Error when installing open3d for conda environment, missing libomp, seg fault when installed #6196

ebruun · 2023-06-03T18:39:30Z

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

The text was updated successfully, but these errors were encountered:

cwreynolds · 2023-06-03T19:21:37Z

(“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 · 2023-06-03T22:12:53Z

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 · 2023-06-15T11:42:53Z

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 · 2023-09-04T02:14:32Z

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 · 2024-03-15T10:59:27Z

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 · 2024-03-15T15:00:08Z

Should be fixed by #6626

ebruun added the build/install Build or installation issue label Jun 3, 2023

ebruun changed the title ~~Summarize the issue and your environments (e.g., "Cannot compile on Ubuntu 20.04 with OpenBLAS")~~ Error when installing open3d for conda environemtn Jun 3, 2023

ebruun changed the title ~~Error when installing open3d for conda environemtn~~ Error when installing open3d for conda environment Jun 3, 2023

ebruun changed the title ~~Error when installing open3d for conda environment~~ Error when installing open3d for conda environment, missing libomp, seg fault when installed Jun 3, 2023

theNded added the bug Not a build issue, this is likely a bug. label Aug 10, 2023

saurabheights mentioned this issue Nov 30, 2023

Build error during build from source on Sonoma M1 Max #6514

Closed

3 tasks

geyang mentioned this issue Dec 20, 2023

M1 Mac 0.17.0 segmentation fault and build error [ SOLVED ] #6545

Open

3 tasks

ssheorey assigned errissa and ssheorey Dec 29, 2023

ssheorey linked a pull request Mar 15, 2024 that will close this issue

Convert OpenMP parallelization to OneAPI::TBB #6626

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Error when installing open3d for conda environment, missing libomp, seg fault when installed #6196

Error when installing open3d for conda environment, missing libomp, seg fault when installed #6196

ebruun commented Jun 3, 2023 •

edited

cwreynolds commented Jun 3, 2023 •

edited

ebruun commented Jun 3, 2023 •

edited

poppigy commented Jun 15, 2023 •

edited

cielixer commented Sep 4, 2023

bschindler commented Mar 15, 2024

ssheorey commented Mar 15, 2024

Error when installing open3d for conda environment, missing libomp, seg fault when installed #6196

Error when installing open3d for conda environment, missing libomp, seg fault when installed #6196

Comments

ebruun commented Jun 3, 2023 • edited

Checklist

Steps to reproduce the issue

I first create a new conda environement with python 3.10:

Then, I install open3d:

Then, I verify installation:

Error message

Open3D, Python and System information

Additional information

cwreynolds commented Jun 3, 2023 • edited

ebruun commented Jun 3, 2023 • edited

poppigy commented Jun 15, 2023 • edited

cielixer commented Sep 4, 2023

bschindler commented Mar 15, 2024

ssheorey commented Mar 15, 2024

ebruun commented Jun 3, 2023 •

edited

cwreynolds commented Jun 3, 2023 •

edited

ebruun commented Jun 3, 2023 •

edited

poppigy commented Jun 15, 2023 •

edited