GLIBCXX version problem when make walking controller #642

jimingda · 2023-07-03T11:58:22Z

jimingda
Jul 3, 2023

When make walking-controller, i came across the following problem, and i checked my GLIBCXX version is 3.4.28, so i update my gcc as belowed, but it says my gcc is already the newest one. Shall i upgrade my libstdc++.so seperately?

(walk) icub@icubsrv:~/icubtraining/walking-controllers/build$ cmake ../
-- Found YARP: /usr/local/src/robot/robotology-superbuild/build/install/lib/cmake/YARP (found version "3.7.0")
-- Found YCM: /usr/local/src/robot/robotology-superbuild/build/install/share/cmake/YCM (found version "0.14.1")
-- Found YARP: /usr/local/src/robot/robotology-superbuild/build/install/lib/cmake/YARP (found version "3.7.0")
-- Found ICUB 1.25.0 (Components: iCubDev ctrlLib skinDynLib iKin iDyn learningMachine perceptiveModels actionPrimitives optimization)
-- Found YARP: /usr/local/src/robot/robotology-superbuild/build/install/lib/cmake/YARP (found version "3.7.0")
-- Found YARP: /usr/local/src/robot/robotology-superbuild/build/install/lib/cmake/YARP (found version "3.7.0")
-- Could NOT find cppad (missing: cppad_LIBRARIES) 
-- Created target YarpUtilities for export WalkingControllers.
-- Created target HumanState for export WalkingControllers.
-- Created target iDynTreeUtilities for export WalkingControllers.
-- Created target TimeProfiler for export WalkingControllers.
-- Created target StdUtilities for export WalkingControllers.
-- Created target SimplifiedModelControllers for export WalkingControllers.
-- Created target RobotInterface for export WalkingControllers.
-- Created target WholeBodyControllers for export WalkingControllers.
-- Created target TrajectoryPlanner for export WalkingControllers.
-- Created target KinDynWrapper for export WalkingControllers.
-- Created target RetargetingHelper for export WalkingControllers.
-- Created target application WalkingModule.
-- Created target application WalkingJoypadModule.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/icub/icubtraining/walking-controllers/build
(walk) icub@icubsrv:~/icubtraining/walking-controllers/build$ make
[ 10%] Built target HumanState
[ 15%] Built target YarpUtilities
[ 20%] Built target iDynTreeUtilities
[ 25%] Built target TimeProfiler
[ 37%] Built target SimplifiedModelControllers
[ 45%] Built target RobotInterface
[ 50%] Built target KinDynWrapper
[ 65%] Built target WholeBodyControllers
[ 75%] Built target TrajectoryPlanner
[ 80%] Built target RetargetingHelper
[ 82%] Linking CXX executable ../../bin/WalkingModule
/usr/bin/ld: /home/icub/miniconda3/envs/walk/lib/libBipedalLocomotionFrameworkSystem.so.0.13.0: undefined reference to `std::condition_variable::wait(std::unique_lock<std::mutex>&)@GLIBCXX_3.4.30'
/usr/bin/ld: /home/icub/miniconda3/envs/walk/lib/libBipedalLocomotionFrameworkVectorsCollection.so.0.13.0: undefined reference to `std::__throw_bad_array_new_length()@GLIBCXX_3.4.29'
collect2: error: ld returned 1 exit status
make[2]: *** [src/WalkingModule/CMakeFiles/WalkingModule.dir/build.make:170: bin/WalkingModule-0.7.0] Error 1
make[1]: *** [CMakeFiles/Makefile2:698: src/WalkingModule/CMakeFiles/WalkingModule.dir/all] Error 2
make: *** [Makefile:130: all] Error 2


(walk) icub@icubsrv:~/icubtraining/walking-controllers/build$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 |grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_DEBUG_MESSAGE_LENGTH


(walk) icub@icubsrv:~/icubtraining/walking-controllers/build$ sudo apt install gcc
Reading package lists... Done
Building dependency tree       
Reading state information... Done
gcc is already the newest version (4:9.3.0-1ubuntu2).

Answered by traversaro

Jul 3, 2023

If you want to compile against a C++ library installed via conda-forge, you also need to install compilers and other development related dependencies via conda:

conda install -c conda-forge compilers make ninja cmake

Furthermore, you need to make sure that you do not have the setup.sh of the robotology-superbuild compiled against apt dependencies in your bashrc, as as mentioned before, you can't mix libraries build with apt dependencies with libraries built with apt dependencies.

View full answer

traversaro · 2023-07-03T12:25:40Z

traversaro
Jul 3, 2023
Maintainer

How are did you installed the dependency required to build walking-controllers? If you are using dependencies provided by conda-forge or robotology conda channels, you should compile it with the conda-forge provided compiler, i.e. the one installed by conda-forge compilers package. If instead you are using apt-provided dependencies, you should make sure that there is no activated conda environment when you build. You can't mix apt and conda provided dependencies.

4 replies

jimingda Jul 3, 2023
Author

Thanks @traversaro
For dependency bipedal-locomotion-framework i installed by
conda install -c conda-forge bipedal-locomotion-framework
as recommended. https://github.com/ami-iit/bipedal-locomotion-framework

traversaro Jul 3, 2023
Maintainer

If you want to compile against a C++ library installed via conda-forge, you also need to install compilers and other development related dependencies via conda:

conda install -c conda-forge compilers make ninja cmake

Furthermore, you need to make sure that you do not have the setup.sh of the robotology-superbuild compiled against apt dependencies in your bashrc, as as mentioned before, you can't mix libraries build with apt dependencies with libraries built with apt dependencies.

Answer selected by pattacini

jimingda Jul 5, 2023
Author

Thank you @traversaro . I found the GLIBCXX_3.4.29 & GLIBCXX_3.4.30 on the conda env lib path.

(walk) icub@icubsrv:~/icubtraining/walking-controllers/build$ strings /home/icub/miniconda3/envs/walk/lib/libstdc++.so.6.0.31 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_3.4.29
GLIBCXX_3.4.30
GLIBCXX_3.4.31
GLIBCXX_TUNABLES
GLIBCXX_DEBUG_MESSAGE_LENGTH

jimingda Jul 7, 2023
Author

I used the source code to install 'bipedal-locomotion-framework' instead, but some error occured. Is that because i didn't install dependency Qhull correctly?

(walk) icub@icubsrv:~/icubtraining/bipedal-locomotion-framework/build$ cmake ../
-- Found YARP: /usr/local/src/robot/robotology-superbuild/build/install/lib/cmake/YARP (found version "3.7.0")
CMake Error at cmake/BipedalLocomotionFrameworkFindDependencies.cmake:58 (find_package):
  By not providing "FindQhull.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "Qhull", but
  CMake did not find one.

  Could not find a package configuration file provided by "Qhull" (requested
  version 8.0.0) with any of the following names:

    QhullConfig.cmake
    qhull-config.cmake

(walk) icub@icubsrv:~/icubtraining/Qhull/qhull-2020.2$ sudo make install
[sudo] password for icub: 
mkdir -p /usr/local/bin
mkdir -p /usr/local/share/doc/qhull
mkdir -p /usr/local/share/doc/qhull/src
mkdir -p /usr/local/include/libqhull
mkdir -p /usr/local/include/libqhull_r
mkdir -p /usr/local/include/libqhullcpp
mkdir -p /usr/local/lib
mkdir -p /usr/local/share/man/man1
mkdir -p /usr/local/lib/pkgconfig
cp bin/qconvex /usr/local/bin
cp bin/qdelaunay /usr/local/bin
cp bin/qhalf /usr/local/bin
cp bin/qhull /usr/local/bin
cp bin/qvoronoi /usr/local/bin
cp bin/rbox /usr/local/bin
cp -p html/qhull.man /usr/local/share/man/man1/qhull.1
cp -p html/rbox.man /usr/local/share/man/man1/rbox.1
cp -p README.txt REGISTER.txt Announce.txt COPYING.txt index.htm /usr/local/share/doc/qhull/
cp -pr html /usr/local/share/doc/qhull/
cp -p src/Changes.txt /usr/local/share/doc/qhull/src/
cp -P lib/* /usr/local/lib
cp src/libqhull/DEPRECATED.txt src/libqhull/*.h /usr/local/include/libqhull
cp src/libqhull_r/*.h /usr/local/include/libqhull_r
cp src/libqhullcpp/*.h /usr/local/include/libqhullcpp
cp src/qhulltest/*.h /usr/local/include/libqhullcpp
for lib in qhullstatic qhullstatic_r qhull_r qhullcpp; \
do sed \
	-e 's#@qhull_VERSION@#8.0.2#' \
	-e 's#@CMAKE_INSTALL_PREFIX@#/usr/local#' \
	-e 's#@LIB_INSTALL_DIR@#lib#' \
	-e 's#@INCLUDE_INSTALL_DIR@#include#' \
	-e 's#@LIBRARY_NAME@#'$lib'#' \
	-e 's#@LIBRARY_DESCRIPTION@#'$lib'#' \
	build/qhull.pc.in > /usr/local/lib/pkgconfig/$lib.pc; \
done

jimingda · 2023-08-29T03:08:44Z

jimingda
Aug 29, 2023
Author

Hi @traversaro

I comment the setup.sh in ~/.bashrc as below,
#source /usr/local/src/robot/robotology-superbuild/build/install/share/robotology-superbuild/setup.sh

and then conda install -c conda-forge compilers make ninja cmake, get the newest version of these tools than system default one.

(walkcontrol) icub@icubsrv:~/icubtraining/walking-controllers/build$ gcc --version
gcc (conda-forge gcc 12.1.0-17) 12.1.0
Copyright (C) 2022 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.

(walkcontrol) icub@icubsrv:~/icubtraining/walking-controllers/build$ make --version
GNU Make 4.3
Built for x86_64-conda-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
(walkcontrol) icub@icubsrv:~/icubtraining/walking-controllers/build$ ninja --version
1.11.1
(walkcontrol) icub@icubsrv:~/icubtraining/walking-controllers/build$ cmake --version
cmake version 3.26.4

CMake suite maintained and supported by Kitware (kitware.com/cmake).

when i make the walking-controller i got the below error,

[ 87%] Building CXX object src/WalkingModule/CMakeFiles/WalkingModule.dir/src/Module.cpp.o
[ 87%] Generating code from thrifts/WalkingCommands.thrift
[ 90%] Building CXX object src/WalkingModule/CMakeFiles/WalkingModule.dir/thrifts/WalkingCommands.cpp.o
[ 92%] Linking CXX executable ../../bin/WalkingModule
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libz.so.1, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_dev.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libjpeg.so.8, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libpng16.so.16, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libavcodec.so.58, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libavutil.so.56, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libACE-6.4.5.so, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_os.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libedit.so.2, needed by /exports/code/robotology-superbuild/build/install/lib/libYARP_os.so.3.7.0, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libipopt.so.1, needed by /usr/local/lib/libidyntree-inverse-kinematics.so, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: warning: libxml2.so.2, needed by /usr/local/lib/libidyntree-modelio.so, not found (try using -rpath or -rpath-link)
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /usr/local/lib/libidyntree-modelio.so: undefined reference to `xmlDocSetRootElement@LIBXML2_2.4.30'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0: undefined reference to `png_create_read_struct@PNG16_0'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0: undefined reference to `avcodec_send_packet@LIBAVCODEC_58'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /exports/code/robotology-superbuild/build/install/lib/libYARP_os.so.3.7.0: undefined reference to `ACE_DLL::close()'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /exports/code/robotology-superbuild/build/install/lib/libYARP_os.so.3.7.0: undefined reference to `ACE_INET_Addr::get_ip_address() const'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /exports/code/robotology-superbuild/build/install/lib/libYARP_os.so.3.7.0: undefined reference to `vtable for ACE_Time_Value'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /exports/code/robotology-superbuild/build/install/lib/libYARP_sig.so.3.7.0: undefined reference to `avcodec_receive_packet@LIBAVCODEC_58'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /usr/local/lib/libidyntree-modelio.so: undefined reference to `xmlDocDumpFormatMemory@LIBXML2_2.4.30'
/home/icub/miniconda3/envs/walkcontrol/bin/ld: /usr/local/lib/libidyntree-modelio-xml.so: undefined reference to `xmlSchemaNewParserCtxt@LIBXML2_2.5.8'

but i can locate the so file in the system

$ locate libYARP_dev.so.3.7.0
/exports/code/robotology-superbuild/build/install/lib/libYARP_dev.so.3.7.0
/exports/code/robotology-superbuild/build/src/YARP/lib/libYARP_dev.so.3.7.0
$ locate libidyntree-modelio.so
/home/icub/icubtraining/idyntree/build/lib/libidyntree-modelio.so
/home/icub/miniconda3/envs/walkcontrol/lib/libidyntree-modelio.so
/home/icub/miniconda3/pkgs/idyntree-9.1.0-py311h1f4174d_1/lib/libidyntree-modelio.so
/home/icub/whole-body-estimators/build/idyntree/build/lib/libidyntree-modelio.so
/usr/local/lib/libidyntree-modelio.so

Thanks in advance.

14 replies

traversaro Aug 29, 2023
Maintainer

Looking at your CMakeCache.txt, it seems that you have yarp installed both in the conda environment and via the robotology-superbuild, it is possible that the two versions are in conflicts. To avoid this kind of problems, I suggest to start from a clean system (like a clean Docker image, or at least a clean conda environment) and use a single way to install your dependencies.

traversaro Aug 29, 2023
Maintainer

And for icub-main, i didn't find the source.

From the ICUB_DIR variables in your CMakeCache.txt :

//The directory containing a CMake configuration file for ICUB.
ICUB_DIR:PATH=/usr/local/src/robot/robotology-superbuild/build/install/lib/cmake/ICUB

jimingda Aug 30, 2023
Author

Thanks.

Start from a clean conda env, i got the same problem as above https://github.com/orgs/robotology/discussions/642#discussioncomment-6853784
It seems that yarp was installed in the conda, but icub-main still from superbuild.

Then i install the icub-main via conda install -c conda-forge -c robotology icub-main
It works now and the make process can finish 100%

After installed, during the run step 4,
I got the following problem.

(wc) icub@icubsrv:~/icubtraining/walking-controllers/build$  YARP_CLOCK=/clock yarprobotinterface --config launch-wholebodydynamics.xml
[INFO] |yarp.os.Port|/icubsrv/yarprobotinterface/126646/clock:i| Port /icubsrv/yarprobotinterface/126646/clock:i active at tcp://192.168.1.12:10055/
[INFO] |yarp.os.Network| Success: port-to-port persistent connection added.
[INFO] |yarp.os.Time| Waiting for clock server to start broadcasting data ...
[INFO] |yarp.os.impl.PortCoreInputUnit|/icubsrv/yarprobotinterface/126646/clock:i| Receiving input from /clock to /icubsrv/yarprobotinterface/126646/clock:i using tcp
[ERROR] |yarp.os.Property| cannot read from yarprobotinterface.ini
[DEBUG] Reading file 
[ERROR] Syntax error while loading  at line 0 . Failed to open file
[FATAL] Config file    not parsed correctly.
Trace requested at /home/conda/feedstock_root/build_artifacts/yarp_1689081344305/work/src/yarprobotinterface/Module.cpp:132 by code called from:
/home/icub/miniconda3/envs/wc/bin/../lib/libYARP_os.so.3(_Z16yarp_print_traceP8_IO_FILEPKcj+0x36) [0x7f778a4ab4e6]
yarprobotinterface(+0xcd65) [0x55f487090d65]
/home/icub/miniconda3/envs/wc/bin/../lib/libYARP_os.so.3(_ZN4yarp2os8RFModule9runModuleERNS0_14ResourceFinderE+0xef) [0x7f778a50508f]
yarprobotinterface(+0x8c1f) [0x55f48708cc1f]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f778a027083]
yarprobotinterface(+0x8cf5) [0x55f48708ccf5]
Segmentation fault (core dumped)

CMakeCache.txt

jimingda Aug 30, 2023
Author

Maybe the reason is there is no launch-wholebodydynamics.xml in the system and i cann't find it too.

traversaro Aug 30, 2023
Maintainer

Start from a clean conda env, i got the same problem as above https://github.com/orgs/robotology/discussions/642#discussioncomment-6853784
It seems that yarp was installed in the conda, but icub-main still from superbuild.

Then i install the icub-main via conda install -c conda-forge -c robotology icub-main
It works now and the make process can finish 100%

Which instructions are you following? If you are installing the superbuild from source, you should not install yarp or icub-main from conda, as otherwise you have two YARPs and two icub-mains, one installed by the robotology-superbuild and one installed by conda, that may not be compatible. The dependencies to install in the conda environment to compile the robotology-superbuild from source are provided in https://github.com/robotology/robotology-superbuild/blob/master/doc/conda-forge.md#source-installation, and do not result in yarp being installed in the conda environment. Even if the compilation is working now, what you have done will result in a fragile setup that could create problems later one, so I would strongly suggest to setup a clean environment before proceeding.

Maybe the reason is there is no launch-wholebodydynamics.xml in the system and i cann't find it too.

That file is installed by whole-body-estimators. This can be installed via the robotology-superbuild if you enable the ROBOTOLOGY_ENABLE_DYNAMICS option, and also walking-controllers can be installed via the robotology-superbuild enabling the ROBOTOLOGY_ENABLE_DYNAMICS_FULL_DEPS CMake option, see https://github.com/robotology/robotology-superbuild/blob/2094861e78745a2c2268a04d41997957baf78cf5/cmake/RobotologySuperbuildLogic.cmake#L67 .

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Robotology

GLIBCXX version problem when make walking controller #642

jimingda Jul 3, 2023

Replies: 2 comments · 18 replies

traversaro Jul 3, 2023 Maintainer

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