GLIBCXX version problem when make walking controller

[jimingda]

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).

[traversaro]

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.

[jimingda]

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]

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.

[jimingda]

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]

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]

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.

[traversaro]

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]

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]

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]

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

[traversaro]

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 .