`GLIBCXX_3.4.30' not found for importing _limap

[cherubicXN]

Thanks for your great work!

While running the quickstart on my machine, I found an issue with importing _limap with the errors as shown below:

(limap) [TITAN] ➜  limap git:(main) ✗ python runners/hypersim/triangulation.py --output_dir outputs/quickstart_triangulation

Traceback (most recent call last):
  File "/home/xn/repo/limap/runners/hypersim/triangulation.py", line 6, in <module>
    from loader import read_scene_hypersim
  File "/home/xn/repo/limap/runners/hypersim/loader.py", line 7, in <module>
    import limap.base as _base
  File "/home/xn/repo/limap/limap/__init__.py", line 3, in <module>
    from _limap import *
ImportError: /home/xn/anaconda3/envs/limap/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/xn/repo/limap/_limap.cpython-39-x86_64-linux-gnu.so)

After checking the code, I found the issue is caused by the sys.path.append at triangulation.py#L4.

When I first import _limap at triangulation.py#L3, the problem is solved.

[B1ueber2y]

Hey thanks for the interest and contribution!

I never came across this issue. Could you provide more details on reproducing it? I do not understand why adding "import _limap" can resolve this issue. Is there any chance that you could clarify on this?

Thanks a lot!

[iago-suarez]

This is something usual when using anaconda. The error is saying that you have compiled the library (/home/xn/repo/limap/_limap.cpython-39-x86_64-linux-gnu.so) with a different C++ version than the one used to compile the python version that you are trying to use (/home/xn/anaconda3/envs/limap/bin/../lib/libstdc++.so.6).

This usually happens because when compiling the limap library in this case, the system compiler and C++ version is used but the correct one would be the anaconda version. A simple fix uses to be installing the proper gcc and cmake version in anaconda. In such a way that the default cmake is the anaconda one instead of the system one.

try with (untested):

conda install cmake

And re-compile the limap library

[cherubicXN]

Hello,

I am currently working with the following runtime environment:

• Ubuntu 22.04.1
• Anaconda 4.13.0
• CUDA 11.7
• Python 3.9
• PyTorch 1.13.0+cu117 (installed using pip install torch==1.13.0+cu117 torchvision==0.14.0+cu117 torchaudio==0.13.0 --extra-index-url https://download.pytorch.org/whl/cu117)

Click to see my CMake Outputs

-- The C compiler identification is GNU 9.5.0
-- The CXX compiler identification is GNU 9.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc-9 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++-9 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Enabling OpenMP support
-- Disabling pixelwise optimization with ceres interpolation.
-- Found METIS: /usr/include (found suitable version "5.1.0", minimum required is "5.1.0")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found AMD headers in: /usr/include/suitesparse
-- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so
-- Found SPQR headers in: /usr/include/suitesparse
-- Found SPQR library: /usr/lib/x86_64-linux-gnu/libspqr.so
-- Found Config headers in: /usr/include/suitesparse
-- Found Config library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so
-- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB.
-- Looking for shm_open in rt
-- Looking for shm_open in rt - found
-- Adding librt to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing).
-- Found METIS: /usr/include (found version "5.1.0")
-- Looking for cholmod_metis
-- Looking for cholmod_metis - found
-- Found SuiteSparse: /usr/include/suitesparse (found suitable version "5.10.1", minimum required is "5.10.1") found components: AMD CAMD CCOLAMD CHOLMOD COLAMD SPQR Config
-- Found required Ceres dependency: Eigen version 3.4.0 in /usr/share/eigen3/cmake
-- Found required Ceres dependency: glog
-- Found required Ceres dependency: gflags
-- Found Ceres version: 2.2.0 installed in: /usr/local with components: [EigenSparse, SparseLinearAlgebraLibrary, LAPACK, SuiteSparse, SchurSpecializations, Multithreading]
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem system unit_test_framework
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found Eigen
--   Includes : /usr/include/eigen3
-- Found FreeImage
--   Includes : /usr/include
--   Libraries : /usr/lib/x86_64-linux-gnu/libfreeimage.so
-- Found Glog
--   Includes : /usr/local/include
--   Libraries : /usr/local/lib/libglog.so
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so
-- Found Glew
--   Includes : /usr/include
--   Libraries : /usr/lib/x86_64-linux-gnu/libGLEW.so
-- Using header-only CGAL
-- Targetting Unix Makefiles
-- Using /usr/bin/g++-9 compiler.
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- Found MPFR: /usr/lib/x86_64-linux-gnu/libmpfr.so
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.48")
-- Boost include dirs: /usr/include
-- Boost libraries:
-- Using gcc version 4 or later. Adding -frounding-math
-- Setting build type to 'RelWithDebInfo' as none was specified.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.7")
-- Found Boost: /usr/include (found version "1.74.0") found components: system serialization
-- pybind11 v2.10.0 dev1
-- Found PythonInterp: /home/xn/anaconda3/envs/limap/bin/python (found suitable version "3.9", minimum required is "3.6")
-- Found PythonLibs: /home/xn/anaconda3/envs/limap/lib/libpython3.9.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
Build type: RelWithDebInfo
-- Creating target: igl::core (igl_core)
-- Configuring done
-- Generating done

I tried implementing @iago-suarez's solution but still encountered the same issue. I believe the main cause is the use of Anaconda. However, I discovered that the compiled _limap module could be successfully imported in the terminal, as shown below:

(limap) [TITAN] ➜  limap git:(main) ✗ python
Python 3.9.0 (default, Nov 15 2020, 14:28:56)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import _limap
>>>

I further investigated the problem by attempting to import _limap before or after triangulation.py#L4, both of which were successful. Since _limap is actually imported at hypersim/loader.py#L5, I set a breakpoint at the beginning of loader.py and then tried importing _limap. Unfortunately, I encountered the same error.

So, my current solution to avoid this issue is importing the _limap or limap in the first.

On my machine, I encounter the same issue with other runners as well, such as ETH3D.

[B1ueber2y]

Maybe the problem can be resolved by linking your existing libstdc++.so file to the anaconda environment by

ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6  {path to anaconda}/envs/limap/bin/../lib/libstdc++.so.6

I never encountered this issue myself but got inspiration from similar issue from another project. Thanks!

[cherubicXN]

It works! Thanks!