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SolveGeneralSparseLinearSystemGraphColoring.cu
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SolveGeneralSparseLinearSystemGraphColoring.cu
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#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <assert.h>
#include "Utilities.cuh"
#include <cuda_runtime.h>
#include <cusparse_v2.h>
#define BLOCKSIZE 256
/**************************/
/* SETTING UP THE PROBLEM */
/**************************/
void setUpTheProblem(double **h_A_dense, double **h_x_dense, double **d_A_dense, double **d_x_dense, const int N) {
// --- Host side dense matrix
h_A_dense[0] = (double*)calloc(N * N, sizeof(*h_A_dense));
// --- Column-major ordering
h_A_dense[0][0] = 0.4612f; h_A_dense[0][4] = -0.0006f; h_A_dense[0][8] = 0.f; h_A_dense[0][12] = 0.0f;
h_A_dense[0][1] = -0.0006f; h_A_dense[0][5] = 0.f; h_A_dense[0][9] = 0.0723f; h_A_dense[0][13] = 0.04f;
h_A_dense[0][2] = 0.3566f; h_A_dense[0][6] = 0.0723f; h_A_dense[0][10] = 0.f; h_A_dense[0][14] = 0.0f;
h_A_dense[0][3] = 0.0f; h_A_dense[0][7] = 0.0f; h_A_dense[0][11] = 1.0f; h_A_dense[0][15] = 0.1f;
h_x_dense[0] = (double *)malloc(N * sizeof(double));
h_x_dense[0][0] = 100.0; h_x_dense[0][1] = 200.0; h_x_dense[0][2] = 400.0; h_x_dense[0][3] = 500.0;
// --- Create device arrays and copy host arrays to them
gpuErrchk(cudaMalloc(&d_A_dense[0], N * N * sizeof(double)));
gpuErrchk(cudaMemcpy(d_A_dense[0], h_A_dense[0], N * N * sizeof(double), cudaMemcpyHostToDevice));
gpuErrchk(cudaMalloc(&d_x_dense[0], N * sizeof(double)));
gpuErrchk(cudaMemcpy(d_x_dense[0], h_x_dense[0], N * sizeof(double), cudaMemcpyHostToDevice));
}
/************************/
/* FROM DENSE TO SPARSE */
/************************/
void fromDenseToSparse(const cusparseHandle_t handle, double *d_A_dense, double **d_A, int **d_A_RowIndices, int **d_A_ColIndices, int *nnz,
cusparseMatDescr_t *descrA, const int N) {
cusparseSafeCall(cusparseCreateMatDescr(&descrA[0]));
cusparseSafeCall(cusparseSetMatType (descrA[0], CUSPARSE_MATRIX_TYPE_GENERAL));
cusparseSafeCall(cusparseSetMatIndexBase(descrA[0], CUSPARSE_INDEX_BASE_ZERO));
nnz[0] = 0; // --- Number of nonzero elements in dense matrix
const int lda = N; // --- Leading dimension of dense matrix
// --- Device side number of nonzero elements per row
int *d_nnzPerVector; gpuErrchk(cudaMalloc(&d_nnzPerVector, N * sizeof(int)));
cusparseSafeCall(cusparseDnnz(handle, CUSPARSE_DIRECTION_ROW, N, N, descrA[0], d_A_dense, lda, d_nnzPerVector, &nnz[0]));
// --- Host side number of nonzero elements per row
int *h_nnzPerVector = (int *)malloc(N * sizeof(int));
gpuErrchk(cudaMemcpy(h_nnzPerVector, d_nnzPerVector, N * sizeof(int), cudaMemcpyDeviceToHost));
printf("Number of nonzero elements in dense matrix = %i\n\n", nnz[0]);
for (int i = 0; i < N; ++i) printf("Number of nonzero elements in row %i = %i \n", i, h_nnzPerVector[i]);
printf("\n");
// --- Device side sparse matrix
gpuErrchk(cudaMalloc(&d_A[0], nnz[0] * sizeof(double)));
gpuErrchk(cudaMalloc(&d_A_RowIndices[0], (N + 1) * sizeof(int)));
gpuErrchk(cudaMalloc(&d_A_ColIndices[0], nnz[0] * sizeof(int)));
cusparseSafeCall(cusparseDdense2csr(handle, N, N, descrA[0], d_A_dense, lda, d_nnzPerVector, d_A[0], d_A_RowIndices[0], d_A_ColIndices[0]));
// --- Host side sparse matrix
double *h_A = (double *)malloc(nnz[0] * sizeof(double));
int *h_A_RowIndices = (int *)malloc((N + 1) * sizeof(*h_A_RowIndices));
int *h_A_ColIndices = (int *)malloc(nnz[0] * sizeof(*h_A_ColIndices));
gpuErrchk(cudaMemcpy(h_A, d_A[0], nnz[0] * sizeof(double), cudaMemcpyDeviceToHost));
gpuErrchk(cudaMemcpy(h_A_RowIndices, d_A_RowIndices[0], (N + 1) * sizeof(int), cudaMemcpyDeviceToHost));
gpuErrchk(cudaMemcpy(h_A_ColIndices, d_A_ColIndices[0], nnz[0] * sizeof(int), cudaMemcpyDeviceToHost));
printf("\nOriginal matrix in CSR format\n\n");
for (int i = 0; i < nnz[0]; ++i) printf("A[%i] = %f ", i, h_A[i]); printf("\n");
printf("\n");
for (int i = 0; i < (N + 1); ++i) printf("h_A_RowIndices[%i] = %i \n", i, h_A_RowIndices[i]); printf("\n");
for (int i = 0; i < nnz[0]; ++i) printf("h_A_ColIndices[%i] = %i \n", i, h_A_ColIndices[i]);
}
/******************/
/* GRAPH COLORING */
/******************/
__global__ void setRowIndices(int *d_B_RowIndices, const int N) {
const int tid = threadIdx.x + blockDim.x * blockIdx.x;
if (tid == N) d_B_RowIndices[tid] = N;
else if (tid < N) d_B_RowIndices[tid] = tid;
}
__global__ void setB(double *d_B, const int N) {
const int tid = threadIdx.x + blockDim.x * blockIdx.x;
if (tid < N) d_B[tid] = 1.f;
}
void graphColoring(const cusparseHandle_t handle, const int nnz, const cusparseMatDescr_t descrA, const double fractionToColor, double *d_A,
const int *d_A_RowIndices, const int *d_A_ColIndices, double **d_B, int **d_B_RowIndices, int **d_B_ColIndices,
cusparseMatDescr_t *descrB, const int N) {
cusparseColorInfo_t info; cusparseSafeCall(cusparseCreateColorInfo(&info));
int ncolors;
int *d_coloring; gpuErrchk(cudaMalloc(&d_coloring, N * sizeof(double)));
gpuErrchk(cudaMalloc(&d_B_ColIndices[0], N * sizeof(double)));
cusparseSafeCall(cusparseDcsrcolor(handle, N, nnz, descrA, d_A, d_A_RowIndices, d_A_ColIndices, &fractionToColor, &ncolors, d_coloring,
d_B_ColIndices[0], info));
int *h_coloring = (int *)malloc(N * sizeof(double));
int *h_B_ColIndices = (int *)malloc(N * sizeof(double));
gpuErrchk(cudaMemcpy(h_coloring, d_coloring, N * sizeof(double), cudaMemcpyDeviceToHost));
gpuErrchk(cudaMemcpy(h_B_ColIndices, d_B_ColIndices[0], N * sizeof(double), cudaMemcpyDeviceToHost));
for (int i = 0; i < N; i++) printf("h_coloring = %i; h_B_ColIndices = %i\n", h_coloring[i], h_B_ColIndices[i]);
gpuErrchk(cudaMalloc(&d_B_RowIndices[0], (N + 1) * sizeof(int)));
int *h_B_RowIndices = (int *)malloc((N + 1) * sizeof(double));
setRowIndices<<<iDivUp(N + 1, BLOCKSIZE), BLOCKSIZE>>>(d_B_RowIndices[0], N);
gpuErrchk(cudaMemcpy(h_B_RowIndices, d_B_RowIndices[0], (N + 1) * sizeof(int), cudaMemcpyDeviceToHost));
printf("\n"); for (int i = 0; i <= N; i++) printf("h_B_RowIndices = %i\n", h_B_RowIndices[i]);
gpuErrchk(cudaMalloc(&d_B[0], N * sizeof(double)));
double *h_B = (double *)malloc(N * sizeof(double));
setB<<<iDivUp(N, BLOCKSIZE), BLOCKSIZE>>>(d_B[0], N);
gpuErrchk(cudaMemcpy(h_B, d_B[0], N * sizeof(double), cudaMemcpyDeviceToHost));
printf("\n"); for (int i = 0; i < N; i++) printf("h_B = %f\n", h_B[i]);
// --- Descriptor for sparse mutation matrix B
cusparseSafeCall(cusparseCreateMatDescr(&descrB[0]));
cusparseSafeCall(cusparseSetMatType (descrB[0], CUSPARSE_MATRIX_TYPE_GENERAL));
cusparseSafeCall(cusparseSetMatIndexBase(descrB[0], CUSPARSE_INDEX_BASE_ZERO));
}
/*************************/
/* MATRIX ROW REORDERING */
/*************************/
void matrixRowReordering(const cusparseHandle_t handle, int nnzA, int nnzB, int *nnzC, cusparseMatDescr_t descrA, cusparseMatDescr_t descrB,
cusparseMatDescr_t *descrC, double *d_A, int *d_A_RowIndices, int *d_A_ColIndices, double *d_B, int *d_B_RowIndices,
int *d_B_ColIndices, double **d_C, int **d_C_RowIndices, int **d_C_ColIndices, const int N) {
// --- Descriptor for sparse matrix C
cusparseSafeCall(cusparseCreateMatDescr(&descrC[0]));
cusparseSafeCall(cusparseSetMatType (descrC[0], CUSPARSE_MATRIX_TYPE_GENERAL));
cusparseSafeCall(cusparseSetMatIndexBase(descrC[0], CUSPARSE_INDEX_BASE_ZERO));
const int lda = N; // --- Leading dimension of dense matrix
// --- Device side sparse matrix
gpuErrchk(cudaMalloc(&d_C_RowIndices[0], (N + 1) * sizeof(int)));
// --- Host side sparse matrices
int *h_C_RowIndices = (int *)malloc((N + 1) * sizeof(int));
// --- Performing the matrix - matrix multiplication
int baseC;
int *nnzTotalDevHostPtr = &nnzC[0];
cusparseSafeCall(cusparseSetPointerMode(handle, CUSPARSE_POINTER_MODE_HOST));
cusparseSafeCall(cusparseXcsrgemmNnz(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, CUSPARSE_OPERATION_NON_TRANSPOSE, N, N, N, descrB, nnzB,
d_B_RowIndices, d_B_ColIndices, descrA, nnzA, d_A_RowIndices, d_A_ColIndices, descrC[0], d_C_RowIndices[0],
nnzTotalDevHostPtr));
if (NULL != nnzTotalDevHostPtr) nnzC[0] = *nnzTotalDevHostPtr;
else {
gpuErrchk(cudaMemcpy(&nnzC[0], d_C_RowIndices + N, sizeof(int), cudaMemcpyDeviceToHost));
gpuErrchk(cudaMemcpy(&baseC, d_C_RowIndices, sizeof(int), cudaMemcpyDeviceToHost));
nnzC -= baseC;
}
gpuErrchk(cudaMalloc(&d_C_ColIndices[0], nnzC[0] * sizeof(int)));
gpuErrchk(cudaMalloc(&d_C[0], nnzC[0] * sizeof(double)));
double *h_C = (double *)malloc(nnzC[0] * sizeof(double));
int *h_C_ColIndices = (int *)malloc(nnzC[0] * sizeof(int));
cusparseSafeCall(cusparseDcsrgemm(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, CUSPARSE_OPERATION_NON_TRANSPOSE, N, N, N, descrB, nnzB,
d_B, d_B_RowIndices, d_B_ColIndices, descrA, nnzA, d_A, d_A_RowIndices, d_A_ColIndices, descrC[0],
d_C[0], d_C_RowIndices[0], d_C_ColIndices[0]));
double *h_C_dense = (double*)malloc(N * N * sizeof(double));
double *d_C_dense; gpuErrchk(cudaMalloc(&d_C_dense, N * N * sizeof(double)));
cusparseSafeCall(cusparseDcsr2dense(handle, N, N, descrC[0], d_C[0], d_C_RowIndices[0], d_C_ColIndices[0], d_C_dense, N));
gpuErrchk(cudaMemcpy(h_C , d_C[0], nnzC[0] * sizeof(double), cudaMemcpyDeviceToHost));
gpuErrchk(cudaMemcpy(h_C_RowIndices, d_C_RowIndices[0], (N + 1) * sizeof(int), cudaMemcpyDeviceToHost));
gpuErrchk(cudaMemcpy(h_C_ColIndices, d_C_ColIndices[0], nnzC[0] * sizeof(int), cudaMemcpyDeviceToHost));
printf("\nResult matrix C in CSR format\n\n");
for (int i = 0; i < nnzC[0]; ++i) printf("C[%i] = %f ", i, h_C[i]); printf("\n");
printf("\n");
for (int i = 0; i < (N + 1); ++i) printf("h_C_RowIndices[%i] = %i \n", i, h_C_RowIndices[i]); printf("\n");
printf("\n");
for (int i = 0; i < nnzC[0]; ++i) printf("h_C_ColIndices[%i] = %i \n", i, h_C_ColIndices[i]);
gpuErrchk(cudaMemcpy(h_C_dense, d_C_dense, N * N * sizeof(double), cudaMemcpyDeviceToHost));
for (int j = 0; j < N; j++) {
for (int i = 0; i < N; i++)
printf("%f \t", h_C_dense[i * N + j]);
printf("\n");
}
}
/******************/
/* ROW REORDERING */
/******************/
void rowReordering(const cusparseHandle_t handle, int nnzA, cusparseMatDescr_t descrB, double *d_B, int *d_B_RowIndices, int *d_B_ColIndices,
double *d_x_dense, double **d_y_dense, const int N) {
gpuErrchk(cudaMalloc(&d_y_dense[0], N * sizeof(double)));
const double alpha = 1.;
const double beta = 0.;
cusparseSafeCall(cusparseDcsrmv(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, N, nnzA, &alpha, descrB, d_B, d_B_RowIndices, d_B_ColIndices, d_x_dense,
&beta, d_y_dense[0]));
double *h_y_dense = (double*)malloc(N * sizeof(double));
gpuErrchk(cudaMemcpy(h_y_dense, d_y_dense[0], N * sizeof(double), cudaMemcpyDeviceToHost));
printf("\nResult vector\n\n");
for (int i = 0; i < N; ++i) printf("h_y[%i] = %f ", i, h_y_dense[i]); printf("\n");
}
/*****************************/
/* SOLVING THE LINEAR SYSTEM */
/*****************************/
void LUDecomposition(const cusparseHandle_t handle, int nnzC, cusparseMatDescr_t descrC, double *d_C, int *d_C_RowIndices, int *d_C_ColIndices,
double *d_x_dense, double **d_y_dense, const int N) {
/******************************************/
/* STEP 1: CREATE DESCRIPTORS FOR L AND U */
/******************************************/
cusparseMatDescr_t descr_L = 0;
cusparseSafeCall(cusparseCreateMatDescr (&descr_L));
cusparseSafeCall(cusparseSetMatIndexBase(descr_L, CUSPARSE_INDEX_BASE_ZERO));
cusparseSafeCall(cusparseSetMatType (descr_L, CUSPARSE_MATRIX_TYPE_GENERAL));
cusparseSafeCall(cusparseSetMatFillMode (descr_L, CUSPARSE_FILL_MODE_LOWER));
cusparseSafeCall(cusparseSetMatDiagType (descr_L, CUSPARSE_DIAG_TYPE_UNIT));
cusparseMatDescr_t descr_U = 0;
cusparseSafeCall(cusparseCreateMatDescr (&descr_U));
cusparseSafeCall(cusparseSetMatIndexBase(descr_U, CUSPARSE_INDEX_BASE_ZERO));
cusparseSafeCall(cusparseSetMatType (descr_U, CUSPARSE_MATRIX_TYPE_GENERAL));
cusparseSafeCall(cusparseSetMatFillMode (descr_U, CUSPARSE_FILL_MODE_UPPER));
cusparseSafeCall(cusparseSetMatDiagType (descr_U, CUSPARSE_DIAG_TYPE_NON_UNIT));
/**************************************************************************************************/
/* STEP 2: QUERY HOW MUCH MEMORY USED IN LU FACTORIZATION AND THE TWO FOLLOWING SYSTEM INVERSIONS */
/**************************************************************************************************/
csrilu02Info_t info_C = 0; cusparseSafeCall(cusparseCreateCsrilu02Info (&info_C));
csrsv2Info_t info_L = 0; cusparseSafeCall(cusparseCreateCsrsv2Info (&info_L));
csrsv2Info_t info_U = 0; cusparseSafeCall(cusparseCreateCsrsv2Info (&info_U));
int pBufferSize_M, pBufferSize_L, pBufferSize_U;
cusparseSafeCall(cusparseDcsrilu02_bufferSize(handle, N, nnzC, descrC, d_C, d_C_RowIndices, d_C_ColIndices, info_C, &pBufferSize_M));
cusparseSafeCall(cusparseDcsrsv2_bufferSize (handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, nnzC, descr_L, d_C, d_C_RowIndices, d_C_ColIndices, info_L, &pBufferSize_L));
cusparseSafeCall(cusparseDcsrsv2_bufferSize (handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, nnzC, descr_U, d_C, d_C_RowIndices, d_C_ColIndices, info_U, &pBufferSize_U));
int pBufferSize = max(pBufferSize_M, max(pBufferSize_L, pBufferSize_U));
void *pBuffer = 0; gpuErrchk(cudaMalloc((void**)&pBuffer, pBufferSize));
/************************************************************************************************/
/* STEP 3: ANALYZE THE THREE PROBLEMS: LU FACTORIZATION AND THE TWO FOLLOWING SYSTEM INVERSIONS */
/************************************************************************************************/
int structural_zero;
cusparseSafeCall(cusparseDcsrilu02_analysis(handle, N, nnzC, descrC, d_C, d_C_RowIndices, d_C_ColIndices, info_C, CUSPARSE_SOLVE_POLICY_NO_LEVEL, pBuffer));
cusparseStatus_t status = cusparseXcsrilu02_zeroPivot(handle, info_C, &structural_zero);
if (CUSPARSE_STATUS_ZERO_PIVOT == status){ printf("A(%d,%d) is missing\n", structural_zero, structural_zero); }
cusparseSafeCall(cusparseDcsrsv2_analysis(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, nnzC, descr_L, d_C, d_C_RowIndices, d_C_ColIndices, info_L, CUSPARSE_SOLVE_POLICY_NO_LEVEL, pBuffer));
cusparseSafeCall(cusparseDcsrsv2_analysis(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, nnzC, descr_U, d_C, d_C_RowIndices, d_C_ColIndices, info_U, CUSPARSE_SOLVE_POLICY_USE_LEVEL, pBuffer));
/************************************/
/* STEP 4: FACTORIZATION: A = L * U */
/************************************/
int numerical_zero;
cusparseSafeCall(cusparseDcsrilu02(handle, N, nnzC, descrC, d_C, d_C_RowIndices, d_C_ColIndices, info_C, CUSPARSE_SOLVE_POLICY_NO_LEVEL, pBuffer));
status = cusparseXcsrilu02_zeroPivot(handle, info_C, &numerical_zero);
if (CUSPARSE_STATUS_ZERO_PIVOT == status){ printf("U(%d,%d) is zero\n", numerical_zero, numerical_zero); }
/*********************/
/* STEP 5: L * z = x */
/*********************/
// --- Allocating the intermediate result vector
double *d_z_dense; gpuErrchk(cudaMalloc(&d_z_dense, N * sizeof(double)));
const double alpha = 1.;
cusparseSafeCall(cusparseDcsrsv2_solve(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, nnzC, &alpha, descr_L, d_C, d_C_RowIndices, d_C_ColIndices, info_L, d_x_dense, d_z_dense, CUSPARSE_SOLVE_POLICY_NO_LEVEL, pBuffer));
/*********************/
/* STEP 5: U * y = z */
/*********************/
gpuErrchk(cudaMalloc(&d_y_dense[0], N * sizeof(double)));
cusparseSafeCall(cusparseDcsrsv2_solve(handle, CUSPARSE_OPERATION_NON_TRANSPOSE, N, nnzC, &alpha, descr_U, d_C, d_C_RowIndices, d_C_ColIndices, info_U, d_z_dense, d_y_dense[0], CUSPARSE_SOLVE_POLICY_USE_LEVEL, pBuffer));
double *h_y_dense = (double *)malloc(N * sizeof(double));
gpuErrchk(cudaMemcpy(h_y_dense, d_y_dense[0], N * sizeof(double), cudaMemcpyDeviceToHost));
printf("\n\nFinal result\n");
for (int k=0; k<N; k++) printf("x[%i] = %f\n", k, h_y_dense[k]);
}
/********/
/* MAIN */
/********/
int main()
{
// --- Initialize cuSPARSE
cusparseHandle_t handle; cusparseSafeCall(cusparseCreate(&handle));
/*************************************************/
/* SETTING UP THE ORIGINAL LINEAR SYSTEM PROBLEM */
/*************************************************/
const int N = 4; // --- Number of rows and columns
double *h_A_dense; double *h_x_dense;
double *d_A_dense; double *d_x_dense;
setUpTheProblem(&h_A_dense, &h_x_dense, &d_A_dense, &d_x_dense, N);
/************************/
/* FROM DENSE TO SPARSE */
/************************/
//--- Descriptor for sparse matrix A
cusparseMatDescr_t descrA;
int *d_A_RowIndices, *d_A_ColIndices;
double *d_A;
int nnzA;
fromDenseToSparse(handle, d_A_dense, &d_A, &d_A_RowIndices, &d_A_ColIndices, &nnzA, &descrA, N);
/******************/
/* GRAPH COLORING */
/******************/
const double fractionToColor = 0.95;
int *d_B_RowIndices, *d_B_ColIndices;
double *d_B;
int nnzB;
cusparseMatDescr_t descrB;
graphColoring(handle, nnzB, descrA, fractionToColor, d_A, d_A_RowIndices, d_A_ColIndices, &d_B, &d_B_RowIndices, &d_B_ColIndices, &descrB, N);
/*************************/
/* MATRIX ROW REORDERING */
/*************************/
int nnzC;
int *d_C_RowIndices, *d_C_ColIndices;
double *d_C;
cusparseMatDescr_t descrC;
matrixRowReordering(handle, nnzA, nnzB, &nnzC, descrA, descrB, &descrC, d_A, d_A_RowIndices, d_A_ColIndices, d_B, d_B_RowIndices, d_B_ColIndices,
&d_C, &d_C_RowIndices, &d_C_ColIndices, N);
/******************/
/* ROW REORDERING */
/******************/
double *d_y_dense;
rowReordering(handle, nnzA, descrB, d_B, d_B_RowIndices, d_B_ColIndices, d_x_dense, &d_y_dense, N);
/*****************************/
/* SOLVING THE LINEAR SYSTEM */
/*****************************/
double *d_xsol_dense;
LUDecomposition(handle, nnzC, descrC, d_C, d_C_RowIndices, d_C_ColIndices, d_y_dense, &d_xsol_dense, N);
}