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Introduce separate version for traced force routine.

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This commit is contained in:
Jan Eitzinger
2021-10-26 09:11:17 +02:00
parent 557c5e4d3f
commit 3c3d27b48a
6 changed files with 677 additions and 179 deletions
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232
src/force-tracing.c Normal file
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@@ -0,0 +1,232 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
*
* This file is part of MD-Bench.
*
* MD-Bench is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License along
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <likwid-marker.h>
#include <timing.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <stats.h>
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#include <stdio.h>
#include <stdlib.h>
#endif
#ifndef VECTOR_WIDTH
# define VECTOR_WIDTH 8
#endif
#ifndef TRACER_CONDITION
# define TRACER_CONDITION (!(timestep % param->every))
#endif
#ifdef MEM_TRACER
# define MEM_TRACER_INIT FILE *mem_tracer_fp; \
if(TRACER_CONDITION) { \
char mem_tracer_fn[128]; \
snprintf(mem_tracer_fn, sizeof mem_tracer_fn, "mem_tracer_%d.out", timestep); \
mem_tracer_fp = fopen(mem_tracer_fn, "w");
}
# define MEM_TRACER_END if(TRACER_CONDITION) { fclose(mem_tracer_fp); }
# define MEM_TRACE(addr, op) if(TRACER_CONDITION) { fprintf(mem_tracer_fp, "%c: %p\n", op, (void *)(&(addr))); }
#else
# define MEM_TRACER_INIT
# define MEM_TRACER_END
# define MEM_TRACE(addr, op)
#endif
#ifdef INDEX_TRACER
# define INDEX_TRACER_INIT FILE *index_tracer_fp; \
if(TRACER_CONDITION) { \
char index_tracer_fn[128]; \
snprintf(index_tracer_fn, sizeof index_tracer_fn, "index_tracer_%d.out", timestep); \
index_tracer_fp = fopen(index_tracer_fn, "w"); \
}
# define INDEX_TRACER_END if(TRACER_CONDITION) { fclose(index_tracer_fp); }
# define INDEX_TRACE_NATOMS(nl, ng, mn) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "N: %d %d %d\n", nl, ng, mn); }
# define INDEX_TRACE_ATOM(a) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "A: %d\n", a); }
# define INDEX_TRACE(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
fprintf(index_tracer_fp, "I: "); \
for(int __j = 0; __j < __e; ++__j) { \
fprintf(index_tracer_fp, "%d ", l[__i + __j]); \
} \
fprintf(index_tracer_fp, "\n"); \
} \
}
# define DIST_TRACE_SORT(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
if(__e > 1) { \
for(int __j = __i; __j < __i + __e - 1; ++__j) { \
for(int __k = __i; __k < __i + __e - (__j - __i) - 1; ++__k) { \
if(l[__k] > l[__k + 1]) { \
int __t = l[__k]; \
l[__k] = l[__k + 1]; \
l[__k + 1] = __t; \
} \
} \
} \
} \
} \
}
# define DIST_TRACE(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
if(__e > 1) { \
fprintf(index_tracer_fp, "D: "); \
for(int __j = 0; __j < __e - 1; ++__j) { \
int __dist = abs(l[__i + __j + 1] - l[__i + __j]); \
fprintf(index_tracer_fp, "%d ", __dist); \
} \
fprintf(index_tracer_fp, "\n"); \
} \
} \
}
#else
# define INDEX_TRACER_INIT
# define INDEX_TRACER_END
# define INDEX_TRACE_NATOMS(nl, ng, mn)
# define INDEX_TRACE_ATOM(a)
# define INDEX_TRACE(l, e)
# define DIST_TRACE_SORT(l, e)
# define DIST_TRACE(l, e)
#endif
double computeForceTracing(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep) {
MEM_TRACER_INIT;
INDEX_TRACER_INIT;
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
INDEX_TRACE_NATOMS(Nlocal, atom->Nghost, neighbor->maxneighs);
double S = getTimeStamp();
LIKWID_MARKER_START("force");
for(int na = 0; na < (first_exec ? 1 : ATOMS_LOOP_RUNS); na++) {
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
MEM_TRACE(atom_x(i), 'R');
MEM_TRACE(atom_y(i), 'R');
MEM_TRACE(atom_z(i), 'R');
INDEX_TRACE_ATOM(i);
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
MEM_TRACE(atom->type(i), 'R');
#endif
#if defined(VARIANT) && VARIANT == stub && defined(NEIGHBORS_LOOP_RUNS) && NEIGHBORS_LOOP_RUNS > 1
#define REPEAT_NEIGHBORS_LOOP
int nmax = first_exec ? 1 : NEIGHBORS_LOOP_RUNS;
for(int nn = 0; nn < (first_exec ? 1 : NEIGHBORS_LOOP_RUNS); nn++) {
#endif
//DIST_TRACE_SORT(neighs, numneighs);
INDEX_TRACE(neighs, numneighs);
//DIST_TRACE(neighs, numneighs);
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
MEM_TRACE(neighs[k], 'R');
MEM_TRACE(atom_x(j), 'R');
MEM_TRACE(atom_y(j), 'R');
MEM_TRACE(atom_z(j), 'R');
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
MEM_TRACE(atom->type(j), 'R');
#endif
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
}
}
#ifdef REPEAT_NEIGHBORS_LOOP
}
#endif
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
MEM_TRACE(fx[i], 'R');
MEM_TRACE(fx[i], 'W');
MEM_TRACE(fy[i], 'R');
MEM_TRACE(fy[i], 'W');
MEM_TRACE(fz[i], 'R');
MEM_TRACE(fz[i], 'W');
}
}
LIKWID_MARKER_STOP("force");
double E = getTimeStamp();
INDEX_TRACER_END;
MEM_TRACER_END;
return E-S;
}

222
src/force.c
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@@ -26,110 +26,23 @@
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <stats.h>
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#include <stdio.h>
#include <stdlib.h>
#endif
#ifndef VECTOR_WIDTH
# define VECTOR_WIDTH 8
#endif
#ifndef TRACER_CONDITION
# define TRACER_CONDITION (!(timestep % param->every))
#endif
#ifdef MEM_TRACER
# define MEM_TRACER_INIT FILE *mem_tracer_fp; \
if(TRACER_CONDITION) { \
char mem_tracer_fn[128]; \
snprintf(mem_tracer_fn, sizeof mem_tracer_fn, "mem_tracer_%d.out", timestep); \
mem_tracer_fp = fopen(mem_tracer_fn, "w");
}
# define MEM_TRACER_END if(TRACER_CONDITION) { fclose(mem_tracer_fp); }
# define MEM_TRACE(addr, op) if(TRACER_CONDITION) { fprintf(mem_tracer_fp, "%c: %p\n", op, (void *)(&(addr))); }
#else
# define MEM_TRACER_INIT
# define MEM_TRACER_END
# define MEM_TRACE(addr, op)
#endif
#ifdef INDEX_TRACER
# define INDEX_TRACER_INIT FILE *index_tracer_fp; \
if(TRACER_CONDITION) { \
char index_tracer_fn[128]; \
snprintf(index_tracer_fn, sizeof index_tracer_fn, "index_tracer_%d.out", timestep); \
index_tracer_fp = fopen(index_tracer_fn, "w"); \
}
# define INDEX_TRACER_END if(TRACER_CONDITION) { fclose(index_tracer_fp); }
# define INDEX_TRACE_NATOMS(nl, ng, mn) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "N: %d %d %d\n", nl, ng, mn); }
# define INDEX_TRACE_ATOM(a) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "A: %d\n", a); }
# define INDEX_TRACE(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
fprintf(index_tracer_fp, "I: "); \
for(int __j = 0; __j < __e; ++__j) { \
fprintf(index_tracer_fp, "%d ", l[__i + __j]); \
} \
fprintf(index_tracer_fp, "\n"); \
} \
}
# define DIST_TRACE_SORT(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
if(__e > 1) { \
for(int __j = __i; __j < __i + __e - 1; ++__j) { \
for(int __k = __i; __k < __i + __e - (__j - __i) - 1; ++__k) { \
if(l[__k] > l[__k + 1]) { \
int __t = l[__k]; \
l[__k] = l[__k + 1]; \
l[__k + 1] = __t; \
} \
} \
} \
} \
} \
}
# define DIST_TRACE(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
if(__e > 1) { \
fprintf(index_tracer_fp, "D: "); \
for(int __j = 0; __j < __e - 1; ++__j) { \
int __dist = abs(l[__i + __j + 1] - l[__i + __j]); \
fprintf(index_tracer_fp, "%d ", __dist); \
} \
fprintf(index_tracer_fp, "\n"); \
} \
} \
}
#else
# define INDEX_TRACER_INIT
# define INDEX_TRACER_END
# define INDEX_TRACE_NATOMS(nl, ng, mn)
# define INDEX_TRACE_ATOM(a)
# define INDEX_TRACE(l, e)
# define DIST_TRACE_SORT(l, e)
# define DIST_TRACE(l, e)
#endif
double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep) {
MEM_TRACER_INIT;
INDEX_TRACER_INIT;
double computeForce(
Parameter *param,
Atom *atom,
Neighbor *neighbor
)
{
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES
MD_FLOAT* fx = atom->fx;
MD_FLOAT* fy = atom->fy;
MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
#endif
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
@@ -137,96 +50,57 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *sta
fz[i] = 0.0;
}
INDEX_TRACE_NATOMS(Nlocal, atom->Nghost, neighbor->maxneighs);
double S = getTimeStamp();
LIKWID_MARKER_START("force");
for(int na = 0; na < (first_exec ? 1 : ATOMS_LOOP_RUNS); na++) {
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
MEM_TRACE(atom_x(i), 'R');
MEM_TRACE(atom_y(i), 'R');
MEM_TRACE(atom_z(i), 'R');
INDEX_TRACE_ATOM(i);
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
MEM_TRACE(atom->type(i), 'R');
#endif
#if defined(VARIANT) && VARIANT == stub && defined(NEIGHBORS_LOOP_RUNS) && NEIGHBORS_LOOP_RUNS > 1
#define REPEAT_NEIGHBORS_LOOP
int nmax = first_exec ? 1 : NEIGHBORS_LOOP_RUNS;
for(int nn = 0; nn < (first_exec ? 1 : NEIGHBORS_LOOP_RUNS); nn++) {
#endif
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
//DIST_TRACE_SORT(neighs, numneighs);
INDEX_TRACE(neighs, numneighs);
//DIST_TRACE(neighs, numneighs);
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
MEM_TRACE(neighs[k], 'R');
MEM_TRACE(atom_x(j), 'R');
MEM_TRACE(atom_y(j), 'R');
MEM_TRACE(atom_z(j), 'R');
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
MEM_TRACE(atom->type(j), 'R');
#endif
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
}
}
#ifdef REPEAT_NEIGHBORS_LOOP
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
}
#endif
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
MEM_TRACE(fx[i], 'R');
MEM_TRACE(fx[i], 'W');
MEM_TRACE(fy[i], 'R');
MEM_TRACE(fy[i], 'W');
MEM_TRACE(fz[i], 'R');
MEM_TRACE(fz[i], 'W');
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
}
LIKWID_MARKER_STOP("force");
double E = getTimeStamp();
INDEX_TRACER_END;
MEM_TRACER_END;
return E-S;
}

17
src/main.c
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@@ -42,7 +42,8 @@
#define HLINE "----------------------------------------------------------------------------\n"
extern double computeForce(Parameter*, Atom*, Neighbor*, Stats*, int, int);
extern double computeForce(Parameter*, Atom*, Neighbor*);
extern double computeForceTracing(Parameter*, Atom*, Neighbor*, Stats*, int, int);
void init(Parameter *param)
{
@@ -211,7 +212,11 @@ int main (int argc, char** argv)
setup(&param, &atom, &neighbor, &stats);
computeThermo(0, &param, &atom);
computeForce(&param, &atom, &neighbor, &stats, 1, 0);
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(PRINT_STATS)
computeForceTracing(&param, &atom, &neighbor, &stats, 1, 0);
#else
computeForce(&param, &atom, &neighbor);
#endif
timer[FORCE] = 0.0;
timer[NEIGH] = 0.0;
@@ -226,7 +231,11 @@ int main (int argc, char** argv)
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
}
timer[FORCE] += computeForce(&param, &atom, &neighbor, &stats, 0, n + 1);
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(PRINT_STATS)
timer[FORCE] += computeForceTracing(&param, &atom, &neighbor, &stats, 0, n + 1);
#else
timer[FORCE] += computeForce(&param, &atom, &neighbor);
#endif
finalIntegrate(&param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
@@ -251,7 +260,9 @@ int main (int argc, char** argv)
printf(HLINE);
printf("Performance: %.2f million atom updates per second\n",
1e-6 * (double) atom.Natoms * param.ntimes / timer[TOTAL]);
#ifdef PRINT_STATS
displayStatistics(&atom, &param, &stats, timer);
#endif
LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS;
}