KeyError: 'honour_petsc_dir' #3185

adominious · 2023-10-24T08:18:13Z

Hi there, when running make_test, I receive the following error

KeyError: 'honour_petsc_dir'

How do I solve this?

The text was updated successfully, but these errors were encountered:

jshipton · 2023-10-24T08:24:50Z

Are you sure that your installation worked @adominious ? It would be a good idea to be clear about what it is that you are trying to do - i.e. that you are trying to use your own installation of PETSc.

adominious · 2023-10-24T08:34:29Z

I am trying to use gusto for my PhD, but I have next to no experience with Linux. I downloaded arch Linux due to a recommendation from a friend.

With a fresh instillation, I tried installing Gusto. I could only complete a successful instillation if I installed PETSc using pacman first, otherwise the instillation would always error at the 'building PETSc' stage

jshipton · 2023-10-24T09:02:02Z

It might be worth starting with reporting the error that you get if you try to install without installing your own PETSc (or did you already do this?)

Given that you have installed your own PETSc, you need to figure out how to link it to your Firedrake installation when you install Firedrake - I am not sure that you have done this, which is why I'm asking if you are sure that your Firedrake installation has worked. Can you upload your firedrake-install.log?

adominious · 2023-10-24T09:13:05Z

Please give me a moment while I try to find the error I get without installing my own PETSc

adominious · 2023-10-24T12:42:29Z

Sorry it took so long, I have the following error:

Traceback (most recent call last):
  File "/home/adamh/firedrake-install", line 1914, in <module>
    install("petsc/")
  File "/home/adamh/firedrake-install", line 1058, in install
    build_and_install_petsc()
  File "/home/adamh/firedrake-install", line 1170, in build_and_install_petsc
    check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options)
  File "/home/adamh/firedrake-install", line 666, in check_call
    log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode())
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/home/adamh/firedrake/bin/python', './configure', 'PETSC_DIR=/home/adamh/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-pnetcdf', '--download-ml', '--download-cmake', '--download-hypre', '--with-debugging=0', '--download-netcdf', '--download-metis', '--download-ptscotch', '--download-pastix', '--download-hwloc', '--download-bison', '--with-fortran-bindings=0', '--download-hdf5', '--download-superlu_dist', '--with-c2html=0', '--download-chaco', '--with-shared-libraries=1', '--download-mumps', '--download-scalapack', '--with-zlib', '--download-suitesparse', '--download-mpich']' returned non-zero exit status 1.


Install log saved in /home/adamh/firedrake-install.log

jshipton · 2023-10-24T12:45:05Z

It'd be a good idea to attach the firedrake-install.log file too. I'm afraid I can't make head or tail of that error but maybe @JDBetteridge, @ksagiyam or @connorjward can? There might also be a PESTc install log that you can attach.

adominious · 2023-10-24T12:47:52Z

Sorry, I think I have attached it?

firedrake-install.log

connorjward · 2023-10-24T12:48:26Z

I am trying to use gusto for my PhD, but I have next to no experience with Linux. I downloaded arch Linux due to a recommendation from a friend.

Arch linux is not really recommended for individuals new to Linux. It is definitely a "thrown in at the deep end" type of distribution. Something like Ubuntu would normally be recommended.

With a fresh instillation, I tried installing Gusto. I could only complete a successful instillation if I installed PETSc using pacman first, otherwise the instillation would always error at the 'building PETSc' stage

You should not be installing PETSc using pacman. The PETSc Firedrake uses has a bunch of extra packages.

adominious · 2023-10-24T12:51:40Z

I think I am starting to wrap my head around Arch, I would like to try and stick with it if possible. I am currently using Xero distribution.

I guessed that useing pacman would not be enough. Can you help with current error?

JDBetteridge · 2023-10-24T12:52:19Z

Just catching up with this. Your friend recommended Arch Linux, but you have no prior experience with Linux at all? I will echo Connor's comment about trying Ubuntu first, unless you intend to learn all aspects of Linux in depth (like maintaining your installation and cosplaying as a sysadmin). Or even Windows subsystem for Linux if you are already a Windows user: guide here

From the install log, it looks like PETSc is being installed by the firedrake install script anyway, is that really the latest install log?

jshipton · 2023-10-24T12:56:14Z

Sorry Jack, the chronology may have got confusing due to my intervention! The original post is an error from trying to use the pacman install of PETSc but I asked @adominious to try a fresh install so that we could see the error if Firedrake was allowed to do it's own thing.

JDBetteridge · 2023-10-24T13:00:31Z

Oh I see. @adominious you do not have a Fortran compiler installed you need to run pacman -S gcc-fortran . Additionally you should make sure that all of the other system requirements for Firedrake are installed (using pacman).

Then when you install use firedrake-install --no-package-manager since the Firedrake install script is not aware of the Arch Linux package manager.

adominious · 2023-10-26T16:09:38Z

Apologies for the delay in response, I did not have access to my laptop.

I believe I have installed all the necessary system requirements now, along with running pacman -S gcc-fortran

I am met with the following error:

File "/home/adamh/firedrake-install", line 1914, in <module>
    install("petsc/")
  File "/home/adamh/firedrake-install", line 1058, in install
    build_and_install_petsc()
  File "/home/adamh/firedrake-install", line 1170, in build_and_install_petsc
    check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options)
  File "/home/adamh/firedrake-install", line 666, in check_call
    log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode())
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/home/adamh/firedrake/bin/python', './configure', 'PETSC_DIR=/home/adamh/firedrake/src/petsc', 'PETSC_ARCH=default', '--download-cmake', '--with-fortran-bindings=0', '--download-superlu_dist', '--download-chaco', '--download-netcdf', '--download-hdf5', '--download-mumps', '--download-pnetcdf', '--with-zlib', '--download-mpich', '--download-scalapack', '--download-hypre', '--download-ptscotch', '--download-bison', '--download-pastix', '--download-hwloc', '--download-metis', '--with-debugging=0', '--with-c2html=0', '--download-suitesparse', '--download-ml', '--with-shared-libraries=1']' returned non-zero exit status 1.


Install log saved in /home/adamh/firedrake-install.log

I think I have attached the corresponding log file below:

firedrake-install.log

JDBetteridge · 2023-10-26T17:35:55Z

Can we see /home/adamh/firedrake/src/petsc/configure.log please?

adominious · 2023-10-27T10:14:30Z

Hello. I have recently wiped my ssd as I believe there was interference between the old installed of PETSc. Doing this proved successful. Running the firedrake make test yeilded the following, is there anything here I need to worry about?

===================================================== FAILURES =====================================================
____________________________________________ test_pyop2_not_initialised ____________________________________________

    @pytest.mark.skipif(
        "PYTEST_XDIST_WORKER_COUNT" in os.environ.keys()
        and int(os.environ["PYTEST_XDIST_WORKER_COUNT"]) > 1,
        reason="Must be run first"
    )
    def test_pyop2_not_initialised():
        """Check that PyOP2 has not been initialised yet.
           The test fails if another test builds a firedrake object not in a fixture."""
>       assert not op2.initialised()
E       assert not True
E        +  where True = <function initialised at 0x7fd4ee2e1440>()
E        +    where <function initialised at 0x7fd4ee2e1440> = op2.initialised

tests/test_0init.py:15: AssertionError
_______________________________________ test_demo_runs[qgbasinmodes.py.rst] ________________________________________

py_file = '/tmp/pytest-of-adamh/pytest-0/test_demo_runs_qgbasinmodes_py0/qgbasinmodes.py'
env = {'BROWSER': 'firefox', 'COLORFGBG': '15;0', 'COLORTERM': 'truecolor', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus', ...}

    @pytest.mark.skipcomplex  # Will need to add a seperate case for a complex demo.
    def test_demo_runs(py_file, env):
>       subprocess.check_call([sys.executable, py_file], env=env)

/home/adamh/firedrake/src/firedrake/tests/demos/test_demos_run.py:60: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

popenargs = (['/home/adamh/firedrake/bin/python', '/tmp/pytest-of-adamh/pytest-0/test_demo_runs_qgbasinmodes_py0/qgbasinmodes.py'],)
kwargs = {'env': {'BROWSER': 'firefox', 'COLORFGBG': '15;0', 'COLORTERM': 'truecolor', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus', ...}}
retcode = 1
cmd = ['/home/adamh/firedrake/bin/python', '/tmp/pytest-of-adamh/pytest-0/test_demo_runs_qgbasinmodes_py0/qgbasinmodes.py']

    def check_call(*popenargs, **kwargs):
        """Run command with arguments.  Wait for command to complete.  If
        the exit code was zero then return, otherwise raise
        CalledProcessError.  The CalledProcessError object will have the
        return code in the returncode attribute.
    
        The arguments are the same as for the call function.  Example:
    
        check_call(["ls", "-l"])
        """
        retcode = call(*popenargs, **kwargs)
        if retcode:
            cmd = kwargs.get("args")
            if cmd is None:
                cmd = popenargs[0]
>           raise CalledProcessError(retcode, cmd)
E           subprocess.CalledProcessError: Command '['/home/adamh/firedrake/bin/python', '/tmp/pytest-of-adamh/pytest-0/test_demo_runs_qgbasinmodes_py0/qgbasinmodes.py']' returned non-zero exit status 1.

/usr/lib/python3.11/subprocess.py:413: CalledProcessError
---------------------------------------------- Captured stdout setup -----------------------------------------------
Output written to '/tmp/pytest-of-adamh/pytest-0/test_demo_runs_qgbasinmodes_py0/qgbasinmodes.py'
----------------------------------------------- Captured stderr call -----------------------------------------------
firedrake:WARNING OMP_NUM_THREADS is not set or is set to a value greater than 1, we suggest setting OMP_NUM_THREADS=1 to improve performance
Traceback (most recent call last):
  File "/tmp/pytest-of-adamh/pytest-0/test_demo_runs_qgbasinmodes_py0/qgbasinmodes.py", line 142, in <module>
    eigenproblem = LinearEigenproblem(
                   ^^^^^^^^^^^^^^^^^^^
  File "/home/adamh/firedrake/src/firedrake/firedrake/eigensolver.py", line 44, in __init__
    raise ImportError(
ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)
_____________________________________________ test_evals_1d[5-1-1e-13] _____________________________________________

n = 5, degree = 1, tolerance = 1e-13

    @pytest.mark.parametrize(('n', 'degree', 'tolerance'),
                             [(5, 1, 1e-13),
                              (10, 1, 1e-13),
                              (20, 1, 1e-13),
                              (30, 1, 1e-13)])
    def test_evals_1d(n, degree, tolerance):
>       true_values, estimates = evals(n, degree=degree)

tests/regression/test_eigensolver.py:53: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/regression/test_eigensolver.py:21: in evals
    eigenprob = LinearEigenproblem(a, bcs=bc, bc_shift=-6666.)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <firedrake.eigensolver.LinearEigenproblem object at 0x7fd4875c4d10>
A = Form([Integral(Conj(Inner(Grad(Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7fd4872407... None)))), 'cell', Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 21506), 'everywhere', {}, None)])
M = None, bcs = <firedrake.bcs.DirichletBC object at 0x7fd487354750>, bc_shift = -6666.0

    def __init__(self, A, M=None, bcs=None, bc_shift=0.0):
        if not SLEPc:
>           raise ImportError(
                "Unable to import SLEPc, eigenvalue computation not possible "
                "(try firedrake-update --slepc)"
            )
E           ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)

firedrake/eigensolver.py:44: ImportError
____________________________________________ test_evals_1d[10-1-1e-13] _____________________________________________

n = 10, degree = 1, tolerance = 1e-13

    @pytest.mark.parametrize(('n', 'degree', 'tolerance'),
                             [(5, 1, 1e-13),
                              (10, 1, 1e-13),
                              (20, 1, 1e-13),
                              (30, 1, 1e-13)])
    def test_evals_1d(n, degree, tolerance):
>       true_values, estimates = evals(n, degree=degree)

tests/regression/test_eigensolver.py:53: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/regression/test_eigensolver.py:21: in evals
    eigenprob = LinearEigenproblem(a, bcs=bc, bc_shift=-6666.)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <firedrake.eigensolver.LinearEigenproblem object at 0x7fd487312410>
A = Form([Integral(Conj(Inner(Grad(Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7fd48722f9... None)))), 'cell', Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 21508), 'everywhere', {}, None)])
M = None, bcs = <firedrake.bcs.DirichletBC object at 0x7fd4873122d0>, bc_shift = -6666.0

    def __init__(self, A, M=None, bcs=None, bc_shift=0.0):
        if not SLEPc:
>           raise ImportError(
                "Unable to import SLEPc, eigenvalue computation not possible "
                "(try firedrake-update --slepc)"
            )
E           ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)

firedrake/eigensolver.py:44: ImportError
____________________________________________ test_evals_1d[20-1-1e-13] _____________________________________________

n = 20, degree = 1, tolerance = 1e-13

    @pytest.mark.parametrize(('n', 'degree', 'tolerance'),
                             [(5, 1, 1e-13),
                              (10, 1, 1e-13),
                              (20, 1, 1e-13),
                              (30, 1, 1e-13)])
    def test_evals_1d(n, degree, tolerance):
>       true_values, estimates = evals(n, degree=degree)

tests/regression/test_eigensolver.py:53: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/regression/test_eigensolver.py:21: in evals
    eigenprob = LinearEigenproblem(a, bcs=bc, bc_shift=-6666.)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <firedrake.eigensolver.LinearEigenproblem object at 0x7fd487116d50>
A = Form([Integral(Conj(Inner(Grad(Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7fd487114e... None)))), 'cell', Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 21510), 'everywhere', {}, None)])
M = None, bcs = <firedrake.bcs.DirichletBC object at 0x7fd4871163d0>, bc_shift = -6666.0

    def __init__(self, A, M=None, bcs=None, bc_shift=0.0):
        if not SLEPc:
>           raise ImportError(
                "Unable to import SLEPc, eigenvalue computation not possible "
                "(try firedrake-update --slepc)"
            )
E           ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)

firedrake/eigensolver.py:44: ImportError
____________________________________________ test_evals_1d[30-1-1e-13] _____________________________________________

n = 30, degree = 1, tolerance = 1e-13

    @pytest.mark.parametrize(('n', 'degree', 'tolerance'),
                             [(5, 1, 1e-13),
                              (10, 1, 1e-13),
                              (20, 1, 1e-13),
                              (30, 1, 1e-13)])
    def test_evals_1d(n, degree, tolerance):
>       true_values, estimates = evals(n, degree=degree)

tests/regression/test_eigensolver.py:53: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/regression/test_eigensolver.py:21: in evals
    eigenprob = LinearEigenproblem(a, bcs=bc, bc_shift=-6666.)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <firedrake.eigensolver.LinearEigenproblem object at 0x7fd4872470d0>
A = Form([Integral(Conj(Inner(Grad(Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7fd48736de... None)))), 'cell', Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 21512), 'everywhere', {}, None)])
M = None, bcs = <firedrake.bcs.DirichletBC object at 0x7fd487247e50>, bc_shift = -6666.0

    def __init__(self, A, M=None, bcs=None, bc_shift=0.0):
        if not SLEPc:
>           raise ImportError(
                "Unable to import SLEPc, eigenvalue computation not possible "
                "(try firedrake-update --slepc)"
            )
E           ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)

firedrake/eigensolver.py:44: ImportError
__________________________________________________ test_evals_2d ___________________________________________________

    def test_evals_2d():
        """2D Eigenvalue convergence test. As with Boffi, we observe that the
        convergence rate convergest to 2 from above."""
>       errors = np.array([poisson_eigenvalue_2d(i) for i in range(5)])

tests/regression/test_eigensolver.py:78: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/regression/test_eigensolver.py:78: in <listcomp>
    errors = np.array([poisson_eigenvalue_2d(i) for i in range(5)])
tests/regression/test_eigensolver.py:65: in poisson_eigenvalue_2d
    ep = LinearEigenproblem(inner(grad(u), grad(v)) * dx,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <firedrake.eigensolver.LinearEigenproblem object at 0x7fd48753bc10>
A = Form([Integral(Conj(Inner(Grad(Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7fd487437d... None)))), 'cell', Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 21514), 'everywhere', {}, None)])
M = None, bcs = <firedrake.bcs.DirichletBC object at 0x7fd487311710>, bc_shift = 666.0

    def __init__(self, A, M=None, bcs=None, bc_shift=0.0):
        if not SLEPc:
>           raise ImportError(
                "Unable to import SLEPc, eigenvalue computation not possible "
                "(try firedrake-update --slepc)"
            )
E           ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)

firedrake/eigensolver.py:44: ImportError
================================================= warnings summary =================================================
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
  /home/adamh/firedrake/src/ufl/ufl/core/ufl_type.py:56: DeprecationWarning: attach_operators_from_hash_data deprecated, please use UFLObject instead.
    warnings.warn("attach_operators_from_hash_data deprecated, please use UFLObject instead.", DeprecationWarning)

../fiat/FIAT/__init__.py:5
  /home/adamh/firedrake/src/fiat/FIAT/__init__.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    import pkg_resources

tests/equation_bcs/test_bcs_reconstruct.py: 12 warnings
tests/equation_bcs/test_equation_bcs.py: 120 warnings
tests/extrusion/test_annulus.py: 8 warnings
tests/extrusion/test_cylinder.py: 18 warnings
tests/extrusion/test_enrichment_1_feec.py: 36 warnings
tests/extrusion/test_extruded_periodic.py: 2 warnings
tests/extrusion/test_facet_integrals_2D.py: 4 warnings
tests/extrusion/test_facet_integrals_3D.py: 4 warnings
tests/extrusion/test_galerkinproj.py: 92 warnings
tests/extrusion/test_helmholtz_scalar.py: 48 warnings
tests/extrusion/test_helmholtz_vector.py: 80 warnings
tests/extrusion/test_interval.py: 6 warnings
tests/extrusion/test_laplace_neumann.py: 92 warnings
tests/extrusion/test_mixed_bcs.py: 140 warnings
tests/extrusion/test_point_eval_cells_extrusion.py: 51 warnings
tests/extrusion/test_point_eval_fs_extrusion.py: 60 warnings
tests/extrusion/test_poisson_neumann.py: 60 warnings
tests/extrusion/test_poisson_strong_bcs_extrusion.py: 12 warnings
tests/extrusion/test_real_tensorproduct.py: 84 warnings
tests/extrusion/test_rhs_side_bcs.py: 8 warnings
tests/extrusion/test_side_strong_bcs.py: 76 warnings
tests/extrusion/test_steady_advection_2D_extr.py: 16 warnings
tests/extrusion/test_steady_advection_3D_extr.py: 48 warnings
tests/extrusion/test_subdomain_extruded.py: 2 warnings
tests/extrusion/test_trace_extr.py: 8 warnings
tests/extrusion/test_two_step.py: 4 warnings
tests/extrusion/test_variable_layers_poisson.py: 4 warnings
tests/extrusion/test_zero_integrand_extrusion.py: 2 warnings
tests/multigrid/test_extruded_semicoarsen.py: 4 warnings
tests/multigrid/test_hiptmair.py: 16 warnings
tests/multigrid/test_inject_refined_extruded.py: 8 warnings
tests/multigrid/test_nested_split.py: 16 warnings
tests/multigrid/test_non_nested.py: 12 warnings
tests/multigrid/test_p_multigrid.py: 120 warnings
tests/multigrid/test_poisson_gmg.py: 16 warnings
tests/multigrid/test_poisson_gmg_extruded.py: 12 warnings
tests/multigrid/test_poisson_gtmg.py: 16 warnings
tests/multigrid/test_two_poisson_gmg.py: 24 warnings
tests/output/test_dumb_checkpoint.py: 14 warnings
tests/output/test_function_plotter.py: 12 warnings
tests/output/test_hdf5file_checkpoint.py: 26 warnings
tests/output/test_io_function.py: 8 warnings
tests/output/test_io_mesh.py: 6 warnings
tests/output/test_plotting.py: 17896 warnings
tests/output/test_pvd_output.py: 180 warnings
tests/regression/test_2dcohomology.py: 56 warnings
tests/regression/test_adjoint_operators.py: 287 warnings
tests/regression/test_adv_diff.py: 36 warnings
tests/regression/test_adv_diff_nonsplit.py: 36 warnings
tests/regression/test_assemble.py: 108 warnings
tests/regression/test_assemble_baseform.py: 306 warnings
tests/regression/test_auxiliary_dm.py: 2 warnings
tests/regression/test_aw.py: 4 warnings
tests/regression/test_bcs.py: 24 warnings
tests/regression/test_bessel_functions.py: 12 warnings
tests/regression/test_bubble.py: 2 warnings
tests/regression/test_cellcoordinate.py: 2 warnings
tests/regression/test_cellorigin.py: 4 warnings
tests/regression/test_cellvolume.py: 1 warning
tests/regression/test_coarse_nullspace.py: 2 warnings
tests/regression/test_coefficient_derivatives.py: 2 warnings
tests/regression/test_constant.py: 2 warnings
tests/regression/test_coordinatederivative.py: 8 warnings
tests/regression/test_dg_advection.py: 12 warnings
tests/regression/test_element_mapping.py: 2 warnings
tests/regression/test_facet_normal.py: 16 warnings
tests/regression/test_facet_orientation.py: 30 warnings
tests/regression/test_facet_split.py: 16 warnings
tests/regression/test_facets.py: 32 warnings
tests/regression/test_fdm.py: 80 warnings
tests/regression/test_fieldsplit_breadcrumbs.py: 2 warnings
tests/regression/test_fieldsplit_fieldsplit_aux_multigrid.py: 10 warnings
tests/regression/test_fieldsplit_split_reorder_bcs.py: 24 warnings
tests/regression/test_fml.py: 4 warnings
tests/regression/test_function.py: 22 warnings
tests/regression/test_helmholtz.py: 52 warnings
tests/regression/test_helmholtz_bernstein.py: 24 warnings
tests/regression/test_helmholtz_mixed.py: 48 warnings
tests/regression/test_helmholtz_nonlinear_diffusion.py: 24 warnings
tests/regression/test_helmholtz_sphere.py: 168 warnings
tests/regression/test_helmholtz_zany.py: 18 warnings
tests/regression/test_hypre_ads.py: 6 warnings
tests/regression/test_hypre_ams.py: 8 warnings
tests/regression/test_identity.py: 32 warnings
tests/regression/test_interior_facets.py: 4 warnings
tests/regression/test_interpolate.py: 24 warnings
tests/regression/test_interpolate_cross_mesh.py: 1209 warnings
tests/regression/test_interpolate_zany.py: 54 warnings
tests/regression/test_interpolation_manual.py: 46 warnings
tests/regression/test_l2pullbacks.py: 150 warnings
tests/regression/test_line_smoother_periodic.py: 2 warnings
tests/regression/test_linear_solver_change_bc.py: 4 warnings
tests/regression/test_locate_cell.py: 4 warnings
tests/regression/test_manifolds.py: 20 warnings
tests/regression/test_manual_quadrature.py: 2 warnings
tests/regression/test_mark_entities.py: 4 warnings
tests/regression/test_mat_type_dense.py: 12 warnings
tests/regression/test_matrix_free.py: 16 warnings
tests/regression/test_mesh_generation.py: 104 warnings
tests/regression/test_mixed_interior_facets.py: 16 warnings
tests/regression/test_mtw.py: 4 warnings
tests/regression/test_nonlinear_helmholtz.py: 24 warnings
tests/regression/test_nonlinear_stokes_hdiv.py: 2 warnings
tests/regression/test_nullspace.py: 34 warnings
tests/regression/test_octahedral_hemisphere.py: 108 warnings
tests/regression/test_p1pc.py: 12 warnings
tests/regression/test_par_loops.py: 4 warnings
tests/regression/test_patch_pc.py: 12 warnings
tests/regression/test_periodic_2d.py: 40 warnings
tests/regression/test_periodic_interval_advection.py: 64 warnings
tests/regression/test_periodic_rectangle_advection.py: 192 warnings
tests/regression/test_piola_mixed_fn.py: 2 warnings
tests/regression/test_planesmoother.py: 8 warnings
tests/regression/test_point_eval_api.py: 57 warnings
tests/regression/test_point_eval_cells.py: 48 warnings
tests/regression/test_point_eval_fs.py: 108 warnings
tests/regression/test_poisson_mixed_no_bcs.py: 36 warnings
tests/regression/test_poisson_mixed_strong_bcs.py: 8 warnings
tests/regression/test_poisson_sphere.py: 90 warnings
tests/regression/test_poisson_strong_bcs.py: 96 warnings
tests/regression/test_poisson_strong_bcs_nitsche.py: 8 warnings
tests/regression/test_project_interp_KMV.py: 48 warnings
tests/regression/test_projection.py: 252 warnings
tests/regression/test_real_space.py: 4 warnings
tests/regression/test_split.py: 2 warnings
tests/regression/test_star_pc.py: 2 warnings
tests/regression/test_steady_advection_2D.py: 16 warnings
tests/regression/test_steady_advection_3D.py: 4 warnings
tests/regression/test_stokes_mini.py: 59 warnings
tests/regression/test_subdomain.py: 9 warnings
tests/regression/test_subdomain_integrals.py: 55 warnings
tests/regression/test_taylor.py: 12 warnings
tests/regression/test_tensor_algebra.py: 69 warnings
tests/regression/test_trace_galerkin_projection.py: 236 warnings
tests/regression/test_ufl.py: 6 warnings
tests/regression/test_upwind_flux.py: 66 warnings
tests/regression/test_vector.py: 38 warnings
tests/regression/test_vector_laplace_on_quadrilaterals.py: 256 warnings
tests/regression/test_vertex_based_limiter.py: 80 warnings
tests/regression/test_vfs_component_bcs.py: 229 warnings
tests/regression/test_zero_forms.py: 430 warnings
tests/regression/test_zero_integrand.py: 13 warnings
tests/slate/test_assemble_tensors.py: 588 warnings
tests/slate/test_darcy_hybridized_mixed.py: 137 warnings
tests/slate/test_facet_tensors.py: 38 warnings
tests/slate/test_facet_tensors_extr.py: 88 warnings
tests/slate/test_linear_algebra.py: 19 warnings
tests/slate/test_matrix_free_hybridization.py: 14 warnings
tests/slate/test_optimise.py: 258 warnings
tests/slate/test_orientations.py: 66 warnings
tests/slate/test_scalar_tensors.py: 108 warnings
tests/slate/test_scalar_tensors_extr.py: 2 warnings
tests/slate/test_slac.py: 156 warnings
tests/slate/test_slate_hybridization.py: 452 warnings
tests/slate/test_slate_hybridization_extr.py: 56 warnings
tests/slate/test_slate_hybridized_mixed_bcs.py: 152 warnings
tests/slate/test_slate_infrastructure.py: 266 warnings
tests/slate/test_slate_mixed_direct.py: 27 warnings
tests/slate/test_subdomains.py: 165 warnings
tests/slate/test_unaryop_precedence.py: 3 warnings
tests/slate/test_variational_prb.py: 488 warnings
tests/slate/test_zany_element_tensors.py: 42 warnings
tests/supermesh/test_assemble_mixed_mass_matrix.py: 40 warnings
tests/supermesh/test_galerkin_projection.py: 34 warnings
tests/supermesh/test_nonnested_project.py: 25 warnings
tests/supermesh/test_periodic.py: 250 warnings
tests/unit/test_fml/test_replace_perp.py: 4 warnings
tests/vertexonly/test_interpolation_from_parent.py: 1308 warnings
tests/vertexonly/test_point_eval_immersed_manifold.py: 6 warnings
tests/vertexonly/test_poisson_inverse_conductivity.py: 2445 warnings
tests/vertexonly/test_swarm.py: 72 warnings
tests/vertexonly/test_vertex_only_fs.py: 2796 warnings
tests/vertexonly/test_vertex_only_manual.py: 17 warnings
tests/vertexonly/test_vertex_only_mesh_generation.py: 164 warnings
  /home/adamh/firedrake/src/ufl/ufl/core/expr.py:275: DeprecationWarning: Expr.ufl_domain() is deprecated, please use extract_unique_domain(expr) instead.
    warnings.warn("Expr.ufl_domain() is deprecated, please "

tests/extrusion/test_fs_abbreviations.py: 8 warnings
tests/extrusion/test_interior_facets_extr.py: 2 warnings
tests/extrusion/test_interval.py: 2 warnings
tests/extrusion/test_mixed_periodic.py: 1 warning
tests/extrusion/test_point_eval_fs_extrusion.py: 1 warning
tests/extrusion/test_steady_advection_2D_extr.py: 1 warning
tests/slate/test_scalar_tensors_extr.py: 1 warning
tests/slate/test_slate_hybridized_mixed_bcs.py: 1 warning
  /home/adamh/firedrake/src/ufl/ufl/finiteelement/elementlist.py:440: UserWarning: Discontinuous Lagrange element requested on interval * interval, creating DQ element.
    warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname())

tests/extrusion/test_fs_abbreviations.py: 8 warnings
tests/extrusion/test_interior_facets_extr.py: 1 warning
tests/extrusion/test_mixed_periodic.py: 2 warnings
tests/extrusion/test_point_eval_fs_extrusion.py: 1 warning
tests/extrusion/test_real_tensorproduct.py: 1 warning
tests/extrusion/test_steady_advection_3D_extr.py: 2 warnings
tests/regression/test_fs_caching.py: 1 warning
tests/regression/test_interpolate_cross_mesh.py: 2 warnings
tests/slate/test_facet_tensors_extr.py: 9 warnings
tests/slate/test_subdomains.py: 5 warnings
tests/vertexonly/test_interpolation_from_parent.py: 6 warnings
  /home/adamh/firedrake/src/ufl/ufl/finiteelement/elementlist.py:440: UserWarning: Discontinuous Lagrange element requested on triangle * interval, creating DQ element.
    warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname())

tests/extrusion/test_meshes.py: 6 warnings
tests/extrusion/test_zero_forms_extrusion.py: 1 warning
tests/regression/test_adjoint_operators.py: 28 warnings
tests/regression/test_circle_manifold.py: 9 warnings
tests/regression/test_constant.py: 4 warnings
tests/regression/test_multiple_domains.py: 4 warnings
tests/regression/test_scaled_mass.py: 198 warnings
tests/regression/test_subdomain_integrals.py: 1 warning
tests/regression/test_zero_forms.py: 398 warnings
tests/slate/test_scalar_tensors.py: 72 warnings
tests/slate/test_scalar_tensors_extr.py: 1 warning
tests/vertexonly/test_interpolation_from_parent.py: 117 warnings
tests/vertexonly/test_poisson_inverse_conductivity.py: 9 warnings
tests/vertexonly/test_vertex_only_fs.py: 47 warnings
  /home/adamh/firedrake/src/firedrake/firedrake/constant.py:63: FutureWarning: Giving Constants a domain is no longer supported. Instead please create a Function in the Real space.
    warnings.warn(

tests/extrusion/test_meshes.py: 1 warning
tests/extrusion/test_real_tensorproduct.py: 1 warning
tests/output/test_io_mesh.py: 1 warning
tests/output/test_pvd_output.py: 2 warnings
tests/regression/test_adjoint_operators.py: 1 warning
tests/regression/test_facet_orientation.py: 3 warnings
tests/regression/test_helmholtz_sphere.py: 2 warnings
tests/regression/test_interior_facets.py: 2 warnings
tests/regression/test_interpolate_cross_mesh.py: 6 warnings
tests/regression/test_linesmoother.py: 1 warning
tests/regression/test_periodic_rectangle_advection.py: 8 warnings
tests/regression/test_point_eval_fs.py: 2 warnings
tests/regression/test_poisson_sphere.py: 6 warnings
tests/regression/test_steady_advection_2D.py: 1 warning
tests/regression/test_vertex_based_limiter.py: 3 warnings
tests/slate/test_assemble_tensors.py: 11 warnings
tests/slate/test_facet_tensors.py: 3 warnings
tests/slate/test_linear_algebra.py: 6 warnings
tests/slate/test_slac.py: 4 warnings
tests/slate/test_slate_hybridization.py: 1 warning
tests/slate/test_slate_hybridized_mixed_bcs.py: 1 warning
tests/slate/test_slate_infrastructure.py: 8 warnings
tests/slate/test_subdomains.py: 5 warnings
tests/vertexonly/test_interpolation_from_parent.py: 3 warnings
  /home/adamh/firedrake/src/ufl/ufl/finiteelement/elementlist.py:440: UserWarning: Discontinuous Lagrange element requested on quadrilateral, creating DQ element.
    warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname())

tests/extrusion/test_mixed_periodic.py: 1 warning
tests/extrusion/test_point_eval_fs_extrusion.py: 2 warnings
tests/extrusion/test_real_tensorproduct.py: 1 warning
tests/extrusion/test_steady_advection_3D_extr.py: 1 warning
tests/slate/test_facet_tensors_extr.py: 9 warnings
tests/slate/test_subdomains.py: 5 warnings
  /home/adamh/firedrake/src/ufl/ufl/finiteelement/elementlist.py:440: UserWarning: Discontinuous Lagrange element requested on quadrilateral * interval, creating DQ element.
    warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname())

tests/extrusion/test_point_eval_cells_extrusion.py::test_2d[False]
tests/regression/test_stokes_mini.py::test_stokes_mini[aij]
tests/vertexonly/test_interpolation_from_parent.py::test_scalar_spatialcoordinate_interpolation[immersedsphere-mesh-100-coords]
  /home/adamh/firedrake/src/loopy/loopy/target/c/compyte/dtypes.py:184: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`.  (Deprecated NumPy 1.24)
    reg.get_or_register_dtype("bool", np.bool8)

tests/multigrid/test_opencascade_poisson.py::test_opencascade_poisson[stepdata0-1]
tests/multigrid/test_opencascade_poisson.py::test_opencascade_poisson[stepdata1-1]
tests/multigrid/test_opencascade_poisson.py::test_opencascade_poisson[stepdata1-2]
tests/multigrid/test_opencascade_poisson.py::test_opencascade_poisson[stepdata0-2]
tests/multigrid/test_opencascade_poisson.py::test_opencascade_poisson[stepdata2-2]
tests/multigrid/test_opencascade_poisson.py::test_opencascade_poisson[stepdata2-1]
  /home/adamh/firedrake/src/firedrake/tests/multigrid/test_opencascade_poisson.py:24: PytestRemovedIn8Warning: pytest.skip(msg=...) is now deprecated, use pytest.skip(reason=...) instead
    pytest.skip(msg="OpenCascade unavailable, skipping test")

tests/output/test_dumb_checkpoint.py: 26 warnings
  /home/adamh/firedrake/src/firedrake/firedrake/checkpointing.py:98: DeprecationWarning: DumbCheckpoint class will soon be deprecated; use CheckpointFile class instead.
    warnings.warn("DumbCheckpoint class will soon be deprecated; use CheckpointFile class instead.",

tests/output/test_hdf5file_checkpoint.py: 24 warnings
  /home/adamh/firedrake/src/firedrake/firedrake/checkpointing.py:376: DeprecationWarning: HDF5File class will soon be deprecated; use CheckpointFile class instead.
    warnings.warn("HDF5File class will soon be deprecated; use CheckpointFile class instead.",

tests/output/test_plotting.py::test_triplot
tests/output/test_plotting.py::test_triplot_quad_mesh
tests/output/test_plotting.py::test_triplot_3d
tests/output/test_plotting.py::test_triplot_3d
  /home/adamh/firedrake/src/firedrake/firedrake/plot.py:159: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.
    cmap = matplotlib.cm.get_cmap("Dark2")

tests/output/test_pvd_output.py::test_can_save_coordinates[interval]
  /home/adamh/firedrake/lib/python3.11/site-packages/matplotlib/animation.py:892: UserWarning: Animation was deleted without rendering anything. This is most likely not intended. To prevent deletion, assign the Animation to a variable, e.g. `anim`, that exists until you output the Animation using `plt.show()` or `anim.save()`.
    warnings.warn(

tests/regression/test_adjoint_operators.py::test_interpolate_hessian_linear_expr
tests/regression/test_adjoint_operators.py::test_interpolate_hessian_nonlinear_expr
tests/regression/test_adjoint_operators.py::test_interpolate_hessian_nonlinear_expr_multi
tests/regression/test_adjoint_operators.py::test_interpolate_hessian_nonlinear_expr_multi_cross_mesh
  /home/adamh/firedrake/src/firedrake/firedrake/adjoint_utils/function.py:112: UserWarning: Could not find overloaded class of type '<class 'int'>'.
    other = create_overloaded_object(other)

tests/regression/test_moore_spence.py::test_moore_spence
  /home/adamh/firedrake/src/firedrake/tests/regression/test_moore_spence.py:11: PytestRemovedIn8Warning: pytest.skip(msg=...) is now deprecated, use pytest.skip(reason=...) instead
    pytest.skip(msg="SLEPc unavailable, skipping eigenvalue test")

tests/regression/test_project_interp_KMV.py: 16 warnings
  /home/adamh/firedrake/src/ufl/ufl/utils/sorting.py:84: UserWarning: Applying str() to a metadata value of type QuadratureRule, don't know if this is safe.
    warnings.warn(f"Applying str() to a metadata value of type {type(value).__name__}, "

tests/regression/test_slepc.py::test_laplace_physical_ev
  /home/adamh/firedrake/src/firedrake/tests/regression/test_slepc.py:15: PytestRemovedIn8Warning: pytest.skip(msg=...) is now deprecated, use pytest.skip(reason=...) instead
    pytest.skip(msg="SLEPc unavailable, skipping eigenvalue test")

tests/vertexonly/test_poisson_inverse_conductivity.py::test_poisson_inverse_conductivity[per_cell]
  /home/adamh/firedrake/lib/python3.11/site-packages/scipy/optimize/_optimize.py:2133: OptimizeWarning: Warning: Desired error not necessarily achieved due to precision loss.
    return terminate(2, msg)

tests/vertexonly/test_vertex_only_manual.py::test_vom_manual_points_outside_domain
  /home/adamh/firedrake/src/firedrake/firedrake/mesh.py:2852: UserWarning: 1 vertices are outside the mesh and have been removed from the VertexOnlyMesh.
    warn(str(error))

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================= short test summary info ==============================================
FAILED tests/test_0init.py::test_pyop2_not_initialised - assert not True
FAILED tests/demos/test_demos_run.py::test_demo_runs[qgbasinmodes.py.rst] - subprocess.CalledProcessError: Command '['/home/adamh/firedrake/bin/python', '/tmp/pytest-of-adamh/pytest-0/tes...
FAILED tests/regression/test_eigensolver.py::test_evals_1d[5-1-1e-13] - ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)
FAILED tests/regression/test_eigensolver.py::test_evals_1d[10-1-1e-13] - ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)
FAILED tests/regression/test_eigensolver.py::test_evals_1d[20-1-1e-13] - ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)
FAILED tests/regression/test_eigensolver.py::test_evals_1d[30-1-1e-13] - ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)
FAILED tests/regression/test_eigensolver.py::test_evals_2d - ImportError: Unable to import SLEPc, eigenvalue computation not possible (try firedrake-update --slepc)
============== 7 failed, 6494 passed, 582 skipped, 200 xfailed, 36955 warnings in 6407.95s (1:46:47) ===============
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WARNING! could be spelling mistake, etc!
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Option left: name:-firedrake_644_pmg_mg_coarse_pc_mg_levels value: 1 source: code
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Option left: name:-firedrake_646_pmg_mg_coarse_pc_mg_levels value: 1 source: code
Option left: name:-firedrake_647_pfas_fas_coarse_pc_mg_levels value: 1 source: code
Option left: name:-firedrake_647_pfas_fas_coarse_snes_fas_levels value: 1 source: code
Option left: name:-firedrake_647_pfas_fas_levels_1_pmg_mg_coarse_pc_mg_levels value: 3 source: code
Option left: name:-firedrake_647_pfas_fas_levels_2_pmg_mg_coarse_pc_mg_levels value: 3 source: code
Option left: name:-firedrake_648_pfas_fas_coarse_pc_mg_levels value: 1 source: code
Option left: name:-firedrake_648_pfas_fas_coarse_snes_fas_levels value: 1 source: code
Option left: name:-firedrake_648_pfas_fas_levels_1_pmg_mg_coarse_pc_mg_levels value: 3 source: code
Option left: name:-firedrake_648_pfas_fas_levels_2_pmg_mg_coarse_pc_mg_levels value: 3 source: code
Option left: name:-firedrake_649_pmg_mg_coarse_pc_mg_levels value: 1 source: code
make: *** [Makefile:91: test] Error 1

I'm also interested in using Gusto. I received the following output when running make test in the firedrake virtual environment. Is there anything here I need to worry about?

================================================= warnings summary =================================================
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
../ufl/ufl/core/ufl_type.py:56
  /home/adamh/firedrake/src/ufl/ufl/core/ufl_type.py:56: DeprecationWarning: attach_operators_from_hash_data deprecated, please use UFLObject instead.
    warnings.warn("attach_operators_from_hash_data deprecated, please use UFLObject instead.", DeprecationWarning)

../fiat/FIAT/__init__.py:5
  /home/adamh/firedrake/src/fiat/FIAT/__init__.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    import pkg_resources

unit-tests/test_distances.py: 4 warnings
unit-tests/test_domain.py: 56 warnings
unit-tests/test_h1_spaces.py: 356 warnings
unit-tests/test_meshes.py: 18 warnings
unit-tests/test_rotated_coords.py: 12 warnings
unit-tests/test_rotated_vectors.py: 12 warnings
unit-tests/test_spherical_coord_transforms.py: 12 warnings
unit-tests/test_spherical_rotations.py: 8 warnings
unit-tests/test_spherical_vector_transforms.py: 32 warnings
unit-tests/fml_tests/test_replace_perp.py: 31 warnings
unit-tests/kernel_tests/test_limit_midpoints_kernel.py: 12 warnings
unit-tests/recovery_tests/test_average_kernel.py: 12 warnings
unit-tests/recovery_tests/test_extruded_boundary_kernel.py: 8 warnings
unit-tests/recovery_tests/test_gauss_elim_kernel.py: 4 warnings
unit-tests/recovery_tests/test_hcurl_boundary_kernel.py: 12 warnings
unit-tests/recovery_tests/test_recovery_1d.py: 96 warnings
unit-tests/recovery_tests/test_recovery_2d_cart.py: 948 warnings
unit-tests/recovery_tests/test_recovery_2d_vert_slice.py: 328 warnings
unit-tests/recovery_tests/test_recovery_3d_cart.py: 1512 warnings
unit-tests/recovery_tests/test_recovery_3d_spherical.py: 76 warnings
unit-tests/recovery_tests/test_reversible_recovery.py: 413 warnings
unit-tests/recovery_tests/test_weighting_kernel.py: 4 warnings
integration-tests/test_fml.py: 56 warnings
integration-tests/balance/test_compressible_balance.py: 1493 warnings
integration-tests/balance/test_saturated_balance.py: 7566 warnings
integration-tests/balance/test_unsaturated_balance.py: 1834 warnings
integration-tests/diffusion/test_diffusion.py: 556 warnings
integration-tests/equations/test_advection_diffusion.py: 264 warnings
integration-tests/equations/test_coupled_transport.py: 3710 warnings
integration-tests/equations/test_dry_compressible.py: 99 warnings
integration-tests/equations/test_forced_advection.py: 5599 warnings
integration-tests/equations/test_incompressible.py: 254 warnings
integration-tests/equations/test_linear_sw_wave.py: 407 warnings
integration-tests/equations/test_moist_compressible.py: 131 warnings
integration-tests/equations/test_sw_fplane.py: 321 warnings
integration-tests/equations/test_sw_linear_triangle.py: 553 warnings
integration-tests/equations/test_sw_triangle.py: 6125 warnings
integration-tests/equations/test_thermal_sw.py: 367 warnings
integration-tests/model/test_checkpointing.py: 1647 warnings
integration-tests/model/test_nc_outputting.py: 667 warnings
integration-tests/model/test_passive_tracer.py: 638 warnings
integration-tests/model/test_prescribed_transport.py: 424 warnings
integration-tests/model/test_time_discretisation.py: 3959 warnings
integration-tests/physics/test_boundary_layer_mixing.py: 795 warnings
integration-tests/physics/test_instant_rain.py: 196 warnings
integration-tests/physics/test_precipitation.py: 736 warnings
integration-tests/physics/test_saturation_adjustment.py: 231 warnings
integration-tests/physics/test_source_sink.py: 230 warnings
integration-tests/physics/test_static_adjustment.py: 194 warnings
integration-tests/physics/test_suppress_vertical_wind.py: 76 warnings
integration-tests/physics/test_surface_fluxes.py: 554 warnings
integration-tests/physics/test_sw_saturation_adjustment.py: 385 warnings
integration-tests/physics/test_wind_drag.py: 221 warnings
integration-tests/transport/test_dg_transport.py: 2792 warnings
integration-tests/transport/test_embedded_dg_advection.py: 4568 warnings
integration-tests/transport/test_limiters.py: 5385 warnings
integration-tests/transport/test_recovered_transport.py: 791 warnings
integration-tests/transport/test_subcycling.py: 832 warnings
integration-tests/transport/test_supg_transport.py: 6776 warnings
integration-tests/transport/test_vector_recovered_space.py: 494 warnings
  /home/adamh/firedrake/src/ufl/ufl/core/expr.py:275: DeprecationWarning: Expr.ufl_domain() is deprecated, please use extract_unique_domain(expr) instead.
    warnings.warn("Expr.ufl_domain() is deprecated, please "

unit-tests/test_distances.py::test_great_arc_angle[firedrake]
unit-tests/test_distances.py::test_great_arc_angle[firedrake]
  /home/adamh/firedrake/src/loopy/loopy/target/c/compyte/dtypes.py:184: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`.  (Deprecated NumPy 1.24)
    reg.get_or_register_dtype("bool", np.bool8)

unit-tests/test_function_spaces.py: 10 warnings
unit-tests/test_h1_spaces.py: 4 warnings
unit-tests/recovery_tests/test_average_kernel.py: 1 warning
unit-tests/recovery_tests/test_gauss_elim_kernel.py: 1 warning
unit-tests/recovery_tests/test_recovery_2d_cart.py: 13 warnings
unit-tests/recovery_tests/test_recovery_3d_cart.py: 17 warnings
unit-tests/recovery_tests/test_reversible_recovery.py: 6 warnings
integration-tests/equations/test_sw_fplane.py: 2 warnings
integration-tests/model/test_nc_outputting.py: 5 warnings
integration-tests/physics/test_source_sink.py: 4 warnings
  /home/adamh/firedrake/src/ufl/ufl/finiteelement/elementlist.py:440: UserWarning: Discontinuous Lagrange element requested on quadrilateral, creating DQ element.
    warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname())

unit-tests/kernel_tests/test_limit_midpoints_kernel.py: 3 warnings
unit-tests/recovery_tests/test_extruded_boundary_kernel.py: 2 warnings
unit-tests/recovery_tests/test_hcurl_boundary_kernel.py: 3 warnings
unit-tests/recovery_tests/test_recovery_2d_vert_slice.py: 2 warnings
unit-tests/recovery_tests/test_recovery_3d_cart.py: 10 warnings
unit-tests/recovery_tests/test_recovery_3d_spherical.py: 4 warnings
integration-tests/balance/test_saturated_balance.py: 5 warnings
integration-tests/balance/test_unsaturated_balance.py: 4 warnings
integration-tests/physics/test_boundary_layer_mixing.py: 3 warnings
integration-tests/physics/test_surface_fluxes.py: 2 warnings
integration-tests/transport/test_limiters.py: 2 warnings
  /home/adamh/firedrake/src/firedrake/firedrake/parloops.py:263: FutureWarning: is_loopy_kernel does not need to be specified
    warnings.warn(

integration-tests/diffusion/test_diffusion.py::test_vector_diffusion[True]
integration-tests/physics/test_boundary_layer_mixing.py::test_boundary_layer_mixing[u-True-True]
integration-tests/transport/test_dg_transport.py::test_dg_transport_vector[advective-slice]
integration-tests/transport/test_dg_transport.py::test_dg_transport_vector[continuity-slice]
  /home/adamh/firedrake/src/ufl/ufl/finiteelement/elementlist.py:440: UserWarning: Discontinuous Lagrange element requested on interval * interval, creating DQ element.
    warnings.warn("Discontinuous Lagrange element requested on %s, creating DQ element." % cell.cellname())

integration-tests/model/test_checkpointing.py: 14 warnings
  /home/adamh/firedrake/src/firedrake/firedrake/checkpointing.py:98: DeprecationWarning: DumbCheckpoint class will soon be deprecated; use CheckpointFile class instead.
    warnings.warn("DumbCheckpoint class will soon be deprecated; use CheckpointFile class instead.",

integration-tests/physics/test_sw_saturation_adjustment.py::test_cond_evap[evaporation]
integration-tests/physics/test_sw_saturation_adjustment.py::test_cond_evap[condensation]
  /home/adamh/firedrake/src/firedrake/firedrake/function.py:326: FutureWarning: The .split() method is deprecated, please use the .subfunctions property instead
    warnings.warn("The .split() method is deprecated, please use the .subfunctions property instead", category=FutureWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== 362 passed, 1 xfailed, 66026 warnings in 8573.21s (2:22:53) ============================

Thank you for all your support so far!

JDBetteridge · 2023-10-27T10:33:39Z

Most of these failures are a result of this issue #3175 and I don't think you need to worry. I think things are working!

I will close this issue, but feel free to open another if you have more problems down the line 🙂

adominious added the question label Oct 24, 2023

JDBetteridge self-assigned this Oct 24, 2023

JDBetteridge mentioned this issue Oct 24, 2023

INSTALL: #3058

Closed

JDBetteridge closed this as completed Oct 27, 2023

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KeyError: 'honour_petsc_dir' #3185

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