Error with reentry induction protocols example

Question

I was running command python3 run.py --np 2 --protocol prepace --prepace_bcl 500 --prebeats 4 --visualize to run the reentry example on my mac, the following error occurred:

Traceback (most recent call last):

  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 729, in <module>

    run()

  File "/Users/abc/openCARP/external/carputils/carputils/tools.py", line 540, in wrapped

    ret = run(args, job)

  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 559, in run

    tissue_init = single_cell_initialization(args, job, steady_state_dir)

  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 708, in single_cell_initialization

    '--imp-par',            'GCaL*{},GK1*{},GNa*{},factorGKur*{},Gto*{},GKs*{},maxIpCa*{},maxINaCa*{}'.format(GCaL[k],GK1[k],GNa[k],factorGKur[k],Gto[k],GKs[k],maxIpCa[k],maxINaCa[k]),

NameError: name 'GCaL' is not defined

Answer 1

Hello,

This issue should have been fixed in this commit: https://git.opencarp.org/openCARP/experiments/-/commit/176e7a46a791dd1e4adc49eeec192d7c387dbfa0

I invite you to download the latest version of the experiments, where this shouldn't happen anymore.

Comments

Thank you. I have downloaded the latest version of the experiments now, yet I found another error:
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: [[61696,1],0]
  Exit code:    1
--------------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 735, in <module>
    run()
  File "/Users/abc/openCARP/external/carputils/carputils/tools.py", line 540, in wrapped
    ret = run(args, job)
  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 566, in run
    model.prepace.prepace(args, job, cmd, meshname, sinus, steady_state_dir, tissue_init)
  File "/Users/abc/openCARP/external/carputils/carputils/model/prepace.py", line 131, in prepace
    os.rename(old_file, new_file)
FileNotFoundError: [Errno 2] No such file or directory: 'prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/vm.igb' -> 'prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/vm_last_beat.igb'

---

Could you provide more from the logs? I am not able to reproduce this error.

---

SETTINGS SUMMARY
================================================================================
Executables
--------------------------------------------------------------------------------
   CARP:              /Users/abc/openCARP/_build/bin/openCARP
   MESHER:            /Users/abc/openCARP/_build/bin/mesher
   BENCH:             /Users/abc/openCARP/_build/bin/bench
   IGBHEAD:           /Users/abc/openCARP/_build/bin/igbhead
   IGBOPS:            /Users/abc/openCARP/_build/bin/igbops
   IGBEXTRACT:        /Users/abc/openCARP/_build/bin/igbextract
   IGBAPD:            /Users/abc/openCARP/_build/bin/igbapd
   MESHALYZER:        /Users/abc/meshalyzer/meshalyzer
   SV2H5B:            /Users/abc/openCARP/external/carputils/bin/bin2h5.py
   SV2H5T:            /Users/abc/openCARP/external/carputils/bin/txt2h5.py
   CLOSEST_HC:        /Users/abc/openCARP/external/carputils/bin/closest_hc
   APDRESTITUTION:    /Users/abc/openCARP/external/carputils/bin/APDrestitution
   TUNECV:            /Users/abc/openCARP/external/carputils/bin/tuneCV
   RESTITUTECV:       /Users/abc/openCARP/external/carputils/bin/restituteCV
   GENERATEMETADATA:  /Users/abc/openCARP/external/carputils/bin/generateMetadata
   MESHTOOL:          /usr/local/bin/meshtool
--------------------------------------------------------------------------------
Command Line Options
--------------------------------------------------------------------------------
   NP:        2
   BUILD:     CPU
   FLAVOR:    petsc
   DRY:       False
   VISUALIZE: True
--------------------------------------------------------------------------------
Solver Option Files
--------------------------------------------------------------------------------
   Parabolic: /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/ilu_cg_opts
   Elliptic:  /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/gamg_cg_opts
--------------------------------------------------------------------------------
Paths
--------------------------------------------------------------------------------
   OPENCARP_SRC:  /Users/abc/openCARP/_build/bin
   MPIEXEC:       /opt/homebrew/bin/mpiexec
--------------------------------------------------------------------------------
System Info
--------------------------------------------------------------------------------
   Python:    3.9.13
   OS:        Unknown
   SETTINGS:  /Users/abc/.config/carputils/settings.yaml
   Email:     yzlhbg@gmail.com
   Name:      Zhuolin Yang
   ORCID:     0000-0000-0000-0000
================================================================================

mkdir \
  -p /Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/2022-06-28_prepace

/Users/abc/openCARP/external/carputils/bin/tuneCV \
  --model Courtemanche \
  --modelpar GCaL-55%,GK1+100%,factorGKur-50%,Gto-65%,GKs+100%,maxIpCa+50%,maxINaCa+60%,GKr*1.6 \
  --converge True \
  --velocity 0.3 \
  --resolution 400.0 \
  --gi 0.14 \
  --ge 0.7 \
  --dt 20 \
  --tol 0.001 \
  --length 2 \
  --lumping True \
  --silent




Conduction velocity testing - parameter summary
________________________________________________________________________________

# system settings
Python 3


# mesh settings
resolution   : 400.0 um
length       : 2.0 cm
surf         : False


# model settings
model        : Courtemanche
model-par    : GCaL-55%,GK1+100%,factorGKur-50%,Gto-65%,GKs+100%,maxIpCa+50%,maxINaCa+60%,GKr*1.6
plugin       :
plug-par     :
svinit       :


# conductivity/velocity settings
velocity     : 0.3 m/s
gil          : 0.14 S/m
gel          : 0.7 S/m
beta         : 0.14 1/cm


# numerical settings
dt           : 20.0 us
ts           : 1
solver tol   : 1e-09
mass lumping : True
op splitting : True
source model : monodomain
stimulus strength : 250.0


Courtemanche  Tissue conductivities for CV =  0.2994
---------------------------------------------
gi =  0.1406 ge =  0.7028
---------------------------------------------
gi (S/m) 0.1406
ge (S/m) 0.7028

Requested mesh does not yet exist - generating it...
#-------------------------------------------------------------------------------
#                               Launching Mesher
#-------------------------------------------------------------------------------

/Users/abc/openCARP/_build/bin/mesher \
  -size[0] 5.0 \
  -size[1] 5.0 \
  -size[2] 0.0 \
  -bath[0] -0.0 \
  -bath[1] -0.0 \
  -bath[2] -0.0 \
  -center[0] 2.5 \
  -center[1] 2.5 \
  -center[2] 0.0 \
  -resolution[0] 400.0 \
  -resolution[1] 400.0 \
  -resolution[2] 400.0 \
  -mesh meshes/2022-06-28_kQAvPDqAoI/block \
  -Elem3D 0 \
  -fibers.rotEndo 0.0 \
  -fibers.rotEpi 0.0 \
  -fibers.sheetEndo 0.0 \
  -fibers.sheetEpi 0.0 \
  -periodic 0 \
  -periodic_tag 1234 \
  -perturb 0.0 \
  -tri2D

Number of points: 15876
Number of triangles: 31250
Using transversely isotropic fiber setup.
Creation of the directory fibrosis_block_50000.0um_resolution_400.0um failed

---

#-------------------------------------------------------------------------------
#               Launching openCARP Simulation 2022-06-28_prepace
#-------------------------------------------------------------------------------

mpiexec -n 2 /Users/abc/openCARP/_build/bin/openCARP \
  -ellip_use_pt 0 \
  -parab_use_pt 0 \
  -parab_options_file /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/ilu_cg_opts \
  -ellip_options_file /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/gamg_cg_opts \
  -meshname meshes/2022-06-28_kQAvPDqAoI/block \
  -gridout_i 2 \
  -experiment 3 \
  -simID 2022-06-28_prepace \
  -numtagreg 2 \
  -tagreg[0].type 4 \
  -tagreg[0].elemfile fibrosis_block_50000.0um_resolution_400.0um/f_fib \
  -tagreg[0].tag 2 \
  -tagreg[1].type 4 \
  -tagreg[1].elemfile fibrosis_block_50000.0um_resolution_400.0um/elems_slow_conductive \
  -tagreg[1].tag 3

L2 : Output directory exists: 2022-06-28_prepace

L2 : Output directory exists: 2022-06-28_prepace


    *** Processing meshes ***

Reading reference mesh: meshes/2022-06-28_kQAvPDqAoI/block.*
L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L4 : Warning: No potential or current stimuli found!

    *** Processing meshes ***

Reading reference mesh: meshes/2022-06-28_kQAvPDqAoI/block.*
L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L4 : Warning: No potential or current stimuli found!
Done in 0.015956 sec.
Done in 0.000035 sec.
Re-tagging reference mesh
Done in 0.016013 sec.
Done in 0.000036 sec.
Re-tagging reference mesh
Processing submeshes
Processing submeshes
All done in 0.022770 sec.
Writing "Autogenerated intracellular Electrics" mesh: block_i
All done in 0.022690 sec.
Writing "Autogenerated intracellular Electrics" mesh: block_i

    *** Destroying physics ***


    *** Destroying physics ***

/Users/abc/openCARP/_build/bin/bench \
  --imp Courtemanche \
  --imp-par GCaL*0.45,GK1*2,GNa*1,factorGKur*0.5,Gto*0.35,GKs*2,maxIpCa*1.5,maxINaCa*1.6 \
  --bcl 500.0 \
  --dt-out 10000.0 \
  --stim-curr 9.5 \
  --stim-dur 2 \
  --numstim 20 \
  --duration 10000.0 \
  --stim-start 0 \
  --dt 0.02 \
  --fout=prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/tVI_stabilization_0 \
  -S 10000.0 \
  -F prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_0_bcl_500.0.sv \
  --no-trace on

Ionic model: Courtemanche
    GCaL                 modifier: *0.45           value: 0.05571
    GK1                  modifier: *2              value: 0.18
    GNa                  modifier: *1              value: 7.8
    factorGKur           modifier: *0.5            value: 0.5
    Gto                  modifier: *0.35           value: 0.05782
    GKs                  modifier: *2              value: 0.258
    maxIpCa              modifier: *1.5            value: 0.4125
    maxINaCa             modifier: *1.6            value: 2560

Outputting the following quantities at each time:
      Time            Vm          Iion   

save_sv(): Saving state vector to file: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_0_bcl_500.0.sv




All done!


setup time          0.001142 s
initialization time 0.003919 s
main loop time      0.087967 s
total ode time      0.060529 s

mn/avg/mx loop time 0.000000 0.000176 0.199000 ms
mn/avg/mx ODE time  0.000000 0.000121 0.017000 ms
real time factor    165.210065


/Users/abc/openCARP/_build/bin/bench \
  --imp Courtemanche \
  --imp-par GCaL*0.225,GK1*1,GNa*0.6,factorGKur*0.5,Gto*0.35,GKs*2,maxIpCa*1.5,maxINaCa*1.6 \
  --bcl 500.0 \
  --dt-out 10000.0 \
  --stim-curr 9.5 \
  --stim-dur 2 \
  --numstim 20 \
  --duration 10000.0 \
  --stim-start 0 \
  --dt 0.02 \
  --fout=prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/tVI_stabilization_1 \
  -S 10000.0 \
  -F prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_1_bcl_500.0.sv \
  --no-trace on

Ionic model: Courtemanche
    GCaL                 modifier: *0.225          value: 0.027855
    GK1                  modifier: *1              value: 0.09
    GNa                  modifier: *0.6            value: 4.68
    factorGKur           modifier: *0.5            value: 0.5
    Gto                  modifier: *0.35           value: 0.05782
    GKs                  modifier: *2              value: 0.258
    maxIpCa              modifier: *1.5            value: 0.4125
    maxINaCa             modifier: *1.6            value: 2560

Outputting the following quantities at each time:
      Time            Vm          Iion   

save_sv(): Saving state vector to file: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_1_bcl_500.0.sv




All done!


setup time          0.000040 s
initialization time 0.003535 s
main loop time      0.087420 s
total ode time      0.059670 s

mn/avg/mx loop time 0.000000 0.000175 0.154000 ms
mn/avg/mx ODE time  0.000000 0.000119 0.016000 ms
real time factor    167.588403


Creation of the directory prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1 failed

---

#-------------------------------------------------------------------------------
#               Launching openCARP Simulation 2022-06-28_prepace
#-------------------------------------------------------------------------------

mpiexec -n 2 /Users/abc/openCARP/_build/bin/openCARP \
  +F /Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/parameters.par \
  -ellip_use_pt 0 \
  -parab_use_pt 0 \
  -parab_options_file /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/ilu_cg_opts \
  -ellip_options_file /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/gamg_cg_opts \
  -num_gregions 2 \
  -gregion[0].num_IDs  2 \
  -gregion[0].ID[0] 1 \
  -gregion[0].ID[1] 2 \
  -gregion[0].g_il  0.1406 \
  -gregion[0].g_it  0.1406 \
  -gregion[0].g_in  0.1406 \
  -gregion[0].g_el  0.7028 \
  -gregion[0].g_et  0.7028 \
  -gregion[0].g_en  0.7028 \
  -gregion[1].num_IDs  1 \
  -gregion[1].ID[0] 3 \
  -gregion[1].g_il  1e-07 \
  -gregion[1].g_it  1e-07 \
  -gregion[1].g_in  1e-07 \
  -gregion[1].g_el  1e-07 \
  -gregion[1].g_et  1e-07 \
  -gregion[1].g_en  1e-07 \
  -imp_region[0].im_sv_init prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_0_bcl_500.0.sv \
  -imp_region[1].im_sv_init prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_1_bcl_500.0.sv \
  -num_stim 1 \
  -num_tsav 1 \
  -tsav[0] 2000.0 \
  -stimulus[0].stimtype 0 \
  -stimulus[0].strength 70 \
  -stimulus[0].duration 2.0 \
  -stimulus[0].npls 4 \
  -stimulus[0].bcl 500.0 \
  -stimulus[0].x0 -200.0 \
  -stimulus[0].xd 400.0 \
  -stimulus[0].y0 -200.0 \
  -stimulus[0].yd 50400.0 \
  -stimulus[0].z0 -200.0 \
  -stimulus[0].zd 400.0 \
  -simID prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1 \
  -dt 20 \
  -spacedt 10 \
  -mass_lumping 1 \
  -timedt 100 \
  -tend 2000.1 \
  -meshname 2022-06-28_prepace/block_i

L2 : Output directory exists: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1

L2 : Output directory exists: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1

L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"!

    *** Processing meshes ***

Reading reference mesh: 2022-06-28_prepace/block_i.*
L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"!

    *** Processing meshes ***

Reading reference mesh: 2022-06-28_prepace/block_i.*
Done in 0.019736 sec.
Renormalised 8 longitudinal and 0 sheet-transverse fibre vectors.
Done in 0.000039 sec.
Processing submeshes
Done in 0.019795 sec.
Renormalised 8 longitudinal and 0 sheet-transverse fibre vectors.
Done in 0.000039 sec.
Processing submeshes
All done in 0.024460 sec.
All done in 0.024496 sec.

    *** Initializing physics ***

Initializing Electrics ..

    *** Initializing physics ***

Initializing Electrics ..

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

Assigning IMPS to tagged regions:
    Ionic model: Courtemanche to tag region(s) [1].
    Ionic model: Courtemanche to tag region(s) [2], [3].

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

Assigning IMPS to tagged regions:
    Ionic model: Courtemanche to tag region(s) [1].
    Ionic model: Courtemanche to tag region(s) [2], [3].
Ionic model: Courtemanche
    GCaL                 modifier: -55%            value: 0.05571
    GK1                  modifier: +100%           value: 0.18
    factorGKur           modifier: -50%            value: 0.5
Ionic model: Courtemanche
    GCaL                 modifier: -55%            value: 0.05571
    GK1                  modifier: +100%           value: 0.18
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

Ionic model: Courtemanche
    GCaL                 modifier: *0.225          value: 0.027855
    GNa                  modifier: *0.6            value: 4.68
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    Gto                  modifier: -65%            value: 0.05782
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

Ionic model: Courtemanche
    GCaL                 modifier: *0.225          value: 0.027855
    GNa                  modifier: *0.6            value: 4.68
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

read_sv(): Initialization using file: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_0_bcl_500.0.sv

read_sv(): Initialization using file: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_1_bcl_500.0.sv

read_sv(): Initialization using file: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_0_bcl_500.0.sv

read_sv(): Initialization using file: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/init_values_stab_1_bcl_500.0.sv

Adjusting dim_t to make dimensions consistent
Adjusting dim_t to make dimensions consistent

    *** Launching simulation ***


    *** Launching simulation ***

PROG    -----     ----    -------    -------|
time    %%comp    time     ctime       ETA  |
0.00    0.0    0.0    0:00:00    0:00:00
L5 : parabolic PDE solver diverged. Reason: NaN or inf encountered.
PROG    -----     ----    -------    -------|
time    %%comp    time     ctime       ETA  |
0.00    0.0    0.0    0:00:00    0:00:00
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
L5 : parabolic PDE solver diverged. Reason: NaN or inf encountered.
--------------------------------------------------------------------------
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: [[54506,1],0]
  Exit code:    1

---

--------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#               Launching openCARP Simulation 2022-06-28_prepace
#-------------------------------------------------------------------------------

mpiexec -n 2 /Users/abc/openCARP/_build/bin/openCARP \
  +F /Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/parameters.par \
  -ellip_use_pt 0 \
  -parab_use_pt 0 \
  -parab_options_file /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/ilu_cg_opts \
  -ellip_options_file /Users/abc/openCARP/external/carputils/carputils/resources/petsc_options/gamg_cg_opts \
  -num_gregions 2 \
  -gregion[0].num_IDs  2 \
  -gregion[0].ID[0] 1 \
  -gregion[0].ID[1] 2 \
  -gregion[0].g_il  0.1406 \
  -gregion[0].g_it  0.1406 \
  -gregion[0].g_in  0.1406 \
  -gregion[0].g_el  0.7028 \
  -gregion[0].g_et  0.7028 \
  -gregion[0].g_en  0.7028 \
  -gregion[1].num_IDs  1 \
  -gregion[1].ID[0] 3 \
  -gregion[1].g_il  1e-07 \
  -gregion[1].g_it  1e-07 \
  -gregion[1].g_in  1e-07 \
  -gregion[1].g_el  1e-07 \
  -gregion[1].g_et  1e-07 \
  -gregion[1].g_en  1e-07 \
  -num_stim 1 \
  -start_statef prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/state.2000.0 \
  -num_tsav 1 \
  -tsav[0] 2500.0 \
  -stimulus[0].start 2000.0 \
  -stimulus[0].stimtype 0 \
  -stimulus[0].strength 70 \
  -stimulus[0].duration 2.0 \
  -stimulus[0].npls 1 \
  -stimulus[0].x0 -200.0 \
  -stimulus[0].xd 400.0 \
  -stimulus[0].y0 -200.0 \
  -stimulus[0].yd 50400.0 \
  -stimulus[0].z0 -200.0 \
  -stimulus[0].zd 400.0 \
  -num_LATs 1 \
  -lats[0].all 0 \
  -lats[0].measurand 0 \
  -lats[0].mode 0 \
  -lats[0].threshold -50 \
  -simID prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1 \
  -dt 20 \
  -spacedt 1 \
  -timedt 100 \
  -mass_lumping 1 \
  -tend 2500.1 \
  -meshname 2022-06-28_prepace/block_i

L2 : Output directory exists: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1

L2 : Output directory exists: prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1


    *** Processing meshes ***

Reading reference mesh: 2022-06-28_prepace/block_i.*
L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"!
L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"!

    *** Processing meshes ***

Reading reference mesh: 2022-06-28_prepace/block_i.*
Done in 0.019605 sec.
Renormalised 8 longitudinal and 0 sheet-transverse fibre vectors.
Done in 0.000036 sec.
Processing submeshes
Done in 0.019648 sec.
Renormalised 8 longitudinal and 0 sheet-transverse fibre vectors.
Done in 0.000039 sec.
Processing submeshes
All done in 0.024188 sec.
All done in 0.024064 sec.

    *** Initializing physics ***

Initializing Electrics ..

    *** Initializing physics ***

Initializing Electrics ..

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

Assigning IMPS to tagged regions:
    Ionic model: Courtemanche to tag region(s) [1].
    Ionic model: Courtemanche to tag region(s) [2], [3].

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

Assigning IMPS to tagged regions:
    Ionic model: Courtemanche to tag region(s) [1].
    Ionic model: Courtemanche to tag region(s) [2], [3].
Ionic model: Courtemanche
    GCaL                 modifier: -55%            value: 0.05571
    GK1                  modifier: +100%           value: 0.18
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

Ionic model: Courtemanche
    GCaL                 modifier: *0.225          value: 0.027855
    GNa                  modifier: *0.6            value: 4.68
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

Ionic model: Courtemanche
    GCaL                 modifier: -55%            value: 0.05571
    GK1                  modifier: +100%           value: 0.18
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

Ionic model: Courtemanche
    GCaL                 modifier: *0.225          value: 0.027855
    GNa                  modifier: *0.6            value: 4.68
    factorGKur           modifier: -50%            value: 0.5
    Gto                  modifier: -65%            value: 0.05782
    GKs                  modifier: +100%           value: 0.258
    maxIpCa              modifier: +50%            value: 0.4125
    maxINaCa             modifier: +60%            value: 2560
    GKr                  modifier: *1.6            value: 0.04704

Restoring time 2000.000000 from prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/state.2000.0.roe (format v1) generated
    by calling program r800 on Tue Dec  8 09:16:06 2020

Restoring time 2000.000000 from prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/state.2000.0.roe (format v1) generated
    by calling program r800 on Tue Dec  8 09:16:06 2020

L5 : expecting 8123 nodes but read 15876 nodes
L5 : expecting 8123 nodes but read 15876 nodes
--------------------------------------------------------------------------
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: [[54302,1],1]
  Exit code:    1
--------------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 735, in <module>
    run()
  File "/Users/abc/openCARP/external/carputils/carputils/tools.py", line 540, in wrapped
    ret = run(args, job)
  File "/Users/abc/openCARP/external/experiments/tutorials/02_EP_tissue/21_reentry_induction/run.py", line 566, in run
    model.prepace.prepace(args, job, cmd, meshname, sinus, steady_state_dir, tissue_init)
  File "/Users/abc/openCARP/external/carputils/carputils/model/prepace.py", line 131, in prepace
    os.rename(old_file, new_file)
FileNotFoundError: [Errno 2] No such file or directory: 'prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/vm.igb' -> 'prepace_block_50000.0um_resolution_400.0um_cv_0.3_with_4_beats_at_500.0_bcl_lump_1/vm_last_beat.igb'