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Added code to sort the contents of all bins to make it comparable to the CPU version

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Martin Bauernfeind 2022-07-11 00:24:48 +02:00
parent c9db6e45fa
commit d1c2249b55
1 changed files with 31 additions and 0 deletions
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31
src/neighbor.cu
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@ -70,6 +70,31 @@ __device__ int coord2bin_device(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin,
return (iz * np.mbiny * np.mbinx + iy * np.mbinx + ix + 1); return (iz * np.mbiny * np.mbinx + iy * np.mbinx + ix + 1);
} }
/* sorts the contents of a bin to make it comparable to the CPU version */
/* uses bubble sort since atoms per bin should be relatively small and can be done in situ */
__global__ void sort_bin_contents_kernel(int* bincount, int* bins, int mbins, int atoms_per_bin){
const int i = blockIdx.x * blockDim.x + threadIdx.x;
if (i >= mbins){
return;
}
int atoms_in_bin = bincount[i];
int* bin_ptr = &bins[i * atoms_per_bin];
int sorted;
do {
sorted = 1;
int tmp;
for(int index = 0; index < atoms_in_bin - 1; index++){
if (bin_ptr[index] > bin_ptr[index + 1]){
tmp = bin_ptr[index];
bin_ptr[index] = bin_ptr[index + 1];
bin_ptr[index + 1] = tmp;
sorted = 0;
}
}
} while (!sorted)
}
__global__ void binatoms_kernel(Atom a, int* bincount, int* bins, int atoms_per_bin, Neighbor_params np, int *resize_needed){ __global__ void binatoms_kernel(Atom a, int* bincount, int* bins, int atoms_per_bin, Neighbor_params np, int *resize_needed){
Atom* atom = &a; Atom* atom = &a;
const int i = blockIdx.x * blockDim.x + threadIdx.x; const int i = blockIdx.x * blockDim.x + threadIdx.x;
@ -571,6 +596,12 @@ void binatoms_cuda(Atom* c_atom, Binning* c_binning, int* c_resize_needed, Neigh
checkCUDAError("binatoms_cuda c_binning->bins resize malloc", cudaMalloc(&c_binning->bins, c_binning->mbins * c_binning->atoms_per_bin * sizeof(int)) ); checkCUDAError("binatoms_cuda c_binning->bins resize malloc", cudaMalloc(&c_binning->bins, c_binning->mbins * c_binning->atoms_per_bin * sizeof(int)) );
} }
} }
atoms_per_bin = c_binning->atoms_per_bin;
const int sortBlocks = ceil((float)mbins / (float)threads_per_block);
/*void sort_bin_contents_kernel(int* bincount, int* bins, int mbins, int atoms_per_bin)*/
sort_bin_contents_kernel<<<sortBlocks, threads_per_block>>>(c_binning->bincount, c_binning->bins, c_binning->mbins, c_binning->atoms_per_bin);
checkCUDAError( "PeekAtLastError sort_bin_contents kernel", cudaPeekAtLastError() );
checkCUDAError( "DeviceSync sort_bin_contents kernel", cudaDeviceSynchronize() );
} }
void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor, const int num_threads_per_block) void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor, const int num_threads_per_block)