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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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50
src/main.c
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@@ -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);