/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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.
{ "no", "box size", "domain decompostion", "PME grid restriction", "maximum allowed grid scaling" };
struct pme_load_balancing_t {
- gmx_bool bSepPMERanks; /**< do we have separate PME ranks? */
- gmx_bool bActive; /**< is PME tuning active? */
- int64_t step_rel_stop; /**< stop the tuning after this value of step_rel */
- gmx_bool bTriggerOnDLB; /**< trigger balancing only on DD DLB */
- gmx_bool bBalance; /**< are we in the balancing phase, i.e. trying different setups? */
- 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 */
- real rbufOuter_coulomb; /**< the outer pairlist buffer size */
- real rbufOuter_vdw; /**< the outer pairlist buffer size */
- real rbufInner_coulomb; /**< the inner pairlist buffer size */
- real rbufInner_vdw; /**< the inner 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 inex (in setup) of the current setup */
- int fastest; /**< index of the fastest setup up till now */
- int lower_limit; /**< don't go below this setup index */
- int start; /**< start of setup index range to consider in stage>0 */
- int end; /**< end of setup index 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 cycles_n; /**< step cycle counter cummulative count */
- double cycles_c; /**< step cycle counter cummulative cycles */
+ gmx_bool bSepPMERanks; /**< do we have separate PME ranks? */
+ gmx_bool bActive; /**< is PME tuning active? */
+ int64_t step_rel_stop; /**< stop the tuning after this value of step_rel */
+ gmx_bool bTriggerOnDLB; /**< trigger balancing only on DD DLB */
+ gmx_bool bBalance; /**< are we in the balancing phase, i.e. trying different setups? */
+ 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 */
+ real rbufOuter_coulomb; /**< the outer pairlist buffer size */
+ real rbufOuter_vdw; /**< the outer pairlist buffer size */
+ real rbufInner_coulomb; /**< the inner pairlist buffer size */
+ real rbufInner_vdw; /**< the inner pairlist buffer size */
+ matrix box_start; /**< the initial simulation box */
+ std::vector<pme_setup_t> setup; /**< the PME+cutoff setups */
+ int cur; /**< the index (in setup) of the current setup */
+ int fastest; /**< index of the fastest setup up till now */
+ int lower_limit; /**< don't go below this setup index */
+ int start; /**< start of setup index range to consider in stage>0 */
+ int end; /**< end of setup index 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 cycles_n; /**< step cycle counter cummulative count */
+ double cycles_c; /**< step cycle counter cummulative cycles */
};
/* TODO The code in this file should call this getter, rather than
return pme_lb != nullptr && pme_lb->bActive;
}
+// TODO Return a unique_ptr to pme_load_balancing_t
void pme_loadbal_init(pme_load_balancing_t **pme_lb_p,
t_commrec *cr,
const gmx::MDLogger &mdlog,
// This is checked by grompp, but it doesn't hurt to check again.
GMX_RELEASE_ASSERT(!(EEL_PME(ir.coulombtype) && EVDW_PME(ir.vdwtype) && ir.rcoulomb != ir.rvdw), "With Coulomb and LJ PME, rcoulomb should be equal to rvdw");
- snew(pme_lb, 1);
+ pme_lb = new pme_load_balancing_t;
pme_lb->bSepPMERanks = !thisRankHasDuty(cr, DUTY_PME);
EwaldBoxZScaler boxScaler(ir);
boxScaler.scaleBox(box, pme_lb->box_start);
- pme_lb->n = 1;
- snew(pme_lb->setup, pme_lb->n);
+ pme_lb->setup.resize(1);
pme_lb->rcut_vdw = ic.rvdw;
pme_lb->rcut_coulomb_start = ir.rcoulomb;
int pme_order,
const gmx_domdec_t *dd)
{
- pme_setup_t *set;
real fac, sp;
real tmpr_coulomb, tmpr_vdw;
int d;
bool grid_ok;
/* 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];
- set->pmedata = nullptr;
+ pme_setup_t set;
+
+ set.pmedata = nullptr;
NumPmeDomains numPmeDomains = getNumPmeDomains(dd);
*/
if (fac > 2.1)
{
- pme_lb->n--;
-
return FALSE;
}
fac *= 1.01;
- clear_ivec(set->grid);
+ clear_ivec(set.grid);
sp = calcFftGrid(nullptr, pme_lb->box_start,
fac*pme_lb->setup[pme_lb->cur].spacing,
minimalPmeGridSize(pme_order),
- &set->grid[XX],
- &set->grid[YY],
- &set->grid[ZZ]);
+ &set.grid[XX],
+ &set.grid[YY],
+ &set.grid[ZZ]);
/* As here we can't easily check if one of the PME ranks
* uses threading, we do a conservative grid check.
* per PME rank along x, which is not a strong restriction.
*/
grid_ok = gmx_pme_check_restrictions(pme_order,
- set->grid[XX], set->grid[YY], set->grid[ZZ],
+ set.grid[XX], set.grid[YY], set.grid[ZZ],
numPmeDomains.x,
true,
false);
}
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)
+ 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;
+ set.rcut_coulomb = pme_lb->rcut_coulomb_start;
}
if (pme_lb->cutoff_scheme == ecutsVERLET)
{
/* Never decrease the Coulomb and VdW list buffers */
- set->rlistOuter = std::max(set->rcut_coulomb + pme_lb->rbufOuter_coulomb,
- pme_lb->rcut_vdw + pme_lb->rbufOuter_vdw);
- set->rlistInner = std::max(set->rcut_coulomb + pme_lb->rbufInner_coulomb,
- pme_lb->rcut_vdw + pme_lb->rbufInner_vdw);
+ set.rlistOuter = std::max(set.rcut_coulomb + pme_lb->rbufOuter_coulomb,
+ pme_lb->rcut_vdw + pme_lb->rbufOuter_vdw);
+ set.rlistInner = std::max(set.rcut_coulomb + pme_lb->rbufInner_coulomb,
+ pme_lb->rcut_vdw + pme_lb->rbufInner_vdw);
}
else
{
/* TODO Remove these lines and pme_lb->cutoff_scheme */
- tmpr_coulomb = set->rcut_coulomb + pme_lb->rbufOuter_coulomb;
+ tmpr_coulomb = set.rcut_coulomb + pme_lb->rbufOuter_coulomb;
tmpr_vdw = pme_lb->rcut_vdw + pme_lb->rbufOuter_vdw;
/* Two (known) bugs with cutoff-scheme=group here:
* - This modification of rlist results in incorrect DD comunication.
* - We should set fr->bTwinRange = (fr->rlistlong > fr->rlist).
*/
- set->rlistOuter = std::min(tmpr_coulomb, tmpr_vdw);
- set->rlistInner = set->rlistOuter;
+ set.rlistOuter = std::min(tmpr_coulomb, tmpr_vdw);
+ set.rlistInner = set.rlistOuter;
}
- set->spacing = sp;
+ set.spacing = sp;
/* The grid efficiency is the size wrt a grid with uniform x/y/z spacing */
- set->grid_efficiency = 1;
+ set.grid_efficiency = 1;
for (d = 0; d < DIM; d++)
{
- set->grid_efficiency *= (set->grid[d]*sp)/norm(pme_lb->box_start[d]);
+ 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_q =
- pme_lb->setup[0].ewaldcoeff_q*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.ewaldcoeff_lj =
+ pme_lb->setup[0].ewaldcoeff_lj*pme_lb->setup[0].rcut_coulomb/set.rcut_coulomb;
- set->count = 0;
- set->cycles = 0;
+ set.count = 0;
+ set.cycles = 0;
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);
+ set.grid[XX], set.grid[YY], set.grid[ZZ], set.rcut_coulomb);
}
+ pme_lb->setup.push_back(set);
return TRUE;
}
}
else
{
- return pme_lb->n;
+ return pme_lb->setup.size();
}
}
* maxRelativeSlowdownAccepted times the fastest setup.
*/
pme_lb->start = pme_lb->lower_limit;
- while (pme_lb->start + 1 < pme_lb->n &&
+ while (pme_lb->start + 1 < static_cast<int>(pme_lb->setup.size()) &&
(pme_lb->setup[pme_lb->start].count == 0 ||
pme_lb->setup[pme_lb->start].cycles >
pme_lb->setup[pme_lb->fastest].cycles*maxRelativeSlowdownAccepted))
}
/* Decrease end only with setups that we timed and that are slow. */
- pme_lb->end = pme_lb->n;
+ pme_lb->end = pme_lb->setup.size();
if (pme_lb->setup[pme_lb->end - 1].count > 0 &&
pme_lb->setup[pme_lb->end - 1].cycles >
pme_lb->setup[pme_lb->fastest].cycles*maxRelativeSlowdownAccepted)
if (pme_lb->stage == 0 && pme_lb->cur > 0 &&
cycles > pme_lb->setup[pme_lb->fastest].cycles*maxRelativeSlowdownAccepted)
{
- pme_lb->n = pme_lb->cur + 1;
+ pme_lb->setup.resize(pme_lb->cur + 1);
/* Done with scanning, go to stage 1 */
switch_to_stage1(pme_lb);
}
do
{
- if (pme_lb->cur+1 < pme_lb->n)
+ if (pme_lb->cur+1 < static_cast<int>(pme_lb->setup.size()))
{
/* We had already generated the next setup */
OK = TRUE;
/* We hit the upper limit for the cut-off,
* the setup should not go further than cur.
*/
- pme_lb->n = pme_lb->cur + 1;
+ pme_lb->setup.resize(pme_lb->cur + 1);
print_loadbal_limited(fp_err, fp_log, step, pme_lb);
/* Switch to the next stage */
switch_to_stage1(pme_lb);
print_pme_loadbal_settings(pme_lb, fplog, mdlog, bNonBondedOnGPU);
}
- /* TODO: Here we should free all pointers in pme_lb,
- * but as it contains pme data structures,
- * we need to first make pme.c free all data.
- */
+ delete pme_lb;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff