/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 51, in <module>
    from .linalg import *
  File "/usr/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: No such file or directory

I have double checked and the file:

/usr/lib/python2.7/site-packages/numpy/linalg/lapack_lite.dll

exists and is 64 bits. I have successfully installed numpy,scipy and sklearn from pip on the cygwin terminal.

Additionally, PyCharm says there are no modules named sklearn, matplotlib and numpy.

When I had a similar problem (couldn't import numpy in Pycharm but on cygwin console), it turned out that cygwin was using a different interpreter as PyCharm.

In PyCharm I had configured the interpreter from C:\Program Files\cygwin\usr\bin\python. In contrast, cygwin was using /bin/python. In PyCharm click File > Settings > Project: yourProjectName > Project Interpreter, click on "Add local" and find the interpreter used by cygwin (in my case C:\Program Files\cygwin\bin\python).

Then open the Python Console in PyCharm via View > Tools Windows > Python Console and try your import statement.