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ImportError: libdynamicedt3d.so.1.8 #1

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fzy139 opened this issue Jul 28, 2019 · 30 comments
Open

ImportError: libdynamicedt3d.so.1.8 #1

fzy139 opened this issue Jul 28, 2019 · 30 comments
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@wkentaro
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@fzy139
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fzy139 commented Jul 28, 2019 •
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Hi,
I'm trying to install octomap with pip in a conda env and it turns out to be that import error.Is there anything else I should install?
ImportError: libdynamicedt3d.so.1.8: cannot open shared object file: No such file or directory

                                                       Thanks a lot!
@wkentaro
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It is working on the Travis: https://travis-ci.com/wkentaro/octomap-python.
Can you check what is the difference between your env and the env on Travis?
e.g., OS

@fzy139
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fzy139 commented Jul 29, 2019

It is working on the Travis: https://travis-ci.com/wkentaro/octomap-python.
Can you check what is the difference between your env and the env on Travis?
e.g., OS

Hi wkentaro,
I've done it.I should install the liboctomap-dev and libdynamicedt3d-dev before I install the octomap-python.Thank for what you've done.

@wkentaro
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It's strange, since these dynamic link libraries should be installed via pip.

Name: octomap-python
Version: 1.8.0.post12
Summary: Python binding of the OctoMap library.
Home-page: https://github.com/wkentaro/octomap-python
Author: None
Author-email: None
License: BSD
Location: /usr/local/lib/python2.7/dist-packages
Requires: numpy
Required-by: 
Files:
  ../../../bin/binvox2bt
  ../../../bin/bt2vrml
  ../../../bin/compare_octrees
  ../../../bin/convert_octree
  ../../../bin/edit_octree
  ../../../bin/eval_octree_accuracy
  ../../../bin/graph2tree
  ../../../bin/log2graph
  ../../../include/dynamicEDT3D/bucketedqueue.h
  ../../../include/dynamicEDT3D/bucketedqueue.hxx
  ../../../include/dynamicEDT3D/dynamicEDT3D.h
  ../../../include/dynamicEDT3D/dynamicEDTOctomap.h
  ../../../include/dynamicEDT3D/point.h
  ../../../include/octomap/AbstractOcTree.h
  ../../../include/octomap/AbstractOccupancyOcTree.h
  ../../../include/octomap/ColorOcTree.h
  ../../../include/octomap/CountingOcTree.h
  ../../../include/octomap/MCTables.h
  ../../../include/octomap/MapCollection.h
  ../../../include/octomap/MapCollection.hxx
  ../../../include/octomap/MapNode.h
  ../../../include/octomap/MapNode.hxx
  ../../../include/octomap/OcTree.h
  ../../../include/octomap/OcTreeBase.h
  ../../../include/octomap/OcTreeBaseImpl.h
  ../../../include/octomap/OcTreeBaseImpl.hxx
  ../../../include/octomap/OcTreeDataNode.h
  ../../../include/octomap/OcTreeDataNode.hxx
  ../../../include/octomap/OcTreeIterator.hxx
  ../../../include/octomap/OcTreeKey.h
  ../../../include/octomap/OcTreeNode.h
  ../../../include/octomap/OcTreeStamped.h
  ../../../include/octomap/OccupancyOcTreeBase.h
  ../../../include/octomap/OccupancyOcTreeBase.hxx
  ../../../include/octomap/Pointcloud.h
  ../../../include/octomap/ScanGraph.h
  ../../../include/octomap/math/Pose6D.h
  ../../../include/octomap/math/Quaternion.h
  ../../../include/octomap/math/Utils.h
  ../../../include/octomap/math/Vector3.h
  ../../../include/octomap/octomap.h
  ../../../include/octomap/octomap_deprecated.h
  ../../../include/octomap/octomap_timing.h
  ../../../include/octomap/octomap_types.h
  ../../../include/octomap/octomap_utils.h
  ../../../share/dynamicEDT3D/dynamicEDT3DConfig-version.cmake
  ../../../share/dynamicEDT3D/dynamicEDT3DConfig.cmake
  ../../../share/dynamic_edt_3d/package.xml
  ../../../share/octomap/octomap-config-version.cmake
  ../../../share/octomap/octomap-config.cmake
  ../../../share/octomap/package.xml
  ../../libdynamicedt3d.a
  ../../libdynamicedt3d.so
  ../../libdynamicedt3d.so.1.8
  ../../libdynamicedt3d.so.1.8.0
  ../../liboctomap.a
  ../../liboctomap.so
  ../../liboctomap.so.1.8
  ../../liboctomap.so.1.8.0
  ../../liboctomath.a
  ../../liboctomath.so
  ../../liboctomath.so.1.8
  ../../liboctomath.so.1.8.0
  ../../pkgconfig/dynamicEDT3D.pc
  ../../pkgconfig/octomap.pc
  octomap.so
  octomap_python-1.8.0.post12.dist-info/INSTALLER
  octomap_python-1.8.0.post12.dist-info/METADATA
  octomap_python-1.8.0.post12.dist-info/RECORD
  octomap_python-1.8.0.post12.dist-info/WHEEL
  octomap_python-1.8.0.post12.dist-info/top_level.txt

@biggzlar
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I have the same issue on macOS Mojave 10.14.6

Installing octomap beforehand did not fix it for me either.

@wkentaro
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Please put the output of pip show --files octomap-python?

@biggzlar
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Thank you for the quick response.

Name: octomap-python
Version: 1.8.0.post12
Summary: Python binding of the OctoMap library.
Home-page: https://github.com/wkentaro/octomap-python
Author: None
Author-email: None
License: BSD
Location: /Users/biggzlar/anaconda3/envs/octo/lib/python3.6/site-packages
Requires: numpy
Required-by:
Files:
  ../../../bin/binvox2bt
  ../../../bin/bt2vrml
  ../../../bin/compare_octrees
  ../../../bin/convert_octree
  ../../../bin/edit_octree
  ../../../bin/eval_octree_accuracy
  ../../../bin/graph2tree
  ../../../bin/log2graph
  ../../../include/dynamicEDT3D/bucketedqueue.h
  ../../../include/dynamicEDT3D/bucketedqueue.hxx
  ../../../include/dynamicEDT3D/dynamicEDT3D.h
  ../../../include/dynamicEDT3D/dynamicEDTOctomap.h
  ../../../include/dynamicEDT3D/point.h
  ../../../include/octomap/AbstractOcTree.h
  ../../../include/octomap/AbstractOccupancyOcTree.h
  ../../../include/octomap/ColorOcTree.h
  ../../../include/octomap/CountingOcTree.h
  ../../../include/octomap/MCTables.h
  ../../../include/octomap/MapCollection.h
  ../../../include/octomap/MapCollection.hxx
  ../../../include/octomap/MapNode.h
  ../../../include/octomap/MapNode.hxx
  ../../../include/octomap/OcTree.h
  ../../../include/octomap/OcTreeBase.h
  ../../../include/octomap/OcTreeBaseImpl.h
  ../../../include/octomap/OcTreeBaseImpl.hxx
  ../../../include/octomap/OcTreeDataNode.h
  ../../../include/octomap/OcTreeDataNode.hxx
  ../../../include/octomap/OcTreeIterator.hxx
  ../../../include/octomap/OcTreeKey.h
  ../../../include/octomap/OcTreeNode.h
  ../../../include/octomap/OcTreeStamped.h
  ../../../include/octomap/OccupancyOcTreeBase.h
  ../../../include/octomap/OccupancyOcTreeBase.hxx
  ../../../include/octomap/Pointcloud.h
  ../../../include/octomap/ScanGraph.h
  ../../../include/octomap/math/Pose6D.h
  ../../../include/octomap/math/Quaternion.h
  ../../../include/octomap/math/Utils.h
  ../../../include/octomap/math/Vector3.h
  ../../../include/octomap/octomap.h
  ../../../include/octomap/octomap_deprecated.h
  ../../../include/octomap/octomap_timing.h
  ../../../include/octomap/octomap_types.h
  ../../../include/octomap/octomap_utils.h
  ../../../share/dynamicEDT3D/dynamicEDT3DConfig-version.cmake
  ../../../share/dynamicEDT3D/dynamicEDT3DConfig.cmake
  ../../../share/dynamic_edt_3d/package.xml
  ../../../share/octomap/octomap-config-version.cmake
  ../../../share/octomap/octomap-config.cmake
  ../../../share/octomap/package.xml
  ../../libdynamicedt3d.1.8.0.dylib
  ../../libdynamicedt3d.1.8.dylib
  ../../libdynamicedt3d.a
  ../../libdynamicedt3d.dylib
  ../../liboctomap.1.8.0.dylib
  ../../liboctomap.1.8.dylib
  ../../liboctomap.a
  ../../liboctomap.dylib
  ../../liboctomath.1.8.0.dylib
  ../../liboctomath.1.8.dylib
  ../../liboctomath.a
  ../../liboctomath.dylib
  ../../pkgconfig/dynamicEDT3D.pc
  ../../pkgconfig/octomap.pc
  octomap.cpython-36m-darwin.so
  octomap_python-1.8.0.post12.dist-info/INSTALLER
  octomap_python-1.8.0.post12.dist-info/METADATA
  octomap_python-1.8.0.post12.dist-info/RECORD
  octomap_python-1.8.0.post12.dist-info/WHEEL
  octomap_python-1.8.0.post12.dist-info/top_level.txt

Error log:

Traceback (most recent call last):
  File "run.py", line 2, in <module>
    import octomap
ImportError: dlopen(/Users/biggzlar/anaconda3/envs/octo/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so, 2): Library not loaded: /private/var/folders/hs/0ggtspzs07bfg6x4dtm1b2880000gn/T/pip-install-_ttpxv31/octomap-python/src/octomap/lib/libdynamicedt3d.1.8.dylib
  Referenced from: /Users/biggzlar/anaconda3/envs/octo/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so
  Reason: image not found

@wkentaro
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It seems dylib is properly installed. Maybe linking fails.
Can you run otool -L /Users/biggzlar/anaconda3/envs/octo/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so?

@wkentaro
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wkentaro commented Aug 20, 2019 •
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FYI: If you are in a rush, you can run pip install octomap-python --no-binary octomap-python to avoid using the wheel file, which is prebuilt and install from source.
But I also want to fix the issue of binary actually.

@biggzlar
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biggzlar commented Aug 20, 2019 •
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Output of otool -L ...:

/Users/biggzlar/anaconda3/envs/octo/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so:
	/private/var/folders/hs/0ggtspzs07bfg6x4dtm1b2880000gn/T/pip-install-_ttpxv31/octomap-python/src/octomap/lib/libdynamicedt3d.1.8.dylib (compatibility version 1.8.0, current version 1.8.0)
	/private/var/folders/hs/0ggtspzs07bfg6x4dtm1b2880000gn/T/pip-install-_ttpxv31/octomap-python/src/octomap/lib/liboctomap.1.8.dylib (compatibility version 1.8.0, current version 1.8.0)
	/private/var/folders/hs/0ggtspzs07bfg6x4dtm1b2880000gn/T/pip-install-_ttpxv31/octomap-python/src/octomap/lib/liboctomath.1.8.dylib (compatibility version 1.8.0, current version 1.8.0)
	@rpath/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1)

What might be of interest is, that when I go to uninstall via pip, it shows the following list of file locations. Maybe this is just an issue with conda environments? I.e. the binary is not searching in the right spot?

    ...
    /Users/biggzlar/anaconda3/envs/octo/lib/libdynamicedt3d.1.8.0.dylib
    /Users/biggzlar/anaconda3/envs/octo/lib/libdynamicedt3d.1.8.dylib
    /Users/biggzlar/anaconda3/envs/octo/lib/libdynamicedt3d.a
    /Users/biggzlar/anaconda3/envs/octo/lib/libdynamicedt3d.dylib
    /Users/biggzlar/anaconda3/envs/octo/lib/liboctomap.1.8.0.dylib
    /Users/biggzlar/anaconda3/envs/octo/lib/liboctomap.1.8.dylib
    ...

@wkentaro
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I think the problem is that the dylib file paths are absolute.
e.g. /private/var/folders/hs/0ggtspzs07bfg6x4dtm1b2880000gn/T/pip-install-_ttpxv31/octomap-python/src/octomap/lib/libdynamicedt3d.1.8.dylib

It should be relative or something like @rpath/libdynamicedt3d.1.8.dylib.
I think this is the problem of the binary generator https://github.com/wkentaro/octomap-python-wheels.

In Ubuntu + Anaconda, it shows like below

% ldd .anaconda3/lib/python3.7/site-packages/octomap.cpython-37m-x86_64-linux-gnu.so
	linux-vdso.so.1 =>  (0x00007ffc9ffb7000)
	libdynamicedt3d.so.1.8 => not found
	liboctomap.so.1.8 => not found
	liboctomath.so.1.8 => not found
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f3361fed000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f3361ce4000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f3361ace000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f33618b1000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f33614e7000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f33625bc000)

but lib is installed

% ls .anaconda3/lib/liboctomap*
.anaconda3/lib/liboctomap.a  .anaconda3/lib/liboctomap.so  .anaconda3/lib/liboctomap.so.1.8  .anaconda3/lib/liboctomap.so.1.8.0

so it works.

python -c 'import octomap'

@wkentaro
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I will work on fixing this, but for short-term you need to use --no-binary option, because I don't think I can fix it immediately

@biggzlar
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Thank you!
Could you give instructions on how to compile the binary myself if I go the --no-binary route?

@wkentaro
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The binary files (e.g., octomap..so, liboctomap..so) are compiled and installed automatically. you just need to run with the options I told.

@wkentaro wkentaro added the bug Something isn't working label Aug 21, 2019
@wkentaro wkentaro self-assigned this Aug 21, 2019
@biggzlar
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Thanks! Sadly, for me, this leads to the same error. The library again isn't found (and searched for in the same temp directory). :(

@wkentaro
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Oh, really. Maybe you need to wait until I solve this

@brunoeducsantos
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Has the binary issue being solved?
I am having the same problem.

@tianyudwang
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Has the binary issue being solved?
I am having the same problem.

Sadly me too.

@LucasBruder
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i was able to fix this by adding the path to the .so to LD_LIBRARY_PATH

@VicSegers VicSegers mentioned this issue May 8, 2020
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@UpstairsCheek
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UpstairsCheek commented Jun 25, 2020 •
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I am having the same issue on macOS Catalina. @LucasBruder can you be more specific?

(py3.6.10) student-net-vpn-2142:octomap-python mgsa$ python -c "import octomap"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: dlopen(/Users/mgsa/sp/py3.6.10/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so, 2): Library not loaded: /private/var/folders/v_/87m7kb0x3sl15z2_cypyd4c40000gn/T/pip-install-1ye7easn/octomap-python/src/octomap/lib/libdynamicedt3d.1.8.dylib
  Referenced from: /Users/mgsa/sp/py3.6.10/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so
  Reason: image not found

@LucasBruder
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I am having the same issue on macOS Catalina. @LucasBruder can you be more specific?

(py3.6.10) student-net-vpn-2142:octomap-python mgsa$ python -c "import octomap"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: dlopen(/Users/mgsa/sp/py3.6.10/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so, 2): Library not loaded: /private/var/folders/v_/87m7kb0x3sl15z2_cypyd4c40000gn/T/pip-install-1ye7easn/octomap-python/src/octomap/lib/libdynamicedt3d.1.8.dylib
  Referenced from: /Users/mgsa/sp/py3.6.10/lib/python3.6/site-packages/octomap.cpython-36m-darwin.so
  Reason: image not found

Something like the below might work, although I've never tried this on OSX

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Users/mgsa/sp/py3.6.10/lib/python3.6/site-packages/
python -c "import octomap"

@UpstairsCheek
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Thank you for your answer. However, it still does not work. I could not install the library as I get back to that image not found error every way I try

@wkentaro
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Let me have a look.

@UpstairsCheek
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Let me have a look.

Do you need any info? Thank you

@wkentaro
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Below command should work in the wild

git clone https://github.com/wkentaro/octomap-python.git
cd octomap-python

wget https://raw.githubusercontent.com/wkentaro/dotfiles/master/local/bin/install_anaconda3.sh
bash ./install_anaconda3.sh .
source .anaconda3/bin/activate

pip install -e .

cd examples
python -c 'import octomap'
./insertPointCloud.py
./getLabels.py

@rhidra rhidra mentioned this issue Jul 27, 2020
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@zbynekwinkler
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I have been able to create "fixed" manylinux wheel following the instructions at How to include external library with python wheel package using the mentioned auditwheel tool.

zbynekwinkler added a commit to robotika/osgar that referenced this issue Oct 29, 2020
@zbynekwinkler
Add octomap python package.
91373bd 
The whl package was fixed to include proper RPATH. For details
see wkentaro/octomap-python#1 (comment)

To run the included example install also the follwing packages:

  pip install glooye imgviz trimesh scipy networkx
@zbynekwinkler
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Feel free to try the fixed package: pip install -i https://osgar.robotika.cz/subt/pip/ octomap-python==1.8.0.post12

@Fabricio9199
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Hello @wkentaro,
Has this bug been fixed yet? I'm having the same problem during import the octomap package.

ImportError: libdynamicedt3d.so.1.8: cannot open shared object file: No such file or directory

I already installed libdynamicedt3d separately on my PC (using apt-get), but the version is 1.9. Is it possible to use this package with the 1.9 version of libdynamicedt? Or, I should use the 1.8 version? Do you know how I can install this lib on 1.8 version?

@kopytjuk
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Feel free to try the fixed package: pip install -i https://osgar.robotika.cz/subt/pip/ octomap-python==1.8.0.post12

Thanks for your work - Is it possible to create such package for other python versions (3.8+), too?

@miiller
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miiller commented Dec 11, 2022

had to add extra_link_args to the Extension in setup.py to resolve this linker issue:

Extension(
            'octomap',
            ['octomap/octomap.pyx'],
            extra_link_args=['-Wl,-rpath,$ORIGIN/../lib'],

$ORIGIN is here the path to the executable, see https://unix.stackexchange.com/questions/22926/where-do-executables-look-for-shared-objects-at-runtime for more info. Depending on how you install with pip, the path will differ. E.g. when installing with pip install -e ./, it should be $ORIGIN/src/octomap/lib.

@raoshashank
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I think this has something to do with the current version of the octomap library that is added as a submodule to the repo. When I clone the repo with --recursive, i am able to import octomap, this is likely because when building the library without the local octomap submodule, the globally installed one is used, which in my case is the latest version of the octomap library.

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