0

I've been struggling to get pytables and the underlying HDF5 library working on python in OS X, so thought I'd give the Enthought distribution a go (which will also greatly simplify deployment across platforms later on).

I installed EPD 7.3 for 64-bit OS X (I'm running 10.8.2), but unfortunately no success, I get the following when trying to load the pytables...

In [4]: import tables
--------------------------------------------------------------------------- ImportError                               Traceback (most recent call last) /<ipython-input-4-389ecae14f10> in <module>()
----> 1 import tables

/Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/__init__.py in <module>()
     57 
     58 # Necessary imports to get versions stored on the Pyrex extension

---> 59 from tables.utilsExtension import getPyTablesVersion, getHDF5Version
     60 
     61 __version__ = getPyTablesVersion()

ImportError: dlopen(/Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/utilsExtension.so, 2): Symbol not found: _SZ_BufftoBuffCompress   Referenced from: /Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/utilsExtension.so Expected in: flat namespace  in /Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/utilsExtension.so

I presume this means that szip, a required library for HDF5, cannot be found? If it is actually missing from EPD (seems odd...), can I install it myself without building HDF5 from source? Or is is just in a strange place?

internals-in
  • 4,798
  • 2
  • 21
  • 38
user2205880
  • 233
  • 2
  • 8

1 Answers1

1

First, I apologize for the problems you are encountering.

It looks as if you are not loading pytables from EPD, but from a former installation. How does PYTHONPATH look like in your environment ?

Generally, EPD is installed somewhere in /Library/Frameworks/Python.framework/Versions/7.3. What does the following do ?

PYTHONPATH= /Library/Frameworks/Python.framework/Versions/7.3/bin/python -c "import tables; print tables.__version__"

or (64 bits version):

PYTHONPATH= /Library/Frameworks/EPD64.framework/Versions/7.3/bin/python -c "import tables; print tables.__version__"

It should return you something like "2.3.1" (the actual tables version available in EPD). If that indeed works, then do make EPD the default python in your environment, you will need to adapt the PATH/PYTHONPATH variables to make it available.

If that still does not work, then can you try the following (adapt for 32 bits):

 PYTHONPATH= /Library/Frameworks/EPD64.framework/Versions/7.3/bin/python -c "import sys; print sys.path"

and paste the output ?

David Cournapeau
  • 78,318
  • 8
  • 63
  • 70
  • This article addresses the issue that David describes: https://support.enthought.com/entries/22094157-OS-X-Conflict-with-installed-packages-in-earlier-Python-installation – Jonathan March Mar 26 '13 at 12:32
  • The command doesn't work for me, but the following does... `/Library/Frameworks/EPD64.framework/Versions/7.3/bin/python -c "import tables; print tables.__version__"` ... but I'm afraid I get the same error. – user2205880 Mar 27 '13 at 02:08
  • Indeed, I forgot about the 64 bits version (my example was for 32 bits). I have updated the instructions: note the PYTHONPATH= prefix to each command to 'reset' PYTHONPATH for each python run. I suspect that the EPD python is trying to load your pytables instead of its own because of how your PYTHONPATH is setup – David Cournapeau Mar 27 '13 at 11:54
  • The suggested command to call python directly returns an identical error message to the original question. PYTHONPATH is not set on my system, and my PATH=/Library/Frameworks/EPD64.framework/Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/CrossPack-AVR/bin which I presume is okay? Any other way that the old pytables could interfere? Is it worth trying the 32-bit version instead? – user2205880 Mar 28 '13 at 02:42
  • Ok, this is definitely strange. Do you confirm you get the exact same error (with a path starting with Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables) ? If so, something else is modifying your sys.path. I have updated my response – David Cournapeau Mar 28 '13 at 20:00
  • Bingo! sys.path included /Users/davidperry/Library/Python/2.7/lib/python/site-packages which included modules from an old install. I renamed the directory and problem solved (as per the solution linked to by Jonathan, except it was the site-packages in my home directory rather than the shared ones). Thank you both! – user2205880 Mar 29 '13 at 10:53