Merge branch '53-create-mpi-fractal-objects' into mpi

gprMax/fractals/fractal_surface.py

@@ -143,7 +143,7 @@ class FractalSurface:
 
         return surfacedims
 
-    def generate_fractal_surface(self):
+    def generate_fractal_surface(self) -> bool:
         """Generate a 2D array with a fractal distribution."""
 
         surfacedims = self.get_surface_dims()
@@ -199,6 +199,8 @@ class FractalSurface:
             - ((self.fractalrange[1] - self.fractalrange[0]) / fractalrange) * fractalmin
         )
 
+        return True
+
 
 class MPIFractalSurface(FractalSurface):
     def __init__(
@@ -218,7 +220,7 @@ class MPIFractalSurface(FractalSurface):
         self.comm = comm
         self.upper_bound = upper_bound
 
-    def generate_fractal_surface(self):
+    def generate_fractal_surface(self) -> bool:
         """Generate a 2D array with a fractal distribution."""
 
         if self.xs == self.xf:
@@ -247,7 +249,7 @@ class MPIFractalSurface(FractalSurface):
             self.start = np.minimum(self.start, self.upper_bound)
             self.stop = np.maximum(self.stop, 0)
             self.stop = np.minimum(self.stop, self.upper_bound)
-            return
+            return False
         else:
             # Create new cartsesian communicator for the Fractal Surface
             comm = self.comm.Split(color=color)
@@ -262,8 +264,17 @@ class MPIFractalSurface(FractalSurface):
         # Check domain decomosition is valid for the Fractal Volume
         if all([dim > 1 for dim in self.comm.dims]):
             raise ValueError(
-                "Fractal surface must be positioned such that its MPI decomposition is 1 in at least"
-                f" 1 dimension. Current decompostion is: {self.comm.dims}"
+                "Fractal surface must be positioned such that its MPI decomposition is 1 in at"
+                f" least 1 dimension. Current decompostion is: {self.comm.dims}"
+            )
+
+        # Check domain decomosition is valid for the Fractal Volume
+        if len(self.grass) > 0 and self.comm.size > 1:
+            raise ValueError(
+                "Grass cannot currently be split across multiple MPI rank. Either change the MPI "
+                " decomposition such that the grass object is contained within a single MPI rank,"
+                " or divide the grass object into multiple sections. Current decompostion is:"
+                f" {self.comm.dims}"
             )
 
         surfacedims = self.get_surface_dims()
@@ -445,3 +456,5 @@ class MPIFractalSurface(FractalSurface):
         logger.debug(
             f"Generated fractal surface: start={self.start}, stop={self.stop}, size={self.size}, fractalrange={self.fractalrange}"
         )
+
+        return True

gprMax/user_objects/cmds_geometry/add_grass.py

@@ -173,14 +173,22 @@ class AddGrass(RotatableMixin, GeometryUserObject):
         else:
             raise ValueError(f"{self.__str__()} dimensions are not specified correctly")
 
-        surface = FractalSurface(xs, xf, ys, yf, zs, zf, frac_dim, seed)
+        surface = grid.create_fractal_surface(xs, xf, ys, yf, zs, zf, frac_dim, seed)
         surface.ID = "grass"
         surface.surfaceID = requestedsurface
 
+        # Create grass geometry parameters
+        # Add grass to the surface here as an MPIFractalSurface needs to
+        # know if grass is present when generate_fractal_surface() is
+        # called
+        g = Grass(n_blades, surface.seed)
+        surface.grass.append(g)
+
         # Set the fractal range to scale the fractal distribution between zero and one
         surface.fractalrange = (0, 1)
         surface.operatingonID = volume.ID
-        surface.generate_fractal_surface()
+        if not surface.generate_fractal_surface():
+            return
         if n_blades > surface.fractalsurface.shape[0] * surface.fractalsurface.shape[1]:
             raise ValueError(
                 f"{self.__str__()} the specified surface is not large "
@@ -220,10 +228,6 @@ class AddGrass(RotatableMixin, GeometryUserObject):
                 surface.fractalrange[0], surface.fractalrange[1], size=1
             )
 
-        # Create grass geometry parameters
-        g = Grass(n_blades, surface.seed)
-        surface.grass.append(g)
-
         # Check to see if grass has been already defined as a material
         if not any(x.ID == "grass" for x in grid.materials):
             create_grass(grid)

gprMax/user_objects/cmds_geometry/fractal_box.py

@@ -116,27 +116,23 @@ class FractalBox(RotatableMixin, GeometryUserObject):
         xf, yf, zf = p2
 
         if frac_dim < 0:
-            logger.exception(
+            raise ValueError(
                 f"{self.__str__()} requires a positive value for the fractal dimension"
             )
-            raise ValueError
         if weighting[0] < 0:
-            logger.exception(
+            raise ValueError(
                 f"{self.__str__()} requires a positive value for the fractal weighting in the x direction"
             )
-            raise ValueError
         if weighting[1] < 0:
-            logger.exception(
+            raise ValueError(
                 f"{self.__str__()} requires a positive value for the fractal weighting in the y direction"
             )
-            raise ValueError
         if weighting[2] < 0:
-            logger.exception(
+            raise ValueError(
                 f"{self.__str__()} requires a positive value for the fractal weighting in the z direction"
             )
         if n_materials < 0:
-            logger.exception(f"{self.__str__()} requires a positive value for the number of bins")
-            raise ValueError
+            raise ValueError(f"{self.__str__()} requires a positive value for the number of bins")
 
         # Find materials to use to build fractal volume, either from mixing
         # models or normal materials.
@@ -146,26 +142,23 @@ class FractalBox(RotatableMixin, GeometryUserObject):
 
         if mixingmodel:
             if nbins == 1:
-                logger.exception(
+                raise ValueError(
                     f"{self.__str__()} must be used with more than one material from the mixing model."
                 )
-                raise ValueError
             if isinstance(mixingmodel, ListMaterial) and nbins > len(mixingmodel.mat):
-                logger.exception(
+                raise ValueError(
                     f"{self.__str__()} too many materials/bins "
                     "requested compared to materials in "
                     "mixing model."
                 )
-                raise ValueError
             # Create materials from mixing model as number of bins now known
             # from fractal_box command.
             mixingmodel.calculate_properties(nbins, grid)
         elif not material:
-            logger.exception(
+            raise ValueError(
                 f"{self.__str__()} mixing model or material with "
                 + "ID {mixing_model_id} does not exist"
             )
-            raise ValueError
 
         self.volume = grid.add_fractal_volume(xs, xf, ys, yf, zs, zf, frac_dim, seed)
         self.volume.ID = ID
@@ -685,12 +678,11 @@ class FractalBox(RotatableMixin, GeometryUserObject):
 
             else:
                 if self.volume.nbins == 1:
-                    logger.exception(
+                    raise ValueError(
                         f"{self.__str__()} is being used with a "
                         "single material and no modifications, "
                         "therefore please use a #box command instead."
                     )
-                    raise ValueError
                 else:
                     if not self.volume.generate_fractal_volume():
                         return

reframe_tests/tests/base_tests.py

@@ -248,6 +248,20 @@ class GprMaxBaseTest(RunOnlyRegressionTest):
             # Set the matplotlib cache to the work filesystem
             self.env_vars["MPLCONFIGDIR"] = "${HOME/home/work}/.config/matplotlib"
 
+    def build_output_file_path(self, filename: str) -> Path:
+        """Build output file Path object from filename.
+
+        Using a function to build this allows mixins to reuse or
+        override it if needed.
+
+        Args:
+            filename: Name of output file with no file extension.
+
+        Returns:
+            Path: Output file Path object
+        """
+        return Path(f"{filename}.h5")
+
     @run_after("init")
     def set_file_paths(self):
         """Set default test input and output files.
@@ -256,7 +270,7 @@ class GprMaxBaseTest(RunOnlyRegressionTest):
         later in the pipeline.
         """
         self.input_file = Path(f"{self.model}.in")
-        self.output_file = Path(f"{self.model}.h5")
+        self.output_file = self.build_output_file_path(self.model)
 
     @run_before("run")
     def configure_test_run(self):

reframe_tests/tests/mixins.py

@@ -35,7 +35,8 @@ class ReceiverMixin(GprMaxMixin):
     def add_receiver_regression_checks(self):
         test_dependency = self.get_test_dependency()
         if test_dependency is not None:
-            reference_file = self.build_reference_filepath(test_dependency.output_file)
+            output_file = self.build_output_file_path(test_dependency.model)
+            reference_file = self.build_reference_filepath(output_file)
         else:
             reference_file = self.build_reference_filepath(self.output_file)
 

reframe_tests/tests/test_geometry.py

@@ -168,7 +168,8 @@ class TestTriangleGeometry(GprMaxRegressionTest):
 @rfm.simple_test
 class TestAddGrassMpi(MpiMixin, TestAddGrass):
     tags = {"test", "mpi", "geometery", "fractal", "surface", "grass"}
-    mpi_layout = parameter([[1, 2, 2], [3, 1, 3], [4, 1, 4]])
+    mpi_layout = parameter([[2, 2, 2]])
+    model = parameter(["add_grass_small"])
     test_dependency = TestAddGrass