libvtkhdf5 contains unmangled symbols
N.B. This is the same issue as was addressed in #18514 (closed), but for a newer HDF5 version. I did not want to resurrect the old issue, so created a new one instead.
When I compile paraview, the libvtkhdf5-pv5.12.so
that gets build contains some unmangled symbols:
paraview-build$ nm -gDC ./lib/libvtkhdf5-pv5.12.so | grep \ H5
00000000003ab190 R H5O_TOKEN_UNDEF_g
00000000003972a0 R H5O_attr_ver_bounds
00000000003b3a00 R H5O_dtype_ver_bounds
00000000003aab60 R H5O_fill_ver_bounds
000000000039d9c0 R H5O_layout_ver_bounds
00000000003ab1a0 R H5O_obj_ver_bounds
00000000003aba90 R H5O_pline_ver_bounds
00000000003b2400 R H5O_sds_hyper_ver_bounds
00000000003b26c0 R H5O_sds_point_ver_bounds
00000000003b18d0 R H5O_sdspace_ver_bounds
000000000044c008 B H5T_HDSETREGREF_ALIGN_g
000000000044c010 B H5T_HOBJREF_ALIGN_g
000000000044c018 B H5T_HVL_ALIGN_g
000000000044c020 B H5T_POINTER_ALIGN_g
000000000044c000 B H5T_REF_ALIGN_g
0000000000300ab0 T H5T__init_native_float_types
00000000003047d0 T H5T__init_native_internal
00000000003943a0 R H5build_settings
This is causing a segfault for a paraview plugin that is compiled and linked against another HDF5 library. Showing the relevant bits of the stacktrace of that crash below:
#61298 0x00007fffe4c293c7 in H5T__init_native_float_types () from /work/imas/opt/EasyBuild/software/ParaView/5.12.0-foss-2023b/lib/libvtkhdf5-pv5.12.so.1
#61299 0x00007fffa9a406f7 in H5T_init () from /work/imas/opt/EasyBuild/software/HDF5/1.14.3-gompi-2023b/lib/libhdf5.so.310
#61300 0x00007fffa9acc4f3 in H5VL_init_phase2 () from /work/imas/opt/EasyBuild/software/HDF5/1.14.3-gompi-2023b/lib/libhdf5.so.310
#61301 0x00007fffa9830362 in H5_init_library () from /work/imas/opt/EasyBuild/software/HDF5/1.14.3-gompi-2023b/lib/libhdf5.so.310
#61302 0x00007fffa9830eb5 in H5open () from /work/imas/opt/EasyBuild/software/HDF5/1.14.3-gompi-2023b/lib/libhdf5.so.310
The problem is that the H5T__init_native_float_types
from libvtkhdf5-pv5.12.so.1
is executed, instead of the one from libhdf5.so.310
.
@jaswant.panchumarti tagging you here, since you were assigned to #18514 (closed)