DMPlex: Unstructured Grids in PETSc¶

This chapter introduces the DMPLEX subclass of DM, which allows the user to handle unstructured grids using the generic DM interface for hierarchy and multi-physics. DMPlex was created to remedy a huge problem in all current PDE simulation codes, namely that the discretization was so closely tied to the data layout and solver that switching discretizations in the same code was not possible. Not only does this preclude the kind of comparison that is necessary for scientific investigation, but it makes library (as opposed to monolithic application) development impossible.

Representing Unstructured Grids¶

The main advantage of DMPlex in representing topology is that it treats all the different pieces of a mesh, e.g. cells, faces, edges, and vertices, in exactly the same way. This allows the interface to be very small and simple, while remaining flexible and general. This also allows “dimension independent programming”, which means that the same algorithm can be used unchanged for meshes of different shapes and dimensions.

All pieces of the mesh are treated as points, which are identified by PetscInts. A mesh is built by relating points to other points, in particular specifying a “covering” relation among the points. For example, an edge is defined by being covered by two vertices, and a triangle can be defined by being covered by three edges (or even by three vertices). In fact, this structure has been known for a long time. It is a Hasse Diagram Hasse Diagram, which is a Directed Acyclic Graph (DAG) representing a cell complex using the covering relation. The graph edges represent the relation, which also encodes a partially ordered set (poset).

For example, we can encode the doublet mesh as in Fig. 6,

Fig. 6 A 2D doublet mesh, two triangles sharing an edge.¶

which can also be represented as the DAG in Fig. 7.

Fig. 7 The Hasse diagram for our 2D doublet mesh, expressed as a DAG.¶

To use the PETSc API, we first consecutively number the mesh pieces. The PETSc convention in 3 dimensions is to number first cells, then vertices, then faces, and then edges. In 2 dimensions the convention is to number faces, vertices, and then edges. The user is free to violate these conventions. In terms of the labels in Fig. 6, these numberings are

\[f_0 \mapsto \mathtt{0}, f_1 \mapsto \mathtt{1}, \quad v_0 \mapsto \mathtt{2}, v_1 \mapsto \mathtt{3}, v_2 \mapsto \mathtt{4}, v_3 \mapsto \mathtt{5}, \quad e_0 \mapsto \mathtt{6}, e_1 \mapsto \mathtt{7}, e_2 \mapsto \mathtt{8}, e_3 \mapsto \mathtt{9}, e_4 \mapsto \mathtt{10} \]

First, we declare the set of points present in a mesh,

DMPlexSetChart(dm, 0, 11);

Note that a chart here corresponds to a semi-closed interval (e.g \([0,11) = \{0,1,\ldots,10\}\)) specifying the range of indices we’d like to use to define points on the current rank. We then define the covering relation, which we call the cone, which are also the in-edges in the DAG. In order to preallocate correctly, we first setup sizes,

DMPlexSetConeSize(dm, 0, 3);
DMPlexSetConeSize(dm, 1, 3);
DMPlexSetConeSize(dm, 6, 2);
DMPlexSetConeSize(dm, 7, 2);
DMPlexSetConeSize(dm, 8, 2);
DMPlexSetConeSize(dm, 9, 2);
DMPlexSetConeSize(dm, 10, 2);
DMSetUp(dm);

and then point values,

DMPlexSetCone(dm, 0, [6, 7, 8]);
DMPlexSetCone(dm, 1, [7, 9, 10]);
DMPlexSetCone(dm, 6, [2, 3]);
DMPlexSetCone(dm, 7, [3, 4]);
DMPlexSetCone(dm, 8, [4, 2]);
DMPlexSetCone(dm, 9, [4, 5]);
DMPlexSetCone(dm, 10, [5, 3]);

There is also an API for the dual relation, using DMPlexSetSupportSize() and DMPlexSetSupport(), but this can be calculated automatically by calling

DMPlexSymmetrize(dm);

In order to support efficient queries, we also want to construct fast search structures and indices for the different types of points, which is done using

DMPlexStratify(dm);

Data on Unstructured Grids¶

The strongest links between solvers and discretizations are

the layout of data over the mesh,
problem partitioning, and
ordering of unknowns.

To enable modularity, we encode the operations above in simple data structures that can be understood by the linear algebra engine in PETSc without any reference to the mesh (topology) or discretization (analysis).

Data Layout¶

Data is associated with a mesh using the PetscSection object. A PetscSection can be thought of as a generalization of PetscLayout, in the same way that a fiber bundle is a generalization of the normal Euclidean basis used in linear algebra. With PetscLayout, we associate a unit vector (\(e_i\)) with every point in the space, and just divide up points between processes. Using PetscSection, we can associate a set of dofs, a small space \(\{e_k\}\), with every point, and though our points must be contiguous like PetscLayout, they can be in any range \([\mathrm{pStart}, \mathrm{pEnd})\).

The sequence for setting up any PetscSection is the following:

Specify the chart,
Specify the number of dofs per point, and
Set up the PetscSection.

For example, using the mesh from Fig. 6, we can lay out data for a continuous Galerkin \(P_3\) finite element method,

PetscInt pStart, pEnd, cStart, cEnd, c, vStart, vEnd, v, eStart, eEnd, e;

DMPlexGetChart(dm, &pStart, &pEnd);
DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);   /* cells */
DMPlexGetHeightStratum(dm, 1, &eStart, &eEnd);   /* edges */
DMPlexGetHeightStratum(dm, 2, &vStart, &vEnd);   /* vertices, equivalent to DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd); */
PetscSectionSetChart(s, pStart, pEnd);
for(c = cStart; c < cEnd; ++c)
    PetscSectionSetDof(s, c, 1);
for(v = vStart; v < vEnd; ++v)
    PetscSectionSetDof(s, v, 1);
for(e = eStart; e < eEnd; ++e)
    PetscSectionSetDof(s, e, 2);
PetscSectionSetUp(s);

DMPlexGetHeightStratum() returns all the points of the requested height in the DAG. Since this problem is in two dimensions the edges are at height 1 and the vertices at height 2 (the cells are always at height 0). One can also use DMPlexGetDepthStratum() to use the depth in the DAG to select the points. DMPlexGetDepth(,&depth) routines the depth of the DAG, hence DMPlexGetDepthStratum(dm,depth-1-h,) returns the same values as DMPlexGetHeightStratum(dm,h,).

For P3 elements there is one degree of freedom at each vertex, 2 along each edge (resulting in a total of 4 degrees of freedom alone each edge including the vertices, thus being able to reproduce a cubic function) and 1 degree of freedom within the cell (the bubble function which is zero along all edges).

Now a PETSc local vector can be created manually using this layout,

PetscSectionGetStorageSize(s, &n);
VecSetSizes(localVec, n, PETSC_DETERMINE);
VecSetFromOptions(localVec);

though it is usually easier to use the DM directly, which also provides global vectors,

DMSetLocalSection(dm, s);
DMGetLocalVector(dm, &localVec);
DMGetGlobalVector(dm, &globalVec);

Partitioning and Ordering¶

In exactly the same way as in MatPartitioning or with MatGetOrdering(), the results of a partition using DMPlexPartition or reordering using DMPlexPermute are encoded in an IS. However, the graph is not the adjacency graph of the problem Jacobian, but the mesh itself. Once the mesh is partitioned and reordered, the data layout from a PetscSection can be used to automatically derive a problem partitioning/ordering.

Influence of Variables on One Another¶

The Jacobian of a problem is intended to represent the influence of some variable on other variables in the problem. Very often, this influence pattern is determined jointly by the computational mesh and discretization. DMCreateMatrix must compute this pattern when it automatically creates the properly preallocated Jacobian matrix. In DMDA the influence pattern, or what we will call variable adjacency, depends only on the stencil since the topology is Cartesian and the discretization is implicitly finite difference. In DMPlex, we allow the user to specify the adjacency topologically, while maintaining good defaults.

The pattern is controlled by two flags. The first flag, useCone, indicates whether variables couple first to their boundary and then to neighboring entities, or the reverse. For example, in finite elements, the variables couple to the set of neighboring cells containing the mesh point, and we set the flag to useCone = PETSC_FALSE. By constrast, in finite volumes, cell variables first couple to the cell boundary, and then to the neighbors, so we set the flag to useCone = PETSC_TRUE. The second flag, useClosure, indicates whether we consider the transitive closure of the neighbor relation above, or just a single level. For example, in finite elements, the entire boundary of any cell couples to the interior, and we set the flag to useClosure = PETSC_TRUE. By contrast, in most finite volume methods, cells couple only across faces, and not through vertices, so we set the flag to useClosure = PETSC_FALSE. However, the power of this method is its flexibility. If we wanted a finite volume method that coupled all cells around a vertex, we could easily prescribe that by changing to useClosure = PETSC_TRUE.

Evaluating Residuals¶

The evaluation of a residual or Jacobian, for most discretizations has the following general form:

Traverse the mesh, picking out pieces (which in general overlap),
Extract some values from the solution vector, associated with this piece,
Calculate some values for the piece, and
Insert these values into the residual vector

DMPlex separates these different concerns by passing sets of points, which are just PetscInts, from mesh traversal routines to data extraction routines and back. In this way, the PetscSection which structures the data inside a Vec does not need to know anything about the mesh inside a DMPlex.

The most common mesh traversal is the transitive closure of a point, which is exactly the transitive closure of a point in the DAG using the covering relation. In other words, the transitive closure consists of all points that cover the given point (generally a cell) plus all points that cover those points, etc. So in 2d the transitive closure for a cell consists of edges and vertices while in 3d it consists of faces, edges, and vertices. Note that this closure can be calculated orienting the arrows in either direction. For example, in a finite element calculation, we calculate an integral over each element, and then sum up the contributions to the basis function coefficients. The closure of the element can be expressed discretely as the transitive closure of the element point in the mesh DAG, where each point also has an orientation. Then we can retrieve the data using PetscSection methods,

PetscScalar *a;
PetscInt     numPoints, *points = NULL, p;

VecGetArray(u,&a);
DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&numPoints,&points);
for (p = 0; p <= numPoints*2; p += 2) {
  PetscInt dof, off, d;

  PetscSectionGetDof(section, points[p], &dof);
  PetscSectionGetOffset(section, points[p], &off);
  for (d = 0; d <= dof; ++d) {
    myfunc(a[off+d]);
  }
}
DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &numPoints, &points);
VecRestoreArray(u, &a);

This operation is so common that we have built a convenience method around it which returns the values in a contiguous array, correctly taking into account the orientations of various mesh points:

const PetscScalar *values;
PetscInt           csize;

DMPlexVecGetClosure(dm, section, u, cell, &csize, &values);
/* Do integral in quadrature loop */
DMPlexVecRestoreClosure(dm, section, u, cell, &csize, &values);
DMPlexVecSetClosure(dm, section, residual, cell, &r, ADD_VALUES);

A simple example of this kind of calculation is in DMPlexComputeL2Diff_Plex() (source). Note that there is no restriction on the type of cell or dimension of the mesh in the code above, so it will work for polyhedral cells, hybrid meshes, and meshes of any dimension, without change. We can also reverse the covering relation, so that the code works for finite volume methods where we want the data from neighboring cells for each face:

PetscScalar *a;
PetscInt     points[2*2], numPoints, p, dofA, offA, dofB, offB;

VecGetArray(u,  &a);
DMPlexGetTransitiveClosure(dm, cell, PETSC_FALSE, &numPoints, &points);
assert(numPoints == 2);
PetscSectionGetDof(section, points[0*2], &dofA);
PetscSectionGetDof(section, points[1*2], &dofB);
assert(dofA == dofB);
PetscSectionGetOffset(section, points[0*2], &offA);
PetscSectionGetOffset(section, points[1*2], &offB);
myfunc(a[offA], a[offB]);
VecRestoreArray(u, &a);

This kind of calculation is used in TS Tutorial ex11.

Networks¶

Built on top of DMPlex, the DMNetwork subclass provides abstractions for representing general unstructured networks such as communication networks, power grid, computer networks, transportation networks, electrical circuits, graphs, and others.

Application flow¶

The general flow of an application code using DMNetwork is as follows:

Create a network object

DMNetworkCreate(MPI_Comm comm, DM *dm);

Create components and register them with the network. A “component” is specific application data at a vertex/edge of the network required for its residual evaluation. For example, components could be resistor, inductor data for circuit applications, edge weights for graph problems, generator/transmission line data for power grids. Components are registered by calling
```
DMNetworkRegisterComponent(DM dm, const char *name, size_t size, PetscInt *compkey);
```
Here, name is the component name, size is the size of component data type, and compkey is an integer key that can be used for setting/getting the component at a vertex or an edge. DMNetwork currently allows upto 16 components to be registered for a network.
A DMNetwork can consist of one or more physical subnetworks. When multiple physical subnetworks are used one can (optionally) provide coupling information between subnetworks which consist only of edges connecting the vertices of the physical subnetworks. The topological sizes of the network are set by calling
```
DMNetworkSetSizes(DM dm, PetscInt Nsubnet, PetscInt nV[], PetscInt nE[], PetscInt NsubnetCouple, PetscInt nec[]);
```
Here, Nsubnet is the number of subnetworks, nV and nE is the number of vertices and edges for each subnetwork, NsubnetCouple is the number of pairs of subnetworks that are coupled, and nec is the number of edges coupling each subnetwork pair. DMNetwork assumes coupling between the subnetworks through coupling edges. For a single network, set Nsubnet = 1, NsubnetCouple = 0, and nec = NULL. Note that the coupling between subnetworks is still an experimental feature and under development.
The next step is to set up the connectivity for the network. This is done by specifying the connectivity within each subnetwork (edgelist) and between subnetworks (edgelistCouple).
```
DMNetworkSetEdgeList(DM dm, PetscInt *edgelist[], PetscInt *edgelistCouple[]);
```
Each element of edgelist is an integer array of size 2*nE[i] containing the edge connectivity for the i-th subnetwork. Each element in edgelistCouple has four entries - from subnetwork number (net.id), from subnetwork vertex number (vertex.id), to subnetwork number (net.id), to subetwork vertex number (vertex.id).

As an example, consider a network comprising of 2 subnetworks that are coupled. The topological information for the network is as follows:

subnetwork 0: v0 — v1 — v2 — v3

subnetwork 1: v1 — v2 — v0

coupling between subnetworks: subnetwork 1: v2 — subnetwork 0: v0

The edgelist and edgelistCouple for this network are

edgelist[0] = {0,1,1,2,2,3}

edgelist[1] = {1,2,2,0}

edgelistCouple[0] = {1,2,0,0}.
The next step is to have DMNetwork to create a bare layout (graph) of the network by calling
```
DMNetworkLayoutSetUp(DM dm);
```
After completing the previous steps, the network graph is set up, but no physics is associated yet. This is done by adding the components and setting the number of variables for the vertices and edges.

A component is added to a vertex/edge by calling
```
DMNetworkAddComponent(DM dm, PetscInt p, PetscInt compkey, void* compdata);
```
where p is the network vertex/edge point in the range obtained by either DMNetworkGetEdgeRange or DMNetworkGetVertexRange, compkey is the component key returned when registering the component (DMNetworkRegisterComponent), and compdata holds the data for the component. DMNetwork supports setting multiple components (max. 36) at a vertex/edge.

DMNetwork currently assumes the component data to be stored in a contiguous chunk of memory. As such, it does not do any packing/unpacking before/after the component data gets distributed. Any such serialization (packing/unpacking) should be done by the application.

The number of variables at each vertex/edge are set by
```
DMNetworkSetNumVariables(DM dm, PetscInt p, PetscInt nvar);
```
or
```
DMNetworkAddNumVariables(DM dm, PetscInt p, PetscInt nvar);
```
Alternatively, the number of variables can be set for a component directly. This allows much finer control, specifically for vertices/edges that have multiple components set on them.
```
DMNetworkSetComponentNumVariables(DM dm, PetscInt p, PetscInt compnum, PetscInt nvar);
```
Set up network internal data structures.
```
DMSetUp(DM dm);
```
Distribute the network (also moves components attached with vertices/edges) to multiple processors.
```
DMNetworkDistribute(DM dm, const char partitioner[], PetscInt overlap, DM *distDM);
```

Associate the DM with a PETSc solver:

KSPSetDM(KSP ksp, DM dm) or SNESSetDM(SNES snes, DM dm) or TSSetDM(TS ts, DM dm).

Utility functions¶

DMNetwork provides several utility functions for operations on the network. The mostly commonly used functions are: obtaining iterators for vertices/edges,

DMNetworkGetEdgeRange(DM dm, PetscInt *eStart, PetscInt *eEnd);

DMNetworkGetVertexRange(DM dm, PetscInt *vStart, PetscInt *vEnd);

DMNetworkGetSubnetworkInfo(DM dm, PetscInt netid, PetscInt *nv, PetscInt *ne, const PetscInt **vtx, const PetscInt **edge);

Checking the “ghost” status of a vertex,

DMNetworkIsGhostVertex(DM dm, PetscInt p, PetscBool *isghost);

and retrieving local/global indices of vertex/edge variables for inserting elements in vectors/matrices.

DMNetworkGetVariableOffset(DM dm, PetscInt p, PetscInt *offset);

DMNetworkGetVariableGlobalOffset(DM dm, PetscInt p, PetscInt *offsetg);

If the number of variables are set at the component level, then their local/global offsets can be retrieved via

DMNetworkGetComponentVariableOffset(DM dm, PetscInt p, PetscInt compnum, PetscInt *offset);

DMNetworkGetComponentVariableGlobalOffset(DM dm, PetscInt p, PetscInt compnum, PetscInt *offsetg);

In network applications, one frequently needs to find the supporting edges for a vertex or the connecting vertices covering an edge. These can be obtained by the following two routines.

DMNetworkGetConnectedVertices(DM dm, PetscInt edge, const PetscInt *vertices[]);

DMNetworkGetSupportingEdges(DM dm, PetscInt vertex, PetscInt *nedges, const PetscInt *edges[]);

Retrieving components¶

The components set at a vertex/edge can be accessed by

DMNetworkGetComponent(DM dm, PetscInt p, PetscInt compnum, PetscInt *compkey, void** component);

compkey is the key set by DMNetworkRegisterComponent. An example of accessing and retrieving the components at vertices is:

PetscInt Start, End, numcomps,key,v,compnum;
void *component;

DMNetworkGetVertexRange(dm, &Start, &End);
for (v=Start; v  < End; v++) {
  DMNetworkGetNumComponents(dm,v, &numcomps);
  for (compnum=0; compnum < numcomps;compnum++) {
    DMNetworkGetComponent(dm,v,compnum, &key, &component);
    compdata = (UserCompDataType)(component);
  }
}

The above example does not explicitly make use the component key. It is used when different component types are set at different vertices. In this case, the compkey is used to differentiate the component type.

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