Segmentation fault using 2D ERT inversion on linux

[Lena-LC]

Problem description

I installed the latest version of pygimly in a fresh environment (named pg15+ on my machine) using the command given on the website . My issue is that when I try to do a topographic inversion of ERT field measure there is a Fatal Python error: Segmentation fault.
I've run the same code on windows and the inversion just worked perfectly fine, i've also created a new environment with pygimly 1.2.1 and the inversion was able to be processed easily on my linux machine.

Your environment

---

Date: mar. déc. 17 21:00:40 2024 CET

            OS : Linux (Ubuntu 24.04)
        CPU(s) : 12
       Machine : x86_64
  Architecture : 64bit
           RAM : 30.7 GiB
   Environment : IPython
   File system : ext4

Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC
12.3.0]

       pygimli : 1.5.3
        pgcore : 1.5.0
         numpy : 1.26.4
    matplotlib : 3.9.1
         scipy : 1.14.1
          tqdm : 4.67.1
       IPython : 8.30.0
       pyvista : 0.44.2

---

Steps to reproduce

So here is the code with the latest set of data I've tried (I've also done it with data formatted for pygimly and some data using the command pg.getExampleData)

r"""
ERT field data with topography
==============================

Simple example of data measured over a slagdump demonstrating:

- 2D inversion with topography
- geometric factor generation
- topography effect
"""
# sphinx_gallery_thumbnail_number = 5
import pygimli as pg
from pygimli.physics import ert
import pygimli.meshtools as mt
from pygimli.frameworks.resolution import resolutionMatrix



###############################################################################
# Get some example data with, typically by a call like
data = ert.load('/home/lena/Documents/Documents/Universite/S9/04_Near_surface_geophy/04_Field_trip_data/G1-22112024/20241119_ddp64.dat')
# that supports various file formats
print(data)
sensors=data.sensorPositions()
# %%



###############################################################################
# The data file does not contain geometric factors (token field 'k'),
# so we create them based on the given topography.
data['k'] = ert.createGeometricFactors(data, numerical=True)
data['rhoa'] = data['k'] * data['r']
###############################################################################
# We initialize the ERTManager for further steps and eventually inversion.
mgr = ert.ERTManager(sr=False)

###############################################################################
# It might be interesting to see the topography effect, i.e the ratio between
# the numerically computed geometry factor and the analytical formula
k0 = ert.createGeometricFactors(data)
ert.showData(data, vals=k0/data['k'], label='Topography effect')

###############################################################################
# The data container has no apparent resistivities (token field 'rhoa') yet.
# We can let the Manager fix this later for us (as we now have the 'k' field),
# or we do it manually.
mgr.checkData(data)
print(data)
# %%


###############################################################################
# The data container does not necessarily contain data errors data errors
# (token field 'err'), requiring us to enter data errors. We can let the
# manager guess some defaults for us automaticly or set them manually
#data['err'] = ert.estimateError(data, relativeError=0.03, absoluteUError=5e-5)
# or manually:
# data['err'] = data_errors  # somehow
ert.show(data, data['rhoa'])

# %%


plc = mt.createParaMeshPLC(data,
                           paraDX=0.25, #Résolution entre capteur (nb triangles entre capteur)
                           paraMaxCellSize=15, #Taille max (surface) du triangle
                           surfaceMeshQuality=33.6, #qualité du maillage
                           #surfaceMeshArea=2000,
                           paraBoundary=5, #de combien on déborde aux extrémités du profil (à gauche et à droite, en %)
                           #boudary=0.1,
                           #addTopo=topo,
                           paraDepth=30, #prof du profil
                           #addNodes=2, #ça raffine. Pas trop certain de l'utilité pour ces données-ci
                          )
                           
for pos in sensors:
    plc.createNode(pos)

mesh = mt.createMesh(plc)

pg.show(mesh)


###############################################################################
# Now the data have all necessary fields ('rhoa', 'err' and 'k') so we can run
# the inversion. The inversion mesh will be created with some optional values
# for the parametric mesh generation.
#
mod = mgr.invert(data, 
                 #lam=10, # Facteur de régularisation
                 verbose=True,
                 mesh = mesh,
                 robust = True, #Norm L1 (False = L2) avec un fort contraste entre les couches L1 marche mieux car lisse moins
                 zWeight= 0.3, #Anisotropie (milieu stratifié < 1 ; variations latérales > 1)
                )

mgr.showResult()

###############################################################################
# We can view the resulting model in the usual way.
mgr.showResultAndFit()
# np.testing.assert_approx_equal(ert.inv.chi2(), 1.10883, significant=3)
# %%
###############################################################################
# Or just plot the model only using your own options.
mgr.showResult(mod, cMin=10, cMax=1000, cMap="Spectral_r", logScale=True)

Expected behavior

Get all the result of the inversion ? Eg the figures

Actual behavior

The kernel just die :

%runfile /home/lena/Documents/Documents/Universite/S9/04_Near_surface_geophy/04_Field_trip_data/ERT_inversion.py --wdir
17/12/24 - 21:04:24 - pyGIMLi - INFO - could not read unified data format for ERT ... try res2dinv
17/12/24 - 21:04:24 - pyGIMLi - INFO - Create default mesh for geometric factor calculation.
ModellingBase::setMesh() copying new mesh ... Found datafile: 64 electrodes
Found: 64 node-electrodes
rMin = 1, rMax = 252
NGauLeg + NGauLag for inverse Fouriertransformation: 14 + 4
Found non-Neumann domain
0.0105294 s
FOP updating mesh dependencies ... 1.956e-06 s
/tmp/spyder-lena/tmpot2fkmkm: line 3: 42782 Segmentation fault      (core dumped) /home/lena/anaconda3/envs/pg15+/bin/python -Xfrozen_modules=off -m spyder_kernels.console -f /home/lena/.local/share/jupyter/runtime/kernel-89c49f7d7589.json

The kernel died, restarting...
 


Fatal Python error: Segmentation fault


Main thread:
Thread 0x00007960c4337740 (most recent call first):
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/pygimli/physics/ert/ert.py", line 192 in simulate
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/pygimli/physics/ert/ert.py", line 385 in createGeometricFactors
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/pygimli/utils/cache.py", line 277 in wrapper
  File "/home/lena/Documents/Documents/Universite/S9/04_Near_surface_geophy/04_Field_trip_data/ERT_inversion.py", line 34 in <module>
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/utils.py", line 209 in exec_encapsulate_locals
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/code_runner.py", line 506 in _exec_code
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/code_runner.py", line 336 in _exec_file
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/code_runner.py", line 165 in runfile

I thank you in advance for you help ! I'd really like to be able to use this latest version ! :)
Best,
Lena

[halbmy]

I've also done it with data formatted for pygimly and some data using the command pg.getExampleData

you mean the segmentation fault also occurs with the original data file from getExampleData?

[Lena-LC]

Yes exactly, here is the error I get when I use data = pg.getExampleData('ert/slagdump.ohm', verbose=True) :

18/12/24 - 09:06:30 - pyGIMLi - INFO - Getting: /home/lena/.cache/pygimli/example-data/gimli-org/example-data/master/ert/slagdump.ohm from https://raw.githubusercontent.com//gimli-org/example-data//master/ert/slagdump.ohm
Found locale decimal_point ',' and change it to: decimal point '.'
   0%|          |0/5435 [00:00 < ?]
18/12/24 - 09:06:31 - pyGIMLi - INFO - Reading /home/lena/.cache/pygimli/example-data/gimli-org/example-data/master/ert/slagdump.ohm (<class 'pgcore._pygimli_.DataContainerERT'>)
18/12/24 - 09:06:31 - pyGIMLi - INFO - Create default mesh for geometric factor calculation.
ModellingBase::setMesh() copying new mesh ... Found topography for surface=114.662 : 114.928
Warning! swap YZ coordinates for sensor positions to meet mesh dimensions.
Found datafile: 38 electrodes
Found: 38 node-electrodes
rMin = 0.999991, rMax = 132.345
NGauLeg + NGauLag for inverse Fouriertransformation: 12 + 4
Found non-Neumann domain
0.0128866 s
FOP updating mesh dependencies ... 4.261e-06 s
/tmp/spyder-lena/tmpu__uwrt3: line 3:  4957 Segmentation fault      (core dumped) /home/lena/anaconda3/envs/pg15+/bin/python -Xfrozen_modules=off -m spyder_kernels.console -f /home/lena/.local/share/jupyter/runtime/kernel-6e0a767197aa.json

The kernel died, restarting...
 


Fatal Python error: Segmentation fault


Thread 0x00007e0ec4e006c0 (most recent call first):
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/threading.py", line 331 in wait
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/threading.py", line 629 in wait
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/tqdm/_monitor.py", line 60 in run
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/threading.py", line 1002 in _bootstrap



Main thread:
Thread 0x00007e0f4f66e740 (most recent call first):
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/pygimli/physics/ert/ert.py", line 192 in simulate
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/pygimli/physics/ert/ert.py", line 385 in createGeometricFactors
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/pygimli/utils/cache.py", line 277 in wrapper
  File "/home/lena/Desktop/plot_02_ert_field_data.py", line 27 in <module>
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/utils.py", line 209 in exec_encapsulate_locals
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/code_runner.py", line 506 in _exec_code
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/code_runner.py", line 336 in _exec_file
  File "/home/lena/anaconda3/envs/pg15+/lib/python3.11/site-packages/spyder_kernels/customize/code_runner.py", line 165 in runfile```