Examples gives keyword/parameters error
EDIT: This only an issue when running the docker from Windows 10, from LinuxMint 19.1, it works fine.
I am running the latest version of the docker (docker.opencarp.org/opencarp/opencarp:latest)
Many of the examples in 02_EP_tissue give the same error as described below.
Running 02_EP_tissue/01_basic_usage by default using
python run.py
gives the following output
================================================================================================================================================
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
MESHALYZER: /usr/local/meshalyzer/meshalyzer
LIMPETGUI: /usr/local/limpetgui/main.py
SV2H5B: /usr/local/lib/python3.6/dist-packages/bin/bin2h5.py
SV2H5T: /usr/local/lib/python3.6/dist-packages/bin/txt2h5.py
CLOSEST_HC: /usr/local/lib/python3.6/dist-packages/bin/closest_hc
APDRESTITUTION: /usr/local/lib/python3.6/dist-packages/bin/APDrestitution
TUNECV: /usr/local/lib/python3.6/dist-packages/bin/tuneCV
RESTITUTECV: /usr/local/lib/python3.6/dist-packages/bin/restituteCV
MESHTOOL: /usr/local/bin/meshtool
LIMPETFE: /usr/local/bin/limpet_fe.py
MAKEDYNAMICMODEL: /usr/local/bin/make_dynamic_model.sh
------------------------------------------------------------------------------------------------------------------------------------------------
Command Line Options
------------------------------------------------------------------------------------------------------------------------------------------------
NP: 1
BUILD: CPU
FLAVOR: petsc
DRY: False
VISUALIZE: False
------------------------------------------------------------------------------------------------------------------------------------------------
Solver Option Files
------------------------------------------------------------------------------------------------------------------------------------------------
Parabolic: /usr/local/lib/python3.6/dist-packages/carputils/resources/petsc_options/ilu_cg_opts
Elliptic: /usr/local/lib/python3.6/dist-packages/carputils/resources/petsc_options/amg_cg_opts
------------------------------------------------------------------------------------------------------------------------------------------------
System Info
------------------------------------------------------------------------------------------------------------------------------------------------
Python: 3.6.9
SETTINGS: /root/.config/carputils/settings.yaml
Email: you@example.com
================================================================================================================================================
Requested mesh does not yet exist - generating it...
#-----------------------------------------------------------------------------------------------------------------------------------------------
# Launching Mesher
#-----------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/bin/mesher \
-size[0] 1.0 \
-size[1] 0.1 \
-size[2] 0.02 \
-bath[0] -0.0 \
-bath[1] -0.0 \
-bath[2] -0.0 \
-center[0] 0.0 \
-center[1] 0.0 \
-center[2] 0.0 \
-resolution[0] 100.0 \
-resolution[1] 100.0 \
-resolution[2] 100.0 \
-mesh meshes/2021-03-04_FMfswahGGJ/block \
-Elem3D 0 \
-fibers.rotEndo 0.0 \
-fibers.rotEpi 0.0 \
-fibers.sheetEndo 90.0 \
-fibers.sheetEpi 90.0 \
-periodic 0 \
-periodic_tag 1234 \
-perturb 0.0
Number of points: 3333
Number of Tetrahedra: 10000
Using orthotropic fiber setup.
Reading file: meshes/2021-03-04_FMfswahGGJ/block.elem
mkdir -p /openCARP/shared/carp/experiments/tutorials/02_EP_tissue/01_basic_usage/2021-03-04_basic_20.0
#-----------------------------------------------------------------------------------------------------------------------------------------------
# Launching CARP Simulation 2021-03-04_basic_20.0
#-----------------------------------------------------------------------------------------------------------------------------------------------
/usr/local/bin/openCARP \
+F basic.par \
-ellip_use_pt 0 \
-parab_use_pt 0 \
-parab_options_file /usr/local/lib/python3.6/dist-packages/carputils/resources/petsc_options/ilu_cg_opts \
-ellip_options_file /usr/local/lib/python3.6/dist-packages/carputils/resources/petsc_options/amg_cg_opts \
-simID 2021-03-04_basic_20.0 \
-meshname meshes/2021-03-04_FMfswahGGJ/block \
-dt 25 \
-tend 20.0 \
-num_phys_regions 2 \
-phys_region[0].name "Intracellular domain" \
-phys_region[0].ptype 0 \
-phys_region[0].num_IDs 1 \
-phys_region[0].ID[0] 1 \
-phys_region[1].name "Extracellular domain" \
-phys_region[1].ptype 1 \
-phys_region[1].num_IDs 1 \
-phys_region[1].ID[0] 1 \
-num_stim 1 \
-stimulus[0].name S1 \
-stimulus[0].stimtype 0 \
-stimulus[0].strength 20.0 \
-stimulus[0].duration 2.0 \
-stimulus[0].x0 -5050.0 \
-stimulus[0].xd 100.0 \
-stimulus[0].y0 -550.0 \
-stimulus[0].yd 1100.0 \
-stimulus[0].z0 -150.0 \
-stimulus[0].zd 300.0
*** Unrecognized keyword
*** Error reading parameters
}```
I see that a similar issue is addressed: https://git.opencarp.org/openCARP/carputilsgui/-/issues/15
Where using the flavor petsc is said to fix it, but it does not work for me.