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h5py import fails with error on undefined H5Pget_fapl_direct #121

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bernstei opened this issue Sep 15, 2022 · 1 comment
Open
1 task done

h5py import fails with error on undefined H5Pget_fapl_direct #121

bernstei opened this issue Sep 15, 2022 · 1 comment
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@bernstei
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bernstei commented Sep 15, 2022 •
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

When installing phono3py from conda-forge inside a github CI action, it ends up with conda-forge::h5py-3.7.0-nompi_py39h63b1161_100

This version provides to a broken h5py that cannot be imported. The trivial script python3 -c "import h5py" fails with the error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/share/miniconda/lib/python3.9/site-packages/h5py/__init__.py", line 33, in <module>
    from . import version
  File "/usr/share/miniconda/lib/python3.9/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: /usr/share/miniconda/lib/python3.9/site-packages/h5py/defs.cpython-39-x86_64-linux-gnu.so: undefined symbol: H5Pget_fapl_direct

I've tried to use conda to install h5py directly (i.e. not as a dependency of phono3py), but rather than the nompi version that is installed as a phono3py dependency, I end up with h5py pkgs/main/linux-64::h5py-3.7.0-py39h737f45e_0, even though I run conda install -c conda-forge h5py=3.7.0, and I don't know enough about conda to be able to test the package without it being added as a phono3py dependency.

Installed packages

# packages in environment at /usr/share/miniconda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
brotlipy                  0.7.0           py39h27cfd23_1003  
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.9.14            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2022.9.14          pyhd8ed1ab_0    conda-forge
cffi                      1.15.0           py39hd667e15_1  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
colorama                  0.4.4              pyhd3eb1b0_0  
conda                     4.14.0           py39hf3d152e_0    conda-forge
conda-content-trust       0.1.1              pyhd3eb1b0_0  
conda-package-handling    1.8.1            py39h7f8727e_0  
cryptography              36.0.0           py39h9ce1e76_0  
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.11.0           py39h27cfd23_0  
freetype                  2.12.1               hca18f0e_0    conda-forge
h5py                      3.7.0           nompi_py39h63b1161_100    conda-forge
hdf5                      1.12.1          nompi_h2750804_100    conda-forge
idna                      3.3                pyhd3eb1b0_0  
jpeg                      9e                   h166bdaf_2    conda-forge
kiwisolver                1.4.2            py39h295c915_0  
krb5                      1.19.2               hac12032_0  
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.35.1               h7274673_9  
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   7.84.0               h91b91d3_0  
libedit                   3.1.20210910         h7f8727e_0  
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  he6710b0_2  
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnghttp2                1.46.0               hce63b2e_0  
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.37               h753d276_4    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              9.3.0               hd4cf53a_17  
libtiff                   4.2.0                h85742a9_0  
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libzlib                   1.2.12               h166bdaf_1    conda-forge
llvm-openmp               14.0.4               he0ac6c6_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
matplotlib-base           3.3.4            py39h2fa2bec_0    conda-forge
ncurses                   6.3                  h7f8727e_2  
numpy                     1.20.3           py39hd249d9e_2    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openblas                  0.3.21          pthreads_h[320](https://github.com/libAtoms/workflow/actions/runs/3063889471/jobs/4946460969#step:7:321)a7e8_3    conda-forge
openssl                   1.1.1q               h166bdaf_0    conda-forge
phono3py                  2.3.2            py39h05a0c83_1    conda-forge
phonopy                   2.15.0           py39hd257fcd_0    conda-forge
pillow                    7.2.0            py39h6f3857e_2    conda-forge
pip                       22.1.2           py39h06a4308_0  
pycosat                   0.6.3            py39h27cfd23_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyopenssl                 22.0.0             pyhd3eb1b0_0  
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39h06a4308_0  
python                    3.9.12               h12debd9_0  
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pyyaml                    6.0              py39hb9d737c_4    conda-forge
readline                  8.1.2                h7f8727e_1  
requests                  2.27.1             pyhd3eb1b0_0  
ruamel_yaml               0.15.100         py39h27cfd23_0  
scipy                     1.5.3            py39hee8e79c_0    conda-forge
setuptools                61.2.0           py39h06a4308_0  
six                       1.16.0             pyhd3eb1b0_1  
spglib                    2.0.1            py39hd257fcd_0    conda-forge
sqlite                    3.38.2               hc218d9a_0  
tk                        8.6.11               h1ccaba5_0  
toolz                     0.11.2             pyhd3eb1b0_0  
tornado                   6.2              py39hb9d737c_0    conda-forge
tqdm                      4.63.0             pyhd3eb1b0_0  
tzdata                    2022a                hda174b7_0  
urllib3                   1.26.8             pyhd3eb1b0_0  
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
zlib                      1.2.12               h7f8727e_1  
zstd                      1.4.9                ha95c52a_0    conda-forge

Environment info

     active environment : None
       user config file : /home/runner/.condarc
 populated config files : 
          conda version : 4.14.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __linux=5.15.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /usr/share/miniconda  (writable)
      conda av data dir : /usr/share/miniconda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /usr/share/miniconda/pkgs
                          /home/runner/.conda/pkgs
       envs directories : /usr/share/miniconda/envs
                          /home/runner/.conda/envs
               platform : linux-64
             user-agent : conda/4.14.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1019-azure ubuntu/20.04.4 glibc/2.31
                UID:GID : 1001:121
             netrc file : None
           offline mode : False

[edited since conda list output seemed wrong]
@bernstei bernstei added the bug label Sep 15, 2022
This was referenced Sep 16, 2022
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@hmaarrfk
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hmaarrfk commented Nov 5, 2024

i have a feeling it is because you are mixing and matching environment with defaults

See
https://conda-forge.org/docs/user/transitioning_from_defaults/

@hmacdope hmacdope mentioned this issue Feb 16, 2025
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