时间戳

首页 > 解决方案 > Cuda 寻找相等的子串

cuda - Cuda 寻找相等的子串

问题描述

函数 compute_kmers 试图找出子串kmer在字符串reference_string中出现的次数，k是 kmer 的长度。这适用于非常小的输入，但在较大的输入上它会发现不同的错误结果。不能确定我做错了什么。

__device__ void compare_elements(char *ref, char *kmer, int k, int *hits, int current)
{
    int equal = 1;
    for(int i=0; i<k; i++)
    {
        if(kmer[i] != ref[i])
        {
            equal =0;
        }
    }
    if(equal == 1)
    {

        hits[current]++;
    }

}

__global__ void compute(char *d_reference_str, char *d_kmer, int reference_length, int k, int *hits)
{


    int current = blockIdx.x * 1024 + threadIdx.x;

    if(current+k<reference_length)
    {
        char *refsubstr = (char *) malloc(k * sizeof(char));
        for(int i=0; i<k; i++)
        {
            refsubstr[i] = d_reference_str[current+i];
        }
        compare_elements(refsubstr, d_kmer, k, hits, current); 
    }
}

__host__ void compute_kmers(char* reference_str, char* kmer, int reference_length, int k, int *hits)
{
    char *d_reference_str;
    char *d_kmer;
    int *d_hits;
    cudaMalloc((void **) &d_reference_str, reference_length*sizeof(char));
    cudaMalloc((void **) &d_kmer, k*sizeof(char));
    cudaMalloc((void **) &d_hits, MAX_REF_LENGTH * sizeof(int));

    cudaMemcpy(d_reference_str, 
    reference_str,reference_length*sizeof(char),cudaMemcpyHostToDevice);
    cudaMemcpy(d_kmer, kmer,k*sizeof(char),cudaMemcpyHostToDevice);
    int numOfBlocks=(reference_length/1024)+1;
    dim3 dimGrid(numOfBlocks, 1);
    dim3 dimBlock(1024, 1);
    compute<<<dimGrid,dimBlock>>>(d_reference_str,d_kmer,reference_length, k, d_hits);

    cudaMemcpy(hits, d_hits, reference_length*sizeof(int),cudaMemcpyDeviceToHost);

    cudaFree(d_reference_str);
    cudaFree(d_kmer);
    cudaFree(d_hits);
}

标签： cudasubstring

解决方案

每当您在内核中使用动态内存分配时，您应该验证返回的指针不为空。如果无法完成请求，malloc 将返回 null。

设备端堆的大小是有限的。它可以通过增加cudaDeviceSetLimit

但是，您不需要复制引用子字符串。可以直接使用参考。

__global__ void compute(char *d_reference_str, char *d_kmer, int reference_length, int k, int *hits)
{


    int current = blockIdx.x * 1024 + threadIdx.x;

    if(current+k<reference_length)
    {
        compare_elements(d_reference_str + current, d_kmer, k, hits, current); 
    }
}

推荐阅读