io: increment version to 3.0.0.

firedrake/checkpointing.py

@@ -519,6 +519,9 @@ class CheckpointFile(object):
     One can also use different number of processes for saving and for loading.
 
     """
+
+    latest_version = '3.0.0'
+
     def __init__(self, filename, mode, comm=COMM_WORLD):
         self.viewer = ViewerHDF5()
         self.filename = filename
@@ -530,7 +533,14 @@ def __init__(self, filename, mode, comm=COMM_WORLD):
         assert self.commkey != MPI.COMM_NULL.py2f()
         self._function_spaces = {}
         self._function_load_utils = {}
-        self.opts = OptionsManager({"dm_plex_view_hdf5_storage_version": "2.1.0"}, "")
+        if mode in [PETSc.Viewer.FileMode.APPEND, PETSc.Viewer.FileMode.A, 'a']:
+            if self.has_attr("/", "dmplex_storage_version"):
+                version = self.get_attr("/", "dmplex_storage_version").decode()
+            else:
+                raise RuntimeError(f"Only files generated with CheckpointFile are supported: got an invalid file ({filename})")
+        else:
+            version = CheckpointFile.latest_version
+        self.opts = OptionsManager({"dm_plex_view_hdf5_storage_version": version}, "")
         r"""DMPlex HDF5 version options."""
 
     def __enter__(self):
@@ -657,12 +667,30 @@ def _save_mesh_topology(self, tmesh):
         perm_is = tmesh._dm_renumbering
         permutation_name = tmesh._permutation_name
         if tmesh_name in self.require_group(self._path_to_topologies()):
+            version_str = self.opts.parameters['dm_plex_view_hdf5_storage_version']
+            version_major, version_minor, version_patch = tuple(int(ver) for ver in version_str.split('.'))
             # Check if the global number of DMPlex points and
             # the global sum of DMPlex cone sizes are consistent.
+            cell_dim = topology_dm.getDimension()
+            if version_major < 3:
+                path = os.path.join(self._path_to_topology(tmesh_name), "topology", "cells")
+            else:
+                path = os.path.join(self._path_to_topology(tmesh_name), "topology")
+            cell_dim1 = self.get_attr(path, "cell_dim")
+            if cell_dim1 != cell_dim:
+                raise ValueError(f"Mesh ({tmesh_name}) already exists in {self.filename}, but the topological dimension is inconsistent: {cell_dim1} ({self.filename}) != {cell_dim} ({tmesh_name})")
             order_array_size, ornt_array_size = dmcommon.compute_point_cone_global_sizes(topology_dm)
-            path = os.path.join(self._path_to_topology(tmesh_name), "topology")
-            order_array_size1 = self.h5pyfile[path]["order"].size
-            ornt_array_size1 = self.h5pyfile[path]["orientation"].size
+            if version_major < 3:
+                path = os.path.join(self._path_to_topology(tmesh_name), "topology")
+                order_array_size1 = self.h5pyfile[path]["order"].size
+                ornt_array_size1 = self.h5pyfile[path]["orientation"].size
+            else:
+                order_array_size1 = 0
+                ornt_array_size1 = 0
+                for d in range(cell_dim + 1):
+                    path = os.path.join(self._path_to_topology(tmesh_name), "topology", "strata", str(d))
+                    order_array_size1 += self.h5pyfile[path]["cone_sizes"].size
+                    ornt_array_size1 += self.h5pyfile[path]["cones"].size
             if order_array_size1 != order_array_size:
                 raise ValueError(f"Mesh ({tmesh_name}) already exists in {self.filename}, but the global number of DMPlex points is inconsistent: {order_array_size1} ({self.filename}) != {order_array_size} ({tmesh_name})")
             if ornt_array_size1 != ornt_array_size:
@@ -1143,11 +1171,6 @@ def _load_mesh_topology(self, tmesh_name, reorder, distribution_parameters):
         plex.setName(tmesh_name)
         # Check format
         path = os.path.join(self._path_to_topology(tmesh_name), "topology")
-        if any(d not in self.h5pyfile for d in [os.path.join(path, "cells"),
-                                                os.path.join(path, "cones"),
-                                                os.path.join(path, "order"),
-                                                os.path.join(path, "orientation")]):
-            raise RuntimeError(f"Unsupported PETSc ViewerHDF5 format used in {self.filename}")
         format = ViewerHDF5.Format.HDF5_PETSC
         self.viewer.pushFormat(format=format)
         plex.distributionSetName(distribution_name)

tests/output/test_io_backward_compat.py

@@ -3,6 +3,7 @@
 from firedrake import *
 from firedrake.mesh import make_mesh_from_coordinates
 from firedrake.utils import IntType
+import shutil
 
 
 test_version = "2024_01_27"
@@ -276,3 +277,34 @@ def test_io_backward_compat_timestepping_load(version):
             f_ = Function(V_)
             _initialise_function(f_, _get_expr_timestepping(V_, i))
             assert assemble(inner(f - f_, f - f_) * dx) < 1.e-16
+
+
+@pytest.mark.skipcomplex
+@pytest.mark.parallel(nprocs=3)
+@pytest.mark.parametrize('version', ["2024_01_27"])
+def test_io_backward_compat_timestepping_append(version, tmpdir):
+    filename = join(filedir, "_".join([basename, version, "timestepping" + ".h5"]))
+    copyname = join(str(tmpdir), "test_io_backward_compat_timestepping_append_dump.h5")
+    copyname = COMM_WORLD.bcast(copyname, root=0)
+    shutil.copyfile(filename, copyname)
+    with CheckpointFile(copyname, "r") as afile:
+        version = afile.opts.parameters['dm_plex_view_hdf5_storage_version']
+        assert version == CheckpointFile.latest_version
+        mesh = afile.load_mesh(mesh_name)
+        f = afile.load_function(mesh, func_name, idx=0)
+        V = f.function_space()
+    with CheckpointFile(copyname, 'a') as afile:
+        version = afile.opts.parameters['dm_plex_view_hdf5_storage_version']
+        assert version == '2.1.0'
+        for i in range(5, 10):
+            _initialise_function(f, _get_expr_timestepping(V, i))
+            afile.save_function(f, idx=i)
+    with CheckpointFile(copyname, "r") as afile:
+        version = afile.opts.parameters['dm_plex_view_hdf5_storage_version']
+        assert version == CheckpointFile.latest_version
+        for i in range(0, 10):
+            f = afile.load_function(mesh, func_name, idx=i)
+            V_ = f.function_space()
+            f_ = Function(V_)
+            _initialise_function(f_, _get_expr_timestepping(V_, i))
+            assert assemble(inner(f - f_, f - f_) * dx) < 1.e-16