`Phie Recovery`

Module: devtests.bidomain.phie_recovery.run

Section author: Anton Prassl <anton.prassl@medunigraz.at>

Test phie recovery in some nodes above a simple slab.

Problem Setup

This example defines a thin cuboid domain (units in microns):

$-1500 \leq x \leq 1500 -2500 \leq y \leq 2500 - 500 \leq z \leq 500$

Run a modomain simulation in a cuboid portion of tissue and recover the $phi_e$ signals above the corners of the geometry. Run the simulation with the same settings in postprocessing mode to recover $phi_e$ based on the previous simulation. Investigate the difference of the two simulation modes (i.e. experiment “0” [normal run] and experiment “4” [postprocess only]).

As with other examples, add the --visualize option to automatically load the results in meshalyzer:

./run.py --visualize

Tests

serial_recv_meth_1

Phie recovery during simulation and as postprocessing step on single core (using FE mass and stiffness matrices)

Tags: FAST SERIAL

Checks:

Compare against stored reference: max_error(phie_recovery.igb)
Compare against stored reference: max_error(phie_recovery_pp.igb)

Last run: 2024-02-29 00:56:53.656178, revision {‘base’: ‘cbf8efd0’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 4d92ddfc}

Runtime: 0:00:01.631200
SIMULATION FAILED TO RUN
  CalledProcessError: Command '/data/prassl_src/carpautotest/repos/carp/CPU/bin/carp.pt' died with <Signals.SIGABRT: 6>. (Unknown error -6)

Last passed: 2024-02-15 00:19:06.884235, revision {‘base’: ‘b048f647’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 92824181}

serial_recv_meth_2

Phie recovery during simulation and as postprocessing step on single core (by integration over element-centered Im using integral solution of Poisson PDE)

Tags: FAST SERIAL

Checks:

Compare against stored reference: max_error(phie_recovery.igb)
Compare against stored reference: max_error(phie_recovery_pp.igb)

Last run: 2024-02-29 00:56:55.314916, revision {‘base’: ‘cbf8efd0’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 4d92ddfc}

Runtime: 0:00:01.376225
SIMULATION FAILED TO RUN
  CalledProcessError: Command '/data/prassl_src/carpautotest/repos/carp/CPU/bin/carp.pt' died with <Signals.SIGABRT: 6>. (Unknown error -6)

Last passed: 2024-02-15 00:19:08.643134, revision {‘base’: ‘b048f647’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 92824181}

parallel_recv_meth_1

Phie recovery during simulation and as postprocessing step on multiple cores (using FE mass and stiffness

Tags: FAST PARALLEL

Checks:

Compare against stored reference: max_error(phie_recovery.igb)
Compare against stored reference: max_error(phie_recovery_pp.igb)

Last run: 2024-02-29 00:56:56.720543, revision {‘base’: ‘cbf8efd0’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 4d92ddfc}

Runtime: 0:00:02.172055
SIMULATION FAILED TO RUN
  CalledProcessError: Command '/home/prassl/install/petsc-3.17.1/linux-gnu-fluid-opt/bin/mpiexec' returned non-zero exit status 134. (Unknown error 134)

Last passed: 2024-02-15 00:19:10.096567, revision {‘base’: ‘b048f647’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 92824181}

parallel_recv_meth_2

Phie recovery during simulation and as postprocessing step on multiple cores (by integration over element-centered Im using integral solution of Poisson PDE)

Tags: FAST PARALLEL

Checks:

Compare against stored reference: max_error(phie_recovery.igb)
Compare against stored reference: max_error(phie_recovery_pp.igb)

Last run: 2024-02-29 00:56:58.924884, revision {‘base’: ‘cbf8efd0’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 4d92ddfc}

Runtime: 0:00:02.264115
SIMULATION FAILED TO RUN
  CalledProcessError: Command '/home/prassl/install/petsc-3.17.1/linux-gnu-fluid-opt/bin/mpiexec' returned non-zero exit status 134. (Unknown error 134)

Last passed: 2024-02-15 00:19:11.344521, revision {‘base’: ‘b048f647’}, dependency revisions {PT_C: 31642c1e,cvsys: 593686bc,eikonal: 5fbbfda3,elasticity: 92824181}