Bug 1623439 - Undefined references to hdf5 libraries
Summary: Undefined references to hdf5 libraries
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: cgnslib
Version: rawhide
Hardware: All
OS: Linux
unspecified
high
Target Milestone: ---
Assignee: Sandro Mani
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2018-08-29 11:10 UTC by Antonio T. (sagitter)
Modified: 2018-08-30 11:24 UTC (History)
5 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2018-08-30 11:24:59 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Antonio T. (sagitter) 2018-08-29 11:10:23 UTC
Description of problem:
Error while running linker during Configure tests when i rebuild my PETsc package on rawhide (see below).

Version-Release number of selected component (if applicable):
cgnslib-3.3.1-5-fc29

How reproducible:
Rebuilding PETsc on current rawhide.

Actual results:
Undefined references of libcgns.so

Expected results:
Correctly linked to hdf5 libraries.

Additional info:

Executing: mpicc  -o /tmp/petsc-o2Wt5g/config.libraries/conftest -Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -fPIC -Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -fPIC -lgfortran -L/usr/lib64/openmpi/lib -lmpi_mpifh -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches  -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 -Wl,-z,now -fPIC   /tmp/petsc-o2Wt5g/config.libraries/conftest.o  -L/usr/lib64/openmpi/lib -lhdf5 -lcgns -ldl 
Possible ERROR while running linker: exit code 256
stderr:
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_INT32_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Pcreate'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tcopy'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_UINT32_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Sget_simple_extent_dims'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Eset_auto2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Sget_simple_extent_ndims'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Aget_type'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fcreate'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Sclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_SCHAR_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Aopen_name'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Gunlink'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Lget_val'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tget_native_type'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Acreate2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Aclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Pset_deflate'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_C_S1_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tset_precision'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dopen2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dget_type'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5P_CLS_LINK_ACCESS_ID_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_FLOAT_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Lunpack_elink_val'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dwrite'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Lcreate_external'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Screate_simple'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Aread'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5check_version'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Iget_name'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Lis_registered'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fget_obj_ids'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Gcreate2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Giterate'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tget_size'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Lexists'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_UCHAR_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Screate'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_IEEE_F32BE_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Literate'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Gopen2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dset_extent'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_IEEE_F64BE_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dget_space'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_UINT64_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Pset_nlinks'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Pclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fflush'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Pset_link_creation_order'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_IEEE_F64LE_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fis_hdf5'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_INT64_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_IEEE_F32LE_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Gget_objinfo'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Sselect_hyperslab'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_INT_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Gclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5P_CLS_GROUP_CREATE_ID_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Ewalk2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Awrite'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Gmove'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Sget_simple_extent_npoints'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5open'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dread'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5garbage_collect'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Pset_libver_bounds'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tget_precision'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tset_size'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Aiterate2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fget_obj_count'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5get_libversion'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fopen'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Fclose'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5P_CLS_FILE_CREATE_ID_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Glink'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5T_NATIVE_DOUBLE_g'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Dcreate2'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Tequal'
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64/libcgns.so: undefined reference to `H5Sget_select_npoints'
collect2: error: ld returned 1 exit status


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