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python-3.xpandasanacondapytableshdfstore

Anaconda3 libhdf5.so.9: cannot open shared object file [works fine on py2.7 but not on py3.4]

I just tried to use pd.HDFStore in IPython Notebook with a Python 3 kernel (Anaconda 2&3 on Ubuntu 14.04)

import pandas as pd
store = pd.HDFStore('/home/Jian/Downloads/test.h5')

but it throws the following error

ImportError: HDFStore requires PyTables, "libhdf5.so.9: cannot open shared object file: No such file or directory" problem importing

I initially thought it's because pytables is somehow missing, but when I check $source activate py34 and $conda list, pytables 3.2.0 is already installed under anaconda python3 environment.

Also, if I switch to Python 2, for example, $source activate py27 and start ipython notebook, it works properly and no import error is thrown.

I guess that I must miss something for configuring pytables under anaconda python 3 env, but I cannot figure it out. Any help is highly appreciated.

Update:

I just tried on a fresh install of Anaconda3-2.3.0-Linux-x86_64 from official website and it ends up with the same error. When I try $locate libhdf5.so.9 in command line, nothing shows up.

Solution

  • This is a known issue that we are working on. When it is fixed, conda update --all will update the libraries and fix the issue.