Posso executar com êxito um script python que usa

from sklearn.cluster import DBSCAN

do prompt do terminal cygwin de 64 bits, que usa uma compilação de 64 bits do python 2.7.

Quando executo o mesmo do pycharm de 64 e 32 bits com-vv opções de intérprete, recebo (as 2 primeiras linhas são a saída detalhada):

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

Eu verifiquei duas vezes e o arquivo:

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

existe e é de 64 bits. Eu instalei com sucesso o numpy, scipy e sklearn do pip no terminal cygwin.

Além disso, PyCharm diz que não há módulos chamadossklearn, matplotlib enumpy.