Hi Åke,
Åke Sandgren <[email protected]> writes:
> The easyconfig contains a run time dep for HDF5 already.
>
> Does that lib contain a link time dep for HDF5? If not then that's where the
> problem is.
Good catch:
[build@admin ~]$ ldd
/trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_hdf.so.4.5.5
...
/trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_hdf.so.4.5.5:
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found
(required by
/trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_core.so.405)
linux-vdso.so.1 => (0x00002aaaaaacd000)
libopencv_core.so.405 =>
/trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_core.so.405
(0x00002aaaaaccf000)
libhdf5.so.8 => /lib64/libhdf5.so.8 (0x00002aaaabc07000)
...
I thought maybe hdf5-1.8.12 from the OS was being picked up and causing
a problem. I ran the build on a cluster node rather than the admin node
where I normally build and everything went fine. libopencv_hdf.so is
now linked to the libhdf5.so from the HDF5 module from EB:
$ ldd
/trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_hdf.so
linux-vdso.so.1 => (0x00002aaaaaacd000)
libopencv_core.so.405 =>
/trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_core.so.405
(0x00002aaaaaccf000)
libhdf5.so.200 =>
/trinity/shared/easybuild/software/HDF5/1.12.1-gompi-2021b/lib/libhdf5.so.200
(0x00002aaaabc07000)
It turns out however that the old HDF5 package from the OS is also
installed on the cluster node (not sure why), so I am still in the dark
about the original problem. At some point I should probably look into
it again.
Cheers,
Loris
> On 3/4/22 09:24, Loris Bennett wrote:
>> Hi,
>> The sanity check for OpenCV-4.5.5-foss-2021b-contrib.eb fails with
>> ImportError:
>> /trinity/shared/easybuild/software/OpenCV/4.5.5-foss-2021b-contrib/lib64/libopencv_hdf.so.405:
>> undefined symbol: H5P_CLS_DATASET_CREATE_ID_g
>> ) (at
>> easybuild/software/EasyBuild/4.5.3/lib/python3.6/site-packages/easybuild/framework/easyblock.py:3424
>> in _sanity_check_step)
>> Does this ring a bell with anyone? Is there a run-time dependency on
>> HDF5 missing?
>> Cheers,
>> Loris
>>
--
Dr. Loris Bennett (Herr/Mr)
ZEDAT, Freie Universität Berlin Email [email protected]
