Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Remove duplicated code and consolidate coo2csr functionality in a single function. #173

Merged
merged 5 commits into from
Jul 2, 2024
Merged

Remove duplicated code and consolidate coo2csr functionality in a single function. #173

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
e27ec57
Make coo2csr a standalone function.
pelesh Jun 23, 2024
d49f561
Remove duplicated coo2csr code.
pelesh Jun 24, 2024
52fa85d
Fix missing header for sort function.
pelesh Jun 25, 2024
f430b29
Rename matrix/utilities.* files
pelesh Jul 2, 2024
31046e4
Fix errors caught by CI.
pelesh Jul 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions resolve/matrix/CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ set(Matrix_SRC
Coo.cpp
MatrixHandler.cpp
MatrixHandlerCpu.cpp
Utilities.cpp
)

# C++ code that depends on CUDA SDK libraries
Expand All @@ -35,6 +36,7 @@ set(Matrix_HEADER_INSTALL
Csr.hpp
Csc.hpp
MatrixHandler.hpp
Utilities.hpp
)

# Build shared library ReSolve::matrix
Expand Down
145 changes: 3 additions & 142 deletions resolve/matrix/Csr.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@

#include "Csr.hpp"
#include "Coo.hpp"
#include <resolve/utilities/misc/IndexValuePair.hpp>
#include <resolve/utilities/logger/Logger.hpp>
#include <resolve/matrix/Utilities.hpp>

namespace ReSolve
{
Expand Down Expand Up @@ -35,7 +35,7 @@ namespace ReSolve
A_coo->symmetric(),
A_coo->expanded())
{
coo2csr(A_coo, memspace);
matrix::coo2csr(A_coo, this, memspace);
}

/**
Expand Down Expand Up @@ -374,149 +374,10 @@ namespace ReSolve
assert(nnz_ == A_coo->getNnz());
assert(is_symmetric_ == A_coo->symmetric()); // <- Do we need to check for this?

return coo2csr(A_coo, memspaceOut);
return matrix::coo2csr(A_coo, this, memspaceOut);
}


int matrix::Csr::coo2csr(matrix::Coo* A_coo, memory::MemorySpace memspace)
{
//count nnzs first
index_type nnz_unpacked = 0;
index_type nnz = A_coo->getNnz();
index_type n = A_coo->getNumRows();
bool symmetric = A_coo->symmetric();
bool expanded = A_coo->expanded();

index_type* nnz_counts = new index_type[n];
std::fill_n(nnz_counts, n, 0);
index_type* coo_rows = A_coo->getRowData(memory::HOST);
index_type* coo_cols = A_coo->getColData(memory::HOST);
real_type* coo_vals = A_coo->getValues( memory::HOST);

index_type* diag_control = new index_type[n]; //for DEDUPLICATION of the diagonal
std::fill_n(diag_control, n, 0);
index_type nnz_unpacked_no_duplicates = 0;
index_type nnz_no_duplicates = nnz;


//maybe check if they exist?
for (index_type i = 0; i < nnz; ++i)
{
nnz_counts[coo_rows[i]]++;
nnz_unpacked++;
nnz_unpacked_no_duplicates++;
if ((coo_rows[i] != coo_cols[i])&& (symmetric) && (!expanded))
{
nnz_counts[coo_cols[i]]++;
nnz_unpacked++;
nnz_unpacked_no_duplicates++;
}
if (coo_rows[i] == coo_cols[i]){
if (diag_control[coo_rows[i]] > 0) {
//duplicate
nnz_unpacked_no_duplicates--;
nnz_no_duplicates--;
}
diag_control[coo_rows[i]]++;
}
}
this->setExpanded(true);
this->setNnzExpanded(nnz_unpacked_no_duplicates);
index_type* csr_ia = new index_type[n+1];
std::fill_n(csr_ia, n + 1, 0);
index_type* csr_ja = new index_type[nnz_unpacked];
real_type* csr_a = new real_type[nnz_unpacked];
index_type* nnz_shifts = new index_type[n];
std::fill_n(nnz_shifts, n , 0);

IndexValuePair* tmp = new IndexValuePair[nnz_unpacked];

csr_ia[0] = 0;

for (index_type i = 1; i < n + 1; ++i){
csr_ia[i] = csr_ia[i - 1] + nnz_counts[i - 1] - (diag_control[i-1] - 1);
}

int r, start;


for (index_type i = 0; i < nnz; ++i){
//which row
r = coo_rows[i];
start = csr_ia[r];

if ((start + nnz_shifts[r]) > nnz_unpacked) {
out::warning() << "index out of bounds (case 1) start: " << start << "nnz_shifts[" << r << "] = " << nnz_shifts[r] << std::endl;
}
if ((r == coo_cols[i]) && (diag_control[r] > 1)) {//diagonal, and there are duplicates
bool already_there = false;
for (index_type j = start; j < start + nnz_shifts[r]; ++j)
{
index_type c = tmp[j].getIdx();
if (c == r) {
real_type val = tmp[j].getValue();
val += coo_vals[i];
tmp[j].setValue(val);
already_there = true;
out::warning() << " duplicate found, row " << c << " adding in place " << j << " current value: " << val << std::endl;
}
}
if (!already_there){ // first time this duplicates appears

tmp[start + nnz_shifts[r]].setIdx(coo_cols[i]);
tmp[start + nnz_shifts[r]].setValue(coo_vals[i]);

nnz_shifts[r]++;
}
} else {//not diagonal
tmp[start + nnz_shifts[r]].setIdx(coo_cols[i]);
tmp[start + nnz_shifts[r]].setValue(coo_vals[i]);
nnz_shifts[r]++;

if ((coo_rows[i] != coo_cols[i]) && (symmetric == 1))
{
r = coo_cols[i];
start = csr_ia[r];

if ((start + nnz_shifts[r]) > nnz_unpacked)
out::warning() << "index out of bounds (case 2) start: " << start << "nnz_shifts[" << r << "] = " << nnz_shifts[r] << std::endl;
tmp[start + nnz_shifts[r]].setIdx(coo_rows[i]);
tmp[start + nnz_shifts[r]].setValue(coo_vals[i]);
nnz_shifts[r]++;
}
}
}
//now sort whatever is inside rows

for (int i = 0; i < n; ++i)
{
//now sorting (and adding 1)
int colStart = csr_ia[i];
int colEnd = csr_ia[i + 1];
int length = colEnd - colStart;
std::sort(&tmp[colStart],&tmp[colStart] + length);
}

for (index_type i = 0; i < nnz_unpacked; ++i)
{
csr_ja[i] = tmp[i].getIdx();
csr_a[i] = tmp[i].getValue();
}

this->setNnz(nnz_no_duplicates);
this->updateData(csr_ia, csr_ja, csr_a, memory::HOST, memspace);

delete [] nnz_counts;
delete [] tmp;
delete [] nnz_shifts;
delete [] csr_ia;
delete [] csr_ja;
delete [] csr_a;
delete [] diag_control;

return 0;
}

/**
* @brief Prints matrix data.
*
Expand Down
2 changes: 0 additions & 2 deletions resolve/matrix/Csr.hpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,6 @@ namespace ReSolve { namespace matrix {

int updateFromCoo(matrix::Coo* mat, memory::MemorySpace memspaceOut);

private:
int coo2csr(matrix::Coo* mat, memory::MemorySpace memspace);
};

}} // namespace ReSolve::matrix
147 changes: 2 additions & 145 deletions resolve/matrix/MatrixHandler.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
#include <resolve/matrix/Csc.hpp>
#include <resolve/matrix/Csr.hpp>
#include <resolve/workspace/LinAlgWorkspace.hpp>
#include <resolve/utilities/misc/IndexValuePair.hpp>
#include <resolve/matrix/Utilities.hpp>
#include "MatrixHandler.hpp"
#include "MatrixHandlerCpu.hpp"

Expand Down Expand Up @@ -116,150 +116,7 @@ namespace ReSolve {
*/
int MatrixHandler::coo2csr(matrix::Coo* A_coo, matrix::Csr* A_csr, memory::MemorySpace memspace)
{
//count nnzs first
index_type nnz_unpacked = 0;
index_type nnz = A_coo->getNnz();
index_type n = A_coo->getNumRows();
bool symmetric = A_coo->symmetric();
bool expanded = A_coo->expanded();

index_type* nnz_counts = new index_type[n];
std::fill_n(nnz_counts, n, 0);
index_type* coo_rows = A_coo->getRowData(memory::HOST);
index_type* coo_cols = A_coo->getColData(memory::HOST);
real_type* coo_vals = A_coo->getValues( memory::HOST);

index_type* diag_control = new index_type[n]; //for DEDUPLICATION of the diagonal
std::fill_n(diag_control, n, 0);
index_type nnz_unpacked_no_duplicates = 0;
index_type nnz_no_duplicates = nnz;


//maybe check if they exist?
for (index_type i = 0; i < nnz; ++i)
{
nnz_counts[coo_rows[i]]++;
nnz_unpacked++;
nnz_unpacked_no_duplicates++;
if ((coo_rows[i] != coo_cols[i])&& (symmetric) && (!expanded))
{
nnz_counts[coo_cols[i]]++;
nnz_unpacked++;
nnz_unpacked_no_duplicates++;
}
if (coo_rows[i] == coo_cols[i]){
if (diag_control[coo_rows[i]] > 0) {
//duplicate
nnz_unpacked_no_duplicates--;
nnz_no_duplicates--;
}
diag_control[coo_rows[i]]++;
}
}
A_csr->setExpanded(true);
A_csr->setNnzExpanded(nnz_unpacked_no_duplicates);
index_type* csr_ia = new index_type[n+1];
std::fill_n(csr_ia, n + 1, 0);
index_type* csr_ja = new index_type[nnz_unpacked];
real_type* csr_a = new real_type[nnz_unpacked];
index_type* nnz_shifts = new index_type[n];
std::fill_n(nnz_shifts, n , 0);

IndexValuePair* tmp = new IndexValuePair[nnz_unpacked];

csr_ia[0] = 0;

for (index_type i = 1; i < n + 1; ++i){
csr_ia[i] = csr_ia[i - 1] + nnz_counts[i - 1] - (diag_control[i-1] - 1);
}

int r, start;


for (index_type i = 0; i < nnz; ++i){
//which row
r = coo_rows[i];
start = csr_ia[r];

if ((start + nnz_shifts[r]) > nnz_unpacked) {
out::warning() << "index out of bounds (case 1) start: " << start << "nnz_shifts[" << r << "] = " << nnz_shifts[r] << std::endl;
}
if ((r == coo_cols[i]) && (diag_control[r] > 1)) {//diagonal, and there are duplicates
bool already_there = false;
for (index_type j = start; j < start + nnz_shifts[r]; ++j)
{
index_type c = tmp[j].getIdx();
if (c == r) {
real_type val = tmp[j].getValue();
val += coo_vals[i];
tmp[j].setValue(val);
already_there = true;
out::warning() << " duplicate found, row " << c << " adding in place " << j << " current value: " << val << std::endl;
}
}
if (!already_there){ // first time this duplicates appears

tmp[start + nnz_shifts[r]].setIdx(coo_cols[i]);
tmp[start + nnz_shifts[r]].setValue(coo_vals[i]);

nnz_shifts[r]++;
}
} else {//not diagonal
tmp[start + nnz_shifts[r]].setIdx(coo_cols[i]);
tmp[start + nnz_shifts[r]].setValue(coo_vals[i]);
nnz_shifts[r]++;

if ((coo_rows[i] != coo_cols[i]) && (symmetric == 1))
{
r = coo_cols[i];
start = csr_ia[r];

if ((start + nnz_shifts[r]) > nnz_unpacked)
out::warning() << "index out of bounds (case 2) start: " << start << "nnz_shifts[" << r << "] = " << nnz_shifts[r] << std::endl;
tmp[start + nnz_shifts[r]].setIdx(coo_rows[i]);
tmp[start + nnz_shifts[r]].setValue(coo_vals[i]);
nnz_shifts[r]++;
}
}
}
//now sort whatever is inside rows

for (int i = 0; i < n; ++i)
{

//now sorting (and adding 1)
int colStart = csr_ia[i];
int colEnd = csr_ia[i + 1];
int length = colEnd - colStart;
std::sort(&tmp[colStart],&tmp[colStart] + length);
}

for (index_type i = 0; i < nnz_unpacked; ++i)
{
csr_ja[i] = tmp[i].getIdx();
csr_a[i] = tmp[i].getValue();
}
#if 0
for (int i = 0; i<n; ++i){
printf("Row: %d \n", i);
for (int j = csr_ia[i]; j<csr_ia[i+1]; ++j){
printf("(%d %16.16f) ", csr_ja[j], csr_a[j]);
}
printf("\n");
}
#endif
A_csr->setNnz(nnz_no_duplicates);
A_csr->updateData(csr_ia, csr_ja, csr_a, memory::HOST, memspace);

delete [] nnz_counts;
delete [] tmp;
delete [] nnz_shifts;
delete [] csr_ia;
delete [] csr_ja;
delete [] csr_a;
delete [] diag_control;

return 0;
return matrix::coo2csr(A_coo, A_csr, memspace);
}

/**
Expand Down
Loading