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nanoporetech / dorado

Oxford Nanopore's Basecaller
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cmake --build cmake-build --config Release -j #144

Closed partha434 closed 12 months ago

partha434 commented 1 year ago

While running cmake --build cmake-build --config Release -j .... I got followign error. Please help. @iiSeymour


[  8%] Built target edlib
[ 11%] Built target dorado_allocator_lib
[ 20%] Built target streamvbyte
[ 25%] Built target htslib_project
[ 36%] Built target minizip
[ 44%] Built target elzip
[ 44%] Built target vbz
[ 46%] Built target vbz_hdf_plugin
[ 48%] Built target dorado_models_lib
[ 51%] Built target dorado_io_lib
[ 81%] Built target dorado_lib
[ 82%] Linking CXX executable bin/dorado
[ 83%] Linking CXX executable dorado_tests
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5check_version: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5check_version: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Initialized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Finalized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_create_keyval'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_set_attr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_free_keyval'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function H5_build_extpath: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function H5_build_extpath: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function H5_build_extpath: error: undefined reference to '__intel_sse4_strrchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5A.o):H5A.c:function H5Aget_name_by_idx: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Aint.o):H5Aint.c:function H5A__read: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Aint.o):H5Aint.c:function H5A__attr_copy_file: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Aint.o):H5Aint.c:function H5A__attr_post_copy_file: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Bcache.o):H5Bcache.c:function H5B__cache_serialize: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cdbg.o):H5Cdbg.c:function H5C_set_prefix: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cimage.o):H5Cimage.c:function H5C__load_cache_image: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5CX.o):H5CX.c:function H5CX_set_apl: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5CX.o):H5CX.c:function H5CX_set_loc: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dbtree2.o):H5Dbtree2.c:function H5D__bt2_idx_insert: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dbtree2.o):H5Dbtree2.c:function H5D__bt2_idx_get_addr: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dbtree2.o):H5Dbtree2.c:function H5D__bt2_idx_remove: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_cmp_addr: error: undefined reference to 'MPI_Aint_diff'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__get_chunk_info_cb: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dcontig.o):H5Dcontig.c:function H5D__contig_fill: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D__create: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D__create: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D_open: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D_open: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dvirtual.o):H5Dvirtual.c:function H5D_virtual_parse_source_name: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Initialized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Finalized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Initialized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Finalized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Fint.o):H5Fint.c:function H5F_prefix_open_file: error: undefined reference to '__intel_sse4_strrchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Fint.o):H5Fint.c:function H5F_prefix_open_file: error: undefined reference to '__intel_sse4_strrchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Gname.o):H5Gname.c:function H5G__component: error: undefined reference to '__intel_sse4_strcspn'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5MM.o):H5MM.c:function H5MM_xstrdup: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5MM.o):H5MM.c:function H5MM_strdup: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Odtype.o):H5Odtype.c:function H5O_dtype_shared_encode: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Odtype.o):H5Odtype.c:function H5O_dtype_shared_encode: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Pdcpl.o):H5Pdcpl.c:function H5P_fill_value_cmp: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Pfapl.o):H5Pfapl.c:function H5P__facc_file_driver_cmp: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Pfapl.o):H5Pfapl.c:function H5P__facc_file_image_info_cmp: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5SMmessage.o):H5SMmessage.c:function H5SM_compare_cb: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_index_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_index_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_udiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_udiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_udiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_i64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_i64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_opt_possible: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__obtain_mpio_mode: error: undefined reference to 'MPI_Gather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_collective_io: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_collective_io: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_collective_io: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allgather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Comm_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Gather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Gatherv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Scatterv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Mprobe'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Get_count'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Imrecv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Isend'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Waitall'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allgather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__filtered_collective_chunk_entry_io: error: undefined reference to 'MPI_Waitall'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Comm_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Allgather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Gather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Allgatherv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Gatherv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Info_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_set_errhandler'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Comm_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Info_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_set_mpio_atomicity: error: undefined reference to 'MPI_File_set_atomicity'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_get_mpio_atomicity: error: undefined reference to 'MPI_File_get_atomicity'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_open'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_get_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_set_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_close'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_close: error: undefined reference to 'MPI_File_close'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Get_elements_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Type_size_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at_all'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at_all'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_Get_elements_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_Type_size_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_flush: error: undefined reference to 'MPI_File_sync'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_truncate: error: undefined reference to 'MPI_File_get_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_truncate: error: undefined reference to 'MPI_File_set_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_vector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_get_extent'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_get_extent'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_create_resized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'MPI_Comm_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'MPI_Comm_set_errhandler'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_dup: error: undefined reference to 'MPI_Info_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_dup: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_cmp: error: undefined reference to 'MPI_Comm_compare'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nkeys'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nkeys'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nthkey'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpio_create_large_type: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpio_create_large_type: error: undefined reference to 'MPI_Type_get_extent'
collect2: error: ld returned 1 exit status
gmake[2]: *** [tests/dorado_tests] Error 1
gmake[1]: *** [tests/CMakeFiles/dorado_tests.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_term_library: error: undefined reference to '__intel_sse4_strlen'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5check_version: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5check_version: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Initialized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Finalized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_create_keyval'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_set_attr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_free_keyval'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function HDfprintf: error: undefined reference to '__intel_sse4_strncat'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function H5_build_extpath: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function H5_build_extpath: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5system.o):H5system.c:function H5_build_extpath: error: undefined reference to '__intel_sse4_strrchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5A.o):H5A.c:function H5Aget_name_by_idx: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Aint.o):H5Aint.c:function H5A__read: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Aint.o):H5Aint.c:function H5A__attr_copy_file: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Aint.o):H5Aint.c:function H5A__attr_post_copy_file: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Bcache.o):H5Bcache.c:function H5B__cache_serialize: error: undefined reference to '__intel_avx_rep_memset'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5B2int.o):H5B2int.c:function H5B2__redistribute2: error: undefined reference to '__intel_avx_memmove'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Error_string'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cdbg.o):H5Cdbg.c:function H5C_set_prefix: error: undefined reference to '__intel_ssse3_strncpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cimage.o):H5Cimage.c:function H5C__load_cache_image: error: undefined reference to 'MPI_Bcast'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5CX.o):H5CX.c:function H5CX_set_apl: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5CX.o):H5CX.c:function H5CX_set_loc: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dbtree2.o):H5Dbtree2.c:function H5D__bt2_idx_insert: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dbtree2.o):H5Dbtree2.c:function H5D__bt2_idx_get_addr: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dbtree2.o):H5Dbtree2.c:function H5D__bt2_idx_remove: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_cmp_addr: error: undefined reference to 'MPI_Aint_diff'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__get_chunk_info_cb: error: undefined reference to '__intel_avx_rep_memcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dcontig.o):H5Dcontig.c:function H5D__contig_fill: error: undefined reference to 'MPI_Barrier'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D__create: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D__create: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D_open: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dint.o):H5Dint.c:function H5D_open: error: undefined reference to '__intel_sse4_strncmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dvirtual.o):H5Dvirtual.c:function H5D_virtual_parse_source_name: error: undefined reference to '__intel_sse4_strchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Initialized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Finalized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Initialized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Finalized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Fint.o):H5Fint.c:function H5F_prefix_open_file: error: undefined reference to '__intel_sse4_strrchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Fint.o):H5Fint.c:function H5F_prefix_open_file: error: undefined reference to '__intel_sse4_strrchr'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Gname.o):H5Gname.c:function H5G__component: error: undefined reference to '__intel_sse4_strcspn'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5MM.o):H5MM.c:function H5MM_xstrdup: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5MM.o):H5MM.c:function H5MM_strdup: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Odtype.o):H5Odtype.c:function H5O_dtype_shared_encode: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Odtype.o):H5Odtype.c:function H5O_dtype_shared_encode: error: undefined reference to '__intel_sse4_strcpy'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Pdcpl.o):H5Pdcpl.c:function H5P_fill_value_cmp: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Pfapl.o):H5Pfapl.c:function H5P__facc_file_driver_cmp: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Pfapl.o):H5Pfapl.c:function H5P__facc_file_image_info_cmp: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5SMmessage.o):H5SMmessage.c:function H5SM_compare_cb: error: undefined reference to '_intel_fast_memcmp'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_index_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_index_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5VM.o):H5VM.c:function H5VM_chunk_scaled: error: undefined reference to '__svml_u64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_idiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_udiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_udiv8_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_udiv8_mask_l9'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_i64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Ztrans.o):H5Ztrans.c:function H5Z__xform_eval_full: error: undefined reference to '__svml_i64div4'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_commit'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_opt_possible: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__obtain_mpio_mode: error: undefined reference to 'MPI_Gather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_collective_io: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_collective_io: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_collective_io: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allgather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__link_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_create_hindexed'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Comm_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Gather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Gatherv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Scatterv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Mprobe'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Get_count'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Imrecv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Isend'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list: error: undefined reference to 'MPI_Waitall'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allreduce'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allgather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__filtered_collective_chunk_entry_io: error: undefined reference to 'MPI_Waitall'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Comm_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Comm_rank'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Allgather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Gather'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Allgatherv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv: error: undefined reference to 'MPI_Gatherv'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Info_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_set_errhandler'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Comm_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Info_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_set_mpio_atomicity: error: undefined reference to 'MPI_File_set_atomicity'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_get_mpio_atomicity: error: undefined reference to 'MPI_File_get_atomicity'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_open'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_get_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_set_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_close'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_close: error: undefined reference to 'MPI_File_close'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Get_elements_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Type_size_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at_all'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at_all'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_set_view'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_Get_elements_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_Type_size_x'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_flush: error: undefined reference to 'MPI_File_sync'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_truncate: error: undefined reference to 'MPI_File_get_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_truncate: error: undefined reference to 'MPI_File_set_size'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype: error: undefined reference to 'MPI_Type_contiguous'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype: error: undefined reference to 'MPI_Type_create_struct'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_create_hindexed_block'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_vector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_get_extent'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_get_extent'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S_mpio_space_type: error: undefined reference to 'MPI_Type_create_resized'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'MPI_Comm_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'MPI_Comm_set_errhandler'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_dup: error: undefined reference to 'MPI_Info_dup'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_dup: error: undefined reference to 'MPI_Info_free'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_cmp: error: undefined reference to 'MPI_Comm_compare'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nkeys'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nkeys'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nthkey'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpio_create_large_type: error: undefined reference to 'MPI_Type_create_hvector'
/cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpio_create_large_type: error: undefined reference to 'MPI_Type_get_extent'
collect2: error: ld returned 1 exit status
gmake[2]: *** [bin/dorado] Error 1
gmake[1]: *** [CMakeFiles/dorado.dir/all] Error 2
gmake: *** [all] Error 2
iiSeymour commented 1 year ago

It looks like /cluster/software/HDF5/1.10.7-iimpi-2021a/lib/libhdf5.a that you are trying to link to was built using the Intel compiler and is using MPI which will need to be linked also.

Is there a reason you are building from source and not using the prebuilt version?

https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.2.4-linux-x64.tar.gz

partha434 commented 1 year ago

While using from the pre-built version, following the below command I got some error...If you can check..

/cluster/projects/nn9337k/dorado-0.2.3-linux-x64/bin/dorado basecaller ./models/dna_r9.4.1_e8_sup@v3.3 ./cluster/projects/nn9337k/pod5_files/sm1.pod5 --modified-bases-models ./models/dna_r9.4.1_e8_sup@v3.3_5mCG@v0 > sm1.sam

[2023-04-14 13:58:09.131] [info] > Creating basecall pipeline [2023-04-14 13:58:15.652] [error] toml::parse: file open error -> /dna_r9.4.1_e8_sup@v3.3/config.toml

iiSeymour commented 1 year ago

In the first draft of your last message you had $model/dna_r9.4.1_e8_sup@v3.3 and the error message /dna_r9.4.1_e8_sup@v3.3/config.toml shows this variable is probably unset so it's looking the fileystem root. You need to make sure the model paths you give to dorado point to the location in which you downloaded the models.

partha434 commented 1 year ago

Hello Seymour, I pointed out the error. Thank you so much. Now it is resolved.

partha434 commented 1 year ago

But now I am getting other error...

Empty sequence and qstring provided for read id 44ee01ff-ff15-4190-9d78-6ad4e0bd57c9

iiSeymour commented 1 year ago

What GPU hardware are you running on? Can you post the output of nvidia-smi

Also, I see you downloaded 0.2.3 but note 0.2.4 is the latest version.

partha434 commented 1 year ago

I tried with the latest 0.2.4 version, but got same error. Here is the output of nvidia-smi...

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 515.43.04    Driver Version: 515.43.04    CUDA Version: 11.7     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  Tesla P100-PCIE...  Off  | 00000000:39:00.0 Off |                    0 |
| N/A   34C    P0    32W / 250W |   7681MiB / 16384MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|    0   N/A  N/A     32630      C   ./bin/dorado                     7679MiB |
+-----------------------------------------------------------------------------+
iiSeymour commented 1 year ago

@partha434 unfortunately dorado doesn't have support for Pascal cards https://github.com/nanoporetech/dorado#platforms

partha434 commented 1 year ago

Is cpu basecalling possible with dorado using more threads?

sklages commented 1 year ago

@partha434 - dorado has no option to control the number of CPU threads to be used, dorado always seems to use between 2 and 5 cores on average. This is really no option IMHO. A single fast5->pod5 file (4K sequences) takes 45s on a fast GPU card and 6h20m when run in cpu-only mode using sup model(s). (Nvidia A100/40G and/or AMD EPYC CPUs).

partha434 commented 1 year ago

Thank you so much @sklages I will try the code on V100 or A100 GPU servers in near future.