ADIOS2

ADIOS2 copied to clipboard

Describe the bug Installing ADIOS2 with pipx install adios2 on macOS 14.4 fails.

To Reproduce A minimal reproducible example is preferred. Or Steps to reproduce the behavior:

1. Run pipx install adios2 in a terminal.
2. Examine the logfile output:

      [80/292] Linking C shared module thirdparty/EVPath/EVPath/adios2/adios2-evpath-modules-2_10/libadios2_cmfabric.so
      FAILED: thirdparty/EVPath/EVPath/adios2/adios2-evpath-modules-2_10/libadios2_cmfabric.so
      : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -w -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.2.sdk -bundle -Wl,-headerpad_max_install_names -L/opt/homebrew/opt/qt@5/lib -o thirdparty/EVPath/EVPath/adios2/adios2-evpath-modules-2_10/libadios2_cmfabric.so thirdparty/EVPath/EVPath/CMakeFiles/cmfabric.dir/cmfabric.c.o thirdparty/EVPath/EVPath/CMakeFiles/cmfabric.dir/ip_config.c.o  -Wl,-rpath,"\$ORIGIN" -Wl,-rpath,@loader_path/../adios2 -Wl,-rpath,"\$ORIGIN/../../adios2"  adios2/libadios2_atl.2.10.0.dylib  /opt/homebrew/Cellar/libfabric/1.20.1/lib/libfabric.dylib && :
      ld: Undefined symbols:
        _INT_CMmalloc, referenced from:
            _CMFABRIC_data_available in cmfabric.c.o
            _CMFABRIC_data_available in cmfabric.c.o
            _CMFABRIC_data_available in cmfabric.c.o
            _libcmfabric_LTX_initiate_conn in cmfabric.c.o
            _libcmfabric_LTX_initiate_conn in cmfabric.c.o
            _libcmfabric_LTX_initiate_conn in cmfabric.c.o
            _libcmfabric_LTX_non_blocking_listen in cmfabric.c.o
            ...
        _INT_CMrealloc, referenced from:
            _libcmfabric_LTX_writev_complete_notify_func in cmfabric.c.o
            _pull_thread in cmfabric.c.o
            _pull_thread in cmfabric.c.o
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      [81/292] Linking C shared library adios2/libadios2_dill.2.10.0.dylib
      [82/292] Building C object thirdparty/ffs/ffs/CMakeFiles/ffs.dir/cod.tab.c.o
      [83/292] Building CXX object thirdparty/KWSys/adios2sys/CMakeFiles/adios2sys_objects.dir/SystemTools.cxx.o
      [84/292] Building C object thirdparty/EVPath/EVPath/CMakeFiles/cmzplenet.dir/cmzplenet.c.o
      ninja: build stopped: subcommand failed.

Expected behavior It should successfully build and install ADIOS2.

Desktop (please complete the following information):

• OS/Platform: macOS 14.4 (Apple M1 Pro)
• Build:

      ADIOS2 build configuration:
        ADIOS Version: 2.10.0.0
        C++ Compiler : AppleClang 15.0.0.15000100
          /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
      
        Installation prefix: /usr/local
              bin: bin
              lib: adios2
          include: adios2/include
            cmake: adios2/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               : OFF
            HDF5_VOL           : OFF
            MHS                : ON
            SST                : ON
            Fortran            : OFF
            MPI                : OFF
            Python             : ON
            PIP                : ON
            Blosc2             : OFF
            BZip2              : OFF
            LIBPRESSIO         : OFF
            MGARD              : OFF
            MGARD_MDR          : OFF
            PNG                : ON
            SZ                 : OFF
            ZFP                : OFF
            DAOS               : OFF
            IME                : OFF
            O_DIRECT           : OFF
            Sodium             : ON
            Catalyst           : OFF
            SysVShMem          : ON
            UCX                : OFF
            ZeroMQ             : OFF
            Profiling          : ON
            Endian_Reverse     : OFF
            Derived_Variable   : OFF
            AWSSDK             : OFF
            GPU_Support        : OFF
            CUDA               : OFF
            Kokkos             : OFF
            Kokkos_CUDA        : OFF
            Kokkos_HIP         : OFF
            Kokkos_SYCL        : OFF
            Campaign           : OFF
          RDMA Transport for Staging: Available

Additional context Logfile: cmd_2024-03-21_23.07.57_pip_errors.log

Following up Was the issue fixed? Please report back.

Odd. This is trying to build the EVPath RDMA module using libfabric, but the ADIOS2/thirdparty/EVPath/CMakeLists.txt explicitly sets EVPATH_NO_RDMA to ON, which should disable any of the EVPath RDMA transports (which aren't used in ADIOS). Clearly it shouldn't be looking for libfabric, but that once looking it has found libfabric is another issue. Presumably you aren't using RDMA on a mac, so in the short term uninstalling libfabric and trying this again should work. Before the final 2.10 release, we'll make disabling RDMA in EVPath more robust.

Ok, uninstalling libfabric fixed the issue for now.

Libfabric got installed as a dependency for ADIOS2 in its Homebrew package (because I had previously done brew install adios2 on this machine). I'm guessing libfabric should probably not be treated as a dependency for ADIOS2 in Homebrew? https://github.com/Homebrew/homebrew-core/blob/c6d4f816f81b66263a5b30be57a3edb76c172cbc/Formula/a/adios2.rb#L29

Huh, news to me that there was a Homebrew recipe for ADIOS. Obviously it's been around for a while. Let me followup with some of the folks involved. Some functionality that was off by default was turned on for release 2.9, so this recipe maybe a bit rotted. Gotta see if someone can fix it.

Yes, we added this a few years ago so we can ship an openPMD-api package in homebrew. The homebrew community is kind enough to maintain it. https://github.com/search?q=org%3AHomebrew+adios2&type=pullrequests

Note that homebrew these days ships for both macOS and Linux.

Is there a dedicated flag in ADIOS2 to explicitly turn off libfabric support? That would then be needed to be added to the package in homebrew, to avoid that the build logic pics up a system libfabric randomly.

I am no ruby developer myself, but luckily the package syntax is pretty self-explanatory: https://github.com/Homebrew/homebrew-core/blob/master/Formula/a/adios2.rb