#include <algorithm>
#include <memory>
+#include <optional>
#include <string>
#include "gromacs/domdec/domdec.h"
InteractionDefinitions idef; /**< Partial local topology */
std::unique_ptr<gmx::VsitePbc> vsitePbc = nullptr; /**< vsite PBC structure */
- int nbonded = 0; /**< The number of bondeds in this struct */
- ListOfLists<int> excl; /**< List of exclusions */
- int excl_count = 0; /**< The total exclusion count for \p excl */
+ int numBondedInteractions = 0; /**< The number of bonded interactions observed */
+ ListOfLists<int> excl; /**< List of exclusions */
+ int excl_count = 0; /**< The total exclusion count for \p excl */
};
/*! \brief Options for setting up gmx_reverse_top_t */
//! \brief Intermolecular reverse ilist
reverse_ilist_t ril_intermol;
- //! The interaction count for the interactions that have to be present
- int numInteractionsToCheck;
+ /*! \brief Data to help check reverse topology construction
+ *
+ * Partitioning could incorrectly miss a bonded interaction.
+ * However, checking for that requires a global communication
+ * stage, which does not otherwise happen during partitioning. So,
+ * for performance, we do that alongside the first global energy
+ * reduction after a new DD is made. These variables handle
+ * whether the check happens, its input for this domain, output
+ * across all domains, and the expected value it should match. */
+ /*! \{ */
+ /*! \brief Number of bonded interactions found in the reverse
+ * topology for this domain. */
+ int numBondedInteractions = 0;
+ /*! \brief Whether to check at the next global communication
+ * stage the total number of bonded interactions found.
+ *
+ * Cleared after that number is found. */
+ bool shouldCheckNumberOfBondedInteractions = false;
+ /*! \brief The total number of bonded interactions found in
+ * the reverse topology across all domains.
+ *
+ * Only has a value after reduction across all ranks, which is
+ * removed when it is again time to check after a new
+ * partition. */
+ std::optional<int> numBondedInteractionsOverAllDomains;
+ //! The number of bonded interactions computed from the full topology
+ int expectedNumGlobalBondedInteractions = 0;
+ /*! \} */
/* Work data structures for multi-threading */
//! \brief Thread work array for local topology generation
}
}
-void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
- t_commrec* cr,
- int local_count,
- const gmx_mtop_t& top_global,
- const gmx_localtop_t* top_local,
+void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ int numBondedInteractionsOverAllDomains,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t* top_local,
gmx::ArrayRef<const gmx::RVec> x,
const matrix box)
{
"Not all bonded interactions have been properly assigned to the domain "
"decomposition cells");
- const int ndiff_tot = local_count - dd->nbonded_global;
+ const int ndiff_tot = numBondedInteractionsOverAllDomains
+ - dd->reverse_top->impl_->expectedNumGlobalBondedInteractions;
for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (DDMASTER(dd))
{
GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
- int rest_global = dd->nbonded_global;
- int rest_local = local_count;
+ int rest_global = dd->reverse_top->impl_->expectedNumGlobalBondedInteractions;
+ int rest = numBondedInteractionsOverAllDomains;
for (int ftype = 0; ftype < F_NRE; ftype++)
{
/* In the reverse and local top all constraints are merged
-ndiff);
}
rest_global -= n;
- rest_local -= cl[ftype];
+ rest -= cl[ftype];
}
}
- int ndiff = rest_local - rest_global;
+ int ndiff = rest - rest_global;
if (ndiff != 0)
{
GMX_LOG(mdlog.warning).appendTextFormatted("%20s of %6d missing %6d", "exclusions", rest_global, -ndiff);
"two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds "
"also see option -ddcheck",
-ndiff_tot,
- cr->dd->nbonded_global,
+ dd->reverse_top->impl_->expectedNumGlobalBondedInteractions,
dd_cutoff_multibody(dd),
dd_cutoff_twobody(dd));
}
fprintf(debug, "The total size of the atom to interaction index is %d integers\n", ril_mt_tot_size);
}
- numInteractionsToCheck = 0;
+ expectedNumGlobalBondedInteractions = 0;
for (const gmx_molblock_t& molblock : mtop.molblock)
{
- numInteractionsToCheck += molblock.nmol * nint_mt[molblock.type];
+ expectedNumGlobalBondedInteractions += molblock.nmol * nint_mt[molblock.type];
}
/* Make an intermolecular reverse top, if necessary */
GMX_RELEASE_ASSERT(mtop.intermolecular_ilist,
"We should have an ilist when intermolecular interactions are on");
- numInteractionsToCheck += make_reverse_ilist(
+ expectedNumGlobalBondedInteractions += make_reverse_ilist(
*mtop.intermolecular_ilist, &atoms_global, options, AtomLinkRule::FirstAtom, &ril_intermol);
}
dd->reverse_top = std::make_unique<gmx_reverse_top_t>(
mtop, inputrec.efep != FreeEnergyPerturbationType::No, rtOptions);
- dd->nbonded_global = dd->reverse_top->impl_->numInteractionsToCheck;
-
dd->haveExclusions = false;
for (const gmx_molblock_t& molb : mtop.molblock)
{
}
}
-/*! \brief Check and when available assign bonded interactions for local atom i
+/*! \brief Determine whether the local domain has responsibility for
+ * any of the bonded interactions for local atom i
+ *
+ * \returns The total number of bonded interactions for this atom for
+ * which this domain is responsible.
*/
-static inline void check_assign_interactions_atom(int i,
- int i_gl,
- int mol,
- int i_mol,
- int numAtomsInMolecule,
- gmx::ArrayRef<const int> index,
- gmx::ArrayRef<const int> rtil,
- gmx_bool bInterMolInteractions,
- int ind_start,
- int ind_end,
- const gmx_ga2la_t& ga2la,
- const gmx_domdec_zones_t* zones,
- const gmx_molblock_t* molb,
- gmx_bool bRCheckMB,
- const ivec rcheck,
- gmx_bool bRCheck2B,
- real rc2,
- t_pbc* pbc_null,
- rvec* cg_cm,
- const t_iparams* ip_in,
- InteractionDefinitions* idef,
- int iz,
- const DDBondedChecking ddBondedChecking,
- int* nbonded_local)
+static inline int assign_interactions_atom(int i,
+ int i_gl,
+ int mol,
+ int i_mol,
+ int numAtomsInMolecule,
+ gmx::ArrayRef<const int> index,
+ gmx::ArrayRef<const int> rtil,
+ gmx_bool bInterMolInteractions,
+ int ind_start,
+ int ind_end,
+ const gmx_ga2la_t& ga2la,
+ const gmx_domdec_zones_t* zones,
+ const gmx_molblock_t* molb,
+ gmx_bool bRCheckMB,
+ const ivec rcheck,
+ gmx_bool bRCheck2B,
+ real rc2,
+ t_pbc* pbc_null,
+ rvec* cg_cm,
+ const t_iparams* ip_in,
+ InteractionDefinitions* idef,
+ int iz,
+ const DDBondedChecking ddBondedChecking)
{
gmx::ArrayRef<const DDPairInteractionRanges> iZones = zones->iZones;
+ int numBondedInteractions = 0;
+
int j = ind_start;
while (j < ind_end)
{
else
{
/* Assign this multi-body bonded interaction to
- * the local node if we have all the atoms involved
+ * the local domain if we have all the atoms involved
* (local or communicated) and the minimum zone shift
* in each dimension is zero, for dimensions
* with 2 DD cells an extra check may be necessary.
if (ddBondedChecking == DDBondedChecking::All
|| !(interaction_function[ftype].flags & IF_LIMZERO))
{
- (*nbonded_local)++;
+ numBondedInteractions++;
}
}
}
j += 1 + nral_rt(ftype);
}
+
+ return numBondedInteractions;
}
/*! \brief This function looks up and assigns bonded interactions for zone iz.
const auto ddBondedChecking = rt->impl_->options.ddBondedChecking;
- int nbonded_local = 0;
+ int numBondedInteractions = 0;
for (int i : atomRange)
{
gmx::ArrayRef<const int> index = rt->impl_->ril_mt[mt].index;
gmx::ArrayRef<const t_iatom> rtil = rt->impl_->ril_mt[mt].il;
- check_assign_interactions_atom(i,
- i_gl,
- mol,
- i_mol,
- rt->impl_->ril_mt[mt].numAtomsInMolecule,
- index,
- rtil,
- FALSE,
- index[i_mol],
- index[i_mol + 1],
- ga2la,
- zones,
- &molb[mb],
- bRCheckMB,
- rcheck,
- bRCheck2B,
- rc2,
- pbc_null,
- cg_cm,
- ip_in,
- idef,
- izone,
- ddBondedChecking,
- &nbonded_local);
+ numBondedInteractions += assign_interactions_atom(i,
+ i_gl,
+ mol,
+ i_mol,
+ rt->impl_->ril_mt[mt].numAtomsInMolecule,
+ index,
+ rtil,
+ FALSE,
+ index[i_mol],
+ index[i_mol + 1],
+ ga2la,
+ zones,
+ &molb[mb],
+ bRCheckMB,
+ rcheck,
+ bRCheck2B,
+ rc2,
+ pbc_null,
+ cg_cm,
+ ip_in,
+ idef,
+ izone,
+ ddBondedChecking);
if (rt->impl_->bIntermolecularInteractions)
index = rt->impl_->ril_intermol.index;
rtil = rt->impl_->ril_intermol.il;
- check_assign_interactions_atom(i,
- i_gl,
- mol,
- i_mol,
- rt->impl_->ril_mt[mt].numAtomsInMolecule,
- index,
- rtil,
- TRUE,
- index[i_gl],
- index[i_gl + 1],
- ga2la,
- zones,
- &molb[mb],
- bRCheckMB,
- rcheck,
- bRCheck2B,
- rc2,
- pbc_null,
- cg_cm,
- ip_in,
- idef,
- izone,
- ddBondedChecking,
- &nbonded_local);
+ numBondedInteractions += assign_interactions_atom(i,
+ i_gl,
+ mol,
+ i_mol,
+ rt->impl_->ril_mt[mt].numAtomsInMolecule,
+ index,
+ rtil,
+ TRUE,
+ index[i_gl],
+ index[i_gl + 1],
+ ga2la,
+ zones,
+ &molb[mb],
+ bRCheckMB,
+ rcheck,
+ bRCheck2B,
+ rc2,
+ pbc_null,
+ cg_cm,
+ ip_in,
+ idef,
+ izone,
+ ddBondedChecking);
}
}
- return nbonded_local;
+ return numBondedInteractions;
}
/*! \brief Set the exclusion data for i-zone \p iz */
}
/*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
-static int make_local_bondeds_excls(gmx_domdec_t* dd,
- gmx_domdec_zones_t* zones,
- const gmx_mtop_t& mtop,
- const int* cginfo,
- gmx_bool bRCheckMB,
- ivec rcheck,
- gmx_bool bRCheck2B,
- real rc,
- t_pbc* pbc_null,
- rvec* cg_cm,
- InteractionDefinitions* idef,
- ListOfLists<int>* lexcls,
- int* excl_count)
+static void make_local_bondeds_excls(gmx_domdec_t* dd,
+ gmx_domdec_zones_t* zones,
+ const gmx_mtop_t& mtop,
+ const int* cginfo,
+ gmx_bool bRCheckMB,
+ ivec rcheck,
+ gmx_bool bRCheck2B,
+ real rc,
+ t_pbc* pbc_null,
+ rvec* cg_cm,
+ InteractionDefinitions* idef,
+ ListOfLists<int>* lexcls,
+ int* excl_count)
{
int nzone_bondeds = 0;
/* Clear the counts */
idef->clear();
- int nbonded_local = 0;
+ dd->reverse_top->impl_->numBondedInteractions = 0;
lexcls->clear();
*excl_count = 0;
idef_t->clear();
}
- rt->impl_->th_work[thread].nbonded = make_bondeds_zone(rt,
- dd->globalAtomIndices,
- *dd->ga2la,
- zones,
- mtop.molblock,
- bRCheckMB,
- rcheck,
- bRCheck2B,
- rc2,
- pbc_null,
- cg_cm,
- idef->iparams.data(),
- idef_t,
- izone,
- gmx::Range<int>(cg0t, cg1t));
+ rt->impl_->th_work[thread].numBondedInteractions =
+ make_bondeds_zone(rt,
+ dd->globalAtomIndices,
+ *dd->ga2la,
+ zones,
+ mtop.molblock,
+ bRCheckMB,
+ rcheck,
+ bRCheck2B,
+ rc2,
+ pbc_null,
+ cg_cm,
+ idef->iparams.data(),
+ idef_t,
+ izone,
+ gmx::Range<int>(cg0t, cg1t));
if (izone < numIZonesForExclusions)
{
for (const thread_work_t& th_work : rt->impl_->th_work)
{
- nbonded_local += th_work.nbonded;
+ dd->reverse_top->impl_->numBondedInteractions += th_work.numBondedInteractions;
}
if (izone < numIZonesForExclusions)
}
}
+ // Note that it's possible for this to still be true from the last
+ // time it was set, e.g. if repartitioning was triggered before
+ // global communication that would have acted on the true
+ // value. This could happen for example when replica exchange took
+ // place soon after a partition.
+ dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions = true;
+ // Clear the old global value, which is now invalid
+ dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.reset();
+
if (debug)
{
fprintf(debug, "We have %d exclusions, check count %d\n", lexcls->numElements(), *excl_count);
}
+}
+
+bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd)
+{
+ return dd.reverse_top->impl_->shouldCheckNumberOfBondedInteractions;
+}
- return nbonded_local;
+int numBondedInteractions(const gmx_domdec_t& dd)
+{
+ return dd.reverse_top->impl_->numBondedInteractions;
+}
+
+void setNumberOfBondedInteractionsOverAllDomains(const gmx_domdec_t& dd, int newValue)
+{
+ GMX_RELEASE_ASSERT(!dd.reverse_top->impl_->numBondedInteractionsOverAllDomains.has_value(),
+ "Cannot set number of bonded interactions because it is already set");
+ dd.reverse_top->impl_->numBondedInteractionsOverAllDomains.emplace(newValue);
+}
+
+void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t* top_local,
+ gmx::ArrayRef<const gmx::RVec> x,
+ const matrix box)
+{
+ GMX_RELEASE_ASSERT(
+ DOMAINDECOMP(cr),
+ "No need to check number of bonded interactions when not using domain decomposition");
+ if (cr->dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions)
+ {
+ GMX_RELEASE_ASSERT(cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.has_value(),
+ "The check for the total number of bonded interactions requires the "
+ "value to have been reduced across all domains");
+ if (cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.value()
+ != cr->dd->reverse_top->impl_->expectedNumGlobalBondedInteractions)
+ {
+ dd_print_missing_interactions(
+ mdlog,
+ cr,
+ cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.value(),
+ top_global,
+ top_local,
+ x,
+ box); // Does not return
+ }
+ // Now that the value is set and the check complete, future
+ // global communication should not compute the value until
+ // after the next partitioning.
+ cr->dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions = false;
+ }
}
void dd_make_local_top(gmx_domdec_t* dd,
}
}
- dd->nbonded_local = make_local_bondeds_excls(dd,
- zones,
- mtop,
- fr->cginfo.data(),
- bRCheckMB,
- rcheck,
- bRCheck2B,
- rc,
- pbc_null,
- cgcm_or_x,
- <op->idef,
- <op->excls,
- &nexcl);
+ make_local_bondeds_excls(dd,
+ zones,
+ mtop,
+ fr->cginfo.data(),
+ bRCheckMB,
+ rcheck,
+ bRCheck2B,
+ rc,
+ pbc_null,
+ cgcm_or_x,
+ <op->idef,
+ <op->excls,
+ &nexcl);
/* The ilist is not sorted yet,
* we can only do this when we have the charge arrays.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff