--- Begin Message ---
Package: src:adios4dolfinx
Version: 0.10.0.post0-4
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202606/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:adios4dolfinx, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:142: Building wheel for python3.14 with "build"
module
I: pybuild base:385: python3.14 -m build --skip-dependency-check --no-isolation
--wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_adios4dolfinx
* Building wheel...
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82:
SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
[... snipped ...]
def write_meshtags(
filename: typing.Union[Path, str],
mesh: dolfinx.mesh.Mesh,
meshtags: dolfinx.mesh.MeshTags,
engine: str = "BP4",
meshtag_name: typing.Optional[str] = None,
):
"""
Write meshtags associated with input mesh to file.
.. note::
For this checkpoint to work, the mesh must be written to file
using :func:`write_mesh` before calling this function.
Args:
filename: Path to save meshtags (with file-extension)
mesh: The mesh associated with the meshtags
meshtags: The meshtags to write to file
engine: Adios2 Engine
meshtag_name: Name of the meshtag. If None, the meshtag name is
used.
"""
tag_entities = meshtags.indices
dim = meshtags.dim
num_tag_entities_local = mesh.topology.index_map(dim).size_local
local_tag_entities = tag_entities[tag_entities < num_tag_entities_local]
local_values = meshtags.values[: len(local_tag_entities)]
num_saved_tag_entities = len(local_tag_entities)
local_start = mesh.comm.exscan(num_saved_tag_entities, op=MPI.SUM)
local_start = local_start if mesh.comm.rank != 0 else 0
global_num_tag_entities = mesh.comm.allreduce(num_saved_tag_entities,
op=MPI.SUM)
dof_layout = mesh.geometry.cmap.create_dof_layout()
num_dofs_per_entity = dof_layout.num_entity_closure_dofs(dim)
entities_to_geometry = dolfinx.cpp.mesh.entities_to_geometry(
mesh._cpp_object, dim, local_tag_entities, False
)
indices =
mesh.geometry.index_map().local_to_global(entities_to_geometry.reshape(-1))
name = meshtag_name or meshtags.name
adios = adios2.ADIOS(mesh.comm)
with ADIOSFile(
adios=adios,
filename=filename,
mode=adios2.Mode.Append,
engine=engine,
io_name="MeshTagWriter",
) as adios_file:
adios_file.file.BeginStep()
# Write meshtag topology
topology_var = adios_file.io.DefineVariable(
name + "_topology",
indices,
shape=[global_num_tag_entities, num_dofs_per_entity],
start=[local_start, 0],
count=[num_saved_tag_entities, num_dofs_per_entity],
)
adios_file.file.Put(topology_var, indices, adios2.Mode.Sync)
# Write meshtag topology
> values_var = adios_file.io.DefineVariable(
name + "_values",
local_values,
shape=[global_num_tag_entities],
start=[local_start],
count=[num_saved_tag_entities],
)
E ValueError: ERROR: variable entity_0_values can't be defined with
an object with type <class 'numpy.ndarray'>, in call to DefineVariable
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_adios4dolfinx/build/adios4dolfinx/checkpointing.py:243:
ValueError
__ test_checkpointing_meshtags_3D[mesh_3D7-read_comm1-GhostMode.shared_facet] __
mesh_3D = <dolfinx.mesh.Mesh object at 0x7feae908a970>
read_comm = <mpi4py.MPI.Intracomm object at 0x7feb1db075a0>
read_mode = GhostMode.shared_facet
tmp_path =
PosixPath('/tmp/pytest-of-sbuild/pytest-1/test_checkpointing_meshtags_3D31')
@pytest.mark.parametrize("read_mode", read_modes)
@pytest.mark.parametrize("read_comm", [MPI.COMM_SELF, MPI.COMM_WORLD])
def test_checkpointing_meshtags_3D(mesh_3D, read_comm, read_mode, tmp_path):
mesh = mesh_3D
hash =
f"{mesh.comm.size}_{mesh.topology.cell_name()}_{mesh.geometry.x.dtype}"
fname = MPI.COMM_WORLD.bcast(tmp_path, root=0)
filename = fname / f"meshtags_1D_{hash}.bp"
if mesh.comm.size != 1:
adios4dolfinx.write_mesh(filename, mesh, engine="BP4")
else:
if MPI.COMM_WORLD.rank == root:
adios4dolfinx.write_mesh(filename, mesh, engine="BP4")
org_maps = []
for dim in range(mesh.topology.dim + 1):
mesh.topology.create_connectivity(dim, mesh.topology.dim)
e_map = mesh.topology.index_map(dim)
num_entities_local = e_map.size_local
entities = np.arange(num_entities_local, dtype=np.int32)
ft = dolfinx.mesh.meshtags(mesh, dim, entities,
e_map.local_range[0] + entities)
ft.name = f"entity_{dim}"
if mesh.comm.size != 1:
adios4dolfinx.write_meshtags(filename, mesh, ft, engine="BP4")
org_map = generate_reference_map(mesh, ft, mesh.comm, root)
org_maps.append(org_map)
else:
if MPI.COMM_WORLD.rank == root:
> adios4dolfinx.write_meshtags(filename, mesh, ft,
> engine="BP4")
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_adios4dolfinx/build/tests/test_meshtags.py:254:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename =
PosixPath('/tmp/pytest-of-sbuild/pytest-1/test_checkpointing_meshtags_3D31/meshtags_1D_1_hexahedron_float32.bp')
mesh = <dolfinx.mesh.Mesh object at 0x7feae908a970>
meshtags = <dolfinx.mesh.MeshTags object at 0x7feae9f095e0>, engine = 'BP4'
meshtag_name = None
def write_meshtags(
filename: typing.Union[Path, str],
mesh: dolfinx.mesh.Mesh,
meshtags: dolfinx.mesh.MeshTags,
engine: str = "BP4",
meshtag_name: typing.Optional[str] = None,
):
"""
Write meshtags associated with input mesh to file.
.. note::
For this checkpoint to work, the mesh must be written to file
using :func:`write_mesh` before calling this function.
Args:
filename: Path to save meshtags (with file-extension)
mesh: The mesh associated with the meshtags
meshtags: The meshtags to write to file
engine: Adios2 Engine
meshtag_name: Name of the meshtag. If None, the meshtag name is
used.
"""
tag_entities = meshtags.indices
dim = meshtags.dim
num_tag_entities_local = mesh.topology.index_map(dim).size_local
local_tag_entities = tag_entities[tag_entities < num_tag_entities_local]
local_values = meshtags.values[: len(local_tag_entities)]
num_saved_tag_entities = len(local_tag_entities)
local_start = mesh.comm.exscan(num_saved_tag_entities, op=MPI.SUM)
local_start = local_start if mesh.comm.rank != 0 else 0
global_num_tag_entities = mesh.comm.allreduce(num_saved_tag_entities,
op=MPI.SUM)
dof_layout = mesh.geometry.cmap.create_dof_layout()
num_dofs_per_entity = dof_layout.num_entity_closure_dofs(dim)
entities_to_geometry = dolfinx.cpp.mesh.entities_to_geometry(
mesh._cpp_object, dim, local_tag_entities, False
)
indices =
mesh.geometry.index_map().local_to_global(entities_to_geometry.reshape(-1))
name = meshtag_name or meshtags.name
adios = adios2.ADIOS(mesh.comm)
with ADIOSFile(
adios=adios,
filename=filename,
mode=adios2.Mode.Append,
engine=engine,
io_name="MeshTagWriter",
) as adios_file:
adios_file.file.BeginStep()
# Write meshtag topology
topology_var = adios_file.io.DefineVariable(
name + "_topology",
indices,
shape=[global_num_tag_entities, num_dofs_per_entity],
start=[local_start, 0],
count=[num_saved_tag_entities, num_dofs_per_entity],
)
adios_file.file.Put(topology_var, indices, adios2.Mode.Sync)
# Write meshtag topology
> values_var = adios_file.io.DefineVariable(
name + "_values",
local_values,
shape=[global_num_tag_entities],
start=[local_start],
count=[num_saved_tag_entities],
)
E ValueError: ERROR: variable entity_0_values can't be defined with
an object with type <class 'numpy.ndarray'>, in call to DefineVariable
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_adios4dolfinx/build/adios4dolfinx/checkpointing.py:243:
ValueError
=========================== short test summary info ============================
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D0-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D0-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D0-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D0-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D1-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D1-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D1-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D1-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D2-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D2-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D2-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D2-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D3-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D3-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D3-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_1D[mesh_1D3-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D0-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D0-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D0-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D0-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D1-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D1-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D1-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D1-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D2-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D2-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D2-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D2-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D3-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D3-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D3-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D3-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D4-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D4-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D4-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D4-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D5-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D5-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D5-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D5-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D6-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D6-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D6-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D6-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D7-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D7-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D7-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_2D[mesh_2D7-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D0-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D0-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D0-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D0-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D1-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D1-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D1-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D1-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D2-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D2-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D2-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D2-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D3-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D3-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D3-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D3-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D4-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D4-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D4-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D4-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D5-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D5-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D5-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D5-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D6-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D6-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D6-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D6-read_comm1-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D7-read_comm0-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D7-read_comm0-GhostMode.shared_facet]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D7-read_comm1-GhostMode.none]
FAILED
tests/test_meshtags.py::test_checkpointing_meshtags_3D[mesh_3D7-read_comm1-GhostMode.shared_facet]
========== 80 failed, 922 passed, 5 skipped, 180 deselected in 14.40s ==========
E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_adios4dolfinx/build; python3.13 -m
pytest -k "not test_original_checkpoint"
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14
3.13" --parallel=2 returned exit code 13
make: *** [debian/rules:13: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
pgpffqaY6LMV6.pgp
