gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t &dd)
{
GMX_RELEASE_ASSERT(dd.comm, "Need a valid dd.comm");
- return dd.comm->updateGroupingPerMoleculetype;
+ return dd.comm->systemInfo.updateGroupingPerMoleculetype;
}
void dd_store_state(gmx_domdec_t *dd, t_state *state)
static void setupUpdateGroups(const gmx::MDLogger &mdlog,
const gmx_mtop_t &mtop,
const t_inputrec &inputrec,
- real cutoffMargin,
- int numMpiRanksTotal,
- gmx_domdec_comm_t *comm)
+ const real cutoffMargin,
+ DDSystemInfo *systemInfo)
{
/* When we have constraints and/or vsites, it is beneficial to use
* update groups (when possible) to allow independent update of groups.
return;
}
- comm->updateGroupingPerMoleculetype = gmx::makeUpdateGroups(mtop);
- comm->useUpdateGroups =
- (!comm->updateGroupingPerMoleculetype.empty() &&
+ systemInfo->updateGroupingPerMoleculetype = gmx::makeUpdateGroups(mtop);
+ systemInfo->useUpdateGroups =
+ (!systemInfo->updateGroupingPerMoleculetype.empty() &&
getenv("GMX_NO_UPDATEGROUPS") == nullptr);
- if (comm->useUpdateGroups)
+ if (systemInfo->useUpdateGroups)
{
int numUpdateGroups = 0;
for (const auto &molblock : mtop.molblock)
{
- numUpdateGroups += molblock.nmol*comm->updateGroupingPerMoleculetype[molblock.type].numBlocks();
+ numUpdateGroups += molblock.nmol*systemInfo->updateGroupingPerMoleculetype[molblock.type].numBlocks();
}
- /* Note: We would like to use dd->nnodes for the atom count estimate,
- * but that is not yet available here. But this anyhow only
- * affect performance up to the second dd_partition_system call.
- */
- int homeAtomCountEstimate = mtop.natoms/numMpiRanksTotal;
- comm->updateGroupsCog =
- std::make_unique<gmx::UpdateGroupsCog>(mtop,
- comm->updateGroupingPerMoleculetype,
- maxReferenceTemperature(inputrec),
- homeAtomCountEstimate);
+ systemInfo->maxUpdateGroupRadius =
+ computeMaxUpdateGroupRadius(mtop,
+ systemInfo->updateGroupingPerMoleculetype,
+ maxReferenceTemperature(inputrec));
/* To use update groups, the large domain-to-domain cutoff distance
* should be compatible with the box size.
*/
- comm->useUpdateGroups = (atomToAtomIntoDomainToDomainCutoff(*comm, 0) < cutoffMargin);
+ systemInfo->useUpdateGroups = (atomToAtomIntoDomainToDomainCutoff(*systemInfo, 0) < cutoffMargin);
- if (comm->useUpdateGroups)
+ if (systemInfo->useUpdateGroups)
{
GMX_LOG(mdlog.info).appendTextFormatted(
"Using update groups, nr %d, average size %.1f atoms, max. radius %.3f nm\n",
numUpdateGroups,
mtop.natoms/static_cast<double>(numUpdateGroups),
- comm->updateGroupsCog->maxUpdateGroupRadius());
+ systemInfo->maxUpdateGroupRadius);
}
else
{
GMX_LOG(mdlog.info).appendTextFormatted("The combination of rlist and box size prohibits the use of update groups\n");
- comm->updateGroupingPerMoleculetype.clear();
- comm->updateGroupsCog.reset(nullptr);
+ systemInfo->updateGroupingPerMoleculetype.clear();
}
}
}
/* Allocate the charge group/atom sorting struct */
comm->sort = std::make_unique<gmx_domdec_sort_t>();
+ /* Generate the simulation system information */
+ DDSystemInfo &systemInfo = comm->systemInfo;
+
/* We need to decide on update groups early, as this affects communication distances */
- comm->useUpdateGroups = false;
+ systemInfo.useUpdateGroups = false;
if (ir->cutoff_scheme == ecutsVERLET)
{
real cutoffMargin = std::sqrt(max_cutoff2(ir->ePBC, box)) - ir->rlist;
- setupUpdateGroups(mdlog, *mtop, *ir, cutoffMargin, cr->nnodes, comm);
- }
+ setupUpdateGroups(mdlog, *mtop, *ir, cutoffMargin, &systemInfo);
- DDSystemInfo &systemInfo = comm->systemInfo;
+ if (systemInfo.useUpdateGroups)
+ {
+ /* Note: We would like to use dd->nnodes for the atom count estimate,
+ * but that is not yet available here. But this anyhow only
+ * affect performance up to the second dd_partition_system call.
+ */
+ const int homeAtomCountEstimate = mtop->natoms/cr->nnodes;
+ comm->updateGroupsCog =
+ std::make_unique<gmx::UpdateGroupsCog>(*mtop,
+ systemInfo.updateGroupingPerMoleculetype,
+ maxReferenceTemperature(*ir),
+ homeAtomCountEstimate);
+ }
+ }
// TODO: Check whether all bondeds are within update groups
systemInfo.haveInterDomainBondeds = (mtop->natoms > gmx_mtop_num_molecules(*mtop) ||
mtop->bIntermolecularInteractions);
systemInfo.haveInterDomainMultiBodyBondeds = (multi_body_bondeds_count(mtop) > 0);
- if (comm->useUpdateGroups)
+ if (systemInfo.useUpdateGroups)
{
dd->splitConstraints = false;
dd->splitSettles = false;
}
else
{
- systemInfo.cutoff = atomToAtomIntoDomainToDomainCutoff(*comm, ir->rlist);
+ systemInfo.cutoff = atomToAtomIntoDomainToDomainCutoff(systemInfo, ir->rlist);
}
systemInfo.minCutoffForMultiBody = 0;
constexpr real c_chanceThatAtomMovesBeyondDomain = 1e-12;
const real limitForAtomDisplacement =
minCellSizeForAtomDisplacement(*mtop, *ir,
- comm->updateGroupingPerMoleculetype,
+ systemInfo.updateGroupingPerMoleculetype,
c_chanceThatAtomMovesBeyondDomain);
GMX_LOG(mdlog.info).appendTextFormatted(
"Minimum cell size due to atom displacement: %.3f nm",
if (options.minimumCommunicationRange > 0)
{
systemInfo.minCutoffForMultiBody =
- atomToAtomIntoDomainToDomainCutoff(*comm, options.minimumCommunicationRange);
+ atomToAtomIntoDomainToDomainCutoff(systemInfo, options.minimumCommunicationRange);
if (options.useBondedCommunication)
{
comm->bBondComm = (systemInfo.minCutoffForMultiBody > systemInfo.cutoff);
}
const bool haveInterDomainVsites =
- (countInterUpdategroupVsites(*mtop, comm->updateGroupingPerMoleculetype) != 0);
+ (countInterUpdategroupVsites(*mtop, comm->systemInfo.updateGroupingPerMoleculetype) != 0);
if (comm->systemInfo.haveInterDomainBondeds ||
haveInterDomainVsites ||
dd->splitConstraints || dd->splitSettles)
{
std::string decompUnits;
- if (comm->useUpdateGroups)
+ if (comm->systemInfo.useUpdateGroups)
{
decompUnits = "atom groups";
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff