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Integrate LAMMPS CUDA versions into master branch

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-08-09 18:53:53 +02:00
parent eb77e1a3bd
commit c18124b066
19 changed files with 1004 additions and 92 deletions
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89
lammps/main.c
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@@ -42,6 +42,7 @@
#include <eam.h>
#include <vtk.h>
#include <util.h>
#include <integrate.h>
#define HLINE "----------------------------------------------------------------------------\n"
@@ -51,15 +52,12 @@ extern double computeForceLJHalfNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceDemFullNeigh(Parameter*, Atom*, Neighbor*, Stats*);
#ifdef USE_SIMD_KERNEL
# define KERNEL_NAME "SIMD"
# define computeForceLJFullNeigh computeForceLJFullNeigh_simd
#else
# define KERNEL_NAME "plain-C"
# define computeForceLJFullNeigh computeForceLJFullNeigh_plain_c
#ifdef CUDA_TARGET
#include <cuda_atom.h>
extern double computeForceLJFullNeigh_cuda(Parameter*, Atom*, Neighbor*, Atom*, Neighbor*);
#endif
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *stats) {
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor, Stats *stats) {
if(param->force_field == FF_EAM) { initEam(eam, param); }
double S, E;
param->lattice = pow((4.0 / param->rho), (1.0 / 3.0));
@@ -82,45 +80,29 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *
setupThermo(param, atom->Natoms);
if(param->input_file == NULL) { adjustThermo(param, atom); }
setupPbc(atom, param);
updatePbc(atom, param);
buildNeighbor(atom, neighbor);
#ifdef CUDA_TARGET
initCuda(atom, neighbor, c_atom, c_neighbor);
#endif
updatePbc(atom, c_atom, param, true);
buildNeighbor(atom, neighbor, c_atom, c_neighbor);
E = getTimeStamp();
return E-S;
}
double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor) {
double S, E;
S = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param);
updateAtomsPbc(atom, c_atom, param);
setupPbc(atom, param);
updatePbc(atom, param);
updatePbc(atom, c_atom, param, true);
//sortAtom(atom);
buildNeighbor(atom, neighbor);
buildNeighbor(atom, neighbor, c_atom, c_neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
return E-S;
}
void initialIntegrate(Parameter *param, Atom *atom) {
for(int i = 0; i < atom->Nlocal; i++) {
atom_vx(i) += param->dtforce * atom_fx(i);
atom_vy(i) += param->dtforce * atom_fy(i);
atom_vz(i) += param->dtforce * atom_fz(i);
atom_x(i) = atom_x(i) + param->dt * atom_vx(i);
atom_y(i) = atom_y(i) + param->dt * atom_vy(i);
atom_z(i) = atom_z(i) + param->dt * atom_vz(i);
}
}
void finalIntegrate(Parameter *param, Atom *atom) {
for(int i = 0; i < atom->Nlocal; i++) {
atom_vx(i) += param->dtforce * atom_fx(i);
atom_vy(i) += param->dtforce * atom_fy(i);
atom_vz(i) += param->dtforce * atom_fz(i);
}
}
void printAtomState(Atom *atom) {
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n", atom->Natoms, atom->Nlocal, atom->Nghost, atom->Nmax);
// int nall = atom->Nlocal + atom->Nghost;
@@ -129,7 +111,7 @@ void printAtomState(Atom *atom) {
// }
}
double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor, Atom *c_atom, Neighbor *c_neighbor, Stats *stats) {
if(param->force_field == FF_EAM) {
return computeForceEam(eam, param, atom, neighbor, stats);
} else if(param->force_field == FF_DEM) {
@@ -145,14 +127,18 @@ double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor,
return computeForceLJHalfNeigh(param, atom, neighbor, stats);
}
#ifdef CUDA_TARGET
return computeForceLJFullNeigh(param, atom, neighbor, c_atom, c_neighbor);
#else
return computeForceLJFullNeigh(param, atom, neighbor, stats);
#endif
}
int main(int argc, char** argv) {
double timer[NUMTIMER];
Eam eam;
Atom atom;
Neighbor neighbor;
Atom atom, c_atom;
Neighbor neighbor, c_neighbor;
Stats stats;
Parameter param;
@@ -240,16 +226,16 @@ int main(int argc, char** argv) {
}
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &stats);
setup(&param, &eam, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
printParameter(&param);
printf("step\ttemp\t\tpressure\n");
computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
#endif
timer[FORCE] = computeForce(&eam, &param, &atom, &neighbor, &stats);
timer[FORCE] = computeForce(&eam, &param, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
timer[NEIGH] = 0.0;
timer[TOTAL] = getTimeStamp();
@@ -258,21 +244,26 @@ int main(int argc, char** argv) {
}
for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param, &atom);
bool reneigh = (n + 1) % param.reneigh_every == 0;
initialIntegrate(reneigh, &param, &atom, &c_atom);
if((n + 1) % param.reneigh_every) {
updatePbc(&atom, &param);
updatePbc(&atom, &c_atom, &param, false);
} else {
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
timer[NEIGH] += reneighbour(&param, &atom, &neighbor, &c_atom, &c_neighbor);
}
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
#endif
timer[FORCE] += computeForce(&eam, &param, &atom, &neighbor, &stats);
finalIntegrate(&param, &atom);
timer[FORCE] += computeForce(&eam, &param, &atom, &neighbor, &c_atom, &c_neighbor, &stats);
finalIntegrate(reneigh, &param, &atom, &c_atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
#ifdef CUDA_TARGET
checkCUDAError("computeThermo atom->x memcpy back", cudaMemcpy(atom.x, c_atom.x, atom.Nmax * sizeof(MD_FLOAT) * 3, cudaMemcpyDeviceToHost));
#endif
computeThermo(n + 1, &param, &atom);
}
@@ -287,11 +278,11 @@ int main(int argc, char** argv) {
printf(HLINE);
printf("Force field: %s\n", ff2str(param.force_field));
printf("Data layout for positions: %s\n", POS_DATA_LAYOUT);
#if PRECISION == 1
#if PRECISION == 1
printf("Using single precision floating point.\n");
#else
#else
printf("Using double precision floating point.\n");
#endif
#endif
printf(HLINE);
printf("System: %d atoms %d ghost atoms, Steps: %d\n", atom.Natoms, atom.Nghost, param.ntimes);
printf("TOTAL %.2fs FORCE %.2fs NEIGH %.2fs REST %.2fs\n",