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Inserting any iCub model into Gazebo world crashes Gazebo with FatalException #1253

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nunoguedelha opened this issue Sep 8, 2022 · 2 comments
Closed

Inserting any iCub model into Gazebo world crashes Gazebo with FatalException #1253

nunoguedelha opened this issue Sep 8, 2022 · 2 comments

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@nunoguedelha
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Steps for reproducing the issue...

  • Install Gazebo and build the superbuild
conda create -n robenv
conda activate robenv
mamba update --all
mamba install -c conda-forge gazebo=11.9.1
mamba install -c conda-forge cmake compilers make ninja pkg-config
mamba install -c conda-forge ace asio assimp boost eigen freetype gazebo glew glfw glm graphviz gsl ipopt irrlicht libjpeg-turbo libmatio libode libxml2 nlohmann_json opencv pkg-config portaudio sdl sdl2 sqlite tinyxml spdlog lua soxr
cd ~/dev
git clone https://github.com/robotology/robotology-superbuild
cd robotology-superbuild
mkdir build
cd build
cmake ..
cmake --build . --config Release --target update-all
cmake --build . --config Release
  • run Gazebo
gazebo --verbose
  • insert an iCub model (e.g. iCubGazeboV3)
    => Gazebo crashes with the error:
[libprotobuf ERROR google/protobuf/descriptor_database.cc:559] Invalid file descriptor data passed to EncodedDescriptorDatabase::Add().
[libprotobuf FATAL google/protobuf/descriptor.cc:1357] CHECK failed: GeneratedDatabase()->Add(encoded_file_descriptor, size):
libc++abi.dylib: terminating with uncaught exception of type google::protobuf::FatalException: CHECK failed: GeneratedDatabase()->Add(encoded_file_descriptor, size):

Details

  • When installing the superbuild dependencies through conda, we dropped qt-main.
  • Superbuild options set through ccmake interface:
 ROBOTOLOGY_ENABLE_DYNAMICS       ON
 ROBOTOLOGY_ENABLE_DYNAMICS_FUL   ON
 ROBOTOLOGY_PROJECT_TAGS          Stable
 ROBOTOLOGY_USES_MATLAB           ON
conda info: 
     active environment : robotologydeps3
    active env location : /Users/nunoguedelha/miniforge3/envs/robotologydeps3
            shell level : 1
       user config file : /Users/nunoguedelha/.condarc
 populated config files : /Users/nunoguedelha/miniforge3/.condarc
                          /Users/nunoguedelha/.condarc
          conda version : 4.14.0
    conda-build version : not installed
         python version : 3.8.13.final.0
       virtual packages : __osx=10.15.7=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/nunoguedelha/miniforge3  (writable)
      conda av data dir : /Users/nunoguedelha/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/nunoguedelha/miniforge3/pkgs
                          /Users/nunoguedelha/.conda/pkgs
       envs directories : /Users/nunoguedelha/miniforge3/envs
                          /Users/nunoguedelha/.conda/envs
               platform : osx-64
             user-agent : conda/4.14.0 requests/2.28.1 CPython/3.8.13 Darwin/19.6.0 OSX/10.15.7
                UID:GID : 501:20
             netrc file : None
           offline mode : False
conda list: 
# packages in environment at /Users/nunoguedelha/miniforge3/envs/robotologydeps3:
#
# Name                    Version                   Build  Channel
ace                       7.0.8                hb486fe8_0    conda-forge
ampl-mp                   3.1.0             h2beb688_1006    conda-forge
asio                      1.24.0               h4da505d_0    conda-forge
assimp                    5.0.1                h1224e73_7    conda-forge
atk-1.0                   2.36.0               he69c4ee_4    conda-forge
blosc                     1.21.1               h97e831e_3    conda-forge
boost                     1.74.0          py310h509978a_5    conda-forge
boost-cpp                 1.74.0               hdbf7018_7    conda-forge
bullet-cpp                3.17                 hcc25f39_1    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
c-compiler                1.5.0                hbf74d83_0    conda-forge
ca-certificates           2022.6.15            h033912b_0    conda-forge
cairo                     1.16.0            he01c77b_1009    conda-forge
cctools                   973.0.1             h76f1dac_10    conda-forge
cctools_osx-64            973.0.1             h2b95895_10    conda-forge
cfitsio                   4.1.0                h2c97ad1_0    conda-forge
clang                     14.0.4               h694c41f_0    conda-forge
clang-14                  14.0.4          default_h55ffa42_0    conda-forge
clang_osx-64              14.0.4               h3a95cd4_2    conda-forge
clangxx                   14.0.4          default_h55ffa42_0    conda-forge
clangxx_osx-64            14.0.4               he1dbc44_2    conda-forge
cmake                     3.24.1               h5291bba_0    conda-forge
compiler-rt               14.0.4               h7fcd477_0    conda-forge
compiler-rt_osx-64        14.0.4               h6df654d_0    conda-forge
compilers                 1.5.0                h694c41f_0    conda-forge
console_bridge            1.0.2                hbb4e6a2_1    conda-forge
cppzmq                    4.8.1                hf09c4ce_0    conda-forge
curl                      7.83.1               h23f1065_0    conda-forge
cxx-compiler              1.5.0                hb8565cd_0    conda-forge
dartsim                   6.12.1               h110914a_0    conda-forge
eigen                     3.4.0                h940c156_0    conda-forge
expat                     2.4.8                h96cf925_0    conda-forge
fcl                       0.7.0                h31ff308_0    conda-forge
ffmpeg                    4.3.2                hbf27d7b_3    conda-forge
flann                     1.9.1             h30321d8_1010    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.94              h10f422b_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fortran-compiler          1.5.0                h14ada62_0    conda-forge
freeimage                 3.18.0               h33ef725_9    conda-forge
freetype                  2.12.1               h3f81eb7_0    conda-forge
freexl                    1.0.6                h0d85af4_0    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
gazebo                    11.9.1               ha2fdce5_2    conda-forge
gdbm                      1.18                 h8a0c380_2    conda-forge
gdk-pixbuf                2.42.8               hb161b9c_0    conda-forge
geos                      3.10.2               he49afe7_0    conda-forge
geotiff                   1.7.1                had63758_1    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
gfortran                  11.3.0               h2c809b3_0    conda-forge
gfortran_impl_osx-64      9.5.0               h2221f41_25    conda-forge
gfortran_osx-64           9.5.0                h18f7dce_0    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
glew                      2.1.0                h046ec9c_2    conda-forge
glfw                      3.3.8                hac89ed1_0    conda-forge
glm                       0.9.9.4              h1b54a9f_2    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
gnutls                    3.6.13               h756fd2b_1    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
graphviz                  2.50.0               h2b5222e_2    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
gtk2                      2.24.33              h7c1209e_2    conda-forge
gts                       0.7.6                hccb3bdf_2    conda-forge
harfbuzz                  3.4.0                h447b35c_0    conda-forge
hdf4                      4.2.15               h0623a88_4    conda-forge
hdf5                      1.12.1          nompi_h0aa1fa2_104    conda-forge
icu                       69.1                 he49afe7_0    conda-forge
imath                     3.1.5                hd9580d2_0    conda-forge
ipopt                     3.14.9               h069150e_1    conda-forge
irrlicht                  1.8.5                he00d70a_2    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jasper                    2.0.33               h013e400_0    conda-forge
jpeg                      9e                   hac89ed1_2    conda-forge
json-c                    0.16                 h01d06f9_0    conda-forge
jsoncpp                   1.9.5                h940c156_1    conda-forge
jxrlib                    1.1                  h35c211d_2    conda-forge
kealib                    1.4.15               h4dab1bc_0    conda-forge
krb5                      1.19.3               hb98e516_0    conda-forge
lame                      3.100             h35c211d_1001    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
ld64                      609                 hc6ad406_10    conda-forge
ld64_osx-64               609                 h1e06c2b_10    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libccd                    2.1                  he49afe7_1    conda-forge
libclang                  13.0.1          default_he082bbe_0    conda-forge
libclang-cpp14            14.0.4          default_h55ffa42_0    conda-forge
libcurl                   7.83.1               h23f1065_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libdap4                   3.20.6               h3e144a0_2    conda-forge
libdeflate                1.13                 h775f41a_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgd                     2.3.3                hb8742e1_1    conda-forge
libgdal                   3.4.2                ha663369_6    conda-forge
libgfortran               5.0.0           10_4_0_h97931a8_25    conda-forge
libgfortran-devel_osx-64  9.5.0               hc2d6858_25    conda-forge
libgfortran5              11.3.0              h082f757_25    conda-forge
libglib                   2.72.1               hfbcb929_0    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
libignition-cmake2        2.15.0               hf0c8a7f_0    conda-forge
libignition-common3       3.13.2               h39c3357_1    conda-forge
libignition-fuel-tools4   4.4.0                h1699cbd_6    conda-forge
libignition-math6         6.11.0          py310h9fb7402_1    conda-forge
libignition-msgs5         5.7.0                h08ae71b_2    conda-forge
libignition-tools1        1.5.0                hd8dcec6_0    conda-forge
libignition-transport8    8.1.0               h4b67353_10    conda-forge
libjpeg-turbo             2.1.3                hac89ed1_0    conda-forge
libkml                    1.3.0             h8fd9edb_1014    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
liblapacke                3.9.0           16_osx64_openblas    conda-forge
libllvm13                 13.0.1               h64f94b2_2    conda-forge
libllvm14                 14.0.4               h41df66c_0    conda-forge
libmatio                  1.5.23               hb7ac2cd_0    conda-forge
libnetcdf                 4.8.1           nompi_h6609ca0_102    conda-forge
libnghttp2                1.47.0               h5aae05b_1    conda-forge
libode                    0.16.2              h9d931ec_10    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libopencv                 4.5.5            py31h1f8f45b_4    conda-forge
libpng                    1.6.37               h5481273_4    conda-forge
libpq                     14.2                 h8ce7ee7_0    conda-forge
libprotobuf               3.19.4               hcf210ce_0    conda-forge
libraw                    0.20.2               hefd3b78_1    conda-forge
librsvg                   2.52.5               h5e5d7d9_2    conda-forge
librttopo                 1.1.0                hec60dd8_9    conda-forge
libsdformat               9.3.0                h6955478_5    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libspatialite             5.0.1               hadde3e2_15    conda-forge
libsqlite                 3.39.3               ha978bb4_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libtar                    1.2.20            h0d85af4_1004    conda-forge
libtiff                   4.4.0                h5e0c7b4_3    conda-forge
libtool                   2.4.6             he49afe7_1008    conda-forge
libusb                    1.0.26             hc2f2c32_100    conda-forge
libuv                     1.44.2               hac89ed1_0    conda-forge
libwebp                   1.2.4                hfa4350a_0    conda-forge
libwebp-base              1.2.4                h775f41a_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.9.12               h7e28ab6_1    conda-forge
libzip                    1.9.2                h6db710c_1    conda-forge
libzlib                   1.2.12               hfe4f2af_2    conda-forge
llvm-openmp               14.0.4               ha654fa7_0    conda-forge
llvm-tools                14.0.4               h41df66c_0    conda-forge
lua                       5.4.4                hf9dbe3d_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
make                      4.3                  h22f3db7_1    conda-forge
metis                     5.1.0             h2e338ed_1006    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
mumps-include             5.2.1               h694c41f_11    conda-forge
mumps-seq                 5.2.1               hea8e22a_11    conda-forge
mysql-common              8.0.30               hc4b2c72_1    conda-forge
mysql-libs                8.0.30               h8658499_1    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nettle                    3.6                  hedd7734_0    conda-forge
ninja                     1.11.0               h1b54a9f_0    conda-forge
nlohmann_json             3.11.2               hbbd2c75_0    conda-forge
nspr                      4.32                 hcd9eead_1    conda-forge
nss                       3.78                 ha8197d3_0    conda-forge
numpy                     1.23.2          py310hf910466_0    conda-forge
octomap                   1.9.7                h940c156_0    conda-forge
ogre                      1.10.12              hf9dbd05_9    conda-forge
openal-soft               1.22.2               h1b54a9f_0    conda-forge
opencv                    4.5.5            py31h2ec42d9_4    conda-forge
openexr                   3.1.5                h6fbc5c6_0    conda-forge
openh264                  2.1.1                hfd3ada9_0    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openssl                   3.0.5                hfd90126_2    conda-forge
pango                     1.50.3               h7f27720_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkg-config                0.29.2            ha3d46e9_1008    conda-forge
poppler                   22.01.0              h9573804_0    conda-forge
poppler-data              0.4.11               hd8ed1ab_0    conda-forge
portaudio                 19.6.0               hf0c8a7f_6    conda-forge
postgresql                14.2                 h0fd25fa_0    conda-forge
proj                      9.0.0                h2364a93_1    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
pugixml                   1.11.4               he49afe7_0    conda-forge
py-opencv                 4.5.5            py31ha188af9_4    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
python                    3.10.6          hc14f532_0_cpython    conda-forge
python_abi                3.10                    2_cp310    conda-forge
qt                        5.12.9               h2a607e2_5    conda-forge
qwt                       6.2.0                h0f3c874_2    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
rhash                     1.4.3                hac89ed1_0    conda-forge
ruby                      3.1.2                hcaea9d7_0    conda-forge
scotch                    6.0.9                h3da7401_2    conda-forge
sdl                       1.2.52               h96cf925_1    conda-forge
sdl2                      2.0.22               hb486fe8_2    conda-forge
setuptools                65.3.0             pyhd8ed1ab_1    conda-forge
sigtool                   0.1.3                h88f4db0_0    conda-forge
simbody                   3.7                  h43072b6_3    conda-forge
snappy                    1.1.9                h6e38e02_1    conda-forge
soxr                      0.1.3                had99412_2    conda-forge
spdlog                    1.10.0               hbb4e6a2_0    conda-forge
sqlite                    3.39.3               h9ae0607_0    conda-forge
swig                      4.0.2                hce5123c_2    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
tbb                       2020.2               h940c156_4    conda-forge
tbb-devel                 2020.2               h940c156_4    conda-forge
tiledb                    2.8.3                h349c43f_1    conda-forge
tinyxml                   2.6.2                h65a07b1_2    conda-forge
tinyxml2                  9.0.0                he49afe7_2    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tzcode                    2022c                h775f41a_0    conda-forge
tzdata                    2022c                h191b570_0    conda-forge
unixodbc                  2.3.10               h7b58acd_0    conda-forge
urdfdom                   2.3.5                h940c156_0    conda-forge
urdfdom_headers           1.1.0                h1b54a9f_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
x264                      1!161.3030           h0d85af4_1    conda-forge
xerces-c                  3.2.3                h6564042_4    conda-forge
xorg-fixesproto           5.0               h0d85af4_1002    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.0.10               h0d85af4_0    conda-forge
xorg-libsm                1.2.3             h0d85af4_1000    conda-forge
xorg-libx11               1.7.2                h0d85af4_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxaw               1.0.14               h0d85af4_1    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                h0d85af4_1    conda-forge
xorg-libxfixes            5.0.3             h0d85af4_1004    conda-forge
xorg-libxmu               1.1.3                h0d85af4_0    conda-forge
xorg-libxpm               3.5.13               h0d85af4_0    conda-forge
xorg-libxrender           0.9.10            h0d85af4_1003    conda-forge
xorg-libxt                1.2.1                h0d85af4_2    conda-forge
xorg-renderproto          0.11.1            h0d85af4_1002    conda-forge
xorg-xextproto            7.3.0             h35c211d_1002    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zlib                      1.2.12               hfe4f2af_2    conda-forge
zstd                      1.5.2                hfa58983_4    conda-forge
zziplib                   0.13.69              h5dbffcc_1    conda-forge
@nunoguedelha nunoguedelha mentioned this issue Sep 8, 2022
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@nunoguedelha
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The Protobuf headers and libraries were being found in the system (/usr/local/include/google/protobuf) instead of Conda install prefix, which can be seen in the Cmake cache:

 Protobuf_DIR                     Protobuf_DIR-NOTFOUND
 Protobuf_INCLUDE_DIR             /usr/local/include
 Protobuf_LIBRARY_DEBUG           /usr/local/lib/libprotobuf.dylib
 Protobuf_LIBRARY_RELEASE         /usr/local/lib/libprotobuf.dylib
 Protobuf_LITE_LIBRARY_DEBUG      /usr/local/lib/libprotobuf-lite.dylib
 Protobuf_LITE_LIBRARY_RELEASE    /usr/local/lib/libprotobuf-lite.dylib
 Protobuf_PROTOC_EXECUTABLE       /Users/nunoguedelha/miniforge3/envs/robotologybin3/bin/protoc
 Protobuf_PROTOC_LIBRARY_DEBUG    /usr/local/lib/libprotoc.dylib
 Protobuf_PROTOC_LIBRARY_RELEAS   /usr/local/lib/libprotoc.dylib

I added to the CMake command line DCMAKE_PREFIX_PATH=$CONDA_PREFIX to force CMake to find protobuf in conda environment.

I now get the CMake config:

Protobuf_DIR                     Protobuf_DIR-NOTFOUND
 Protobuf_INCLUDE_DIR             /Users/nunoguedelha/miniforge3/envs/robotologydeps3/include
 Protobuf_LIBRARY_DEBUG           /Users/nunoguedelha/miniforge3/envs/robotologydeps3/lib/libprotobuf.dylib
 Protobuf_LIBRARY_RELEASE         /Users/nunoguedelha/miniforge3/envs/robotologydeps3/lib/libprotobuf.dylib
 Protobuf_LITE_LIBRARY_DEBUG      /Users/nunoguedelha/miniforge3/envs/robotologydeps3/lib/libprotobuf-lite.dylib
 Protobuf_LITE_LIBRARY_RELEASE    /Users/nunoguedelha/miniforge3/envs/robotologydeps3/lib/libprotobuf-lite.dylib
 Protobuf_PROTOC_EXECUTABLE       /Users/nunoguedelha/miniforge3/envs/robotologydeps3/bin/protoc
 Protobuf_PROTOC_LIBRARY_DEBUG    /Users/nunoguedelha/miniforge3/envs/robotologydeps3/lib/libprotoc.dylib
 Protobuf_PROTOC_LIBRARY_RELEAS   /Users/nunoguedelha/miniforge3/envs/robotologydeps3/lib/libprotoc.dylib

Rebuilding...

@traversaro
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I guess this was fixed by rebuilding against the correct libprotobuf libraries, if anyone is still experiencing this issue, please open a new issue, thanks!

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@traversaro @nunoguedelha