Refactor matrix file I/O (#184)

* Import proper CSR from Matrix Market file. * Remove nnz_expanded_ sparse matrix member variable and supporting accessor methods (i.e. resolve document invariants for nnz_expanded_ or remove it entirely) resolves #166. * Fix ReSolve::io::writeMatrixToFile calls Sparse::print, which writes out 0-indexed coordinates of matrix data, when the matrix market coordinate format is 1-indexed. Resolves #179. * Resolve Sparse::updateData reads nnz from nnz_expanded_ if the is_expanded_ flag is set. Resolves #176. * Update tests to verify the new matrix I/O code. * Improve doxygen documentation in io.cpp.
ORNL · Sep 20, 2024 · b326fbd · b326fbd
1 parent cc8e57a
commit b326fbd
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diff --git a/README.md b/README.md
@@ -91,6 +91,7 @@ Primary authors of this project are Kasia &#346;wirydowicz and Slaven Peles.
 
 ReSolve project would not be possible without significant contributions from (in alphabetic order):
 - Maksudul Alam
+- Kaleb Brunhoeber
 - Ryan Danehy
 - Nicholson Koukpaizan
 - Jaelyn Litzinger

diff --git a/examples/r_KLU_GLU.cpp b/examples/r_KLU_GLU.cpp
@@ -35,7 +35,6 @@ int main(int argc, char *argv[])
   std::string matrixFileNameFull;
   std::string rhsFileNameFull;
 
-  ReSolve::matrix::Coo* A_coo;
   ReSolve::matrix::Csr* A;
   ReSolve::LinAlgWorkspaceCUDA* workspace_CUDA = new ReSolve::LinAlgWorkspaceCUDA;
   workspace_CUDA->initializeHandles();
@@ -82,39 +81,34 @@ int main(int argc, char *argv[])
       std::cout << "Failed to open file " << rhsFileNameFull << "\n";
       return -1;
     }
+    bool is_expand_symmetric = true;
     if (i == 0) {
-      A_coo = ReSolve::io::readMatrixFromFile(mat_file);
-      A = new ReSolve::matrix::Csr(A_coo->getNumRows(),
-                                   A_coo->getNumColumns(),
-                                   A_coo->getNnz(),
-                                   A_coo->symmetric(),
-                                   A_coo->expanded());
-
-      rhs = ReSolve::io::readRhsFromFile(rhs_file);
+      A = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
+
+      rhs = ReSolve::io::createArrayFromFile(rhs_file);
       x = new real_type[A->getNumRows()];
       vec_rhs = new vector_type(A->getNumRows());
       vec_x = new vector_type(A->getNumRows());
       vec_x->allocate(ReSolve::memory::HOST);//for KLU
       vec_x->allocate(ReSolve::memory::DEVICE);
       vec_r = new vector_type(A->getNumRows());
     } else {
-      ReSolve::io::readAndUpdateMatrix(mat_file, A_coo);
-      ReSolve::io::readAndUpdateRhs(rhs_file, &rhs);
+      ReSolve::io::updateMatrixFromFile(mat_file, A);
+      ReSolve::io::updateArrayFromFile(rhs_file, &rhs);
     }
     std::cout<<"Finished reading the matrix and rhs, size: "<<A->getNumRows()<<" x "<<A->getNumColumns()<< ", nnz: "<< A->getNnz()<< ", symmetric? "<<A->symmetric()<< ", Expanded? "<<A->expanded()<<std::endl;
     mat_file.close();
     rhs_file.close();
 
-    //Now convert to CSR.
+    // Update host and device data.
     if (i < 1) {
-      A->updateFromCoo(A_coo, ReSolve::memory::HOST);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
       vec_rhs->setDataUpdated(ReSolve::memory::HOST);
     } else { 
-      A->updateFromCoo(A_coo, ReSolve::memory::DEVICE);
+      A->copyData(ReSolve::memory::DEVICE);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::DEVICE);
     }
-    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnzExpanded()<<std::endl;
+    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnz()<<std::endl;
     //Now call direct solver
     int status;
     if (i < 1) {

diff --git a/examples/r_KLU_GLU_matrix_values_update.cpp b/examples/r_KLU_GLU_matrix_values_update.cpp
@@ -37,9 +37,8 @@ int main(int argc, char *argv[])
   std::string matrixFileNameFull;
   std::string rhsFileNameFull;
 
-  ReSolve::matrix::Coo* A_coo;
-  ReSolve::matrix::Coo* A_exp_coo;
   ReSolve::matrix::Csr* A;
+  ReSolve::matrix::Csr* A_exp;
   ReSolve::LinAlgWorkspaceCUDA* workspace_CUDA = new ReSolve::LinAlgWorkspaceCUDA;
   workspace_CUDA->initializeHandles();
   ReSolve::MatrixHandler* matrix_handler =  new ReSolve::MatrixHandler(workspace_CUDA);
@@ -84,15 +83,11 @@ int main(int argc, char *argv[])
       std::cout << "Failed to open file " << rhsFileNameFull << "\n";
       return -1;
     }
+    bool is_expand_symmetric = true;
     if (i == 0) {
-      A_coo = ReSolve::io::readMatrixFromFile(mat_file);
-      A = new ReSolve::matrix::Csr(A_coo->getNumRows(),
-                                   A_coo->getNumColumns(),
-                                   A_coo->getNnz(),
-                                   A_coo->symmetric(),
-                                   A_coo->expanded());
-
-      rhs = ReSolve::io::readRhsFromFile(rhs_file);
+      A = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
+
+      rhs = ReSolve::io::createArrayFromFile(rhs_file);
       x = new real_type[A->getNumRows()];
       vec_rhs = new vector_type(A->getNumRows());
       vec_x = new vector_type(A->getNumRows());
@@ -101,29 +96,28 @@ int main(int argc, char *argv[])
       vec_r = new vector_type(A->getNumRows());
     } else {
       if (i==1) {
-        A_exp_coo = ReSolve::io::readMatrixFromFile(mat_file);
+        A_exp = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
       } else {
-        ReSolve::io::readAndUpdateMatrix(mat_file, A_exp_coo);
+        ReSolve::io::updateMatrixFromFile(mat_file, A_exp);
       }
       std::cout<<"Updating values of A_coo!"<<std::endl; 
-      A_coo->updateValues(A_exp_coo->getValues(ReSolve::memory::HOST), ReSolve::memory::HOST, ReSolve::memory::HOST);
-      //ReSolve::io::readAndUpdateMatrix(mat_file, A_coo);
-      ReSolve::io::readAndUpdateRhs(rhs_file, &rhs);
+      A->updateValues(A_exp->getValues(ReSolve::memory::HOST), ReSolve::memory::HOST, ReSolve::memory::HOST);
+      //ReSolve::io::updateMatrixFromFile(mat_file, A);
+      ReSolve::io::updateArrayFromFile(rhs_file, &rhs);
     }
       std::cout<<"Finished reading the matrix and rhs, size: "<<A->getNumRows()<<" x "<<A->getNumColumns()<< ", nnz: "<< A->getNnz()<< ", symmetric? "<<A->symmetric()<< ", Expanded? "<<A->expanded()<<std::endl;
       mat_file.close();
       rhs_file.close();
 
-      //Now convert to CSR.
+      // Update host and device data.
       if (i < 1) { 
-        A->updateFromCoo(A_coo, ReSolve::memory::HOST);
         vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
         vec_rhs->setDataUpdated(ReSolve::memory::HOST);
       } else { 
-        A->updateFromCoo(A_coo, ReSolve::memory::DEVICE);
+        A->copyData(ReSolve::memory::DEVICE);
         vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::DEVICE);
       }
-      std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnzExpanded()<<std::endl;
+      std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnz()<<std::endl;
       //Now call direct solver
       int status;
       if (i < 1){
@@ -165,6 +159,7 @@ int main(int argc, char *argv[])
 
     //now DELETE
     delete A;
+    delete A_exp;
     delete KLU;
     delete GLU;
     delete [] x;

diff --git a/examples/r_KLU_KLU.cpp b/examples/r_KLU_KLU.cpp
@@ -35,7 +35,6 @@ int main(int argc, char *argv[])
   std::string matrixFileNameFull;
   std::string rhsFileNameFull;
 
-  ReSolve::matrix::Coo* A_coo;
   ReSolve::matrix::Csr* A;
   ReSolve::LinAlgWorkspaceCpu* workspace = new ReSolve::LinAlgWorkspaceCpu();
   ReSolve::MatrixHandler* matrix_handler = new ReSolve::MatrixHandler(workspace);
@@ -80,22 +79,18 @@ int main(int argc, char *argv[])
       std::cout << "Failed to open file " << rhsFileNameFull << "\n";
       return -1;
     }
+    bool is_expand_symmetric = true;
     if (i == 0) {
-      A_coo = ReSolve::io::readMatrixFromFile(mat_file);
-      A = new ReSolve::matrix::Csr(A_coo->getNumRows(),
-                                   A_coo->getNumColumns(),
-                                   A_coo->getNnz(),
-                                   A_coo->symmetric(),
-                                   A_coo->expanded());
-
-      rhs = ReSolve::io::readRhsFromFile(rhs_file);
+      A = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
+
+      rhs = ReSolve::io::createArrayFromFile(rhs_file);
       x = new real_type[A->getNumRows()];
       vec_rhs = new vector_type(A->getNumRows());
       vec_x = new vector_type(A->getNumRows());
       vec_r = new vector_type(A->getNumRows());
     } else {
-      ReSolve::io::readAndUpdateMatrix(mat_file, A_coo);
-      ReSolve::io::readAndUpdateRhs(rhs_file, &rhs);
+      ReSolve::io::updateMatrixFromFile(mat_file, A);
+      ReSolve::io::updateArrayFromFile(rhs_file, &rhs);
     }
     std::cout << "Finished reading the matrix and rhs, size: " << A->getNumRows()
               << " x "           << A->getNumColumns()
@@ -105,16 +100,14 @@ int main(int argc, char *argv[])
     mat_file.close();
     rhs_file.close();
 
-    //Now convert to CSR.
+    // Update data.
     if (i < 2) { 
-      A->updateFromCoo(A_coo, ReSolve::memory::HOST);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
       vec_rhs->setDataUpdated(ReSolve::memory::HOST);
     } else { 
-      A->updateFromCoo(A_coo, ReSolve::memory::HOST);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
     }
-    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnzExpanded()<<std::endl;
+    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnz()<<std::endl;
     //Now call direct solver
     int status;
 

diff --git a/examples/r_KLU_KLU_standalone.cpp b/examples/r_KLU_KLU_standalone.cpp
@@ -31,7 +31,6 @@ int main(int argc, char *argv[])
   std::string fileId;
   std::string rhsId;
 
-  ReSolve::matrix::Coo* A_coo;
   ReSolve::matrix::Csr* A;
   ReSolve::LinAlgWorkspaceCpu* workspace = new ReSolve::LinAlgWorkspaceCpu();
   ReSolve::MatrixHandler* matrix_handler = new ReSolve::MatrixHandler(workspace);
@@ -65,14 +64,10 @@ int main(int argc, char *argv[])
     std::cout << "Failed to open file " << rhsFileName << "\n";
     return -1;
   }
-  A_coo = ReSolve::io::readMatrixFromFile(mat_file);
-  A = new ReSolve::matrix::Csr(A_coo->getNumRows(),
-                               A_coo->getNumColumns(),
-                               A_coo->getNnz(),
-                               A_coo->symmetric(),
-                               A_coo->expanded());
-
-  rhs = ReSolve::io::readRhsFromFile(rhs_file);
+  bool is_expand_symmetric = true;
+  A = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
+
+  rhs = ReSolve::io::createArrayFromFile(rhs_file);
   x = new real_type[A->getNumRows()];
   vec_rhs = new vector_type(A->getNumRows());
   vec_x = new vector_type(A->getNumRows());
@@ -81,11 +76,9 @@ int main(int argc, char *argv[])
   mat_file.close();
   rhs_file.close();
 
-  //Now convert to CSR.
-  A->updateFromCoo(A_coo, ReSolve::memory::HOST);
   vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
   vec_rhs->setDataUpdated(ReSolve::memory::HOST);
-  std::cout << "COO to CSR completed. Expanded NNZ: " << A->getNnzExpanded() << std::endl;
+  std::cout << "COO to CSR completed. Expanded NNZ: " << A->getNnz() << std::endl;
   //Now call direct solver
   int status;
   KLU->setup(A);

diff --git a/examples/r_KLU_cusolverrf_redo_factorization.cpp b/examples/r_KLU_cusolverrf_redo_factorization.cpp
@@ -35,7 +35,6 @@ int main(int argc, char *argv[] )
   std::string matrixFileNameFull;
   std::string rhsFileNameFull;
 
-  ReSolve::matrix::Coo* A_coo;
   ReSolve::matrix::Csr* A;
 
   ReSolve::LinAlgWorkspaceCUDA* workspace_CUDA = new ReSolve::LinAlgWorkspaceCUDA;
@@ -93,37 +92,32 @@ int main(int argc, char *argv[] )
       std::cout << "Failed to open file " << rhsFileNameFull << "\n";
       return -1;
     }
+    bool is_expand_symmetric = true;
     if (i == 0) {
-      A_coo = ReSolve::io::readMatrixFromFile(mat_file);
-      A = new ReSolve::matrix::Csr(A_coo->getNumRows(),
-                                   A_coo->getNumColumns(),
-                                   A_coo->getNnz(),
-                                   A_coo->symmetric(),
-                                   A_coo->expanded());
-
-      rhs = ReSolve::io::readRhsFromFile(rhs_file);
+      A = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
+
+      rhs = ReSolve::io::createArrayFromFile(rhs_file);
       x = new real_type[A->getNumRows()];
       vec_rhs = new vector_type(A->getNumRows());
       vec_x = new vector_type(A->getNumRows());
       vec_r = new vector_type(A->getNumRows());
     } else {
-      ReSolve::io::readAndUpdateMatrix(mat_file, A_coo);
-      ReSolve::io::readAndUpdateRhs(rhs_file, &rhs);
+      ReSolve::io::updateMatrixFromFile(mat_file, A);
+      ReSolve::io::updateArrayFromFile(rhs_file, &rhs);
     }
     std::cout<<"Finished reading the matrix and rhs, size: "<<A->getNumRows()<<" x "<<A->getNumColumns()<< ", nnz: "<< A->getNnz()<< ", symmetric? "<<A->symmetric()<< ", Expanded? "<<A->expanded()<<std::endl;
     mat_file.close();
     rhs_file.close();
 
-    //Now convert to CSR.
+    // Update host and device data.
     if (i < 2) { 
-      matrix_handler->coo2csr(A_coo, A, ReSolve::memory::HOST);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
       vec_rhs->setDataUpdated(ReSolve::memory::HOST);
     } else { 
-      matrix_handler->coo2csr(A_coo, A, ReSolve::memory::DEVICE);
+      A->copyData(ReSolve::memory::DEVICE);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::DEVICE);
     }
-    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnzExpanded()<<std::endl;
+    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnz()<<std::endl;
     //Now call direct solver
     if (i < 2) {
       KLU->setup(A);
@@ -215,7 +209,6 @@ int main(int argc, char *argv[] )
 
   //now DELETE
   delete A;
-  delete A_coo;
   delete KLU;
   delete Rf;
   delete [] x;

diff --git a/examples/r_KLU_rf.cpp b/examples/r_KLU_rf.cpp
@@ -35,7 +35,6 @@ int main(int argc, char *argv[] )
   std::string matrixFileNameFull;
   std::string rhsFileNameFull;
 
-  ReSolve::matrix::Coo* A_coo;
   ReSolve::matrix::Csr* A;
 
   ReSolve::LinAlgWorkspaceCUDA* workspace_CUDA = new ReSolve::LinAlgWorkspaceCUDA;
@@ -82,38 +81,33 @@ int main(int argc, char *argv[] )
       std::cout << "Failed to open file " << rhsFileNameFull << "\n";
       return -1;
     }
+    bool is_expand_symmetric = true;
     if (i == 0) {
-      A_coo = ReSolve::io::readMatrixFromFile(mat_file);
-      A = new ReSolve::matrix::Csr(A_coo->getNumRows(),
-                                   A_coo->getNumColumns(),
-                                   A_coo->getNnz(),
-                                   A_coo->symmetric(),
-                                   A_coo->expanded());
-
-      rhs = ReSolve::io::readRhsFromFile(rhs_file);
+      A = ReSolve::io::createCsrFromFile(mat_file, is_expand_symmetric);
+
+      rhs = ReSolve::io::createArrayFromFile(rhs_file);
       x = new real_type[A->getNumRows()];
       vec_rhs = new vector_type(A->getNumRows());
       vec_x = new vector_type(A->getNumRows());
       vec_r = new vector_type(A->getNumRows());
     }
     else {
-      ReSolve::io::readAndUpdateMatrix(mat_file, A_coo);
-      ReSolve::io::readAndUpdateRhs(rhs_file, &rhs);
+      ReSolve::io::updateMatrixFromFile(mat_file, A);
+      ReSolve::io::updateArrayFromFile(rhs_file, &rhs);
     }
     std::cout<<"Finished reading the matrix and rhs, size: "<<A->getNumRows()<<" x "<<A->getNumColumns()<< ", nnz: "<< A->getNnz()<< ", symmetric? "<<A->symmetric()<< ", Expanded? "<<A->expanded()<<std::endl;
     mat_file.close();
     rhs_file.close();
 
-    //Now convert to CSR.
+    // Update host and device data.
     if (i < 2) { 
-      A->updateFromCoo(A_coo, ReSolve::memory::HOST);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::HOST);
       vec_rhs->setDataUpdated(ReSolve::memory::HOST);
     } else { 
-      A->updateFromCoo(A_coo, ReSolve::memory::DEVICE);
+      A->copyData(ReSolve::memory::DEVICE);
       vec_rhs->update(rhs, ReSolve::memory::HOST, ReSolve::memory::DEVICE);
     }
-    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnzExpanded()<<std::endl;
+    std::cout<<"COO to CSR completed. Expanded NNZ: "<< A->getNnz()<<std::endl;
     //Now call direct solver
     int status;
     if (i < 2){