-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
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*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "perf_est.h"
-#include "physics.h"
-#include "vec.h"
-#include "mtop_util.h"
-#include "types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "nbnxn_search.h"
#include "nbnxn_consts.h"
-
/* Computational cost of bonded, non-bonded and PME calculations.
* This will be machine dependent.
* The numbers here are accurate for Intel Core2 and AMD Athlon 64
* although not so much that the numbers need to be adjusted.
*/
-/* Cost of a pair interaction in the "group" cut-off scheme" */
-#define C_GR_FQ 1.5
-#define C_GR_QLJ_CUT 1.5
-#define C_GR_QLJ_TAB 2.0
-#define C_GR_LJ_CUT 1.0
-#define C_GR_LJ_TAB 1.75
+/* Cost of a pair interaction in the "group" cut-off scheme */
+#define C_GR_FQ 1.5
+#define C_GR_QLJ_CUT 1.5
+#define C_GR_QLJ_TAB 2.0
+#define C_GR_LJ_CUT 1.0
+#define C_GR_LJ_TAB 1.75
/* Cost of 1 water with one Q/LJ atom */
-#define C_GR_QLJW_CUT 2.0
-#define C_GR_QLJW_TAB 2.25
+#define C_GR_QLJW_CUT 2.0
+#define C_GR_QLJW_TAB 2.25
/* Cost of 1 water with one Q atom or with 1/3 water (LJ negligible) */
-#define C_GR_QW 1.75
+#define C_GR_QW 1.75
-/* Cost of a pair interaction in the "Verlet" cut-off scheme" */
-#define C_VT_LJ 0.30
-#define C_VT_QLJ_RF 0.40
-#define C_VT_Q_RF 0.30
-#define C_VT_QLJ_TAB 0.55
-#define C_VT_Q_TAB 0.50
+/* Cost of a pair interaction in the "Verlet" cut-off scheme, QEXP is Ewald */
+#define C_VT_LJ 0.30
+#define C_VT_QRF_LJ 0.40
+#define C_VT_QRF 0.30
+#define C_VT_QEXP_LJ 0.55
+#define C_VT_QEXP 0.50
+/* Extra cost for expensive LJ interaction, e.g. pot-switch or LJ-PME */
+#define C_VT_LJEXP_ADD 0.20
/* Cost of PME, with all components running with SSE instructions */
/* Cost of particle reordering and redistribution */
*/
ndx = 0;
ndx_excl = 0;
+#if __ICC == 1400 || __ICL == 1400
+#pragma novector /* Work-around for incorrect vectorization */
+#endif
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
}
static void pp_group_load(gmx_mtop_t *mtop, t_inputrec *ir, matrix box,
- int *nq_tot,
+ int *nq_tot, int *nlj_tot,
double *cost_pp,
- gmx_bool *bChargePerturbed)
+ gmx_bool *bChargePerturbed, gmx_bool *bTypePerturbed)
{
t_atom *atom;
int mb, nmol, atnr, cg, a, a0, ncqlj, ncq, nclj;
{
*bChargePerturbed = TRUE;
}
+ if (atom[a].type != atom[a].typeB)
+ {
+ *bTypePerturbed = TRUE;
+ }
/* This if this atom fits into water optimization */
if (!((a == a0 && bQ && bLJ) ||
(a == a0+1 && bQ && !bLJ) ||
}
}
- *nq_tot = nq + nqlj + nw*3;
+ *nq_tot = nq + nqlj + nw*3;
+ *nlj_tot = nlj + nqlj + nw;
if (debug)
{
}
static void pp_verlet_load(gmx_mtop_t *mtop, t_inputrec *ir, matrix box,
- int *nq_tot,
+ int *nq_tot, int *nlj_tot,
double *cost_pp,
- gmx_bool *bChargePerturbed)
+ gmx_bool *bChargePerturbed, gmx_bool *bTypePerturbed)
{
t_atom *atom;
int mb, nmol, atnr, cg, a, a0, nqlj, nq, nlj;
gmx_bool bQRF;
t_iparams *iparams;
gmx_moltype_t *molt;
- float r_eff;
+ real r_eff;
+ double c_qlj, c_q, c_lj;
double nat;
+ /* Conversion factor for reference vs SIMD kernel performance.
+ * The factor is about right for SSE2/4, but should be 2 higher for AVX256.
+ */
+#ifdef GMX_DOUBLE
+ const real nbnxn_refkernel_fac = 4.0;
+#else
+ const real nbnxn_refkernel_fac = 8.0;
+#endif
bQRF = (EEL_RF(ir->coulombtype) || ir->coulombtype == eelCUT);
{
*bChargePerturbed = TRUE;
}
+ if (atom[a].type != atom[a].typeB)
+ {
+ *bTypePerturbed = TRUE;
+ }
}
}
nlj = mtop->natoms - nqlj - nq;
- *nq_tot = nqlj + nq;
+ *nq_tot = nqlj + nq;
+ *nlj_tot = nqlj + nlj;
/* Effective cut-off for cluster pair list of 4x4 atoms */
r_eff = ir->rlist + nbnxn_get_rlist_effective_inc(NBNXN_CPU_CLUSTER_I_SIZE, mtop->natoms/det(box));
nqlj, nq, nlj, ir->rlist, r_eff);
}
+ /* Determine the cost per pair interaction */
+ c_qlj = (bQRF ? C_VT_QRF_LJ : C_VT_QEXP_LJ);
+ c_q = (bQRF ? C_VT_QRF : C_VT_QEXP);
+ c_lj = C_VT_LJ;
+ if (ir->vdw_modifier == eintmodPOTSWITCH || EVDW_PME(ir->vdwtype))
+ {
+ c_qlj += C_VT_LJEXP_ADD;
+ c_lj += C_VT_LJEXP_ADD;
+ }
+ if (EVDW_PME(ir->vdwtype) && ir->ljpme_combination_rule == eljpmeLB)
+ {
+ /* We don't have LJ-PME LB comb. rule kernels, we use slow kernels */
+ c_qlj *= nbnxn_refkernel_fac;
+ c_q *= nbnxn_refkernel_fac;
+ c_lj *= nbnxn_refkernel_fac;
+ }
+
/* For the PP non-bonded cost it is (unrealistically) assumed
* that all atoms are distributed homogeneously in space.
*/
/* Convert mtop->natoms to double to avoid int overflow */
nat = mtop->natoms;
- *cost_pp = 0.5*(nqlj*nat*(bQRF ? C_VT_QLJ_RF : C_VT_QLJ_TAB) +
- nq*nat*(bQRF ? C_VT_Q_RF : C_VT_Q_TAB) +
- nlj*nat*C_VT_LJ)
+ *cost_pp = 0.5*nat*(nqlj*c_qlj + nq*c_q + nlj*c_lj)
*4/3*M_PI*r_eff*r_eff*r_eff/det(box);
}
float pme_load_estimate(gmx_mtop_t *mtop, t_inputrec *ir, matrix box)
{
t_atom *atom;
- int mb, nmol, atnr, cg, a, a0, nq_tot;
- gmx_bool bBHAM, bLJcut, bChargePerturbed, bWater, bQ, bLJ;
+ int mb, nmol, atnr, cg, a, a0, nq_tot, nlj_tot, f;
+ gmx_bool bBHAM, bLJcut, bChargePerturbed, bTypePerturbed;
+ gmx_bool bWater, bQ, bLJ;
double cost_bond, cost_pp, cost_redist, cost_spread, cost_fft, cost_solve, cost_pme;
float ratio;
t_iparams *iparams;
if (ir->cutoff_scheme == ecutsGROUP)
{
- pp_group_load(mtop, ir, box, &nq_tot, &cost_pp, &bChargePerturbed);
+ pp_group_load(mtop, ir, box,
+ &nq_tot, &nlj_tot, &cost_pp,
+ &bChargePerturbed, &bTypePerturbed);
}
else
{
- pp_verlet_load(mtop, ir, box, &nq_tot, &cost_pp, &bChargePerturbed);
+ pp_verlet_load(mtop, ir, box,
+ &nq_tot, &nlj_tot, &cost_pp,
+ &bChargePerturbed, &bTypePerturbed);
}
- cost_redist = C_PME_REDIST*nq_tot;
- cost_spread = C_PME_SPREAD*nq_tot*pow(ir->pme_order, 3);
- cost_fft = C_PME_FFT*ir->nkx*ir->nky*ir->nkz*log(ir->nkx*ir->nky*ir->nkz);
- cost_solve = C_PME_SOLVE*ir->nkx*ir->nky*ir->nkz;
+ cost_redist = 0;
+ cost_spread = 0;
+ cost_fft = 0;
+ cost_solve = 0;
- if (ir->efep != efepNO && bChargePerturbed)
+ if (EEL_PME(ir->coulombtype))
{
- /* All PME work, except redist & spline coefficient calculation, doubles */
- cost_spread *= 2;
- cost_fft *= 2;
- cost_solve *= 2;
+ f = ((ir->efep != efepNO && bChargePerturbed) ? 2 : 1);
+ cost_redist += C_PME_REDIST*nq_tot;
+ cost_spread += f*C_PME_SPREAD*nq_tot*pow(ir->pme_order, 3);
+ cost_fft += f*C_PME_FFT*ir->nkx*ir->nky*ir->nkz*log(ir->nkx*ir->nky*ir->nkz);
+ cost_solve += f*C_PME_SOLVE*ir->nkx*ir->nky*ir->nkz;
+ }
+
+ if (EVDW_PME(ir->vdwtype))
+ {
+ f = ((ir->efep != efepNO && bTypePerturbed) ? 2 : 1);
+ if (ir->ljpme_combination_rule == eljpmeLB)
+ {
+ /* LB combination rule: we have 7 mesh terms */
+ f *= 7;
+ }
+ cost_redist += C_PME_REDIST*nlj_tot;
+ cost_spread += f*C_PME_SPREAD*nlj_tot*pow(ir->pme_order, 3);
+ cost_fft += f*C_PME_FFT*ir->nkx*ir->nky*ir->nkz*log(ir->nkx*ir->nky*ir->nkz);
+ cost_solve += f*C_PME_SOLVE*ir->nkx*ir->nky*ir->nkz;
}
cost_pme = cost_redist + cost_spread + cost_fft + cost_solve;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff