/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2008, The GROMACS development team.
+ * Copyright (c) 2012,2014, 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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+ * in the README & COPYING files - if they are missing, get the
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* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
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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 "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
+ * in single precision. In double precision PME mesh is slightly cheaper,
+ * 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 1 water with one Q/LJ atom */
+#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
+
+/* 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 */
+#define C_PME_REDIST 12.0
+/* Cost of q spreading and force interpolation per charge (mainly memory) */
+#define C_PME_SPREAD 0.30
+/* Cost of fft's, will be multiplied with N log(N) */
+#define C_PME_FFT 0.20
+/* Cost of pme_solve, will be multiplied with N */
+#define C_PME_SOLVE 0.50
-int n_bonded_dx(gmx_mtop_t *mtop,gmx_bool bExcl)
+/* Cost of a bonded interaction divided by the number of (pbc_)dx nrequired */
+#define C_BOND 5.0
+
+int n_bonded_dx(gmx_mtop_t *mtop, gmx_bool bExcl)
{
- int mb,nmol,ftype,ndxb,ndx_excl;
- int ndx;
- gmx_moltype_t *molt;
-
- /* Count the number of pbc_rvec_sub calls required for bonded interactions.
- * This number is also roughly proportional to the computational cost.
- */
- ndx = 0;
- ndx_excl = 0;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molt = &mtop->moltype[mtop->molblock[mb].type];
- nmol = mtop->molblock[mb].nmol;
- for(ftype=0; ftype<F_NRE; ftype++) {
- if (interaction_function[ftype].flags & IF_BOND) {
- switch (ftype) {
- case F_POSRES: ndxb = 1; break;
- case F_CONNBONDS: ndxb = 0; break;
- default: ndxb = NRAL(ftype) - 1; break;
- }
- ndx += nmol*ndxb*molt->ilist[ftype].nr/(1 + NRAL(ftype));
- }
+ int mb, nmol, ftype, ndxb, ndx_excl;
+ int ndx;
+ gmx_moltype_t *molt;
+
+ /* Count the number of pbc_rvec_sub calls required for bonded interactions.
+ * This number is also roughly proportional to the computational cost.
+ */
+ 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];
+ nmol = mtop->molblock[mb].nmol;
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_BOND)
+ {
+ switch (ftype)
+ {
+ case F_POSRES:
+ case F_FBPOSRES: ndxb = 1; break;
+ case F_CONNBONDS: ndxb = 0; break;
+ default: ndxb = NRAL(ftype) - 1; break;
+ }
+ ndx += nmol*ndxb*molt->ilist[ftype].nr/(1 + NRAL(ftype));
+ }
+ }
+ if (bExcl)
+ {
+ ndx_excl += nmol*(molt->excls.nra - molt->atoms.nr)/2;
+ }
+ else
+ {
+ ndx_excl = 0;
+ }
}
- if (bExcl) {
- ndx_excl += nmol*(molt->excls.nra - molt->atoms.nr)/2;
- } else {
- ndx_excl = 0;
+
+ if (debug)
+ {
+ fprintf(debug, "ndx bonded %d exclusions %d\n", ndx, ndx_excl);
+ }
+
+ ndx += ndx_excl;
+
+ return ndx;
+}
+
+static void pp_group_load(gmx_mtop_t *mtop, t_inputrec *ir, matrix box,
+ int *nq_tot, int *nlj_tot,
+ double *cost_pp,
+ gmx_bool *bChargePerturbed, gmx_bool *bTypePerturbed)
+{
+ t_atom *atom;
+ int mb, nmol, atnr, cg, a, a0, ncqlj, ncq, nclj;
+ gmx_bool bBHAM, bLJcut, bWater, bQ, bLJ;
+ int nw, nqlj, nq, nlj;
+ float fq, fqlj, flj, fljtab, fqljw, fqw;
+ t_iparams *iparams;
+ gmx_moltype_t *molt;
+
+ bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
+
+ bLJcut = ((ir->vdwtype == evdwCUT) && !bBHAM);
+
+ /* 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
+ * in single precision. In double precision PME mesh is slightly cheaper,
+ * although not so much that the numbers need to be adjusted.
+ */
+ fq = C_GR_FQ;
+ fqlj = (bLJcut ? C_GR_QLJ_CUT : C_GR_QLJ_TAB);
+ flj = (bLJcut ? C_GR_LJ_CUT : C_GR_LJ_TAB);
+ /* Cost of 1 water with one Q/LJ atom */
+ fqljw = (bLJcut ? C_GR_QLJW_CUT : C_GR_QLJW_TAB);
+ /* Cost of 1 water with one Q atom or with 1/3 water (LJ negligible) */
+ fqw = C_GR_QW;
+
+ iparams = mtop->ffparams.iparams;
+ atnr = mtop->ffparams.atnr;
+ nw = 0;
+ nqlj = 0;
+ nq = 0;
+ nlj = 0;
+ *bChargePerturbed = FALSE;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ atom = molt->atoms.atom;
+ nmol = mtop->molblock[mb].nmol;
+ a = 0;
+ for (cg = 0; cg < molt->cgs.nr; cg++)
+ {
+ bWater = !bBHAM;
+ ncqlj = 0;
+ ncq = 0;
+ nclj = 0;
+ a0 = a;
+ while (a < molt->cgs.index[cg+1])
+ {
+ bQ = (atom[a].q != 0 || atom[a].qB != 0);
+ bLJ = (iparams[(atnr+1)*atom[a].type].lj.c6 != 0 ||
+ iparams[(atnr+1)*atom[a].type].lj.c12 != 0);
+ if (atom[a].q != atom[a].qB)
+ {
+ *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) ||
+ (a == a0+2 && bQ && !bLJ && atom[a].q == atom[a-1].q) ||
+ (a == a0+3 && !bQ && bLJ)))
+ {
+ bWater = FALSE;
+ }
+ if (bQ && bLJ)
+ {
+ ncqlj++;
+ }
+ else
+ {
+ if (bQ)
+ {
+ ncq++;
+ }
+ if (bLJ)
+ {
+ nclj++;
+ }
+ }
+ a++;
+ }
+ if (bWater)
+ {
+ nw += nmol;
+ }
+ else
+ {
+ nqlj += nmol*ncqlj;
+ nq += nmol*ncq;
+ nlj += nmol*nclj;
+ }
+ }
+ }
+
+ *nq_tot = nq + nqlj + nw*3;
+ *nlj_tot = nlj + nqlj + nw;
+
+ if (debug)
+ {
+ fprintf(debug, "nw %d nqlj %d nq %d nlj %d\n", nw, nqlj, nq, nlj);
+ }
+
+ /* For the PP non-bonded cost it is (unrealistically) assumed
+ * that all atoms are distributed homogeneously in space.
+ * Factor 3 is used because a water molecule has 3 atoms
+ * (and TIP4P effectively has 3 interactions with (water) atoms)).
+ */
+ *cost_pp = 0.5*(fqljw*nw*nqlj +
+ fqw *nw*(3*nw + nq) +
+ fqlj *nqlj*nqlj +
+ fq *nq*(3*nw + nqlj + nq) +
+ flj *nlj*(nw + nqlj + nlj))
+ *4/3*M_PI*ir->rlist*ir->rlist*ir->rlist/det(box);
+}
+
+static void pp_verlet_load(gmx_mtop_t *mtop, t_inputrec *ir, matrix box,
+ int *nq_tot, int *nlj_tot,
+ double *cost_pp,
+ 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;
+ 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);
+
+ iparams = mtop->ffparams.iparams;
+ atnr = mtop->ffparams.atnr;
+ nqlj = 0;
+ nq = 0;
+ *bChargePerturbed = FALSE;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ atom = molt->atoms.atom;
+ nmol = mtop->molblock[mb].nmol;
+ a = 0;
+ for (a = 0; a < molt->atoms.nr; a++)
+ {
+ if (atom[a].q != 0 || atom[a].qB != 0)
+ {
+ if (iparams[(atnr+1)*atom[a].type].lj.c6 != 0 ||
+ iparams[(atnr+1)*atom[a].type].lj.c12 != 0)
+ {
+ nqlj += nmol;
+ }
+ else
+ {
+ nq += nmol;
+ }
+ }
+ if (atom[a].q != atom[a].qB)
+ {
+ *bChargePerturbed = TRUE;
+ }
+ if (atom[a].type != atom[a].typeB)
+ {
+ *bTypePerturbed = TRUE;
+ }
+ }
}
- }
- if (debug)
- fprintf(debug,"ndx bonded %d exclusions %d\n",ndx,ndx_excl);
+ nlj = mtop->natoms - 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));
- ndx += ndx_excl;
+ if (debug)
+ {
+ fprintf(debug, "nqlj %d nq %d nlj %d rlist %.3f r_eff %.3f\n",
+ 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;
+ }
- return ndx;
+ /* 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*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)
+float pme_load_estimate(gmx_mtop_t *mtop, t_inputrec *ir, matrix box)
{
- t_atom *atom;
- int mb,nmol,atnr,cg,a,a0,ncqlj,ncq,nclj;
- gmx_bool bBHAM,bLJcut,bChargePerturbed,bWater,bQ,bLJ;
- double nw,nqlj,nq,nlj;
- double cost_bond,cost_pp,cost_spread,cost_fft,cost_solve,cost_pme;
- float fq,fqlj,flj,fljtab,fqljw,fqw,fqspread,ffft,fsolve,fbond;
- float ratio;
- t_iparams *iparams;
- gmx_moltype_t *molt;
-
- bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
-
- bLJcut = ((ir->vdwtype == evdwCUT) && !bBHAM);
-
- /* 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
- * in single precision. In double precision PME mesh is slightly cheaper,
- * although not so much that the numbers need to be adjusted.
- */
- fq = 1.5;
- fqlj = (bLJcut ? 1.5 : 2.0 );
- flj = (bLJcut ? 1.0 : 1.75);
- /* Cost of 1 water with one Q/LJ atom */
- fqljw = (bLJcut ? 2.0 : 2.25);
- /* Cost of 1 water with one Q atom or with 1/3 water (LJ negligible) */
- fqw = 1.75;
- /* Cost of q spreading and force interpolation per charge (mainly memory) */
- fqspread = 0.55;
- /* Cost of fft's, will be multiplied with N log(N) */
- ffft = 0.20;
- /* Cost of pme_solve, will be multiplied with N */
- fsolve = 0.80;
- /* Cost of a bonded interaction divided by the number of (pbc_)dx nrequired */
- fbond = 5.0;
-
- iparams = mtop->ffparams.iparams;
- atnr = mtop->ffparams.atnr;
- nw = 0;
- nqlj = 0;
- nq = 0;
- nlj = 0;
- bChargePerturbed = FALSE;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molt = &mtop->moltype[mtop->molblock[mb].type];
- atom = molt->atoms.atom;
- nmol = mtop->molblock[mb].nmol;
- a = 0;
- for(cg=0; cg<molt->cgs.nr; cg++) {
- bWater = !bBHAM;
- ncqlj = 0;
- ncq = 0;
- nclj = 0;
- a0 = a;
- while (a < molt->cgs.index[cg+1]) {
- bQ = (atom[a].q != 0 || atom[a].qB != 0);
- bLJ = (iparams[(atnr+1)*atom[a].type].lj.c6 != 0 ||
- iparams[(atnr+1)*atom[a].type].lj.c12 != 0);
- if (atom[a].q != atom[a].qB) {
- bChargePerturbed = TRUE;
- }
- /* This if this atom fits into water optimization */
- if (!((a == a0 && bQ && bLJ) ||
- (a == a0+1 && bQ && !bLJ) ||
- (a == a0+2 && bQ && !bLJ && atom[a].q == atom[a-1].q) ||
- (a == a0+3 && !bQ && bLJ)))
- bWater = FALSE;
- if (bQ && bLJ) {
- ncqlj++;
- } else {
- if (bQ)
- ncq++;
- if (bLJ)
- nclj++;
- }
- a++;
- }
- if (bWater) {
- nw += nmol;
- } else {
- nqlj += nmol*ncqlj;
- nq += nmol*ncq;
- nlj += nmol*nclj;
- }
+ t_atom *atom;
+ 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;
+ gmx_moltype_t *molt;
+
+ /* 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
+ * in single precision. In double precision PME mesh is slightly cheaper,
+ * although not so much that the numbers need to be adjusted.
+ */
+
+ iparams = mtop->ffparams.iparams;
+ atnr = mtop->ffparams.atnr;
+
+ cost_bond = C_BOND*n_bonded_dx(mtop, TRUE);
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ pp_group_load(mtop, ir, box,
+ &nq_tot, &nlj_tot, &cost_pp,
+ &bChargePerturbed, &bTypePerturbed);
+ }
+ else
+ {
+ pp_verlet_load(mtop, ir, box,
+ &nq_tot, &nlj_tot, &cost_pp,
+ &bChargePerturbed, &bTypePerturbed);
+ }
+
+ cost_redist = 0;
+ cost_spread = 0;
+ cost_fft = 0;
+ cost_solve = 0;
+
+ if (EEL_PME(ir->coulombtype))
+ {
+ 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;
}
- }
- if (debug)
- fprintf(debug,"nw %g nqlj %g nq %g nlj %g\n",nw,nqlj,nq,nlj);
-
- cost_bond = fbond*n_bonded_dx(mtop,TRUE);
-
- /* For the PP non-bonded cost it is (unrealistically) assumed
- * that all atoms are distributed homogeneously in space.
- */
- cost_pp = 0.5*(fqljw*nw*nqlj +
- fqw *nw*(3*nw + nq) +
- fqlj *nqlj*nqlj +
- fq *nq*(3*nw + nqlj + nq) +
- flj *nlj*(nw + nqlj + nlj))
- *4/3*M_PI*ir->rlist*ir->rlist*ir->rlist/det(box);
-
- cost_spread = fqspread*(3*nw + nqlj + nq)*pow(ir->pme_order,3);
- cost_fft = ffft*ir->nkx*ir->nky*ir->nkz*log(ir->nkx*ir->nky*ir->nkz);
- cost_solve = fsolve*ir->nkx*ir->nky*ir->nkz;
-
- if (ir->efep != efepNO && bChargePerturbed) {
- /* All PME work, except the spline coefficient calculation, doubles */
- cost_spread *= 2;
- cost_fft *= 2;
- cost_solve *= 2;
- }
-
- cost_pme = cost_spread + cost_fft + cost_solve;
-
- ratio = cost_pme/(cost_bond + cost_pp + cost_pme);
-
- if (debug) {
- fprintf(debug,
- "cost_bond %f\n"
- "cost_pp %f\n"
- "cost_spread %f\n"
- "cost_fft %f\n"
- "cost_solve %f\n",
- cost_bond,cost_pp,cost_spread,cost_fft,cost_solve);
-
- fprintf(debug,"Estimate for relative PME load: %.3f\n",ratio);
- }
-
- return ratio;
+
+ cost_pme = cost_redist + cost_spread + cost_fft + cost_solve;
+
+ ratio = cost_pme/(cost_bond + cost_pp + cost_pme);
+
+ if (debug)
+ {
+ fprintf(debug,
+ "cost_bond %f\n"
+ "cost_pp %f\n"
+ "cost_redist %f\n"
+ "cost_spread %f\n"
+ "cost_fft %f\n"
+ "cost_solve %f\n",
+ cost_bond, cost_pp, cost_redist, cost_spread, cost_fft, cost_solve);
+
+ fprintf(debug, "Estimate for relative PME load: %.3f\n", ratio);
+ }
+
+ return ratio;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff