*
* \param [in] ir The input parameter record
*/
-static bool supportsDynamicPairlistGenerationInterval(const t_inputrec &ir)
+static bool supportsDynamicPairlistGenerationInterval(const t_inputrec& ir)
{
- return
- ir.cutoff_scheme == ecutsVERLET &&
- EI_DYNAMICS(ir.eI) &&
- !(EI_MD(ir.eI) && ir.etc == etcNO) &&
- ir.verletbuf_tol > 0;
+ return ir.cutoff_scheme == ecutsVERLET && EI_DYNAMICS(ir.eI)
+ && !(EI_MD(ir.eI) && ir.etc == etcNO) && ir.verletbuf_tol > 0;
}
/*! \brief Cost of non-bonded kernels
* We determine the extra cost of the non-bonded kernels compared to
* a reference nstlist value of 10 (which is the default in grompp).
*/
-static const int nbnxnReferenceNstlist = 10;
+static const int nbnxnReferenceNstlist = 10;
//! The values to try when switching
-const int nstlist_try[] = { 20, 25, 40, 50, 80, 100 };
+const int nstlist_try[] = { 20, 25, 40, 50, 80, 100 };
//! Number of elements in the neighborsearch list trials.
-#define NNSTL (sizeof(nstlist_try)/sizeof(nstlist_try[0]))
+#define NNSTL (sizeof(nstlist_try) / sizeof(nstlist_try[0]))
/* Increase nstlist until the size of the pair-list increased by
* \p c_nbnxnListSizeFactor??? or more, but never more than
* \p c_nbnxnListSizeFactor??? + \p c_nbnxnListSizeFactorMargin.
*/
// CPU: pair-search is a factor ~1.5 slower than the non-bonded kernel.
//! Target pair-list size increase ratio for CPU
-static const float c_nbnxnListSizeFactorCpu = 1.25;
+static const float c_nbnxnListSizeFactorCpu = 1.25;
// Intel KNL: pair-search is a factor ~2-3 slower than the non-bonded kernel.
//! Target pair-list size increase ratio for Intel KNL
-static const float c_nbnxnListSizeFactorIntelXeonPhi = 1.4;
+static const float c_nbnxnListSizeFactorIntelXeonPhi = 1.4;
// GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel.
//! Target pair-list size increase ratio for GPU
-static const float c_nbnxnListSizeFactorGPU = 1.4;
+static const float c_nbnxnListSizeFactorGPU = 1.4;
//! Never increase the size of the pair-list more than the factor above plus this margin
-static const float c_nbnxnListSizeFactorMargin = 0.1;
-
-void increaseNstlist(FILE *fp, t_commrec *cr,
- t_inputrec *ir, int nstlist_cmdline,
- const gmx_mtop_t *mtop,
- const matrix box,
- bool useOrEmulateGpuForNonbondeds,
- const gmx::CpuInfo &cpuinfo)
+static const float c_nbnxnListSizeFactorMargin = 0.1;
+
+void increaseNstlist(FILE* fp,
+ t_commrec* cr,
+ t_inputrec* ir,
+ int nstlist_cmdline,
+ const gmx_mtop_t* mtop,
+ const matrix box,
+ bool useOrEmulateGpuForNonbondeds,
+ const gmx::CpuInfo& cpuinfo)
{
if (!EI_DYNAMICS(ir->eI))
{
return;
}
- float listfac_ok, listfac_max;
- int nstlist_orig, nstlist_prev;
- real rlist_inc, rlist_ok, rlist_max;
- real rlist_new, rlist_prev;
- size_t nstlist_ind = 0;
- gmx_bool bBox, bDD, bCont;
- const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
- const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
- const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
- const char *box_err = "Can not increase nstlist because the box is too small";
- const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
- char buf[STRLEN];
+ float listfac_ok, listfac_max;
+ int nstlist_orig, nstlist_prev;
+ real rlist_inc, rlist_ok, rlist_max;
+ real rlist_new, rlist_prev;
+ size_t nstlist_ind = 0;
+ gmx_bool bBox, bDD, bCont;
+ const char* nstl_gpu =
+ "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe "
+ "optimum depends on your CPU and GPU resources.\nYou might want to try several "
+ "nstlist values.\n";
+ const char* nve_err = "Can not increase nstlist because an NVE ensemble is used";
+ const char* vbd_err =
+ "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
+ const char* box_err = "Can not increase nstlist because the box is too small";
+ const char* dd_err = "Can not increase nstlist because of domain decomposition limitations";
+ char buf[STRLEN];
if (nstlist_cmdline <= 0)
{
}
/* With a GPU and fixed nstlist suggest tuning nstlist */
- if (fp != nullptr &&
- useOrEmulateGpuForNonbondeds &&
- ir->nstlist < nstlist_try[0] &&
- !supportsDynamicPairlistGenerationInterval(*ir))
+ if (fp != nullptr && useOrEmulateGpuForNonbondeds && ir->nstlist < nstlist_try[0]
+ && !supportsDynamicPairlistGenerationInterval(*ir))
{
fprintf(fp, nstl_gpu, ir->nstlist);
}
if (ir->verletbuf_tol == 0 && useOrEmulateGpuForNonbondeds)
{
- gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
+ gmx_fatal(FARGS,
+ "You are using an old tpr file with a GPU, please generate a new tpr file with "
+ "an up to date version of grompp");
}
if (ir->verletbuf_tol < 0)
return;
}
- GMX_RELEASE_ASSERT(supportsDynamicPairlistGenerationInterval(*ir), "In all cases that do not support dynamic nstlist, we should have returned with an appropriate message above");
+ GMX_RELEASE_ASSERT(supportsDynamicPairlistGenerationInterval(*ir),
+ "In all cases that do not support dynamic nstlist, we should have returned "
+ "with an appropriate message above");
if (useOrEmulateGpuForNonbondeds)
{
- listfac_ok = c_nbnxnListSizeFactorGPU;
+ listfac_ok = c_nbnxnListSizeFactorGPU;
}
else if (cpuinfo.brandString().find("Xeon Phi") != std::string::npos)
{
- listfac_ok = c_nbnxnListSizeFactorIntelXeonPhi;
+ listfac_ok = c_nbnxnListSizeFactorIntelXeonPhi;
}
else
{
- listfac_ok = c_nbnxnListSizeFactorCpu;
+ listfac_ok = c_nbnxnListSizeFactorCpu;
}
- listfac_max = listfac_ok + c_nbnxnListSizeFactorMargin;
+ listfac_max = listfac_ok + c_nbnxnListSizeFactorMargin;
- nstlist_orig = ir->nstlist;
+ nstlist_orig = ir->nstlist;
if (nstlist_cmdline > 0)
{
if (fp)
{
- sprintf(buf, "Getting nstlist=%d from command line option",
- nstlist_cmdline);
+ sprintf(buf, "Getting nstlist=%d from command line option", nstlist_cmdline);
}
ir->nstlist = nstlist_cmdline;
}
- ListSetupType listType = (useOrEmulateGpuForNonbondeds ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
+ ListSetupType listType =
+ (useOrEmulateGpuForNonbondeds ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
/* Allow rlist to make the list a given factor larger than the list
nstlist_prev = ir->nstlist;
ir->nstlist = nbnxnReferenceNstlist;
const real rlistWithReferenceNstlist =
- calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
- -1, listSetup);
- ir->nstlist = nstlist_prev;
+ calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
+ ir->nstlist = nstlist_prev;
/* Determine the pair list size increase due to zero interactions */
- rlist_inc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j,
- mtop->natoms/det(box));
- rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_ok) - rlist_inc;
- rlist_max = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_max) - rlist_inc;
+ rlist_inc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j, mtop->natoms / det(box));
+ rlist_ok = (rlistWithReferenceNstlist + rlist_inc) * std::cbrt(listfac_ok) - rlist_inc;
+ rlist_max = (rlistWithReferenceNstlist + rlist_inc) * std::cbrt(listfac_max) - rlist_inc;
if (debug)
{
- fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
- rlist_inc, rlist_ok, rlist_max);
+ fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n", rlist_inc,
+ rlist_ok, rlist_max);
}
nstlist_prev = nstlist_orig;
}
/* Set the pair-list buffer size in ir */
- rlist_new =
- calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
+ rlist_new = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
/* Does rlist fit in the box? */
bBox = (gmx::square(rlist_new) < max_cutoff2(ir->ePBC, box));
/* Check if rlist fits in the domain decomposition */
if (inputrec2nboundeddim(ir) < DIM)
{
- gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
+ gmx_incons(
+ "Changing nstlist with domain decomposition and unbounded dimensions is "
+ "not implemented yet");
}
bDD = change_dd_cutoff(cr, box, gmx::ArrayRef<const gmx::RVec>(), rlist_new);
}
if (debug)
{
- fprintf(debug, "nstlist %d rlist %.3f bBox %s bDD %s\n",
- ir->nstlist, rlist_new, gmx::boolToString(bBox), gmx::boolToString(bDD));
+ fprintf(debug, "nstlist %d rlist %.3f bBox %s bDD %s\n", ir->nstlist, rlist_new,
+ gmx::boolToString(bBox), gmx::boolToString(bDD));
}
bCont = FALSE;
/* Increase nstlist */
nstlist_prev = ir->nstlist;
rlist_prev = rlist_new;
- bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
+ bCont = (nstlist_ind + 1 < NNSTL && rlist_new < rlist_ok);
}
else
{
}
nstlist_ind++;
- }
- while (bCont);
+ } while (bCont);
if (!bBox || !bDD)
{
}
else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
{
- sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
- nstlist_orig, ir->nstlist,
- ir->rlist, rlist_new);
+ sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g", nstlist_orig,
+ ir->nstlist, ir->rlist, rlist_new);
if (MASTER(cr))
{
fprintf(stderr, "%s\n\n", buf);
{
fprintf(fp, "%s\n\n", buf);
}
- ir->rlist = rlist_new;
+ ir->rlist = rlist_new;
}
}
* \param[in] ic The nonbonded interactions constants
* \param[in,out] listParams The list setup parameters
*/
-static void
-setDynamicPairlistPruningParameters(const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- const matrix box,
- const bool useGpuList,
- const VerletbufListSetup &listSetup,
- const bool userSetNstlistPrune,
- const interaction_const_t *ic,
- PairlistParams *listParams)
+static void setDynamicPairlistPruningParameters(const t_inputrec* ir,
+ const gmx_mtop_t* mtop,
+ const matrix box,
+ const bool useGpuList,
+ const VerletbufListSetup& listSetup,
+ const bool userSetNstlistPrune,
+ const interaction_const_t* ic,
+ PairlistParams* listParams)
{
listParams->lifetime = ir->nstlist - 1;
*/
int listLifetime = tunedNstlistPrune - (useGpuList ? 0 : 1);
listParams->nstlistPrune = tunedNstlistPrune;
- listParams->rlistInner =
- calcVerletBufferSize(*mtop, det(box), *ir,
- tunedNstlistPrune, listLifetime,
- -1, listSetup);
+ listParams->rlistInner = calcVerletBufferSize(*mtop, det(box), *ir, tunedNstlistPrune,
+ listLifetime, -1, listSetup);
/* On the GPU we apply the dynamic pruning in a rolling fashion
* every c_nbnxnGpuRollingListPruningInterval steps,
* so keep nstlistPrune a multiple of the interval.
*/
tunedNstlistPrune += useGpuList ? c_nbnxnGpuRollingListPruningInterval : 1;
- }
- while (!userSetNstlistPrune &&
- tunedNstlistPrune < ir->nstlist &&
- listParams->rlistInner == interactionCutoff);
+ } while (!userSetNstlistPrune && tunedNstlistPrune < ir->nstlist
+ && listParams->rlistInner == interactionCutoff);
if (userSetNstlistPrune)
{
else
{
/* Determine the pair list size increase due to zero interactions */
- real rlistInc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j,
- mtop->natoms/det(box));
+ real rlistInc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j, mtop->natoms / det(box));
/* Dynamic pruning is only useful when the inner list is smaller than
* the outer. The factor 0.99 ensures at least 3% list size reduction.
* Note that in such cases the first sub-condition is likely also false.
*/
listParams->useDynamicPruning =
- (listParams->rlistInner + rlistInc < 0.99*(listParams->rlistOuter + rlistInc) &&
- listParams->nstlistPrune < listParams->lifetime);
+ (listParams->rlistInner + rlistInc < 0.99 * (listParams->rlistOuter + rlistInc)
+ && listParams->nstlistPrune < listParams->lifetime);
}
if (!listParams->useDynamicPruning)
{
/* These parameters should not be used, but set them to useful values */
- listParams->nstlistPrune = -1;
- listParams->rlistInner = listParams->rlistOuter;
+ listParams->nstlistPrune = -1;
+ listParams->rlistInner = listParams->rlistOuter;
}
}
* \param[in] rList List cut-off radius
* \param[in] interactionCutoff The interaction cut-off, use for printing the list buffer size
*/
-static std::string formatListSetup(const std::string &listName,
+static std::string formatListSetup(const std::string& listName,
int nstList,
int nstListForSpacing,
real rList,
}
listSetup += "updated every ";
// Make the shortest int format string that fits nstListForSpacing
- std::string nstListFormat = "%" + gmx::formatString("%zu", gmx::formatString("%d", nstListForSpacing).size()) + "d";
+ std::string nstListFormat =
+ "%" + gmx::formatString("%zu", gmx::formatString("%d", nstListForSpacing).size()) + "d";
listSetup += gmx::formatString(nstListFormat.c_str(), nstList);
listSetup += gmx::formatString(" steps, buffer %.3f nm, rlist %.3f nm\n",
rList - interactionCutoff, rList);
return listSetup;
}
-void setupDynamicPairlistPruning(const gmx::MDLogger &mdlog,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
+void setupDynamicPairlistPruning(const gmx::MDLogger& mdlog,
+ const t_inputrec* ir,
+ const gmx_mtop_t* mtop,
matrix box,
- const interaction_const_t *ic,
- PairlistParams *listParams)
+ const interaction_const_t* ic,
+ PairlistParams* listParams)
{
GMX_RELEASE_ASSERT(listParams->rlistOuter > 0, "With the nbnxn setup rlist should be > 0");
/* Initialize the parameters to no dynamic list pruning */
listParams->useDynamicPruning = false;
- const VerletbufListSetup ls =
- {
- IClusterSizePerListType[listParams->pairlistType],
- JClusterSizePerListType[listParams->pairlistType]
- };
+ const VerletbufListSetup ls = { IClusterSizePerListType[listParams->pairlistType],
+ JClusterSizePerListType[listParams->pairlistType] };
/* Currently emulation mode does not support dual pair-lists */
- const bool useGpuList = (listParams->pairlistType == PairlistType::HierarchicalNxN);
+ const bool useGpuList = (listParams->pairlistType == PairlistType::HierarchicalNxN);
- if (supportsDynamicPairlistGenerationInterval(*ir) &&
- getenv("GMX_DISABLE_DYNAMICPRUNING") == nullptr)
+ if (supportsDynamicPairlistGenerationInterval(*ir) && getenv("GMX_DISABLE_DYNAMICPRUNING") == nullptr)
{
/* Note that nstlistPrune can have any value independently of nstlist.
* Actually applying rolling pruning is only useful when
* nstlistPrune < nstlist -1
*/
- char *env = getenv("GMX_NSTLIST_DYNAMICPRUNING");
+ char* env = getenv("GMX_NSTLIST_DYNAMICPRUNING");
bool userSetNstlistPrune = (env != nullptr);
if (userSetNstlistPrune)
{
- char *end;
+ char* end;
listParams->nstlistPrune = strtol(env, &end, 10);
- if (!end || (*end != 0) ||
- !(listParams->nstlistPrune > 0 && listParams->nstlistPrune < ir->nstlist))
+ if (!end || (*end != 0)
+ || !(listParams->nstlistPrune > 0 && listParams->nstlistPrune < ir->nstlist))
{
- gmx_fatal(FARGS, "Invalid value passed in GMX_NSTLIST_DYNAMICPRUNING=%s, should be > 0 and < nstlist", env);
+ gmx_fatal(FARGS,
+ "Invalid value passed in GMX_NSTLIST_DYNAMICPRUNING=%s, should be > 0 "
+ "and < nstlist",
+ env);
}
}
else
{
static_assert(c_nbnxnDynamicListPruningMinLifetime % c_nbnxnGpuRollingListPruningInterval == 0,
- "c_nbnxnDynamicListPruningMinLifetime sets the starting value for nstlistPrune, which should be divisible by the rolling pruning interval for efficiency reasons.");
+ "c_nbnxnDynamicListPruningMinLifetime sets the starting value for "
+ "nstlistPrune, which should be divisible by the rolling pruning interval "
+ "for efficiency reasons.");
// TODO: Use auto-tuning to determine nstlistPrune
listParams->nstlistPrune = c_nbnxnDynamicListPruningMinLifetime;
}
- setDynamicPairlistPruningParameters(ir, mtop, box, useGpuList, ls,
- userSetNstlistPrune, ic,
+ setDynamicPairlistPruningParameters(ir, mtop, box, useGpuList, ls, userSetNstlistPrune, ic,
listParams);
if (listParams->useDynamicPruning && useGpuList)
* rolling pruning interval slightly shorter than nstlistTune,
* thus giving correct results, but a slightly lower efficiency.
*/
- GMX_RELEASE_ASSERT(listParams->nstlistPrune >= c_nbnxnGpuRollingListPruningInterval,
- ( "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->numRollingPruningParts = listParams->nstlistPrune/c_nbnxnGpuRollingListPruningInterval;
+ GMX_RELEASE_ASSERT(listParams->nstlistPrune >= c_nbnxnGpuRollingListPruningInterval, ("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->numRollingPruningParts =
+ listParams->nstlistPrune / c_nbnxnGpuRollingListPruningInterval;
}
else
{
std::string mesg;
- const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
+ const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
if (listParams->useDynamicPruning)
{
- 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->numRollingPruningParts > 1 ? ", rolling" : "");
+ 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->numRollingPruningParts > 1 ? ", rolling" : "");
mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
- mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, listParams->rlistInner, interactionCutoff);
+ mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist,
+ listParams->rlistInner, interactionCutoff);
}
else
{
- mesg += gmx::formatString("Using a %dx%d pair-list setup:\n",
- ls.cluster_size_i, ls.cluster_size_j);
+ mesg += gmx::formatString("Using a %dx%d pair-list setup:\n", ls.cluster_size_i, ls.cluster_size_j);
mesg += formatListSetup("", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
}
if (supportsDynamicPairlistGenerationInterval(*ir))
{
const VerletbufListSetup listSetup1x1 = { 1, 1 };
- const real rlistOuter =
- calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
- -1, listSetup1x1);
- real rlistInner = rlistOuter;
+ const real rlistOuter = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist,
+ ir->nstlist - 1, -1, listSetup1x1);
+ real rlistInner = rlistOuter;
if (listParams->useDynamicPruning)
{
int listLifeTime = listParams->nstlistPrune - (useGpuList ? 0 : 1);
- rlistInner =
- calcVerletBufferSize(*mtop, det(box), *ir, listParams->nstlistPrune, listLifeTime,
- -1, listSetup1x1);
+ rlistInner = calcVerletBufferSize(*mtop, det(box), *ir, listParams->nstlistPrune,
+ listLifeTime, -1, listSetup1x1);
}
- mesg += gmx::formatString("At tolerance %g kJ/mol/ps per atom, equivalent classical 1x1 list would be:\n",
- ir->verletbuf_tol);
+ mesg += gmx::formatString(
+ "At tolerance %g kJ/mol/ps per atom, equivalent classical 1x1 list would be:\n",
+ ir->verletbuf_tol);
if (listParams->useDynamicPruning)
{
mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, rlistOuter, interactionCutoff);
- mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, rlistInner, interactionCutoff);
+ mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, rlistInner,
+ interactionCutoff);
}
else
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff