Actual source code: ex18.c

      1: static char help[] = "Demonstrates the use of the COO interface to PETSc matrices for finite element computations\n\n";

      3: /*
      4:      The COO interface for PETSc matrices provides a convenient way to provide finite element stiffness matrices to PETSc matrix that should work
      5:    well on both CPUs and GPUs. It is an alternative to using MatSetValues()

      7:      This example is intended for people who are NOT using DMPLEX or libCEED or any other higher-level infrastructure for finite elements;
      8:    it is only to demonstrate the concepts in a simple way for those people who are interested and for those people who are using PETSc for
      9:    linear algebra solvers but are managing their own finite element process.

     11:      Please do NOT use this example as a starting point to writing your own finite element code from scratch!

     13:      Each element in this example has three vertices; hence the usage below needs to be adjusted for elements of a different number of vertices.
     14: */

     16: #include <petscmat.h>
     17: #include "ex18.h"

     19: static PetscErrorCode CreateFEStruct(FEStruct *fe)
     20: {
     21:   PetscFunctionBeginUser;
     22:   fe->Nv = 5;
     23:   fe->Ne = 3;
     24:   PetscCall(PetscMalloc1(3 * fe->Ne, &fe->vertices));
     25:   /* the three vertices associated with each element in order of element */
     26:   fe->vertices[0 + 0] = 0;
     27:   fe->vertices[0 + 1] = 1;
     28:   fe->vertices[0 + 2] = 2;
     29:   fe->vertices[3 + 0] = 2;
     30:   fe->vertices[3 + 1] = 1;
     31:   fe->vertices[3 + 2] = 3;
     32:   fe->vertices[6 + 0] = 2;
     33:   fe->vertices[6 + 1] = 4;
     34:   fe->vertices[6 + 2] = 3;
     35:   fe->n               = 5;
     36:   PetscFunctionReturn(PETSC_SUCCESS);
     37: }

     39: static PetscErrorCode DestroyFEStruct(FEStruct *fe)
     40: {
     41:   PetscFunctionBeginUser;
     42:   PetscCall(PetscFree(fe->vertices));
     43:   PetscCall(PetscFree(fe->coo));
     44:   PetscFunctionReturn(PETSC_SUCCESS);
     45: }

     47: static PetscErrorCode CreateMatrix(FEStruct *fe, Mat *A)
     48: {
     49:   PetscInt *oor, *ooc, cnt = 0;

     51:   PetscFunctionBeginUser;
     52:   PetscCall(MatCreate(PETSC_COMM_WORLD, A));
     53:   PetscCall(MatSetSizes(*A, fe->n, fe->n, PETSC_DECIDE, PETSC_DECIDE));
     54:   PetscCall(MatSetFromOptions(*A));

     56:   /* determine for each entry in each element stiffness matrix the global row and column */
     57:   /* since the element is triangular with piecewise linear basis functions there are three degrees of freedom per element, one for each vertex */
     58:   PetscCall(PetscMalloc2(3 * 3 * fe->Ne, &oor, 3 * 3 * fe->Ne, &ooc));
     59:   for (PetscInt e = 0; e < fe->Ne; e++) {
     60:     for (PetscInt vi = 0; vi < 3; vi++) {
     61:       for (PetscInt vj = 0; vj < 3; vj++) {
     62:         oor[cnt]   = fe->vertices[3 * e + vi];
     63:         ooc[cnt++] = fe->vertices[3 * e + vj];
     64:       }
     65:     }
     66:   }
     67:   PetscCall(MatSetPreallocationCOO(*A, 3 * 3 * fe->Ne, oor, ooc));
     68:   PetscCall(PetscFree2(oor, ooc));

     70:   /* determine the offset into the COO value array the offset of each element stiffness; there are 9 = 3*3 entries for each element stiffness */
     71:   /* for lists of elements with different numbers of degrees of freedom associated with each element the offsets will not be uniform */
     72:   PetscCall(PetscMalloc1(fe->Ne, &fe->coo));
     73:   fe->coo[0] = 0;
     74:   for (PetscInt e = 1; e < fe->Ne; e++) fe->coo[e] = fe->coo[e - 1] + 3 * 3;
     75:   PetscFunctionReturn(PETSC_SUCCESS);
     76: }

     78: static PetscErrorCode FillMatrixCPU(FEStruct *fe, Mat A)
     79: {
     80:   PetscScalar s[9];

     82:   PetscFunctionBeginUser;
     83:   /* simulation of traditional PETSc CPU based finite assembly process */
     84:   for (PetscInt e = 0; e < fe->Ne; e++) {
     85:     for (PetscInt vi = 0; vi < 3; vi++) {
     86:       for (PetscInt vj = 0; vj < 3; vj++) s[3 * vi + vj] = vi + 2 * vj;
     87:     }
     88:     PetscCall(MatSetValues(A, 3, fe->vertices + 3 * e, 3, fe->vertices + 3 * e, s, ADD_VALUES));
     89:   }
     90:   PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
     91:   PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
     92:   PetscFunctionReturn(PETSC_SUCCESS);
     93: }

     95: /*
     96:    Shows an example of tracking element offsets explicitly, which allows for
     97:    mixed-topology meshes and combining both volume and surface parts into the weak form.
     98: */
     99: static PetscErrorCode FillMatrixCPUCOO(FEStruct *fe, Mat A)
    100: {
    101:   PetscScalar *v, *s;

    103:   PetscFunctionBeginUser;
    104:   /* simulation of CPU based finite assembly process with COO */
    105:   PetscCall(PetscMalloc1(3 * 3 * fe->Ne, &v));
    106:   for (PetscInt e = 0; e < fe->Ne; e++) {
    107:     s = v + fe->coo[e]; /* point to location in COO of current element stiffness */
    108:     for (PetscInt vi = 0; vi < 3; vi++) {
    109:       for (PetscInt vj = 0; vj < 3; vj++) s[3 * vi + vj] = vi + 2 * vj;
    110:     }
    111:   }
    112:   PetscCall(MatSetValuesCOO(A, v, ADD_VALUES));
    113:   PetscCall(PetscFree(v));
    114:   PetscFunctionReturn(PETSC_SUCCESS);
    115: }

    117: /*
    118:   Uses a multi-dimensional indexing technique that works for homogeneous meshes
    119:   such as single-topology with volume integral only.
    120: */
    121: static PetscErrorCode FillMatrixCPUCOO3d(FEStruct *fe, Mat A)
    122: {
    123:   PetscScalar(*s)[3][3];

    125:   PetscFunctionBeginUser;
    126:   /* simulation of CPU based finite assembly process with COO */
    127:   PetscCall(PetscMalloc1(fe->Ne, &s));
    128:   for (PetscInt e = 0; e < fe->Ne; e++) {
    129:     for (PetscInt vi = 0; vi < 3; vi++) {
    130:       for (PetscInt vj = 0; vj < 3; vj++) s[e][vi][vj] = vi + 2 * vj;
    131:     }
    132:   }
    133:   PetscCall(MatSetValuesCOO(A, (PetscScalar *)s, INSERT_VALUES));
    134:   PetscCall(PetscFree(s));
    135:   PetscFunctionReturn(PETSC_SUCCESS);
    136: }

    138: int main(int argc, char **args)
    139: {
    140:   Mat         A, B;
    141:   FEStruct    fe;
    142:   PetscMPIInt size;
    143:   PetscBool   is_kokkos, is_cuda;

    145:   PetscFunctionBeginUser;
    146:   PetscCall(PetscInitialize(&argc, &args, NULL, help));
    147:   PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD, &size));
    148:   PetscCheck(size <= 1, PETSC_COMM_WORLD, PETSC_ERR_WRONG_MPI_SIZE, "Demonstration is only for sequential runs");

    150:   PetscCall(CreateFEStruct(&fe));

    152:   PetscCall(CreateMatrix(&fe, &B));
    153:   PetscCall(MatDuplicate(B, MAT_DO_NOT_COPY_VALUES, &A));
    154:   PetscCall(MatDestroy(&B));

    156:   PetscCall(FillMatrixCPU(&fe, A));
    157:   PetscCall(MatView(A, PETSC_VIEWER_STDOUT_WORLD));

    159:   PetscCall(MatZeroEntries(A));
    160:   PetscCall(FillMatrixCPUCOO(&fe, A));
    161:   PetscCall(MatView(A, PETSC_VIEWER_STDOUT_WORLD));

    163:   PetscCall(MatZeroEntries(A));
    164:   PetscCall(FillMatrixCPUCOO3d(&fe, A));
    165:   PetscCall(MatView(A, PETSC_VIEWER_STDOUT_WORLD));

    167:   PetscCall(MatZeroEntries(A));
    168:   PetscCall(PetscObjectBaseTypeCompare((PetscObject)A, MATSEQAIJKOKKOS, &is_kokkos));
    169:   PetscCall(PetscObjectBaseTypeCompare((PetscObject)A, MATSEQAIJCUSPARSE, &is_cuda));
    170: #if defined(PETSC_HAVE_KOKKOS)
    171:   if (is_kokkos) PetscCall(FillMatrixKokkosCOO(&fe, A));
    172: #endif
    173: #if defined(PETSC_HAVE_CUDA)
    174:   if (is_cuda) PetscCall(FillMatrixCUDACOO(&fe, A));
    175: #endif
    176:   PetscCall(MatView(A, PETSC_VIEWER_STDOUT_WORLD));

    178:   PetscCall(MatDestroy(&A));
    179:   PetscCall(DestroyFEStruct(&fe));
    180:   PetscCall(PetscFinalize());
    181:   return 0;
    182: }

    184: /*TEST
    185:   build:
    186:     requires: cuda kokkos_kernels
    187:     depends: ex18cu.cu ex18kok.kokkos.cxx

    189:   testset:
    190:     filter: grep -v "type"
    191:     output_file: output/ex18_1.out

    193:     test:
    194:       suffix: kok
    195:       requires: kokkos_kernels
    196:       args: -mat_type aijkokkos

    198:     test:
    199:       suffix: cuda
    200:       requires: cuda
    201:       args: -mat_type aijcusparse

    203:     test:
    204:       suffix: hip
    205:       requires: hip
    206:       args: -mat_type aijhipsparse

    208: TEST*/