Error when installing open3d for conda environment, missing libomp, seg fault when installed

[ebruun]

Checklist

• I have searched for similar issues.
• For Python issues, I have tested with the latest development wheel.
• I have checked the release documentation and the latest documentation (for master branch).

Steps to reproduce the issue

I first create a new conda environement with python 3.10:

conda create -n o3d_test python=3.10

Then, I install open3d:

pip install open3d

Then, I verify installation:

python -c "import open3d as o3d; print(o3d.__version__)"

Error message

Full terminal output:
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/homebrew/anaconda3/envs/o3d_test/lib/python3.10/site-packages/open3d/__init__.py", line 93, in <module>
    from open3d.cpu.pybind import (core, camera, data, geometry, io, pipelines,
ImportError: dlopen(/opt/homebrew/anaconda3/envs/o3d_test/lib/python3.10/site-packages/open3d/cpu/pybind.cpython-310-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/libomp/lib/libomp.dylib
  Referenced from: /opt/homebrew/anaconda3/envs/o3d_test/lib/python3.10/site-packages/open3d/cpu/pybind.cpython-310-darwin.so
  Reason: tried: '/opt/homebrew/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

Open3D, Python and System information

- Operating system: macOS 12.0.1
- Python version: Python 3.10.11
- Open3D version: 0.17.0
- System architecture: apple-silicon
- Is this a remote workstation?: no
- How did you install Open3D?: pip
- Compiler version (if built from source): N/A

Additional information

No response

[cwreynolds]

(“Wait, I understood that reference” — some superhero movie)

I ran into the same thing on my first Open3d install on macOS (see #6032). Try this:

brew install libomp

and see if your build works, like mine did after that. You might have to install Homebrew first if you have not already.

[ebruun]

hmm okay so doing the above suggested seems to work when I run it in a bare-bones conda environment that is built from just the following environment.yml

name: o3d_test
channels:
  - r
  - conda-forge
  - defaults
dependencies:
  - python==3.10.11
  - pip:
    - open3d==0.17.0
prefix: /opt/homebrew/anaconda3/envs/o3d_test

But if I create the conda environment with another package, e.g. compas-fab, things seem to break

name: o3d_test
channels:
  - r
  - conda-forge
  - defaults
dependencies:
  - python==3.10.11
  - compas_fab==0.27.0
  - pip:
    - open3d==0.17.0
prefix: /opt/homebrew/anaconda3/envs/o3d_test

now I get a seg fault:

zsh: segmentation fault  python -c "import open3d as o3d; print(o3d.__version__)"

[poppigy]

Is there any workaround here? It worked a few days ago, but now I always have segfaults. I recreated a conda env and reinstalled open3d (version 0.17.0).

pip show open3d
Name: open3d
Version: 0.17.0

python -c "import open3d; print(open3d.__version__)"
[1]    4431 segmentation fault  python -c "import open3d; print(open3d.__version__)"

upd: have decided to try open3d==0.15.1, and now I can run it

[cielixer]

Hi, i have been recently digging this problem for days, and found out some temporary solution.

I did lldb python and run -c "import open3d", found out that libomp causes the problem in multi thread settings.

Process 11193 stopped
* thread #11, stop reason = EXC_BAD_ACCESS (code=1, address=0x8)
    frame #0: 0x0000000101e08f50 libomp.dylib`void __kmp_suspend_64<false, true>(int, kmp_flag_64<false, true>*) + 48
libomp.dylib`__kmp_suspend_64<false, true>:
->  0x101e08f50 <+48>: ldr    x19, [x8, w0, sxtw #3]
    0x101e08f54 <+52>: mov    x0, x19
    0x101e08f58 <+56>: bl     0x101e08694               ; __kmp_suspend_initialize_thread
    0x101e08f5c <+60>: mov    x0, x19
  thread #12, stop reason = EXC_BAD_ACCESS (code=1, address=0x10)
    frame #0: 0x0000000101e08f50 libomp.dylib`void __kmp_suspend_64<false, true>(int, kmp_flag_64<false, true>*) + 48
libomp.dylib`__kmp_suspend_64<false, true>:
->  0x101e08f50 <+48>: ldr    x19, [x8, w0, sxtw #3]
    0x101e08f54 <+52>: mov    x0, x19
    0x101e08f58 <+56>: bl     0x101e08694               ; __kmp_suspend_initialize_thread
    0x101e08f5c <+60>: mov    x0, x19
  thread #13, stop reason = EXC_BAD_ACCESS (code=1, address=0x18)
    frame #0: 0x0000000101e08f50 libomp.dylib`void __kmp_suspend_64<false, true>(int, kmp_flag_64<false, true>*) + 48
libomp.dylib`__kmp_suspend_64<false, true>:
->  0x101e08f50 <+48>: ldr    x19, [x8, w0, sxtw #3]
    0x101e08f54 <+52>: mov    x0, x19
    0x101e08f58 <+56>: bl     0x101e08694               ; __kmp_suspend_initialize_thread
    0x101e08f5c <+60>: mov    x0, x19
  thread #14, stop reason = EXC_BAD_ACCESS (code=1, address=0x20)
    frame #0: 0x0000000101e08f50 libomp.dylib`void __kmp_suspend_64<false, true>(int, kmp_flag_64<false, true>*) + 48
libomp.dylib`__kmp_suspend_64<false, true>:
->  0x101e08f50 <+48>: ldr    x19, [x8, w0, sxtw #3]
    0x101e08f54 <+52>: mov    x0, x19
    0x101e08f58 <+56>: bl     0x101e08694               ; __kmp_suspend_initialize_thread
    0x101e08f5c <+60>: mov    x0, x19
  thread #15, stop reason = EXC_BAD_ACCESS (code=1, address=0x28)
    frame #0: 0x0000000101e08f50 libomp.dylib`void __kmp_suspend_64<false, true>(int, kmp_flag_64<false, true>*) + 48
libomp.dylib`__kmp_suspend_64<false, true>:
->  0x101e08f50 <+48>: ldr    x19, [x8, w0, sxtw #3]
    0x101e08f54 <+52>: mov    x0, x19
    0x101e08f58 <+56>: bl     0x101e08694               ; __kmp_suspend_initialize_thread
    0x101e08f5c <+60>: mov    x0, x19
  thread #16, stop reason = EXC_BAD_ACCESS (code=1, address=0x30)
    frame #0: 0x0000000101e08f50 libomp.dylib`void __kmp_suspend_64<false, true>(int, kmp_flag_64<false, true>*) + 48
libomp.dylib`__kmp_suspend_64<false, true>:
->  0x101e08f50 <+48>: ldr    x19, [x8, w0, sxtw #3]
    0x101e08f54 <+52>: mov    x0, x19
    0x101e08f58 <+56>: bl     0x101e08694               ; __kmp_suspend_initialize_thread
    0x101e08f5c <+60>: mov    x0, x19
Target 0: (python) stopped.

It's not a perfect solution, when setting the openmp's number of threads to 1 solved the problem.

export OMP_NUM_THREADS=1

This worked for me in Ventura 13.4.1 with Apple M1 Pro in conda environment, i am using python=3.10.12 and open3d=1.16.1.

[bschindler]

The issue is that open3d ships its own libopenmp, but conda has its own version. So 2 versions of openmp get loaded and things explode.
I found a fix for the conda case, but its less than ideal, to put it mildly. In my case, I cannot switch to the available conda builds because they don't have GUI mode...

install_name_tool -change "@loader_path/../libomp.dylib" "@rpath/libomp.dylib" /path/to/conda/env/lib/python3.8/site-packages/open3d/cpu/pybind.cpython-38-darwin.so

[ssheorey]

Should be fixed by #6626