Issues in compilation

[EdmundBenedict]

Hi, I am very sorry to bother you, but I have been having issues with compiling the HOPR code. It seems to get through the download and compilation of HDF5 and CGN fine, and gets through the HOPR compilation until it gets to the linking stage, then fails with the error:

[100%] Linking Fortran executable bin/hopr /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(cg_ftoc.c.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(cgns_error.c.o): relocation R_X86_64_32 against symbolcgns_error_mess' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(cgns_internals.c.o): relocation R_X86_64_32S against undefined symbol posit_stack' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(cgns_io.c.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(cgnslib.c.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(ADF_interface.c.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../share/GNU-MPI/CGNS/build/build/lib/libcgns.a(ADF_internals.c.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC ../share/GNU-MPI/HDF5/build/lib/libhdf5_fortran.a(H5Pf.o): In functionh5pset_fapl_mpio_c': H5Pf.c:(.text+0x2c7d): undefined reference to MPI_Comm_f2c' H5Pf.c:(.text+0x2c89): undefined reference toMPI_Info_f2c' ../share/GNU-MPI/HDF5/build/lib/libhdf5_fortran.a(H5Pf.o): In function h5pget_fapl_mpio_c': H5Pf.c:(.text+0x2cd5): undefined reference toMPI_Comm_c2f' H5Pf.c:(.text+0x2ce2): undefined reference to MPI_Info_c2f' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5.o): In functionH5_init_library': H5.c:(.text+0x111e): undefined reference to MPI_Initialized' H5.c:(.text+0x1128): undefined reference toMPI_Finalized' H5.c:(.text+0x12f8): undefined reference to OMPI_C_MPI_COMM_NULL_COPY_FN' H5.c:(.text+0x1309): undefined reference toMPI_Comm_create_keyval' H5.c:(.text+0x131c): undefined reference to ompi_mpi_comm_self' H5.c:(.text+0x1323): undefined reference toMPI_Comm_set_attr' H5.c:(.text+0x1333): undefined reference to MPI_Comm_free_keyval' H5.c:(.text+0x1353): undefined reference toMPI_Error_string' H5.c:(.text+0x13d9): undefined reference to MPI_Error_string' H5.c:(.text+0x15d3): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5AC.o): In function H5AC_create': H5AC.c:(.text+0x3a9d): undefined reference toompi_mpi_comm_null' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5C.o): In function H5C_protect': H5C.c:(.text+0x9db9): undefined reference toompi_mpi_comm_null' H5C.c:(.text+0x9e38): undefined reference to ompi_mpi_byte' H5C.c:(.text+0x9e42): undefined reference toMPI_Bcast' H5C.c:(.text+0xa20a): undefined reference to ompi_mpi_comm_null' H5C.c:(.text+0xa230): undefined reference toompi_mpi_byte' H5C.c:(.text+0xa23a): undefined reference to MPI_Bcast' H5C.c:(.text+0xa32f): undefined reference toompi_mpi_byte' H5C.c:(.text+0xa341): undefined reference to MPI_Bcast' H5C.c:(.text+0xaa3e): undefined reference toompi_mpi_comm_null' H5C.c:(.text+0xb0b7): undefined reference to MPI_Error_string' H5C.c:(.text+0xb32d): undefined reference toMPI_Error_string' H5C.c:(.text+0xc090): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Cimage.o): In functionH5Cload_cache_image': H5Cimage.c:(.text+0x2149): undefined reference to ompi_mpi_byte' H5Cimage.c:(.text+0x2156): undefined reference toMPI_Bcast' H5Cimage.c:(.text+0x234b): undefined reference to ompi_mpi_byte' H5Cimage.c:(.text+0x235a): undefined reference toMPI_Bcast' H5Cimage.c:(.text+0x237a): undefined reference to MPI_Error_string' H5Cimage.c:(.text+0x3802): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Cimage.o): In function `H5Cprep_image_for_file_close': H5Cimage.c:(.text+0x40bd): undefined reference to ompi_mpi_unsigned' H5Cimage.c:(.text+0x40d0): undefined reference toMPI_Bcast' H5Cimage.c:(.text+0x42d2): undefined reference to ompi_mpi_unsigned' H5Cimage.c:(.text+0x42e3): undefined reference toMPI_Bcast' H5Cimage.c:(.text+0x4831): undefined reference to MPI_Error_string' H5Cimage.c:(.text+0x4986): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5CX.o): In function H5CX_set_apl': H5CX.c:(.text+0x1320): undefined reference toompi_mpi_comm_null' H5CX.c:(.text+0x132b): undefined reference to MPI_Barrier' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5CX.o): In functionH5CX_set_loc': H5CX.c:(.text+0x1624): undefined reference to ompi_mpi_comm_null' H5CX.c:(.text+0x162b): undefined reference toMPI_Barrier' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dchunk.o): In function H5D__chunk_allocate': H5Dchunk.c:(.text+0xbfe2): undefined reference toompi_mpi_comm_null' H5Dchunk.c:(.text+0xc08e): undefined reference to MPI_Type_free' H5Dchunk.c:(.text+0xc09f): undefined reference toMPI_Type_free' H5Dchunk.c:(.text+0xcc63): undefined reference to MPI_Error_string' H5Dchunk.c:(.text+0xcd11): undefined reference toMPI_Error_string' H5Dchunk.c:(.text+0xcfcc): undefined reference to ompi_mpi_byte' H5Dchunk.c:(.text+0xcfe2): undefined reference toMPI_Type_create_hindexed' H5Dchunk.c:(.text+0xd002): undefined reference to MPI_Error_string' H5Dchunk.c:(.text+0xd11c): undefined reference toMPI_Type_commit' H5Dchunk.c:(.text+0xd13c): undefined reference to MPI_Error_string' H5Dchunk.c:(.text+0xd28d): undefined reference toompi_mpi_byte' H5Dchunk.c:(.text+0xd2a0): undefined reference to MPI_Type_create_hvector' H5Dchunk.c:(.text+0xd2c0): undefined reference toMPI_Error_string' H5Dchunk.c:(.text+0xd34f): undefined reference to MPI_Type_commit' H5Dchunk.c:(.text+0xd36f): undefined reference toMPI_Error_string' H5Dchunk.c:(.text+0xd450): undefined reference to MPI_Barrier' H5Dchunk.c:(.text+0xd4de): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dcontig.o): In function H5D__contig_fill': H5Dcontig.c:(.text+0x14eb): undefined reference toompi_mpi_comm_null' H5Dcontig.c:(.text+0x16fc): undefined reference to ompi_mpi_comm_null' H5Dcontig.c:(.text+0x19f4): undefined reference toMPI_Barrier' H5Dcontig.c:(.text+0x1a14): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dio.o): In functionH5Dioinfo_adjust.isra.2.part.3': H5Dio.c:(.text+0x790): undefined reference to ompi_mpi_comm_null' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Eint.o): In functionH5E_walk2_cb': H5Eint.c:(.text+0x147): undefined reference to MPI_Initialized' H5Eint.c:(.text+0x151): undefined reference toMPI_Finalized' H5Eint.c:(.text+0x26b): undefined reference to ompi_mpi_comm_world' H5Eint.c:(.text+0x275): undefined reference toMPI_Comm_rank' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Eint.o): In function H5E_walk1_cb': H5Eint.c:(.text+0x3f3): undefined reference toMPI_Initialized' H5Eint.c:(.text+0x3fd): undefined reference to MPI_Finalized' H5Eint.c:(.text+0x51b): undefined reference toompi_mpi_comm_world' H5Eint.c:(.text+0x525): undefined reference to MPI_Comm_rank' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Fsuper.o): In functionH5Fsuper_read': H5Fsuper.c:(.text+0x12cf): undefined reference to ompi_mpi_comm_null' H5Fsuper.c:(.text+0x12ed): undefined reference toompi_mpi_byte' H5Fsuper.c:(.text+0x12ff): undefined reference to MPI_Bcast' H5Fsuper.c:(.text+0x131f): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Z.o): In function H5Z__flush_file_cb': H5Z.c:(.text+0xdb): undefined reference toompi_mpi_comm_null' H5Z.c:(.text+0xe5): undefined reference to MPI_Barrier' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5ACmpio.o): In functionH5ACreceive_haddr_list': H5ACmpio.c:(.text+0x1ac): undefined reference to ompi_mpi_unsigned' H5ACmpio.c:(.text+0x1c6): undefined reference toMPI_Bcast' H5ACmpio.c:(.text+0x20c): undefined reference to MPI_Error_string' H5ACmpio.c:(.text+0x2c7): undefined reference toompi_mpi_byte' H5ACmpio.c:(.text+0x2d6): undefined reference to MPI_Bcast' H5ACmpio.c:(.text+0x302): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5ACmpio.o): In function `H5ACpropagate_flushed_and_still_clean_entries_list': H5ACmpio.c:(.text+0x5ac): undefined reference to ompi_mpi_unsigned' H5ACmpio.c:(.text+0x5c1): undefined reference toMPI_Bcast' H5ACmpio.c:(.text+0x6a4): undefined reference to MPI_Error_string' H5ACmpio.c:(.text+0x84e): undefined reference toompi_mpi_byte' H5ACmpio.c:(.text+0x85a): undefined reference to MPI_Bcast' H5ACmpio.c:(.text+0x99f): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5ACmpio.o): In function H5AC__run_sync_point': H5ACmpio.c:(.text+0x1683): undefined reference toMPI_Barrier' H5ACmpio.c:(.text+0x16d6): undefined reference to ompi_mpi_unsigned' H5ACmpio.c:(.text+0x16eb): undefined reference toMPI_Bcast' H5ACmpio.c:(.text+0x1790): undefined reference to MPI_Barrier' H5ACmpio.c:(.text+0x18b5): undefined reference toMPI_Barrier' H5ACmpio.c:(.text+0x18d5): undefined reference to MPI_Error_string' H5ACmpio.c:(.text+0x1a29): undefined reference toMPI_Barrier' H5ACmpio.c:(.text+0x1a79): undefined reference to MPI_Barrier' H5ACmpio.c:(.text+0x1c24): undefined reference toMPI_Error_string' H5ACmpio.c:(.text+0x1d29): undefined reference to MPI_Barrier' H5ACmpio.c:(.text+0x1da4): undefined reference toMPI_Error_string' H5ACmpio.c:(.text+0x1e4c): undefined reference to MPI_Error_string' H5ACmpio.c:(.text+0x1f5c): undefined reference toompi_mpi_byte' H5ACmpio.c:(.text+0x1f71): undefined reference to MPI_Bcast' H5ACmpio.c:(.text+0x1f95): undefined reference toMPI_Error_string' H5ACmpio.c:(.text+0x2019): undefined reference to MPI_Error_string' H5ACmpio.c:(.text+0x209f): undefined reference toMPI_Error_string' H5ACmpio.c:(.text+0x21f2): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Cmpio.o): In functionH5C_apply_candidate_list': H5Cmpio.c:(.text+0xd9e): undefined reference to ompi_mpi_byte' H5Cmpio.c:(.text+0xdbb): undefined reference toMPI_File_set_view' H5Cmpio.c:(.text+0xddb): undefined reference to MPI_Error_string' H5Cmpio.c:(.text+0xf3d): undefined reference toMPI_File_write_at_all' H5Cmpio.c:(.text+0xf5d): undefined reference to MPI_Error_string' H5Cmpio.c:(.text+0x102c): undefined reference toMPI_File_set_view' H5Cmpio.c:(.text+0x10b6): undefined reference to MPI_Error_string' H5Cmpio.c:(.text+0x11b9): undefined reference toompi_mpi_byte' H5Cmpio.c:(.text+0x11cf): undefined reference to MPI_Type_create_hindexed' H5Cmpio.c:(.text+0x11ef): undefined reference toMPI_Error_string' H5Cmpio.c:(.text+0x1297): undefined reference to MPI_Type_commit' H5Cmpio.c:(.text+0x12b7): undefined reference toMPI_Error_string' H5Cmpio.c:(.text+0x1364): undefined reference to MPI_Type_free' H5Cmpio.c:(.text+0x1382): undefined reference toMPI_Type_free' H5Cmpio.c:(.text+0x13a8): undefined reference to MPI_Error_string' H5Cmpio.c:(.text+0x14db): undefined reference toMPI_Error_string' H5Cmpio.c:(.text+0x1571): undefined reference to ompi_mpi_byte' H5Cmpio.c:(.text+0x1582): undefined reference toMPI_Type_create_hindexed' H5Cmpio.c:(.text+0x15a2): undefined reference to MPI_Error_string' H5Cmpio.c:(.text+0x1618): undefined reference toMPI_Type_commit' H5Cmpio.c:(.text+0x1638): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dmpio_get_sum_chunk.isra.0': H5Dmpio.c:(.text+0x25d): undefined reference to ompi_mpi_op_sum' H5Dmpio.c:(.text+0x269): undefined reference toompi_mpi_int' H5Dmpio.c:(.text+0x27a): undefined reference to MPI_Allreduce' H5Dmpio.c:(.text+0x2a4): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In function H5D__filtered_collective_chunk_entry_io.isra.1': H5Dmpio.c:(.text+0xc43): undefined reference toMPI_Waitall' H5Dmpio.c:(.text+0x1132): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dmpio_array_gatherv.constprop.5': H5Dmpio.c:(.text+0x13dd): undefined reference to MPI_Comm_size' H5Dmpio.c:(.text+0x13ea): undefined reference toMPI_Comm_rank' H5Dmpio.c:(.text+0x13f1): undefined reference to ompi_mpi_op_sum' H5Dmpio.c:(.text+0x13f8): undefined reference toompi_mpi_int' H5Dmpio.c:(.text+0x140d): undefined reference to MPI_Allreduce' H5Dmpio.c:(.text+0x1493): undefined reference toompi_mpi_int' H5Dmpio.c:(.text+0x14af): undefined reference to MPI_Gather' H5Dmpio.c:(.text+0x14d5): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x14f0): undefined reference to MPI_Gatherv' H5Dmpio.c:(.text+0x1544): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x1638): undefined reference to ompi_mpi_int' H5Dmpio.c:(.text+0x1656): undefined reference toMPI_Allgather' H5Dmpio.c:(.text+0x16db): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x16f0): undefined reference toMPI_Allgatherv' H5Dmpio.c:(.text+0x1744): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x17ec): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x1894): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x192a): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In function H5D__construct_filtered_io_info_list': H5Dmpio.c:(.text+0x2200): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x2208): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x222b): undefined reference toMPI_Scatterv' H5Dmpio.c:(.text+0x2446): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x2468): undefined reference toMPI_Isend' H5Dmpio.c:(.text+0x24ef): undefined reference to MPI_Waitall' H5Dmpio.c:(.text+0x25d8): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x25e0): undefined reference to MPI_Get_count' H5Dmpio.c:(.text+0x2635): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x2645): undefined reference to MPI_Imrecv' H5Dmpio.c:(.text+0x268b): undefined reference toMPI_Mprobe' H5Dmpio.c:(.text+0x26bb): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x280a): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x295d): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x2a34): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x2efb): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:(.text+0x2fd5): more undefined references toMPI_Error_string' follow ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In function H5D__link_chunk_filtered_collective_io': H5Dmpio.c:(.text+0x30a4): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x31f0): undefined reference to MPI_Type_free' H5Dmpio.c:(.text+0x321e): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x323a): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x35b7): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x3671): undefined reference to ompi_mpi_unsigned_long_long' H5Dmpio.c:(.text+0x368f): undefined reference toMPI_Allgather' H5Dmpio.c:(.text+0x39ca): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x3ba2): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x3bb6): undefined reference to MPI_Type_create_hindexed' H5Dmpio.c:(.text+0x3bd6): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x3d11): undefined reference to MPI_Type_commit' H5Dmpio.c:(.text+0x3d31): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x3de2): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x3df6): undefined reference toMPI_Type_create_hindexed' H5Dmpio.c:(.text+0x3e16): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x3f2f): undefined reference toMPI_Type_commit' H5Dmpio.c:(.text+0x400f): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dmulti_chunk_filtered_collective_io': H5Dmpio.c:(.text+0x44b3): undefined reference to ompi_mpi_op_max' H5Dmpio.c:(.text+0x44ba): undefined reference toompi_mpi_unsigned_long_long' H5Dmpio.c:(.text+0x4516): undefined reference to MPI_Allreduce' H5Dmpio.c:(.text+0x47c1): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x4897): undefined reference to ompi_mpi_c_bool' H5Dmpio.c:(.text+0x48be): undefined reference toMPI_Allgather' H5Dmpio.c:(.text+0x491b): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x494e): undefined reference toMPI_Type_contiguous' H5Dmpio.c:(.text+0x4960): undefined reference to MPI_Type_commit' H5Dmpio.c:(.text+0x4986): undefined reference toMPI_Type_contiguous' H5Dmpio.c:(.text+0x4998): undefined reference to MPI_Type_commit' H5Dmpio.c:(.text+0x4bb7): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x4bd0): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x4c6b): undefined reference toompi_mpi_byte' H5Dmpio.c:(.text+0x4e12): undefined reference to MPI_Type_free' H5Dmpio.c:(.text+0x4e2f): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x4fa2): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x5072): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x5105): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x5197): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:(.text+0x5229): more undefined references to MPI_Error_string' follow ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dinter_collective_io': H5Dmpio.c:(.text+0x52f8): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x538e): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x53aa): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x54d6): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x54f6): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dlink_chunk_collective_io': H5Dmpio.c:(.text+0x5782): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x58b3): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x58e1): undefined reference to MPI_Type_free' H5Dmpio.c:(.text+0x58fd): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x5b2c): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x5b40): undefined reference toMPI_Bcast' H5Dmpio.c:(.text+0x5f57): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x6442): undefined reference toMPI_Type_create_struct' H5Dmpio.c:(.text+0x6462): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x6557): undefined reference toMPI_Type_commit' H5Dmpio.c:(.text+0x6577): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x6750): undefined reference toMPI_Type_create_struct' H5Dmpio.c:(.text+0x6770): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x6815): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x6975): undefined reference to MPI_Type_commit' H5Dmpio.c:(.text+0x69cd): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x69e6): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x6a81): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x6a9e): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x6bd4): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In function `H5Dmulti_chunk_collective_io': H5Dmpio.c:(.text+0x7041): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x7136): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x723e): undefined reference to MPI_Type_free' H5Dmpio.c:(.text+0x7264): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x7303): undefined reference to MPI_Type_free' H5Dmpio.c:(.text+0x7314): undefined reference toMPI_Error_string' H5Dmpio.c:(.text+0x76d0): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x76ed): undefined reference toMPI_Gather' H5Dmpio.c:(.text+0x77fa): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x7809): undefined reference toMPI_Bcast' H5Dmpio.c:(.text+0x782c): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x795d): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In function H5D__mpio_opt_possible': H5Dmpio.c:(.text+0x7c8f): undefined reference toompi_mpi_op_bor' H5Dmpio.c:(.text+0x7c9b): undefined reference to ompi_mpi_unsigned' H5Dmpio.c:(.text+0x7caa): undefined reference toMPI_Allreduce' H5Dmpio.c:(.text+0x7d86): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dcontig_collective_read': H5Dmpio.c:(.text+0x7fb8): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x805e): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x807a): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x8116): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x8136): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Dmpio.o): In functionH5Dcontig_collective_write': H5Dmpio.c:(.text+0x8478): undefined reference to ompi_mpi_byte' H5Dmpio.c:(.text+0x851e): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x853a): undefined reference to MPI_Error_string' H5Dmpio.c:(.text+0x85d6): undefined reference toMPI_Type_free' H5Dmpio.c:(.text+0x85f6): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Fmpi.o): In functionH5F_mpi_get_comm': H5Fmpi.c:(.text+0x253): undefined reference to ompi_mpi_comm_null' H5Fmpi.c:(.text+0x2f1): undefined reference toompi_mpi_comm_null' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Fmpi.o): In function H5F_mpi_retrieve_comm': H5Fmpi.c:(.text+0x810): undefined reference toompi_mpi_comm_null' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpi.o): In function H5FD_mpi_get_comm': H5FDmpi.c:(.text+0xee): undefined reference toompi_mpi_comm_null' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpi.o): In function H5FD_mpi_comm_info_dup': H5FDmpi.c:(.text+0x1ef): undefined reference toompi_mpi_comm_null' H5FDmpi.c:(.text+0x1f6): undefined reference to ompi_mpi_info_null' H5FDmpi.c:(.text+0x223): undefined reference toMPI_Comm_dup' H5FDmpi.c:(.text+0x23d): undefined reference to MPI_Info_dup' H5FDmpi.c:(.text+0x24c): undefined reference toompi_mpi_errors_return' H5FDmpi.c:(.text+0x255): undefined reference to MPI_Comm_set_errhandler' H5FDmpi.c:(.text+0x2dd): undefined reference toMPI_Comm_free' H5FDmpi.c:(.text+0x2f3): undefined reference to MPI_Info_free' H5FDmpi.c:(.text+0x324): undefined reference toMPI_Error_string' H5FDmpi.c:(.text+0x3b4): undefined reference to MPI_Error_string' H5FDmpi.c:(.text+0x444): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpi.o): In function H5FD_mpi_comm_info_free': H5FDmpi.c:(.text+0x506): undefined reference toompi_mpi_comm_null' H5FDmpi.c:(.text+0x510): undefined reference to MPI_Comm_free' H5FDmpi.c:(.text+0x519): undefined reference toompi_mpi_info_null' H5FDmpi.c:(.text+0x526): undefined reference to MPI_Info_free' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5FD_mpio_write': H5FDmpio.c:(.text+0xe8): undefined reference to ompi_mpi_byte' H5FDmpio.c:(.text+0x189): undefined reference toMPI_File_write_at' H5FDmpio.c:(.text+0x1a3): undefined reference to MPI_Get_elements_x' H5FDmpio.c:(.text+0x1ba): undefined reference toMPI_Type_size_x' H5FDmpio.c:(.text+0x24b): undefined reference to ompi_mpi_byte' H5FDmpio.c:(.text+0x25a): undefined reference toMPI_File_set_view' H5FDmpio.c:(.text+0x2b2): undefined reference to MPI_File_write_at' H5FDmpio.c:(.text+0x2c1): undefined reference toompi_mpi_byte' H5FDmpio.c:(.text+0x2da): undefined reference to MPI_File_set_view' H5FDmpio.c:(.text+0x2fa): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x388): undefined reference to MPI_File_write_at_all' H5FDmpio.c:(.text+0x3a8): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x494): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x583): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x609): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x6ed): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:(.text+0x7a2): more undefined references to MPI_Error_string' follow ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5FD_mpio_read': H5FDmpio.c:(.text+0x868): undefined reference to ompi_mpi_byte' H5FDmpio.c:(.text+0x8fb): undefined reference toMPI_File_read_at' H5FDmpio.c:(.text+0x915): undefined reference to MPI_Get_elements_x' H5FDmpio.c:(.text+0x92f): undefined reference toMPI_Type_size_x' H5FDmpio.c:(.text+0x9ce): undefined reference to ompi_mpi_byte' H5FDmpio.c:(.text+0x9d8): undefined reference toMPI_File_set_view' H5FDmpio.c:(.text+0xa37): undefined reference to MPI_File_read_at' H5FDmpio.c:(.text+0xa55): undefined reference toMPI_Bcast' H5FDmpio.c:(.text+0xa6a): undefined reference to ompi_mpi_byte' H5FDmpio.c:(.text+0xa83): undefined reference toMPI_File_set_view' H5FDmpio.c:(.text+0xab0): undefined reference to MPI_Get_elements_x' H5FDmpio.c:(.text+0xac3): undefined reference toompi_mpi_long_long_int' H5FDmpio.c:(.text+0xad2): undefined reference to MPI_Bcast' H5FDmpio.c:(.text+0xaf2): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0xba0): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0xc2f): undefined reference toMPI_File_read_at' H5FDmpio.c:(.text+0xc60): undefined reference to MPI_File_read_at_all' H5FDmpio.c:(.text+0xc7c): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0xd64): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0xdea): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0xe70): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0xf25): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:(.text+0xfda): more undefined references to MPI_Error_string' follow ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5FD_mpio_close': H5FDmpio.c:(.text+0x11e3): undefined reference to MPI_File_close' H5FDmpio.c:(.text+0x1224): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In function H5FD_mpio_truncate': H5FDmpio.c:(.text+0x157b): undefined reference toompi_mpi_byte' H5FDmpio.c:(.text+0x158a): undefined reference to MPI_Bcast' H5FDmpio.c:(.text+0x15bc): undefined reference toMPI_File_set_size' H5FDmpio.c:(.text+0x15cd): undefined reference to MPI_Barrier' H5FDmpio.c:(.text+0x15f8): undefined reference toMPI_File_get_size' H5FDmpio.c:(.text+0x1618): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x1695): undefined reference toMPI_Barrier' H5FDmpio.c:(.text+0x16b5): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x174f): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x17fc): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x1884): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In function H5FD_mpio_flush': H5FDmpio.c:(.text+0x1959): undefined reference toMPI_File_sync' H5FDmpio.c:(.text+0x197c): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5FD_mpio_open': H5FDmpio.c:(.text+0x1c88): undefined reference to ompi_mpi_comm_null' H5FDmpio.c:(.text+0x1c8f): undefined reference toompi_mpi_info_null' H5FDmpio.c:(.text+0x1cfd): undefined reference to ompi_mpi_comm_self' H5FDmpio.c:(.text+0x1d7e): undefined reference toMPI_File_open' H5FDmpio.c:(.text+0x1d9e): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x1e35): undefined reference toMPI_Comm_free' H5FDmpio.c:(.text+0x1e46): undefined reference to MPI_Info_free' H5FDmpio.c:(.text+0x1e7b): undefined reference toMPI_Comm_rank' H5FDmpio.c:(.text+0x1e92): undefined reference to MPI_Comm_size' H5FDmpio.c:(.text+0x1eb2): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x1f3d): undefined reference to MPI_File_close' H5FDmpio.c:(.text+0x1f64): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x205e): undefined reference to MPI_File_get_size' H5FDmpio.c:(.text+0x2072): undefined reference toompi_mpi_byte' H5FDmpio.c:(.text+0x2081): undefined reference to MPI_Bcast' H5FDmpio.c:(.text+0x20e9): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x21c0): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x223e): undefined reference toMPI_File_set_size' H5FDmpio.c:(.text+0x225b): undefined reference to MPI_Error_string' H5FDmpio.c:(.text+0x2306): undefined reference toMPI_Barrier' H5FDmpio.c:(.text+0x235e): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5Pset_fapl_mpio': H5FDmpio.c:(.text+0x244b): undefined reference to ompi_mpi_comm_null' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5Pget_fapl_mpio': H5FDmpio.c:(.text+0x2686): undefined reference to ompi_mpi_comm_null' H5FDmpio.c:(.text+0x2720): undefined reference toMPI_Comm_dup' H5FDmpio.c:(.text+0x273e): undefined reference to ompi_mpi_info_null' H5FDmpio.c:(.text+0x274c): undefined reference toMPI_Info_dup' H5FDmpio.c:(.text+0x2863): undefined reference to ompi_mpi_info_null' H5FDmpio.c:(.text+0x288a): undefined reference toMPI_Error_string' H5FDmpio.c:(.text+0x291b): undefined reference to MPI_Comm_free' H5FDmpio.c:(.text+0x29e4): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In function H5FD_set_mpio_atomicity': H5FDmpio.c:(.text+0x3962): undefined reference toMPI_File_set_atomicity' H5FDmpio.c:(.text+0x398c): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5FDmpio.o): In functionH5FD_get_mpio_atomicity': H5FDmpio.c:(.text+0x3a4c): undefined reference to MPI_File_get_atomicity' H5FDmpio.c:(.text+0x3a94): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o): In function H5S_mpio_create_point_datatype': H5Smpio.c:(.text+0x38): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x4d): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0x146): undefined reference toMPI_Type_create_hindexed_block' H5Smpio.c:(.text+0x162): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x1ed): undefined reference toMPI_Type_create_hindexed_block' H5Smpio.c:(.text+0x20d): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x2a5): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x2d4): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x3bb): undefined reference toMPI_Type_create_hindexed_block' H5Smpio.c:(.text+0x3f3): undefined reference to MPI_Type_create_struct' H5Smpio.c:(.text+0x428): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x451): undefined reference to MPI_Type_commit' H5Smpio.c:(.text+0x46e): undefined reference toMPI_Type_commit' H5Smpio.c:(.text+0x48a): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x543): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x604): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x68a): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o): In function H5S_mpio_create_large_type': H5Smpio.c:(.text+0xbb2): undefined reference toMPI_Type_contiguous' H5Smpio.c:(.text+0xbd4): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0xbe4): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0xc04): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0xc21): undefined reference toMPI_Type_get_extent' H5Smpio.c:(.text+0xc7e): undefined reference to MPI_Type_create_struct' H5Smpio.c:(.text+0xc90): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0xc98): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0xca0): undefined reference toMPI_Type_commit' H5Smpio.c:(.text+0xcd9): undefined reference to MPI_Type_create_hvector' H5Smpio.c:(.text+0xd03): undefined reference toMPI_Type_create_hvector' H5Smpio.c:(.text+0xd15): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0xd32): undefined reference toMPI_Type_commit' H5Smpio.c:(.text+0xd52): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0xe0a): undefined reference toMPI_Type_create_hvector' H5Smpio.c:(.text+0xe2a): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0xeb4): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0xf3a): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0xfc0): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x1046): undefined reference to MPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:(.text+0x10cc): more undefined references toMPI_Error_string' follow ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o): In function H5S_mpio_hyper_type': H5Smpio.c:(.text+0x135f): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x1370): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0x13d5): undefined reference toMPI_Type_contiguous' H5Smpio.c:(.text+0x13ef): undefined reference to MPI_Type_get_extent' H5Smpio.c:(.text+0x1430): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x143a): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x147b): undefined reference toMPI_Type_get_extent' H5Smpio.c:(.text+0x1633): undefined reference to ompi_mpi_byte' H5Smpio.c:(.text+0x16be): undefined reference toMPI_Type_create_hindexed' H5Smpio.c:(.text+0x16cb): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x16eb): undefined reference toMPI_Type_create_resized' H5Smpio.c:(.text+0x16f6): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x1726): undefined reference toMPI_Type_create_hvector' H5Smpio.c:(.text+0x174b): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x17ce): undefined reference toMPI_Type_vector' H5Smpio.c:(.text+0x17db): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x1802): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x187b): undefined reference to ompi_mpi_byte' H5Smpio.c:(.text+0x18de): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x1985): undefined reference to MPI_Type_commit' H5Smpio.c:(.text+0x19c5): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x1a51): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x1add): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x1b68): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x1c22): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o): In function H5S_obtain_datatype': H5Smpio.c:(.text+0x1dd4): undefined reference toMPI_Type_create_hvector' H5Smpio.c:(.text+0x1de6): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x1fd7): undefined reference toompi_mpi_datatype_null' H5Smpio.c:(.text+0x2089): undefined reference to MPI_Type_create_struct' H5Smpio.c:(.text+0x20a6): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x20e5): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0x2105): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x2196): undefined reference to MPI_Type_create_struct' H5Smpio.c:(.text+0x21c9): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x21e5): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x230d): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x2331): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x23fc): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x241c): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x24b9): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x24d2): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x2564): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x25f6): undefined reference to MPI_Type_create_hindexed' H5Smpio.c:(.text+0x261b): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x2820): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x2987): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o): In function H5S_mpio_span_hyper_type': H5Smpio.c:(.text+0x2aa8): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x2ab2): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0x2b18): undefined reference toMPI_Type_commit' H5Smpio.c:(.text+0x2b43): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x2b78): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x2b9a): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0x2bbd): undefined reference toMPI_Type_contiguous' H5Smpio.c:(.text+0x2bcd): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x2be6): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x2bf0): undefined reference to MPI_Type_contiguous' H5Smpio.c:(.text+0x2c04): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x2c16): undefined reference to MPI_Type_get_extent' H5Smpio.c:(.text+0x2c7d): undefined reference toMPI_Type_create_struct' H5Smpio.c:(.text+0x2c8f): undefined reference to MPI_Type_free' H5Smpio.c:(.text+0x2c97): undefined reference toMPI_Type_free' H5Smpio.c:(.text+0x2cb3): undefined reference to MPI_Type_commit' H5Smpio.c:(.text+0x2cd3): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x2e24): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x2ecc): undefined reference toMPI_Error_string' H5Smpio.c:(.text+0x2f54): undefined reference to MPI_Error_string' H5Smpio.c:(.text+0x2ff9): undefined reference toMPI_Error_string' ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:(.text+0x307f): more undefined references to MPI_Error_string' follow ../share/GNU-MPI/HDF5/build/lib/libhdf5.a(H5Smpio.o): In functionH5S_mpio_space_type': H5Smpio.c:(.text+0x3311): undefined reference to ompi_mpi_byte' H5Smpio.c:(.text+0x3358): undefined reference toompi_mpi_byte' H5Smpio.c:(.text+0x3697): undefined reference to `ompi_mpi_byte' /usr/bin/ld: final link failed: Symbol needs debug section which does not exist collect2: error: ld returned 1 exit status CMakeFiles/hopr.dir/build.make:106: recipe for target 'bin/hopr' failed make[2]: [bin/hopr] Error 1 CMakeFiles/Makefile2:68: recipe for target 'CMakeFiles/hopr.dir/all' failed make[1]: [CMakeFiles/hopr.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2

I have tried setting LIBS_USE_MPI to false, and this does remove the MPI error messages, but the "can not be used when making a PIE object; recompile with -fPIC" error messages remain, even after adding the -fPIC flags. This is on a Ubuntu 18.04.5 LTS system, but I cannot figure out what I'm doing wrong Thank you very much

[flexi-framework]

Hi, sorry for the late response. There seems to be an issue with compiling HDF5 within hopr when using MPI. However, if the HDF5 is compiled manually (i.e. outside of hopr), everything works fine. I hope we can identify the issue and fix it soon. But this only causes the MPI error messages.

However, I cannot reproduce the persisting error message of "can not be used when making a PIE object; recompile with -fPIC". Could you please provide some more details?

• The last merge 2 weeks ago changed the CMake structure of the project. Do you have this problem with a clean build "from scratch" with an up-to-date repository?
• What is your CMake configuration? I assume you build HDF5 and CGNS within the hopr project?
• Could you tell us which compiler and which version you use?

I hope we can then find the issue.

[EdmundBenedict]

Hi, thank you for your response.

I cloned the repository a week ago first, and have redownloaded it several times since then, so the repository should be up to date. In the first few tries, I did not alter the Cmake configuration at all, so it had the form:

CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /home/edders/hopr/hopr
HOPR_YPLUSESTIMATOR OFF
LIBS_BUILD_CGNS ON
LIBS_BUILD_CGNS_INT 32
LIBS_BUILD_CGNS_TAG v3.4.1
LIBS_BUILD_HDF5 ON
LIBS_USE_MKL OFF
LIBS_USE_MPI ON

Although I have also tried with debug options, and yes, when I set LIBS_BUILD_HDF5 = OFF the MPI errors disappear. The Cmake version I use is 3.10.2 and the compiler is gfortran-5.5.0

-- The C compiler identification is GNU 5.5.0 -- Check for working C compiler: /home/linuxbrew/.linuxbrew/bin/cc -- Check for working C compiler: /home/linuxbrew/.linuxbrew/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long -- Check size of long - done -- Check size of off_t -- Check size of offt - done -- The Fortran compiler identification is GNU 5.5.0 -- Check for working Fortran compiler: /home/linuxbrew/.linuxbrew/bin/gfortran -- Check for working Fortran compiler: /home/linuxbrew/.linuxbrew/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /home/linuxbrew/.linuxbrew/bin/gfortran supports Fortran 90 -- Checking whether /home/linuxbrew/.linuxbrew/bin/gfortran supports Fortran 90 -- yes -- Detecting Fortran/C Interface -- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling -- Fortran name mangling convention: LOWERCASE -- Testing Fortran Fortran2003 - OK -- Testing Fortran Fortran2008TS - OK -- Testing Fortran Fortran2008 - OK -- Testing Fortran Sizeof_int - OK -- Testing Fortran FortranConcat - Fail -- Performing Test CHECK_HAVE_STAT64_STRUCT -- Performing Test CHECK_HAVE_STAT64_STRUCT - Failed -- Configuring done -- Generating done -- Build files have been written to: /home/edders/hopr/hopr/share/GNU-MPI/CGNS/build/src/cgns-build

I apologise for the delay in my response, Edmund

[flexi-framework]

Hi, sorry for my late response. I tried to compile hopr with your CMake settings and also with CMake 3.1.2 and the GNU 5 Compiler on Ubuntu 20.04 and with the standard 7.3 Compiler on Ubuntu 18.04. Unfortunately, I could not reproduce the error; all cases I've tried worked fine with LIBS_BUILD_HDF5=OFF. So there seems to be something strange going on. There are some ideas I have left:

• You can checkout the old CMake configuration at commit 0aa58a9. Does it work with this?
• Is there a special reason you use the relatively old GNU 5 instead of the standard 7.3 of Ubuntu 18.04? Updating the compiler might help to solve the issue
• Could you please try to also compile CGNS by yourself? If it is linked in a standard location, hopr should be able to locate it. CGNS also builds with CMake. You should set the flags: -DCMAKE_INSTALL_PREFIX=INSERT_HERE_YOUR_WANTED_PATH/ -DCGNS_ENABLE_FORTRAN=ON -DCGNS_BUILD_SHARED=OFF -DCGNS_USE_SHARED=OFF -DCMAKE_BUILD_TYPE=Release -DCGNS_BUILD_CGNSTOOLS=OFF -DCGNS_ENABLE_HDF5=OFF -DCGNS_ENABLE_PARALLEL=OFF -DCGNS_ENABLE_TESTS=OFF -DCMAKE_SKIP_RPATH=ON

I hope something helps. Please keep us posted.

[EdmundBenedict]

Thank you for all of your help! The old CMake configuration from commit 0aa58a9 runs fine, with no issues in compilation even with HOPR_BUILD_HDF5 and HOPR_BUILD_CGNS on, and all the tutorials seem to run fine with the resultant binary. About gcc, it is slightly strange: when I call "gcc --version" it outputs 5.5.0, but I have gcc-7 installed, although the compiler seems to link to gcc-7 in the CMake configuration file:

CMAKE_C_COMPILER /usr/bin/cc
CMAKE_C_COMPILER_AR /usr/bin/gcc-ar-7
CMAKE_C_COMPILER_RANLIB /usr/bin/gcc-ranlib-7
... CMAKE_Fortran_COMPILER /usr/bin/f95
CMAKE_Fortran_COMPILER_AR /usr/bin/gcc-ar-7
CMAKE_Fortran_COMPILER_RANLIB */usr/bin/gcc-ranlib-7

It uses gcc-5 when I call "make":

checking for config linux-gnu... found compiler '/usr/bin/mpicc' is GNU gcc-5.5.0 compiler '/usr/bin/mpif90' is GNU gfortran-5.5.0 compiler 'g++' is GNU g++-5.5.0 ... -- The C compiler identification is GNU 5.5.0 ... -- The Fortran compiler identification is GNU 5.5.0

Perhaps I need to change the priority of the gcc compilers. I will try to compile CGNS and let you know if there are any developments. Thanks again!