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Add percentage of atoms within cutoff radius when using GROMACS reference version

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-25 14:19:48 +01:00
parent fdd18df816
commit e637a26844
3 changed files with 21 additions and 4 deletions
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8
gromacs/force_lj.c
View File

@ -83,6 +83,9 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
fix += delx * force; fix += delx * force;
fiy += dely * force; fiy += dely * force;
fiz += delz * force; fiz += delz * force;
addStat(stats->atoms_within_cutoff, 1);
} else {
addStat(stats->atoms_outside_cutoff, 1);
} }
} }
} }
@ -93,8 +96,9 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
} }
} }
addStat(stats->calculated_forces, 1);
addStat(stats->num_neighs, numneighs); addStat(stats->num_neighs, numneighs);
addStat(stats->force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH); addStat(stats->force_iters, (long long int)((double)numneighs * CLUSTER_DIM_M / CLUSTER_DIM_N));
} }
LIKWID_MARKER_STOP("force"); LIKWID_MARKER_STOP("force");
@ -250,7 +254,7 @@ double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
addStat(stats->calculated_forces, 1); addStat(stats->calculated_forces, 1);
addStat(stats->num_neighs, numneighs); addStat(stats->num_neighs, numneighs);
addStat(stats->force_iters, numneighs / 2); addStat(stats->force_iters, (long long int)((double)numneighs * CLUSTER_DIM_M / CLUSTER_DIM_N));
} }
LIKWID_MARKER_STOP("force"); LIKWID_MARKER_STOP("force");

2
gromacs/includes/stats.h
View File

@ -29,6 +29,8 @@ typedef struct {
long long int calculated_forces; long long int calculated_forces;
long long int num_neighs; long long int num_neighs;
long long int force_iters; long long int force_iters;
long long int atoms_within_cutoff;
long long int atoms_outside_cutoff;
} Stats; } Stats;
void initStats(Stats *s); void initStats(Stats *s);

15
gromacs/stats.c
View File

@ -9,10 +9,13 @@ void initStats(Stats *s) {
s->calculated_forces = 0; s->calculated_forces = 0;
s->num_neighs = 0; s->num_neighs = 0;
s->force_iters = 0; s->force_iters = 0;
s->atoms_within_cutoff = 0;
s->atoms_outside_cutoff = 0;
} }
void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer) { void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer) {
#ifdef COMPUTE_STATS #ifdef COMPUTE_STATS
const int MxN = CLUSTER_DIM_M * CLUSTER_DIM_N; const int MxN = CLUSTER_DIM_M * CLUSTER_DIM_N;
double avg_atoms_cluster = (double)(atom->Nlocal) / (double)(atom->Nclusters_local); double avg_atoms_cluster = (double)(atom->Nlocal) / (double)(atom->Nclusters_local);
double force_useful_volume = 1e-9 * ( (double)(atom->Nlocal * (param->ntimes + 1)) * (sizeof(MD_FLOAT) * 6 + sizeof(int)) + double force_useful_volume = 1e-9 * ( (double)(atom->Nlocal * (param->ntimes + 1)) * (sizeof(MD_FLOAT) * 6 + sizeof(int)) +
@ -20,9 +23,11 @@ void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer
double avg_neigh_atom = (stats->num_neighs * CLUSTER_DIM_N) / (double)(atom->Nlocal * (param->ntimes + 1)); double avg_neigh_atom = (stats->num_neighs * CLUSTER_DIM_N) / (double)(atom->Nlocal * (param->ntimes + 1));
double avg_neigh_cluster = (double)(stats->num_neighs) / (double)(stats->calculated_forces); double avg_neigh_cluster = (double)(stats->num_neighs) / (double)(stats->calculated_forces);
double avg_simd = stats->force_iters / (double)(atom->Nlocal * (param->ntimes + 1)); double avg_simd = stats->force_iters / (double)(atom->Nlocal * (param->ntimes + 1));
#ifdef EXPLICIT_TYPES
#ifdef EXPLICIT_TYPES
force_useful_volume += 1e-9 * (double)((atom->Nlocal * (param->ntimes + 1)) + stats->num_neighs) * sizeof(int); force_useful_volume += 1e-9 * (double)((atom->Nlocal * (param->ntimes + 1)) + stats->num_neighs) * sizeof(int);
#endif #endif
printf("Statistics:\n"); printf("Statistics:\n");
printf("\tVector width: %d, Processor frequency: %.4f GHz\n", VECTOR_WIDTH, param->proc_freq); printf("\tVector width: %d, Processor frequency: %.4f GHz\n", VECTOR_WIDTH, param->proc_freq);
printf("\tAverage atoms per cluster: %.4f\n", avg_atoms_cluster); printf("\tAverage atoms per cluster: %.4f\n", avg_atoms_cluster);
@ -33,5 +38,11 @@ void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer
printf("\tTotal number of SIMD iterations: %lld\n", stats->force_iters); printf("\tTotal number of SIMD iterations: %lld\n", stats->force_iters);
printf("\tUseful read data volume for force computation: %.2fGB\n", force_useful_volume); printf("\tUseful read data volume for force computation: %.2fGB\n", force_useful_volume);
printf("\tCycles/SIMD iteration: %.4f\n", timer[FORCE] * param->proc_freq * 1e9 / stats->force_iters); printf("\tCycles/SIMD iteration: %.4f\n", timer[FORCE] * param->proc_freq * 1e9 / stats->force_iters);
#ifdef USE_REFERENCE_VERSION
const double eff_pct = (double)stats->atoms_within_cutoff / (double)(stats->atoms_within_cutoff + stats->atoms_outside_cutoff) * 100.0;
printf("\tAtoms within/outside cutoff radius: %lld/%lld (%.2f%%)\n", stats->atoms_within_cutoff, stats->atoms_outside_cutoff, eff_pct);
#endif
#endif #endif
} }