import h5py: undefined symbol: H5Ovisit_by_name

To assist reproducing bugs, please include the following:

• Operating System Ubuntu 16.04.2 LTS
• Python version 3.6
• Where Python was acquired: Anaconda
• h5py version 2.9.0.post0
• HDF5 version 1.10.4
• The full traceback/stack trace shown (if it appears)

h5py.version.info contains the needed versions, which can be displayed by

python -c 'import h5py; print(h5py.version.info)'

where python should be substituted for the path to python used to install h5py with.

I installed mpi hdf5 as following:

export CC=mpicc
python setup.py configure --mpi 
python setup.py build
python setup.py install

but when in import h5py, it shows that /home/studenter/haoyut/anaconda3/lib/python3.6/site-packages/h5py/defs.cpython-36m-x86_64-linux-gnu.so: undefined symbol: H5Ovisit_by_name

it seems with lib things, I have add this to my .bashrc: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/studenter/haoyut/local_install/hdf5-1.10.4/install/lib export LD_RUN_PATH=$LD_RUN_PATH:/home/studenter/haoyut/local_install/hdf5-1.10.4/install/lib

[lldelisle]

Unfortunately the problem is still present. I still have the issue when I use python 3.7: With conda:

conda activate justh5pypy3.6
python -c "import h5py"
# No issue
conda install python=3.7
python -c "import h5py"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python3.7/site-packages/h5py/__init__.py", line 36, in <module>
    from ._conv import register_converters as _register_converters
  File "h5py/h5r.pxd", line 21, in init h5py._conv
  File "h5py/_objects.pxd", line 12, in init h5py.h5r
  File "h5py/_objects.pyx", line 1, in init h5py._objects
ImportError: /usr/lib/python3.7/site-packages/h5py/defs.cpython-37m-x86_64-linux-gnu.so: undefined symbol: H5Ovisit_by_name

If you need more log, do not hesitate. Thanks,

Lucille

[tacaswell]

I am going to close this as a packaging issue that has been resolved.