moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update stubbed force calculation

Browse Source 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2021-04-07 00:46:51 +02:00
parent 77a0774208
commit 706f1c38f2
5 changed files with 43 additions and 42 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
config.mk
View File

@ -6,4 +6,4 @@ DATA_TYPE ?= DP
DATA_LAYOUT ?= SOA DATA_LAYOUT ?= SOA
#Feature options #Feature options
OPTIONS += -DALIGNMENT=64 OPTIONS += -DALIGNMENT=64 -DLIKWID_PERFMON

6
include_GCC.mk
View File

@ -11,5 +11,7 @@ CFLAGS = -O3 -march=znver1 -ffast-math -funroll-loops # -fopenmp
ASFLAGS = -masm=intel ASFLAGS = -masm=intel
LFLAGS = LFLAGS =
DEFINES = -D_GNU_SOURCE DEFINES = -D_GNU_SOURCE
INCLUDES = #INCLUDES =
LIBS = -lm #LIBS = -lm
INCLUDES = $(LIKWID_INC)
LIBS = -lm $(LIKWID_LIB) -llikwid

57
src/core/force.c
View File

@ -31,7 +31,8 @@ double computeForce(
Parameter *param, Parameter *param,
Atom *atom, Atom *atom,
Neighbor *neighbor, Neighbor *neighbor,
int profile) int profile,
int ntimes)
{ {
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
int* neighs; int* neighs;
@ -52,38 +53,40 @@ double computeForce(
LIKWID_MARKER_START("force"); LIKWID_MARKER_START("force");
} }
for(int t = 0; t < ntimes; t++) {
#pragma omp parallel for #pragma omp parallel for
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs]; neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i]; int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i); MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i); MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i); MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0; MD_FLOAT fix = 0;
MD_FLOAT fiy = 0; MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0; MD_FLOAT fiz = 0;
for(int k = 0; k < numneighs; k++) { for(int k = 0; k < numneighs; k++) {
int j = neighs[k]; int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j); MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j); MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j); MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) { if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq; MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6; MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon; MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force; fix += delx * force;
fiy += dely * force; fiy += dely * force;
fiz += delz * force; fiz += delz * force;
}
} }
}
fx[i] += fix; fx[i] += fix;
fy[i] += fiy; fy[i] += fiy;
fz[i] += fiz; fz[i] += fiz;
}
} }
if(profile) { if(profile) {

6
src/main.c
View File

@ -47,7 +47,7 @@ typedef enum {
NUMTIMER NUMTIMER
} timertype; } timertype;
extern double computeForce( Parameter*, Atom*, Neighbor*, int); extern double computeForce( Parameter*, Atom*, Neighbor*, int, int);
void init(Parameter *param) void init(Parameter *param)
{ {
@ -205,7 +205,7 @@ int main (int argc, char** argv)
setup(&param, &atom, &neighbor); setup(&param, &atom, &neighbor);
computeThermo(0, &param, &atom); computeThermo(0, &param, &atom);
computeForce(&param, &atom, &neighbor, 1); computeForce(&param, &atom, &neighbor, 1, 1);
timer[FORCE] = 0.0; timer[FORCE] = 0.0;
timer[NEIGH] = 0.0; timer[NEIGH] = 0.0;
@ -221,7 +221,7 @@ int main (int argc, char** argv)
timer[NEIGH] += reneighbour(&param, &atom, &neighbor); timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
} }
timer[FORCE] += computeForce(&param, &atom, &neighbor, 1); timer[FORCE] += computeForce(&param, &atom, &neighbor, 1, 1);
finalIntegrate(&param, &atom); finalIntegrate(&param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) { if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {

14
src/stub.c
View File

@ -16,7 +16,7 @@
#define LATTICE_DISTANCE 10.0 #define LATTICE_DISTANCE 10.0
#define NEIGH_DISTANCE 1.0 #define NEIGH_DISTANCE 1.0
extern double computeForce( Parameter*, Atom*, Neighbor*, int); extern double computeForce( Parameter*, Atom*, Neighbor*, int, int);
void init(Parameter *param) { void init(Parameter *param) {
param->epsilon = 1.0; param->epsilon = 1.0;
@ -103,7 +103,7 @@ int main(int argc, const char *argv[]) {
initAtom(atom); initAtom(atom);
DEBUG("Creating atoms...\n"); DEBUG("Creating atoms...\n");
const int atoms_per_unit_cell = 16; const int atoms_per_unit_cell = 8;
for(int i = 0; i < param.nx; ++i) { for(int i = 0; i < param.nx; ++i) {
for(int j = 0; j < param.ny; ++j) { for(int j = 0; j < param.ny; ++j) {
@ -158,7 +158,7 @@ int main(int argc, const char *argv[]) {
} }
} }
const double estim_volume = (double)(atom->Nlocal * 6 * sizeof(MD_FLOAT) + (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0; const double estim_volume = (double)(atom->Nlocal * 6 * sizeof(MD_FLOAT) + atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0;
printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz); printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz);
printf("Atoms per unit cell: %d\n", atoms_per_unit_cell); printf("Atoms per unit cell: %d\n", atoms_per_unit_cell);
printf("Total number of atoms: %d\n", atom->Nlocal); printf("Total number of atoms: %d\n", atom->Nlocal);
@ -171,13 +171,9 @@ int main(int argc, const char *argv[]) {
DEBUG("Building neighbor lists...\n"); DEBUG("Building neighbor lists...\n");
buildNeighbor(atom, &neighbor); buildNeighbor(atom, &neighbor);
DEBUG("Computing forces...\n"); DEBUG("Computing forces...\n");
computeForce(&param, atom, &neighbor, 0); computeForce(&param, atom, &neighbor, 0, 1);
double T_accum = 0.0;
for(int i = 0; i < param.ntimes; i++) {
T_accum += computeForce(&param, atom, &neighbor, 1);
}
double T_accum = computeForce(&param, atom, &neighbor, 1, param.ntimes);
printf("Total time: %.4f, Time/force: %.4f\n", T_accum, T_accum / param.ntimes); printf("Total time: %.4f, Time/force: %.4f\n", T_accum, T_accum / param.ntimes);
LIKWID_MARKER_CLOSE; LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS; return EXIT_SUCCESS;