/* When dynamic pair-list pruning is requested, we need to prune
* at nstlistPrune steps.
*/
- if (nbv->pairlistSets().isDynamicPairlistPruningStep(step))
+ if (nbv->pairlistSets().isDynamicPruningStepCpu(step))
{
/* Prune the pair-list beyond fr->ic->rlistPrune using
* the current coordinates of the atoms.
*/
wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
- nbv->dispatchPruneKernel(ilocality, fr->shift_vec);
+ nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
}
}
}
-/*! \brief
- * Launch the dynamic rolling pruning GPU task.
- *
- * We currently alternate local/non-local list pruning in odd-even steps
- * (only pruning every second step without DD).
- *
- * \param[in] cr The communication record
- * \param[in] nbv Nonbonded verlet structure
- * \param[in] inputrec The input record
- * \param[in] step The current MD step
- */
-static inline void launchGpuRollingPruning(const t_commrec *cr,
- const nonbonded_verlet_t *nbv,
- const t_inputrec *inputrec,
- const int64_t step)
-{
- /* We should not launch the rolling pruning kernel at a search
- * step or just before search steps, since that's useless.
- * Without domain decomposition we prune at even steps.
- * With domain decomposition we alternate local and non-local
- * pruning at even and odd steps.
- */
- int numRollingParts = nbv->pairlistSets().params().numRollingParts;
- GMX_ASSERT(numRollingParts == nbv->pairlistSets().params().nstlistPrune/2,
- "Since we alternate local/non-local at even/odd steps, "
- "we need numRollingParts<=nstlistPrune/2 for correctness and == for efficiency");
- int stepWithCurrentList = nbv->pairlistSets().numStepsWithPairlist(step);
- bool stepIsEven = ((stepWithCurrentList & 1) == 0);
- if (stepWithCurrentList > 0 &&
- stepWithCurrentList < inputrec->nstlist - 1 &&
- (stepIsEven || havePPDomainDecomposition(cr)))
- {
- Nbnxm::gpu_launch_kernel_pruneonly(nbv->gpu_nbv,
- stepIsEven ? Nbnxm::InteractionLocality::Local : Nbnxm::InteractionLocality::NonLocal,
- numRollingParts);
- }
-}
-
static void do_force_cutsVERLET(FILE *fplog,
const t_commrec *cr,
const gmx_multisim_t *ms,
wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
Nbnxm::gpu_clear_outputs(nbv->gpu_nbv, flags);
- /* Is dynamic pair-list pruning activated? */
- if (nbv->pairlistSets().params().useDynamicPruning)
+ if (nbv->pairlistSets().isDynamicPruningStepGpu(step))
{
- launchGpuRollingPruning(cr, nbv, inputrec, step);
+ nbv->dispatchPruneKernelGpu(step);
}
wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
wallcycle_stop(wcycle, ewcLAUNCH_GPU);
/*! \brief Constructor producing a struct with dynamic pruning disabled
*/
NbnxnListParameters(Nbnxm::KernelType kernelType,
- real rlist);
-
- PairlistType pairlistType; //!< The type of cluster-pair list
- bool useDynamicPruning; //!< Are we using dynamic pair-list pruning
- int nstlistPrune; //!< Pair-list dynamic pruning interval
- real rlistOuter; //!< Cut-off of the larger, outer pair-list
- real rlistInner; //!< Cut-off of the smaller, inner pair-list
- int numRollingParts; //!< The number parts to divide the pair-list into for rolling pruning, a value of 1 gives no rolling pruning
+ real rlist,
+ bool haveMultipleDomains);
+
+ PairlistType pairlistType; //!< The type of cluster-pair list
+ real rlistOuter; //!< Cut-off of the larger, outer pair-list
+ real rlistInner; //!< Cut-off of the smaller, inner pair-list
+ bool haveMultipleDomains; //!< True when using DD with multiple domains
+ bool useDynamicPruning; //!< Are we using dynamic pair-list pruning
+ int nstlistPrune; //!< Pair-list dynamic pruning interval
+ int numRollingPruningParts; //!< The number parts to divide the pair-list into for rolling pruning, a value of 1 gives no rolling pruning
+ int lifetime; //!< Lifetime in steps of the pair-list
};
/*! \brief Resources that can be used to execute non-bonded kernels on */
return step - outerListCreationStep_;
}
- //! Returns whether step is a dynamic list pruning step, for CPU lists only
- bool isDynamicPairlistPruningStep(int64_t step) const
+ //! Returns whether step is a dynamic list pruning step, for CPU lists
+ bool isDynamicPruningStepCpu(int64_t step) const
{
return (params_.useDynamicPruning &&
numStepsWithPairlist(step) % params_.nstlistPrune == 0);
}
+ //! Returns whether step is a dynamic list pruning step, for GPU lists
+ bool isDynamicPruningStepGpu(int64_t step) const
+ {
+ const int age = numStepsWithPairlist(step);
+
+ return (params_.useDynamicPruning &&
+ age > 0 &&
+ age < params_.lifetime &&
+ (params_.haveMultipleDomains || age % 2 == 0));
+ }
+
//! Changes the pair-list outer and inner radius
void changeRadii(real rlistOuter,
real rlistInner)
return *pairlistSets_;
}
- //! Dispatches the dynamic pruning kernel for the given locality
- void dispatchPruneKernel(Nbnxm::InteractionLocality iLocality,
- const rvec *shift_vec);
+ //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
+ void dispatchPruneKernelCpu(Nbnxm::InteractionLocality iLocality,
+ const rvec *shift_vec);
+
+ //! Dispatches the dynamic pruning kernel for GPU lists
+ void dispatchPruneKernelGpu(int64_t step)
+ {
+ const bool stepIsEven = (pairlistSets().numStepsWithPairlist(step) % 2 == 0);
+
+ Nbnxm::gpu_launch_kernel_pruneonly(gpu_nbv,
+ stepIsEven ? Nbnxm::InteractionLocality::Local : Nbnxm::InteractionLocality::NonLocal,
+ pairlistSets().params().numRollingPruningParts);
+ }
//! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
void dispatchNonbondedKernel(Nbnxm::InteractionLocality iLocality,
const bool haveMultipleDomains = (DOMAINDECOMP(cr) && cr->dd->nnodes > 1);
- NbnxnListParameters listParams(nbv->kernelSetup().kernelType, ir->rlist);
+ NbnxnListParameters listParams(nbv->kernelSetup().kernelType,
+ ir->rlist,
+ havePPDomainDecomposition(cr));
setupDynamicPairlistPruning(mdlog, ir, mtop, box, fr->ic,
&listParams);
const interaction_const_t *ic,
NbnxnListParameters *listParams)
{
+ listParams->lifetime = ir->nstlist - 1;
+
/* When nstlistPrune was set by the user, we need to execute one loop
* iteration to determine rlistInner.
* Otherwise we compute rlistInner and increase nstlist as long as
*/
listParams->useDynamicPruning =
(listParams->rlistInner + rlistInc < 0.99*(listParams->rlistOuter + rlistInc) &&
- listParams->nstlistPrune < ir->nstlist - 1);
+ listParams->nstlistPrune < listParams->lifetime);
}
if (!listParams->useDynamicPruning)
( "With dynamic list pruning on GPUs pruning frequency must be at least as large as the rolling pruning interval (" +
std::to_string(c_nbnxnGpuRollingListPruningInterval) +
").").c_str() );
- listParams->numRollingParts = listParams->nstlistPrune/c_nbnxnGpuRollingListPruningInterval;
+ listParams->numRollingPruningParts = listParams->nstlistPrune/c_nbnxnGpuRollingListPruningInterval;
}
else
{
- listParams->numRollingParts = 1;
+ listParams->numRollingPruningParts = 1;
}
}
{
mesg += gmx::formatString("Using a dual %dx%d pair-list setup updated with dynamic%s pruning:\n",
ls.cluster_size_i, ls.cluster_size_j,
- listParams->numRollingParts > 1 ? ", rolling" : "");
+ listParams->numRollingPruningParts > 1 ? ", rolling" : "");
mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, listParams->rlistInner, interactionCutoff);
}
/*! \cond INTERNAL */
NbnxnListParameters::NbnxnListParameters(const Nbnxm::KernelType kernelType,
- const real rlist) :
- useDynamicPruning(false),
- nstlistPrune(-1),
+ const real rlist,
+ const bool haveMultipleDomains) :
rlistOuter(rlist),
rlistInner(rlist),
- numRollingParts(1)
+ haveMultipleDomains(haveMultipleDomains),
+ useDynamicPruning(false),
+ nstlistPrune(-1),
+ numRollingPruningParts(1),
+ lifetime(-1)
{
if (!Nbnxm::kernelTypeUsesSimplePairlist(kernelType))
{
}
void
-nonbonded_verlet_t::dispatchPruneKernel(const Nbnxm::InteractionLocality iLocality,
- const rvec *shift_vec)
+nonbonded_verlet_t::dispatchPruneKernelCpu(const Nbnxm::InteractionLocality iLocality,
+ const rvec *shift_vec)
{
pairlistSets_->dispatchPruneKernel(iLocality, nbat, shift_vec, kernelSetup_.kernelType);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff