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[Bug] Cannot build wheels on linux x86 #3545

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loguille opened this issue Jan 10, 2025 · 4 comments
Open

[Bug] Cannot build wheels on linux x86 #3545

loguille opened this issue Jan 10, 2025 · 4 comments
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@johnkerl

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@loguille
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Hello,
I'm encounting an issue regarding the build of tiledbsoma from source. Indeed I would like to install tiledbsoma on my server but I encounted the error :

>>> import tiledbsoma
Illegal instruction (core dumped)

As mentionned in issue 2580. I'm then trying to build tiledbsoma from source.

/home/guillel/TileDB-SOMA/libtiledbsoma/src/reindexer/reindexer.h:37:10: fatal error: format: No such file or directory
         37 | #include <format>
            |          ^~~~~~~~
      compilation terminated.
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:79: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/reindexer/reindexer.cc.o] Error 1
      gmake[4]: *** [CMakeFiles/Makefile2:253: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/all] Error 2
      gmake[4]: *** Waiting for unfinished jobs....
      [  4%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_benchmark_function.cpp.o
      [  4%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_run_for_at_least.cpp.o
      [  5%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_stats.cpp.o
      [  5%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generator_exception.cpp.o
      [  6%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generators.cpp.o
      [  6%] Built target TILEDBSOMA_NANOARROW_OBJECT
      [  7%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generators_random.cpp.o
      [  8%] Building CXX object src/CMakeFiles/TILEDB_SOMA_GEOMETRY_OBJECTS.dir/geometry/multipolygon.cc.o
      [  9%] Building CXX object src/CMakeFiles/TILEDB_SOMA_GEOMETRY_OBJECTS.dir/geometry/operators/io/read.cc.o
      [  9%] Building CXX object src/CMakeFiles/TILEDB_SOMA_GEOMETRY_OBJECTS.dir/geometry/operators/io/write.cc.o
      [ 10%] Building CXX object src/CMakeFiles/TILEDB_SOMA_GEOMETRY_OBJECTS.dir/geometry/operators/envelope.cc.o
      [ 10%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_automake.cpp.o
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      [ 11%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_compact.cpp.o
      [ 12%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_console.cpp.o
      [ 13%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_cumulative_base.cpp.o
      [ 13%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_event_listener.cpp.o
      [ 14%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_helpers.cpp.o
      [ 14%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_junit.cpp.o
      [ 15%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_multi.cpp.o
      [ 16%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_registrars.cpp.o
      [ 16%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_sonarqube.cpp.o
      [ 16%] Built target TILEDB_SOMA_GEOMETRY_OBJECTS
      [ 17%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_streaming_base.cpp.o
      [ 17%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_tap.cpp.o
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      [ 66%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2.dir/catch2/matchers/internal/catch_matchers_impl.cpp.o
      [ 67%] Linking CXX static library libCatch2.a
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      gmake[3]: *** [Makefile:146: all] Error 2
      gmake[2]: *** [CMakeFiles/libtiledbsoma.dir/build.make:86: libtiledbsoma-prefix/src/libtiledbsoma-stamp/libtiledbsoma-build] Error 2
      gmake[1]: *** [CMakeFiles/Makefile2:158: CMakeFiles/libtiledbsoma.dir/all] Error 2
      gmake: *** [Makefile:91: all] Error 2
      Checking: /home/guillel/TileDB-SOMA/dist/lib/libtiledbsoma.so exists: False
      Checking: /home/guillel/TileDB-SOMA/dist/lib64/libtiledbsoma.so exists: False
      Checking: /home/guillel/TileDB-SOMA/dist/lib/x86_64-linux-gnu/libtiledbsoma.so exists: False
      libtiledbsoma.so: cannot open shared object file: No such file or directory
      Traceback (most recent call last):
        File "/home/guillel/miniconda3/envs/new_tiledb/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/guillel/miniconda3/envs/new_tiledb/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/guillel/miniconda3/envs/new_tiledb/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 438, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 426, in _build
          return self._build_with_temp_dir(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
          self.run_setup()
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 274, in <module>
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-5zt50r_b/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
          cmd_obj.run()
        File "<string>", line 226, in run
        File "<string>", line 188, in find_or_build_package_data
        File "/home/guillel/miniconda3/envs/new_tiledb/lib/python3.12/subprocess.py", line 571, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command '['./bld', '--tiledb=/home/guillel/TileDB-SOMA/dist']' returned non-zero exit status 2.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for tiledbsoma
Failed to build tiledbsoma
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (tiledbsoma)

I use python 3.12.8 on a server linux x86

Thanks for the help

Loïc
@johnkerl
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Hi Loïc!

What is your GCC/G++ version? We require >= 13 as we are using C++ 20, and, old GCC/G++ < 13 lack support for std::format.

@johnkerl johnkerl self-assigned this Jan 10, 2025
@loguille
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Hi,
Thanks, now tiledbsoma can be installed but when I import the packages I get the same error as previously

Python 3.12.8 | packaged by conda-forge | (main, Dec  5 2024, 14:24:40) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tiledbsoma
Illegal instruction (core dumped)

Do you have any recommendation ?

Many thanks.

@johnkerl
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Hello @loguille !

Can you please share the output of:

  • uname -a
  • grep avx2 /proc/cpuinfo
  • g++ --version

?

@loguille
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Yes for sure, here is the output I got :

  • uname -a
    Linux eomix02 5.15.0-56-generic #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

  • grep avx2 /proc/cpuinfo
    no output

  • g++ version

g++ (conda-forge gcc 13.3.0-1) 13.3.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Many thanks

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