I've built my virtual environment solely from PyPi (and it's a requirement). Everything installs well, but I'm facing run time error: E ImportError: libmkl_rt.so: cannot open shared object file: No such file or directory. This is used by scipy for multi-threading. This error can be avoided when installing nomkl package, which is available only from anaconda.
Since I can install only using pip, I can install intel-scipy, intel-numpy, etc. that come with multi-threading support. However, these packages only provide scipy-1.1.0 and numpy-1.15.1, which do not meet Snorkel's requirements.
Has anyone tried a pip-only installation and gotten things to work?
Here's my complete error log.
from snorkel.labeling import LFAnalysis
../../build/myProject/venv/lib/python3.6/site-packages/snorkel/labeling/__init__.py:3: in <module>
from .analysis import LFAnalysis # noqa: F401
../../build/myProject/venv/lib/python3.6/site-packages/snorkel/labeling/analysis.py:8: in <module>
from sklearn.metrics import confusion_matrix
../../build/myProject/venv/lib/python3.6/site-packages/sklearn/__init__.py:76: in <module>
from .base import clone
../../build/myProject/venv/lib/python3.6/site-packages/sklearn/base.py:16: in <module>
from .utils import _IS_32BIT
../../build/myProject/venv/lib/python3.6/site-packages/sklearn/utils/__init__.py:20: in <module>
from .validation import (as_float_array,
../../build/myProject/venv/lib/python3.6/site-packages/sklearn/utils/validation.py:21: in <module>
from .fixes import _object_dtype_isnan
../../build/myProject/venv/lib/python3.6/site-packages/sklearn/utils/fixes.py:18: in <module>
from scipy.sparse.linalg import lsqr as sparse_lsqr # noqa
../../build/myProject/venv/lib/python3.6/site-packages/scipy/sparse/linalg/__init__.py:113: in <module>
from .isolve import *
../../build/myProject/venv/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/__init__.py:6: in <module>
from .iterative import *
../../build/myProject/venv/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/iterative.py:10: in <module>
from . import _iterative
E ImportError: libmkl_rt.so: cannot open shared object file: No such file or directory
System info
Here's the list of relevant packages in my current environment (using standard numpy and scipy, and not Intel's).
Issue description
I've built my virtual environment solely from PyPi (and it's a requirement). Everything installs well, but I'm facing run time error:
E ImportError: libmkl_rt.so: cannot open shared object file: No such file or directory
. This is used byscipy
for multi-threading. This error can be avoided when installingnomkl
package, which is available only fromanaconda
.Since I can install only using
pip
, I can installintel-scipy
,intel-numpy
, etc. that come with multi-threading support. However, these packages only providescipy-1.1.0
andnumpy-1.15.1
, which do not meet Snorkel's requirements.Has anyone tried a
pip
-only installation and gotten things to work?Here's my complete error log.
System info
Here's the list of relevant packages in my current environment (using standard
numpy
andscipy
, and not Intel's).