installing openCARP and carputils on linux cluster

Question

Hi, 

I installed openCARP and carputils on my desktop using docker, everything went fine.
Then I tried to install them on our linux cluster following the instructions (git close and pip3 for carputils and dnf install ./opencarp-v3.1-Linux.rpm for openCARP).
The installation seems to have worked but when I try to run the first example run.py in 01_basic_bench, I get the errors below. Maybe you see quickly what I am doing wrong?
Thank you and best regards,   Luca

(opencarp_gab) [pavarino@headnode1 01_basic_bench]$ ./run.py --help

Traceback (most recent call last):

  File "/home/pavarino/opencarp/experiments/tutorials/01_EP_single_cell/01_basic_bench/./run.py", line 557, in <module>

    run()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/tools.py", line 450, in wrapped

    prs = parser()

  File "/home/pavarino/opencarp/experiments/tutorials/01_EP_single_cell/01_basic_bench/./run.py", line 359, in parser

    parser = tools.standard_parser()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/tools.py", line 172, in standard_parser

    builds = tuple(settings.config.CARP_EXE_DIR.keys())

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/settings/settings.py", line 48, in config

    self._config = config.load()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/settings/config.py", line 173, in load

    fname = filename()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/settings/config.py", line 121, in filename

    msg = NOSETTINGS_TEMPLATE.format('\n    - '.join(candidates))

TypeError: sequence item 0: expected str instance, NoneType found

Comments

Hi Luca,

what's the output of calling "cusummary"? This script is located in carputils/bin.

Then, what's the content of the settings.yaml file that is referred to in the output of cusummary?

Answer 1

Hi, there is an issue here that has to be fixed, but it is also seems to mean that your carputils settings file is not found: where is it located?

I also see that you are using an old release of openCARP, could you try to use a more recent one and see if you still encounter this issue? (See https://git.opencarp.org/openCARP/openCARP/-/releases)

Cheers,

Marie

Comments

I was able to reproduce your issue when removing my settings.yaml files.
Try setting the CARPUTILS_SETTINGS environment variable to the full path of your settings file, or put your settings file in `$HOME/.config/carputils/'.

I will also fix this error raising.

Cheers,
Marie

Answer 2

The output of calling "cusummary" in carputils/bin  is:

 ./cusummary

Traceback (most recent call last):

  File "/home/pavarino/opencarp/carputils/bin/./cusummary", line 11, in <module>

    args = standard_parser().parse_args()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/tools.py", line 172, in standard_parser

    builds = tuple(settings.config.CARP_EXE_DIR.keys())

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/settings/settings.py", line 48, in config

    self._config = config.load()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/settings/config.py", line 173, in load

    fname = filename()

  File "/home/pavarino/.local/lib/python3.9/site-packages/carputils/settings/config.py", line 121, in filename

    msg = NOSETTINGS_TEMPLATE.format('\n    - '.join(candidates))

TypeError: sequence item 0: expected str instance, NoneType found

Answer 3

The settings.yaml file is:

# openCARP executables directory

# Specify as many alternative directories as you like, and use the key (e.g.

# 'CPU'/'GPU') with the --build flag on the command line to select which one

# to run with. Whether the build uses GPU or not is determined automatically.

CARP_EXE_DIR:

    CPU: /usr/local/bin

# Other paths

MESHALYZER_DIR: /usr/local/meshalyzer

LIMPETGUI_DIR:  /usr/local/limpetgui

MESH_DIR:       /usr/local/meshes

MESHTOOL_DIR:   /usr/local/bin

# Execution settings and configuration defaults

# Some of these can be overridden on the command line

MPIEXEC:       mpiexec    # Affects desktop only

SILENT:        No         # choose Yes or No

VISUALIZE:     No         # visualization default (Yes, No)

FLAVOR:        petsc      # choose petsc, direct or pt

DIRECT_SOLVER: MUMPS      # choose MUMPS, SUPERLU_DIST or PASTIX

PURK_SOLVER:   GMRES      # choose GMRES, MUMPS, SUPERLU_DIST or PASTIX

PLATFORM:      desktop    # choose default hardware profile

BUILD:         CPU        # choose default CARP build (CPU, GPU)

# Regression testing settings

# The path to a directory containing the reference solution repositories

# (required):

REGRESSION_REF: /home/pavarino/carp-tests-reference

# Default packages to run tests from (can use the Python subpackage notation

# to select specific submodules, e.g. devtests.mechanics):

REGRESSION_PKG:  []

# Examples

#    - devtests

#    - benchmarks

#    - devtests.mechanics # Would cause duplication with full devtests above

# Uncomment the following line to control the location of temporary

# files generated by the regression testing framework. By default, temporary

# files are generated in your system /tmp

REGRESSION_TEMP: None

# Uncomment to limit resources

# MAX_NP:      32         # set maximum number of processes

# Personal information

EMAIL: you@example.com # Email for notifications

NAME: Your Name # Name of the user

ORCID: 0000-0000-0000-0000 # ORCID of the user

(opencarp_gab) [pavarino@headn