hdf5 / h5py ImportError: libhdf5.so.7

Question

I'm working on a project involving network messaging queues (msgpack, zmq, ...) on a RHEL 6.3 (x86_64) system. I was installing the most recent packages of glib, gevent, pygobject, pygtk, and such in order to get pylab / matplotlib to work (which hasn't been successful either).

After giving up I went back to my code and somehow I had managed to wreck my hdf5 / h5py installation - h5py can't find libhdf5.so.7 on import. I immediately reinstalled hdf5-1.8.9 in /usr/local/hdf5 on RHEL 6.3 (x86_64) as follows:

./configure --prefix=/usr/local/hdf5 make make check sudo make install make check install 

which seemed to work just fine. Then I went to reinstall h5py (in python 2.7.3):

python2.7 setup.py build --hdf5=/usr/local/hdf5/ python2.7 setup.py test   # optional # sudo python2.7 setup.py install 

which fails to import the _errors file in the tests, like so:

====================================================================== ERROR: _hl.tests.test_attrs_data (unittest.loader.ModuleImportFailure) ---------------------------------------------------------------------- ImportError: Failed to import test module: _hl.tests.test_attrs_data Traceback (most recent call last):   File "/usr/local/lib/python2.7/unittest/loader.py", line 252, in _find_tests     module = self._get_module_from_name(name)   File "/usr/local/lib/python2.7/unittest/loader.py", line 230, in _get_module_from_name     __import__(name)   File "/home/cronburg/Downloads/h5py-2.0.1/build/lib.linux-x86_64-2.7/h5py/_hl/tests/test_attrs_data.py", line 5, in <module>     import h5py   File "/home/cronburg/Downloads/h5py-2.0.1/build/lib.linux-x86_64-2.7/h5py/__init__.py", line 1, in <module>     from h5py import _errors ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory   ---------------------------------------------------------------------- Ran 12 tests in 0.001s  FAILED (errors=12) 

h5py was working fine before I went to install the aforementioned packages / tarballs, and I don't remember touching anything that even remotely looked like hdf5. Any ideas?

EDIT: Trying to locate the file only shows it in the location i untarred it:

cronburg@rhel:~/Downloads/h5py-2.0.1$ locate libhdf5.so.7 /home/cronburg/tmp/hdf5-1.8.9/hdf5/lib/libhdf5.so.7 /home/cronburg/tmp/hdf5-1.8.9/hdf5/lib/libhdf5.so.7.0.3 /home/cronburg/tmp/hdf5-1.8.9/src/.libs/libhdf5.so.7 /home/cronburg/tmp/hdf5-1.8.9/src/.libs/libhdf5.so.7.0.3 

Answer 1

take a look on: http://rpm.pbone.net/index.php3/stat/3/srodzaj/1/search/libhdf5.so.7()(64bit)

Or should try this repo: https://ius.io/Packages/

I prefer always use the most updated python version, in a package format.

https://dl.iuscommunity.org/pub/ius/stable/Redhat/6/x86_64/repoview/python27.html

sudo yum install -y https://centos6.iuscommunity.org/ius-release.rpm sudo yum install -y python27 sudo yum install -y python27-devel 

Do a pip install and be happy:

$ sudo pip install h5py Installing collected packages: h5py Successfully installed h5py-2.6.0