"Duplicate symbols" linker error with Boost 1.81 #320

AlexBork · 2023-01-16T15:01:56Z

After updating Boost from Version 1.79 to 1.81, compilation fails during the linking process of the Storm library due to multiple duplicate symbol errors, apparently stemming from the same two files.

Console output:

[ 93%] Linking CXX shared library ../../lib/libstorm.dylib
duplicate symbol 'boost::phoenix::placeholders::uarg9' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg8' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg7' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg6' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg5' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg4' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg3' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg2' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg1' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
duplicate symbol 'boost::phoenix::placeholders::uarg10' in:
    CMakeFiles/storm.dir/abstraction/MenuGameRefiner.cpp.o
    CMakeFiles/storm.dir/modelchecker/abstraction/GameBasedMdpModelChecker.cpp.o
ld: 10 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

The text was updated successfully, but these errors were encountered:

AlexBork · 2023-01-16T15:02:55Z

I will look further into this, mostly just wanted to document this in case anyone also wants to perform a Boost update.

volkm · 2023-01-16T15:07:37Z

Might be a Booost issue:
boostorg/phoenix#111

AlexBork · 2023-01-16T15:38:00Z

Yep, also just stumbled upon that one. I guess best idea for now is to throw a warning if that Boost version is detected? I will also try out the workaround.

sjunges · 2023-01-16T16:31:06Z

Does it compile with -DBOOST_PHOENIX_STL_TUPLE_H_ ??

In that case: check for boost version, and if it is 1.81 or newer, use this flag?

volkm · 2023-01-16T16:31:55Z

I am currently trying to see if that indeed works.

abadithela · 2023-01-17T10:10:34Z

Hi, I get this error as well, which ends with:

clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [lib/libstorm.dylib] Error 1
make[2]: *** [src/storm/CMakeFiles/storm.dir/all] Error 2
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
make: *** [check] Error 2

How do I add that tag during compilation? Can you please provide the command for that?

abadithela · 2023-01-17T10:16:58Z

When I try to check for all dependencies using cmake .. command inside the build folder, I get the following warnings:

CMake Warning at /usr/local/Cellar/cmake/3.25.1/share/cmake/Modules/FindBoost.cmake:1384 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/local/Cellar/cmake/3.25.1/share/cmake/Modules/FindBoost.cmake:1507 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/local/Cellar/cmake/3.25.1/share/cmake/Modules/FindBoost.cmake:2118 (_Boost_MISSING_DEPENDENCIES)
  resources/3rdparty/CMakeLists.txt:83 (find_package)
  CMakeLists.txt:435 (include)

I get these warnings for both versions 1.6.4 and 1.7.0 (stable releases of storm)

AlexBork · 2023-01-17T10:29:05Z

It indeed appears to be an issue with Boost. @volkm has submitted a pull request that automatically adds the flag. I will check it today.
For now, you can either downgrade to a previous Boost Version or add the -DBOOST_PHOENIX_STL_TUPLE_H_ to the cmake call.
The warning you describe is automatically thrown by cmake, so it is not something directly related to Storm. My guess is that there is no cmake version yet where compatibility with Boost 1.81 is checked.

volkm · 2023-01-17T11:45:22Z

The latest storm version should work again now.

@abadithela: Your compilation should be successful after updating Storm. If the issue persists, feel free to reopen this issue.

abadithela · 2023-01-17T17:40:44Z

Hi @volkm:

I am using storm-1.7.0 and the corresponding version of stormy (1.7.0). I added the workaround that you have here in the CMakeLists.txt inside the resources folder for Storm-1.7.0. I then built that version of Storm and it was successful. However, then in building the stormy version, I get a similar error like above. I was thinking that a similar fix would work also in stormpy. Where do I add it? Also in the resources/pybind11/CMakeLists.txt? That file doesn't seem to have anything regarding boost so I am not sure if that's the correct place to put it in...

[100%] Linking CXX shared module /Users/apurvabadithela/Documents/software/stormpy-1.7.0/lib/stormpy/core.cpython-310-darwin.so
ld: warning: -undefined dynamic_lookup may not work with chained fixups
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duplicate symbol 'boost::phoenix::placeholders::uarg7' in:
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duplicate symbol 'boost::phoenix::placeholders::uarg6' in:
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    CMakeFiles/core.dir/src/core/transformation.cpp.o
ld: 100 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [/Users/apurvabadithela/Documents/software/stormpy-1.7.0/lib/stormpy/core.cpython-310-darwin.so] Error 1
make[2]: *** [CMakeFiles/core.dir/all] Error 2
make[1]: *** [CMakeFiles/core.dir/rule] Error 2
make: *** [core] Error 2
Traceback (most recent call last):
  File "/Users/apurvabadithela/Documents/software/stormpy-1.7.0/setup.py", line 238, in <module>
    setup(
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/__init__.py", line 87, in setup
    return distutils.core.setup(**attrs)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/dist.py", line 1208, in run_command
    super().run_command(command)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/command/develop.py", line 34, in run
    self.install_for_development()
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/command/develop.py", line 114, in install_for_development
    self.run_command('build_ext')
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
    self.distribution.run_command(command)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/dist.py", line 1208, in run_command
    super().run_command(command)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/Users/apurvabadithela/Documents/software/stormpy-1.7.0/setup.py", line 196, in run
    self.build_extension(ext, cmake_args, build_args)
  File "/Users/apurvabadithela/Documents/software/stormpy-1.7.0/setup.py", line 235, in build_extension
    subprocess.check_call(['cmake', '--build', '.', '--target', ext.name] + build_args, cwd=self.build_temp)
  File "/Users/apurvabadithela/opt/anaconda3/envs/pacti_env/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--target', 'core', '--config', 'Debug', '--', '-j8']' returned non-zero exit status 2.

volkm · 2023-01-17T17:48:44Z

I saw the same problem with stormpy. Please see the following PR moves-rwth/stormpy#108 for how to add the workaround in stormpy. Note that we will soon merge this into the main branch of stormpy as well.

AlexBork added bug broken dependency labels Jan 16, 2023

AlexBork self-assigned this Jan 16, 2023

volkm mentioned this issue Jan 16, 2023

Workaround for issue with Boost Phoenix 1.81 #321

Merged

AlexBork removed the bug label Jan 17, 2023

AlexBork closed this as completed in #321 Jan 17, 2023

volkm mentioned this issue Jan 17, 2023

Workaround for issue with Boost 1.81 moves-rwth/stormpy#108

Merged

tquatmann mentioned this issue Jun 14, 2023

unsuccessful installation moves-rwth/homebrew-storm#8

Closed

volkm mentioned this issue Mar 3, 2024

Linking error when installing Stormpy moves-rwth/stormpy#159

Closed

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"Duplicate symbols" linker error with Boost 1.81 #320

"Duplicate symbols" linker error with Boost 1.81 #320

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volkm commented Jan 17, 2023

"Duplicate symbols" linker error with Boost 1.81 #320

"Duplicate symbols" linker error with Boost 1.81 #320

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AlexBork commented Jan 16, 2023

AlexBork commented Jan 16, 2023

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