Segfault in ik command

[adithyamurali]

Hi @mjd3

Thanks for this amazing repo. I get an error when running the following test script in my Ubuntu 18.04 machine:

import numpy as np
from tracikpy import TracIKSolver

ee_pose = np.array([[ 0.0525767 , -0.64690764, -0.7607537 , 0.        ],
                    [-0.90099786, -0.35923817,  0.24320937, 0.2       ],
                    [-0.43062577,  0.67265031, -0.60174996, 0.4       ],
                    [ 0.        ,  0.        ,  0.        , 1.        ]])

ik_solver = TracIKSolver(
    "data/franka_panda.urdf",
    "panda_link0",
    "panda_hand",
)
qout = ik_solver.ik(ee_pose, qinit=np.zeros(ik_solver.number_of_joints))
print(qout)

There is a segfault at line ik_solver.ik:
KDL FKSolver is failing: Segmentation fault (core dumped)

I was wondering if you have seen this error before?

[adithyamurali]

I installed the package with the steps in the readme:

sudo apt-get install libeigen3-dev liborocos-kdl-dev libkdl-parser-dev liburdf-dev libnlopt-dev
git clone https://github.com/mjd3/tracikpy.git
pip install tracikpy/

[adithyamurali]

I believe the error is happening in these lines:
https://github.com/mjd3/tracikpy/blob/main/tracikpy/src/nlopt_ik.cpp#L354
https://github.com/mjd3/tracikpy/blob/main/tracikpy/src/nlopt_ik.cpp#L407

[mjd3]

Hmmm, I am not able to reproduce this error. I have added an Ubuntu 18.04 workflow to testing as well as Dockerfiles for Ubuntu 18.04 and Ubuntu 20.04 and all of these pass the unit tests without issue (see #3). Can you install with the test option (using pip install tracikpy[test]) and then run pytest from the root directory of the project to see if that passes?

[adithyamurali]

Thanks for the debuging steps. I have a small correction: actually in the first post above, I installed as pip install trackikpy[test] and that's how I ended up with the segfault error.

If I just install with pip install tracikpy/ without the test option, I get a separate error: ModuleNotFoundError: No module named tracikpy.swig.trac_ik_wrap when trying to import the library: from tracikpy import TracIKSolver

[mjd3]

Ah, this suggests that the install is not working. Can you try with pip install tracikpy --verbose and see if the SWIG binding fails to build? Also, make sure you have SWIG installed (on Ubuntu, you can check with swig -version from the command line).

[adithyamurali]

Yes, it seems I do have swig installed, here's the output of swig -version:

SWIG Version 3.0.12
Compiled with g++ [x86_64-pc-linux-gnu]
Configured options: +pcre
Please see http://www.swig.org for reporting bugs and further information

When I installed with the --verbose option, there were no build errors. Here's the full output:

`Using pip 21.1.3 from /home/admurali/anaconda3/envs/rlgpu/lib/python3.7/site-packages/pip (python 3.7)
Non-user install because site-packages writeable
Created temporary directory: /tmp/pip-ephem-wheel-cache-wdc8wzmh
Created temporary directory: /tmp/pip-req-tracker-ulmy33cn
Initialized build tracking at /tmp/pip-req-tracker-ulmy33cn
Created build tracker: /tmp/pip-req-tracker-ulmy33cn
Entered build tracker: /tmp/pip-req-tracker-ulmy33cn
Created temporary directory: /tmp/pip-install-guvp44w5
Processing ./tracikpy
Created temporary directory: /tmp/pip-req-build-168qvv_i
DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
pip 21.3 will remove support for this functionality. You can find discussion regarding this at pypa/pip#7555.
Added file:///home/admurali/ws/tracikpy to build tracker '/tmp/pip-req-tracker-ulmy33cn'
Running setup.py (path:/tmp/pip-req-build-168qvv_i/setup.py) egg_info for package from file:///home/admurali/ws/tracikpy
Created temporary directory: /tmp/pip-pip-egg-info-eooyqyjb
Running command python setup.py egg_info
running egg_info
creating /tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info
writing /tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/PKG-INFO
writing dependency_links to /tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/dependency_links.txt
writing requirements to /tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/requires.txt
writing top-level names to /tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/top_level.txt
writing manifest file '/tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/SOURCES.txt'
reading manifest file '/tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/SOURCES.txt'
writing manifest file '/tmp/pip-pip-egg-info-eooyqyjb/tracikpy.egg-info/SOURCES.txt'
Source in /tmp/pip-req-build-168qvv_i has version 0.1.0, which satisfies requirement tracikpy==0.1.0 from file:///home/admurali/ws/tracikpy
Removed tracikpy==0.1.0 from file:///home/admurali/ws/tracikpy from build tracker '/tmp/pip-req-tracker-ulmy33cn'
Requirement already satisfied: numpy in /home/admurali/anaconda3/envs/rlgpu/lib/python3.7/site-packages (from tracikpy==0.1.0) (1.21.1)
Created temporary directory: /tmp/pip-unpack-ui5goh
Building wheels for collected packages: tracikpy
Created temporary directory: /tmp/pip-wheel-2z11bl_7
Building wheel for tracikpy (setup.py) ... Destination directory: /tmp/pip-wheel-2z11bl_7
Running command /home/admurali/anaconda3/envs/rlgpu/bin/python3.7 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-168qvv_i/setup.py'"'"'; file='"'"'/tmp/pip-req-build-168qvv_i/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-2z11bl_7
running bdist_wheel
running build
running build_py
running build_ext
building 'tracikpy.swig._trac_ik_wrap' extension
swigging tracikpy/swig/trac_ik.i to tracikpy/swig/trac_ik_wrap.cpp
swig -python -c++ -Itracikpy/include -o tracikpy/swig/trac_ik_wrap.cpp tracikpy/swig/trac_ik.i
creating build
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/tracikpy
creating build/temp.linux-x86_64-3.7/tracikpy/swig
creating build/temp.linux-x86_64-3.7/tracikpy/src
gcc -pthread -B /home/admurali/anaconda3/envs/rlgpu/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itracikpy/include -I/usr/include/eigen3 -I/home/admurali/anaconda3/envs/rlgpu/include/python3.7m -c tracikpy/swig/trac_ik_wrap.cpp -o build/temp.linux-x86_64-3.7/tracikpy/swig/trac_ik_wrap.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/admurali/anaconda3/envs/rlgpu/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itracikpy/include -I/usr/include/eigen3 -I/home/admurali/anaconda3/envs/rlgpu/include/python3.7m -c tracikpy/src/trac_ik.cpp -o build/temp.linux-x86_64-3.7/tracikpy/src/trac_ik.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/admurali/anaconda3/envs/rlgpu/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itracikpy/include -I/usr/include/eigen3 -I/home/admurali/anaconda3/envs/rlgpu/include/python3.7m -c tracikpy/src/nlopt_ik.cpp -o build/temp.linux-x86_64-3.7/tracikpy/src/nlopt_ik.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
tracikpy/src/nlopt_ik.cpp: In member function ‘int NLOPT_IK::NLOPT_IK::CartToJnt(const KDL::JntArray&, const KDL::Frame&, KDL::JntArray&, KDL::Twist, const KDL::JntArray&)’:
tracikpy/src/nlopt_ik.cpp:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (q_init.data.size() != types.size())
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
gcc -pthread -B /home/admurali/anaconda3/envs/rlgpu/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itracikpy/include -I/usr/include/eigen3 -I/home/admurali/anaconda3/envs/rlgpu/include/python3.7m -c tracikpy/src/kdl_tl.cpp -o build/temp.linux-x86_64-3.7/tracikpy/src/kdl_tl.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/tracikpy
creating build/lib.linux-x86_64-3.7/tracikpy/swig
g++ -pthread -shared -B /home/admurali/anaconda3/envs/rlgpu/compiler_compat -L/home/admurali/anaconda3/envs/rlgpu/lib -Wl,-rpath=/home/admurali/anaconda3/envs/rlgpu/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/tracikpy/swig/trac_ik_wrap.o build/temp.linux-x86_64-3.7/tracikpy/src/trac_ik.o build/temp.linux-x86_64-3.7/tracikpy/src/nlopt_ik.o build/temp.linux-x86_64-3.7/tracikpy/src/kdl_tl.o -lorocos-kdl -lnlopt -lurdf -lkdl_parser -o build/lib.linux-x86_64-3.7/tracikpy/swig/_trac_ik_wrap.cpython-37m-x86_64-linux-gnu.so
copying tracikpy/trac_ik_solver.py -> build/lib.linux-x86_64-3.7/tracikpy
copying tracikpy/version.py -> build/lib.linux-x86_64-3.7/tracikpy
copying tracikpy/init.py -> build/lib.linux-x86_64-3.7/tracikpy
copying tracikpy/swig/trac_ik_wrap.py -> build/lib.linux-x86_64-3.7/tracikpy/swig
copying tracikpy/swig/init.py -> build/lib.linux-x86_64-3.7/tracikpy/swig
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/tracikpy
creating build/bdist.linux-x86_64/wheel/tracikpy/swig
copying build/lib.linux-x86_64-3.7/tracikpy/swig/_trac_ik_wrap.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/tracikpy/swig
copying build/lib.linux-x86_64-3.7/tracikpy/swig/trac_ik_wrap.py -> build/bdist.linux-x86_64/wheel/tracikpy/swig
copying build/lib.linux-x86_64-3.7/tracikpy/swig/init.py -> build/bdist.linux-x86_64/wheel/tracikpy/swig
copying build/lib.linux-x86_64-3.7/tracikpy/trac_ik_solver.py -> build/bdist.linux-x86_64/wheel/tracikpy
copying build/lib.linux-x86_64-3.7/tracikpy/version.py -> build/bdist.linux-x86_64/wheel/tracikpy
copying build/lib.linux-x86_64-3.7/tracikpy/init.py -> build/bdist.linux-x86_64/wheel/tracikpy
running install_egg_info
running egg_info
creating tracikpy.egg-info
writing tracikpy.egg-info/PKG-INFO
writing dependency_links to tracikpy.egg-info/dependency_links.txt
writing requirements to tracikpy.egg-info/requires.txt
writing top-level names to tracikpy.egg-info/top_level.txt
writing manifest file 'tracikpy.egg-info/SOURCES.txt'
reading manifest file 'tracikpy.egg-info/SOURCES.txt'
writing manifest file 'tracikpy.egg-info/SOURCES.txt'
Copying tracikpy.egg-info to build/bdist.linux-x86_64/wheel/tracikpy-0.1.0-py3.7.egg-info
running install_scripts
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.linux-x86_64/wheel/tracikpy-0.1.0.dist-info/WHEEL
creating '/tmp/pip-wheel-2z11bl_7/tracikpy-0.1.0-cp37-cp37m-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'tracikpy/init.py'
adding 'tracikpy/trac_ik_solver.py'
adding 'tracikpy/version.py'
adding 'tracikpy/swig/init.py'
adding 'tracikpy/swig/_trac_ik_wrap.cpython-37m-x86_64-linux-gnu.so'
adding 'tracikpy/swig/trac_ik_wrap.py'
adding 'tracikpy-0.1.0.dist-info/LICENSE'
adding 'tracikpy-0.1.0.dist-info/METADATA'
adding 'tracikpy-0.1.0.dist-info/WHEEL'
adding 'tracikpy-0.1.0.dist-info/top_level.txt'
adding 'tracikpy-0.1.0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
done
Created wheel for tracikpy: filename=tracikpy-0.1.0-cp37-cp37m-linux_x86_64.whl size=3115277 sha256=bca5f73733ee383684b581a020fdf9891480666db2910afabd018d98239412c2
Stored in directory: /tmp/pip-ephem-wheel-cache-wdc8wzmh/wheels/5f/2d/2f/182aa95356f03e834b6b0100ad29fd64ca37fcb953f587b3b7
Successfully built tracikpy
Installing collected packages: tracikpy

Successfully installed tracikpy-0.1.0
Removed build tracker: '/tmp/pip-req-tracker-ulmy33cn'`

[mjd3]

Hmm yes it does seem like the install is working correctly. So after this successful install you are unable to import?

[adithyamurali]

Yeah after this installation, here's the error trace i get when running from tracikpy import TracIKSolver:

<ipython-input-1-4093a645420a> in <module>()
      1 import numpy as np
----> 2 from tracikpy import TracIKSolver
      3 
      4 ee_pose = np.array([[ 0.0525767 , -0.64690764, -0.7607537 , 0.        ],
      5                     [-0.90099786, -0.35923817,  0.24320937, 0.2       ],

/home/admurali/ws/tracikpy/tracikpy/__init__.py in <module>()
----> 1 from .trac_ik_solver import TracIKSolver

/home/admurali/ws/tracikpy/tracikpy/trac_ik_solver.py in <module>()
      7 import numpy as np
      8 
----> 9 from .swig.trac_ik_wrap import TRAC_IK
     10 
     11 

ModuleNotFoundError: No module named 'tracikpy.swig.trac_ik_wrap'

[mjd3]

Are you installing with pip install -e? Does that file (tracikpy/swig/trac_ik_wrap.py) exist after building the swig bindings? Sorry for the issues! Hoping we can get this figured out although it is hard to debug something of this nature if I am unable to reproduce myself (e.g., in docker).

[mjd3]

@adithyamurali were you able to resolve?