Åke Sandgren <[email protected]> writes: > well, is the HDF5 develop package installed on the cluster node or just the > runtime lib?
You're right of course. hdf5-devel is on the admin node but not on the cluster node. Thanks, Loris > On 3/4/22 11:35, Loris Bennett wrote: >> 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]
