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facebookresearch / habitat-sim

A flexible, high-performance 3D simulator for Embodied AI research.
https://aihabitat.org/
MIT License
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Error Undefined Symbol for habitat_sim_bindings #179

Closed SenZHANG-GitHub closed 5 years ago

SenZHANG-GitHub commented 5 years ago

Steps to reproduce

  1. CentOS release 6.9 (Linux version 2.6.32-696.16.1.el6.x86_64 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) )
  2. Complier: gcc 7.2.0
  3. Compilation status: success (I suppose)
  4. python version: 3.6.5 (GCC 4.9.3 on linux) (I add export /usr/local/gcc/7.2.0/lib64/libstdc++.so.6 to fix a runtime issue w.r.t incompatible old versions of libstdc++.so.6)

Observed Results

Runtime error when I tried to impose habitat_sim. Could you give me some suggestions to fix this?

(habitat) szha2609@login4:~/src$ py Python 3.6.5 (default, May 3 2018, 10:16:57) [GCC 4.9.3] on linux Type "help", "copyright", "credits" or "license" for more information.

import habitat_sim Traceback (most recent call last): File "", line 1, in File "/home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/init.py", line 12, i n from .nav import File "/home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/nav/init.py", line 1 , in from .greedy_geodesic_follower import GreedyGeodesicFollower File "/home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/nav/greedy_geodesic_foll ower.py", line 6, in import habitat_sim.agent File "/home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/agent/init.py", line 7, in from .agent import File "/home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/agent/agent.py", line 14 , in import habitat_sim.bindings as hsim File "/home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/bindings/init.py", l ine 24, in from habitat_sim._ext.habitat_sim_bindings import Simulator as SimulatorBackend ImportError: /home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/_ext/habitat_sim_bi ndings.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZN6google14FlagRegistererC1INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEPKcS9_S9_PTSB

Relevant Code

Compilation Information is attached in compilation_info.txt.

compilation_info.txt

SenZHANG-GitHub commented 5 years ago

"ldd /home/szha2609/venv/habitat/lib/python3.6/site-packages/habitat_sim-0.1.2-py3.6-linux-x86_64.egg/habitat_sim/_ext/habitat_sim_bi ndings.cpython-36m-x86_64-linux-gnu.so" gives the following results. Anything missing or incorrect?

    linux-vdso.so.1 =>  (0x00007ffcf38d6000)
/usr/local/gcc/7.2.0/lib64/libstdc++.so.6 (0x00002b8f61567000)
libz.so.1 => /usr/local/zlib/1.2.8/lib/libz.so.1 (0x00002b8f618fe000)
librt.so.1 => /lib64/librt.so.1 (0x00002b8f61b2e000)
libgomp.so.1 => /usr/local/gcc/7.2.0/lib64/libgomp.so.1 (0x00002b8f61d36000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b8f61f64000)
libGL.so.1 => /usr/lib64/libGL.so.1 (0x00002b8f62181000)
libEGL.so.1 => /home/szha2609/usr/lib64/libEGL.so.1 (0x00002b8f6240a000)
libCorradePluginManager.so.2 => /home/szha2609/src/habitat-sim/build/lib.linux-x86_64-3.6/habitat_sim/_ext/libCorradePluginManager.so.2 (0x00002b8f6262d000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b8f6283e000)
libCorradeUtility.so.2 => /home/szha2609/src/habitat-sim/build/lib.linux-x86_64-3.6/habitat_sim/_ext/libCorradeUtility.so.2 (0x00002b8f62a42000)
libgflags.so.2.2 => /usr/local/gflags/2.2.1/lib/libgflags.so.2.2 (0x00002b8f62c8f000)
libm.so.6 => /lib64/libm.so.6 (0x00002b8f62ec8000)
libgcc_s.so.1 => /usr/local/gcc/7.2.0/lib64/libgcc_s.so.1 (0x00002b8f6314c000)
libc.so.6 => /lib64/libc.so.6 (0x00002b8f63363000)
/lib64/ld-linux-x86-64.so.2 (0x0000003dc4600000)
libglapi.so.0 => /usr/lib64/libglapi.so.0 (0x00002b8f636f7000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00002b8f63925000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00002b8f63b45000)
libXdamage.so.1 => /usr/lib64/libXdamage.so.1 (0x00002b8f63d57000)
libXfixes.so.3 => /usr/lib64/libXfixes.so.3 (0x00002b8f63f59000)
libX11-xcb.so.1 => /usr/lib64/libX11-xcb.so.1 (0x00002b8f6415f000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00002b8f64360000)
libxcb-glx.so.0 => /usr/lib64/libxcb-glx.so.0 (0x00002b8f6469d000)
libxcb-dri2.so.0 => /usr/lib64/libxcb-dri2.so.0 (0x00002b8f648b6000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00002b8f64aba000)
libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x00002b8f64cdf000)
libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x00002b8f64ee5000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00002b8f650f2000)
libxcb-xfixes.so.0 => /usr/lib64/libxcb-xfixes.so.0 (0x00002b8f6531a000)
libxcb-render.so.0 => /usr/lib64/libxcb-render.so.0 (0x00002b8f65522000)
libxcb-shape.so.0 => /usr/lib64/libxcb-shape.so.0 (0x00002b8f6572e000)
libgbm.so.1 => /usr/lib64/libgbm.so.1 (0x00002b8f65931000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00002b8f65b3d000)
mosra commented 5 years ago

The project uses, IIRC, bundled gflags (used by glog I think), and in your case it seems like it compiled with the bundled version but then is trying to use the system-wide library from /usr/local/gflags/2.2.1/lib/libgflags.so.2.2 and those two are different, causing the missing symbol failure. Or maybe, due to how you preload the other libstdc++.so, it also accidentally picked up a different gflags version?

Is there any libgflags.so anywhere else on your system? Can you try running with the LD_LIBRARY_PATH environment variable set to that location? Or LD_PRELOAD that library?

SenZHANG-GitHub commented 5 years ago

The project uses, IIRC, bundled gflags (used by glog I think), and in your case it seems like it compiled with the bundled version but then is trying to use the system-wide library from /usr/local/gflags/2.2.1/lib/libgflags.so.2.2 and those two are different, causing the missing symbol failure. Or maybe, due to how you preload the other libstdc++.so, it also accidentally picked up a different gflags version?

Is there any libgflags.so anywhere else on your system? Can you try running with the LD_LIBRARY_PATH environment variable set to that location? Or LD_PRELOAD that library?

Thanks a lot. Should be exactly the problem. I previously add -Dgflags_DIR=/usr/local/gflags/2.2.1/lib/cmake/gflags to setup.py to avoid the following warning:

CMake Warning at deps/glog/CMakeLists.txt:49 (find_package): By not providing "Findgflags.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "gflags", but CMake did not find one.

Could not find a package configuration file provided by "gflags" (requested version 2.2.0) with any of the following names:

gflagsConfig.cmake
gflags-config.cmake

Add the installation prefix of "gflags" to CMAKE_PREFIX_PATH or set "gflags_DIR" to a directory containing one of the above files. If "gflags" provides a separate development package or SDK, be sure it has been installed.

Now I just remove -Dgflags_DIR=/usr/local/gflags/2.2.1/lib/cmake/gflags and recompile regardless of this warning. The compilation still succeed and get no problem to import habitat_sim now. Though another issue occurs when I run example.py (Segmentation fault (core dumped)). Trying to identify the problem and reading other issues now.

The recompilation log is attached for anyone interested in it.

wo_gflags_compilation.log

mosra commented 4 years ago

Just FYI, this is being fixed on our side in #247.

SenZHANG-GitHub commented 4 years ago

Just FYI, this is being fixed on our side in #247.

Thanks!