JuliaPy / JuliaPy/PythonCall.jl

segmentation fault with multi-threading

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Description

I have this MWE, where I get segmentation faults (frequently, but not deterministically), when trying to run some script that uses multi-threading on the Julia side.

I have used before launching `ipython3`:

```bash
export JULIA_NUM_THREADS=4
```

(my computer has 4 cores - 8 threads).

The MWE is:

```python
Python 3.10.4 (main, Jun 29 2022, 12:14:53) [GCC 11.2.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 7.31.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from juliacall import Main as jl

In [2]: import numpy as np

In [3]: jl.seval("""
...: function test(x)
...: partial = zeros(Threads.nthreads())
...: Threads.@threads for i in 1:Threads.nthreads()
...: for j in i:Threads.nthreads():length(x)
...: partial[i] += x[j]
...: end
...: end
...: return sum(partial)
...: end
...: """)
Out[3]: test (generic function with 1 method)

In [4]: x = np.random.random((10_000,))

In [5]: %timeit jl.test(x)
72.2 µs ± 35.9 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [6]: %timeit jl.test(x)
Segmentation fault (core dumped)

```

Here I have emulated the error using the `%timeit` macro from `ipython`, but my actual error I get after some runs of a function of my package:

```python
In [1]: from juliacall import Main as jl

In [2]: jl.seval("using CellListMap")

In [3]: import numpy as np

In [5]: x = np.random.random((10_000,3))

In [6]: nb = jl.neighborlist(x.transpose(), 0.05)

In [7]: nb = jl.neighborlist(x.transpose(), 0.05)

In [8]: nb = jl.neighborlist(x.transpose(), 0.05)

In [9]: nb = jl.neighborlist(x.transpose(), 0.05)

In [10]: nb = jl.neighborlist(x.transpose(), 0.05)

In [11]: nb = jl.neighborlist(x.transpose(), 0.05)

In [12]: nb = jl.neighborlist(x.transpose(), 0.05)

In [13]: nb = jl.neighborlist(x.transpose(), 0.05)

In [14]: nb = jl.neighborlist(x.transpose(), 0.05)

In [15]: nb = jl.neighborlist(x.transpose(), 0.05)

In [16]: nb = jl.neighborlist(x.transpose(), 0.05)

In [17]: nb = jl.neighborlist(x.transpose(), 0.05)

In [18]: nb = jl.neighborlist(x.transpose(), 0.05)

In [19]: nb = jl.neighborlist(x.transpose(), 0.05)
Segmentation fault (core dumped)
```

`%timeit` runs the function multiple times, there seems to be some memory corruption, or memory overflow, causing the error.

Anyway, even if you have only some hint on how to debug this, I will be very thankful.

(even in the simplest example above, the segfaults only occur with multi-threading).

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the MWE from `from juliacall import Main as jl` with `JULIA_NUM_THREADS=4`, then compare repeated calls to `jl.test` under IPython `%timeit`. The issue is done when the threaded example and repeated `jl.neighborlist` calls no longer produce a segmentation fault, or the failure is isolated to a specific entry point.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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