Experiment 07_extracellular does not work
Summary
When running the experiment 07_extracellular, I get an error about an unrecognized keyword:
*** Unrecognized keyword pt_opts_ellip.amg_smooth_steps
*** Error reading parameters
Error: 2021-05-12_ecg_250.0_um_monodomain_tm_endo_ab_mid_dur_60.0_ms/init_acts_LATs-thresh.dat does not exist!
What version of openCARP are you using?
From source (Commit 422b1d33)
What operating system and processor architecture are you using?
Linux - Mageia 7
$ uname -a
Linux noffke 5.10.30-desktop-1.mga7 #1 SMP Wed Apr 14 22:52:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$ /usr/bin/gcc --version
gcc (Mageia 8.4.0-1.mga7) 8.4.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Steps to reproduce
~/projects/modeling/openCARP/external/experiments/tutorials/02_EP_tissue/07_extracellular $ python3 ./run.py --sourceModel monodomain --duration 60 --visualize
What is the current bug behavior?
Experiment fails.
What is the expected correct behavior?
Experiment succeeds.
Relevant logs and/or screenshots
$ python3 ./run.py --sourceModel monodomain --duration 60 --visualize
========================================================================================================================================
SETTINGS SUMMARY
========================================================================================================================================
Executables
----------------------------------------------------------------------------------------------------------------------------------------
CARP: /usr/local/bin/openCARP
MESHER: /usr/local/bin/mesher
BENCH: /usr/local/bin/bench
IGBHEAD: /usr/local/bin/igbhead
IGBOPS: /usr/local/bin/igbops
IGBEXTRACT: /usr/local/bin/igbextract
IGBAPD: /usr/local/bin/igbapd
SV2H5B: /home/pnoffke/projects/modeling/openCARP/external/carputils/bin/bin2h5.py
SV2H5T: /home/pnoffke/projects/modeling/openCARP/external/carputils/bin/txt2h5.py
CLOSEST_HC: /home/pnoffke/projects/modeling/openCARP/external/carputils/bin/closest_hc
APDRESTITUTION: /home/pnoffke/projects/modeling/openCARP/external/carputils/bin/APDrestitution
TUNECV: /home/pnoffke/projects/modeling/openCARP/external/carputils/bin/tuneCV
RESTITUTECV: /home/pnoffke/projects/modeling/openCARP/external/carputils/bin/restituteCV
MESHTOOL: /usr/local/bin/meshtool
----------------------------------------------------------------------------------------------------------------------------------------
Command Line Options
----------------------------------------------------------------------------------------------------------------------------------------
NP: 1
BUILD: CPU
FLAVOR: pt
DRY: False
VISUALIZE: True
----------------------------------------------------------------------------------------------------------------------------------------
System Info
----------------------------------------------------------------------------------------------------------------------------------------
Python: 3.7.10
SETTINGS: ./settings.yaml
Email: patrick.noffke@hillrom.com
========================================================================================================================================
Requested mesh already exists, skipping generation.
Reading file: meshes/2021-05-11_DsDBBrjBpx/block.elem
Writing file: /home/pnoffke/projects/modeling/openCARP/external/experiments/tutorials/02_EP_tissue/07_extracellular/ecg.pts
mkdir \
-p /home/pnoffke/projects/modeling/openCARP/external/experiments/tutorials/02_EP_tissue/07_extracellular/2021-05-12_ecg_250.0_um_monodomain_tm_endo_ab_mid_dur_60.0_ms
#---------------------------------------------------------------------------------------------------------------------------------------
# Launching CARP Simulation Extracellular potentials and ECGs
#---------------------------------------------------------------------------------------------------------------------------------------
/usr/local/bin/openCARP \
+F /home/pnoffke/projects/modeling/openCARP/external/carputils/carputils/resources/options/pt_ell_amg \
+F /home/pnoffke/projects/modeling/openCARP/external/carputils/carputils/resources/options/pt_para_amg \
-ellip_use_pt 1 \
-parab_use_pt 1 \
-num_imp_regions 9 \
-imp_region[0].im TT2 \
-imp_region[0].im_param "flags=ENDO,Gks*0.45,GNa*1.0" \
-imp_region[0].name VE-BASE-ENDO \
-imp_region[0].num_IDs 1 \
-imp_region[0].ID[0] 125 \
-imp_region[1].im TT2 \
-imp_region[1].im_param "flags=MCELL,Gks*2.48,GNa*1.0" \
-imp_region[1].name VE-BASE-MCELL \
-imp_region[1].num_IDs 1 \
-imp_region[1].ID[0] 150 \
-imp_region[2].im TT2 \
-imp_region[2].im_param "flags=EPI,Gks*0.86,GNa*1.0" \
-imp_region[2].name VE-BASE-EPI \
-imp_region[2].num_IDs 1 \
-imp_region[2].ID[0] 175 \
-imp_region[3].im TT2 \
-imp_region[3].im_param "flags=ENDO,Gks*0.56,GNa*1.0" \
-imp_region[3].name VE-CENTRAL-ENDO \
-imp_region[3].num_IDs 1 \
-imp_region[3].ID[0] 225 \
-imp_region[4].im TT2 \
-imp_region[4].im_param "flags=MCELL,Gks*3.1,GNa*1.0" \
-imp_region[4].name VE-CENTRAL-MCELL \
-imp_region[4].num_IDs 1 \
-imp_region[4].ID[0] 250 \
-imp_region[5].im TT2 \
-imp_region[5].im_param "flags=EPI,Gks*1.1,GNa*1.0" \
-imp_region[5].name VE-CENTRAL-EPI \
-imp_region[5].num_IDs 1 \
-imp_region[5].ID[0] 275 \
-imp_region[6].im TT2 \
-imp_region[6].im_param "flags=ENDO,Gks*0.67,GNa*1.0" \
-imp_region[6].name VE-APEX-ENDO \
-imp_region[6].num_IDs 1 \
-imp_region[6].ID[0] 325 \
-imp_region[7].im TT2 \
-imp_region[7].im_param "flags=MCELL,Gks*3.72,GNa*1.0" \
-imp_region[7].name VE-APEX-MCELL \
-imp_region[7].num_IDs 1 \
-imp_region[7].ID[0] 350 \
-imp_region[8].im TT2 \
-imp_region[8].im_param "flags=EPI,Gks*1.29,GNa*1.0" \
-imp_region[8].name VE-APEX-EPI \
-imp_region[8].num_IDs 1 \
-imp_region[8].ID[0] 375 \
-num_gregions 3 \
-gregion[0].num_IDs 3 \
-gregion[0].ID[0] 125 \
-gregion[0].ID[1] 225 \
-gregion[0].ID[2] 325 \
-gregion[0].g_il 0.174 \
-gregion[0].g_it 0.174 \
-gregion[0].g_in 0.174 \
-gregion[0].g_el 0.625 \
-gregion[0].g_et 0.625 \
-gregion[0].g_en 0.625 \
-gregion[1].num_IDs 3 \
-gregion[1].ID[0] 150 \
-gregion[1].ID[1] 250 \
-gregion[1].ID[2] 350 \
-gregion[1].g_il 0.174 \
-gregion[1].g_it 0.174 \
-gregion[1].g_in 0.174 \
-gregion[1].g_el 0.625 \
-gregion[1].g_et 0.625 \
-gregion[1].g_en 0.625 \
-gregion[2].num_IDs 3 \
-gregion[2].ID[0] 175 \
-gregion[2].ID[1] 275 \
-gregion[2].ID[2] 375 \
-gregion[2].g_il 0.174 \
-gregion[2].g_it 0.174 \
-gregion[2].g_in 0.174 \
-gregion[2].g_el 0.625 \
-gregion[2].g_et 0.625 \
-gregion[2].g_en 0.625 \
-num_stim 1 \
-stimulus[0].stimtype 0 \
-stimulus[0].strength 100.0 \
-stimulus[0].duration 1.0 \
-stimulus[0].npls 1 \
-stimulus[0].x0 -500.0 \
-stimulus[0].xd 1250.0 \
-stimulus[0].y0 24375.0 \
-stimulus[0].yd 1250.0 \
-stimulus[0].z0 -625.0 \
-stimulus[0].zd 1250.0 \
-dt 100 \
-parab_solve 1 \
-spacedt 0.1 \
-timedt 1.0 \
-num_LATs 1 \
-lats[0].ID LATs \
-lats[0].all 0 \
-lats[0].measurand 0 \
-lats[0].threshold -10 \
-lats[0].method 1 \
-phie_rec_ptf /home/pnoffke/projects/modeling/openCARP/external/experiments/tutorials/02_EP_tissue/07_extracellular/ecg \
-bidomain 0 \
-num_phys_regions 2 \
-phys_region[0].name "Intracellular domain" \
-phys_region[0].ptype 0 \
-phys_region[0].num_IDs 9 \
-phys_region[0].ID[0] 125 \
-phys_region[0].ID[1] 150 \
-phys_region[0].ID[2] 175 \
-phys_region[0].ID[3] 225 \
-phys_region[0].ID[4] 250 \
-phys_region[0].ID[5] 275 \
-phys_region[0].ID[6] 325 \
-phys_region[0].ID[7] 350 \
-phys_region[0].ID[8] 375 \
-phys_region[1].name "Extracellular domain" \
-phys_region[1].ptype 1 \
-phys_region[1].num_IDs 9 \
-phys_region[1].ID[0] 125 \
-phys_region[1].ID[1] 150 \
-phys_region[1].ID[2] 175 \
-phys_region[1].ID[3] 225 \
-phys_region[1].ID[4] 250 \
-phys_region[1].ID[5] 275 \
-phys_region[1].ID[6] 325 \
-phys_region[1].ID[7] 350 \
-phys_region[1].ID[8] 375 \
-meshname meshes/2021-05-11_DsDBBrjBpx/block \
-tend 60.0 \
-simID 2021-05-12_ecg_250.0_um_monodomain_tm_endo_ab_mid_dur_60.0_ms \
-gridout_i 3 \
-gridout_e 3
*** Unrecognized keyword pt_opts_ellip.amg_smooth_steps
*** Error reading parameters
Error: 2021-05-12_ecg_250.0_um_monodomain_tm_endo_ab_mid_dur_60.0_ms/init_acts_LATs-thresh.dat does not exist!
Traceback (most recent call last):
File "./run.py", line 878, in <module>
run()
File "/home/pnoffke/projects/modeling/openCARP/external/carputils/carputils/tools.py", line 505, in wrapped
ret = run(args, job)
File "./run.py", line 452, in run
job.meshalyzer(geom, data, view)
File "/home/pnoffke/projects/modeling/openCARP/external/carputils/carputils/job/job.py", line 599, in meshalyzer
cmd = [settings.execs.MESHALYZER, geom] + args
File "/home/pnoffke/projects/modeling/openCARP/external/carputils/carputils/settings/paths.py", line 70, in __getattr__
raise self._exception(attr, path)
carputils.settings.exceptions.CARPUtilsMissingPathError: The path for MESHALYZER was not found (/usr/local/meshalyzer/meshalyzer)
(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's tough to read otherwise.)
Possible fixes
(If you can, link to the line of code that might be responsible for the problem)