Sorry, I am not sure why my code’s format changed when I copied and pasted,
trying again...
#include <deal.II/base/conditional_ostream.h>
#include <deal.II/base/index_set.h>
#include <deal.II/base/mpi.h>
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/petsc_sparse_matrix.h>
using namespace dealii;
class OneBodyHamiltonianOperator
{
public:
/**
* Declare type for container size.
*/
using size_type = dealii::types::global_dof_index;
OneBodyHamiltonianOperator(const dealii::IndexSet &a_local_row_set,
const uint32_t a_my_proc,
const uint32_t a_num_procs);
/// Destructor
~OneBodyHamiltonianOperator();
private:
dealii::PETScWrappers::MPI::SparseMatrix m_H1;
dealii::DynamicSparsityPattern m_dynamic_sparsity_pattern;
};
OneBodyHamiltonianOperator::OneBodyHamiltonianOperator(
const dealii::IndexSet &a_local_row_set,
const uint32_t a_my_proc,
const uint32_t a_num_procs)
{
dealii::IndexSet local_owned_rows(a_local_row_set.size());
local_owned_rows.add_range(*a_local_row_set.begin(),
*a_local_row_set.begin() +
a_local_row_set.n_elements());
dealii::IndexSet local_owned_columns(a_local_row_set.size());
local_owned_columns.add_range(0, a_local_row_set.size());
m_dynamic_sparsity_pattern.reinit(a_local_row_set.size(),
a_local_row_set.size(),
local_owned_rows);
for (dealii::IndexSet::ElementIterator i = a_local_row_set.begin();
i != a_local_row_set.end();
++i)
{
for (uint32_t j = 0; j < a_local_row_set.size(); ++j)
{
auto ith = *i;
m_dynamic_sparsity_pattern.add(ith, j);
}
}
m_H1.reinit(local_owned_rows,
local_owned_rows,
m_dynamic_sparsity_pattern,
MPI_COMM_WORLD);
for (dealii::IndexSet::ElementIterator i = a_local_row_set.begin();
i != a_local_row_set.end();
++i)
{
auto ith = *i;
for (uint32_t j = 0; j < m_dynamic_sparsity_pattern.row_length(ith); ++j)
{
m_H1.add(ith,
m_dynamic_sparsity_pattern.column_number(ith, j),
1); // added 1 for test value
}
}
m_H1.compress(dealii::VectorOperation::add);
}
OneBodyHamiltonianOperator::~OneBodyHamiltonianOperator()
{}
void
test(const int &n_proc, const int &my_proc, const ConditionalOStream &pcout)
{
auto nbas = 64;
auto nchannels = 2;
IndexSet local_row_set =
Utilities::create_evenly_distributed_partitioning(my_proc,
n_proc,
nbas * nchannels);
OneBodyHamiltonianOperator H1(local_row_set, my_proc, n_proc);
}
int
main(int argc, char **argv)
{
Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
MPI_Comm comm(MPI_COMM_WORLD);
const auto my_proc = Utilities::MPI::this_mpi_process(comm);
const auto n_proc = Utilities::MPI::n_mpi_processes(comm);
ConditionalOStream pcout(std::cout, (my_proc == 0));
test(n_proc, my_proc, pcout);
return 0;
}
> On Jan 5, 2021, at 11:03 PM, Wolfgang Bangerth <bange...@colostate.edu> wrote:
>
> On 1/5/21 11:32 AM, Zachary Streeter wrote:
>> Yes, I want to use the constructor with the dynamic sparsity pattern. So
>> with your suggestion in mind, would that just be the following:
>> dealii::IndexSet local_owned(a_local_row_set.size());
>> local_owned.add_range(*a_local_row_set.begin(),
>> *a_local_row_set.begin() +
>> a_local_row_set.n_elements());
>> m_dynamic_sparsity_pattern.reinit(a_local_row_set.size(),
>> a_local_row_set.size(),
>> local_owned);
>> std::vector<size_type> local_rows_per_process(num_procs,
>> a_local_row_set.n_elements() );
>
> This creates a vector of size num_procs in which all entries are equal to
> a_local_row_set.n_elements(). But why would all processors have the same
> number of rows? And are you sure that a_local_row_set.n_elements() is the
> same number on all processors anyway?
>
>> std::vector<size_type> local_columns_per_process(num_procs,
>> a_local_row_set.n_elements() ); // before used a_local_row_set.size() here!
>> m_H1.reinit(MPI_COMM_WORLD, m_dynamic_sparsity_pattern,
>> local_rows_per_process, local_columns_per_process, my_proc);
>
> I would try to stick with the fourth reinit() function here:
> https://dealii.org/developer/doxygen/deal.II/classPETScWrappers_1_1MPI_1_1SparseMatrix.html#a645ab9f99494a47ebb6492e92e707130
> It's the simplest to use because every processor only has to pass an IndexSet
> object that describes which rows (and columns) it owns.
>
> Best
> W.
>
> --
> ------------------------------------------------------------------------
> Wolfgang Bangerth email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
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