/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 4.6.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
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* For more info, check our website at http://www.gromacs.org
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+ *
* And Hey:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
/* Parameters and setting for one PP-PME setup */
typedef struct {
- real rcut_coulomb; /* Coulomb cut-off */
- real rlist; /* pair-list cut-off */
- real rlistlong; /* LR pair-list cut-off */
- int nstcalclr; /* frequency of evaluating long-range forces for group scheme */
- 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 */
- 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 */
+ real rcut_coulomb; /* Coulomb cut-off */
+ real rlist; /* pair-list cut-off */
+ real rlistlong; /* LR pair-list cut-off */
+ int nstcalclr; /* frequency of evaluating long-range forces for group scheme */
+ 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 */
+ 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;
/* In the initial scan, step by grids that are at least a factor 0.8 coarser */
*/
#define PME_LB_ACCEL_TOL 1.02
-enum { epmelblimNO, epmelblimBOX, epmelblimDD, epmelblimNR };
+enum {
+ epmelblimNO, epmelblimBOX, epmelblimDD, epmelblimNR
+};
const char *pmelblim_str[epmelblimNR] =
{ "no", "box size", "domain decompostion" };
struct pme_load_balancing {
- int nstage; /* the current maximum number of stages */
-
- real cut_spacing; /* the minimum cutoff / PME grid spacing ratio */
- real rcut_vdw; /* Vdw cutoff (does not change) */
- real rcut_coulomb_start; /* Initial electrostatics cutoff */
- int nstcalclr_start; /* Initial electrostatics cutoff */
- real rbuf_coulomb; /* the pairlist buffer size */
- real rbuf_vdw; /* the pairlist buffer size */
- matrix box_start; /* the initial simulation box */
- int n; /* the count of setup as well as the allocation size */
- pme_setup_t *setup; /* the PME+cutoff setups */
- int cur; /* the current setup */
- int fastest; /* fastest setup up till now */
- int start; /* start of setup range to consider in stage>0 */
- int end; /* end of setup range to consider in stage>0 */
- int elimited; /* was the balancing limited, uses enum above */
- int cutoff_scheme; /* Verlet or group cut-offs */
-
- int stage; /* the current stage */
+ int nstage; /* the current maximum number of stages */
+
+ real cut_spacing; /* the minimum cutoff / PME grid spacing ratio */
+ real rcut_vdw; /* Vdw cutoff (does not change) */
+ real rcut_coulomb_start; /* Initial electrostatics cutoff */
+ int nstcalclr_start; /* Initial electrostatics cutoff */
+ real rbuf_coulomb; /* the pairlist buffer size */
+ real rbuf_vdw; /* the pairlist buffer size */
+ matrix box_start; /* the initial simulation box */
+ int n; /* the count of setup as well as the allocation size */
+ pme_setup_t *setup; /* the PME+cutoff setups */
+ int cur; /* the current setup */
+ int fastest; /* fastest setup up till now */
+ int start; /* start of setup range to consider in stage>0 */
+ int end; /* end of setup range to consider in stage>0 */
+ int elimited; /* was the balancing limited, uses enum above */
+ int cutoff_scheme; /* Verlet or group cut-offs */
+
+ int stage; /* the current stage */
};
void pme_loadbal_init(pme_load_balancing_t *pme_lb_p,
- const t_inputrec *ir,matrix box,
+ const t_inputrec *ir, matrix box,
const interaction_const_t *ic,
gmx_pme_t pmedata)
{
pme_load_balancing_t pme_lb;
- real spm,sp;
- int d;
+ real spm, sp;
+ int d;
- snew(pme_lb,1);
+ snew(pme_lb, 1);
/* Any number of stages >= 2 is supported */
pme_lb->nstage = 2;
pme_lb->cutoff_scheme = ir->cutoff_scheme;
- if(pme_lb->cutoff_scheme == ecutsVERLET)
+ if (pme_lb->cutoff_scheme == ecutsVERLET)
{
pme_lb->rbuf_coulomb = ic->rlist - ic->rcoulomb;
pme_lb->rbuf_vdw = pme_lb->rbuf_coulomb;
}
else
{
- if(ic->rcoulomb > ic->rlist)
+ if (ic->rcoulomb > ic->rlist)
{
pme_lb->rbuf_coulomb = ic->rlistlong - ic->rcoulomb;
}
{
pme_lb->rbuf_coulomb = ic->rlist - ic->rcoulomb;
}
- if(ic->rvdw > ic->rlist)
+ if (ic->rvdw > ic->rlist)
{
pme_lb->rbuf_vdw = ic->rlistlong - ic->rvdw;
}
}
}
- copy_mat(box,pme_lb->box_start);
- if (ir->ePBC==epbcXY && ir->nwall==2)
+ copy_mat(box, pme_lb->box_start);
+ if (ir->ePBC == epbcXY && ir->nwall == 2)
{
- svmul(ir->wall_ewald_zfac,pme_lb->box_start[ZZ],pme_lb->box_start[ZZ]);
+ svmul(ir->wall_ewald_zfac, pme_lb->box_start[ZZ], pme_lb->box_start[ZZ]);
}
pme_lb->n = 1;
- snew(pme_lb->setup,pme_lb->n);
+ 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->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].ewaldcoeff = ic->ewaldcoeff;
pme_lb->setup[0].pmedata = pmedata;
-
+
spm = 0;
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
sp = norm(pme_lb->box_start[d])/pme_lb->setup[0].grid[d];
if (sp > spm)
}
static gmx_bool pme_loadbal_increase_cutoff(pme_load_balancing_t pme_lb,
- int pme_order)
+ int pme_order)
{
pme_setup_t *set;
- real fac,sp;
- real tmpr_coulomb,tmpr_vdw;
- int d;
+ real fac, sp;
+ real tmpr_coulomb, tmpr_vdw;
+ int d;
/* Try to add a new setup with next larger cut-off to the list */
pme_lb->n++;
- srenew(pme_lb->setup,pme_lb->n);
- set = &pme_lb->setup[pme_lb->n-1];
+ srenew(pme_lb->setup, pme_lb->n);
+ set = &pme_lb->setup[pme_lb->n-1];
set->pmedata = NULL;
fac = 1;
{
fac *= 1.01;
clear_ivec(set->grid);
- sp = calc_grid(NULL,pme_lb->box_start,
+ sp = calc_grid(NULL, pme_lb->box_start,
fac*pme_lb->setup[pme_lb->cur].spacing,
&set->grid[XX],
&set->grid[YY],
/* In parallel we can't have grids smaller than 2*pme_order,
* and we would anyhow not gain much speed at these grid sizes.
*/
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
if (set->grid[d] <= 2*pme_order)
{
set->rcut_coulomb = pme_lb->cut_spacing*sp;
- if(pme_lb->cutoff_scheme == ecutsVERLET)
+ if (pme_lb->cutoff_scheme == ecutsVERLET)
{
set->rlist = set->rcut_coulomb + pme_lb->rbuf_coulomb;
/* We dont use LR lists with Verlet, but this avoids if-statements in further checks */
{
tmpr_coulomb = set->rcut_coulomb + pme_lb->rbuf_coulomb;
tmpr_vdw = pme_lb->rcut_vdw + pme_lb->rbuf_vdw;
- set->rlist = min(tmpr_coulomb,tmpr_vdw);
- set->rlistlong = max(tmpr_coulomb,tmpr_vdw);
-
+ set->rlist = min(tmpr_coulomb, tmpr_vdw);
+ set->rlistlong = max(tmpr_coulomb, tmpr_vdw);
+
/* Set the long-range update frequency */
- if(set->rlist == set->rlistlong)
+ if (set->rlist == set->rlistlong)
{
/* No long-range interactions if the short-/long-range cutoffs are identical */
set->nstcalclr = 0;
}
- else if(pme_lb->nstcalclr_start==0 || pme_lb->nstcalclr_start==1)
+ else if (pme_lb->nstcalclr_start == 0 || pme_lb->nstcalclr_start == 1)
{
/* We were not doing long-range before, but now we are since rlist!=rlistlong */
set->nstcalclr = 1;
else
{
/* We were already doing long-range interactions from the start */
- if(pme_lb->rcut_vdw > pme_lb->rcut_coulomb_start)
+ if (pme_lb->rcut_vdw > pme_lb->rcut_coulomb_start)
{
/* We were originally doing long-range VdW-only interactions.
* If rvdw is still longer than rcoulomb we keep the original nstcalclr,
}
}
}
-
+
set->spacing = sp;
/* The grid efficiency is the size wrt a grid with uniform x/y/z spacing */
set->grid_efficiency = 1;
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
set->grid_efficiency *= (set->grid[d]*sp)/norm(pme_lb->box_start[d]);
}
if (debug)
{
- fprintf(debug,"PME loadbal: grid %d %d %d, coulomb cutoff %f\n",
- set->grid[XX],set->grid[YY],set->grid[ZZ],set->rcut_coulomb);
+ fprintf(debug, "PME loadbal: grid %d %d %d, coulomb cutoff %f\n",
+ set->grid[XX], set->grid[YY], set->grid[ZZ], set->rcut_coulomb);
}
return TRUE;
}
-static void print_grid(FILE *fp_err,FILE *fp_log,
+static void print_grid(FILE *fp_err, FILE *fp_log,
const char *pre,
const char *desc,
const pme_setup_t *set,
double cycles)
{
- char buf[STRLEN],buft[STRLEN];
+ char buf[STRLEN], buft[STRLEN];
if (cycles >= 0)
{
- sprintf(buft,": %.1f M-cycles",cycles*1e-6);
+ sprintf(buft, ": %.1f M-cycles", cycles*1e-6);
}
else
{
buft[0] = '\0';
}
- sprintf(buf,"%-11s%10s pme grid %d %d %d, coulomb cutoff %.3f%s",
+ sprintf(buf, "%-11s%10s pme grid %d %d %d, coulomb cutoff %.3f%s",
pre,
- desc,set->grid[XX],set->grid[YY],set->grid[ZZ],set->rcut_coulomb,
+ desc, set->grid[XX], set->grid[YY], set->grid[ZZ], set->rcut_coulomb,
buft);
if (fp_err != NULL)
{
- fprintf(fp_err,"\r%s\n",buf);
+ fprintf(fp_err, "\r%s\n", buf);
}
if (fp_log != NULL)
{
- fprintf(fp_log,"%s\n",buf);
+ fprintf(fp_log, "%s\n", buf);
}
}
}
}
-static void print_loadbal_limited(FILE *fp_err,FILE *fp_log,
+static void print_loadbal_limited(FILE *fp_err, FILE *fp_log,
gmx_large_int_t step,
pme_load_balancing_t pme_lb)
{
- char buf[STRLEN],sbuf[22];
+ char buf[STRLEN], sbuf[22];
- sprintf(buf,"step %4s: the %s limited the PME load balancing to a coulomb cut-off of %.3f",
- gmx_step_str(step,sbuf),
+ sprintf(buf, "step %4s: the %s limited 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);
if (fp_err != NULL)
{
- fprintf(fp_err,"\r%s\n",buf);
+ fprintf(fp_err, "\r%s\n", buf);
}
if (fp_log != NULL)
{
- fprintf(fp_log,"%s\n",buf);
+ fprintf(fp_log, "%s\n", buf);
}
}
}
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,
+ 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)
+ nonbonded_verlet_t *nbv,
+ gmx_pme_t *pmedata,
+ gmx_large_int_t step)
{
- gmx_bool OK;
+ gmx_bool OK;
pme_setup_t *set;
- double cycles_fast;
- char buf[STRLEN],sbuf[22];
- real rtab;
- gmx_bool bUsesSimpleTables = TRUE;
+ double cycles_fast;
+ char buf[STRLEN], sbuf[22];
+ real rtab;
+ gmx_bool bUsesSimpleTables = TRUE;
if (pme_lb->stage == pme_lb->nstage)
{
if (PAR(cr))
{
- gmx_sumd(1,&cycles,cr);
+ gmx_sumd(1, &cycles, cr);
cycles /= cr->nnodes;
}
return TRUE;
}
- sprintf(buf, "step %4s: ", gmx_step_str(step,sbuf));
- print_grid(fp_err,fp_log,buf,"timed with",set,cycles);
+ sprintf(buf, "step %4s: ", gmx_step_str(step, sbuf));
+ print_grid(fp_err, fp_log, buf, "timed with", set, cycles);
if (set->count <= 2)
{
if (debug)
{
- fprintf(debug,"The performance for grid %d %d %d went from %.3f to %.1f M-cycles, this is more than %f\n"
+ fprintf(debug, "The performance for grid %d %d %d went from %.3f to %.1f M-cycles, this is more than %f\n"
"Increased the number stages to %d"
" and ignoring the previous performance\n",
- set->grid[XX],set->grid[YY],set->grid[ZZ],
- cycles*1e-6,set->cycles*1e-6,PME_LB_ACCEL_TOL,
+ set->grid[XX], set->grid[YY], set->grid[ZZ],
+ cycles*1e-6, set->cycles*1e-6, PME_LB_ACCEL_TOL,
pme_lb->nstage);
}
}
- set->cycles = min(set->cycles,cycles);
+ set->cycles = min(set->cycles, cycles);
}
if (set->cycles < pme_lb->setup[pme_lb->fastest].cycles)
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);
}
if (OK && ir->ePBC != epbcNONE)
{
OK = (sqr(pme_lb->setup[pme_lb->cur+1].rlistlong)
- <= max_cutoff2(ir->ePBC,state->box));
+ <= max_cutoff2(ir->ePBC, state->box));
if (!OK)
{
pme_lb->elimited = epmelblimBOX;
if (DOMAINDECOMP(cr))
{
- OK = change_dd_cutoff(cr,state,ir,
+ OK = change_dd_cutoff(cr, state, ir,
pme_lb->setup[pme_lb->cur].rlistlong);
if (!OK)
{
* the setup should not go further than cur.
*/
pme_lb->n = pme_lb->cur + 1;
- print_loadbal_limited(fp_err,fp_log,step,pme_lb);
+ print_loadbal_limited(fp_err, fp_log, step, pme_lb);
/* Switch to the next stage */
switch_to_stage1(pme_lb);
}
if (pme_lb->stage > 0 && pme_lb->end == 1)
{
- pme_lb->cur = 0;
+ pme_lb->cur = 0;
pme_lb->stage = pme_lb->nstage;
}
else if (pme_lb->stage > 0 && pme_lb->end > 1)
if (DOMAINDECOMP(cr) && pme_lb->stage > 0)
{
- OK = change_dd_cutoff(cr,state,ir,pme_lb->setup[pme_lb->cur].rlistlong);
+ OK = change_dd_cutoff(cr, state, ir, pme_lb->setup[pme_lb->cur].rlistlong);
if (!OK)
{
/* Failsafe solution */
pme_lb->end = pme_lb->cur;
pme_lb->cur = pme_lb->start;
pme_lb->elimited = epmelblimDD;
- print_loadbal_limited(fp_err,fp_log,step,pme_lb);
+ print_loadbal_limited(fp_err, fp_log, step, pme_lb);
}
}
if (pme_lb->cutoff_scheme == ecutsVERLET &&
nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
{
- nbnxn_cuda_pme_loadbal_update_param(nbv->cu_nbv,ic);
+ nbnxn_cuda_pme_loadbal_update_param(nbv->cu_nbv, ic);
}
else
{
- init_interaction_const_tables(NULL,ic,bUsesSimpleTables,
+ init_interaction_const_tables(NULL, ic, bUsesSimpleTables,
rtab);
}
if (pme_lb->cutoff_scheme == ecutsVERLET && nbv->ngrp > 1)
{
- init_interaction_const_tables(NULL,ic,bUsesSimpleTables,
+ init_interaction_const_tables(NULL, ic, bUsesSimpleTables,
rtab);
}
* copying part of the old pointers.
*/
gmx_pme_reinit(&set->pmedata,
- cr,pme_lb->setup[0].pmedata,ir,
+ cr, pme_lb->setup[0].pmedata, ir,
set->grid);
}
*pmedata = set->pmedata;
if (debug)
{
- print_grid(NULL,debug,"","switched to",set,-1);
+ print_grid(NULL, debug, "", "switched to", set, -1);
}
if (pme_lb->stage == pme_lb->nstage)
{
- print_grid(fp_err,fp_log,"","optimal",set,-1);
+ print_grid(fp_err, fp_log, "", "optimal", set, -1);
}
return TRUE;
return setup->grid[XX]*setup->grid[YY]*setup->grid[ZZ];
}
-static void print_pme_loadbal_setting(FILE *fplog,
- char *name,
- const pme_setup_t *setup)
+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->grid[XX],setup->grid[YY],setup->grid[ZZ],
- setup->spacing,1/setup->ewaldcoeff);
+ setup->rcut_coulomb, setup->rlist,
+ setup->grid[XX], setup->grid[YY], setup->grid[ZZ],
+ setup->spacing, 1/setup->ewaldcoeff);
}
static void print_pme_loadbal_settings(pme_load_balancing_t pme_lb,
- FILE *fplog)
+ FILE *fplog)
{
- double pp_ratio,grid_ratio;
+ 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_lb->setup[pme_lb->cur].rlist/pme_lb->setup[0].rlistlong, 3.0);
grid_ratio = pme_grid_points(&pme_lb->setup[pme_lb->cur])/
(double)pme_grid_points(&pme_lb->setup[0]);
- fprintf(fplog,"\n");
- fprintf(fplog," P P - P M E L O A D B A L A N C I N G\n");
- fprintf(fplog,"\n");
+ fprintf(fplog, "\n");
+ fprintf(fplog, " P P - P M E L O A D B A L A N C I N G\n");
+ fprintf(fplog, "\n");
/* Here we only warn when the optimal setting is the last one */
if (pme_lb->elimited != epmelblimNO &&
pme_lb->cur == pme_loadbal_end(pme_lb)-1)
{
- fprintf(fplog," NOTE: The PP/PME load balancing was limited by the %s,\n",
+ fprintf(fplog, " NOTE: The PP/PME load balancing was limited by the %s,\n",
pmelblim_str[pme_lb->elimited]);
- fprintf(fplog," you might not have reached a good load balance.\n");
+ fprintf(fplog, " you might not have reached a good load balance.\n");
if (pme_lb->elimited == epmelblimDD)
{
- fprintf(fplog," Try different mdrun -dd settings or lower the -dds value.\n");
+ fprintf(fplog, " Try different mdrun -dd settings or lower the -dds value.\n");
}
- fprintf(fplog,"\n");
- }
- fprintf(fplog," PP/PME load balancing changed the cut-off and PME settings:\n");
- fprintf(fplog," particle-particle PME\n");
- fprintf(fplog," rcoulomb rlist grid spacing 1/beta\n");
- print_pme_loadbal_setting(fplog,"initial",&pme_lb->setup[0]);
- print_pme_loadbal_setting(fplog,"final" ,&pme_lb->setup[pme_lb->cur]);
- 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");
+ fprintf(fplog, "\n");
+ }
+ fprintf(fplog, " PP/PME load balancing changed the cut-off and PME settings:\n");
+ fprintf(fplog, " particle-particle PME\n");
+ fprintf(fplog, " rcoulomb rlist grid spacing 1/beta\n");
+ print_pme_loadbal_setting(fplog, "initial", &pme_lb->setup[0]);
+ print_pme_loadbal_setting(fplog, "final", &pme_lb->setup[pme_lb->cur]);
+ 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");
}
void pme_loadbal_done(pme_load_balancing_t pme_lb, FILE *fplog)
{
if (fplog != NULL && (pme_lb->cur > 0 || pme_lb->elimited != epmelblimNO))
{
- print_pme_loadbal_settings(pme_lb,fplog);
+ print_pme_loadbal_settings(pme_lb, fplog);
}
/* TODO: Here we should free all pointers in pme_lb,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff