-/* -*- 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.
*
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*
- * This source code is part of
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- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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+ * control is crucial - bugs must be traceable. We will be happy to
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "smalloc.h"
-#include "network.h"
-#include "calcgrid.h"
-#include "pme.h"
-#include "vec.h"
-#include "domdec.h"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "force.h"
-#include "macros.h"
+#include "gmxpre.h"
+
#include "pme_loadbal.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+
/* Parameters and setting for one PP-PME setup */
typedef struct {
real rcut_coulomb; /* Coulomb cut-off */
real spacing; /* (largest) PME grid spacing */
ivec grid; /* the PME grid dimensions */
real grid_efficiency; /* ineffiency factor for non-uniform grids <= 1 */
- real ewaldcoeff; /* the Ewald coefficient */
+ real ewaldcoeff_q; /* Electrostatic Ewald coefficient */
+ real ewaldcoeff_lj; /* LJ Ewald coefficient, only for the call to send_switchgrid */
gmx_pme_t pmedata; /* the data structure used in the PME code */
-
int count; /* number of times this setup has been timed */
double cycles; /* the fastest time for this setup in cycles */
} pme_setup_t;
#define PME_LB_ACCEL_TOL 1.02
enum {
- epmelblimNO, epmelblimBOX, epmelblimDD, epmelblimNR
+ epmelblimNO, epmelblimBOX, epmelblimDD, epmelblimPMEGRID, epmelblimNR
};
const char *pmelblim_str[epmelblimNR] =
-{ "no", "box size", "domain decompostion" };
+{ "no", "box size", "domain decompostion", "PME grid restriction" };
struct pme_load_balancing {
int nstage; /* the current maximum number of stages */
pme_lb->n = 1;
snew(pme_lb->setup, pme_lb->n);
- pme_lb->rcut_vdw = ic->rvdw;
- pme_lb->rcut_coulomb_start = ir->rcoulomb;
- pme_lb->nstcalclr_start = ir->nstcalclr;
-
- pme_lb->cur = 0;
- pme_lb->setup[0].rcut_coulomb = ic->rcoulomb;
- pme_lb->setup[0].rlist = ic->rlist;
- pme_lb->setup[0].rlistlong = ic->rlistlong;
- pme_lb->setup[0].nstcalclr = ir->nstcalclr;
- pme_lb->setup[0].grid[XX] = ir->nkx;
- pme_lb->setup[0].grid[YY] = ir->nky;
- pme_lb->setup[0].grid[ZZ] = ir->nkz;
- pme_lb->setup[0].ewaldcoeff = ic->ewaldcoeff;
+ pme_lb->rcut_vdw = ic->rvdw;
+ pme_lb->rcut_coulomb_start = ir->rcoulomb;
+ pme_lb->nstcalclr_start = ir->nstcalclr;
+
+ pme_lb->cur = 0;
+ pme_lb->setup[0].rcut_coulomb = ic->rcoulomb;
+ pme_lb->setup[0].rlist = ic->rlist;
+ pme_lb->setup[0].rlistlong = ic->rlistlong;
+ pme_lb->setup[0].nstcalclr = ir->nstcalclr;
+ pme_lb->setup[0].grid[XX] = ir->nkx;
+ pme_lb->setup[0].grid[YY] = ir->nky;
+ pme_lb->setup[0].grid[ZZ] = ir->nkz;
+ pme_lb->setup[0].ewaldcoeff_q = ic->ewaldcoeff_q;
+ pme_lb->setup[0].ewaldcoeff_lj = ic->ewaldcoeff_lj;
pme_lb->setup[0].pmedata = pmedata;
*pme_lb_p = pme_lb;
}
-static gmx_bool pme_loadbal_increase_cutoff(pme_load_balancing_t pme_lb,
- int pme_order)
+static gmx_bool pme_loadbal_increase_cutoff(pme_load_balancing_t pme_lb,
+ int pme_order,
+ const gmx_domdec_t *dd)
{
pme_setup_t *set;
+ int npmenodes_x, npmenodes_y;
real fac, sp;
real tmpr_coulomb, tmpr_vdw;
int d;
+ gmx_bool grid_ok;
/* Try to add a new setup with next larger cut-off to the list */
pme_lb->n++;
set = &pme_lb->setup[pme_lb->n-1];
set->pmedata = NULL;
+ get_pme_nnodes(dd, &npmenodes_x, &npmenodes_y);
+
fac = 1;
do
{
+ /* Avoid infinite while loop, which can occur at the minimum grid size.
+ * Note that in practice load balancing will stop before this point.
+ * The factor 2.1 allows for the extreme case in which only grids
+ * of powers of 2 are allowed (the current code supports more grids).
+ */
+ if (fac > 2.1)
+ {
+ pme_lb->n--;
+
+ return FALSE;
+ }
+
fac *= 1.01;
clear_ivec(set->grid);
sp = calc_grid(NULL, pme_lb->box_start,
&set->grid[YY],
&set->grid[ZZ]);
- /* In parallel we can't have grids smaller than 2*pme_order,
- * and we would anyhow not gain much speed at these grid sizes.
+ /* As here we can't easily check if one of the PME nodes
+ * uses threading, we do a conservative grid check.
+ * This means we can't use pme_order or less grid lines
+ * per PME node along x, which is not a strong restriction.
*/
- for (d = 0; d < DIM; d++)
- {
- if (set->grid[d] <= 2*pme_order)
- {
- pme_lb->n--;
-
- return FALSE;
- }
- }
+ gmx_pme_check_restrictions(pme_order,
+ set->grid[XX], set->grid[YY], set->grid[ZZ],
+ npmenodes_x, npmenodes_y,
+ TRUE,
+ FALSE,
+ &grid_ok);
}
- while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing);
+ while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing || !grid_ok);
set->rcut_coulomb = pme_lb->cut_spacing*sp;
+ if (set->rcut_coulomb < pme_lb->rcut_coulomb_start)
+ {
+ /* This is unlikely, but can happen when e.g. continuing from
+ * a checkpoint after equilibration where the box shrank a lot.
+ * We want to avoid rcoulomb getting smaller than rvdw
+ * and there might be more issues with decreasing rcoulomb.
+ */
+ set->rcut_coulomb = pme_lb->rcut_coulomb_start;
+ }
if (pme_lb->cutoff_scheme == ecutsVERLET)
{
set->grid_efficiency *= (set->grid[d]*sp)/norm(pme_lb->box_start[d]);
}
/* The Ewald coefficient is inversly proportional to the cut-off */
- set->ewaldcoeff =
- pme_lb->setup[0].ewaldcoeff*pme_lb->setup[0].rcut_coulomb/set->rcut_coulomb;
+ set->ewaldcoeff_q =
+ pme_lb->setup[0].ewaldcoeff_q*pme_lb->setup[0].rcut_coulomb/set->rcut_coulomb;
+ /* We set ewaldcoeff_lj in set, even when LJ-PME is not used */
+ set->ewaldcoeff_lj =
+ pme_lb->setup[0].ewaldcoeff_lj*pme_lb->setup[0].rcut_coulomb/set->rcut_coulomb;
set->count = 0;
set->cycles = 0;
}
static void print_loadbal_limited(FILE *fp_err, FILE *fp_log,
- gmx_large_int_t step,
+ gmx_int64_t step,
pme_load_balancing_t pme_lb)
{
char buf[STRLEN], sbuf[22];
- sprintf(buf, "step %4s: the %s limited the PME load balancing to a coulomb cut-off of %.3f",
+ sprintf(buf, "step %4s: the %s limits the PME load balancing to a coulomb cut-off of %.3f",
gmx_step_str(step, sbuf),
pmelblim_str[pme_lb->elimited],
pme_lb->setup[pme_loadbal_end(pme_lb)-1].rcut_coulomb);
pme_lb->cur = pme_lb->start - 1;
}
-gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
- t_commrec *cr,
- FILE *fp_err,
- FILE *fp_log,
- t_inputrec *ir,
- t_state *state,
- double cycles,
- interaction_const_t *ic,
- nonbonded_verlet_t *nbv,
- gmx_pme_t *pmedata,
- gmx_large_int_t step)
+gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
+ t_commrec *cr,
+ FILE *fp_err,
+ FILE *fp_log,
+ t_inputrec *ir,
+ t_state *state,
+ double cycles,
+ interaction_const_t *ic,
+ struct nonbonded_verlet_t *nbv,
+ gmx_pme_t *pmedata,
+ gmx_int64_t step)
{
gmx_bool OK;
pme_setup_t *set;
else
{
/* Find the next setup */
- OK = pme_loadbal_increase_cutoff(pme_lb, ir->pme_order);
+ OK = pme_loadbal_increase_cutoff(pme_lb, ir->pme_order, cr->dd);
+
+ if (!OK)
+ {
+ pme_lb->elimited = epmelblimPMEGRID;
+ }
}
if (OK && ir->ePBC != epbcNONE)
set = &pme_lb->setup[pme_lb->cur];
- ic->rcoulomb = set->rcut_coulomb;
- ic->rlist = set->rlist;
- ic->rlistlong = set->rlistlong;
- ir->nstcalclr = set->nstcalclr;
- ic->ewaldcoeff = set->ewaldcoeff;
-
- bUsesSimpleTables = uses_simple_tables(ir->cutoff_scheme, nbv, 0);
- if (pme_lb->cutoff_scheme == ecutsVERLET &&
- nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
+ ic->rcoulomb = set->rcut_coulomb;
+ ic->rlist = set->rlist;
+ ic->rlistlong = set->rlistlong;
+ ir->nstcalclr = set->nstcalclr;
+ ic->ewaldcoeff_q = set->ewaldcoeff_q;
+ /* TODO: centralize the code that sets the potentials shifts */
+ if (ic->coulomb_modifier == eintmodPOTSHIFT)
{
- nbnxn_cuda_pme_loadbal_update_param(nbv->cu_nbv, ic);
+ ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
}
- else
+ if (EVDW_PME(ic->vdwtype))
{
- init_interaction_const_tables(NULL, ic, bUsesSimpleTables,
- rtab);
+ /* We have PME for both Coulomb and VdW, set rvdw equal to rcoulomb */
+ ic->rvdw = set->rcut_coulomb;
+ ic->ewaldcoeff_lj = set->ewaldcoeff_lj;
+ if (ic->vdw_modifier == eintmodPOTSHIFT)
+ {
+ real crc2;
+
+ ic->dispersion_shift.cpot = -pow(ic->rvdw, -6.0);
+ ic->repulsion_shift.cpot = -pow(ic->rvdw, -12.0);
+ ic->sh_invrc6 = -ic->dispersion_shift.cpot;
+ crc2 = sqr(ic->ewaldcoeff_lj*ic->rvdw);
+ ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, -6.0);
+ }
}
- if (pme_lb->cutoff_scheme == ecutsVERLET && nbv->ngrp > 1)
+ bUsesSimpleTables = uses_simple_tables(ir->cutoff_scheme, nbv, 0);
+ nbnxn_cuda_pme_loadbal_update_param(nbv, ic);
+
+ /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
+ * also sharing texture references. To keep the code simple, we don't
+ * treat texture references as shared resources, but this means that
+ * the coulomb_tab texture ref will get updated by multiple threads.
+ * Hence, to ensure that the non-bonded kernels don't start before all
+ * texture binding operations are finished, we need to wait for all ranks
+ * to arrive here before continuing.
+ *
+ * Note that we could omit this barrier if GPUs are not shared (or
+ * texture objects are used), but as this is initialization code, there
+ * is not point in complicating things.
+ */
+#ifdef GMX_THREAD_MPI
+ if (PAR(cr) && use_GPU(nbv))
{
- init_interaction_const_tables(NULL, ic, bUsesSimpleTables,
- rtab);
+ gmx_barrier(cr);
}
+#endif /* GMX_THREAD_MPI */
+
+ /* Usually we won't need the simple tables with GPUs.
+ * But we do with hybrid acceleration and with free energy.
+ * To avoid bugs, we always re-initialize the simple tables here.
+ */
+ init_interaction_const_tables(NULL, ic, bUsesSimpleTables, rtab);
if (cr->duty & DUTY_PME)
{
else
{
/* Tell our PME-only node to switch grid */
- gmx_pme_send_switchgrid(cr, set->grid, set->ewaldcoeff);
+ gmx_pme_send_switchgrid(cr, set->grid, set->ewaldcoeff_q, set->ewaldcoeff_lj);
}
if (debug)
return setup->grid[XX]*setup->grid[YY]*setup->grid[ZZ];
}
+static real pme_loadbal_rlist(const pme_setup_t *setup)
+{
+ /* With the group cut-off scheme we can have twin-range either
+ * for Coulomb or for VdW, so we need a check here.
+ * With the Verlet cut-off scheme rlist=rlistlong.
+ */
+ if (setup->rcut_coulomb > setup->rlist)
+ {
+ return setup->rlistlong;
+ }
+ else
+ {
+ return setup->rlist;
+ }
+}
+
static void print_pme_loadbal_setting(FILE *fplog,
char *name,
const pme_setup_t *setup)
fprintf(fplog,
" %-7s %6.3f nm %6.3f nm %3d %3d %3d %5.3f nm %5.3f nm\n",
name,
- setup->rcut_coulomb, setup->rlist,
+ setup->rcut_coulomb, pme_loadbal_rlist(setup),
setup->grid[XX], setup->grid[YY], setup->grid[ZZ],
- setup->spacing, 1/setup->ewaldcoeff);
+ setup->spacing, 1/setup->ewaldcoeff_q);
}
static void print_pme_loadbal_settings(pme_load_balancing_t pme_lb,
- FILE *fplog)
+ t_commrec *cr,
+ FILE *fplog,
+ gmx_bool bNonBondedOnGPU)
{
double pp_ratio, grid_ratio;
- pp_ratio = pow(pme_lb->setup[pme_lb->cur].rlist/pme_lb->setup[0].rlistlong, 3.0);
+ pp_ratio = pow(pme_loadbal_rlist(&pme_lb->setup[pme_lb->cur])/pme_loadbal_rlist(&pme_lb->setup[0]), 3.0);
grid_ratio = pme_grid_points(&pme_lb->setup[pme_lb->cur])/
(double)pme_grid_points(&pme_lb->setup[0]);
fprintf(fplog, " cost-ratio %4.2f %4.2f\n",
pp_ratio, grid_ratio);
fprintf(fplog, " (note that these numbers concern only part of the total PP and PME load)\n");
- fprintf(fplog, "\n");
+
+ if (pp_ratio > 1.5 && !bNonBondedOnGPU)
+ {
+ md_print_warn(cr, fplog,
+ "NOTE: PME load balancing increased the non-bonded workload by more than 50%%.\n"
+ " For better performance, use (more) PME ranks (mdrun -npme),\n"
+ " or if you are beyond the scaling limit, use fewer total ranks (or nodes).\n");
+ }
+ else
+ {
+ fprintf(fplog, "\n");
+ }
}
-void pme_loadbal_done(pme_load_balancing_t pme_lb, FILE *fplog)
+void pme_loadbal_done(pme_load_balancing_t pme_lb,
+ t_commrec *cr, FILE *fplog,
+ gmx_bool bNonBondedOnGPU)
{
if (fplog != NULL && (pme_lb->cur > 0 || pme_lb->elimited != epmelblimNO))
{
- print_pme_loadbal_settings(pme_lb, fplog);
+ print_pme_loadbal_settings(pme_lb, cr, fplog, bNonBondedOnGPU);
}
/* TODO: Here we should free all pointers in pme_lb,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff