moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Ported the binatoms method to cuda - not used in the program yet

Browse Source
This commit is contained in:
Martin Bauernfeind 2022-07-06 01:09:11 +02:00
parent 71798f5ec5
commit b65199308d
1 changed files with 56 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

56
src/neighbor.cu
View File

@ -70,6 +70,28 @@ __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);
} }
__global__ void binatoms_kernel(Atom a, int* bincount, int* bins, int atoms_per_bin, Neighbor_params np, int *resize_needed){
Atom* atom = &a;
const int i = blockIdx.x * blockDim.x + threadIdx.x;
int nall = atom->Nlocal + atom->Nghost;
if(i >= nall){
return;
}
MD_FLOAT x = atom_x(i);
MD_FLOAT y = atom_y(i);
MD_FLOAT z = atom_z(i);
int ibin = coord2bin_device(x, y, z, np);
int ac = atomicIncrement(bincount[ibin]);
if(ac < atoms_per_bin){
bins[ibin * atoms_per_bin + ac] = i;
} else {
atomicMax(resize_needed, ac);
}
}
__global__ void compute_neighborhood(Atom a, Neighbor neigh, Neighbor_params np, int nstencil, int* stencil, __global__ void compute_neighborhood(Atom a, Neighbor neigh, Neighbor_params np, int nstencil, int* stencil,
int* bins, int atoms_per_bin, int *bincount, int *new_maxneighs, MD_FLOAT cutneighsq){ int* bins, int atoms_per_bin, int *bincount, int *new_maxneighs, MD_FLOAT cutneighsq){
const int i = blockIdx.x * blockDim.x + threadIdx.x; const int i = blockIdx.x * blockDim.x + threadIdx.x;
@ -517,6 +539,40 @@ void sortAtom(Atom* atom) {
#endif #endif
} }
void binatoms_cuda(Atom *c_atom, int** c_bincount, int** c_bins, int** c_resize_needed, int mbins, NeighborParams *np, const int threads_per_block)
{
int nall = c_atom->Nlocal + c_atom->Nghost;
int resize = 1;
if(*c_bincount == NULL){
checkCUDAError("binatoms_cuda c_bincount malloc", cudaMalloc(c_bincount, mbins * sizeof(int)) );
}
if(*c_bins == NULL){
checkCUDAError("binatoms_cuda c_bins malloc", cudaMalloc(c_bins, mbins * atoms_per_bin * sizeof(int)) );
}
if(*c_resize_needed == NULL){
checkCUDAError("binatoms_cuda c_resize_needed malloc", cudaMalloc(&c_resize_needed, sizeof(int)) );
}
const int num_blocks = ceil((float)nall-> / (float)num_threads_per_block);
while(resize > 0) {
resize = 0;
checkCUDAError("binatoms_cuda c_bincount memset", cudaMemset(*c_bincount, 0, mbins * sizeof(int)));
checkCUDAError("binatoms_cuda c_resize_needed memset", cudaMemset(*c_resize_needed, 0, sizeof(int)) );
/*binatoms_kernel(Atom a, int* bincount, int* bins, int atoms_per_bin, Neighbor_params np, int *resize_needed) */
binatoms_kernel<<<num_blocks, threads_per_block>>>(*c_atom, *c_bincount, *c_bins, atoms_per_bin, *np, *c_resize_needed);
checkCUDAError("binatoms_cuda c_resize_needed memcpy back", cudaMemcpy(&resize, *c_resize_needed, sizeof(int), cudaMemcpyDeviceToHost) );
if(resize) {
cudaFree(*c_bins);
atoms_per_bin *= 2;
checkCUDAError("binatoms_cuda c_bins resize malloc", cudaMalloc(c_bins, mbins * atoms_per_bin * sizeof(int)) );
}
}
}
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)
{ {
int nall = atom->Nlocal + atom->Nghost; int nall = atom->Nlocal + atom->Nghost;