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Small changes in buildNeighbor to initialize the bincount list and other arrays only once

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Martin Bauernfeind 2022-07-13 14:42:34 +02:00
parent 5a6d1851ed
commit fb304f240b
1 changed files with 32 additions and 28 deletions
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58
src/neighbor.cu
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@ -194,6 +194,17 @@ static int nstencil; // # of bins in stencil
static int* stencil; // stencil list of bin offsets static int* stencil; // stencil list of bin offsets
static MD_FLOAT binsizex, binsizey, binsizez; static MD_FLOAT binsizex, binsizey, binsizez;
static int* c_stencil = NULL;
static int* c_resize_needed = NULL;
static int* c_new_maxneighs = NULL;
static Binning c_binning{
.mbins = 0;
.atoms_per_bin = 0;
.bincount = NULL;
.bins = 0;
};
static int coord2bin(MD_FLOAT, MD_FLOAT , MD_FLOAT); static int coord2bin(MD_FLOAT, MD_FLOAT , MD_FLOAT);
static MD_FLOAT bindist(int, int, int); static MD_FLOAT bindist(int, int, int);
@ -568,12 +579,6 @@ void binatoms_cuda(Atom* c_atom, Binning* c_binning, int* c_resize_needed, Neigh
{ {
int nall = c_atom->Nlocal + c_atom->Nghost; int nall = c_atom->Nlocal + c_atom->Nghost;
int resize = 1; int resize = 1;
if(c_binning->bincount == NULL){
checkCUDAError("binatoms_cuda c_binning->bincount malloc", cudaMalloc((void**)(&c_binning->bincount), c_binning->mbins * sizeof(int)) );
}
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)) );
}
const int num_blocks = ceil((float)nall / (float)threads_per_block); const int num_blocks = ceil((float)nall / (float)threads_per_block);
@ -585,10 +590,10 @@ void binatoms_cuda(Atom* c_atom, Binning* c_binning, int* c_resize_needed, Neigh
/*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( "PeekAtLastError binatoms kernel", cudaPeekAtLastError() ); checkCUDAError( "PeekAtLastError binatoms kernel", cudaPeekAtLastError() );
checkCUDAError( "DeviceSync binatoms kernel", cudaDeviceSynchronize() ); checkCUDAError( "DeviceSync binatoms kernel", cudaDeviceSynchronize() );
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);
@ -611,16 +616,18 @@ void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *
cudaProfilerStart(); cudaProfilerStart();
/* upload stencil */ /* upload stencil */
int* c_stencil; // TODO move all of this initialization into its own method
// TODO move this to be done once at the start if(c_stencil == NULL){
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 ));
}
Binning c_binning; if(c_binning.mbins == 0){
c_binning.mbins = mbins; c_binning.mbins = mbins;
c_binning.atoms_per_bin = atoms_per_bin; c_binning.atoms_per_bin = atoms_per_bin;
checkCUDAError( "buildNeighbor c_binning->bincount malloc", cudaMalloc((void**)&(c_binning.bincount), mbins * sizeof(int)) ); checkCUDAError( "buildNeighbor c_binning->bincount malloc", cudaMalloc((void**)&(c_binning.bincount), c_binning.mbins * sizeof(int)) );
checkCUDAError( "buidlNeighbor c_binning->bins malloc", cudaMalloc((void**)&(c_binning.bins), c_binning.mbins * c_binning.atoms_per_bin * sizeof(int)) ); checkCUDAError( "buidlNeighbor c_binning->bins malloc", cudaMalloc((void**)&(c_binning.bins), c_binning.mbins * c_binning.atoms_per_bin * sizeof(int)) );
}
Neighbor_params np{ Neighbor_params np{
.xprd = xprd, .xprd = xprd,
@ -640,14 +647,16 @@ void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *
.mbinz = mbinz .mbinz = mbinz
}; };
int* c_resize_needed; if(c_resize_needed == NULL){
checkCUDAError("buildNeighbor c_resize_needed malloc", cudaMalloc((void**)&c_resize_needed, sizeof(int)) ); checkCUDAError("buildNeighbor c_resize_needed malloc", cudaMalloc((void**)&c_resize_needed, sizeof(int)) );
}
/* bin local & ghost atoms */ /* bin local & ghost atoms */
binatoms_cuda(c_atom, &c_binning, c_resize_needed, &np, num_threads_per_block); binatoms_cuda(c_atom, &c_binning, c_resize_needed, &np, num_threads_per_block);
int* c_new_maxneighs; if(c_new_maxneighs == NULL){
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; int resize = 1;
@ -701,10 +710,5 @@ void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *
neighbor->maxneighs = c_neighbor->maxneighs; neighbor->maxneighs = c_neighbor->maxneighs;
cudaProfilerStop(); cudaProfilerStop();
cudaFree(c_new_maxneighs);
cudaFree(c_stencil);
cudaFree(c_binning.bincount);
cudaFree(c_binning.bins);
} }
} }