rtree causes crash during Dataset init

[MaximeRM]

Qgis crashes when testing the encoder. Error on the terminal below:

With python 3.12; Ubuntu 24.04.

Potentially related to this: qgis/QGIS#56599

QGIS died on signal 11
This GDB supports auto-downloading debuginfo from the following URLs:
  <https://debuginfod.ubuntu.com>
Enable debuginfod for this session? (y or [n]) [answered N; input not from terminal]
Debuginfod has been disabled.
To make this setting permanent, add 'set debuginfod enabled off' to .gdbinit.

warning: could not find '.gnu_debugaltlink' file for /usr/bin/qgis.bin
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Operation not permitted.
No thread selected
No stack.
gdb returned 256
Aborted (core dumped)

[ptresson]

I've reproduced the crash with a fresh conda environment with python 3.12. with defaut parameters during encoding. I'll see what can be used to work around this. The QGIS issue seems to suggest we are not the only ones having problems with python 3.12, it may be outside the scope of the plugin.

[ptresson]

crash happens during the creation of a torchgeo RasterDatatsetmore precisely.
More precisely, the crash happens during the init of an Handle IndexHandle, inside a Rtree in a GeoDataset.
So the issue is GIS related and not due to deep learning dependencies or RAM or such.

[ptresson]

working env:

Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import rasterio
>>> rasterio.show_versions()
rasterio info:
  rasterio: 1.3.9
      GDAL: 3.8.3
      PROJ: 9.3.1
      GEOS: 3.12.1
 PROJ DATA: /home/tresson/mambaforge/envs/geosam/share/proj
 GDAL DATA: /home/tresson/mambaforge/envs/geosam/share/gdal

System:
    python: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
executable: /home/tresson/mambaforge/envs/geosam/bin/python
   machine: Linux-6.8.0-40-generic-x86_64-with-glibc2.35

Python deps:
    affine: 2.4.0
     attrs: 23.2.0
   certifi: 2024.02.02
     click: 8.1.7
     cligj: 0.7.2
    cython: None
     numpy: 1.26.4
    snuggs: 1.4.7
click-plugins: None
setuptools: 69.1.0
>>>

broken env:

import rasterio
rasterio.show_versions()
rasterio info:
  rasterio: 1.3.11
      GDAL: 3.9.2
      PROJ: 9.4.1
      GEOS: 3.12.2
 PROJ DATA: /home/tresson/mambaforge/envs/test/share/proj
 GDAL DATA: /home/tresson/mambaforge/envs/test/share/gdal

System:
    python: 3.12.5 | packaged by conda-forge | (main, Aug  8 2024, 18:57:17) [GCC 12.4.0]
executable: /home/tresson/mambaforge/envs/test/bin/python3
   machine: Linux-6.8.0-40-generic-x86_64-with-glibc2.35

Python deps:
    affine: 2.4.0
     attrs: 24.2.0
   certifi: 2024.08.30
     click: 8.1.7
     cligj: 0.7.2
    cython: None
     numpy: 2.1.1
    snuggs: 1.4.7
click-plugins: None
setuptools: 73.0.1

[ptresson]

related:
qgis/QGIS#57320

creating an rtree index in the QGIS python console is sufficient to cause the crash

[ptresson]

a working solution seem to uninstall pip rtree and install it via package manager

https://geo-sam.readthedocs.io/en/latest/blog/2024/05-02_crash_on_QGIS.html
coolzhao/Geo-SAM#43

[ptresson]

several solutions have been found:

• limit to QGIS < 3.36 (which does seem a bad idea)
• link to other ressources on how to solve the issue
• For our usage, uninstalling rtree > 1.0 after torchgeo install (since its a dependencie), then installing rtree < 1.0 via pip seem to work. this will need post installation checkups but could work. Such post installation scripts could be of use for other conflicts such as proj and rasterio versions or others (see Package installation issue with pyproj #17)