I just cloned a working miniconda environment carnd-term1-gpu that had tensorflow with gpu working using tensorflow version '0.12.1'. The environment had a lot of other python packages installed. I wanted to upgrade to the latest version of tensorflow so I did the following based on tensorflow Ubuntu:
1) cloned the existing working environment as tflow
conda create --name tflow --clone carnd-term1-gpu
This completed successfully.
2) source activate tflow and install using pip
source activate tflow
(tflow) xx@pc:~$ pip install --ignore-installed --upgrade https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow_gpu-1.1.0-cp35-cp35m-linux_x86_64.whl
Now I try to run the old environment assuming that it should not be changed.
source activate carnd-term1-gpu
ipython
Then from ipython prompt type import numpy as np and get following:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-4ee716103900> in <module>()
----> 1 import numpy as np
/home/ai/miniconda3/envs/carnd-term1-gpu/lib/python3.5/site-packages/numpy/__init__.py in <module>()
140 return loader(*packages, **options)
141
--> 142 from . import add_newdocs
143 __all__ = ['add_newdocs',
144 'ModuleDeprecationWarning',
/home/ai/miniconda3/envs/carnd-term1-gpu/lib/python3.5/site-packages/numpy/add_newdocs.py in <module>()
11 from __future__ import division, absolute_import, print_function
12
---> 13 from numpy.lib import add_newdoc
14
15 ###############################################################################
/home/ai/miniconda3/envs/carnd-term1-gpu/lib/python3.5/site-packages/numpy/lib/__init__.py in <module>()
6 from numpy.version import version as __version__
7
----> 8 from .type_check import *
9 from .index_tricks import *
10 from .function_base import *
/home/ai/miniconda3/envs/carnd-term1-gpu/lib/python3.5/site-packages/numpy/lib/type_check.py in <module>()
9 'common_type']
10
---> 11 import numpy.core.numeric as _nx
12 from numpy.core.numeric import asarray, asanyarray, array, isnan, \
13 obj2sctype, zeros
/home/ai/miniconda3/envs/carnd-term1-gpu/lib/python3.5/site-packages/numpy/core/__init__.py in <module>()
51 from . import shape_base
52 from .shape_base import *
---> 53 from . import einsumfunc
54 from .einsumfunc import *
55 del nt
ImportError: cannot import name 'einsumfunc'
I thought I was protected by cloning a separate environment and only changing that environment, however it seems that the install in one environment changed behavior in the other environment. Exactly what I thought I was avoiding! What went wrong and how do I fix this? The new environment seems to work fine so far.
I checked the file dates in both environments. The carnd-term1-gpu environment had files that were dated the same day that I did the upgrade in the tflow environment. Any ideas on how that could happen?
I tried adding the missing file einsumfunc.py to my carnd-term1-gpu environment and started Ipython again. This time when I did import numpy as np a different file could not be imported. So it looks like my carnd-term1-gpu environment is corrupted.
Comparing conda list for each environment and looking only at numpy, I see the following:
For tflow environment:
numpy 1.11.3 <pip>
numpy 1.12.1 <pip>
numpy 1.11.3 py35_blas_openblas_200 [blas_openblas] conda-forge
And for carnd-term1-gpu environment:
numpy 1.11.3 <pip>
numpy 1.11.3 py35_blas_openblas_200 [blas_openblas] conda-forge
I then looked at revisions using conda list --revisions. Both environments only show a single revision of rev 0. Likewise looking at conda-meta/history only shows the original creation dates of Jan. 13th for carnd-term1-gpu and May 9 for tflow. So the combination of this version of pip:
pip 9.0.1 py35_0 conda-forge
combined with this wheel:
https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow_gpu-1.1.0-cp35-cp35m-linux_x86_64.whl
somehow corrupted the environment carnd-term1-gpu. This seems like either a bug or I somehow got a corrupted wheel from the tensorflow site? If it is the later, how could it corrupt a different environment than the one installed from?
Note version of pip was same in both environments.
I did the following to investigate what files changed on the date that I did the install.
find /home/ai/miniconda3/envs/carnd-term1-gpu/ -type f -newermt 2017-05-09 -ls | wc -l
This showed 669 files were created/modified. Most of these were in /site-packages/numpy/, but six.py, pyparsing.py,/setuptools/,/pkg_resources/,easy_install.py,/werkzeug/ were also affected.
conda --version is 4.2.12
I tried the following to get my old environment going again.
conda env export > environment.yml
conda env create -f environment.yml -n sdc-gpu
This resulted in following errors:
Could not import setuptools which is required to install from a source distribution.
Traceback (most recent call last):
File "/home/ai/miniconda3/envs/sdc-gpu/lib/python3.5/site-packages/pip/req/req_install.py", line 387, in setup_py
import setuptools # noqa
File "/home/ai/miniconda3/envs/sdc-gpu/lib/python3.5/site-packages/setuptools/__init__.py", line 12, in <module>
import setuptools.version
File "/home/ai/miniconda3/envs/sdc-gpu/lib/python3.5/site-packages/setuptools/version.py", line 1, in <module>
import pkg_resources
File "/home/ai/miniconda3/envs/sdc-gpu/lib/python3.5/site-packages/pkg_resources/__init__.py", line 70, in <module>
import packaging.version
ImportError: No module named 'packaging'
CondaValueError: Value error: pip returned an error.
