1 static char help[] = "Demonstrates the use of the COO interface to PETSc matrices for finite element computations\n\n"; 2 3 /* 4 The COO interface for PETSc matrices provides a convenient way to provide finite element element stiffness matrices to PETSc matrix that should work 5 well on both CPUs and GPUs. It is an alternative to using MatSetValues() 6 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. 10 11 Please do NOT use this example as a starting point to writing your own finite element code from scratch! 12 13 Each element in this example has three vertices; hence the the usage below needs to be adjusted for elements of a different number of vertices. 14 */ 15 16 #include <petscmat.h> 17 #include "ex18.h" 18 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(0); 37 } 38 39 static PetscErrorCode DestroyFEStruct(FEStruct *fe) 40 { 41 PetscFunctionBeginUser; 42 PetscCall(PetscFree(fe->vertices)); 43 PetscCall(PetscFree(fe->coo)); 44 PetscFunctionReturn(0); 45 } 46 47 static PetscErrorCode CreateMatrix(FEStruct *fe,Mat *A) 48 { 49 PetscInt *oor,*ooc,cnt = 0; 50 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)); 55 56 /* determine for each entry in each element stiffness matrix the global row and colum */ 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)); 69 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 assocated 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++) { 75 fe->coo[e] = fe->coo[e-1] + 3*3; 76 } 77 PetscFunctionReturn(0); 78 } 79 80 static PetscErrorCode FillMatrixCPU(FEStruct *fe,Mat A) 81 { 82 PetscScalar s[9]; 83 84 PetscFunctionBeginUser; 85 /* simulation of traditional PETSc CPU based finite assembly process */ 86 for (PetscInt e=0; e<fe->Ne; e++) { 87 for (PetscInt vi=0; vi<3; vi++) { 88 for (PetscInt vj=0; vj<3; vj++) { 89 s[3*vi+vj] = vi+2*vj; 90 } 91 } 92 PetscCall(MatSetValues(A,3,fe->vertices + 3*e,3, fe->vertices + 3*e,s,ADD_VALUES)); 93 } 94 PetscCall(MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY)); 95 PetscCall(MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY)); 96 PetscFunctionReturn(0); 97 } 98 99 /* 100 Shows an example of tracking element offsets explicitly, which allows for 101 mixed-topology meshes and combining both volume and surface parts into the weak form. 102 */ 103 static PetscErrorCode FillMatrixCPUCOO(FEStruct *fe,Mat A) 104 { 105 PetscScalar *v,*s; 106 107 PetscFunctionBeginUser; 108 /* simulation of CPU based finite assembly process with COO */ 109 PetscCall(PetscMalloc1(3*3*fe->Ne,&v)); 110 for (PetscInt e=0; e<fe->Ne; e++) { 111 s = v + fe->coo[e]; /* point to location in COO of current element stiffness */ 112 for (PetscInt vi=0; vi<3; vi++) { 113 for (PetscInt vj=0; vj<3; vj++) { 114 s[3*vi+vj] = vi+2*vj; 115 } 116 } 117 } 118 PetscCall(MatSetValuesCOO(A,v,ADD_VALUES)); 119 PetscCall(PetscFree(v)); 120 PetscFunctionReturn(0); 121 } 122 123 /* 124 Uses a multi-dimensional indexing technique that works for homogeneous meshes 125 such as single-topology with volume integral only. 126 */ 127 static PetscErrorCode FillMatrixCPUCOO3d(FEStruct *fe,Mat A) 128 { 129 PetscScalar (*s)[3][3]; 130 131 PetscFunctionBeginUser; 132 /* simulation of CPU based finite assembly process with COO */ 133 PetscCall(PetscMalloc1(fe->Ne,&s)); 134 for (PetscInt e=0; e<fe->Ne; e++) { 135 for (PetscInt vi=0; vi<3; vi++) { 136 for (PetscInt vj=0; vj<3; vj++) { 137 s[e][vi][vj] = vi+2*vj; 138 } 139 } 140 } 141 PetscCall(MatSetValuesCOO(A,(PetscScalar*)s,INSERT_VALUES)); 142 PetscCall(PetscFree(s)); 143 PetscFunctionReturn(0); 144 } 145 146 int main(int argc, char **args) 147 { 148 Mat A; 149 FEStruct fe; 150 PetscMPIInt size; 151 PetscBool is_kokkos,is_cuda; 152 153 PetscCall(PetscInitialize(&argc,&args,(char*)0,help)); 154 PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD,&size)); 155 PetscCheck(size <= 1,PETSC_COMM_WORLD,PETSC_ERR_WRONG_MPI_SIZE,"Demonstration is only for sequential runs"); 156 157 PetscCall(CreateFEStruct(&fe)); 158 PetscCall(CreateMatrix(&fe,&A)); 159 160 PetscCall(FillMatrixCPU(&fe,A)); 161 PetscCall(MatView(A,PETSC_VIEWER_STDOUT_WORLD)); 162 163 PetscCall(MatZeroEntries(A)); 164 PetscCall(FillMatrixCPUCOO(&fe,A)); 165 PetscCall(MatView(A,PETSC_VIEWER_STDOUT_WORLD)); 166 167 PetscCall(MatZeroEntries(A)); 168 PetscCall(FillMatrixCPUCOO3d(&fe,A)); 169 PetscCall(MatView(A,PETSC_VIEWER_STDOUT_WORLD)); 170 171 PetscCall(MatZeroEntries(A)); 172 PetscCall(PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJKOKKOS,&is_kokkos)); 173 PetscCall(PetscObjectBaseTypeCompare((PetscObject)A,MATSEQAIJCUSPARSE,&is_cuda)); 174 #if defined(PETSC_HAVE_KOKKOS) 175 if (is_kokkos) PetscCall(FillMatrixKokkosCOO(&fe,A)); 176 #endif 177 #if defined(PETSC_HAVE_CUDA) 178 if (is_cuda) PetscCall(FillMatrixCUDACOO(&fe,A)); 179 #endif 180 PetscCall(MatView(A,PETSC_VIEWER_STDOUT_WORLD)); 181 182 PetscCall(MatDestroy(&A)); 183 PetscCall(DestroyFEStruct(&fe)); 184 PetscCall(PetscFinalize()); 185 return 0; 186 } 187 188 /*TEST 189 build: 190 requires: cuda kokkos_kernels 191 depends: ex18cu.cu ex18kok.kokkos.cxx 192 193 testset: 194 filter: grep -v "type" 195 output_file: output/ex18_1.out 196 197 test: 198 suffix: kok 199 requires: kokkos_kernels 200 args: -mat_type aijkokkos 201 202 test: 203 suffix: cuda 204 requires: cuda 205 args: -mat_type aijcusparse 206 207 TEST*/ 208