Examples give errores on Debian10/Ubuntu2020
When I start the containers using
docker-compose up
Navigate to /tutorials/02_stimulation
, enter an ID
, and click run, I get:
Running ...
======================================================================
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
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: pt
DRY: False
VISUALIZE: True
----------------------------------------------------------------------
System Info
----------------------------------------------------------------------
Python: 3.6.9
SETTINGS: /root/.config/carputils/settings.yaml
Email: you@example.com
======================================================================
Requested mesh already exists, skipping generation.
----------------------------------------------
stimulus[0]
x0: -5050.0 xd: 100.0
y0: -100.0 yd: 200.0
z0: -100.0 zd: 200.0
----------------------------------------------
----------------------------------------------
stimulus[1]
x0: 4950.0 xd: 100.0
y0: -100.0 yd: 200.0
z0: -100.0 zd: 200.0
----------------------------------------------
mkdir -p /tutorials/02_EP_tissue/02_stimulation/foobar
#---------------------------------------------------------------------
# Launching CARP Simulation foobar
#---------------------------------------------------------------------
/usr/local/bin/openCARP \
+F stimtest.par \
+F /usr/local/lib/python3.6/dist-packages/carputils-0.0.0-py3.6-linux-x86_64.egg/carputils/resources/options/pt_ell_amg \
+F /usr/local/lib/python3.6/dist-packages/carputils-0.0.0-py3.6-linux-x86_64.egg/carputils/resources/options/pt_para_amg \
-ellip_use_pt 1 \
-parab_use_pt 1 \
-meshname meshes/2020-10-26_eOKYLwmXdN/block \
-gridout_i 3 \
-simID foobar \
-stimulus[0].x0 -5050.0 \
-stimulus[0].xd 100.0 \
-stimulus[0].y0 -100.0 \
-stimulus[0].yd 200.0 \
-stimulus[0].z0 -100.0 \
-stimulus[0].zd 200.0 \
-stimulus[0].stimtype 2 \
-stimulus[0].strength 2e3 \
-stimulus[1].x0 4950.0 \
-stimulus[1].xd 100.0 \
-stimulus[1].y0 -100.0 \
-stimulus[1].yd 200.0 \
-stimulus[1].z0 -100.0 \
-stimulus[1].zd 200.0 \
-gridout_i 3 \
-gridout_e 3
*** Unrecognized keyword pt_opts_ellip.amg_smooth_steps
*** Error reading parameters
OpenMP thread utilization: 1 / 1 threads.
Meshtool - conversion failure
Something went wrong......Try again
Canceled Process
For /tutorials/04_limpet_fe
I get:
Running ...
======================================================================
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
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: pt
DRY: False
VISUALIZE: True
----------------------------------------------------------------------
System Info
----------------------------------------------------------------------
Python: 3.6.9
SETTINGS: /root/.config/carputils/settings.yaml
Email: you@example.com
======================================================================
mkdir -p /tutorials/01_EP_single_cell/04_limpet_fe/egg
#---------------------------------------------------------------------
# Generating C source files
#---------------------------------------------------------------------
/usr/local/bin/limpet_fe.py my_MBRDR.model /usr/local/bin/../physics/limpet/models/imp_list.txt
Traceback (most recent call last):
File "/usr/local/bin/limpet_fe.py", line 1691, in <module>
external_units = parse_external_units(imp_list)
File "/usr/local/bin/limpet_fe.py", line 68, in parse_external_units
f = open(filename, "r")
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/../physics/limpet/models/imp_list.txt'
Something went wrong......Try again
Canceled Process
My guess is that somehow the tutorials in the container, pulled from https://git.opencarp.org/openCARP/experiments/tree/webGUI-tutorials are outdated.