mdsynthesis/datreant.data installation: pytables/HDF5 version clashes

25 views
Skip to first unread message

Oliver Beckstein

unread,
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-3.2.3.1.tar.gz
Complete output from command python setup.py egg_info:
* Using Python 2.7.12 (default, Jul 7 2016, 11:24:27)
* USE_PKGCONFIG: True
.. ERROR:: HDF5 1.10 release not supported. HDF5 v1.8 release required. Found version v1.10.0

This is a known issue: https://github.com/PyTables/PyTables/issues/545

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

--
Oliver Beckstein * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com

orbe...@gmail.com

unread,
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 datreant.data mdsynthesis

This seems to be working.

David Dotson

unread,
Jul 27, 2016, 12:39:51 AM7/27/16
to orbe...@gmail.com, 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. :/

David

--
You received this message because you are subscribed to the Google Groups "datreant" group.
To unsubscribe from this group and stop receiving emails from it, send an email to datreant+u...@googlegroups.com.
To post to this group, send email to datr...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/datreant/110976c2-00e1-4514-8087-081ac0404e54%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Max Linke

unread,
Jul 27, 2016, 10:09:02 AM7/27/16
to datreant
https://github.com/PyTables/PyTables/blob/4d707ffed34582bc6603f4f2e47f4a25ba7e4d86/setup.py#L428

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
Reply all
Reply to author
Forward
0 new messages