Segmentation fault when instantiating a simulation

[dbrnz]

As per the attached. This is with version 0.20260623.0.

$ python crash.py
got simulation
getting instance
[1]    62979 segmentation fault  python crash.py

crash.zip

[agarny]

Hi @dbrnz, I have just given this a try (after doing uv pip install libopencor which installed version 0.20260619.0) and I got the following:

$ python crash.py
got simulation
getting instance
running instance
run instance!

[dbrnz]

Ditto, all is well for me with version 0.20260619.0. Version 0.20260623.0 though crashes (see above), which was installed by pyproject.toml having:

[tool.uv.sources]
libopencor = { git = "https://github.com/opencor/libopencor.git" }

uv.lock shows:

[[package]]
name = "libopencor"
version = "0.20260623.0"
source = { git = "https://github.com/opencor/libopencor.git#21c8a2d0ccf9c43fdac32058aeeeb5cba899817f" }

[agarny]

Thanks, that's good to know! I will look into it on Monday. It ought to be a quick and easy fix.

[agarny]

Ok, having just released a new version of libOpenCOR (1.20260708.2) and everything seems to be fine:

$ uv pip list | grep libopencor
Using Python 3.13.14 environment at: /Users/Alan/venv/libOpenCOR
$ uv pip install libopencor
Using Python 3.13.14 environment at: /Users/Alan/venv/libOpenCOR
Resolved 2 packages in 158ms
Prepared 1 package in 857ms
Installed 1 package in 21ms
 + libopencor==1.20260708.2
$ uv pip list | grep libopencor
Using Python 3.13.14 environment at: /Users/Alan/venv/libOpenCOR
libopencor                    1.20260708.2
$ python crash.py
got simulation
getting instance
running instance
run instance!

So, from what I can tell, everything is fine. Can you please confirm that this is also the case for you (and, if so, then close this issue)?

[dbrnz]

All is well with 1.20260708.2 installed from PyPi. However there is still a seg fault when built locally (by setting [tool.uv.sources]); in this case, uv.lock has:

[[package]]
name = "libopencor"
version = "1.20260708.2"
source = { git = "https://github.com/opencor/libopencor.git#749efd9c9389ae8f6e9b7728465213a0ad6d8429" }
dependencies = [
    { name = "numpy" },
]

so it is the correct version and commit.

I'm happy to install from PyPi -- the build from GitHub used to work though -- was this originally the only way to install libOpenCOR for Python?

[agarny]

All is well with 1.20260708.2 installed from PyPi. However there is still a seg fault when built locally (by setting [tool.uv.sources])

Hmm... strange, because I also tried using uv pip install ~/libOpenCOR and it all worked fine too. But... it's true that I have never tried using [tool.uv.sources]. Do you have something that I could try locally?

I'm happy to install from PyPi -- the build from GitHub used to work though -- was this originally the only way to install libOpenCOR for Python?

No, my intention was always to make it possible for people to install from both source and PyPI.

[dbrnz]

Here's a pyproject.toml for which uv sync will build and install libOpenCOR from GitHub.

[project]
name = "agarny"
version = "0.1.0"
requires-python = "==3.13.*"
dependencies = [
    "libopencor"
]

[tool.uv.sources]
libopencor = { git = "https://github.com/opencor/libopencor.git" }

Strangely, when I run uv run python crash.py there is no seg fault message even though the simulation fails, whereas with the virtual environment active (source .venv/bin/activate) python crash.py reports the seg fault.

$ uv run python crash.py
got simulation
getting instance


$ source .venv/bin/activate
$ python crash.py
got simulation
getting instance
[1]    65875 segmentation fault  python crash.py

[agarny]

Ok, I have created a new folder and then added your pyproject.toml file to it (after replacing agarny with pyloc 🙂). From there, I did:

$ python3 -m venv ~/venv/pyloc
$ source ~/venv/pyloc/bin/activate
$ uv pip list
Using Python 3.14.6 environment at: /Users/Alan/venv/pyloc
Package Version
------- -------
pip     26.1.2
$ uv cache clean  # Just to be on the safe side.
Clearing cache at: /Users/Alan/.cache/uv
Removed 60302 files (4.8GiB)
$ python crash.py
Traceback (most recent call last):
  File "/Users/Alan/Desktop/pyloc/crash.py", line 1, in <module>
    import libopencor as loc
ModuleNotFoundError: No module named 'libopencor'
$ uv pip install .
Using Python 3.14.6 environment at: /Users/Alan/venv/pyloc
    Updated https://github.com/opencor/libopencor.git (749efd9c9389ae8f6e9b7728465213a0ad6d8429)
Resolved 3 packages in 9.12s
      Built pyloc @ file:///Users/Alan/Desktop/pyloc
      Built libopencor @ git+https://github.com/opencor/libopencor.git@749efd9c9389ae8f6e9b7728465213a0ad6d8429
Prepared 3 packages in 48.19s
Installed 3 packages in 48ms
 + libopencor==1.20260708.2 (from git+https://github.com/opencor/libopencor.git@749efd9c9389ae8f6e9b7728465213a0ad6d8429)
 + numpy==2.5.1
 + pyloc==0.1.0 (from file:///Users/Alan/Desktop/pyloc)
$ uv pip list
Using Python 3.14.6 environment at: /Users/Alan/venv/pyloc
Package    Version
---------- ------------
libopencor 1.20260708.2
numpy      2.5.1
pip        26.1.2
pyloc      0.1.0
$ python crash.py
got simulation
getting instance
running instance
run instance!

So, again, everything is fine for me... 🤷‍♂️

[dbrnz]

Hmm, one difference is that you use Python to create the environment and pip to install the packages, whereas I just use uv.

Starting in a clean directory:

$ ls -la
total 32
drwxr-xr-x@   5 dbro078  1403514002   160  9 Jul 08:40 .
drwxr-xr-x  120 dbro078  1403514002  3840  9 Jul 08:34 ..
-rw-------@   1 dbro078  1403514002  5139  9 Jul 08:34 crash.cellml
-rw-r--r--@   1 dbro078  1403514002   833  9 Jul 08:34 crash.py
-rw-r--r--@   1 dbro078  1403514002   195  9 Jul 08:35 pyproject.toml

$ cat pyproject.toml
[project]
name = "agarny"
version = "0.1.0"
requires-python = "==3.13.*"
dependencies = [
    "libopencor"
]

[tool.uv.sources]
libopencor = { git = "https://github.com/opencor/libopencor.git" }

Created virtual environment and install packages:

$ uv sync
Using CPython 3.13.0
Creating virtual environment at: .venv
Resolved 3 packages in 775ms
Installed 2 packages in 20ms
 + libopencor==1.20260708.2 (from git+https://github.com/opencor/libopencor.git@749efd9c9389ae8f6e9b7728465213a0ad6d8429)
 + numpy==2.5.1

$ uv pip list
Package    Version
---------- ------------
libopencor 1.20260708.2
numpy      2.5.1

A silent exception when using uv run:

$ uv run python crash.py
got simulation
getting instance

A Seg fault reported when the virtual environment has been activated and Python is used directly:

$ source .venv/bin/activate

(agarny) $ python crash.py
got simulation
getting instance
[1]    92600 segmentation fault  python crash.py

Although still silent about the exception when run via uv:

(agarny) $ uv run python crash.py
got simulation
getting instance

[agarny]

Interesting, it all works fine for me!

$ uv cache clean
Clearing cache at: /Users/Alan/.cache/uv
Removed 27207 files (3.4GiB)

$ ls -al
total 32
drwxr-xr-x@ 5 Alan  staff   160  9 Jul 11:31 .
drwx------@ 7 Alan  staff   224  9 Jul 11:31 ..
-rw-r--r--@ 1 Alan  staff  4906  9 Jul 11:31 crash.cellml
-rw-r--r--@ 1 Alan  staff   833  9 Jul 11:31 crash.py
-rw-r--r--@ 1 Alan  staff   194  9 Jul 11:31 pyproject.toml

$ cat pyproject.toml
[project]
name = "pyloc"
version = "0.1.0"
requires-python = "==3.13.*"
dependencies = [
    "libopencor"
]

[tool.uv.sources]
libopencor = { git = "https://github.com/opencor/libopencor.git" }

$ uv sync
Using CPython 3.13.14 interpreter at: /opt/homebrew/opt/python@3.13/bin/python3.13
Creating virtual environment at: .venv
    Updated https://github.com/opencor/libopencor.git (749efd9c9389ae8f6e9b7728465213a0ad6d8429)
Resolved 3 packages in 25.97s
      Built libopencor @ git+https://github.com/opencor/libopencor.git@749efd9c9389ae8f6e9b7728465213a0ad6d8429
Prepared 2 packages in 1m 42s
Installed 2 packages in 33ms
 + libopencor==1.20260708.2 (from git+https://github.com/opencor/libopencor.git@749efd9c9389ae8f6e9b7728465213a0ad6d8429)
 + numpy==2.5.1

$ uv run python crash.py
got simulation
getting instance
running instance
run instance!

$ source .venv/bin/activate

(pyloc) $ python crash.py
got simulation
getting instance
running instance
run instance!

(pyloc) $ uv run python crash.py
got simulation
getting instance
running instance
run instance!

[dbrnz]

Hmm, it must be something about my system... I'll do some testing on my other laptop, that should have no prior knowledge of libOpenCOR.

[agarny]

Going to try on my vanilla macOS 26 VM too.

[agarny]

Ok, just to confirm that everything works fine using my vanilla macOS 26 VM (to which I installed a fresh copy of Xcode + command line tools). So, for me, there is no problem at all.