void build_rigid_body_vectors(libMesh::ImplicitSystem& input_system, MatNullSpace& nullsp_sys)
{
// --- Set up some temporary variables to simplify code
// System matrix pointer (only used to get the proper vector dimensions)
libMesh::PetscMatrix<libMesh::Number> * mat_sys = libMesh::cast_ptr<libMesh::PetscMatrix<libMesh::Number>* >(input_system.matrix);
/// Mesh address
const libMesh::MeshBase& mesh_sys = input_system.get_mesh();
// System number
unsigned int sys_number = input_system.number();
// --- Set the coordinates vector structure as the same of rigidity matrix
Vec coord_vec_PETSC;
PetscInt local_N;
MatGetLocalSize(mat_sys->mat(),NULL,&local_N);
VecCreate(mesh_sys.comm().get(),&coord_vec_PETSC);
VecSetSizes(coord_vec_PETSC,local_N,mat_sys->n());
VecSetBlockSize(coord_vec_PETSC,mesh_sys.mesh_dimension());
VecSetFromOptions(coord_vec_PETSC);
libMesh::PetscVector<libMesh::Number> coord_vec(coord_vec_PETSC,mesh_sys.comm());
// --- Fill the coordinates vector
auto node_it = mesh_sys.local_nodes_begin();
auto node_it_end = mesh_sys.local_nodes_end();
unsigned int dof_number = 0;
for( ; node_it != node_it_end; ++node_it)
{
const libMesh::Node* node = *node_it;
for(unsigned int var=0; var<node->n_dofs(sys_number); var++)
{
dof_number = node->dof_number(sys_number,var,0);
coord_vec.set(dof_number,node->operator ()(var));
}
}
MatNullSpaceCreateRigidBody(coord_vec.vec(),&nullsp_sys);
VecDestroy(&coord_vec_PETSC);
};
int main(int argc, char** argv)
{
PC pc;
PetscErrorCode ierr;
PetscInt m, nn, M, j, k, ne = 4;
PetscReal* coords;
Vec x, rhs;
Mat A;
KSP ksp;
PetscMPIInt npe, rank;
PetscInitialize(&argc, &argv, NULL, NULL);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &npe);
CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Linear elasticity in 3D", "");
{
char nestring[256];
ierr = PetscSNPrintf(nestring, sizeof nestring, "number of elements in each direction, ne+1 must be a multiple of %D (sizes^{1/3})",
(PetscInt)(PetscPowReal((PetscReal)npe, 1.0 / 3.0) + 0.5));
ierr = PetscOptionsInt("-ne", nestring, "", ne, &ne, NULL);
}
ierr = PetscOptionsEnd();
CHKERRQ(ierr);
const HpddmOption* const opt = HpddmOptionGet();
{
HpddmOptionParse(opt, argc, argv, rank == 0);
if (rank) HpddmOptionRemove(opt, "verbosity");
}
nn = ne + 1;
M = 3 * nn * nn * nn;
if (npe == 2) {
if (rank == 1)
m = 0;
else
m = nn * nn * nn;
npe = 1;
}
else {
m = nn * nn * nn / npe;
if (rank == npe - 1) m = nn * nn * nn - (npe - 1) * m;
}
m *= 3;
ierr = KSPCreate(PETSC_COMM_WORLD, &ksp);
CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);
CHKERRQ(ierr);
int i;
{
PetscInt Istart, Iend, jj, ic;
const PetscInt NP = (PetscInt)(PetscPowReal((PetscReal)npe, 1.0 / 3.0) + 0.5);
const PetscInt ipx = rank % NP, ipy = (rank % (NP * NP)) / NP, ipz = rank / (NP * NP);
const PetscInt Ni0 = ipx * (nn / NP), Nj0 = ipy * (nn / NP), Nk0 = ipz * (nn / NP);
const PetscInt Ni1 = Ni0 + (m > 0 ? (nn / NP) : 0), Nj1 = Nj0 + (nn / NP), Nk1 = Nk0 + (nn / NP);
PetscInt *d_nnz, *o_nnz, osz[4] = {0, 9, 15, 19}, nbc;
if (npe != NP * NP * NP) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "npe=%d: npe^{1/3} must be integer", npe);
if (nn != NP * (nn / NP)) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "-ne %d: (ne+1)%(npe^{1/3}) must equal zero", ne);
ierr = PetscMalloc1(m + 1, &d_nnz);
CHKERRQ(ierr);
ierr = PetscMalloc1(m + 1, &o_nnz);
CHKERRQ(ierr);
for (i = Ni0, ic = 0; i < Ni1; i++) {
for (j = Nj0; j < Nj1; j++) {
for (k = Nk0; k < Nk1; k++) {
nbc = 0;
if (i == Ni0 || i == Ni1 - 1) nbc++;
if (j == Nj0 || j == Nj1 - 1) nbc++;
if (k == Nk0 || k == Nk1 - 1) nbc++;
for (jj = 0; jj < 3; jj++, ic++) {
d_nnz[ic] = 3 * (27 - osz[nbc]);
o_nnz[ic] = 3 * osz[nbc];
}
}
}
}
if (ic != m) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "ic %D does not equal m %D", ic, m);
ierr = MatCreate(PETSC_COMM_WORLD, &A);
CHKERRQ(ierr);
ierr = MatSetSizes(A, m, m, M, M);
CHKERRQ(ierr);
ierr = MatSetBlockSize(A, 3);
CHKERRQ(ierr);
ierr = MatSetType(A, MATAIJ);
CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A, 0, d_nnz);
CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A, 0, d_nnz, 0, o_nnz);
CHKERRQ(ierr);
ierr = PetscFree(d_nnz);
CHKERRQ(ierr);
ierr = PetscFree(o_nnz);
CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A, &Istart, &Iend);
CHKERRQ(ierr);
if (m != Iend - Istart) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "m %D does not equal Iend %D - Istart %D", m, Iend, Istart);
ierr = VecCreate(PETSC_COMM_WORLD, &x);
CHKERRQ(ierr);
ierr = VecSetSizes(x, m, M);
CHKERRQ(ierr);
ierr = VecSetBlockSize(x, 3);
CHKERRQ(ierr);
ierr = VecSetFromOptions(x);
CHKERRQ(ierr);
ierr = VecDuplicate(x, &rhs);
CHKERRQ(ierr);
ierr = PetscMalloc1(m + 1, &coords);
CHKERRQ(ierr);
coords[m] = -99.0;
PetscReal h = 1.0 / ne;
for (i = Ni0, ic = 0; i < Ni1; i++) {
for (j = Nj0; j < Nj1; j++) {
for (k = Nk0; k < Nk1; k++, ic++) {
coords[3 * ic] = h * (PetscReal)i;
coords[3 * ic + 1] = h * (PetscReal)j;
coords[3 * ic + 2] = h * (PetscReal)k;
}
}
}
}
PetscReal s_r[SIZE_ARRAY_R] = {30, 0.1, 20, 10};
PetscReal x_r[SIZE_ARRAY_R] = {0.5, 0.4, 0.4, 0.4};
PetscReal y_r[SIZE_ARRAY_R] = {0.5, 0.5, 0.4, 0.4};
PetscReal z_r[SIZE_ARRAY_R] = {0.5, 0.45, 0.4, 0.35};
PetscReal r[SIZE_ARRAY_R] = {0.5, 0.5, 0.4, 0.4};
AssembleSystem(A, rhs, s_r[0], x_r[0], y_r[0], z_r[0], r[0], ne, npe, rank, nn, m);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
MatNullSpace matnull;
Vec vec_coords;
PetscScalar* c;
ierr = VecCreate(MPI_COMM_WORLD, &vec_coords);
CHKERRQ(ierr);
ierr = VecSetBlockSize(vec_coords, 3);
CHKERRQ(ierr);
ierr = VecSetSizes(vec_coords, m, PETSC_DECIDE);
CHKERRQ(ierr);
ierr = VecSetUp(vec_coords);
CHKERRQ(ierr);
ierr = VecGetArray(vec_coords, &c);
CHKERRQ(ierr);
for (i = 0; i < m; i++) c[i] = coords[i];
ierr = VecRestoreArray(vec_coords, &c);
CHKERRQ(ierr);
ierr = MatNullSpaceCreateRigidBody(vec_coords, &matnull);
CHKERRQ(ierr);
ierr = MatSetNearNullSpace(A, matnull);
CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&matnull);
CHKERRQ(ierr);
ierr = VecDestroy(&vec_coords);
CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
double time = MPI_Wtime();
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
time = MPI_Wtime() - time;
ierr = PetscPrintf(PETSC_COMM_WORLD, "--- PC setup = %f\n", time);
CHKERRQ(ierr);
float t_time[SIZE_ARRAY_R];
int t_its[SIZE_ARRAY_R];
{
{
ierr = KSPSolve(ksp, rhs, x);
CHKERRQ(ierr);
ierr = KSPReset(ksp);
CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = VecZeroEntries(x);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
time = MPI_Wtime();
ierr = KSPSolve(ksp, rhs, x);
CHKERRQ(ierr);
MPI_Barrier(PETSC_COMM_WORLD);
t_time[i] = MPI_Wtime() - time;
PetscInt its;
ierr = KSPGetIterationNumber(ksp, &its);
CHKERRQ(ierr);
t_its[i] = its;
ierr = ComputeError(A, rhs, x);
CHKERRQ(ierr);
if (i == (SIZE_ARRAY_R - 1))
AssembleSystem(A, rhs, s_r[0], x_r[0], y_r[0], z_r[0], r[0], ne, npe, rank, nn, m);
else
AssembleSystem(A, rhs, s_r[i + 1], x_r[i + 1], y_r[i + 1], z_r[i + 1], r[i + 1], ne, npe, rank, nn, m);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t%d\t%f\n", i + 1, t_its[i], t_time[i]);
CHKERRQ(ierr);
if (i > 0) {
t_its[0] += t_its[i];
t_time[0] += t_time[i];
}
}
if (SIZE_ARRAY_R > 1) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "------------------------\n\t%d\t%f\n", t_its[0], t_time[0]);
CHKERRQ(ierr);
}
}
{
ierr = KSPGetPC(ksp, &pc);
CHKERRQ(ierr);
HpddmCustomOperator H;
H._A = A;
H._M = pc;
H._mv = mv;
H._precond = precond;
H._b = rhs;
H._x = x;
int n;
MatGetLocalSize(A, &n, NULL);
{
ierr = VecZeroEntries(x);
K* pt_rhs;
K* pt_x;
VecGetArray(rhs, &pt_rhs);
VecGetArray(x, &pt_x);
int previous = HpddmOptionVal(opt, "verbosity");
if (previous > 0) HpddmOptionRemove(opt, "verbosity");
HpddmCustomOperatorSolve(&H, n, H._mv, H._precond, pt_rhs, pt_x, 1, &PETSC_COMM_WORLD);
if (previous > 0) {
char buffer[20];
snprintf(buffer, 20, "%d", previous);
char* concat = malloc(strlen("-hpddm_verbosity ") + strlen(buffer) + 1);
strcpy(concat, "-hpddm_verbosity ");
strcat(concat, buffer);
HpddmOptionParseString(opt, concat);
free(concat);
}
VecRestoreArray(x, &pt_x);
VecRestoreArray(rhs, &pt_rhs);
previous = HpddmOptionVal(opt, "krylov_method");
if(previous == 4 || previous == 5) HpddmDestroyRecycling();
ierr = KSPReset(ksp);
CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = VecZeroEntries(x);
CHKERRQ(ierr);
K* pt_rhs;
K* pt_x;
VecGetArray(rhs, &pt_rhs);
VecGetArray(x, &pt_x);
MPI_Barrier(PETSC_COMM_WORLD);
time = MPI_Wtime();
t_its[i] = HpddmCustomOperatorSolve(&H, n, H._mv, H._precond, pt_rhs, pt_x, 1, &PETSC_COMM_WORLD);
MPI_Barrier(PETSC_COMM_WORLD);
t_time[i] = MPI_Wtime() - time;
VecRestoreArray(x, &pt_x);
VecRestoreArray(rhs, &pt_rhs);
ierr = ComputeError(A, rhs, x);
CHKERRQ(ierr);
if (i != (SIZE_ARRAY_R - 1)) {
AssembleSystem(A, rhs, s_r[i + 1], x_r[i + 1], y_r[i + 1], z_r[i + 1], r[i + 1], ne, npe, rank, nn, m);
ierr = KSPSetOperators(ksp, A, A);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
}
}
for (i = 0; i < SIZE_ARRAY_R; ++i) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "%d\t%d\t%f\n", i + 1, t_its[i], t_time[i]);
CHKERRQ(ierr);
if (i > 0) {
t_its[0] += t_its[i];
t_time[0] += t_time[i];
}
}
if (SIZE_ARRAY_R > 1) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "------------------------\n\t%d\t%f\n", t_its[0], t_time[0]);
CHKERRQ(ierr);
}
}
ierr = KSPDestroy(&ksp);
CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr);
ierr = VecDestroy(&rhs);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = PetscFree(coords);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}