opencl写的程序运行在FPGA上反而比CPU上差

最近在学习opencl，写了一段smith-waterman算法计算得分矩阵的程序，运行在FPGA上反而比CPU上性能差。因为是初学，不知道写的哪里有问题。
附上代码：

__kernel void __attribute__ ((reqd_work_group_size(512,512,1)))
krnl_sw(
     __global int* ref,
     __global int* alt,
     __global int* sw,
     __global int* btrack,
     const int overhangStrategy,
     const int match,
     const int mismatch,
     const int open,
     const int extend,
     const int ncol,
     const int nrow
     ) {

 int col = get_global_id(0);
 int row = get_global_id(1);

 for (k = 2;k<ncol+nrow-1;k++)
{
    if(col + row == k)
    { 
            up_score = sw[(row - 1)*ncol + col] + extend*(row-1) + open ;
            left_score = sw[row*ncol + col - 1] + extend*(row-1) + open ;
            up_left_score = sw[(row - 1)*ncol + col - 1] + diag_score(ref[col - 1], alt[row - 1], match, mismatch);
            sw[row*ncol + col] = max(up_score, left_score);
            sw[row*ncol + col] = max(up_left_score, sw[row*ncol + col]);

    }
}
  return;
}

大致的计算过程是初始化矩阵第一行和第一列，然后延对角线放向逐次计算斜对角上矩阵的得分。

计算512*512的矩阵，运行10次，CPU上耗时100ms不到，FPGA上反而是几十秒，慢了近1000倍....