kernel_gpu1.cu

#include <assert.h>
#include <stdio.h>

#include "kernel.h"
#include "matrix.h"
#include "timer.h"

#define THRESHOLD 0.000001
#define YMAX 32
#define BLOCK_DIM 16

__global__ void spmspm(COOMatrix *result, CSRMatrix *A, CSCMatrix *B, float bias) {

    unsigned int r = blockIdx.y*blockDim.y + threadIdx.y;
    unsigned int c = blockIdx.x*blockDim.x + threadIdx.x;
    unsigned int temp = 0;


    if(r < A->numRows && c < B->numCols) {
        
        unsigned int rowPtrA = A->rowPtrs[r]; // Index of the current rowPtrs element
        unsigned int nnzA = A->rowPtrs[r + 1] - rowPtrA;  // Number of non zero elements in A

        if(nnzA > 0){
            unsigned int *colIdxsA = A->colIdxs + rowPtrA;
            float *valueA = A->values + rowPtrA;

            // Loop over B columns
            unsigned int colPtrB = B->colPtrs[c];
            unsigned int nnzB = B->colPtrs[c + 1] - colPtrB;

            if(nnzB > 0){
                unsigned int *rowIdxsB = B->rowIdxs + colPtrB;
                float *valueB = B->values + colPtrB;

                // Loop and find intersection
                float sum = 0;
                unsigned int ia = 0;
                unsigned int ib = 0;

                // Loop over segment of non zero elements in the row of A and col of B
                while(ia < nnzA && ib < nnzB){
                    unsigned int colIdx = colIdxsA[ia];
                    unsigned int rowIdx = rowIdxsB[ib];
                    if(colIdx < rowIdx) {
                        ia++;
                    } else if(colIdx > rowIdx) {
                        ib++;
                    } else {
                        sum += valueA[ia] * valueB[ib];
                        ia++;
                        ib++;
                    }
                }
                // Sync threads
                // Write to Result
                if(sum > THRESHOLD || sum < -THRESHOLD) {
                    sum += bias;

                    //Remove negative and zero values
                    if(sum > 0) {
                        if(sum>YMAX) {
                            sum = YMAX;
                        }
                        
                        temp = atomicAdd(&result->nnz, 1);
                        result->colIdxs[temp] = c;
                        result->values[temp] = sum;
                        result->rowIdxs[temp] = r;
                    }
                }
            }
        }
    }                                    
}

void findNonzeroRows(Vector* v, CSRMatrix* A) {
    unsigned int nnz = 0;
    for(unsigned int r = 0; r < A->numRows; ++r) {
        unsigned int rowPtrA = A->rowPtrs[r];
        unsigned int nnzA = A->rowPtrs[r + 1] - rowPtrA;
        if(nnzA > 0) {
            if(nnz >= v->capacity) {
                expandVectorCapacity(v, 2*v->capacity);
            }
            v->data[nnz] = r;
            ++nnz;
        }
    }
    v->nnz = nnz;
}

COOMatrix* createEmptyCOO_d(unsigned int numRows, unsigned int numCols, unsigned int capacity) {
    COOMatrix cooShadow;
    cooShadow.numRows = numRows;
    cooShadow.numCols = numCols;
    cooShadow.nnz = 0;
    cooShadow.capacity = capacity;
    cudaMalloc((void**) &cooShadow.rowIdxs, capacity*sizeof(unsigned int));
    cudaMalloc((void**) &cooShadow.colIdxs, capacity*sizeof(unsigned int));
    cudaMalloc((void**) &cooShadow.values, capacity*sizeof(float));
    COOMatrix* coo_d;
    cudaMalloc((void**) &coo_d, sizeof(COOMatrix));
    cudaMemcpy(coo_d, &cooShadow, sizeof(COOMatrix), cudaMemcpyHostToDevice);
    cudaDeviceSynchronize();
    return coo_d;
}

void copyCOOfromGPU(COOMatrix* coo_d, COOMatrix* coo) {
    COOMatrix cooShadow;
    cudaMemcpy(&cooShadow, coo_d, sizeof(COOMatrix), cudaMemcpyDeviceToHost);
    assert(coo->numRows == cooShadow.numRows);
    assert(coo->numCols == cooShadow.numCols);
    assert(coo->capacity >= cooShadow.nnz);
    coo->nnz = cooShadow.nnz;
    cudaMemcpy(coo->rowIdxs, cooShadow.rowIdxs, cooShadow.nnz*sizeof(unsigned int), cudaMemcpyDeviceToHost);
    cudaMemcpy(coo->colIdxs, cooShadow.colIdxs, cooShadow.nnz*sizeof(unsigned int), cudaMemcpyDeviceToHost);
    cudaMemcpy(coo->values, cooShadow.values, cooShadow.nnz*sizeof(float), cudaMemcpyDeviceToHost);
    cudaDeviceSynchronize();
}

CSRMatrix* createEmptyCSR_d(unsigned int numRows, unsigned int numCols, unsigned int capacity) {
    CSRMatrix csrShadow;
    csrShadow.numRows = numRows;
    csrShadow.numCols = numCols;
    csrShadow.nnz = 0;
    csrShadow.capacity = capacity;
    cudaMalloc((void**) &csrShadow.rowPtrs, (numRows + 1)*sizeof(unsigned int));
    cudaMalloc((void**) &csrShadow.colIdxs, capacity*sizeof(unsigned int));
    cudaMalloc((void**) &csrShadow.values, capacity*sizeof(float));
    CSRMatrix* csr_d;
    cudaMalloc((void**) &csr_d, sizeof(CSRMatrix));
    cudaMemcpy(csr_d, &csrShadow, sizeof(CSRMatrix), cudaMemcpyHostToDevice);
    cudaDeviceSynchronize();
    return csr_d;
}

void copyCSRtoGPU(CSRMatrix* csr, CSRMatrix* csr_d) {
    CSRMatrix csrShadow;
    cudaMemcpy(&csrShadow, csr_d, sizeof(CSRMatrix), cudaMemcpyDeviceToHost);
    assert(csrShadow.numRows == csr->numRows);
    assert(csrShadow.numCols == csr->numCols);
    assert(csrShadow.capacity >= csr->nnz);
    csrShadow.nnz = csr->nnz;
    cudaMemcpy(csrShadow.rowPtrs, csr->rowPtrs, (csr->numRows + 1)*sizeof(unsigned int), cudaMemcpyHostToDevice);
    cudaMemcpy(csrShadow.colIdxs, csr->colIdxs, csr->nnz*sizeof(unsigned int), cudaMemcpyHostToDevice);
    cudaMemcpy(csrShadow.values, csr->values, csr->nnz*sizeof(float), cudaMemcpyHostToDevice);
    cudaDeviceSynchronize();
}

CSCMatrix* createCSCfromCSC_d(CSCMatrix* csc) {
    CSCMatrix cscShadow;
    cscShadow.numRows = csc->numRows;
    cscShadow.numCols = csc->numCols;
    cscShadow.nnz = csc->nnz;
    cscShadow.capacity = csc->capacity;
    cudaMalloc((void**) &cscShadow.colPtrs, (csc->numCols + 1)*sizeof(unsigned int));
    cudaMalloc((void**) &cscShadow.rowIdxs, csc->capacity*sizeof(unsigned int));
    cudaMalloc((void**) &cscShadow.values, csc->capacity*sizeof(float));
    cudaMemcpy(cscShadow.colPtrs, csc->colPtrs, (csc->numCols + 1)*sizeof(unsigned int), cudaMemcpyHostToDevice);
    cudaMemcpy(cscShadow.rowIdxs, csc->rowIdxs, csc->capacity*sizeof(unsigned int), cudaMemcpyHostToDevice);
    cudaMemcpy(cscShadow.values, csc->values, csc->capacity*sizeof(float), cudaMemcpyHostToDevice);
    CSCMatrix* csc_d;
    cudaMalloc((void**) &csc_d, sizeof(CSCMatrix));
    cudaMemcpy(csc_d, &cscShadow, sizeof(CSCMatrix), cudaMemcpyHostToDevice);
    cudaDeviceSynchronize();
    return csc_d;
}

void sparseNN(Vector* result, COOMatrix* featureVectors, COOMatrix** layerWeights, float bias, unsigned int numLayers) {

    Timer timer;

    // Convert featureVectors to CSR
    startTime(&timer);
    CSRMatrix* Y0 = createEmptyCSR(featureVectors->numRows, featureVectors->numCols, 4*featureVectors->nnz); // Assuming 4*nnz is enough for all Y vectors
    convertCOOtoCSR(featureVectors, Y0);
    CSRMatrix* Y0_d = createEmptyCSR_d(featureVectors->numRows, featureVectors->numCols, 4*featureVectors->nnz); // Assuming 4*nnz is enough for all Y vectors
    stopTimeAndPrint(&timer, "Convert feature vectors to CSR");

    // Convert layer weights to CSC
    startTime(&timer);
    CSCMatrix* W[numLayers];
    CSCMatrix* W_d[numLayers];
    for(unsigned int layer = 0; layer < numLayers; ++layer) {
        W[layer] = createCSCfromCOO(layerWeights[layer]);
        W_d[layer] = createCSCfromCSC_d(W[layer]);
    }
    stopTimeAndPrint(&timer, "Convert weights to CSR");

    // Temporary buffer
    startTime(&timer);
    COOMatrix *tmp = createEmptyCOO(Y0->numRows, Y0->numCols, Y0->capacity);
    COOMatrix *tmp_d = createEmptyCOO_d(Y0->numRows, Y0->numCols, Y0->capacity);
    stopTimeAndPrint(&timer, "Allocate temporary buffer");

    // Loop over layers
    CSRMatrix *Yin = Y0;
    COOMatrix *Yout = tmp;
    CSRMatrix *Yin_d = Y0_d;
    COOMatrix *Yout_d = tmp_d;
    // Configurations
    dim3 threadsPerBlock(BLOCK_DIM,BLOCK_DIM);
    dim3 blocksPerGrid((threadsPerBlock.x + Y0->numCols - 1)/threadsPerBlock.x,(threadsPerBlock.y + Y0->numRows - 1)/threadsPerBlock.y);

    for(unsigned int layer = 0; layer < numLayers; ++layer) {

        printf("Computing layer %u (SpMSpM)\n", layer);
        
        // Copy to GPU
        startTime(&timer);
        copyCSRtoGPU(Yin, Yin_d);
        cudaMemset(&Yout_d->nnz, 0, sizeof(unsigned int));
        stopTimeAndPrint(&timer, "    Copy CSR to GPU and clear COO");

        // SpMSpM
        startTime(&timer);
         spmspm <<< blocksPerGrid, threadsPerBlock >>> (Yout_d, Yin_d, W_d[layer], bias);
        cudaDeviceSynchronize();
        stopTimeAndPrint(&timer, "    SpMSpM");

        // Copy from GPU
        startTime(&timer);
        copyCOOfromGPU(Yout_d, Yout);
        stopTimeAndPrint(&timer, "    Copy COO from GPU");
      

        // Convert COO to CSR
        startTime(&timer);
        convertCOOtoCSR(Yout, Yin);
        stopTimeAndPrint(&timer, "    Converting COO to CSR");
    

    }

    // Find nonzero rows
    startTime(&timer);
    findNonzeroRows(result, Yin);
    stopTimeAndPrint(&timer, "Find nonzero rows");

    // Free buffers
    startTime(&timer);
    freeCSR(Y0);
    for(unsigned int layer = 0; layer < numLayers; ++layer) {
        freeCSC(W[layer]);
    }
    freeCOO(tmp);
    stopTimeAndPrint(&timer, "Deallocate memory");

}