Zachary,
I haven't tried to debug your code snippets, but would suggest to take a look
how step-40 sets up and builds the sparsity pattern. There, we call
make_sparsity_pattern(), which really just adds certain entries to the
sparsity pattern like you do, so if you understand how the set up works in
step-40, you should be able to understand what you need to do in your case.
Best
W.
On 12/20/20 10:21 AM, Zachary Streeter wrote:
I should mention how I am creating my dynamic sparsity pattern. The structure
is like this:
dsp.reinit(local_number_of_rows, number_of_columns); // the number of rows is
divided among processors
for (int i =0; i < local_number_of_rows; ++i )
for (int j = 0; j < number_of_columns; ++j )
dsp( i, j ) = stuff_calculated
This gives me a local dsp and I thought the IndexSet add_range() above will
put this local dsp to the correct global index set.
On Sunday, December 20, 2020 at 10:53:33 AM UTC-6 Zachary Streeter wrote:
Hi there,
I am trying to build a parallel PETSc sparse matrix by building a local
sparsity pattern and subsequently distributing the pattern to all
processes so I then have the full sparsity pattern for the PETSc sparse
matrix (I read this needs to be done but please correct me if I am wrong).
When I try to reinit the PETSc sparse matrix I get a segfault so I am
hunting down the problem.
My understanding for “distribute_sparsity_pattern” is it sends local
sparsity patterns to all other processes and saves the full global pattern
in the dynamic sparsity pattern you passed in. So I figured that after I
call this function, my local number of rows should be the global number of
rows but the number of rows is the same as before I called this function
(i.e. the actual local number of rows) so I think I am not using this
function correctly and my PETSc sparse matrix doesn’t have the global
dynamic sparsity pattern I think it must have, which results in a segfault.
NOTE: The matrix is a square matrix with rows and columns of size “nbas *
nchannels” and the rows are divided amongst the processes.
Here is the code for distributing my locally built sparsity pattern dsp:
IndexSet local_owned( nbas * nchannels * nbas * nchannels ); \\ allocate
global sized index set
local_owned.add_range( LocalStart(), LocalEnd() ); \\ start of local row
first column and end of last local row at last column
SparsityTools::distribute_sparsity_pattern( dsp, local_owned, comm,
local_owned );
Here is the code for initializing my PETSc sparse matrix:
std::vector<size_type> local_rows_per_process( num_procs); // allocate a
vector of length number of process
std::vector<size_type> local_columns_per_process( num_procs, nbas *
nchannels); // columns are full length and rows are divided by num_procs
for(int i=0; i < num_procs; ++i )
{
local_rows_per_process[ i ] = i * local_rows; // Saw this in a test but
initially thought this should just all be local_rows for each i
}
Matrix.reinit( comm, dsp, local_rows_per_process,
local_columns_per_process, my_proc);
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