Can't install ADIOS2 with parallel HDF5 support #4648

Aaron-Hsieh-0129 · 2025-10-06T07:24:13Z

Aaron-Hsieh-0129
Oct 6, 2025

I'm trying to use ADIOS2 with parallel HDF5 support. But when I build ADIOS2 with specified HDF5 path (parallel version), it shows errors like the following. I can install ADIOS2 with serial HDF5 but I fail to install it with parallel HDF5.

[ 84%] Building CXX object bindings/C/CMakeFiles/adios2_c_mpi.dir/adios2/c/adios2_c_adios_mpi.cpp.o
[ 84%] Building CXX object source/utils/CMakeFiles/adios_reorganize_mpi.dir/Utils.cpp.o
[ 85%] Linking CXX executable ../../../../../bin/sst_conn_tool
[ 85%] Building CXX object bindings/C/CMakeFiles/adios2_c_mpi.dir/adios2/c/adios2_c_io_mpi.cpp.o
../../../../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_dxpl_mpio'
../../../../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_fapl_mpio'
make[2]: *** [source/adios2/toolkit/sst/util/CMakeFiles/sst_conn_tool.dir/build.make:147: bin/sst_conn_tool] Error 2
make[1]: *** [CMakeFiles/Makefile2:1944: source/adios2/toolkit/sst/util/CMakeFiles/sst_conn_tool.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 86%] Linking CXX shared library ../../lib64/libadios2_c_mpi.so
[ 86%] Built target adios2_c_mpi
[ 86%] Linking CXX executable ../../bin/adios2_reorganize_mpi
../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_dxpl_mpio'
../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_fapl_mpio'
make[2]: *** [source/utils/CMakeFiles/adios_reorganize_mpi.dir/build.make:134: bin/adios2_reorganize_mpi] Error 2
make[1]: *** [CMakeFiles/Makefile2:2041: source/utils/CMakeFiles/adios_reorganize_mpi.dir/all] Error 2
[ 86%] Linking CXX shared library ../../lib64/libadios2_cxx11.so
[ 89%] Built target adios2_cxx11
[ 89%] Linking CXX executable ../../bin/bpls
[ 89%] Built target bpls
make: *** [Makefile:136: all] Error 2

It seems that ADIOS2 can't find some libraries (parallel related) HDF5 but I think I've installed and specified the correct parallel version of HDF5 as the h5pcc shown.

./h5pcc -showconfig 
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
                   HDF5 Version: 1.14.5
                  Configured on: Sun Oct  5 03:30:33 CST 2025
                  Configured by: [email protected]
                    Host system: x86_64-pc-linux-gnu
              Uname information: Linux un-ln01.twcc.ai 4.18.0-305.131.1.el8_4.x86_64 #1 SMP Fri May 17 03:52:29 EDT 2024 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /work/aaron900129/hdf5_install

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: static, shared
  Statically Linked Executables: 
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
                Extra libraries: -lz -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpicc
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API -I/work/aaron900129/hdf5-1.14.5/src/H5FDsubfiling
                    AM_CPPFLAGS: 
                        C Flags: 
                     H5 C Flags:   -c99 -Minform=warn   -s   -O3
                     AM C Flags: 
               Shared C Library: yes
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++
                      C++ Flags: 
                   H5 C++ Flags:  -std=c++11 -Minform=warn   -s  -O4
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: yes

                           Java: no


Features:
---------
                     Parallel HDF5: yes
  Parallel Filtered Dataset Writes: yes
                Large Parallel I/O: yes
                High-level library: yes
Dimension scales w/ new references: no
                  Build HDF5 Tests: yes
                  Build HDF5 Tools: yes
                   Build GIF Tools: no
                      Threadsafety: no
               Default API mapping: v114
    With deprecated public symbols: yes
            I/O filters (external): deflate(zlib)
                  _Float16 support: no
                     Map (H5M) API: no
                        Direct VFD: no
                        Mirror VFD: no
                     Subfiling VFD: no
                (Read-Only) S3 VFD: no
              (Read-Only) HDFS VFD: no
    Packages w/ extra debug output: none
                       API tracing: no
              Using memory checker: no
                  Use file locking: best-effort
         Strict file format checks: no
      Optimization instrumentation: no

This is my configuration command and output for building ADIOS2

 cmake .. \
  -DCMAKE_BUILD_TYPE=Release \
  -DCMAKE_INSTALL_PREFIX=/work/aaron900129/adios2_install \
  -DCMAKE_C_COMPILER=mpicc \
  -DCMAKE_CXX_COMPILER=mpic++ \
  -DADIOS2_USE_MPI=ON \
  -DADIOS2_USE_HDF5=ON \
  -DADIOS2_USE_Kokkos=ON \
  -DKokkos_ROOT=/work/aaron900129/kokkos_install \
  -DHDF5_ROOT=/work/aaron900129/hdf5_install
-- The C compiler identification is NVHPC 24.9.0
-- The CXX compiler identification is NVHPC 24.9.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR) 
-- Found OpenMP_C: -mp (found version "5.1")
-- Found OpenMP: TRUE (found version "5.1") found components: C
-- Could NOT find SZ (missing: SZ_LIBRARY ZSTD_LIBRARY SZ_INCLUDE_DIR) 
-- Could NOT find mgard (missing: mgard_DIR)
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) (Required is at least version "1.6.0")
-- Found CUDAToolkit: /work/aaron900129/cuda/targets/x86_64-linux/include (found version "12.6.20")
-- Found OpenMP_CXX: -mp (found version "5.1")
-- Found OpenMP: TRUE (found version "5.1") found components: CXX
-- Enabled Kokkos devices: OPENMP;SERIAL;CUDA
-- kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to the appropriate compiler for Kokkos
-- The CUDA compiler identification is NVIDIA 12.6.20 with host compiler GNU 9.4.0
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - done
-- Check for working CUDA compiler: /work/aaron900129/cuda/bin/nvcc - skipped
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done
-- Looking for a Fortran compiler
-- Looking for a Fortran compiler - /usr/bin/f95
-- The Fortran compiler identification is GNU 8.4.1
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/f95 - skipped
-- Performing Test ADIOS2_HAVE_FORTRAN_F03_ARGS
-- Performing Test ADIOS2_HAVE_FORTRAN_F03_ARGS - Success
-- Performing Test ADIOS2_HAVE_FORTRAN_GNU_ARGS
-- Performing Test ADIOS2_HAVE_FORTRAN_GNU_ARGS - Success
-- Found MPI_C: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpicc (found version "3.1")
-- Found MPI_CXX: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ (found version "3.1")
-- Found MPI_Fortran: /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/lib/libmpi_usempif08.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C Fortran CXX
-- Could NOT find ZeroMQ (missing: ZeroMQ_LIBRARY ZeroMQ_INCLUDE_DIR) (Required is at least version "4.1")
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.4.2")
-- Checking for module 'dspaces'
--   Package 'dspaces', required by 'virtual:world', not found
-- Could NOT find DataSpaces (missing: DATASPACES_VERSION DATASPACES_INCLUDE_DIR DATASPACES_LIBRARIES) (Required is at least version "2.1.1")
-- Found HDF5: /work/aaron900129/hdf5_install/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.14.5") found components: C
-- Could NOT find IME (missing: IME_LIBRARY IME_INCLUDE_DIR) 
-- Found Python: /work/aaron900129/miniconda3/bin/python3.12 (found suitable version "3.12.9", minimum required is "3.8") found components: Interpreter Development Development.Module Development.Embed
-- Found PythonModule_mpi4py: /work/aaron900129/miniconda3/lib/python3.12/site-packages/mpi4py
-- Checking for module 'libfabric'
--   Package 'libfabric', required by 'virtual:world', not found
-- Could NOT find LIBFABRIC (missing: LIBFABRIC_LIBRARIES) (Required is at least version "1.6")
-- Performing Test ADIOS2_HAVE_MPI_CLIENT_SERVER
-- Performing Test ADIOS2_HAVE_MPI_CLIENT_SERVER - Failed
-- Checking for module 'ucx'
--   Found ucx, version 1.13.0
-- Found UCX: /usr/lib64/libucp.so;/usr/lib64/libuct.so;/usr/lib64/libucs.so;/usr/lib64/libucm.so (found suitable version "1.13.0", minimum required is "1.9.0")
-- Could NOT find DAOS (missing: DAOS_LIBRARY DFS_LIBRARY DAOS_INCLUDE_DIR) 
-- Looking for shmget
-- Looking for shmget - found
-- Could NOT find Sodium (missing: sodium_LIBRARY_RELEASE sodium_LIBRARY_DEBUG sodium_INCLUDE_DIR) 
-- Could NOT find SQLite3 (missing: SQLite3_INCLUDE_DIR SQLite3_LIBRARY) 
-- Performing Test ADIOS2_USE_Fortran_flag_argument_mismatch
-- Performing Test ADIOS2_USE_Fortran_flag_argument_mismatch - Failed
-- Checking for O_DIRECT
-- Performing Test O_DIRECT_WORKS
-- Performing Test O_DIRECT_WORKS - Success

-- ADIOS2 ThirdParty: Configuring KWSys
-- Checking whether wstring is available
-- Checking whether wstring is available - yes
-- Checking whether C compiler has ptrdiff_t in stddef.h
-- Checking whether C compiler has ptrdiff_t in stddef.h - yes
-- Checking whether C compiler has ssize_t in unistd.h
-- Checking whether C compiler has ssize_t in unistd.h - yes
-- Checking whether CXX compiler has setenv
-- Checking whether CXX compiler has setenv - yes
-- Checking whether CXX compiler has unsetenv
-- Checking whether CXX compiler has unsetenv - yes
-- Checking whether CXX compiler has environ in stdlib.h
-- Checking whether CXX compiler has environ in stdlib.h - no
-- Checking whether CXX compiler has utimes
-- Checking whether CXX compiler has utimes - yes
-- Checking whether CXX compiler has utimensat
-- Checking whether CXX compiler has utimensat - yes
-- Checking whether CXX compiler struct stat has st_mtim member
-- Checking whether CXX compiler struct stat has st_mtim member - yes
-- Checking whether CXX compiler struct stat has st_mtimespec member
-- Checking whether CXX compiler struct stat has st_mtimespec member - no
-- Checking whether <ext/stdio_filebuf.h> is available
-- Checking whether <ext/stdio_filebuf.h> is available - yes

-- ADIOS2 ThirdParty: Configuring perfstubs

-- ADIOS2 ThirdParty: Configuring pybind11

-- ADIOS2 ThirdParty: Configuring pugixml

-- ADIOS2 ThirdParty: Configuring nlohmann_json

-- ADIOS2 ThirdParty: Configuring yaml-cpp

-- ADIOS2 ThirdParty: Configuring atl
CMake Deprecation Warning at thirdparty/atl/atl/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of double
-- Check size of double - done
-- Check size of float
-- Check size of float - done
-- Check size of int
-- Check size of int - done
-- Check size of short
-- Check size of short - done
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file stdlib.h
-- Looking for include file stdlib.h - found
-- Looking for include file string.h
-- Looking for include file string.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file windows.h
-- Looking for include file windows.h - not found
-- Looking for fork
-- Looking for fork - found
-- Found atl: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1")

-- ADIOS2 ThirdParty: Configuring dill
CMake Deprecation Warning at thirdparty/dill/dill/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- Check size of void*
-- Check size of void* - done
-- Check size of long
-- Check size of long - done
-- DILL - Disabling emulation
-- Found Perl: /work/aaron900129/miniconda3/bin/perl (found version "5.32.1")
-- base.ops argument is  -build_shared
-- Looking for include file stdarg.h
-- Looking for include file stdarg.h - found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for include file sys/mman.h
-- Looking for include file sys/mman.h - found
-- Looking for __clear_cache
-- Looking for __clear_cache - found
-- Found dill: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/dill/dill/dill-config.cmake (found version "3.0.0")

-- ADIOS2 ThirdParty: Configuring ffs
CMake Deprecation Warning at thirdparty/ffs/ffs/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- Check size of off_t
-- Check size of off_t - done
-- Check size of long double
-- Check size of long double - done
-- Check size of long long
-- Check size of long long - done
-- Check size of size_t
-- Check size of size_t - done
-- Looking for socket
-- Looking for socket - found
-- Found BISON: /usr/bin/bison (found version "3.0.4")
-- Found FLEX: /usr/bin/flex (found version "2.6.1")
-- Found dill: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/dill/dill/dill-config.cmake (found suitable version "3.0.0", minimum required is "3.0.0")
-- Found atl: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/atl/atl/atl-config.cmake (found suitable version "2.2.1", minimum required is "2.2.1")
-- Looking for netdb.h
-- Looking for netdb.h - found
-- Looking for netinet/in.h
-- Looking for netinet/in.h - found
-- Looking for sockLib.h
-- Looking for sockLib.h - not found
-- Looking for sys/select.h
-- Looking for sys/select.h - found
-- Looking for sys/socket.h
-- Looking for sys/socket.h - found
-- Looking for sys/times.h
-- Looking for sys/times.h - found
-- Looking for sys/uio.h
-- Looking for sys/uio.h - found
-- Looking for sys/un.h
-- Looking for sys/un.h - found
-- Looking for winsock.h
-- Looking for winsock.h - not found
-- Looking for strtof
-- Looking for strtof - found
-- Looking for strtod
-- Looking for strtod - found
-- Looking for strtold
-- Looking for strtold - found
-- Looking for getdomainname
-- Looking for getdomainname - found
-- Check size of struct iovec
-- Check size of struct iovec - done
-- Performing Test HAS_IOV_BASE_IOVEC
-- Performing Test HAS_IOV_BASE_IOVEC - Success
-- Found atl: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1")
-- Found ffs: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/ffs/ffs/ffs-config.cmake (found version "3.0.0")

-- ADIOS2 ThirdParty: Configuring enet
CMake Deprecation Warning at thirdparty/enet/enet/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- Looking for getaddrinfo
-- Looking for getaddrinfo - found
-- Looking for getnameinfo
-- Looking for getnameinfo - found
-- Looking for gethostbyaddr_r
-- Looking for gethostbyaddr_r - found
-- Looking for gethostbyname_r
-- Looking for gethostbyname_r - found
-- Looking for poll
-- Looking for poll - found
-- Looking for fcntl
-- Looking for fcntl - found
-- Looking for inet_pton
-- Looking for inet_pton - found
-- Looking for inet_ntop
-- Looking for inet_ntop - found
-- Performing Test HAS_MSGHDR_FLAGS
-- Performing Test HAS_MSGHDR_FLAGS - Success
-- Performing Test HAS_SOCKLEN_T
-- Performing Test HAS_SOCKLEN_T - Success
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
-- Found enet: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/enet/enet/enet-config.cmake (found version "1.3.14")

-- ADIOS2 ThirdParty: Configuring EVPath
CMake Deprecation Warning at thirdparty/EVPath/EVPath/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- Performing Test HAVE_MATH
-- Performing Test HAVE_MATH - Success
-- Found atl: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/atl/atl/atl-config.cmake (found suitable version "2.2.1", minimum required is "2.2.1")
-- Found ffs: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/ffs/ffs/ffs-config.cmake (found suitable version "3.0.0", minimum required is "3.0.0")
-- Looking for clock_gettime
-- Looking for clock_gettime - found
-- Looking for sys/epoll.h
-- Looking for sys/epoll.h - found
CMake Warning (dev) at thirdparty/EVPath/EVPath/CMakeLists.txt:583 (add_custom_command):
  The following keywords are not supported when using
  add_custom_command(OUTPUT): SOURCE.

  Policy CMP0175 is not set: add_custom_command() rejects invalid arguments.
  Run "cmake --help-policy CMP0175" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Looking for hostlib.h
-- Looking for hostlib.h - not found
-- Looking for sys/sockio.h
-- Looking for sys/sockio.h - not found
-- Looking for winsock2.h
-- Looking for winsock2.h - not found
-- Performing Test HAVE_FDS_BITS
-- Performing Test HAVE_FDS_BITS - Failed
-- Looking for writev
-- Looking for writev - found
-- Looking for uname
-- Looking for uname - found
-- Looking for getloadavg
-- Looking for getloadavg - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for getifaddrs
-- Looking for getifaddrs - found
-- Found EVPath: /work/aaron900129/ADIOS2-2.10.2/build/thirdparty/EVPath/EVPath/EVPathConfigCommon.cmake (found version "4.5.0")

-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
-- Performing Test ADIOS2_HAVE_FORTRAN_SUBMODULES
-- Performing Test ADIOS2_HAVE_FORTRAN_SUBMODULES - Success

ADIOS2 build configuration:
  ADIOS Version: 2.10.2
  C++ Compiler : NVHPC 24.9.0 
    /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++

  Fortran Compiler : GNU 8.4.1 
    /usr/bin/f95

  Installation prefix: /work/aaron900129/adios2_install
        bin: bin
        lib: lib64
    include: include
      cmake: lib64/cmake/adios2
     python: lib/python3.12/site-packages

  Features:
    Library Type: shared
    Build Type:   Release
    Testing: OFF
    Examples: OFF
    Build Options:
      DataMan            : OFF
      DataSpaces         : OFF
      HDF5               : ON
      HDF5_VOL           : ON
      MHS                : ON
      SST                : ON
      Fortran            : ON
      MPI                : ON
      Python             : ON
      PIP                : OFF
      Blosc2             : OFF
      BZip2              : OFF
      LIBPRESSIO         : OFF
      MGARD              : OFF
      MGARD_MDR          : OFF
      PNG                : OFF
      SZ                 : OFF
      ZFP                : ON
      DAOS               : OFF
      IME                : OFF
      O_DIRECT           : ON
      Sodium             : OFF
      Catalyst           : OFF
      SysVShMem          : ON
      UCX                : ON
      ZeroMQ             : OFF
      Profiling          : ON
      Endian_Reverse     : OFF
      Derived_Variable   : OFF
      AWSSDK             : OFF
      GPU_Support        : ON
      CUDA               : OFF
      Kokkos             : ON
      Kokkos_CUDA        : ON
      Kokkos_HIP         : OFF
      Kokkos_SYCL        : OFF
      Campaign           : OFF
    Possible RDMA DataPlanes for SST:  UCX
-- Configuring done (61.3s)
-- Generating done (1.0s)
-- Build files have been written to: /work/aaron900129/ADIOS2-2.10.2/build

Could anyone please help me find out what did I do wrong? I really want to use ADIOS2 with parallel HDF5 support. Thanks in advance!

Answered by pnorbert

Oct 6, 2025

Can you check your environment, path, LD_LIBRARY_PATH? Maybe during compiling separate tools, the compiler finds a serial hdf5 installation and uses that instead of your intended one. The cmake commands don't set the dependencies explicitly at that point, so other versions of the dependencies can cause this issue.

View full answer

vicentebolea · 2025-10-06T12:26:53Z

vicentebolea
Oct 6, 2025
Maintainer

This might be due to HDF5_IS_PARALLEL being incorrectly absent or OFF

1 reply

pnorbert Oct 6, 2025
Maintainer

HDF5_IS_PARALLEL is absent in my build, and it still works fine.
test/ADIOS2-2.10.2/build$ grep -r HDF5_IS_PARALLEL comes up empty for me

pnorbert · 2025-10-06T12:51:01Z

pnorbert
Oct 6, 2025
Maintainer

I cannot see any obviuus issue with the paths from your log. Can you please run make VERBOSE=1 to see the compile command for bindings/C/CMakeFiles/adios2_c_mpi.dir/adios2/c/adios2_c_io_mpi.cpp.o.

0 replies

Aaron-Hsieh-0129 · 2025-10-06T13:27:58Z

Aaron-Hsieh-0129
Oct 6, 2025
Author

Thanks for the quick replying!!!
I tried to add the HDF5_IS_PARALLEL flag but it showed the same errors. Here is the make VERBOSE=1 output.
There is no this file under bindings/C/CMakeFiles/adios2_c_mpi.dir/adios2/c/adios2_c_io_mpi.cpp.o and the folder is empty.

[ 77%] Linking CXX executable ../../../../../bin/sst_conn_tool
cd /work/aaron900129/ADIOS2-2.10.2/build/source/adios2/toolkit/sst/util && /work/aaron900129/local/bin/cmake -E cmake_link_script CMakeFiles/sst_conn_tool.dir/link.txt --verbose=1
/work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -fast -O3 -DNDEBUG CMakeFiles/sst_conn_tool.dir/sst_conn_tool.c.o CMakeFiles/sst_conn_tool.dir/sst_conn_tool.cxx.o ../CMakeFiles/sst.dir/dp/dp.c.o ../CMakeFiles/sst.dir/dp/dummy_dp.c.o ../CMakeFiles/sst.dir/dp/evpath_dp.c.o ../CMakeFiles/sst.dir/cp/cp_reader.c.o ../CMakeFiles/sst.dir/cp/cp_writer.c.o ../CMakeFiles/sst.dir/cp/cp_common.c.o ../CMakeFiles/sst.dir/cp/ffs_marshal.c.o ../CMakeFiles/sst.dir/sst_comm.cpp.o ../CMakeFiles/sst.dir/dp/ucx_dp.c.o ../CMakeFiles/sst.dir/cp/ffs_zfp.c.o -o ../../../../../bin/sst_conn_tool  -Wl,-rpath,/work/aaron900129/ADIOS2-2.10.2/build/lib64: ../../../../../lib64/libadios2_core_mpi.so.2.10.2 ../../../../../lib64/libadios2_core.so.2.10.2 ../../../../../lib64/libadios2_evpath.so.2.10.2 ../../../../../lib64/libadios2_ffs.so.2.10.2 ../../../../../lib64/libadios2_atl.so.2.10.2 ../../../../../lib64/libadios2_perfstubs.so.2.10.2 -ldl -lm /usr/lib64/libucp.so /usr/lib64/libuct.so /usr/lib64/libucs.so /usr/lib64/libucm.so /work/aaron900129/zfp_install/lib64/libzfp.so.1.0.1 -Wl,-rpath-link,/work/aaron900129/ADIOS2-2.10.2/build/lib64
make  -f source/utils/CMakeFiles/adios_reorganize_mpi.dir/build.make source/utils/CMakeFiles/adios_reorganize_mpi.dir/depend
make[2]: Entering directory '/work/aaron900129/ADIOS2-2.10.2/build'
cd /work/aaron900129/ADIOS2-2.10.2/build && /work/aaron900129/local/bin/cmake -E cmake_depends "Unix Makefiles" /work/aaron900129/ADIOS2-2.10.2 /work/aaron900129/ADIOS2-2.10.2/source/utils /work/aaron900129/ADIOS2-2.10.2/build /work/aaron900129/ADIOS2-2.10.2/build/source/utils /work/aaron900129/ADIOS2-2.10.2/build/source/utils/CMakeFiles/adios_reorganize_mpi.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/work/aaron900129/ADIOS2-2.10.2/build'
make  -f source/utils/CMakeFiles/adios_reorganize_mpi.dir/build.make source/utils/CMakeFiles/adios_reorganize_mpi.dir/build
make[2]: Entering directory '/work/aaron900129/ADIOS2-2.10.2/build'
[ 77%] Building CXX object source/utils/CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/main.cpp.o
cd /work/aaron900129/ADIOS2-2.10.2/build/source/utils && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DADIOS2_USE_MPI -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -MD -MT source/utils/CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/main.cpp.o -MF CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/main.cpp.o.d -o CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/main.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/source/utils/adios_reorganize/main.cpp
../../../../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_dxpl_mpio'
../../../../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_fapl_mpio'
make[2]: *** [source/adios2/toolkit/sst/util/CMakeFiles/sst_conn_tool.dir/build.make:147: bin/sst_conn_tool] Error 2
make[2]: Leaving directory '/work/aaron900129/ADIOS2-2.10.2/build'
make[1]: *** [CMakeFiles/Makefile2:1944: source/adios2/toolkit/sst/util/CMakeFiles/sst_conn_tool.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 78%] Building CXX object source/utils/CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/Reorganize.cpp.o
cd /work/aaron900129/ADIOS2-2.10.2/build/source/utils && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DADIOS2_USE_MPI -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -MD -MT source/utils/CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/Reorganize.cpp.o -MF CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/Reorganize.cpp.o.d -o CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/Reorganize.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/source/utils/adios_reorganize/Reorganize.cpp
[ 79%] Building CXX object bindings/C/CMakeFiles/adios2_c.dir/adios2/c/adios2_c_operator.cpp.o
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/C && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -Dadios2_c_EXPORTS -I/work/aaron900129/ADIOS2-2.10.2/bindings/C -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -fPIC -MD -MT bindings/C/CMakeFiles/adios2_c.dir/adios2/c/adios2_c_operator.cpp.o -MF CMakeFiles/adios2_c.dir/adios2/c/adios2_c_operator.cpp.o.d -o CMakeFiles/adios2_c.dir/adios2/c/adios2_c_operator.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/bindings/C/adios2/c/adios2_c_operator.cpp
[ 79%] Building CXX object source/utils/CMakeFiles/adios_reorganize_mpi.dir/Utils.cpp.o
cd /work/aaron900129/ADIOS2-2.10.2/build/source/utils && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DADIOS2_USE_MPI -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -MD -MT source/utils/CMakeFiles/adios_reorganize_mpi.dir/Utils.cpp.o -MF CMakeFiles/adios_reorganize_mpi.dir/Utils.cpp.o.d -o CMakeFiles/adios_reorganize_mpi.dir/Utils.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/source/utils/Utils.cpp
[ 80%] Building CXX object bindings/CXX11/CMakeFiles/adios2_cxx11.dir/adios2/cxx11/VariableNT.cpp.o
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/CXX11 && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -Dadios2_cxx11_EXPORTS -I/work/aaron900129/ADIOS2-2.10.2/bindings/CXX11 -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -fPIC -MD -MT bindings/CXX11/CMakeFiles/adios2_cxx11.dir/adios2/cxx11/VariableNT.cpp.o -MF CMakeFiles/adios2_cxx11.dir/adios2/cxx11/VariableNT.cpp.o.d -o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/VariableNT.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/bindings/CXX11/adios2/cxx11/VariableNT.cpp
[ 80%] Linking CXX shared library ../../lib64/libadios2_c.so
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/C && /work/aaron900129/local/bin/cmake -E cmake_link_script CMakeFiles/adios2_c.dir/link.txt --verbose=1
/work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -fPIC -fast -O3 -DNDEBUG -shared -Wl,-soname,libadios2_c.so.2.10 -o ../../lib64/libadios2_c.so.2.10.2 CMakeFiles/adios2_c.dir/adios2/c/adios2_c_adios.cpp.o CMakeFiles/adios2_c.dir/adios2/c/adios2_c_io.cpp.o CMakeFiles/adios2_c.dir/adios2/c/adios2_c_engine.cpp.o CMakeFiles/adios2_c.dir/adios2/c/adios2_c_variable.cpp.o CMakeFiles/adios2_c.dir/adios2/c/adios2_c_attribute.cpp.o CMakeFiles/adios2_c.dir/adios2/c/adios2_c_operator.cpp.o  -Wl,-rpath,/work/aaron900129/ADIOS2-2.10.2/build/lib64: ../../lib64/libadios2_core.so.2.10.2 -Wl,-rpath-link,/work/aaron900129/ADIOS2-2.10.2/build/lib64
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/C && /work/aaron900129/local/bin/cmake -E cmake_symlink_library ../../lib64/libadios2_c.so.2.10.2 ../../lib64/libadios2_c.so.2.10 ../../lib64/libadios2_c.so
make[2]: Leaving directory '/work/aaron900129/ADIOS2-2.10.2/build'
[ 80%] Built target adios2_c
[ 80%] Building CXX object bindings/CXX11/CMakeFiles/adios2_cxx11.dir/adios2/cxx11/fstream/ADIOS2fstream.cpp.o
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/CXX11 && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -Dadios2_cxx11_EXPORTS -I/work/aaron900129/ADIOS2-2.10.2/bindings/CXX11 -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -fPIC -MD -MT bindings/CXX11/CMakeFiles/adios2_cxx11.dir/adios2/cxx11/fstream/ADIOS2fstream.cpp.o -MF CMakeFiles/adios2_cxx11.dir/adios2/cxx11/fstream/ADIOS2fstream.cpp.o.d -o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/fstream/ADIOS2fstream.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/bindings/CXX11/adios2/cxx11/fstream/ADIOS2fstream.cpp
[ 80%] Linking CXX executable ../../bin/adios2_reorganize_mpi
cd /work/aaron900129/ADIOS2-2.10.2/build/source/utils && /work/aaron900129/local/bin/cmake -E cmake_link_script CMakeFiles/adios_reorganize_mpi.dir/link.txt --verbose=1
/work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -fast -O3 -DNDEBUG CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/main.cpp.o CMakeFiles/adios_reorganize_mpi.dir/adios_reorganize/Reorganize.cpp.o CMakeFiles/adios_reorganize_mpi.dir/Utils.cpp.o -o ../../bin/adios2_reorganize_mpi  -Wl,-rpath,/work/aaron900129/ADIOS2-2.10.2/build/lib64: ../../lib64/libadios2_core_mpi.so.2.10.2 ../../lib64/libadios2_core.so.2.10.2 -Wl,-rpath-link,/work/aaron900129/ADIOS2-2.10.2/build/lib64
../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_dxpl_mpio'
../../lib64/libadios2_core_mpi.so.2.10.2: undefined reference to `H5Pset_fapl_mpio'
make[2]: *** [source/utils/CMakeFiles/adios_reorganize_mpi.dir/build.make:134: bin/adios2_reorganize_mpi] Error 2
make[2]: Leaving directory '/work/aaron900129/ADIOS2-2.10.2/build'
make[1]: *** [CMakeFiles/Makefile2:2041: source/utils/CMakeFiles/adios_reorganize_mpi.dir/all] Error 2
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cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/CXX11 && /work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -Dadios2_cxx11_EXPORTS -I/work/aaron900129/ADIOS2-2.10.2/bindings/CXX11 -I/work/aaron900129/ADIOS2-2.10.2/source -I/work/aaron900129/ADIOS2-2.10.2/build/source -fast -O3 -DNDEBUG --c++11 -fPIC -MD -MT bindings/CXX11/CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Group.cpp.o -MF CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Group.cpp.o.d -o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Group.cpp.o -c /work/aaron900129/ADIOS2-2.10.2/bindings/CXX11/adios2/cxx11/Group.cpp
[ 80%] Linking CXX shared library ../../lib64/libadios2_cxx11.so
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/CXX11 && /work/aaron900129/local/bin/cmake -E cmake_link_script CMakeFiles/adios2_cxx11.dir/link.txt --verbose=1
/work/aaron900129/kokkos_install/bin/kokkos_launch_compiler /work/aaron900129/kokkos_install/bin/nvcc_wrapper /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ /work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ -fPIC -fast -O3 -DNDEBUG -shared -Wl,-soname,libadios2_cxx11.so.2.10 -o ../../lib64/libadios2_cxx11.so.2.10.2 CMakeFiles/adios2_cxx11.dir/adios2/cxx11/ADIOS.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Attribute.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Engine.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/IO.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Operator.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Query.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Types.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Variable.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/VariableNT.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/fstream/ADIOS2fstream.cpp.o CMakeFiles/adios2_cxx11.dir/adios2/cxx11/Group.cpp.o  -Wl,-rpath,/work/aaron900129/ADIOS2-2.10.2/build/lib64: ../../lib64/libadios2_core.so.2.10.2 -Wl,-rpath-link,/work/aaron900129/ADIOS2-2.10.2/build/lib64
cd /work/aaron900129/ADIOS2-2.10.2/build/bindings/CXX11 && /work/aaron900129/local/bin/cmake -E cmake_symlink_library ../../lib64/libadios2_cxx11.so.2.10.2 ../../lib64/libadios2_cxx11.so.2.10 ../../lib64/libadios2_cxx11.so
make[2]: Leaving directory '/work/aaron900129/ADIOS2-2.10.2/build'
[ 80%] Built target adios2_cxx11
make[1]: Leaving directory '/work/aaron900129/ADIOS2-2.10.2/build'
make: *** [Makefile:136: all] Error 2

I hope the information can help, if you need anything else for debugging please tell me. Thanks!

0 replies

pnorbert · 2025-10-06T14:35:28Z

pnorbert
Oct 6, 2025
Maintainer

The issue is at compiling/linking the first executable (adios2_reorganize_mpi) which is using libadios2_core_mpi.so.2.10.2, which in turn depend on parallel hdf5. The commands in my builds look similar, and the compiler is supposed to find the .so's dependencies automatically. I checked with NVHPC on Perlmutter and it builds just fine.

I don't know why it is not working as supposed to in your environment.

However, I had CUDA on and Kokkos OFF. I am not able to build with the available Kokkos module on that machine, so cannot exactly replicate your build.

0 replies

Aaron-Hsieh-0129 · 2025-10-06T14:50:44Z

Aaron-Hsieh-0129
Oct 6, 2025
Author

I tried to built only with HDF5 and turned Kokkos off, but it showed the same errors. So it's probably due to ADIOS2, HDF5, or the compiler. Could you tell me how you built your HDF5? Maybe I did something wrong.

This is my configuration command for parallel HDF5

./configure --enable-parallel --enable-shared --enable-cxx --enable-unsupported --prefix=/work/aaron900129/hdf5_install --disable-nonstandard-feature-float16 \
            CC=/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpicc \
            CXX=/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpic++ \
            FC=/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/bin/mpifort

0 replies

pnorbert · 2025-10-06T14:54:38Z

pnorbert
Oct 6, 2025
Maintainer

Can you check your environment, path, LD_LIBRARY_PATH? Maybe during compiling separate tools, the compiler finds a serial hdf5 installation and uses that instead of your intended one. The cmake commands don't set the dependencies explicitly at that point, so other versions of the dependencies can cause this issue.

0 replies

Aaron-Hsieh-0129 · 2025-10-06T15:05:11Z

Aaron-Hsieh-0129
Oct 6, 2025
Author

You're right!!!! It's because of the LD_LIBRARY_PATH. Thank you soooo much! I've stuck on this problem for a week, you're a life saver.

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