Help with step 4 of the subduction-2d example

Hello, I completed a new pylith installation and it went well, however one of the examples will not process and I’m confused by the errors. Below I give my installation details and the problem with the subduction-2d (step 4) example. Any help would be greatly appreciated.

Here are my pylith installation details

----------------local install pylith installation details---------------williamharbert@Williams-MacBook-Pro subduction-2d % pylith --version
Platform:
Hostname: Williams-MacBook-Pro.local
Operating system: Darwin
Kernel: 21.5.0
Version: Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64
Machine: x86_64
Processor: i386

PyLith
Release v3.0.0

PETSc
Configured on 2022-06-02 16:46:16 -0400, GIT branch: branch-not-available, revision: v3.17.1-527-ge1a1509ab6

Spatialdata
Release v3.0.0

MPI standard: 3.1, implementation: MPICH, version: 3.4.2
HDF5 version: 1.12.1
NetCDF version: 4.8.1
Proj version: 8.1.1

Python
v3.9.7 of CPython compiled with Clang 13.0.0 (clang-1300.0.29.30)
numpy: v1.22.4 from /Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/numpy
spatialdata: v3.0.0 from /Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/spatialdata
h5py: v3.6.0 from /Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/h5py
netCDF4: v1.5.7 from /Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/netCDF4
pythia: v1.0.0 from /Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia

If you publish results based on computations with PyLith please cite the following:
(use --include-citations during your simulations to display a list specific to your computation):

@Manual{PyLith:software,
title = {PyLith v3.0.0},
author = {Aagaard, B. and Knepley, M. and Williams, C.},
organization = {Computational Infrastructure for Geodynamics (CIG)},
address = {University of California, Davis},
year = {2022},
doi = {http://doi.org/10.5281/zenodo.6622161}
}

@Manual{PyLith:manual,
title = {PyLith User Manual, Version 3.0.0},
author = {Aagaard, B. and Knepley, M. and Williams, C.},
organization = {Computational Infrastructure for Geodynamics (CIG)},
address = {University of California, Davis},
year = {2022},
note = {PyLith — PyLith 3.0.0dev documentation}
}

@Article{Aagaard:Knepley:Williams:JGR:2013,
author = {Aagaard, B.~T. and Knepley, M.~G. and Wiliams, C.~A.},
title = {A domain decomposition approach to implementing fault slip in finite-element models of quasi-static and dynamic crustal deformation},
journal = {Journal of Geophysical Research Solid Earth},
year = {2013},
volume = {118},
pages = {3059–3079},
doi = {10.1002/jgrb.50217}
}
-----------------------------------------Errors generated from step 4 of the subduction-2d example--------------
pylith step04_afterslip.cfg

Traceback (most recent call last):

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/bin/pylith”, line 28, in

start(applicationClass=PyLithApp)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/applications/init.py”, line 42, in start

shell.run(**kwds)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/applications/Shell.py”, line 123, in run

app.applyConfiguration(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 71, in applyConfiguration

context.configureComponent(self)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/ConfigContext.py”, line 65, in configureComponent

component.configureComponents(self)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 112, in configureComponents

self.inventory.configureComponents(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Inventory.py”, line 97, in configureComponents

component.applyConfiguration(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 71, in applyConfiguration

context.configureComponent(self)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/ConfigContext.py”, line 65, in configureComponent

component.configureComponents(self)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 112, in configureComponents

self.inventory.configureComponents(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Inventory.py”, line 97, in configureComponents

component.applyConfiguration(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 71, in applyConfiguration

context.configureComponent(self)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/ConfigContext.py”, line 65, in configureComponent

component.configureComponents(self)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 112, in configureComponents

self.inventory.configureComponents(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Inventory.py”, line 97, in configureComponents

component.applyConfiguration(context)

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pythia/pyre/inventory/Configurable.py”, line 74, in applyConfiguration

self._configure()

File “/Users/williamharbert/Downloads/pylith-3.0.0-macOS-11.6.6-x86_64/lib/python3.9/site-packages/pylith/bc/DirichletTimeDependent.py”, line 122, in _configure

raise ValueError("'constrained_dof' must be a zero based integer array of indices corresponding to the "

ValueError: ‘constrained_dof’ must be a zero based integer array of indices corresponding to the constrained degrees of freedom.

-------------------------end of error messages--------------------------------------------------------------------------

Any help or suggestions would be greatly appreciated! Thank you.

As noted in the README.md file, examples/subduction-2d/step04_afterslip has not been updated for PyLith v3. It uses fault friction which has not be reimplemented in v3.

Thank you!