Description of problem: Please, fix undefined references. Executing: /opt/rh/devtoolset-9/root/usr/bin/gcc -o /tmp/petsc-eg1dgwbj/config.libraries/conftest -Wl,-z,relro -fPIC -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic /tmp/petsc-eg1dgwbj/config.libraries/conftest.o -lcgns -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_INT32_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5P_CLS_FILE_CREATE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Pcreate' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tcopy' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_UINT32_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Sget_simple_extent_dims' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Eset_auto2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Sget_simple_extent_ndims' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Aget_type' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fcreate' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Sclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_SCHAR_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Aopen_name' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Gunlink' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Lget_val' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tget_native_type' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Acreate2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Aclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Pset_deflate' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_C_S1_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tset_precision' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dopen2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dget_type' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_FLOAT_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Lunpack_elink_val' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dwrite' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Lcreate_external' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Screate_simple' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Aread' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5check_version' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Iget_name' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Lis_registered' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fget_obj_ids' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5P_CLS_GROUP_CREATE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Gcreate2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Giterate' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tget_size' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Lexists' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_UCHAR_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Screate' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_IEEE_F32BE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Literate' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Gopen2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dset_extent' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_IEEE_F64BE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dget_space' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5P_CLS_FILE_ACCESS_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_UINT64_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Pset_nlinks' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Pclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fflush' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Pset_link_creation_order' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5P_CLS_LINK_ACCESS_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_IEEE_F64LE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fis_hdf5' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_INT64_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_IEEE_F32LE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Gget_objinfo' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Sselect_hyperslab' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_INT_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Gclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Ewalk2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Awrite' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Gmove' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Sget_simple_extent_npoints' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5open' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dread' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5garbage_collect' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Pset_libver_bounds' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tget_precision' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tset_size' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Aiterate2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fget_obj_count' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5P_CLS_DATASET_CREATE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5get_libversion' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fopen' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Fclose' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Glink' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5T_NATIVE_DOUBLE_g' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Dcreate2' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Tequal' /opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /lib/../lib64/libcgns.so: undefined reference to `H5Sget_select_npoints' collect2: error: ld returned 1 exit status Version-Release number of selected component (if applicable): 3.2.1-2 How reproducible: Linking to libcgns.so
Dave - cgnslib should be linked against the hdf5 library. Any idea why it isn't?
Sorry, I don't know what happened to this. Anyway, I'm confused. libcgns is linked against libdf5. It looks as if it's petsc that needs -lhdf5. $ readelf -d /usr/lib64/libcgns.so.3.4|grep hdf5 0x0000000000000001 (NEEDED) Shared library: [libhdf5.so.8] (I should probably orphan it anyway, with other things.)
I suspect that this issue is caused by using different GCC version (GCC-9 in my build against GCC-4 of cgnslib on EPEL7). PETSc is now pushed on EPEL7 without the cgns support. I will try to rebuild with it and GCC-4
It's not linked against libhdf5: [orion@rhel7 ~]$ ldd /usr/lib64/libcgns.so.3.2 linux-vdso.so.1 => (0x00007ffeeaf90000) libc.so.6 => /lib64/libc.so.6 (0x00007f54b9c10000) /lib64/ld-linux-x86-64.so.2 (0x00007f54ba2a6000) [orion@rhel7 ~]$ rpmlint cgnslib cgnslib.x86_64: W: undefined-non-weak-symbol /usr/lib64/libcgns.so.3.2 H5T_NATIVE_SCHAR_g cgnslib.x86_64: W: undefined-non-weak-symbol /usr/lib64/libcgns.so.3.2 H5P_CLS_DATASET_CREATE_g ... The gcc version shouldn't matter.
Sorry, I realize I'd got a version from copr. I don't know what's going on here. If I simply rebuild it for el7 in mock or koji scratch, it is linked correctly, unlike the version in the repo. I've never touched it, I just wanted to stop it dying when I was packaging petsc. I'll trigger a rebuild for now, but I'll drop it later. It looks as thought it needs substantial work, like to separate out the library without the graphics etc.
FEDORA-EPEL-2021-09f2e092cc has been pushed to the Fedora EPEL 7 testing repository. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2021-09f2e092cc See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-EPEL-2021-09f2e092cc has been pushed to the Fedora EPEL 7 stable repository. If problem still persists, please make note of it in this bug report.