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The program now does the binning on the GPU via the binatoms_cuda method

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This commit is contained in:
Martin Bauernfeind 2022-07-10 18:05:06 +02:00
parent fa409c016c
commit 0967e8f671
2 changed files with 50 additions and 55 deletions
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2
src/includes/neighbor.h
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@ -53,6 +53,6 @@ extern void setupNeighbor();
extern void binatoms(Atom*); extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*); extern void buildNeighbor(Atom*, Neighbor*);
extern void sortAtom(Atom*); extern void sortAtom(Atom*);
extern void binatoms_cuda(Atom*, Binning*, int**, Neighbor_params*, const int); extern void binatoms_cuda(Atom*, Binning*, int*, Neighbor_params*, const int);
extern void buildNeighbor_cuda(Atom*, Neighbor*, Atom*, Neighbor*, const int); extern void buildNeighbor_cuda(Atom*, Neighbor*, Atom*, Neighbor*, const int);
#endif #endif

63
src/neighbor.cu
View File

@ -539,7 +539,7 @@ void sortAtom(Atom* atom) {
#endif #endif
} }
void binatoms_cuda(Atom* c_atom, Binning* c_binning, int** c_resize_needed, NeighborParams *np, const int threads_per_block) void binatoms_cuda(Atom* c_atom, Binning* c_binning, int* c_resize_needed, NeighborParams *np, const int threads_per_block)
{ {
int nall = c_atom->Nlocal + c_atom->Nghost; int nall = c_atom->Nlocal + c_atom->Nghost;
int resize = 1; int resize = 1;
@ -549,21 +549,18 @@ void binatoms_cuda(Atom* c_atom, Binning* c_binning, int** c_resize_needed, Neig
if(c_binning->bins == NULL){ if(c_binning->bins == NULL){
checkCUDAError("binatoms_cuda c_binning->bins malloc", cudaMalloc((void**)(&c_binning->bins), c_binning->mbins * c_binning->atoms_per_bin * sizeof(int)) ); checkCUDAError("binatoms_cuda c_binning->bins malloc", cudaMalloc((void**)(&c_binning->bins), c_binning->mbins * c_binning->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); const int num_blocks = ceil((float)nall-> / (float)num_threads_per_block);
while(resize > 0) { while(resize > 0) {
resize = 0; resize = 0;
checkCUDAError("binatoms_cuda c_binning->bincount memset", cudaMemset(c_binning->bincount, 0, c_binning->mbins * sizeof(int))); checkCUDAError("binatoms_cuda c_binning->bincount memset", cudaMemset(c_binning->bincount, 0, c_binning->mbins * sizeof(int)));
checkCUDAError("binatoms_cuda c_resize_needed memset", cudaMemset(*c_resize_needed, 0, 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 c_binning->atoms_per_bin, Neighbor_params np, int *resize_needed) */ /*binatoms_kernel(Atom a, int* bincount, int* bins, int c_binning->atoms_per_bin, Neighbor_params np, int *resize_needed) */
binatoms_kernel<<<num_blocks, threads_per_block>>>(*c_atom, c_binning->bincount, c_binning->bins, c_binning->atoms_per_bin, *np, *c_resize_needed); binatoms_kernel<<<num_blocks, threads_per_block>>>(*c_atom, c_binning->bincount, c_binning->bins, c_binning->atoms_per_bin, *np, c_resize_needed);
checkCUDAError("binatoms_cuda c_resize_needed memcpy back", cudaMemcpy(&resize, *c_resize_needed, sizeof(int), cudaMemcpyDeviceToHost) ); checkCUDAError("binatoms_cuda c_resize_needed memcpy back", cudaMemcpy(&resize, c_resize_needed, sizeof(int), cudaMemcpyDeviceToHost) );
if(resize) { if(resize) {
cudaFree(c_binning->bins); cudaFree(c_binning->bins);
@ -576,39 +573,20 @@ void binatoms_cuda(Atom* c_atom, Binning* c_binning, int** c_resize_needed, Neig
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;
c_neighbor->maxneighs = neighbor->maxneighs; c_neighbor->maxneighs = neighbor->maxneighs;
/* extend c_neighbor arrays if necessary */
if(nall > nmax) {
nmax = nall;
if(c_neighbor->numneigh) cudaFree(c_neighbor->numneigh);
if(c_neighbor->neighbors) cudaFree(c_neighbor->neighbors);
checkCUDAError( "buildNeighbor c_numneigh malloc", cudaMalloc((void**)&(c_neighbor->numneigh), nmax * sizeof(int)) );
checkCUDAError( "buildNeighbor c_neighbors malloc", cudaMalloc((void**)&(c_neighbor->neighbors), nmax * c_neighbor->maxneighs * sizeof(int)) );
}
checkCUDAError( "buildNeighbor c_atom->x memcpy back", cudaMemcpy(atom->x, c_atom->x, sizeof(MD_FLOAT) * 3 * c_atom->Nmax, cudaMemcpyDeviceToHost) );
/* bin local & ghost atoms */
binatoms(atom);
int resize = 1;
cudaProfilerStart(); cudaProfilerStart();
/* upload stencil */ /* upload stencil */
int* c_stencil; int* c_stencil;
// TODO move this to be done once at the start // TODO move this to be done once at the start
checkCUDAError( "buildNeighbor c_n_stencil malloc", cudaMalloc((void**)&c_stencil, nstencil * sizeof(int)) ); checkCUDAError( "buildNeighbor c_n_stencil malloc", cudaMalloc((void**)&c_stencil, nstencil * sizeof(int)) );
checkCUDAError( "buildNeighbor c_n_stencil memcpy", cudaMemcpy(c_stencil, stencil, nstencil * sizeof(int), cudaMemcpyHostToDevice )); checkCUDAError( "buildNeighbor c_n_stencil memcpy", cudaMemcpy(c_stencil, stencil, nstencil * sizeof(int), cudaMemcpyHostToDevice ));
int *c_bincount; Binning c_binning;
checkCUDAError( "buildNeighbor c_bincount malloc", cudaMalloc((void**)&c_bincount, mbins * sizeof(int)) ); c_binning->mbins = mbins;
checkCUDAError( "buildNeighbor c_bincount memcpy", cudaMemcpy(c_bincount, bincount, mbins * sizeof(int), cudaMemcpyHostToDevice) ); c_binning->atoms_per_bin = atoms_per_bin;
checkCUDAError( "buildNeighbor c_binning->bincount malloc", cudaMalloc((void**)&(c_binning->bincount), mbins * sizeof(int)) );
int *c_bins; checkCUDAError( "buidlNeighbor c_binning->bins malloc", cudaMalloc((void**)&(c_binning->bins), c_binning->mbins * c_binning->atoms_per_bin * sizeof(int)) );
checkCUDAError( "buidlNeighbor c_bins malloc", cudaMalloc((void**)&c_bins, mbins * atoms_per_bin * sizeof(int)) );
checkCUDAError( "buildNeighbor c_bins memcpy", cudaMemcpy(c_bins, bins, mbins * atoms_per_bin * sizeof(int), cudaMemcpyHostToDevice ) );
Neighbor_params np{ Neighbor_params np{
.xprd = xprd, .xprd = xprd,
@ -628,9 +606,26 @@ void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *
.mbinz = mbinz .mbinz = mbinz
}; };
int* c_resize_needed;
checkCUDAError("buildNeighbor c_resize_needed malloc", cudaMalloc((void**)&c_resize_needed, sizeof(int)) );
/* bin local & ghost atoms */
binatoms_cuda(c_atom, &c_binning, c_resize_needed, &np, num_threads_per_block);
int* c_new_maxneighs; int* c_new_maxneighs;
checkCUDAError("c_new_maxneighs malloc", cudaMalloc((void**)&c_new_maxneighs, sizeof(int) )); checkCUDAError("c_new_maxneighs malloc", cudaMalloc((void**)&c_new_maxneighs, sizeof(int) ));
int resize = 1;
/* extend c_neighbor arrays if necessary */
if(nall > nmax) {
nmax = nall;
if(c_neighbor->numneigh) cudaFree(c_neighbor->numneigh);
if(c_neighbor->neighbors) cudaFree(c_neighbor->neighbors);
checkCUDAError( "buildNeighbor c_numneigh malloc", cudaMalloc((void**)&(c_neighbor->numneigh), nmax * sizeof(int)) );
checkCUDAError( "buildNeighbor c_neighbors malloc", cudaMalloc((void**)&(c_neighbor->neighbors), nmax * c_neighbor->maxneighs * sizeof(int)) );
}
/* loop over each atom, storing neighbors */ /* loop over each atom, storing neighbors */
while(resize) { while(resize) {
resize = 0; resize = 0;
@ -644,7 +639,7 @@ void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *
* */ * */
compute_neighborhood<<<num_blocks, num_threads_per_block>>>(*c_atom, *c_neighbor, compute_neighborhood<<<num_blocks, num_threads_per_block>>>(*c_atom, *c_neighbor,
np, nstencil, c_stencil, np, nstencil, c_stencil,
c_bins, atoms_per_bin, c_bincount, c_binning->bins, atoms_per_bin, c_binning->bincount,
c_new_maxneighs, c_new_maxneighs,
cutneighsq); cutneighsq);
@ -675,7 +670,7 @@ void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *
cudaFree(c_new_maxneighs); cudaFree(c_new_maxneighs);
cudaFree(c_stencil); cudaFree(c_stencil);
cudaFree(c_bincount); cudaFree(c_binning->bincount);
cudaFree(c_bins); cudaFree(c_binning->bins);
} }
} }