Comments (3)
vdejager
commented on June 13, 2024
after successfully compiling commit f1420cc (25th of may) I tried to compile HEAD today with the same modules loaded on our HPC. I'm now getting many errors and a failing build. I've added the build commands and output below.
Any idea how to get this working on the latest code?
module load 2021
module load CMake/3.20.1-GCCcore-10.3.0
module load zstd/1.4.9-GCCcore-10.3.0
module load HDF5/1.10.7-iimpi-2021a
module load CUDA/11.3.1
module load OpenSSL/1.1
cmake -S . -B cmake-build -DOPENSSL_INCLUDE_DIR=/sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/include/openssl -DOPENSSL_SSL_LIBRARY=/sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/lib64/libssl.so -DOPENSSL_CRYPTO_LIBRARY=/sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/lib64/libcrypto.so
cmake --build cmake-build --config Release -- -j
ctest --test-dir cmake-build$ cmake -S . -B cmake-build
`
-- Submodule update
-- Found HDF5: /sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a;/sw/arch/Centos8/EB_production/2021/software/Szip/2.1.1-GCCcore-10.3.0/lib/libsz.so;/sw/arch/Centos8/EB_production/2021/software/zlib/1.2.11-GCCcore-10.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so;/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5_cpp.a;/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a;/sw/arch/Centos8/EB_production/2021/software/Szip/2.1.1-GCCcore-10.3.0/lib/libsz.so;/sw/arch/Centos8/EB_production/2021/software/zlib/1.2.11-GCCcore-10.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so (found version "1.10.7") found components: C CXX HL
-- Using prebuilt Koi from
-- Found koi_lib
-- Found pod5-0.0.19-Linux
-- Found torch-1.10.2-Linux
-- Caffe2: CUDA detected: 11.3
-- Caffe2: CUDA nvcc is: /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/bin/nvcc
-- Caffe2: CUDA toolkit directory: /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1
-- Caffe2: Header version is: 11.3
-- Found cuDNN: v8.. (include: /projects/0/lwc2020006/software/dorado_latest/dorado/dorado/3rdparty/fake_cudnn, library: /projects/0/lwc2020006/software/dorado_latest/dorado/dorado/3rdparty/fake_cudnn)
-- /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/libnvrtc.so shorthash is 1ea278b5
-- Automatic GPU detection failed. Building for common architectures.
-- Autodetected CUDA architecture(s): 3.5;5.0;5.2;6.0;6.1;7.0;7.5;8.0;8.6;8.6+PTX
-- Added CUDA NVCC flags for: -gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=sm_75;-gencode;arch=compute_80,code=sm_80;-gencode;arch=compute_86,code=sm_86;-gencode;arch=compute_86,code=compute_86
-- Found OpenSSL: /sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/lib64/libcrypto.so (found version "1.1.1g")
-- Using CMake version 3.20.1
CMake Deprecation Warning at dorado/3rdparty/elzip/extlibs/minizip/CMakeLists.txt:56 (cmake_policy):
The OLD behavior for policy CMP0074 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
-- Using ZLIB 1.2.12.1
-- Using OpenSSL 1.1.1g
-- Character encoding support requires iconv
-- The following features have been enabled:
* MZ_COMPAT, Enables compatibility layer
* MZ_ZLIB, Enables ZLIB compression
* MZ_FETCH_LIBS, Enables fetching third-party libraries if not found
* MZ_OPENSSL, Enables OpenSSL for encryption
* MZ_LIBBSD, Build with libbsd for crypto random
-- The following features have been disabled:
* MZ_BZIP2, Enables BZIP2 compression
* MZ_LZMA, Enables LZMA & XZ compression
* MZ_ZSTD, Enables ZSTD compression
* MZ_LIBCOMP, Enables Apple compression
* MZ_FORCE_FETCH_LIBS, Enables fetching third-party libraries always
* MZ_PKCRYPT, Enables PKWARE traditional encryption
* MZ_WZAES, Enables WinZIP AES encryption
* MZ_SIGNING, Enables zip signing support
* MZ_ICONV, Enables iconv string encoding conversion library
* MZ_COMPRESS_ONLY, Only support compression
* MZ_DECOMPRESS_ONLY, Only support decompression
* MZ_FILE32_API, Builds using posix 32-bit file api
* MZ_BUILD_TESTS, Builds minizip test executable
* MZ_BUILD_UNIT_TESTS, Builds minizip unit test project
* MZ_BUILD_FUZZ_TESTS, Builds minizip fuzzer executables
* MZ_CODE_COVERAGE, Builds with code coverage flags
-- Building version 1.0.3
-- Found HDF5: /sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a;/sw/arch/Centos8/EB_production/2021/software/Szip/2.1.1-GCCcore-10.3.0/lib/libsz.so;/sw/arch/Centos8/EB_production/2021/software/zlib/1.2.11-GCCcore-10.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so (found suitable version "1.10.7", minimum required is "1.8.16")
-- CUDA toolkit dir is /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1
-- Configuring done
WARNING: Target "dorado_lib" requests linking to directory "/projects/0/lwc2020006/software/dorado_latest/dorado/dorado/3rdparty/fake_cudnn". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "dorado" requests linking to directory "/projects/0/lwc2020006/software/dorado_latest/dorado/dorado/3rdparty/fake_cudnn". Targets may link only to libraries. CMake is dropping the item.
CMake Warning at CMakeLists.txt:140 (add_executable):
Cannot generate a safe runtime search path for target dorado because files
in some directories may conflict with libraries in implicit directories:
runtime library [libcufft.so.10] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib64 may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
runtime library [libcurand.so.10] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib64 may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
runtime library [libcublas.so.11] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib64 may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
runtime library [libnvrtc.so.11.2] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
Some of these libraries may not be found correctly.
WARNING: Target "dorado_tests" requests linking to directory "/projects/0/lwc2020006/software/dorado_latest/dorado/dorado/3rdparty/fake_cudnn". Targets may link only to libraries. CMake is dropping the item.
CMake Warning at tests/CMakeLists.txt:7 (add_executable):
Cannot generate a safe runtime search path for target dorado_tests because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libcufft.so.10] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib64 may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
runtime library [libcurand.so.10] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib64 may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
runtime library [libcublas.so.11] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib64 may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
runtime library [libnvrtc.so.11.2] in /sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib may be hidden by files in:
/sw/arch/Centos8/EB_production/2021/software/CUDA/11.3.1/lib/stubs
Some of these libraries may not be found correctly.
-- Generating done
-- Build files have been written to: /projects/0/lwc2020006/software/dorado_latest/dorado/cmake-build
Consolidate compiler generated dependencies of target minizip
Consolidate compiler generated dependencies of target hdf_test_utils
[ 22%] Built target minizip
[ 33%] Built target streamvbyte
[ 36%] Built target hdf_test_utils
Consolidate compiler generated dependencies of target elzip
Consolidate compiler generated dependencies of target vbz
[ 42%] Built target elzip
[ 49%] Built target vbz
Consolidate compiler generated dependencies of target vbz_hdf_plugin
[ 52%] Built target vbz_hdf_plugin
Consolidate compiler generated dependencies of target vbz_test
Consolidate compiler generated dependencies of target vbz_hdf_plugin_test
Consolidate compiler generated dependencies of target dorado_lib
[ 58%] Built target vbz_test
[ 60%] Linking CXX executable ../../../../../bin/vbz_hdf_plugin_test
[ 61%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/read_pipeline/ReadPipeline.cpp.o
[ 63%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/cli/basecaller.cpp.o
[ 65%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/nn/CRFModel.cpp.o
[ 66%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/read_pipeline/ScalerNode.cpp.o
[ 68%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/read_pipeline/BasecallerNode.cpp.o
[ 69%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/data_loader/DataLoader.cpp.o
[ 71%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/read_pipeline/WriterNode.cpp.o
[ 73%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/decode/CPUDecoder.cpp.o
[ 74%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/decode/beam_search.cpp.o
[ 76%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/utils/stitch.cpp.o
[ 77%] Building CXX object CMakeFiles/dorado_lib.dir/dorado/utils/tensor_utils.cpp.o
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Initialized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Finalized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'OMPI_C_MPI_COMM_NULL_COPY_FN'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_create_keyval'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'ompi_mpi_comm_self'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_set_attr'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Comm_free_keyval'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5.o):H5.c:function H5_init_library: error: undefined reference to 'MPI_Error_string'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5AC.o):H5AC.c:function H5AC_create: error: undefined reference to 'ompi_mpi_comm_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'ompi_mpi_comm_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'ompi_mpi_byte'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'ompi_mpi_byte'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'ompi_mpi_comm_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'ompi_mpi_byte'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Bcast'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'ompi_mpi_comm_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5C.o):H5C.c:function H5C_protect: error: undefined reference to 'MPI_Error_string'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cimage.o):H5Cimage.c:function H5C__load_cache_image: error: undefined reference to 'ompi_mpi_byte'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cimage.o):H5Cimage.c:function H5C__load_cache_image: error: undefined reference to 'MPI_Bcast'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cimage.o):H5Cimage.c:function H5C__prep_image_for_file_close: error: undefined reference to 'ompi_mpi_unsigned'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cimage.o):H5Cimage.c:function H5C__prep_image_for_file_close: error: undefined reference to 'ompi_mpi_unsigned'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5CX.o):H5CX.c:function H5CX_set_apl: error: undefined reference to 'MPI_Barrier'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5CX.o):H5CX.c:function H5CX_set_loc: error: undefined reference to 'MPI_Barrier'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_create_hindexed'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_commit'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_create_hvector'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_commit'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Barrier'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dchunk.o):H5Dchunk.c:function H5D__chunk_allocate: error: undefined reference to 'MPI_Type_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dcontig.o):H5Dcontig.c:function H5D__contig_fill: error: undefined reference to 'MPI_Barrier'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Initialized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Finalized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'ompi_mpi_comm_world'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk2_cb: error: undefined reference to 'MPI_Comm_rank'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Initialized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Finalized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'ompi_mpi_comm_world'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Eint.o):H5Eint.c:function H5E__walk1_cb: error: undefined reference to 'MPI_Comm_rank'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5ACmpio.o):H5ACmpio.c:function H5AC__receive_haddr_list.part.0: error: undefined reference to 'ompi_mpi_unsigned'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5ACmpio.o):H5ACmpio.c:function H5AC__propagate_flushed_and_still_clean_entries_list.part.0: error: undefined reference to 'ompi_mpi_unsigned'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_create_hindexed'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_commit'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_create_hindexed'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Cmpio.o):H5Cmpio.c:function H5C_apply_candidate_list: error: undefined reference to 'MPI_Type_commit'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__filtered_collective_chunk_entry_io: error: undefined reference to 'MPI_Waitall'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Comm_size'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Comm_rank'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'ompi_mpi_op_sum'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'ompi_mpi_int'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Allreduce'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'ompi_mpi_int'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Gather'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Gatherv'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'ompi_mpi_int'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Allgather'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_array_gatherv.constprop.0: error: undefined reference to 'MPI_Allgatherv'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list.part.0: error: undefined reference to 'MPI_Scatterv'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list.part.0: error: undefined reference to 'MPI_Isend'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list.part.0: error: undefined reference to 'MPI_Get_count'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list.part.0: error: undefined reference to 'MPI_Imrecv'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list.part.0: error: undefined reference to 'MPI_Mprobe'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__construct_filtered_io_info_list.part.0: error: undefined reference to 'MPI_Waitall'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'ompi_mpi_unsigned_long_long'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'ompi_mpi_op_max'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allreduce'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'ompi_mpi_c_bool'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Allgather'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_contiguous'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_filtered_collective_io: error: undefined reference to 'MPI_Type_contiguous'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_get_sum_chunk.part.0.isra.0: error: undefined reference to 'ompi_mpi_op_sum'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_get_sum_chunk.part.0.isra.0: error: undefined reference to 'ompi_mpi_int'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_get_sum_chunk.part.0.isra.0: error: undefined reference to 'MPI_Allreduce'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__multi_chunk_collective_io: error: undefined reference to 'MPI_Gather'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__chunk_collective_io: error: undefined reference to 'ompi_mpi_unsigned_long_long'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__chunk_collective_io: error: undefined reference to 'MPI_Allgather'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__chunk_collective_io: error: undefined reference to 'MPI_Type_create_struct'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__chunk_collective_io: error: undefined reference to 'MPI_Type_create_struct'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__chunk_collective_io: error: undefined reference to 'MPI_Type_create_hindexed'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_opt_possible: error: undefined reference to 'ompi_mpi_op_bor'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Dmpio.o):H5Dmpio.c:function H5D__mpio_opt_possible: error: undefined reference to 'MPI_Allreduce'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'ompi_mpi_info_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Info_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'ompi_mpi_errors_return'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_set_errhandler'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Comm_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_dup: error: undefined reference to 'MPI_Info_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'MPI_Comm_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'ompi_mpi_info_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpi.o):H5FDmpi.c:function H5FD_mpi_comm_info_free: error: undefined reference to 'MPI_Info_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_Get_elements_x'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_Type_size_x'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_set_view'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_set_view'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_write: error: undefined reference to 'MPI_File_write_at_all'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Get_elements_x'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Type_size_x'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_set_view'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_set_view'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_Get_elements_x'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'ompi_mpi_long_long_int'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_read: error: undefined reference to 'MPI_File_read_at_all'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_truncate: error: undefined reference to 'MPI_File_get_size'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_truncate: error: undefined reference to 'MPI_File_set_size'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_flush: error: undefined reference to 'MPI_File_sync'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_close: error: undefined reference to 'MPI_File_close'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'ompi_mpi_info_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'ompi_mpi_comm_self'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_open'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_rank'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_size'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_get_size'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Comm_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_Info_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_close'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_mpio_open: error: undefined reference to 'MPI_File_set_size'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Comm_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'ompi_mpi_info_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Info_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5Pget_fapl_mpio: error: undefined reference to 'MPI_Comm_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_set_mpio_atomicity: error: undefined reference to 'MPI_File_set_atomicity'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5FDmpio.o):H5FDmpio.c:function H5FD_get_mpio_atomicity: error: undefined reference to 'MPI_File_get_atomicity'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_contiguous'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_contiguous'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_get_extent'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_create_hvector'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_get_extent'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_get_extent'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_create_resized'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_reg_hyper_type: error: undefined reference to 'MPI_Type_vector'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype.part.0: error: undefined reference to 'MPI_Type_create_hindexed_block'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype.part.0: error: undefined reference to 'MPI_Type_create_hindexed_block'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype.part.0: error: undefined reference to 'MPI_Type_create_hindexed_block'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype.part.0: error: undefined reference to 'MPI_Type_create_hindexed_block'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_create_point_datatype.part.0: error: undefined reference to 'MPI_Type_create_struct'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype.constprop.0: error: undefined reference to 'MPI_Type_create_hvector'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype.constprop.0: error: undefined reference to 'MPI_Type_create_struct'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype.constprop.0: error: undefined reference to 'ompi_mpi_datatype_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype.constprop.0: error: undefined reference to 'ompi_mpi_datatype_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__obtain_datatype.constprop.0: error: undefined reference to 'ompi_mpi_datatype_null'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5Smpio.o):H5Smpio.c:function H5S__mpio_span_hyper_type: error: undefined reference to 'MPI_Type_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'MPI_Comm_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'ompi_mpi_errors_return'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_dup: error: undefined reference to 'MPI_Comm_set_errhandler'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_dup: error: undefined reference to 'MPI_Info_dup'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_dup: error: undefined reference to 'MPI_Info_free'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_comm_cmp: error: undefined reference to 'MPI_Comm_compare'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nkeys'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nkeys'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpi_info_cmp: error: undefined reference to 'MPI_Info_get_nthkey'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-2021a/lib/libhdf5.a(H5mpi.o):H5mpi.c:function H5_mpio_create_large_type: error: undefined reference to 'MPI_Type_create_hvector'
/sw/arch/Centos8/EB_production/2021/software/HDF5/1.10.7-gompi-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]: *** [dorado/3rdparty/hdf_plugins/vbz_plugin/test/CMakeFiles/vbz_hdf_plugin_test.dir/build.make:131: bin/vbz_hdf_plugin_test] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:1258: dorado/3rdparty/hdf_plugins/vbz_plugin/test/CMakeFiles/vbz_hdf_plugin_test.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
[ 79%] Linking CXX static library lib/libdorado_lib.a
[ 87%] Built target dorado_lib
gmake: *** [Makefile:166: all] Error 2
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vellamike
commented on June 13, 2024
@vdejager could you try this again? We've made many improvements to install ability since June.
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vdejager
commented on June 13, 2024
I tried this again, but I still run into the same HDF5lib related error. I've tried several options on our HPC, but none worked. It alwasy fails at building the vbz_hdf_plugin.
I'm currently using
#
cmake -S . -B cmake-build -DOPENSSL_INCLUDE_DIR=/sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/include/openssl -DOPENSSL_SSL_LIBRARY=/sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/lib64/libssl.so -DOPENSSL_CRYPTO_LIBRARY=/sw/arch/Centos8/EB_production/2021/software/OpenSSL/1.1/lib64/libcrypto.so
# this step fails at building the vbz_hdf_plugin :
cmake --build cmake-build --config Release -- -j
maybe I'm missing something.. The currently loaded modules are::
Currently Loaded Modules:
1) 2021 6) cURL/7.76.0-GCCcore-10.3.0 11) binutils/2.36.1-GCCcore-10.3.0 16) zstd/1.4.9-GCCcore-10.3.0 21) libpciaccess/0.16-GCCcore-10.3.0 26) gompi/2021a
2) GCCcore/10.3.0 7) XZ/5.2.5-GCCcore-10.3.0 12) numactl/2.0.14-GCCcore-10.3.0 17) CUDA/11.3.1 22) hwloc/2.4.1-GCCcore-10.3.0 27) HDF5/1.10.7-gompi-2021a
3) ncurses/6.2-GCCcore-10.3.0 8) libarchive/3.5.1-GCCcore-10.3.0 13) UCX/1.10.0-GCCcore-10.3.0 18) OpenSSL/1.1 23) libevent/2.1.12-GCCcore-10.3.0
4) zlib/1.2.11-GCCcore-10.3.0 9) gzip/1.10-GCCcore-10.3.0 14) Szip/2.1.1-GCCcore-10.3.0 19) GCC/10.3.0 24) libfabric/1.12.1-GCCcore-10.3.0
5) bzip2/1.0.8-GCCcore-10.3.0 10) lz4/1.9.3-GCCcore-10.3.0 15) CMake/3.20.1-GCCcore-10.3.0 20) libxml2/2.9.10-GCCcore-10.3.0 25) OpenMPI/4.1.1-GCC-10.3.0
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Related Issues (20)
- demultiplex HOT 4
- Question: BAM vs FASTQ basecalling outputs HOT 4
- Basecaller with --modified-bases-models option HOT 2
- CUDA device requested but no devices found HOT 4
- Basecall process 100% but memory is still occupied for a long time HOT 4
- Empty values for columns "template_start" and "template_duration" in summary for barcoded reads HOT 1
- Dafult preset lr:hq for Dorado version-v0.6 HOT 1
- Problem building with cmake on an intel macbook pro 2020. HOT 5
- Running duplex still 0% for the last 12 hours HOT 8
- Barcode demultiplexing with dorado 0.6.1 HOT 2
- basecalling with hac v4.2 vs v4.3 model HOT 1
- Trimming existing datasets returns malformed fastq files HOT 1
- Corrupted aux data for read HOT 3
- Putting a link to Dorado binaries in a public workflow or document
- Read splitting HOT 3
- No POD5 or FAST5 data found in path HOT 3
- dorado v7.3.9 adapter trimming HOT 1
- trimming confusion HOT 10
- Dorado demultiplexing question HOT 2
- Dorado basecalling what's next ? Correlation with modkit output and transposable elements HOT 2
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