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-fvisibility-inlines-hidden breaks libprotobuf (and potentially other software) #73

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pitrou opened this issue May 11, 2022 · 14 comments
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bug Something isn't working

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@pitrou
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pitrou commented May 11, 2022

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

The -fvisibility-inlines-hidden compiler option is described thusly in the GCC wiki:

This causes all inlined class member functions to have hidden visibility, causing significant export symbol table size & binary size reductions

This looks theoretically harmless, except that whether class member are defined inline may depend on exact compilation options.

One typical example is when a function declaration depends on whether NDEBUG is enabled. This is exactly what libprotobuf 3.20.1 does (but not 3.19.4):

#if defined(NDEBUG) || defined(_MSC_VER)
  ~InternalMetadata() {
    if (HasMessageOwnedArenaTag()) {
      delete reinterpret_cast<Arena*>(ptr_ - kMessageOwnedArenaTagMask);
    }
  }
#else
  ~InternalMetadata();
#endif

What happens is then:

  • conda-forge compiles libprotobuf 3.20.1 with NDEBUG defined (release mode), so ~InternalMetadata, being inlined, isn't exported by libprotobuf.so
  • third-party software, when compiling and linking in debug mode against libprotobuf (so with NDEBUG not defined), expects to find the ~InternalMetadata in libprotobuf.so, and fails

Installed packages

# packages in environment at /home/antoine/miniconda3/envs/pyarrow:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_sysroot_linux-64_curr_repodata_hack 3                   h5bd9786_13    conda-forge
abseil-cpp                20211102.0           h27087fc_1    conda-forge
aiobotocore               1.4.2                    pypi_0    pypi
aiohttp                   3.7.4.post0              pypi_0    pypi
aioitertools              0.8.0                    pypi_0    pypi
alabaster                 0.7.12                   pypi_0    pypi
archery                   0.1.0                     dev_0    <develop>
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
async-timeout             3.0.1                    pypi_0    pypi
attrs                     21.2.0                   pypi_0    pypi
autopep8                  1.5.7                    pypi_0    pypi
aws-c-auth                0.6.11              h2f9c894_10    conda-forge
aws-c-cal                 0.5.17               h6b4091c_0    conda-forge
aws-c-common              0.6.20               h166bdaf_0    conda-forge
aws-c-compression         0.2.14              h8333888_10    conda-forge
aws-c-event-stream        0.2.7               h3c68b06_43    conda-forge
aws-c-http                0.6.14               h6db1ea3_1    conda-forge
aws-c-io                  0.10.22              h991c0f4_0    conda-forge
aws-c-mqtt                0.7.10              h9f869e8_15    conda-forge
aws-c-s3                  0.1.38               h1c0cbb8_4    conda-forge
aws-c-sdkutils            0.1.2                h8333888_1    conda-forge
aws-checksums             0.1.12               h8333888_9    conda-forge
aws-crt-cpp               0.17.28              h070cc90_2    conda-forge
aws-sdk-cpp               1.9.253              h0519c9a_0    conda-forge
babel                     2.9.1                    pypi_0    pypi
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.1                pyhd3eb1b0_0    defaults
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.10.0                   pypi_0    pypi
benchmark                 1.6.1                h9c3ff4c_0    conda-forge
binutils                  2.36.1               hdd6e379_2    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_9    conda-forge
black                     22.3.0             pyhd8ed1ab_0    conda-forge
blinker                   1.4                      pypi_0    pypi
boost-cpp                 1.71.0               h7f8727e_1    defaults
botocore                  1.20.106                 pypi_0    pypi
breathe                   4.31.0                   pypi_0    pypi
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotlipy                  0.7.0                    pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
c-compiler                1.4.2                h166bdaf_0    conda-forge
ca-certificates           2022.4.26            h06a4308_0    defaults
certifi                   2021.10.8        py39hf3d152e_2    conda-forge
cffi                      1.14.6                   pypi_0    pypi
chardet                   4.0.0                    pypi_0    pypi
charset-normalizer        2.0.7                    pypi_0    pypi
clang                     13.0.1               ha770c72_0    conda-forge
clang-13                  13.0.1          default_hc23dcda_0    conda-forge
clangxx                   13.0.1          default_ha53f305_0    conda-forge
click                     8.0.3                    pypi_0    pypi
cmake                     3.23.1               h5432695_0    conda-forge
cmake-format              0.6.13                   pypi_0    pypi
cmakelang                 0.6.13                   pypi_0    pypi
compilers                 1.4.2                ha770c72_0    conda-forge
contextlib2               21.6.0                   pypi_0    pypi
crc32c                    2.2                      pypi_0    pypi
cryptography              35.0.0                   pypi_0    pypi
cxx-compiler              1.4.2                h924138e_0    conda-forge
cython                    0.29.28          py39h5a03fae_2    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1                    pypi_0    pypi
deprecated                1.2.13                   pypi_0    pypi
docutils                  0.16                     pypi_0    pypi
doxygen                   1.9.2                hb166930_0    conda-forge
executing                 0.8.3              pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h27087fc_0    conda-forge
flake8                    4.0.1                    pypi_0    pypi
flask                     2.0.1                    pypi_0    pypi
flatbuffers               2.0.6                h27087fc_0    conda-forge
fortran-compiler          1.4.2                h2a4ca65_0    conda-forge
fsspec                    2021.10.0                pypi_0    pypi
gcc                       10.3.0               he2824d0_9    conda-forge
gcc_impl_linux-64         10.3.0              hf2f2afa_16    conda-forge
gcc_linux-64              10.3.0               hc39de41_9    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
gfortran                  10.3.0               h18518b4_9    conda-forge
gfortran_impl_linux-64    10.3.0              h73f4979_16    conda-forge
gfortran_linux-64         10.3.0               hb09a455_9    conda-forge
gitdb                     4.0.7                    pypi_0    pypi
github3-py                2.0.0                    pypi_0    pypi
gitpython                 3.1.24                   pypi_0    pypi
glog                      0.6.0                h6f12383_0    conda-forge
gmock                     1.11.0               h924138e_0    conda-forge
google-cloud-cpp          1.40.1               hf2015ea_0    conda-forge
googleapis-common-protos  1.53.0                   pypi_0    pypi
googleapis-cpp            0.10.0              haea4d6a_24    conda-forge
googleapis-storage-testbench 0.7.0                    pypi_0    pypi
grpc-cpp                  1.45.2               he70e3f0_3    conda-forge
grpcio                    1.41.0                   pypi_0    pypi
gtest                     1.11.0               h924138e_0    conda-forge
gunicorn                  20.1.0                   pypi_0    pypi
gxx                       10.3.0               he2824d0_9    conda-forge
gxx_impl_linux-64         10.3.0              hf2f2afa_16    conda-forge
gxx_linux-64              10.3.0               h2593f52_9    conda-forge
httpbin                   0.7.0                    pypi_0    pypi
hypothesis                6.23.2                   pypi_0    pypi
icu                       58.2              hf484d3e_1000    conda-forge
idna                      3.3                      pypi_0    pypi
imagesize                 1.2.0                    pypi_0    pypi
importlib-metadata        4.8.1                    pypi_0    pypi
iniconfig                 1.1.1                    pypi_0    pypi
ipython                   8.3.0            py39hf3d152e_0    conda-forge
itsdangerous              2.0.1                    pypi_0    pypi
jedi                      0.18.1           py39hf3d152e_1    conda-forge
jeepney                   0.7.1                    pypi_0    pypi
jinja2                    3.0.2                    pypi_0    pypi
jira                      3.0.1                    pypi_0    pypi
jmespath                  0.10.0                   pypi_0    pypi
jwcrypto                  1.0                      pypi_0    pypi
kernel-headers_linux-64   3.10.0              h4a8ded7_13    conda-forge
keyring                   23.2.1                   pypi_0    pypi
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libblas                   3.9.0           14_linux64_openblas    conda-forge
libboost                  1.71.0               haf77d95_1    defaults
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcblas                  3.9.0           14_linux64_openblas    conda-forge
libclang-cpp13            13.0.1          default_hc23dcda_0    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   7.83.0               h7bff187_0    conda-forge
libedit                   3.1.20210910         h7f8727e_0    defaults
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     10.3.0              he6cfe16_16    conda-forge
libgcc-ng                 11.2.0              h1d223b6_16    conda-forge
libgfortran-ng            11.2.0              h69a702a_16    conda-forge
libgfortran5              11.2.0              h5c6108e_16    conda-forge
libgomp                   11.2.0              h1d223b6_16    conda-forge
libgoogle-cloud           1.40.1               hf2015ea_0    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           14_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_3    conda-forge
libllvm13                 13.0.1               hf817b99_2    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_0    conda-forge
libprotobuf               3.20.1               h6239696_0    conda-forge
libsanitizer              10.3.0              h26c7422_16    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-devel_linux-64  10.3.0              he6cfe16_16    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_16    conda-forge
libthrift                 0.16.0               h519c5ea_1    conda-forge
libutf8proc               2.7.0                h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.43.0               h7f98852_0    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
llvmlite                  0.38.0           py39h7d9a04d_1    conda-forge
lz4                       4.0.0            py39h029007f_1    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
markupsafe                2.0.1                    pypi_0    pypi
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mccabe                    0.6.1                    pypi_0    pypi
multidict                 5.2.0                    pypi_0    pypi
mypy_extensions           0.4.3            py39hf3d152e_5    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nlohmann_json             3.10.5               h9c3ff4c_0    conda-forge
numba                     0.55.1           py39h56b8d98_0    conda-forge
numpy                     1.21.6           py39h18676bf_0    conda-forge
numpydoc                  1.1.0                    pypi_0    pypi
oauthlib                  3.1.1                    pypi_0    pypi
openssl                   1.1.1o               h166bdaf_0    conda-forge
orc                       1.7.4                h6c59b99_0    conda-forge
packaging                 21.0                     pypi_0    pypi
pandas                    1.4.2            py39h1832856_1    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pip                       22.0.4             pyhd8ed1ab_0    conda-forge
platformdirs              2.5.1              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0                    pypi_0    pypi
prompt-toolkit            3.0.29             pyha770c72_0    conda-forge
prompt_toolkit            3.0.29               hd8ed1ab_0    conda-forge
protobuf                  3.18.0                   pypi_0    pypi
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py                        1.10.0                   pypi_0    pypi
pyarrow                   8.0.0.dev533+g7a69bbf18           dev_0    <develop>
pycodestyle               2.8.0                    pypi_0    pypi
pycparser                 2.20                     pypi_0    pypi
pydata-sphinx-theme       0.7.2                    pypi_0    pypi
pyflakes                  2.4.0                    pypi_0    pypi
pygit2                    1.7.0                    pypi_0    pypi
pygithub                  1.55                     pypi_0    pypi
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.2.0                    pypi_0    pypi
pynacl                    1.4.0                    pypi_0    pypi
pyparsing                 2.4.7                    pypi_0    pypi
pytest                    6.2.5                    pypi_0    pypi
pytest-lazy-fixture       0.6.3                    pypi_0    pypi
pytest-repeat             0.9.1                    pypi_0    pypi
python                    3.9.12          h9a8a25e_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-dotenv             0.19.1                   pypi_0    pypi
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
rapidjson                 1.1.0             he1b5a44_1002    conda-forge
raven                     6.10.0                   pypi_0    pypi
re2                       2022.04.01           h27087fc_0    conda-forge
readline                  8.1.2                h7f8727e_1    defaults
requests                  2.26.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
requests-toolbelt         0.9.1                    pypi_0    pypi
responses                 0.16.0                   pypi_0    pypi
rhash                     1.4.1                h7f98852_0    conda-forge
ruamel-yaml               0.17.16                  pypi_0    pypi
ruamel-yaml-clib          0.2.6                    pypi_0    pypi
s2n                       1.3.11               h8d01263_0    conda-forge
s3fs                      2021.10.0                pypi_0    pypi
scalpl                    0.4.2                    pypi_0    pypi
schema                    0.7.4                    pypi_0    pypi
scipy                     1.8.0            py39hee8e79c_1    conda-forge
secretstorage             3.3.1                    pypi_0    pypi
semver                    2.13.0                   pypi_0    pypi
setuptools                62.1.0           py39hf3d152e_0    conda-forge
setuptools-scm            6.3.2                    pypi_0    pypi
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     4.0.0                    pypi_0    pypi
snappy                    1.1.9                hbd366e4_0    conda-forge
snowballstemmer           2.1.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
soupsieve                 2.2.1                    pypi_0    pypi
sphinx                    4.3.2                    pypi_0    pypi
sphinx-tabs               3.2.0                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.5                    pypi_0    pypi
sqlite                    3.38.5               h4ff8645_0    conda-forge
stack_data                0.2.0              pyhd8ed1ab_0    conda-forge
sysroot_linux-64          2.17                h4a8ded7_13    conda-forge
thrift-compiler           0.16.0               h519c5ea_1    conda-forge
thrift-cpp                0.16.0               h3e2b116_1    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2                   pypi_0    pypi
tomli                     1.2.1                    pypi_0    pypi
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.3            py39hb9d737c_0    conda-forge
typing-extensions         3.10.0.2                 pypi_0    pypi
typing_extensions         4.2.0              pyha770c72_1    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
uritemplate               4.1.1                    pypi_0    pypi
urllib3                   1.26.7                   pypi_0    pypi
valgrind                  3.18.1               hf817b99_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
werkzeug                  2.0.2                    pypi_0    pypi
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
wrapt                     1.13.2                   pypi_0    pypi
xz                        5.2.5                h516909a_1    conda-forge
yarl                      1.7.0                    pypi_0    pypi
zipp                      3.6.0                    pypi_0    pypi
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

Environment info

active environment : pyarrow
    active env location : /home/antoine/miniconda3/envs/pyarrow
            shell level : 1
       user config file : /home/antoine/.condarc
 populated config files : /home/antoine/.condarc
          conda version : 4.12.0
    conda-build version : 3.21.8
         python version : 3.7.12.final.0
       virtual packages : __cuda=11.4=0
                          __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/antoine/miniconda3  (writable)
      conda av data dir : /home/antoine/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/antoine/miniconda3/pkgs
                          /home/antoine/.conda/pkgs
       envs directories : /home/antoine/miniconda3/envs
                          /home/antoine/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.7.12 Linux/5.4.0-109-generic ubuntu/20.04.4 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
@pitrou pitrou added the bug Something isn't working label May 11, 2022
@pitrou
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pitrou commented May 11, 2022

Also cc @xhochy @h-vetinari @jakirkham as libprotobuf maintainers (since that package is affected).

@xhochy
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xhochy commented May 11, 2022

cc @conda-forge/libprotobuf

@pitrou
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pitrou commented May 11, 2022

I also reported the issue to the protobuf issue tracker: protocolbuffers/protobuf#9947

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xhochy commented May 11, 2022

@pitrou Can you post the compiler error you get? I fail to build a minimal reproducible example and I also struggle to understand what could go wrong here.

@pitrou
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pitrou commented May 11, 2022

There is no compiler error. The error happens at runtime:

$ ./build-test/debug/arrow-flight-test 
./build-test/debug/arrow-flight-test: symbol lookup error: /home/antoine/miniconda3/envs/pyarrow/lib/libarrow_flight.so.900: undefined symbol: _ZN6google8protobuf8internal16InternalMetadataD1Ev
$ c++filt _ZN6google8protobuf8internal16InternalMetadataD1Ev
google::protobuf::internal::InternalMetadata::~InternalMetadata()

@xhochy
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xhochy commented May 11, 2022

This should have been caught by the linker earlier. Also this would mean that you could not link against any destructor in a lib. The above code changes behaviour depending on the definitions but it doesn't change inline-vs-not-inline.

@pitrou
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pitrou commented May 11, 2022

The code does change inline-vs-not-inline (a member function which is defined inside the class body is implicitly inline).

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xhochy commented May 11, 2022

Ah, I implicitly read ~InternalMetadata() {}

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xhochy commented May 11, 2022

Keeping the discussion for now in the upstream Arrow issue until we fully understand what is going wrong here.

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xhochy commented May 12, 2022

@pitrou
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pitrou commented May 17, 2022

protocolbuffers/protobuf#9947 was closed as won't fix so this will have to be fixed on the conda-forge side.

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Some packages need to tweak the compiler flags (for example). Would suggest just making this change in the feedstock for now

benmwebb added a commit to salilab/npctransport that referenced this issue Jun 3, 2022
Builds are failing with protobuf 3.20.1 at runtime with
ImportError: libimp_npctransport.so.0: undefined symbol:
_ZN6google8protobuf8internal16InternalMetadataD1Ev

This appears to be because protobuf was built in release
mode (with NDEBUG defined) but we are (perhaps) building
in debug mode (without NDEBUG). Relates
conda-forge/ctng-compiler-activation-feedstock#73.
@pitrou
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pitrou commented Jun 28, 2022

Not wanting to put any pressure, but it would be nice to get this fixed at some point :-)

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pitrou commented Jul 20, 2022

Finally, a fix was accepted for protocolbuffers/protobuf#9947 and should be in the upcoming protobuf 21.3.

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