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Runtime error due to recent commit dune-pdelab

Summary

Runtime error if multiple compartment are present during the time-step phase (i.e. stepper.evolve() )

This appears to be related with recent commits in the dune-pdelab branch (feature/dune-assembler/main) since compilation with older branch of pdelab (7db65040546acc793433d47a5ddd8fcf70cb3f91) does not result in a runtime error.

Steps to reproduce

How can this be reproduced? If you can, point to specific files/configurations where the bug occurs docker:

docker build -t dune-copasi . docker run -v $PWD:/dunecopasi dune-copasi --config=test_mitchell_schaefer.ini ---> runtime error (see below)

standard compilation: pull & compile latest dune-pdelab branch feature/dune-assembler/main ./dune-common/bin/dunecontrol --opts=./dune-copasi/dune-copasi.opts --only=dune-copasi cd dune-copasi/test ../build-cmake/bin/dune-copasi --config=test_mitchell_schaefer.ini ---> runtime error (see below)

What is the current bug behaviour?

Running dune-copasi result in a runtime error! (probably related to recent changes in the pdelab branch)

What is the expected correct behaviour?

Normal simulation without throw ...

Relevant logs, screenshots, files...?

Building the docker container en running it with an example with more than 1 component will yield the runtime error. One component seems to work just fine! (Related to nested indexing?)

Expand to see logs 
...
[2024-01-19 20:06:41.105] [info] Creating mass/stiffness local operator
[2024-01-19 20:06:41.109] [info] Local operator is non-linear
[2024-01-19 20:06:41.109] [info] Creating linear solver with 'RestartedGMRes' type
[2024-01-19 20:06:41.109] [info] Creating linear solver preconditioner with 'SSOR' type
[2024-01-19 20:06:41.109] [info] Creating non-linear solver with 'Newton' type
[2024-01-19 20:06:41.123] [info] Creating time-stepping solver with 'Alexander2' type
[2024-01-19 20:06:41.123] [info] Evolving system: 0.00e+00s -> 5.00e+03s
[2024-01-19 20:06:41.123] [info] Evaluating time step: 0.00e+00s + 1.00e+01s -> 1.00e+01s
terminate called after throwing an instance of 'Dune::ISTLError'
  what():  ISTLError [operator[]:/duneci/install/include/dune/istl/basearray.hh:334]: index 1 not in compressed array
[9bb2bcbe79b1:00001] *** Process received signal ***
[9bb2bcbe79b1:00001] Signal: Aborted (6)
[9bb2bcbe79b1:00001] Signal code:  (-6)
[9bb2bcbe79b1:00001] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3c510)[0x7f52f3a7e510]
[9bb2bcbe79b1:00001] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x8a0fc)[0x7f52f3acc0fc]
[9bb2bcbe79b1:00001] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x12)[0x7f52f3a7e472]
[9bb2bcbe79b1:00001] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f52f3a684b2]
[9bb2bcbe79b1:00001] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa09eb)[0x7f52f3dc99eb]
[9bb2bcbe79b1:00001] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xaffca)[0x7f52f3dd8fca]
[9bb2bcbe79b1:00001] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xb0035)[0x7f52f3dd9035]
[9bb2bcbe79b1:00001] [ 7] dune-copasi(+0x15d17b)[0x55dc99e7b17b]
[9bb2bcbe79b1:00001] [ 8] dune-copasi(+0x3e78b0)[0x55dc9a1058b0]
[9bb2bcbe79b1:00001] [ 9] dune-copasi(+0x3e257d)[0x55dc9a10057d]
[9bb2bcbe79b1:00001] [10] dune-copasi(+0x3d936f)[0x55dc9a0f736f]
[9bb2bcbe79b1:00001] [11] dune-copasi(+0x3d6bf9)[0x55dc9a0f4bf9]
[9bb2bcbe79b1:00001] [12] dune-copasi(+0x29b609)[0x55dc99fb9609]
[9bb2bcbe79b1:00001] [13] dune-copasi(+0x2958bb)[0x55dc99fb38bb]
[9bb2bcbe79b1:00001] [14] dune-copasi(+0x2fffa9)[0x55dc9a01dfa9]
[9bb2bcbe79b1:00001] [15] dune-copasi(+0x2febf9)[0x55dc9a01cbf9]
[9bb2bcbe79b1:00001] [16] dune-copasi(+0x3f5678)[0x55dc9a113678]
[9bb2bcbe79b1:00001] [17] dune-copasi(+0x3f593c)[0x55dc9a11393c]
[9bb2bcbe79b1:00001] [18] dune-copasi(+0x1a1c25)[0x55dc99ebfc25]
[9bb2bcbe79b1:00001] [19] dune-copasi(+0x1a195e)[0x55dc99ebf95e]
[9bb2bcbe79b1:00001] [20] dune-copasi(+0x1637ed)[0x55dc99e817ed]
[9bb2bcbe79b1:00001] [21] dune-copasi(+0x15a429)[0x55dc99e78429]
[9bb2bcbe79b1:00001] [22] /lib/x86_64-linux-gnu/libc.so.6(+0x276ca)[0x7f52f3a696ca]
[9bb2bcbe79b1:00001] [23] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85)[0x7f52f3a69785]
[9bb2bcbe79b1:00001] [24] dune-copasi(+0x157fc1)[0x55dc99e75fc1]
[9bb2bcbe79b1:00001] *** End of error message ***
[9bb2bcbe79b1:00001] *** Process received signal ***
[9bb2bcbe79b1:00001] Signal: Segmentation fault (11)
[9bb2bcbe79b1:00001] Signal code:  (128)
[9bb2bcbe79b1:00001] Failing at address: (nil)
[9bb2bcbe79b1:00001] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3c510)[0x7f52f3a7e510]
[9bb2bcbe79b1:00001] [ 1] /lib/x86_64-linux-gnu/libc.so.6(abort+0x170)[0x7f52f3a6854f]
[9bb2bcbe79b1:00001] [ 2] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa09eb)[0x7f52f3dc99eb]
[9bb2bcbe79b1:00001] [ 3] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xaffca)[0x7f52f3dd8fca]
[9bb2bcbe79b1:00001] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xb0035)[0x7f52f3dd9035]
[9bb2bcbe79b1:00001] [ 5] dune-copasi(+0x15d17b)[0x55dc99e7b17b]
[9bb2bcbe79b1:00001] [ 6] dune-copasi(+0x3e78b0)[0x55dc9a1058b0]
[9bb2bcbe79b1:00001] [ 7] dune-copasi(+0x3e257d)[0x55dc9a10057d]
[9bb2bcbe79b1:00001] [ 8] dune-copasi(+0x3d936f)[0x55dc9a0f736f]
[9bb2bcbe79b1:00001] [ 9] dune-copasi(+0x3d6bf9)[0x55dc9a0f4bf9]
[9bb2bcbe79b1:00001] [10] dune-copasi(+0x29b609)[0x55dc99fb9609]
[9bb2bcbe79b1:00001] [11] dune-copasi(+0x2958bb)[0x55dc99fb38bb]
[9bb2bcbe79b1:00001] [12] dune-copasi(+0x2fffa9)[0x55dc9a01dfa9]
[9bb2bcbe79b1:00001] [13] dune-copasi(+0x2febf9)[0x55dc9a01cbf9]
[9bb2bcbe79b1:00001] [14] dune-copasi(+0x3f5678)[0x55dc9a113678]
[9bb2bcbe79b1:00001] [15] dune-copasi(+0x3f593c)[0x55dc9a11393c]
[9bb2bcbe79b1:00001] [16] dune-copasi(+0x1a1c25)[0x55dc99ebfc25]
[9bb2bcbe79b1:00001] [17] dune-copasi(+0x1a195e)[0x55dc99ebf95e]
[9bb2bcbe79b1:00001] [18] dune-copasi(+0x1637ed)[0x55dc99e817ed]
[9bb2bcbe79b1:00001] [19] dune-copasi(+0x15a429)[0x55dc99e78429]
[9bb2bcbe79b1:00001] [20] /lib/x86_64-linux-gnu/libc.so.6(+0x276ca)[0x7f52f3a696ca]
[9bb2bcbe79b1:00001] [21] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85)[0x7f52f3a69785]
[9bb2bcbe79b1:00001] [22] dune-copasi(+0x157fc1)[0x55dc99e75fc1]
[9bb2bcbe79b1:00001] *** End of error message ***

Reproducing input

| Input data | none | Simulation Case | Multiple components for simulation in one domain | | GMSH grid file: none | Run config file: test/test_mitchell_schaefer.ini

Ideas how to fix this?

Add them here, if you have any.

@santiago.ospina - Do you have any idea ? I think one of the following pdelab commits is the origin: 9550d5999035edd4a1602ba45e049a1aeb2d2bd9 152990884bd4715e77c7d81955c2d54d55a77a15 7fa535e73689628c9aada4e0e2959de26fc53a48

Edited by Dylan Vermoortele