Error while running example with meshalyzer

Question

Hi all,

I was trying this example: https://opencarp.org/documentation/examples/visualization/meshalyzer, yet while I run python3 run.py [--np n] [--bidomain], this error occurred:

usage: run.py [-h] [--np NP] [--np-job NP_JOB] [--tpp TPP]

              [--runtime HH:MM:SS] [--build {CPU}]

              [--flavor {petsc,petsc-pipelined,boomeramg,boomeramg-pipelined,parasails,pt,direct}]

              [--platform {desktop,archer,archer24c,archer2,archer_intel,archer_camel,bwunicluster,curie,horeka,marconi,marconi_slurm,marconi_debug,medtronic,mephisto,smuc_f,smuc_t,smuc_i,vsc2,vsc3,vsc4,wopr}]

              [--queue QUEUE] [--vectorized-fe VECTORIZED_FE] [--dry-run]

              [--checkpoint CHECKPOINT] [--restore RESTORE]

              [--generate-parfile GENERATE_PARFILE]

              [--polling-param POLLING_PARAM [POLLING_PARAM ...]]

              [--polling-range min:max:num [min:max:num ...]]

              [--polling-file POLLING_FILE]

              [--sampling-type {linear,geometric,lhs}] [--stress-models]

              [--material-models] [--ionic-models] [--CARP-opts CARP_OPTS]

              [--postprocess {phie,optic,activation,axial,filament,efield,mechanics} [{phie,optic,activation,axial,filament,efield,mechanics} ...]]

              [--bundle [EXP_NAME]] [--push-bundle [PUSH_BUNDLE]]

              [--release-bundle] [--bundle-output] [--gdb [PROC ...]]

              [--lldb [PROC ...]] [--ddd [PROC ...]] [--ddt]

              [--valgrind [OUTFILE]] [--valgrind-options [OPT=VAL ...]]

              [--map] [--scalasca] [--ID ID] [--suffix SUFFIX]

              [--overwrite-behaviour {prompt,error,delete,overwrite,append}]

              [--silent] [--visualize] [--mech-element {P1-P0,P1-P1-DB,MINI}]

              [--mech-with-inertia] [--webGUI] [--bidomain] [--tend TEND]

              [--monitor [MONITOR]] [--APDshorten APDSHORTEN] [--clean]

error: unrecognized arguments: [--np n] [--bidomain]

Answer 1

Hi!

You have to remove the brackets:

python3 run.py --np 2 --bidomain

Comments

An error occurred while running the example:

  *** Initializing physics ***

Initializing Electrics ..

Setting up ionic models and plugins
-----------------------------------

Assigning IMPS to tagged regions:

Setting up ionic models and plugins
-----------------------------------

Assigning IMPS to tagged regions:
L5 : Illegal IM specified: MBRDR

L5 : Run bench --list-imps for a list of all available models.

L5 : Illegal IM specified: MBRDR

L5 : Run bench --list-imps for a list of all available models.

--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[60031,1],0]
  Exit code:    1

---

This example is using the deprecated named MBRDR, which is not used in the new naming convention of ionic models.

In order to fix this, you should replace in `example.par` `MBRDR` by `DrouhardRoberge`, which is the new name of the model .

Thanks for noticing, it will be fixed soon.