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Change data layout for force arrays according to position

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-03-18 01:40:51 +01:00
parent e7737e9151
commit 719330807b
6 changed files with 41 additions and 43 deletions
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7
lammps/atom.c
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@ -440,16 +440,17 @@ void growAtom(Atom *atom) {
#ifdef AOS #ifdef AOS
atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3); atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
atom->fx = (MD_FLOAT*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
#else #else
atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->y = (MD_FLOAT*) reallocate(atom->y, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->y = (MD_FLOAT*) reallocate(atom->y, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->z = (MD_FLOAT*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->z = (MD_FLOAT*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fx = (MD_FLOAT*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fy = (MD_FLOAT*) reallocate(atom->fy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fz = (MD_FLOAT*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
#endif #endif
atom->vx = (MD_FLOAT*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->vx = (MD_FLOAT*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vy = (MD_FLOAT*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->vy = (MD_FLOAT*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vz = (MD_FLOAT*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->vz = (MD_FLOAT*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fx = (MD_FLOAT*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fy = (MD_FLOAT*) reallocate(atom->fy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fz = (MD_FLOAT*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int)); atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int));
} }

8
lammps/force_eam.c
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@ -41,7 +41,7 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
int* neighs; int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; int ntypes = atom->ntypes; MD_FLOAT* fp = eam->fp; int ntypes = atom->ntypes; MD_FLOAT* fp = eam->fp;
MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline; MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline;
MD_FLOAT rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; MD_FLOAT rdrho = eam->rdrho; MD_FLOAT rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; MD_FLOAT rdrho = eam->rdrho;
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot; int nrho = eam->nrho; int nrho_tot = eam->nrho_tot;
@ -200,9 +200,9 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
} }
} }
fx[i] = fix; atom_fx(i) = fix;
fy[i] = fiy; atom_fy(i) = fiy;
fz[i] = fiz; atom_fz(i) = fiz;
addStat(stats->total_force_neighs, numneighs); addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH); addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
} }

37
lammps/force_lj.c
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@ -31,9 +31,6 @@
double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) { double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
int* neighs; int* neighs;
MD_FLOAT* fx = atom->fx;
MD_FLOAT* fy = atom->fy;
MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES #ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6; MD_FLOAT sigma6 = param->sigma6;
@ -41,9 +38,9 @@ double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
#endif #endif
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0; atom_fx(i) = 0.0;
fy[i] = 0.0; atom_fy(i) = 0.0;
fz[i] = 0.0; atom_fz(i) = 0.0;
} }
double S = getTimeStamp(); double S = getTimeStamp();
@ -94,9 +91,9 @@ double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
} }
} }
fx[i] += fix; atom_fx(i) += fix;
fy[i] += fiy; atom_fy(i) += fiy;
fz[i] += fiz; atom_fz(i) += fiz;
addStat(stats->total_force_neighs, numneighs); addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH); addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
@ -110,9 +107,6 @@ double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) { double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
int* neighs; int* neighs;
MD_FLOAT* fx = atom->fx;
MD_FLOAT* fy = atom->fy;
MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES #ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6; MD_FLOAT sigma6 = param->sigma6;
@ -120,9 +114,9 @@ double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
#endif #endif
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0; atom_fx(i) = 0.0;
fy[i] = 0.0; atom_fy(i) = 0.0;
fz[i] = 0.0; atom_fz(i) = 0.0;
} }
double S = getTimeStamp(); double S = getTimeStamp();
@ -167,17 +161,16 @@ double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
// We do not need to update forces for ghost atoms // We do not need to update forces for ghost atoms
if(j < Nlocal) { if(j < Nlocal) {
// TODO: Experiment with AoS layout for forces atom_fx(j) -= delx * force;
fx[j] -= delx * force; atom_fy(j) -= dely * force;
fy[j] -= dely * force; atom_fz(j) -= delz * force;
fz[j] -= delz * force;
} }
} }
} }
fx[i] += fix; atom_fx(i) += fix;
fy[i] += fiy; atom_fy(i) += fiy;
fz[i] += fiz; atom_fz(i) += fiz;
addStat(stats->total_force_neighs, numneighs); addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH); addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);

6
lammps/includes/atom.h
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@ -52,11 +52,17 @@ extern void growAtom(Atom*);
#define atom_x(i) atom->x[(i) * 3 + 0] #define atom_x(i) atom->x[(i) * 3 + 0]
#define atom_y(i) atom->x[(i) * 3 + 1] #define atom_y(i) atom->x[(i) * 3 + 1]
#define atom_z(i) atom->x[(i) * 3 + 2] #define atom_z(i) atom->x[(i) * 3 + 2]
#define atom_fx(i) atom->fx[(i) * 3 + 0]
#define atom_fy(i) atom->fx[(i) * 3 + 1]
#define atom_fz(i) atom->fx[(i) * 3 + 2]
#else #else
#define POS_DATA_LAYOUT "SoA" #define POS_DATA_LAYOUT "SoA"
#define atom_x(i) atom->x[i] #define atom_x(i) atom->x[i]
#define atom_y(i) atom->y[i] #define atom_y(i) atom->y[i]
#define atom_z(i) atom->z[i] #define atom_z(i) atom->z[i]
#define atom_fx(i) atom->fx[i]
#define atom_fy(i) atom->fy[i]
#define atom_fz(i) atom->fz[i]
#endif #endif
#endif #endif

13
lammps/main.c
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@ -93,13 +93,12 @@ double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
} }
void initialIntegrate(Parameter *param, Atom *atom) { void initialIntegrate(Parameter *param, Atom *atom) {
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz; MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) { for(int i = 0; i < atom->Nlocal; i++) {
vx[i] += param->dtforce * fx[i]; vx[i] += param->dtforce * atom_fx(i);
vy[i] += param->dtforce * fy[i]; vy[i] += param->dtforce * atom_fy(i);
vz[i] += param->dtforce * fz[i]; vz[i] += param->dtforce * atom_fz(i);
atom_x(i) = atom_x(i) + param->dt * vx[i]; atom_x(i) = atom_x(i) + param->dt * vx[i];
atom_y(i) = atom_y(i) + param->dt * vy[i]; atom_y(i) = atom_y(i) + param->dt * vy[i];
atom_z(i) = atom_z(i) + param->dt * vz[i]; atom_z(i) = atom_z(i) + param->dt * vz[i];
@ -111,9 +110,9 @@ void finalIntegrate(Parameter *param, Atom *atom) {
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz; MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) { for(int i = 0; i < atom->Nlocal; i++) {
vx[i] += param->dtforce * fx[i]; vx[i] += param->dtforce * atom_fx(i);
vy[i] += param->dtforce * fy[i]; vy[i] += param->dtforce * atom_fy(i);
vz[i] += param->dtforce * fz[i]; vz[i] += param->dtforce * atom_fz(i);
} }
} }

13
lammps/tracing.c
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@ -30,7 +30,6 @@ void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timest
INDEX_TRACER_INIT; INDEX_TRACER_INIT;
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
int* neighs; int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
INDEX_TRACE_NATOMS(Nlocal, atom->Nghost, neighbor->maxneighs); INDEX_TRACE_NATOMS(Nlocal, atom->Nghost, neighbor->maxneighs);
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
@ -60,12 +59,12 @@ void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timest
#endif #endif
} }
MEM_TRACE(fx[i], 'R'); MEM_TRACE(atom_fx(i), 'R');
MEM_TRACE(fx[i], 'W'); MEM_TRACE(atom_fx(i), 'W');
MEM_TRACE(fy[i], 'R'); MEM_TRACE(atom_fy(i), 'R');
MEM_TRACE(fy[i], 'W'); MEM_TRACE(atom_fy(i), 'W');
MEM_TRACE(fz[i], 'R'); MEM_TRACE(atom_fz(i), 'R');
MEM_TRACE(fz[i], 'W'); MEM_TRACE(atom_fz(i), 'W');
} }
INDEX_TRACER_END; INDEX_TRACER_END;