implement alignment optimizations, currently disabled since they are not working correctly on GPU

bioem_cuda.cu

@@ -116,7 +116,7 @@ __global__ void multComplexMap(const mycomplex_t* convmap, const mycomplex_t* re
 {
 	if (myBlockIdxX >= NumberMaps) return;
 	const mycomplex_t* myin = &refmap[myBlockIdxX * MapSize + Offset];
-	mycuComplex_t* myout = &out[(myBlockIdxX * MapSize)];
+	mycuComplex_t* myout = &out[myBlockIdxX * MapSize];
 	for(int i = myThreadIdxX; i < NumberPixelsTotal; i += myBlockDimX)
 	{
 		myout[i].x = convmap[i][0] * myin[i][0] + convmap[i][1] * myin[i][1];
@@ -339,7 +339,7 @@ int bioem_cuda::deviceStartRun()
 		for (int i = 0; i < 2; i++)
 		{
 			int n[2] = {param.param_device.NumberPixels, param.param_device.NumberPixels};
-			if (cufftPlanMany(&plan[i], 2, n, NULL, 1, 0, NULL, 1, 0, MY_CUFFT_C2R, i ? (maxRef % CUDA_FFTS_AT_ONCE) : CUDA_FFTS_AT_ONCE) != CUFFT_SUCCESS)
+			if (cufftPlanMany(&plan[i], 2, n, NULL, 1, param.FFTMapSize, NULL, 1, 0, MY_CUFFT_C2R, i ? (maxRef % CUDA_FFTS_AT_ONCE) : CUDA_FFTS_AT_ONCE) != CUFFT_SUCCESS)
 			{
 				cout << "Error planning CUFFT\n";
 				exit(1);

include/param.h

@@ -33,6 +33,7 @@ public:
 	bioem_param_device param_device;
 
 	int FFTMapSize;
+	int Alignment;
 	mycomplex_t* refCTF;
 	myfloat3_t* CtfParam;
 

param.cpp

@@ -180,8 +180,6 @@ int bioem_param::readParameters()
 
 	}
 	input.close();
-	param_device.NumberFFTPixels1D = param_device.NumberPixels / 2 + 1;
-	FFTMapSize = param_device.NumberPixels * param_device.NumberFFTPixels1D;
 	cout << " +++++++++++++++++++++++++++++++++++++++++ \n";
 
 	cout << "Preparing FFTs\n";
@@ -189,6 +187,7 @@ int bioem_param::readParameters()
 	mycomplex_t *tmp_map, *tmp_map2;
 	tmp_map = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param_device.NumberPixels * param_device.NumberPixels);
 	tmp_map2 = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param_device.NumberPixels * param_device.NumberPixels);
+	Alignment = 64;
 
 	fft_plan_c2c_forward = myfftw_plan_dft_2d(param_device.NumberPixels, param_device.NumberPixels, tmp_map, tmp_map2, FFTW_FORWARD, FFTW_MEASURE | FFTW_DESTROY_INPUT);
 	fft_plan_c2c_backward = myfftw_plan_dft_2d(param_device.NumberPixels, param_device.NumberPixels, tmp_map, tmp_map2, FFTW_BACKWARD, FFTW_MEASURE | FFTW_DESTROY_INPUT);
@@ -204,6 +203,17 @@ int bioem_param::readParameters()
 	myfftw_free(tmp_map);
 	myfftw_free(tmp_map2);
 	fft_plans_created = 1;
+
+	param_device.NumberFFTPixels1D = param_device.NumberPixels / 2 + 1;
+	FFTMapSize = param_device.NumberPixels * param_device.NumberFFTPixels1D;
+
+	//Does currently not work with custom alignment on GPU
+	/*if (FFTMapSize % Alignment)
+	{
+		FFTMapSize += Alignment - FFTMapSize % Alignment;
+	}
+	cout << "Using MAP Size " << FFTMapSize << " (Alignment " << Alignment << ", Unaligned Size " << param_device.NumberPixels * param_device.NumberFFTPixels1D << ")\n";*/
+
 	cout << " +++++++++++++++++++++++++++++++++++++++++ \n";
 
 	return(0);