Restrict adios2 to main until new release (#135) (#141)

* Restrict adios2 to main until new release (#135)

* Restrict adios2 to main until new release due to: ornladios/ADIOS2#4287

* Simplify try except

* Try new adios2 version

* Fix readpos

* Move to default and source installation

* Apply suggestions from code review

* Flattened topo as partition input (#126)

* Flattened topo as partition input

* Bump adios2 version on CI

* Add create connectivity prior to computing midpoints (#123)

* ADd incompatibility check to test for adios2 and numpy (#142)

.github/workflows/test_package.yml

@@ -52,7 +52,7 @@ jobs:
       artifact_name: "legacy_checkpoint_mpich"
 
   test-code:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     needs:
       [create-datasets, create-legacy-datasets, check-formatting, get_image_tag]
     container: ghcr.io/fenics/dolfinx/dolfinx:${{ needs.get_image_tag.outputs.image }}

.github/workflows/test_package_openmpi.yml

@@ -38,7 +38,7 @@ jobs:
 
     strategy:
       matrix:
-        adios2: ["default", "v2.9.2", "v2.10.0"]
+        adios2: ["default", "v2.10.2"]
     steps:
       - uses: actions/checkout@v4
 

.github/workflows/test_redhat.yml

@@ -37,7 +37,7 @@ jobs:
 
     strategy:
       matrix:
-        adios2: ["v2.10.0"]
+        adios2: ["v2.10.2"]
     steps:
       - uses: actions/checkout@v4
 

docs/meshtags.py

@@ -33,6 +33,7 @@
 
     # Compute midpoints of entities
     entities = np.arange(e_map.size_local, dtype=np.int32)
+    mesh.topology.create_connectivity(i, mesh.topology.dim)
     entity_midpoints[i] = dolfinx.mesh.compute_midpoints(mesh, i, entities)
     # Associate each local index with its global index
     values = np.arange(e_map.size_local, dtype=np.int32) + e_map.local_range[0]
@@ -67,6 +68,7 @@ def verify_meshtags(filename: Path):
         meshtags = adios4dolfinx.read_meshtags(filename, read_mesh, meshtag_name=f"meshtags_{i}")
 
         # Compute midpoints for all local entities on process
+        read_mesh.topology.create_connectivity(i, read_mesh.topology.dim)
         midpoints = dolfinx.mesh.compute_midpoints(read_mesh, i, meshtags.indices)
         # Compare locally computed midpoint with reference data
         for global_pos, midpoint in zip(meshtags.values, midpoints):

src/adios4dolfinx/__init__.py

@@ -24,10 +24,7 @@
 
 meta = metadata("adios4dolfinx")
 __version__ = meta["Version"]
-try:
-    __author__ = meta["Author"]
-except KeyError:
-    pass
+__author__ = meta.get("Author", "")
 __license__ = meta["License"]
 __email__ = meta["Author-email"]
 __program_name__ = meta["Name"]

src/adios4dolfinx/checkpointing.py

@@ -564,7 +564,7 @@ def read_mesh_data(
         )
 
         def partitioner(comm: MPI.Intracomm, n, m, topo):
-            assert len(partition_graph.offsets) - 1 == topo.num_nodes
+            assert len(topo[0]) % (len(partition_graph.offsets) - 1) == 0
             return partition_graph
     else:
         partitioner = dolfinx.cpp.mesh.create_cell_partitioner(ghost_mode)

src/adios4dolfinx/legacy_readers.py

@@ -152,7 +152,7 @@ def read_dofmap_legacy(
         # Extract dofmap data
         global_dofs = np.zeros_like(cells, dtype=np.int64)
         input_cell_positions = cells - local_cell_range[0]
-        read_pos = in_offsets[input_cell_positions].astype(np.int32) + dof_pos - in_offsets[0]
+        read_pos = (in_offsets[input_cell_positions] + dof_pos - in_offsets[0]).astype(np.int32)
         global_dofs = mapped_dofmap[read_pos]
         del input_cell_positions, read_pos
 

tests/test_attributes.py

@@ -2,12 +2,18 @@
 
 from mpi4py import MPI
 
+import adios2
 import numpy as np
 import pytest
+from packaging.version import parse as _v
 
 import adios4dolfinx
 
 
+@pytest.mark.skipif(
+    _v(np.__version__) >= _v("2.0.0") and _v(adios2.__version__) < _v("2.10.2"),
+    reason="Cannot use numpy>=2.0.0 and adios2<2.10.2",
+)
 @pytest.mark.parametrize("comm", [MPI.COMM_SELF, MPI.COMM_WORLD])
 def test_read_write_attributes(comm, tmp_path):
     attributes1 = {

tests/test_mesh_writer.py

@@ -48,11 +48,13 @@ def compute_distance_matrix(points_A, points_B, tol=1e-12):
         new_cell_map = mesh_adios.topology.index_map(mesh_adios.topology.dim)
         assert cell_map.size_local == new_cell_map.size_local
         assert cell_map.num_ghosts == new_cell_map.num_ghosts
+        mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
         midpoints = dolfinx.mesh.compute_midpoints(
             mesh,
             mesh.topology.dim,
             np.arange(cell_map.size_local + cell_map.num_ghosts, dtype=np.int32),
         )
+        mesh_adios.topology.create_connectivity(mesh_adios.topology.dim, mesh_adios.topology.dim)
         new_midpoints = dolfinx.mesh.compute_midpoints(
             mesh_adios,
             mesh_adios.topology.dim,

tests/test_meshtags.py

@@ -80,6 +80,7 @@ def generate_reference_map(
     Returns:
         Root rank returns the map, all other ranks return None
     """
+    mesh.topology.create_connectivity(meshtag.dim, mesh.topology.dim)
     midpoints = dolfinx.mesh.compute_midpoints(mesh, meshtag.dim, meshtag.indices)
     e_map = mesh.topology.index_map(meshtag.dim)
     value_to_midpoint = {}