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First crude attempt at parallelizing neighborhood computation (only the part after binning the atoms is parallelized with cuda)

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This commit is contained in:
Martin Bauernfeind
2022-06-26 16:25:59 +02:00
parent 757d4329f3
commit c49278cb21
4 changed files with 130 additions and 58 deletions
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35
src/force.cu
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@@ -126,25 +126,9 @@ extern "C" {
int get_num_threads() {
const char *num_threads_env = getenv("NUM_THREADS");
int num_threads = 0;
if(num_threads_env == nullptr)
num_threads = 32;
else {
num_threads = atoi(num_threads_env);
}
return num_threads;
}
void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom *c_atom) {
void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom *c_atom, const int num_threads_per_block) {
const int Nlocal = atom->Nlocal;
const int num_threads = get_num_threads();
const int num_threads_per_block = num_threads; // this should be multiple of 32 as operations are performed at the level of warps
const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block);
kernel_final_integrate <<< num_blocks, num_threads_per_block >>> (param->dtforce, Nlocal, *c_atom);
@@ -157,12 +141,9 @@ void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom
}
}
void cuda_initial_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom *c_atom) {
void cuda_initial_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom *c_atom, const int num_threads_per_block) {
const int Nlocal = atom->Nlocal;
const int num_threads = get_num_threads();
const int num_threads_per_block = num_threads; // this should be multiple of 32 as operations are performed at the level of warps
const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block);
kernel_initial_integrate <<< num_blocks, num_threads_per_block >>> (param->dtforce, param->dt, Nlocal, *c_atom);
@@ -182,7 +163,8 @@ double computeForce(
Atom *atom,
Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor
Neighbor *c_neighbor,
int num_threads_per_block
)
{
int Nlocal = atom->Nlocal;
@@ -192,8 +174,6 @@ double computeForce(
MD_FLOAT epsilon = param->epsilon;
#endif
const int num_threads = get_num_threads();
c_atom->Natoms = atom->Natoms;
c_atom->Nlocal = atom->Nlocal;
c_atom->Nghost = atom->Nghost;
@@ -219,14 +199,11 @@ double computeForce(
cudaProfilerStart();
checkCUDAError( "c_atom->x memcpy", cudaMemcpy(c_atom->x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
if(reneighbourHappenend) {
checkCUDAError( "c_neighbor->numneigh memcpy", cudaMemcpy(c_neighbor->numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) );
checkCUDAError( "c_neighbor->neighbors memcpy", cudaMemcpy(c_neighbor->neighbors, neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs, cudaMemcpyHostToDevice) );
if(!reneighbourHappenend) {
checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
}
const int num_threads_per_block = num_threads; // this should be multiple of 32 as operations are performed at the level of warps
const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block);
double S = getTimeStamp();

1
src/includes/neighbor.h
View File

@@ -46,4 +46,5 @@ extern void setupNeighbor();
extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*);
extern void sortAtom(Atom*);
extern void buildNeighbor_cuda(Atom*, Neighbor*, Atom*, Neighbor*, const int);
#endif

50
src/main.c
View File

@@ -45,10 +45,14 @@
#define HLINE "----------------------------------------------------------------------------\n"
extern void cuda_final_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom *c_atom);
extern void cuda_initial_integrate(bool doReneighbour, Parameter *param, Atom *atom, Atom *c_atom);
extern void cuda_final_integrate(bool doReneighbour, Parameter *param,
Atom *atom, Atom *c_atom,
const int num_threads_per_block);
extern void cuda_initial_integrate(bool doReneighbour, Parameter *param,
Atom *atom, Atom *c_atom,
const int num_threads_per_block);
extern double computeForce(bool, Parameter*, Atom*, Neighbor*, Atom*, Neighbor*);
extern double computeForce(bool, Parameter*, Atom*, Neighbor*, Atom*, Neighbor*, const int);
extern double computeForceTracing(Parameter*, Atom*, Neighbor*, Stats*, int, int);
extern double computeForceEam(Eam* eam, Parameter*, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep);
@@ -111,7 +115,8 @@ double setup(
Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor,
Stats *stats)
Stats *stats,
const int num_threads_per_block)
{
if(param->force_field == FF_EAM) { initEam(eam, param); }
double S, E;
@@ -131,7 +136,7 @@ double setup(
adjustThermo(param, atom);
setupPbc(atom, param);
updatePbc(atom, param);
buildNeighbor(atom, neighbor);
buildNeighbor_cuda(atom, neighbor, c_atom, c_neighbor, num_threads_per_block);
E = getTimeStamp();
initCudaAtom(atom, neighbor, c_atom, c_neighbor);
@@ -142,7 +147,10 @@ double setup(
double reneighbour(
Parameter *param,
Atom *atom,
Neighbor *neighbor)
Neighbor *neighbor,
Atom *c_atom,
Neighbor *c_neighbor,
const int num_threads_per_block)
{
double S, E;
@@ -152,7 +160,7 @@ double reneighbour(
setupPbc(atom, param);
updatePbc(atom, param);
//sortAtom(atom);
buildNeighbor(atom, neighbor);
buildNeighbor(atom, neighbor, c_atom, c_neighbor, num_threads_per_block);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
@@ -206,6 +214,19 @@ const char* ff2str(int ff)
return "invalid";
}
int get_num_threads() {
const char *num_threads_env = getenv("NUM_THREADS");
int num_threads = 0;
if(num_threads_env == nullptr)
num_threads = 32;
else {
num_threads = atoi(num_threads_env);
}
return num_threads;
}
int main(int argc, char** argv)
{
double timer[NUMTIMER];
@@ -286,7 +307,10 @@ int main(int argc, char** argv)
}
}
setup(&param, &eam, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
// this should be multiple of 32 as operations are performed at the level of warps
const int num_threads_per_block = get_num_threads();
setup(&param, &eam, &atom, &neighbor, &c_atom, &c_neighbor, &stats, num_threads_per_block);
computeThermo(0, &param, &atom);
if(param.force_field == FF_EAM) {
computeForceEam(&eam, &param, &atom, &neighbor, &stats, 1, 0);
@@ -294,7 +318,7 @@ int main(int argc, char** argv)
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(COMPUTE_STATS)
computeForceTracing(&param, &atom, &neighbor, &stats, 1, 0);
#else
computeForce(true, &param, &atom, &neighbor, &c_atom, &c_neighbor);
computeForce(true, &param, &atom, &neighbor, &c_atom, &c_neighbor, num_threads_per_block);
#endif
}
@@ -310,10 +334,10 @@ int main(int argc, char** argv)
const bool doReneighbour = (n + 1) % param.every == 0;
cuda_initial_integrate(doReneighbour, &param, &atom, &c_atom);
cuda_initial_integrate(doReneighbour, &param, &atom, &c_atom, num_threads_per_block);
if(doReneighbour) {
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
timer[NEIGH] += reneighbour(&param, &atom, &neighbor, &c_atom, &c_neighbor, num_threads_per_block);
} else {
updatePbc(&atom, &param);
}
@@ -324,11 +348,11 @@ int main(int argc, char** argv)
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(COMPUTE_STATS)
timer[FORCE] += computeForceTracing(&param, &atom, &neighbor, &stats, 0, n + 1);
#else
timer[FORCE] += computeForce(doReneighbour, &param, &atom, &neighbor, &c_atom, &c_neighbor);
timer[FORCE] += computeForce(doReneighbour, &param, &atom, &neighbor, &c_atom, &c_neighbor, num_threads_per_block);
#endif
}
cuda_final_integrate(doReneighbour, &param, &atom, &c_atom);
cuda_final_integrate(doReneighbour, &param, &atom, &c_atom, num_threads_per_block);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
computeThermo(n + 1, &param, &atom);

102
src/neighbor.cu
View File

@@ -67,9 +67,10 @@ __device__ int coord2bin_device(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin,
return (iz * np.mbiny * np.mbinx + iy * np.mbinx + ix + 1);
}
__global__ void compute_neighborhood(Atom a, Neighbor neigh, int Nlocal, 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){
const int i = blockIdx.x * blockDim.x + threadIdx.x;
const int Nlocal = a.Nlocal;
if( i >= Nlocal ) {
return;
}
@@ -513,41 +514,110 @@ void sortAtom(Atom* atom) {
#endif
}
void buildNeighbor_cuda(Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor)
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;
/* extend atom arrays if necessary */
c_atom->Natoms = atom->Natoms;
c_atom->Nlocal = atom->Nlocal;
c_atom->Nghost = atom->Nghost;
c_atom->Nmax = atom->Nmax;
c_atom->ntypes = atom->ntypes;
c_neighbor->maxneighs = neighbor->maxneighs;
/* extend c_neighbor arrays if necessary */
if(nall > nmax) {
nmax = nall;
if(neighbor->numneigh) cudaFreeHost(neighbor->numneigh);
if(neighbor->neighbors) cudaFreeHost(neighbor->neighbors);
checkCUDAError( "buildNeighbor numneigh", cudaMallocHost((void**)&(neighbor->numneigh), nmax * sizeof(int)) );
checkCUDAError( "buildNeighbor neighbors", cudaMallocHost((void**)&(neighbor->neighbors), nmax * neighbor->maxneighs * sizeof(int)) );
// neighbor->numneigh = (int*) malloc(nmax * sizeof(int));
// neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*));
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)) );
}
/* bin local & ghost atoms */
binatoms(atom);
int resize = 1;
cudaProfilerStart();
checkCUDAError( "c_atom->x memcpy", cudaMemcpy(c_atom->x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
/* upload stencil */
int* c_stencil;
// 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 memcpy", cudaMemcpy(c_stencil, stencil, nstencil * sizeof(int), cudaMemcpyHostToDevice ));
int *c_bincount;
checkCUDAError( "buildNeighbor c_bincount malloc", cudaMalloc((void**)&c_bincount, mbins * sizeof(int)) );
checkCUDAError( "buildNeighbor c_bincount memcpy", cudaMemcpy(c_bincount, bincount, mbins * sizeof(int), cudaMemcpyHostToDevice) );
int *c_bins;
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{
.xprd = xprd,
.yprd = yprd,
.zprd = zprd,
.bininvx = bininvx,
.bininvy = bininvy,
.bininvz = bininvz,
.mbinxlo = mbinxlo,
.mbinylo = mbinylo,
.mbinzlo = mbinzlo,
.nbinx = nbinx,
.nbiny = nbiny,
.nbinz = nbinz,
.mbinx = mbinx,
.mbiny = mbiny,
.mbinz = mbinz
};
int* c_new_maxneighs;
checkCUDAError("c_new_maxneighs malloc", cudaMalloc((void**)&c_new_maxneighs, sizeof(int) ));
/* loop over each atom, storing neighbors */
while(resize) {
int new_maxneighs = neighbor->maxneighs;
resize = 0;
// TODO allocate space for and then copy all necessary components
// TODO dont forget to copy the atom positions over
checkCUDAError("c_new_maxneighs memset", cudaMemset(c_new_maxneighs, c_neighbor->maxneighs, sizeof(int) ));
// TODO call compute_neigborhood kernel here
const int num_blocks = ceil((float)atom->Nlocal / (float)num_threads_per_block);
/*compute_neighborhood(Atom a, Neighbor neigh, Neighbor_params np, int nstencil, int* stencil,
int* bins, int atoms_per_bin, int *bincount, int *new_maxneighs)
* */
compute_neighborhood<<<num_blocks, num_threads_per_block>>>(*c_Atom, *c_neighbor,
np, nstencil, c_stencil,
c_bins, atoms_per_bin, c_bincount,
c_new_maxneighs);
// TODO copy the value of c_new_maxneighs back to host and check if it has been modified
int new_maxneighs;
checkCUDAError("c_new_maxneighs memcpy back", cudaMemcpy(&new_maxneighs, c_new_maxneighs, sizeof(int), cudaMemcpyDeviceToHost));
if (new_maxneighs > c_neighbor->maxneighs){
resize = 1;
}
if(resize) {
printf("RESIZE %d\n", neighbor->maxneighs);
neighbor->maxneighs = new_maxneighs * 1.2;
free(neighbor->neighbors);
neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int));
printf("RESIZE %d\n", c_neighbor->maxneighs);
c_neighbor->maxneighs = new_maxneighs * 1.2;
cudaFree(c_neighbor->neighbors);
checkCUDAError("c_neighbor->neighbors resize malloc",
cudaMalloc((void**)(&c_neighbor->neighbors),
c_atom->Nmax * c_neighbor->maxneighs * sizeof(int)));
}
}
neighbor->maxneighs = c_neighbor->maxneighs;
cudaProfilerStop();
cudaFree(c_new_maxneighs);
cudaFree(c_n_stencil);
cudaFree(c_bincount);
cudaFree(c_bins);
}
}