undefined symbol: H5Pset_fapl_ros3

[brianpenghe]

I'm using linux but have this problem! I followed this issue but it couldn't help me solve this. https://github.com/scverse/scvi-tools/issues?q=H5Pset_fapl_ros3#issue-1235458517

import scvi
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [2], in <cell line: 1>()
----> 1 import scvi

File /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/scvi/__init__.py:10, in <module>
      7 from ._settings import settings
      9 # this import needs to come after prior imports to prevent circular import
---> 10 from . import data, model, external, utils
     12 # https://github.com/python-poetry/poetry/pull/2366#issuecomment-652418094
     13 # https://github.com/python-poetry/poetry/issues/144#issuecomment-623927302
     14 try:

File /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/scvi/data/__init__.py:1, in <module>
----> 1 from anndata import read_csv, read_h5ad, read_loom, read_text
      3 from ._datasets import (
      4     annotation_simulation,
      5     brainlarge_dataset,
   (...)
     22     synthetic_iid,
     23 )
     24 from ._manager import AnnDataManager

File /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/anndata/__init__.py:7, in <module>
      5 if not within_flit():
      6     del within_flit
----> 7     from ._core.anndata import AnnData
      8     from ._core.merge import concat
      9     from ._core.raw import Raw

File /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/anndata/_core/anndata.py:17, in <module>
     14 from typing import Iterable, Sequence, Mapping, MutableMapping  # Generic ABCs
     15 from typing import Tuple, List  # Generic
---> 17 import h5py
     18 from natsort import natsorted
     19 import numpy as np

File /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/h5py/__init__.py:33, in <module>
     30     else:
     31         raise
---> 33 from . import version
     35 if version.hdf5_version_tuple != version.hdf5_built_version_tuple:
     36     _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
     37            "this may cause problems").format(
     38             '{0}.{1}.{2}'.format(*version.hdf5_version_tuple),
     39             '{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple)
     40     ))

File /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/h5py/version.py:15, in <module>
     10 """
     11     Versioning module for h5py.
     12 """
     14 from collections import namedtuple
---> 15 from . import h5 as _h5
     16 import sys
     17 import numpy

File h5py/h5.pyx:1, in init h5py.h5()

ImportError: /opt/conda/envs/scvi-env2/lib/python3.9/site-packages/h5py/defs.cpython-39-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3

Any ideas?

[brianpenghe]

The error was gone after I installed a a slightly newer version of h5py. Does it sound reasonable?

(scvi-env2) jupyter@ph12-new:~$ pip install h5py==3.6.0
Collecting h5py==3.6.0
  Downloading h5py-3.6.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 41.3 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.14.5 in /opt/conda/envs/scvi-env2/lib/python3.9/site-packages (from h5py==3.6.0) (1.22.3)
Installing collected packages: h5py
  Attempting uninstall: h5py
    Found existing installation: h5py 3.2.1
    Uninstalling h5py-3.2.1:
      Successfully uninstalled h5py-3.2.1
Successfully installed h5py-3.6.0

[watiss]

Hi Brian. I'm not too sure what is causing this. In this issue, people are saying that they got away with forcing h5py to an older version. But if you can get it to work with the newest version, I'd just use that. Otherwise, feel free to ask away on their github.

[brianpenghe]

OK I'm having another issue now

import scvi
/opt/conda/envs/scvi-env2/lib/python3.9/site-packages/h5py/__init__.py:36: UserWarning: h5py is running against HDF5 1.12.1 when it was built against 1.10.6, this may cause problems
  _warn(("h5py is running against HDF5 {0} when it was built against {1}, "

and scanpy doesn't work. So I indeed may try an older version

[adamgayoso]

closing due to inactivity