* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <cstring>
-#include <algorithm>
-#include <vector>
-
-#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/arraysize.h"
-
typedef struct
{
const char* name;
static void pr_difftime(FILE* out, double dt)
{
- int ndays, nhours, nmins, nsecs;
- gmx_bool bPrint, bPrinted;
+ int ndays, nhours, nmins, nsecs;
+ bool bPrint, bPrinted;
ndays = static_cast<int>(dt / (24 * 3600));
dt = dt - 24 * 3600 * ndays;
void clear_nrnb(t_nrnb* nrnb)
{
- int i;
-
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
nrnb->n[i] = 0.0;
}
}
-void add_nrnb(t_nrnb* dest, t_nrnb* s1, t_nrnb* s2)
-{
- int i;
-
- for (i = 0; (i < eNRNB); i++)
- {
- dest->n[i] = s1->n[i] + s2->n[i];
- }
-}
-
void print_nrnb(FILE* out, t_nrnb* nrnb)
{
- int i;
-
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
if (nrnb->n[i] > 0)
{
}
}
-void _inc_nrnb(t_nrnb* nrnb, int enr, int inc, char gmx_unused* file, int gmx_unused line)
-{
- nrnb->n[enr] += inc;
-#ifdef DEBUG_NRNB
- printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n", nbdata[enr].name, enr, inc, file, line);
-#endif
-}
-
/* Returns in enr is the index of a full nbnxn VdW kernel */
-static gmx_bool nrnb_is_nbnxn_vdw_kernel(int enr)
+static bool nrnb_is_nbnxn_vdw_kernel(int enr)
{
return (enr >= eNR_NBNXN_LJ_RF && enr <= eNR_NBNXN_LJ_E);
}
/* Returns in enr is the index of an nbnxn kernel addition (LJ modification) */
-static gmx_bool nrnb_is_nbnxn_kernel_addition(int enr)
+static bool nrnb_is_nbnxn_kernel_addition(int enr)
{
return (enr >= eNR_NBNXN_ADD_LJ_FSW && enr <= eNR_NBNXN_ADD_LJ_EWALD_E);
}
+void atomicNrnbIncrement(t_nrnb* nrnb, int index, int increment)
+{
+#pragma omp atomic
+ nrnb->n[index] += increment;
+}
+
void print_flop(FILE* out, t_nrnb* nrnb, double* nbfs, double* mflop)
{
- int i, j;
double mni, frac, tfrac, tflop;
const char* myline =
"-----------------------------------------------------------------------------";
*nbfs = 0.0;
- for (i = 0; (i < eNR_NBKERNEL_TOTAL_NR); i++)
+ for (int i = 0; (i < eNR_NBKERNEL_TOTAL_NR); i++)
{
if (std::strstr(nbdata[i].name, "W3-W3") != nullptr)
{
}
}
tflop = 0;
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
tflop += 1e-6 * nrnb->n[i] * nbdata[i].flop;
}
}
*mflop = 0.0;
tfrac = 0.0;
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
mni = 1e-6 * nrnb->n[i];
/* Skip empty entries and nbnxn additional flops,
if (nrnb_is_nbnxn_vdw_kernel(i))
{
/* Possibly add the cost of an LJ switch/Ewald function */
- for (j = eNR_NBNXN_ADD_LJ_FSW; j <= eNR_NBNXN_ADD_LJ_EWALD; j += 2)
+ for (int j = eNR_NBNXN_ADD_LJ_FSW; j <= eNR_NBNXN_ADD_LJ_EWALD; j += 2)
{
int e_kernel_add;
{
return nbdata[enr].name;
}
-
-static const int force_index[] = {
- eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER, eNR_RB,
- eNR_DISRES, eNR_ORIRES, eNR_POSRES, eNR_FBPOSRES, eNR_NS,
-};
-#define NFORCE_INDEX asize(force_index)
-
-static const int constr_index[] = { eNR_SHAKE, eNR_SHAKE_RIJ, eNR_SETTLE, eNR_UPDATE,
- eNR_PCOUPL, eNR_CONSTR_VIR, eNR_CONSTR_V };
-#define NCONSTR_INDEX asize(constr_index)
-
-static double pr_av(FILE* log, t_commrec* cr, double fav, const double ftot[], const char* title)
-{
- int i, perc;
- double dperc, unb;
-
- unb = 0;
- if (fav > 0)
- {
- fav /= cr->nnodes - cr->npmenodes;
- fprintf(log, "\n %-26s", title);
- for (i = 0; (i < cr->nnodes); i++)
- {
- dperc = (100.0 * ftot[i]) / fav;
- unb = std::max(unb, dperc);
- perc = static_cast<int>(dperc);
- fprintf(log, "%3d ", perc);
- }
- if (unb > 0)
- {
- perc = static_cast<int>(10000.0 / unb);
- fprintf(log, "%6d%%\n\n", perc);
- }
- else
- {
- fprintf(log, "\n\n");
- }
- }
- return unb;
-}
-
-void pr_load(FILE* log, t_commrec* cr, t_nrnb nrnb[])
-{
- t_nrnb av;
-
- std::vector<double> ftot(cr->nnodes);
- std::vector<double> stot(cr->nnodes);
- for (int i = 0; (i < cr->nnodes); i++)
- {
- add_nrnb(&av, &av, &(nrnb[i]));
- /* Cost due to forces */
- for (int j = 0; (j < eNR_NBKERNEL_TOTAL_NR); j++)
- {
- ftot[i] += nrnb[i].n[j] * cost_nrnb(j);
- }
- for (int j = 0; (j < NFORCE_INDEX); j++)
- {
- ftot[i] += nrnb[i].n[force_index[j]] * cost_nrnb(force_index[j]);
- }
- /* Due to shake */
- for (int j = 0; (j < NCONSTR_INDEX); j++)
- {
- stot[i] += nrnb[i].n[constr_index[j]] * cost_nrnb(constr_index[j]);
- }
- }
- for (int j = 0; (j < eNRNB); j++)
- {
- av.n[j] = av.n[j] / static_cast<double>(cr->nnodes - cr->npmenodes);
- }
-
- fprintf(log, "\nDetailed load balancing info in percentage of average\n");
-
- fprintf(log, " Type RANK:");
- for (int i = 0; (i < cr->nnodes); i++)
- {
- fprintf(log, "%3d ", i);
- }
- fprintf(log, "Scaling\n");
- fprintf(log, "---------------------------");
- for (int i = 0; (i < cr->nnodes); i++)
- {
- fprintf(log, "----");
- }
- fprintf(log, "-------\n");
-
- for (int j = 0; (j < eNRNB); j++)
- {
- double unb = 100.0;
- if (av.n[j] > 0)
- {
- double dperc;
- int perc;
- fprintf(log, " %-26s", nrnb_str(j));
- for (int i = 0; (i < cr->nnodes); i++)
- {
- dperc = (100.0 * nrnb[i].n[j]) / av.n[j];
- unb = std::max(unb, dperc);
- perc = static_cast<int>(dperc);
- fprintf(log, "%3d ", perc);
- }
- if (unb > 0)
- {
- perc = static_cast<int>(10000.0 / unb);
- fprintf(log, "%6d%%\n", perc);
- }
- else
- {
- fprintf(log, "\n");
- }
- }
- }
- double fav = 0;
- double sav = 0;
- for (int i = 0; (i < cr->nnodes); i++)
- {
- fav += ftot[i];
- sav += stot[i];
- }
- double uf = pr_av(log, cr, fav, ftot.data(), "Total Force");
- double us = pr_av(log, cr, sav, stot.data(), "Total Constr.");
-
- double unb = (uf * fav + us * sav) / (fav + sav);
- if (unb > 0)
- {
- unb = 10000.0 / unb;
- fprintf(log, "\nTotal Scaling: %.0f%% of max performance\n\n", unb);
- }
-}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_GMXLIB_NRNB_H
#define GMX_GMXLIB_NRNB_H
-#include <stdio.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#define eNR_NBKERNEL_NONE (-1)
+#include <array>
+#include <cstdint>
+#include <cstdio>
enum
{
struct t_nrnb
{
- double n[eNRNB] = { 0 };
+ std::array<double, eNRNB> n = { 0 };
};
-struct t_commrec;
-
void clear_nrnb(t_nrnb* nrnb);
-void add_nrnb(t_nrnb* dest, t_nrnb* s1, t_nrnb* s2);
-
void print_nrnb(FILE* out, t_nrnb* nrnb);
-void _inc_nrnb(t_nrnb* nrnb, int enr, int inc, char* file, int line);
-
-#ifdef DEBUG_NRNB
-# define inc_nrnb(nrnb, enr, inc) _inc_nrnb(nrnb, enr, inc, __FILE__, __LINE__)
-#else
-# define inc_nrnb(nrnb, enr, inc) (nrnb)->n[enr] += inc
-#endif
+/*! \brief Increment the nonbonded kernel flop counters
+ *
+ * \param nrnb The nonbonded kernel flop counters.
+ * \param index Which counter to incrememnt.
+ * \param increment How much to increment the counter by.
+ */
+static inline void inc_nrnb(t_nrnb* nrnb, int index, int increment)
+{
+ nrnb->n[index] += increment;
+}
+/*! \brief Atomic increment of nonbonded kernel flop counters
+ *
+ * \param nrnb The nonbonded kernel flop counters.
+ * \param index Which counter to incrememnt.
+ * \param increment How much to increment the counter by.
+ *
+ * Same as inc_nrnb but includes omp atomic pragma
+ */
+void atomicNrnbIncrement(t_nrnb* nrnb, int index, int increment);
void print_flop(FILE* out, t_nrnb* nrnb, double* nbfs, double* mflop);
/* Calculates the non-bonded forces and flop count.
void print_perf(FILE* out, double nodetime, double realtime, int64_t nsteps, double delta_t, double nbfs, double mflop);
/* Prints the performance, nbfs and mflop come from print_flop */
-void pr_load(FILE* log, struct t_commrec* cr, t_nrnb nrnb[]);
-/* Print detailed load balancing info */
-
int cost_nrnb(int enr);
/* Cost in i860 cycles of this component of MD */
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff