mdsynthesis/ installation: pytables/HDF5 version clashes

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Oliver Beckstein

Jul 26, 2016, 7:46:37 PM7/26/16
to datreant
I tried to install

pip install mdsynthesis

on Mac OS X 10.11.6 but it failed because of a version problem: the real problem is pytables:

pip install tables

Collecting tables
Using cached tables-
Complete output from command python egg_info:
* Using Python 2.7.12 (default, Jul 7 2016, 11:24:27)
.. ERROR:: HDF5 1.10 release not supported. HDF5 v1.8 release required. Found version v1.10.0

This is a known issue:

Assuming that I don't want to use conda, does anyone have any great ideas?

I have mac ports and installed the hdf5-18 package:

sudo port install hdf5-18

but so far I have not figured out how to make pip pick up the alternative hdf-18 libs in /opt/local/lib/hdf5-18/


Oliver Beckstein *
skype: orbeckst *

Jul 26, 2016, 8:04:04 PM7/26/16
to datreant
A workaround on my system relies on the fact that macports installs a working pytables. Thus, I can set up a dirty virtualenv and work there...

    mkvirtualenv --system-site-packages stable
    pip install datreant.core mdsynthesis

This seems to be working.

David Dotson

Jul 27, 2016, 12:39:51 AM7/27/16
to, datreant

Glad it ended up working alright. HDF5 1.10 has been a headache for the PyTables devs, so things are a bit off right now. For example, in ArchLinux, the pytables package maintainers are packaging HDF5 libs v1.8 for this very reason.

Unfortunately there's nothing we can do at the level of datreant. :/


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Max Linke

Jul 27, 2016, 10:09:02 AM7/27/16
to datreant

According to this you should be able to tell pytables during installation about special HDF installations. So

HDF5_DIR=/your/1.8/install/loc pip install PyTables

could work. I haven't tried it myself.

best Max
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