void TestBasicFunctionality() throw (Exception)
{
/*
* We need to make sure here that the matrix is loaded with the appropriate parallel layout. Petsc's
* default puts 1331 rows in each processor. This wouldn't be possible in a real bidomain simulation
* because implies that equations V_665 an Phi_e_665 are solved in different processors.
*/
unsigned num_nodes = 1331;
DistributedVectorFactory factory(num_nodes);
Vec parallel_layout = factory.CreateVec(2);
Mat system_matrix;
PetscTools::ReadPetscObject(system_matrix, "linalg/test/data/matrices/cube_6000elems_half_activated.mat", parallel_layout);
PetscTools::Destroy(parallel_layout);
// Set rhs = A * [1 0 1 0 ... 1 0]'
Vec one_zeros = factory.CreateVec(2);
Vec rhs = factory.CreateVec(2);
for (unsigned node_index=0; node_index<2*num_nodes; node_index+=2)
{
PetscVecTools::SetElement(one_zeros, node_index, 1.0);
PetscVecTools::SetElement(one_zeros, node_index+1, 0.0);
}
PetscVecTools::Finalise(one_zeros);
MatMult(system_matrix, one_zeros, rhs);
PetscTools::Destroy(one_zeros);
LinearSystem ls = LinearSystem(rhs, system_matrix);
ls.SetAbsoluteTolerance(1e-9);
ls.SetKspType("cg");
ls.SetPcType("none");
ls.AssembleFinalLinearSystem();
Vec solution = ls.Solve();
DistributedVector distributed_solution = factory.CreateDistributedVector(solution);
DistributedVector::Stripe vm(distributed_solution, 0);
DistributedVector::Stripe phi_e(distributed_solution, 1);
for (DistributedVector::Iterator index = distributed_solution.Begin();
index!= distributed_solution.End();
++index)
{
/*
* Although we're trying to enforce the solution to be [1 0 ... 1 0], the system is singular and
* therefore it has infinite solutions. I've (migb) found that the use of different preconditioners
* lead to different solutions ([0.8 -0.2 ... 0.8 -0.2], [0.5 -0.5 ... 0.5 -0.5], ...)
*
* If we were using PETSc null space, it would find the solution that satisfies x'*v=0,
* being v the null space of the system (v=[1 1 ... 1])
*/
TS_ASSERT_DELTA(vm[index] - phi_e[index], 1.0, 1e-6);
}
// Coverage (setting PC type after first solve)
ls.SetPcType("blockdiagonal");
PetscTools::Destroy(system_matrix);
PetscTools::Destroy(rhs);
PetscTools::Destroy(solution);
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR <= 3) //PETSc 3.0 to PETSc 3.3
//The PETSc developers changed this one, but later changed it back again!
const PCType pc;
#else
PCType pc;
#endif
PC prec;
KSPGetPC(ls.mKspSolver, &prec);
PCGetType(prec, &pc);
// Although we call it "blockdiagonal", PETSc considers this PC a generic SHELL preconditioner
TS_ASSERT( strcmp(pc,"shell")==0 );
}
void TestChebyshevVsCG() throw (Exception)
{
unsigned num_nodes = 1331;
DistributedVectorFactory factory(num_nodes);
Vec parallel_layout = factory.CreateVec(2);
unsigned cg_its;
unsigned chebyshev_its;
Timer::Reset();
{
Mat system_matrix;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_matrix, "linalg/test/data/matrices/cube_6000elems_half_activated.mat", parallel_layout);
Vec system_rhs;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_rhs, "linalg/test/data/matrices/cube_6000elems_half_activated.vec", parallel_layout);
LinearSystem ls = LinearSystem(system_rhs, system_matrix);
ls.SetMatrixIsSymmetric();
ls.SetAbsoluteTolerance(1e-9);
ls.SetKspType("cg");
ls.SetPcType("bjacobi");
Vec solution = ls.Solve();
cg_its = ls.GetNumIterations();
PetscTools::Destroy(system_matrix);
PetscTools::Destroy(system_rhs);
PetscTools::Destroy(solution);
}
Timer::PrintAndReset("CG");
{
Mat system_matrix;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_matrix, "linalg/test/data/matrices/cube_6000elems_half_activated.mat", parallel_layout);
Vec system_rhs;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_rhs, "linalg/test/data/matrices/cube_6000elems_half_activated.vec", parallel_layout);
LinearSystem ls = LinearSystem(system_rhs, system_matrix);
ls.SetMatrixIsSymmetric();
ls.SetAbsoluteTolerance(1e-9);
ls.SetKspType("chebychev");
ls.SetPcType("bjacobi");
Vec solution = ls.Solve();
chebyshev_its = ls.GetNumIterations();
PetscTools::Destroy(system_matrix);
PetscTools::Destroy(system_rhs);
PetscTools::Destroy(solution);
}
Timer::Print("Chebyshev");
TS_ASSERT_LESS_THAN(cg_its, 15u); // Takes 14 iterations with 16 cores
TS_ASSERT_LESS_THAN(chebyshev_its, 17u); // Takes 16 iterations with 16 cores
PetscTools::Destroy(parallel_layout);
}
void TestBetterThanNoPreconditioning()
{
unsigned num_nodes = 1331;
DistributedVectorFactory factory(num_nodes);
Vec parallel_layout = factory.CreateVec(2);
unsigned point_jacobi_its;
unsigned block_diag_its;
Timer::Reset();
{
Mat system_matrix;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_matrix, "linalg/test/data/matrices/cube_6000elems_half_activated.mat", parallel_layout);
Vec system_rhs;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_rhs, "linalg/test/data/matrices/cube_6000elems_half_activated.vec", parallel_layout);
LinearSystem ls = LinearSystem(system_rhs, system_matrix);
ls.SetAbsoluteTolerance(1e-9);
ls.SetKspType("cg");
ls.SetPcType("none");
Vec solution = ls.Solve();
point_jacobi_its = ls.GetNumIterations();
PetscTools::Destroy(system_matrix);
PetscTools::Destroy(system_rhs);
PetscTools::Destroy(solution);
}
Timer::PrintAndReset("No preconditioning");
{
Mat system_matrix;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_matrix, "linalg/test/data/matrices/cube_6000elems_half_activated.mat", parallel_layout);
Vec system_rhs;
// Note that this test deadlocks if the file's not on the disk
PetscTools::ReadPetscObject(system_rhs, "linalg/test/data/matrices/cube_6000elems_half_activated.vec", parallel_layout);
LinearSystem ls = LinearSystem(system_rhs, system_matrix);
ls.SetAbsoluteTolerance(1e-9);
ls.SetKspType("cg");
ls.SetPcType("blockdiagonal");
Vec solution = ls.Solve();
block_diag_its = ls.GetNumIterations();
// Coverage (setting PC type after using blockdiagonal solve)
ls.SetPcType("blockdiagonal");
PetscTools::Destroy(system_matrix);
PetscTools::Destroy(system_rhs);
PetscTools::Destroy(solution);
}
Timer::Print("Block diagonal preconditioner");
std::cout << block_diag_its << " " << point_jacobi_its << std::endl;
TS_ASSERT_LESS_THAN_EQUALS(block_diag_its, point_jacobi_its);
PetscTools::Destroy(parallel_layout);
}