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Add support for AoS data layout

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2021-03-20 18:32:50 +01:00
parent b39957421c
commit 3f7edb5dbf
6 changed files with 93 additions and 77 deletions
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3
Makefile
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@ -5,6 +5,7 @@ TARGET = MDBench-$(TAG)
BUILD_DIR = ./$(TAG)
SRC_DIR = ./src
MAKE_DIR = ./
FLAGS = #-DAOS
Q ?= @
#DO NOT EDIT BELOW
@ -14,7 +15,7 @@ INCLUDES += -I./src/includes
VPATH = $(SRC_DIR)
ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s,$(wildcard $(SRC_DIR)/*.c))
OBJ = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o,$(wildcard $(SRC_DIR)/*.c))
CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(INCLUDES)
CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(INCLUDES) ${FLAGS}
${TARGET}: $(BUILD_DIR) $(OBJ)

10
src/atom.c
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@ -111,9 +111,9 @@ void createAtom(Atom *atom, Parameter *param)
growAtom(atom);
}
atom->x[atom->Nlocal] = xtmp;
atom->y[atom->Nlocal] = ytmp;
atom->z[atom->Nlocal] = ztmp;
set_atom_x(atom, atom->Nlocal, xtmp);
set_atom_y(atom, atom->Nlocal, ytmp);
set_atom_z(atom, atom->Nlocal, ztmp);
atom->vx[atom->Nlocal] = vxtmp;
atom->vy[atom->Nlocal] = vytmp;
atom->vz[atom->Nlocal] = vztmp;
@ -136,9 +136,13 @@ void growAtom(Atom *atom)
int nold = atom->Nmax;
atom->Nmax += DELTA;
#ifdef AOS
atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
#else
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->z = (MD_FLOAT*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
#endif
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->vz = (MD_FLOAT*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));

19
src/includes/atom.h
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@ -35,4 +35,23 @@ typedef struct {
extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern void growAtom(Atom*);
#ifdef AOS
inline const char *posDataLayout() { return "AoS"; }
inline void set_atom_x(Atom *atom, int i, MD_FLOAT x) { atom->x[i * 3 + 0] = x; }
inline void set_atom_y(Atom *atom, int i, MD_FLOAT y) { atom->x[i * 3 + 1] = y; }
inline void set_atom_z(Atom *atom, int i, MD_FLOAT z) { atom->x[i * 3 + 2] = z; }
inline MD_FLOAT get_atom_x(Atom *atom, int i) { return atom->x[i * 3 + 0]; }
inline MD_FLOAT get_atom_y(Atom *atom, int i) { return atom->x[i * 3 + 1]; }
inline MD_FLOAT get_atom_z(Atom *atom, int i) { return atom->x[i * 3 + 2]; }
#else
inline const char *posDataLayout() { return "SoA"; }
inline void set_atom_x(Atom *atom, int i, MD_FLOAT x) { atom->x[i] = x; }
inline void set_atom_y(Atom *atom, int i, MD_FLOAT y) { atom->y[i] = y; }
inline void set_atom_z(Atom *atom, int i, MD_FLOAT z) { atom->z[i] = z; }
inline MD_FLOAT get_atom_x(Atom *atom, int i) { return atom->x[i]; }
inline MD_FLOAT get_atom_y(Atom *atom, int i) { return atom->y[i]; }
inline MD_FLOAT get_atom_z(Atom *atom, int i) { return atom->z[i]; }
#endif
#endif

21
src/main.c
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@ -116,7 +116,6 @@ double reneighbour(
void initialIntegrate(Parameter *param, Atom *atom)
{
MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z;
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;
@ -124,9 +123,9 @@ void initialIntegrate(Parameter *param, Atom *atom)
vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i];
vz[i] += param->dtforce * fz[i];
x[i] += param->dt * vx[i];
y[i] += param->dt * vy[i];
z[i] += param->dt * vz[i];
set_atom_x(atom, i, get_atom_x(atom, i) + param->dt * vx[i]);
set_atom_y(atom, i, get_atom_y(atom, i) + param->dt * vy[i]);
set_atom_z(atom, i, get_atom_z(atom, i) + param->dt * vz[i]);
}
}
@ -149,7 +148,6 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT S, E;
@ -166,9 +164,9 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = x[i];
MD_FLOAT ytmp = y[i];
MD_FLOAT ztmp = z[i];
MD_FLOAT xtmp = get_atom_x(atom, i);
MD_FLOAT ytmp = get_atom_y(atom, i);
MD_FLOAT ztmp = get_atom_z(atom, i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
@ -176,9 +174,9 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - x[j];
MD_FLOAT dely = ytmp - y[j];
MD_FLOAT delz = ztmp - z[j];
MD_FLOAT delx = xtmp - get_atom_x(atom, j);
MD_FLOAT dely = ytmp - get_atom_y(atom, j);
MD_FLOAT delz = ztmp - get_atom_z(atom, j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) {
@ -293,6 +291,7 @@ int main (int argc, char** argv)
computeThermo(-1, &param, &atom);
printf(HLINE);
printf("Data layout for positions: %s\n", posDataLayout());
#if PRECISION == 1
printf("Using single precision floating point.\n");
#else

20
src/neighbor.c
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@ -184,9 +184,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
/* bin local & ghost atoms */
binatoms(atom);
int resize = 1;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
/* loop over each atom, storing neighbors */
while(resize) {
@ -196,9 +193,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
for(int i = 0; i < atom->Nlocal; i++) {
int* neighptr = &(neighbor->neighbors[i * neighbor->maxneighs]);
int n = 0;
MD_FLOAT xtmp = x[i];
MD_FLOAT ytmp = y[i];
MD_FLOAT ztmp = z[i];
MD_FLOAT xtmp = get_atom_x(atom, i);
MD_FLOAT ytmp = get_atom_y(atom, i);
MD_FLOAT ztmp = get_atom_z(atom, i);
int ibin = coord2bin(xtmp, ytmp, ztmp);
for(int k = 0; k < nstencil; k++) {
@ -212,9 +209,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
continue;
}
MD_FLOAT delx = xtmp - x[j];
MD_FLOAT dely = ytmp - y[j];
MD_FLOAT delz = ztmp - z[j];
MD_FLOAT delx = xtmp - get_atom_x(atom, j);
MD_FLOAT dely = ytmp - get_atom_y(atom, j);
MD_FLOAT delz = ztmp - get_atom_z(atom, j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if( rsq <= cutneighsq ) {
@ -309,9 +306,6 @@ int coord2bin(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin)
void binatoms(Atom *atom)
{
int nall = atom->Nlocal + atom->Nghost;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
int resize = 1;
while(resize > 0) {
@ -322,7 +316,7 @@ void binatoms(Atom *atom)
}
for(int i = 0; i < nall; i++) {
int ibin = coord2bin(x[i], y[i], z[i]);
int ibin = coord2bin(get_atom_x(atom, i), get_atom_y(atom, i), get_atom_z(atom, i));
if(bincount[ibin] < atoms_per_bin) {
int ac = bincount[ibin]++;

97
src/pbc.c
View File

@ -48,17 +48,14 @@ void initPbc()
void updatePbc(Atom *atom, Parameter *param)
{
int nlocal = atom->Nlocal;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nghost; i++) {
x[nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd;
y[nlocal + i] = y[BorderMap[i]] + PBCy[i] * yprd;
z[nlocal + i] = z[BorderMap[i]] + PBCz[i] * zprd;
set_atom_x(atom, nlocal + i, get_atom_x(atom, BorderMap[i]) + PBCx[i] * xprd);
set_atom_y(atom, nlocal + i, get_atom_y(atom, BorderMap[i]) + PBCy[i] * yprd);
set_atom_z(atom, nlocal + i, get_atom_z(atom, BorderMap[i]) + PBCz[i] * zprd);
}
}
@ -66,31 +63,31 @@ void updatePbc(Atom *atom, Parameter *param)
* to periodic boundary conditions */
void updateAtomsPbc(Atom *atom, Parameter *param)
{
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nlocal; i++) {
MD_FLOAT x = get_atom_x(atom, i);
MD_FLOAT y = get_atom_y(atom, i);
MD_FLOAT z = get_atom_z(atom, i);
if(x[i] < 0.0) {
x[i] += xprd;
} else if(x[i] >= xprd) {
x[i] -= xprd;
if(x < 0.0) {
set_atom_x(atom, i, x + xprd);
} else if(x >= xprd) {
set_atom_x(atom, i, x - xprd);
}
if(y[i] < 0.0) {
y[i] += yprd;
} else if(y[i] >= yprd) {
y[i] -= yprd;
if(y < 0.0) {
set_atom_y(atom, i, y + yprd);
} else if(y >= yprd) {
set_atom_y(atom, i, y - yprd);
}
if(z[i] < 0.0) {
z[i] += zprd;
} else if(z[i] >= zprd) {
z[i] -= zprd;
if(z < 0.0) {
set_atom_z(atom, i, z + zprd);
} else if(z >= zprd) {
set_atom_z(atom, i, z - zprd);
}
}
}
@ -102,7 +99,6 @@ void updateAtomsPbc(Atom *atom, Parameter *param)
#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
void setupPbc(Atom *atom, Parameter *param)
{
MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
@ -113,42 +109,45 @@ void setupPbc(Atom *atom, Parameter *param)
if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
growAtom(atom);
x = atom->x; y = atom->y; z = atom->z;
}
if (Nghost + 7 >= NmaxGhost) {
growPbc();
}
MD_FLOAT x = get_atom_x(atom, i);
MD_FLOAT y = get_atom_y(atom, i);
MD_FLOAT z = get_atom_z(atom, i);
/* Setup ghost atoms */
/* 6 planes */
if (x[i] < Cutneigh) { ADDGHOST(+1,0,0); }
if (x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
if (y[i] < Cutneigh) { ADDGHOST(0,+1,0); }
if (y[i] >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
if (z[i] < Cutneigh) { ADDGHOST(0,0,+1); }
if (z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
if (x < Cutneigh) { ADDGHOST(+1,0,0); }
if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
if (y < Cutneigh) { ADDGHOST(0,+1,0); }
if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
if (z < Cutneigh) { ADDGHOST(0,0,+1); }
if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
/* 8 corners */
if (x[i] < Cutneigh && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x[i] < Cutneigh && y[i] >= Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x < Cutneigh && y >= Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
/* 12 edges */
if (x[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x[i] >= (xprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,0,+1); }
if (x[i] >= (xprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
if (y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
if (y[i] < Cutneigh && x[i] < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y[i] < Cutneigh && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y[i] >= (yprd-Cutneigh) && x[i] < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y[i] >= (yprd-Cutneigh) && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); }
if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y >= (yprd-Cutneigh) && x >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
}
// increase by one to make it the ghost atom count
atom->Nghost = Nghost + 1;