h5py: undefined symbol: H5Pset_fapl_ros3
To assist reproducing bugs, please include the following:
- Operating System: Ubuntu 18 Docker
- Python version: 3.8
- Where Python was acquired: Conda
- h5py version (e.g. 2.6): results in error
- HDF5 version (e.g. 1.8.17): 1.10.6
- The full traceback/stack trace shown (if it appears)
Dear everyone,
I am using a Docker container based on jupyter/minimal-notebook:latest. It already has a miniconda with Python 3.
Next, I installed h5py (was a dependency of something else). However, when attempting to use it I get:
(sc-analysis) jovyan@7171d029a008:~$ python -c 'import h5py; print(h5py.version.info)'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/conda/envs/sc-analysis/lib/python3.8/site-packages/h5py/__init__.py", line 33, in <module>
from . import version
File "/opt/conda/envs/sc-analysis/lib/python3.8/site-packages/h5py/version.py", line 15, in <module>
from . import h5 as _h5
File "h5py/h5.pyx", line 1, in init h5py.h5
ImportError: /opt/conda/envs/sc-analysis/lib/python3.8/site-packages/h5py/defs.cpython-38-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3
Do you have any idea? I can share the full container if required. Thanks.
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Comments: 19 (5 by maintainers)
Commits related to this issue
- h5py issue in building through mamba https://github.com/h5py/h5py/issues/1880 — committed to yanhui09/laca by yanhui09 2 years ago
- Try limiting h5py version https://github.com/h5py/h5py/issues/1880#issuecomment-823241926 — committed to gibsramen/evident by gibsramen 2 years ago
- Fix h5py installation issue (#20) Try limiting h5py version https://github.com/h5py/h5py/issues/1880#issuecomment-823241926 — committed to biocore/evident by gibsramen 2 years ago
- XFEL: pin h5py due to a mamba mismatch Happens when using mamba to install h5py/hdf5 from conda-forge, while installing psana from lcls-i See h5py/h5py#1880 and conda-forge/h5py-feedstock#92 — committed to cctbx/cctbx_project by phyy-nx 2 years ago
- XFEL: pin h5py due to a mamba mismatch Happens when using mamba to install h5py/hdf5 from conda-forge, while installing psana from lcls-i See h5py/h5py#1880 and conda-forge/h5py-feedstock#92 — committed to cctbx/cctbx_project by phyy-nx 2 years ago
- Unpin everything The psana=4.0.47 and h5py<3.2 pins are mutually incompatible, apparently related to the packages zlib/libzlib. The h5py issue in h5py/h5py#1880 and conda-forge/h5py-feedstock#92 is n... — committed to cctbx/cctbx_project by dwpaley 2 years ago
- Unpin everything The psana=4.0.47 and h5py<3.2 pins are mutually incompatible, apparently related to the packages zlib/libzlib. The h5py issue in h5py/h5py#1880 and conda-forge/h5py-feedstock#92 is n... — committed to cctbx/cctbx_project by dwpaley 2 years ago
- Unpin everything (#828) XFEL conda environments: the previous psana=4.0.47 and h5py<3.2 pins were mutually incompatible, apparently related to the packages zlib/libzlib. The h5py issue in h5py/h5py#1... — committed to cctbx/cctbx_project by dwpaley 2 years ago
- H5Pset_fapl_ros3 error h5py/h5py#1880 — committed to atharva-2001/tardis by atharva-2001 a year ago
- install via pip in build step H5Pset_fapl_ros3 error h5py/h5py#1880 — committed to atharva-2001/tardis by atharva-2001 a year ago
- Try fix for https://github.com/h5py/h5py/issues/1880 — committed to berquist/pymolresponse by berquist a year ago
- Revert "Try fix for https://github.com/h5py/h5py/issues/1880" This reverts commit 4f44b9803c707c02038985a07ab3ced722e7aff2. — committed to berquist/pymolresponse by berquist a year ago
- [WIP] Basic Benchmarks Using ASV (#2260) * Initial commit * Comment old benchmarks temporarily * Add timeout * Change the tests workflow to run benchmarks * Replace ASV config file by tem... — committed to tardis-sn/tardis by atharva-2001 a year ago
I just hit this too (I’m also using Mamba). I worked around the issue for now by forcing
h5py<3.2in myenvironment.yml.The error is due to the HDF5 library being used not matching the configuration h5py was built with. This sounds like whichever source(s) of libraries mamba is using, they’re not consistent (which is a mamba problem).
Update: This issue only occurs when installing the package with mamba (https://github.com/mamba-org/mamba), but not with Conda. Feel free to close if you think that it’s not your responsibility.
I am getting the same error at @tschaka1904 without mamba, from conda-forge. Installation from pip avoids the issue.
Also just ran into this:
defs.cpython-38-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3Seems like that this as a recent issue for me, as I was able to built it just fine a couple of weeks back. What’s the preferred workaround or even solution?