CUDA to solve many “small/moderate” linear systems

Question

Some background info on the problem I am trying to speed up using CUDA:

I have a large number of small/moderate same-sized linear systems I need to solve independently. Each linear system is square, real, dense, invertible, and non-symmetric. These are actually matrix systems so each system look like, AX = B, where A, X, and B are (nxn) matrixes.

In this previous question I ask CUBLAS batch and matrix sizes , where I learn cuBLAS batch operations give best performance for matrix of size 100x100 or smaller.

I still have an issue because the matrices I am working with have 100 < n < 700. So, the matrices are of moderate size where cuBLAS batch operations are not give best performance, and regular BLAS (cusolverDnDgetrf, cusolverDnDgetrs) also are not give better performance than MATLAB (look at timings below).

I did some timing compared to MATLAB, for solving a single system, and found regular BLAS is better for matrices of size (4096x4096) or larger. I make a random matrix of size (nxn), for n=64,256,512,1024,4096,16384, and only time the factorization and back/forward solve, no transfers across PCIE.

DOUBLE PRECISION CUDA (GTX 1080ti) vs MATLAB (backslash)

(GPU) 64: 0.001157 sec (MATLAB) 64: 0.000205 sec

(GPU) 256: 0.01161 sec (MATLAB) 256: 0.007762 sec

(GPU) 512: 0.026348 sec (MATLAB) 512: 0.008550 sec

(GPU) 1024: 0.064357 sec (MATLAB) 1024: 0.036280 sec

(GPU) 4096: 0.734908 sec (MATLAB) 4096: 1.174442 sec

(GPU) 16384: 32.962229 sec (MATLAB) 16384: 68.691236 sec

These timing make me conclude that iterating one by one over my matrices calling non-batch inversion method will be slower than MATLAB. Also, for my moderate sized matrices, batch cuBLAS batch inversion method will not perform well, according to CUBLAS batch and matrix sizes .

Is there other approach I should consider to speed up my code with CUDA? Or am I misunderstanding something?

 /*  How to use
 *      ./cuSolverDn_LinearSolver                     // Default: cholesky
 *     ./cuSolverDn_LinearSolver -R=chol -filefile>   // cholesky factorization
 *     ./cuSolverDn_LinearSolver -R=lu -file<file>     // LU with partial pivoting
 *     ./cuSolverDn_LinearSolver -R=qr -file<file>     // QR factorization
 *
 *  Remark: the absolute error on solution x is meaningless without knowing condition number of A.
 *     The relative error on residual should be close to machine zero, i.e. 1.e-15.
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <assert.h>

#include <cuda_runtime.h>

#include "cublas_v2.h"
#include "cusolverDn.h"
#include "helper_cuda.h"

#include "helper_cusolver.h"
int linearSolverLU(
    cusolverDnHandle_t handle,
    int n,
    const double *Acopy,
    int lda,
    const double *b,
    double *x)
{
    int bufferSize = 0;
    int *info = NULL;
    double *buffer = NULL;
    double *A = NULL;
    int *ipiv = NULL; // pivoting sequence
    int h_info = 0;
    double start, stop;
    double time_solve;

    checkCudaErrors(cusolverDnDgetrf_bufferSize(handle, n, n, (double*)Acopy, lda, &bufferSize));

    checkCudaErrors(cudaMalloc(&info, sizeof(int)));
    checkCudaErrors(cudaMalloc(&buffer, sizeof(double)*bufferSize));
    checkCudaErrors(cudaMalloc(&A, sizeof(double)*lda*n));
    checkCudaErrors(cudaMalloc(&ipiv, sizeof(int)*n));


    // prepare a copy of A because getrf will overwrite A with L
    checkCudaErrors(cudaMemcpy(A, Acopy, sizeof(double)*lda*n, cudaMemcpyDeviceToDevice));
    checkCudaErrors(cudaMemset(info, 0, sizeof(int)));

    start = second();
    start = second();

    checkCudaErrors(cusolverDnDgetrf(handle, n, n, A, lda, buffer, ipiv, info));
    checkCudaErrors(cudaMemcpy(&h_info, info, sizeof(int), cudaMemcpyDeviceToHost));

    if ( 0 != h_info ){
        fprintf(stderr, "Error: LU factorization failed\n");
    }

    //checkCudaErrors(cudaMemcpy(x, b, sizeof(double)*n, cudaMemcpyDeviceToDevice));
    checkCudaErrors(cudaMemcpy(x, b, sizeof(double)*lda*n, cudaMemcpyDeviceToDevice));
    //checkCudaErrors(cusolverDnDgetrs(handle, CUBLAS_OP_N, n, 1, A, lda, ipiv, x, n, info));
    checkCudaErrors(cusolverDnDgetrs(handle, CUBLAS_OP_N, n, n, A, lda, ipiv, x, n, info));
    checkCudaErrors(cudaDeviceSynchronize());
    stop = second();

    time_solve = stop - start;
    fprintf (stdout, "timing: LU = %10.6f sec\n", time_solve);

    if (info  ) { checkCudaErrors(cudaFree(info  )); }
    if (buffer) { checkCudaErrors(cudaFree(buffer)); }
    if (A     ) { checkCudaErrors(cudaFree(A)); }
    if (ipiv  ) { checkCudaErrors(cudaFree(ipiv));}

    return 0;
}
void generate_random_dense_matrix(int M, int N, double **outA)
{
    int i, j;
    double rMax = (double)RAND_MAX;
    double *A   = (double *)malloc(sizeof(double) * M * N);

    // For each column
    for (j = 0; j < N; j++)
    {
        // For each row
        for (i = 0; i < M; i++)
        {
            double dr = (double)rand();
            A[j * M + i] = (dr / rMax) * 100.0;
        //printf("A[j * M + i] = %f \n",A[j * M + i]);
        }
    }

    *outA = A;
}

int main (int argc, char *argv[])
{
    struct testOpts opts;
    cusolverDnHandle_t handle = NULL;
    cublasHandle_t cublasHandle = NULL; // used in residual evaluation
    cudaStream_t stream = NULL;

    int rowsA = 0; // number of rows of A
    int colsA = 0; // number of columns of A
    int nnzA  = 0; // number of nonzeros of A
    int baseA = 0; // base index in CSR format
    int lda   = 0; // leading dimension in dense matrix

    // CSR(A) from I/O
    int *h_csrRowPtrA = NULL;
    int *h_csrColIndA = NULL;
    double *h_csrValA = NULL;

    double *h_A = NULL; // dense matrix from CSR(A)
    double *h_x = NULL; // a copy of d_x
    double *h_b = NULL; // b = ones(m,1)
    double *h_r = NULL; // r = b - A*x, a copy of d_r

    double *d_A = NULL; // a copy of h_A
    double *d_x = NULL; // x = A \ b
    double *d_b = NULL; // a copy of h_b
    double *d_r = NULL; // r = b - A*x

    // the constants are used in residual evaluation, r = b - A*x
    const double minus_one = -1.0;
    const double one = 1.0;

    double x_inf = 0.0;
    double r_inf = 0.0;
    double A_inf = 0.0;
    int errors = 0;


    colsA = 660;
    rowsA = colsA;
    int NN = colsA;
    int MM = rowsA;
    lda = rowsA;

    // Generate inputs
    srand(9384);  
    generate_random_dense_matrix(MM, NN, &h_A);
    generate_random_dense_matrix(MM, NN, &h_b);

    parseCommandLineArguments(argc, argv, opts);

    if (NULL == opts.testFunc)
    {
        //opts.testFunc = "chol"; // By default running Cholesky as NO solver selected with -R option.
    opts.testFunc = "lu";  
    //opts.testFunc = "qr"; 
    }

    findCudaDevice(argc, (const char **)argv);

    /*
    printf("step 1: read matrix market format\n");

    if (opts.sparse_mat_filename == NULL)
    {
        opts.sparse_mat_filename =  sdkFindFilePath("gr_900_900_crg.mtx", argv[0]);
        if (opts.sparse_mat_filename != NULL)
            printf("Using default input file [%s]\n", opts.sparse_mat_filename);
        else
            printf("Could not find gr_900_900_crg.mtx\n");
    }
    else
    {
        printf("Using input file [%s]\n", opts.sparse_mat_filename);
    }

    if (opts.sparse_mat_filename == NULL)
    {
        fprintf(stderr, "Error: input matrix is not provided\n");
        return EXIT_FAILURE;
    }

    if (loadMMSparseMatrix<double>(opts.sparse_mat_filename, 'd', true , &rowsA, &colsA,
               &nnzA, &h_csrValA, &h_csrRowPtrA, &h_csrColIndA, true))
    {
        exit(EXIT_FAILURE);
    }
    baseA = h_csrRowPtrA[0]; // baseA = {0,1}

    printf("sparse matrix A is %d x %d with %d nonzeros, base=%d\n", rowsA, colsA, nnzA, baseA);

    if ( rowsA != colsA )
    {
        fprintf(stderr, "Error: only support square matrix\n");
        exit(EXIT_FAILURE);
    }

    printf("step 2: convert CSR(A) to dense matrix\n");

    lda = opts.lda ? opts.lda : rowsA;
    if (lda < rowsA)
    {
        fprintf(stderr, "Error: lda must be greater or equal to dimension of A\n");
        exit(EXIT_FAILURE);
    }
    */
    //h_A = (double*)malloc(sizeof(double)*lda*colsA);
    h_x = (double*)malloc(sizeof(double)*lda*colsA);
    //h_b = (double*)malloc(sizeof(double)*rowsA);
    h_r = (double*)malloc(sizeof(double)*lda*rowsA);
    assert(NULL != h_A);
    assert(NULL != h_x);
    assert(NULL != h_b);
    assert(NULL != h_r);

    /*
    memset(h_A, 0, sizeof(double)*lda*colsA); 
    for(int row = 0 ; row < rowsA ; row++)
    {
        const int start = h_csrRowPtrA[row  ] - baseA;
        const int end   = h_csrRowPtrA[row+1] - baseA;
        for(int colidx = start ; colidx < end ; colidx++)
        {
            const int col = h_csrColIndA[colidx] - baseA;
            const double Areg = h_csrValA[colidx];
            h_A[row + col*lda] = Areg;
        }
    }

    printf("step 3: set right hand side vector (b) to 1\n");
    for(int row = 0 ; row < rowsA ; row++)
    {
        h_b[row] = 1.0;
    }
    */
    // verify if A is symmetric or not.
    if ( 0 == strcmp(opts.testFunc, "chol") )
    {
        int issym = 1;
        for(int j = 0 ; j < colsA ; j++)
        {
            for(int i = j ; i < rowsA ; i++)
            {
                double Aij = h_A[i + j*lda];
                double Aji = h_A[j + i*lda];
                if ( Aij != Aji )
                {
                    issym = 0;
                    break;
                }
            }
        }
        if (!issym)
        {
            printf("Error: A has no symmetric pattern, please use LU or QR \n");
            exit(EXIT_FAILURE);
        }
    }

    checkCudaErrors(cusolverDnCreate(&handle));
    checkCudaErrors(cublasCreate(&cublasHandle));
    checkCudaErrors(cudaStreamCreate(&stream));

    checkCudaErrors(cusolverDnSetStream(handle, stream));
    checkCudaErrors(cublasSetStream(cublasHandle, stream));


    checkCudaErrors(cudaMalloc((void **)&d_A, sizeof(double)*lda*colsA));
    checkCudaErrors(cudaMalloc((void **)&d_x, sizeof(double)*lda*colsA));
    checkCudaErrors(cudaMalloc((void **)&d_b, sizeof(double)*lda*rowsA));
    checkCudaErrors(cudaMalloc((void **)&d_r, sizeof(double)*lda*rowsA));

    printf("step 4: prepare data on device\n");
    checkCudaErrors(cudaMemcpy(d_A, h_A, sizeof(double)*lda*colsA, cudaMemcpyHostToDevice));
    checkCudaErrors(cudaMemcpy(d_b, h_b, sizeof(double)*lda*rowsA, cudaMemcpyHostToDevice));

    printf("step 5: solve A*x = b \n");
    // d_A and d_b are read-only
    if ( 0 == strcmp(opts.testFunc, "chol") )
    {
        linearSolverCHOL(handle, rowsA, d_A, lda, d_b, d_x);
    }
    else if ( 0 == strcmp(opts.testFunc, "lu") )
    {
        //printf("hi \n");
        linearSolverLU(handle, rowsA, d_A, lda, d_b, d_x);
    }
    else if ( 0 == strcmp(opts.testFunc, "qr") )
    {
        linearSolverQR(handle, rowsA, d_A, lda, d_b, d_x);
    }
    else
    {
        fprintf(stderr, "Error: %s is unknown function\n", opts.testFunc);
        exit(EXIT_FAILURE);
    }
    printf("step 6: evaluate residual\n");
    checkCudaErrors(cudaMemcpy(d_r, d_b, sizeof(double)*lda*rowsA, cudaMemcpyDeviceToDevice));

    // r = b - A*x
    checkCudaErrors(cublasDgemm_v2(
        cublasHandle,
        CUBLAS_OP_N,
        CUBLAS_OP_N,
        rowsA,
        colsA,
        colsA,
        &minus_one,
        d_A,
        lda,
        d_x,
        rowsA,
        &one,
        d_r,
        rowsA));

    checkCudaErrors(cudaMemcpy(h_x, d_x, sizeof(double)*lda*colsA, cudaMemcpyDeviceToHost));
    checkCudaErrors(cudaMemcpy(h_r, d_r, sizeof(double)*lda*rowsA, cudaMemcpyDeviceToHost));

    x_inf = vec_norminf(colsA, h_x);
    r_inf = vec_norminf(rowsA, h_r);
    A_inf = mat_norminf(rowsA, colsA, h_A, lda);


    printf("x[0] = %f\n", h_x[0]);
    printf("r[0] = %f\n", h_r[0]);
    printf("|b - A*x| = %E \n", r_inf);
    printf("|A| = %E \n", A_inf);
    printf("|x| = %E \n", x_inf);
    printf("|b - A*x|/(|A|*|x|) = %E \n", r_inf/(A_inf * x_inf));

    if (handle) { checkCudaErrors(cusolverDnDestroy(handle)); }
    if (cublasHandle) { checkCudaErrors(cublasDestroy(cublasHandle)); }
    if (stream) { checkCudaErrors(cudaStreamDestroy(stream)); }

    if (h_csrValA   ) { free(h_csrValA); }
    if (h_csrRowPtrA) { free(h_csrRowPtrA); }
    if (h_csrColIndA) { free(h_csrColIndA); }

    if (h_A) { free(h_A); }
    if (h_x) { free(h_x); }
    if (h_b) { free(h_b); }
    if (h_r) { free(h_r); }

    if (d_A) { checkCudaErrors(cudaFree(d_A)); }
    if (d_x) { checkCudaErrors(cudaFree(d_x)); }
    if (d_b) { checkCudaErrors(cudaFree(d_b)); }
    if (d_r) { checkCudaErrors(cudaFree(d_r)); }

    return 0;
}

Answer 1

Try using two or more parallel streams (with one linear system each) on the GPU, possibly this helps utilizing a bigger part of the GPU.

For timing measurments and hardware utilization use the visual profiler instead of CPU time measurements.

Another point is, that the GTX (consumer) GPUs perform pretty bad on double preision. If you have the chance, try to use a Tesla GPU instead.

Answer 2

MATLAB提供了一种使用pagefun调用GPU阵列的cublas批处理接口的方法。