-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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-
- * This program is free software; you can redistribute it and/or
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2008, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
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*
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+ * consider that scientific software is very special. Version
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+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#include "gromacs/timing/wallcycle.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "wallcycle.h"
-#include <string.h>
+#include "config.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "md_logging.h"
-#include "string2.h"
+#include <stdlib.h>
+#include <string.h>
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
/* DEBUG_WCYCLE adds consistency checking for the counters.
* It checks if you stop a counter different from the last
#endif
int ewc_prev;
gmx_cycles_t cycle_prev;
- gmx_large_int_t reset_counters;
+ gmx_int64_t reset_counters;
#ifdef GMX_MPI
MPI_Comm mpi_comm_mygroup;
#endif
"Run", "Step", "PP during PME", "Domain decomp.", "DD comm. load",
"DD comm. bounds", "Vsite constr.", "Send X to PME", "Neighbor search", "Launch GPU ops.",
"Comm. coord.", "Born radii", "Force", "Wait + Comm. F", "PME mesh",
- "PME redist. X/F", "PME spread/gather", "PME 3D-FFT", "PME 3D-FFT Comm.", "PME solve",
+ "PME redist. X/F", "PME spread/gather", "PME 3D-FFT", "PME 3D-FFT Comm.", "PME solve LJ", "PME solve Elec",
"PME wait for PP", "Wait + Recv. PME F", "Wait GPU nonlocal", "Wait GPU local", "NB X/F buffer ops.",
- "Vsite spread", "Write traj.", "Update", "Constraints", "Comm. energies",
- "Enforced rotation", "Add rot. forces", "Test"
+ "Vsite spread", "COM pull force",
+ "Write traj.", "Update", "Constraints", "Comm. energies",
+ "Enforced rotation", "Add rot. forces", "Coordinate swapping", "IMD", "Test"
};
static const char *wcsn[ewcsNR] =
"DD redist.", "DD NS grid + sort", "DD setup comm.",
"DD make top.", "DD make constr.", "DD top. other",
"NS grid local", "NS grid non-loc.", "NS search local", "NS search non-loc.",
- "Bonded F", "Nonbonded F", "Ewald F correction",
+ "Listed F", "Nonbonded F", "Ewald F correction",
"NB X buffer ops.", "NB F buffer ops."
};
return gmx_cycles_have_counter();
}
-gmx_wallcycle_t wallcycle_init(FILE *fplog, int resetstep, t_commrec *cr,
+gmx_wallcycle_t wallcycle_init(FILE *fplog, int resetstep, t_commrec gmx_unused *cr,
int nthreads_pp, int nthreads_pme)
{
gmx_wallcycle_t wc;
void wallcycle_sum(t_commrec *cr, gmx_wallcycle_t wc)
{
wallcc_t *wcc;
- double *cycles;
+ double cycles[ewcNR+ewcsNR];
double cycles_n[ewcNR+ewcsNR], buf[ewcNR+ewcsNR], *cyc_all, *buf_all;
int i, j;
int nsum;
}
snew(wc->cycles_sum, ewcNR+ewcsNR);
- cycles = wc->cycles_sum;
wcc = wc->wcc;
}
#endif
- MPI_Allreduce(cycles, buf, nsum, MPI_DOUBLE, MPI_SUM,
+ MPI_Allreduce(cycles, wc->cycles_sum, nsum, MPI_DOUBLE, MPI_SUM,
cr->mpi_comm_mysim);
- for (i = 0; i < nsum; i++)
- {
- cycles[i] = buf[i];
- }
if (wc->wcc_all != NULL)
{
sfree(cyc_all);
}
}
+ else
#endif
+ {
+ for (i = 0; i < nsum; i++)
+ {
+ wc->cycles_sum[i] = cycles[i];
+ }
+ }
}
static void print_cycles(FILE *fplog, double c2t, const char *name,
- int nthreads_tot,
int nnodes, int nthreads,
- int n, double c, double tot)
+ int ncalls, double c_sum, double tot)
{
- char num[11];
- char thstr[6];
+ char nnodes_str[6];
+ char nthreads_str[6];
+ char ncalls_str[11];
double wallt;
- if (c > 0)
+ if (c_sum > 0)
{
- if (n > 0)
+ if (ncalls > 0)
{
- snprintf(num, sizeof(num), "%10d", n);
+ snprintf(ncalls_str, sizeof(ncalls_str), "%10d", ncalls);
+ if (nnodes < 0)
+ {
+ snprintf(nnodes_str, sizeof(nnodes_str), "N/A");
+ }
+ else
+ {
+ snprintf(nnodes_str, sizeof(nnodes_str), "%4d", nnodes);
+ }
if (nthreads < 0)
{
- snprintf(thstr, sizeof(thstr), "N/A");
+ snprintf(nthreads_str, sizeof(nthreads_str), "N/A");
}
else
{
- snprintf(thstr, sizeof(thstr), "%4d", nthreads);
+ snprintf(nthreads_str, sizeof(nthreads_str), "%4d", nthreads);
}
}
else
{
- sprintf(num, " ");
- sprintf(thstr, " ");
+ nnodes_str[0] = 0;
+ nthreads_str[0] = 0;
+ ncalls_str[0] = 0;
}
/* Convert the cycle count to wallclock time for this task */
- if (nthreads > 0)
- {
- /* Cycle count has been multiplied by the thread count,
- * correct for the number of threads used.
- */
- wallt = c*c2t*nthreads_tot/(double)(nnodes*nthreads);
- }
- else
- {
- /* nthreads=-1 signals total run time, no correction required */
- wallt = c*c2t;
- }
- fprintf(fplog, " %-19.19s %4d %4s %10s %10.3f %12.3f %5.1f\n",
- name, nnodes, thstr, num, wallt, c*1e-9, 100*c/tot);
+ wallt = c_sum*c2t;
+
+ fprintf(fplog, " %-19.19s %4s %4s %10s %10.3f %14.3f %5.1f\n",
+ name, nnodes_str, nthreads_str, ncalls_str, wallt,
+ c_sum*1e-9, 100*c_sum/tot);
}
}
}
}
+static void print_header(FILE *fplog, int nrank_pp, int nth_pp, int nrank_pme, int nth_pme)
+{
+ int nrank_tot = nrank_pp + nrank_pme;
+ if (0 == nrank_pme)
+ {
+ fprintf(fplog, "On %d MPI rank%s", nrank_tot, nrank_tot == 1 ? "" : "s");
+ if (nth_pp > 1)
+ {
+ fprintf(fplog, ", each using %d OpenMP threads", nth_pp);
+ }
+ /* Don't report doing PP+PME, because we can't tell here if
+ * this is RF, etc. */
+ }
+ else
+ {
+ fprintf(fplog, "On %d MPI rank%s doing PP", nrank_pp, nrank_pp == 1 ? "" : "s");
+ if (nth_pp > 1)
+ {
+ fprintf(fplog, ",%s using %d OpenMP threads", nrank_pp > 1 ? " each" : "", nth_pp);
+ }
+ fprintf(fplog, ", and\non %d MPI rank%s doing PME", nrank_pme, nrank_pme == 1 ? "" : "s");
+ if (nth_pme > 1)
+ {
+ fprintf(fplog, ",%s using %d OpenMP threads", nrank_pme > 1 ? " each" : "", nth_pme);
+ }
+ }
+
+ fprintf(fplog, "\n\n");
+ fprintf(fplog, " Computing: Num Num Call Wall time Giga-Cycles\n");
+ fprintf(fplog, " Ranks Threads Count (s) total sum %%\n");
+}
+
void wallcycle_print(FILE *fplog, int nnodes, int npme, double realtime,
gmx_wallcycle_t wc, wallclock_gpu_t *gpu_t)
{
- double *cycles;
- double c2t, tot, tot_gpu, tot_cpu_overlap, gpu_cpu_ratio, sum, tot_k;
+ double *cyc_sum;
+ double tot, tot_for_pp, tot_for_rest, tot_gpu, tot_cpu_overlap, gpu_cpu_ratio, tot_k;
+ double c2t, c2t_pp, c2t_pme;
int i, j, npp, nth_pp, nth_pme, nth_tot;
char buf[STRLEN];
const char *hline = "-----------------------------------------------------------------------------";
nth_pp = wc->nthreads_pp;
nth_pme = wc->nthreads_pme;
- cycles = wc->cycles_sum;
-
- if (npme > 0)
- {
- npp = nnodes - npme;
-
- nth_tot = npp*nth_pp + npme*nth_pme;
- }
- else
- {
- npp = nnodes;
- npme = nnodes;
+ cyc_sum = wc->cycles_sum;
- nth_tot = npp*nth_pp;
- }
+ npp = nnodes - npme;
+ nth_tot = npp*nth_pp + npme*nth_pme;
- tot = cycles[ewcRUN];
+ /* When using PME-only nodes, the next line is valid for both
+ PP-only and PME-only nodes because they started ewcRUN at the
+ same time. */
+ tot = cyc_sum[ewcRUN];
+ tot_for_pp = 0;
/* Conversion factor from cycles to seconds */
if (tot > 0)
{
- c2t = realtime/tot;
+ c2t = realtime/tot;
+ c2t_pp = c2t * nth_tot / (double) (npp*nth_pp);
+ c2t_pme = c2t * nth_tot / (double) (npme*nth_pme);
}
else
{
- c2t = 0;
+ c2t = 0;
+ c2t_pp = 0;
+ c2t_pme = 0;
}
fprintf(fplog, "\n R E A L C Y C L E A N D T I M E A C C O U N T I N G\n\n");
- fprintf(fplog, " Computing: Nodes Th. Count Wall t (s) G-Cycles %c\n", '%');
+ print_header(fplog, npp, nth_pp, npme, nth_pme);
+
fprintf(fplog, "%s\n", hline);
- sum = 0;
for (i = ewcPPDURINGPME+1; i < ewcNR; i++)
{
- if (!is_pme_subcounter(i))
+ if (is_pme_subcounter(i))
+ {
+ /* Do not count these at all */
+ }
+ else if (npme > 0 && is_pme_counter(i))
+ {
+ /* Print timing information for PME-only nodes, but add an
+ * asterisk so the reader of the table can know that the
+ * walltimes are not meant to add up. The asterisk still
+ * fits in the required maximum of 19 characters. */
+ char buffer[STRLEN];
+ snprintf(buffer, STRLEN, "%s *", wcn[i]);
+ print_cycles(fplog, c2t_pme, buffer,
+ npme, nth_pme,
+ wc->wcc[i].n, cyc_sum[i], tot);
+ }
+ else
{
- print_cycles(fplog, c2t, wcn[i], nth_tot,
- is_pme_counter(i) ? npme : npp,
- is_pme_counter(i) ? nth_pme : nth_pp,
- wc->wcc[i].n, cycles[i], tot);
- sum += cycles[i];
+ /* Print timing information when it is for a PP or PP+PME
+ node */
+ print_cycles(fplog, c2t_pp, wcn[i],
+ npp, nth_pp,
+ wc->wcc[i].n, cyc_sum[i], tot);
+ tot_for_pp += cyc_sum[i];
}
}
if (wc->wcc_all != NULL)
for (j = 0; j < ewcNR; j++)
{
snprintf(buf, 20, "%-9.9s %-9.9s", wcn[i], wcn[j]);
- print_cycles(fplog, c2t, buf, nth_tot,
- is_pme_counter(i) ? npme : npp,
- is_pme_counter(i) ? nth_pme : nth_pp,
+ print_cycles(fplog, c2t_pp, buf,
+ npp, nth_pp,
wc->wcc_all[i*ewcNR+j].n,
wc->wcc_all[i*ewcNR+j].c,
tot);
}
}
}
- print_cycles(fplog, c2t, "Rest", nth_tot, npp, -1, 0, tot-sum, tot);
+ tot_for_rest = tot * (npp * nth_pp) / (double) nth_tot;
+ print_cycles(fplog, c2t_pp, "Rest",
+ npp, nth_pp,
+ -1, tot_for_rest - tot_for_pp, tot);
fprintf(fplog, "%s\n", hline);
- print_cycles(fplog, c2t, "Total", nth_tot, nnodes, -1, 0, tot, tot);
+ print_cycles(fplog, c2t, "Total",
+ npp, nth_pp,
+ -1, tot, tot);
fprintf(fplog, "%s\n", hline);
+ if (npme > 0)
+ {
+ fprintf(fplog,
+ "(*) Note that with separate PME ranks, the walltime column actually sums to\n"
+ " twice the total reported, but the cycle count total and %% are correct.\n"
+ "%s\n", hline);
+ }
+
if (wc->wcc[ewcPMEMESH].n > 0)
{
+ fprintf(fplog, " Breakdown of PME mesh computation\n");
fprintf(fplog, "%s\n", hline);
for (i = ewcPPDURINGPME+1; i < ewcNR; i++)
{
if (is_pme_subcounter(i))
{
- print_cycles(fplog, c2t, wcn[i], nth_tot,
- is_pme_counter(i) ? npme : npp,
- is_pme_counter(i) ? nth_pme : nth_pp,
- wc->wcc[i].n, cycles[i], tot);
+ print_cycles(fplog, npme > 0 ? c2t_pme : c2t_pp, wcn[i],
+ npme > 0 ? npme : npp, nth_pme,
+ wc->wcc[i].n, cyc_sum[i], tot);
}
}
fprintf(fplog, "%s\n", hline);
}
#ifdef GMX_CYCLE_SUBCOUNTERS
+ fprintf(fplog, " Breakdown of PP computation\n");
fprintf(fplog, "%s\n", hline);
for (i = 0; i < ewcsNR; i++)
{
- print_cycles(fplog, c2t, wcsn[i], nth_tot, npp, nth_pp,
- wc->wcsc[i].n, cycles[ewcNR+i], tot);
+ print_cycles(fplog, c2t_pp, wcsn[i],
+ npp, nth_pp,
+ wc->wcsc[i].n, cyc_sum[ewcNR+i], tot);
}
fprintf(fplog, "%s\n", hline);
#endif
{
tot_cpu_overlap += wc->wcc[ewcPMEMESH].c;
}
- tot_cpu_overlap *= c2t * 1000; /* convert s to ms */
+ tot_cpu_overlap *= realtime*1000/tot; /* convert s to ms */
fprintf(fplog, "\n GPU timings\n%s\n", hline);
fprintf(fplog, " Computing: Count Wall t (s) ms/step %c\n", '%');
}
if (wc->wcc[ewcNB_XF_BUF_OPS].n > 0 &&
- (cycles[ewcDOMDEC] > tot*0.1 ||
- cycles[ewcNS] > tot*0.1))
+ (cyc_sum[ewcDOMDEC] > tot*0.1 ||
+ cyc_sum[ewcNS] > tot*0.1))
{
/* Only the sim master calls this function, so always print to stderr */
if (wc->wcc[ewcDOMDEC].n == 0)
md_print_warn(NULL, fplog,
"NOTE: %d %% of the run time was spent in pair search,\n"
" you might want to increase nstlist (this has no effect on accuracy)\n",
- (int)(100*cycles[ewcNS]/tot+0.5));
+ (int)(100*cyc_sum[ewcNS]/tot+0.5));
}
else
{
"NOTE: %d %% of the run time was spent in domain decomposition,\n"
" %d %% of the run time was spent in pair search,\n"
" you might want to increase nstlist (this has no effect on accuracy)\n",
- (int)(100*cycles[ewcDOMDEC]/tot+0.5),
- (int)(100*cycles[ewcNS]/tot+0.5));
+ (int)(100*cyc_sum[ewcDOMDEC]/tot+0.5),
+ (int)(100*cyc_sum[ewcNS]/tot+0.5));
}
}
- if (cycles[ewcMoveE] > tot*0.05)
+ if (cyc_sum[ewcMoveE] > tot*0.05)
{
/* Only the sim master calls this function, so always print to stderr */
md_print_warn(NULL, fplog,
"NOTE: %d %% of the run time was spent communicating energies,\n"
" you might want to use the -gcom option of mdrun\n",
- (int)(100*cycles[ewcMoveE]/tot+0.5));
+ (int)(100*cyc_sum[ewcMoveE]/tot+0.5));
}
}
-extern gmx_large_int_t wcycle_get_reset_counters(gmx_wallcycle_t wc)
+extern gmx_int64_t wcycle_get_reset_counters(gmx_wallcycle_t wc)
{
if (wc == NULL)
{
return wc->reset_counters;
}
-extern void wcycle_set_reset_counters(gmx_wallcycle_t wc, gmx_large_int_t reset_counters)
+extern void wcycle_set_reset_counters(gmx_wallcycle_t wc, gmx_int64_t reset_counters)
{
if (wc == NULL)
{
#else
-void wallcycle_sub_start(gmx_wallcycle_t gmx_unused wc, int gmx_unused ewcs) {}
-void wallcycle_sub_stop(gmx_wallcycle_t gmx_unused wc, int gmx_unused ewcs) {}
+void wallcycle_sub_start(gmx_wallcycle_t gmx_unused wc, int gmx_unused ewcs)
+{
+}
+void wallcycle_sub_stop(gmx_wallcycle_t gmx_unused wc, int gmx_unused ewcs)
+{
+}
#endif /* GMX_CYCLE_SUBCOUNTERS */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff