Cuda 寻找相等的子串

Question

函数compute_kmers试图找出子字符串kmer在字符串reference_string中出现了多少次， k是kmer的长度。这适用于非常小的输入，但在大的输入上它会发现不同的错误结果。不确定我做错了什么。

__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);
}

Answer 1

无论何时在内核中使用动态内存分配，都应该验证返回的指针不为空。 malloc returns 如果无法满足请求，则为 null。

设备端堆的大小有限。可以通过 cudaDeviceSetLimit

增加

但是，您不需要复制引用子字符串。可以直接使用引用。

__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); 
    }
}

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