Different Kernel Executions times

Please post the section of your host code that measures the kernel execution times.

#include "timing.h"# include <Windows.h>
double get_wall_time(){
    LARGE_INTEGER time,freq;
    if (!QueryPerformanceFrequency(&freq)){
        //  Handle error
        return 0;
    }
    if (!QueryPerformanceCounter(&time)){
        //  Handle error
        return 0;
    }
    return (double)time.QuadPart / freq.QuadPart;
}
-----------------------------------------------------------------------------
runKernerl(...){
/* Set Kernel Arguments */
	for(i=0; i < num_arguments;i++)
	status = clSetKernelArg(kernel, i, sizeof(cl_mem), &buffer);
	/* Run kernel the kernel */
	status = clEnqueueTask(cmdqueue,kernel,0,NULL,NULL);
	checkError(status, "Failed to launch kernel");
	/* Wait for command queue to complete pending events */
	status = clFinish(cmdqueue);
	/* Read the device output buffer to the host output array */
	checkError(status, "Failed to finish");
}
-----------------------------------------------------------------------------
ini_kernel_bi = get_wall_time();
runKernel(context, cluster_kernel, cmd_queue, 6, 0, NULL, buffers, NULL , NULL);
end_kernel_bi = get_wall_time();
printf("Time:%f", end_kernel_bi - ini_kernel_bi);

Try moving clSetKernelArg and checkError outside of the timing region and only time clEnqueueTask and clFinish.

The function you are using is a high-precision timer. I personally also use the same function on Windows. This function provides accurate time measurement up to a few microseconds or maybe even less.

Interesting, did you figure out the problem? Which board are you using? Try to use the profiler to check the actual kernel runtime.