/* In domdec_top.c */
-/*! \brief Print error output when interactions are missing */
-[[noreturn]] 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,
- gmx::ArrayRef<const gmx::RVec> x,
- const matrix box);
-
/*! \brief Generate and store the reverse topology */
void dd_make_reverse_top(FILE* fplog,
gmx_domdec_t* dd,
const t_inputrec& inputrec,
gmx::DDBondedChecking ddBondedChecking);
-/*! \brief Set that the number of bonded interactions in the local
- * topology should be checked via observables reduction. */
-void scheduleCheckOfLocalTopology(gmx_domdec_t* dd, int numBondedInteractionsToReduce);
-
-/*! \brief Return whether the total bonded interaction count across
- * domains should be checked this step. */
-bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd);
-
-//! Return the number of bonded interactions in this domain.
-int numBondedInteractions(const gmx_domdec_t& dd);
-
-/*! \brief Set total bonded interaction count across domains. */
-void setNumberOfBondedInteractionsOverAllDomains(const gmx_domdec_t& dd, int newValue);
-
-/*! \brief Check whether bonded interactions are missing from the reverse topology
- * produced by domain decomposition.
- *
- * Must only be called when DD is active.
- *
- * \param[in] mdlog Logger
- * \param[in] cr Communication object
- * \param[in] top_global Global topology for the error message
- * \param[in] top_local Local topology for the error message
- * \param[in] x Position vector for the error message
- * \param[in] box Box matrix for the error message
- */
-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);
-
/*! \brief Generate the local topology and virtual site data
*
* \returns Total count of bonded interactions in the local topology on this domain */
};
-/*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
-static int nral_rt(int ftype)
+int nral_rt(int ftype)
{
int nral = NRAL(ftype);
if (interaction_function[ftype].flags & IF_VSITE)
return nral;
}
-/*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
-static gmx_bool dd_check_ftype(const int ftype, const ReverseTopOptions rtOptions)
+bool dd_check_ftype(const int ftype, const ReverseTopOptions& rtOptions)
{
return ((((interaction_function[ftype].flags & IF_BOND) != 0U)
&& ((interaction_function[ftype].flags & IF_VSITE) == 0U)
|| (rtOptions.includeSettles && ftype == F_SETTLE));
}
-/*! \brief Checks whether interactions have been assigned for one function type
- *
- * Loops over a list of interactions in the local topology of one function type
- * and flags each of the interactions as assigned in the global \p isAssigned list.
- * Exits with an inconsistency error when an interaction is assigned more than once.
- */
-static void flagInteractionsForType(const int ftype,
- const InteractionList& il,
- const reverse_ilist_t& ril,
- const gmx::Range<int>& atomRange,
- const int numAtomsPerMolecule,
- gmx::ArrayRef<const int> globalAtomIndices,
- gmx::ArrayRef<int> isAssigned)
-{
- const int nril_mol = ril.index[numAtomsPerMolecule];
- const int nral = NRAL(ftype);
-
- for (int i = 0; i < il.size(); i += 1 + nral)
- {
- // ia[0] is the interaction type, ia[1, ...] the atom indices
- const int* ia = il.iatoms.data() + i;
- // Extract the global atom index of the first atom in this interaction
- const int a0 = globalAtomIndices[ia[1]];
- /* Check if this interaction is in
- * the currently checked molblock.
- */
- if (atomRange.isInRange(a0))
- {
- // The molecule index in the list of this molecule type
- const int moleculeIndex = (a0 - atomRange.begin()) / numAtomsPerMolecule;
- const int atomOffset = (a0 - atomRange.begin()) - moleculeIndex * numAtomsPerMolecule;
- const int globalAtomStartInMolecule = atomRange.begin() + moleculeIndex * numAtomsPerMolecule;
- int j_mol = ril.index[atomOffset];
- bool found = false;
- while (j_mol < ril.index[atomOffset + 1] && !found)
- {
- const int j = moleculeIndex * nril_mol + j_mol;
- const int ftype_j = ril.il[j_mol];
- /* Here we need to check if this interaction has
- * not already been assigned, since we could have
- * multiply defined interactions.
- */
- if (ftype == ftype_j && ia[0] == ril.il[j_mol + 1] && isAssigned[j] == 0)
- {
- /* Check the atoms */
- found = true;
- for (int a = 0; a < nral; a++)
- {
- if (globalAtomIndices[ia[1 + a]]
- != globalAtomStartInMolecule + ril.il[j_mol + 2 + a])
- {
- found = false;
- }
- }
- if (found)
- {
- isAssigned[j] = 1;
- }
- }
- j_mol += 2 + nral_rt(ftype_j);
- }
- if (!found)
- {
- gmx_incons("Some interactions seem to be assigned multiple times");
- }
- }
- }
-}
-
-/*! \brief Help print error output when interactions are missing in a molblock
- *
- * \note This function needs to be called on all ranks (contains a global summation)
- */
-static std::string printMissingInteractionsMolblock(t_commrec* cr,
- const gmx_reverse_top_t& rt,
- const char* moltypename,
- const reverse_ilist_t& ril,
- const gmx::Range<int>& atomRange,
- const int numAtomsPerMolecule,
- const int numMolecules,
- const InteractionDefinitions& idef)
-{
- const int nril_mol = ril.index[numAtomsPerMolecule];
- std::vector<int> isAssigned(numMolecules * nril_mol, 0);
- gmx::StringOutputStream stream;
- gmx::TextWriter log(&stream);
-
- for (int ftype = 0; ftype < F_NRE; ftype++)
- {
- if (dd_check_ftype(ftype, rt.options()))
- {
- flagInteractionsForType(
- ftype, idef.il[ftype], ril, atomRange, numAtomsPerMolecule, cr->dd->globalAtomIndices, isAssigned);
- }
- }
-
- gmx_sumi(isAssigned.size(), isAssigned.data(), cr);
-
- const int numMissingToPrint = 10;
- int i = 0;
- for (int mol = 0; mol < numMolecules; mol++)
- {
- int j_mol = 0;
- while (j_mol < nril_mol)
- {
- int ftype = ril.il[j_mol];
- int nral = NRAL(ftype);
- int j = mol * nril_mol + j_mol;
- if (isAssigned[j] == 0 && !(interaction_function[ftype].flags & IF_VSITE))
- {
- if (DDMASTER(cr->dd))
- {
- if (i == 0)
- {
- log.writeLineFormatted("Molecule type '%s'", moltypename);
- log.writeLineFormatted(
- "the first %d missing interactions, except for exclusions:",
- numMissingToPrint);
- }
- log.writeStringFormatted("%20s atoms", interaction_function[ftype].longname);
- int a = 0;
- for (; a < nral; a++)
- {
- log.writeStringFormatted("%5d", ril.il[j_mol + 2 + a] + 1);
- }
- while (a < 4)
- {
- log.writeString(" ");
- a++;
- }
- log.writeString(" global");
- for (int a = 0; a < nral; a++)
- {
- log.writeStringFormatted("%6d",
- atomRange.begin() + mol * numAtomsPerMolecule
- + ril.il[j_mol + 2 + a] + 1);
- }
- log.ensureLineBreak();
- }
- i++;
- if (i >= numMissingToPrint)
- {
- break;
- }
- }
- j_mol += 2 + nral_rt(ftype);
- }
- }
-
- return stream.toString();
-}
-
-/*! \brief Help print error output when interactions are missing */
-static void printMissingInteractionsAtoms(const gmx::MDLogger& mdlog,
- t_commrec* cr,
- const gmx_mtop_t& mtop,
- const InteractionDefinitions& idef)
-{
- const gmx_reverse_top_t& rt = *cr->dd->reverse_top;
-
- /* Print the atoms in the missing interactions per molblock */
- int a_end = 0;
- for (const gmx_molblock_t& molb : mtop.molblock)
- {
- const gmx_moltype_t& moltype = mtop.moltype[molb.type];
- const int a_start = a_end;
- a_end = a_start + molb.nmol * moltype.atoms.nr;
- const gmx::Range<int> atomRange(a_start, a_end);
-
- auto warning = printMissingInteractionsMolblock(cr,
- rt,
- *(moltype.name),
- rt.interactionListForMoleculeType(molb.type),
- atomRange,
- moltype.atoms.nr,
- molb.nmol,
- idef);
-
- GMX_LOG(mdlog.warning).appendText(warning);
- }
-}
-
-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)
-{
- int cl[F_NRE];
- gmx_domdec_t* dd = cr->dd;
-
- GMX_LOG(mdlog.warning)
- .appendText(
- "Not all bonded interactions have been properly assigned to the domain "
- "decomposition cells");
-
- const int ndiff_tot = numBondedInteractionsOverAllDomains
- - dd->reverse_top->expectedNumGlobalBondedInteractions();
-
- for (int ftype = 0; ftype < F_NRE; ftype++)
- {
- const int nral = NRAL(ftype);
- cl[ftype] = top_local->idef.il[ftype].size() / (1 + nral);
- }
-
- gmx_sumi(F_NRE, cl, cr);
-
- if (DDMASTER(dd))
- {
- GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
- int rest_global = dd->reverse_top->expectedNumGlobalBondedInteractions();
- int rest = numBondedInteractionsOverAllDomains;
- for (int ftype = 0; ftype < F_NRE; ftype++)
- {
- /* In the reverse and local top all constraints are merged
- * into F_CONSTR. So in the if statement we skip F_CONSTRNC
- * and add these constraints when doing F_CONSTR.
- */
- if (dd_check_ftype(ftype, dd->reverse_top->options()) && ftype != F_CONSTRNC)
- {
- int n = gmx_mtop_ftype_count(top_global, ftype);
- if (ftype == F_CONSTR)
- {
- n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
- }
- int ndiff = cl[ftype] - n;
- if (ndiff != 0)
- {
- GMX_LOG(mdlog.warning)
- .appendTextFormatted("%20s of %6d missing %6d",
- interaction_function[ftype].longname,
- n,
- -ndiff);
- }
- rest_global -= n;
- rest -= cl[ftype];
- }
- }
-
- int ndiff = rest - rest_global;
- if (ndiff != 0)
- {
- GMX_LOG(mdlog.warning).appendTextFormatted("%20s of %6d missing %6d", "exclusions", rest_global, -ndiff);
- }
- }
-
- printMissingInteractionsAtoms(mdlog, cr, top_global, top_local->idef);
- write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr, -1, as_rvec_array(x.data()), box);
-
- std::string errorMessage;
-
- if (ndiff_tot > 0)
- {
- errorMessage =
- "One or more interactions were assigned to multiple domains of the domain "
- "decompostion. Please report this bug.";
- }
- else
- {
- errorMessage = gmx::formatString(
- "%d of the %d bonded interactions could not be calculated because some atoms "
- "involved moved further apart than the multi-body cut-off distance (%g nm) or the "
- "two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds "
- "also see option -ddcheck",
- -ndiff_tot,
- dd->reverse_top->expectedNumGlobalBondedInteractions(),
- dd_cutoff_multibody(dd),
- dd_cutoff_twobody(dd));
- }
- gmx_fatal_collective(FARGS, cr->mpi_comm_mygroup, MASTER(cr), "%s", errorMessage.c_str());
-}
-
/*! \brief Return global topology molecule information for global atom index \p i_gl */
static void global_atomnr_to_moltype_ind(ArrayRef<const MolblockIndices> molblockIndices,
int i_gl,
return numBondedInteractions;
}
-void scheduleCheckOfLocalTopology(gmx_domdec_t* dd, const int numBondedInteractionsToReduce)
-{
- dd->localTopologyChecker->numBondedInteractionsToReduce = numBondedInteractionsToReduce;
- // 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->localTopologyChecker->shouldCheckNumberOfBondedInteractions = true;
- // Clear the old global value, which is now invalid
- dd->localTopologyChecker->numBondedInteractionsOverAllDomains.reset();
-}
-
-bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd)
-{
- return dd.localTopologyChecker->shouldCheckNumberOfBondedInteractions;
-}
-
-int numBondedInteractions(const gmx_domdec_t& dd)
-{
- return dd.localTopologyChecker->numBondedInteractionsToReduce;
-}
-
-void setNumberOfBondedInteractionsOverAllDomains(const gmx_domdec_t& dd, int newValue)
-{
- GMX_RELEASE_ASSERT(!dd.localTopologyChecker->numBondedInteractionsOverAllDomains.has_value(),
- "Cannot set number of bonded interactions because it is already set");
- dd.localTopologyChecker->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->localTopologyChecker->shouldCheckNumberOfBondedInteractions)
- {
- GMX_RELEASE_ASSERT(cr->dd->localTopologyChecker->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->localTopologyChecker->numBondedInteractionsOverAllDomains.value()
- != cr->dd->reverse_top->expectedNumGlobalBondedInteractions())
- {
- dd_print_missing_interactions(
- mdlog,
- cr,
- cr->dd->localTopologyChecker->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->localTopologyChecker->shouldCheckNumberOfBondedInteractions = false;
- }
-}
-
int dd_make_local_top(gmx_domdec_t* dd,
gmx_domdec_zones_t* zones,
int npbcdim,
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief This file defines functions used by the domdec module
+ * while managing the construction, use and error checking for
+ * topologies local to a DD rank.
+ *
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
+
+#include <string>
+#include <vector>
+
+#include "gromacs/domdec/localtopologychecker.h"
+
+#include "gromacs/domdec/domdec_internal.h"
+#include "gromacs/domdec/reversetopology.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/textwriter.h"
+
+#include "dump.h"
+
+using gmx::ArrayRef;
+using gmx::RVec;
+
+/*! \brief Checks whether interactions have been assigned for one function type
+ *
+ * Loops over a list of interactions in the local topology of one function type
+ * and flags each of the interactions as assigned in the global \p isAssigned list.
+ * Exits with an inconsistency error when an interaction is assigned more than once.
+ */
+static void flagInteractionsForType(const int ftype,
+ const InteractionList& il,
+ const reverse_ilist_t& ril,
+ const gmx::Range<int>& atomRange,
+ const int numAtomsPerMolecule,
+ ArrayRef<const int> globalAtomIndices,
+ ArrayRef<int> isAssigned)
+{
+ const int nril_mol = ril.index[numAtomsPerMolecule];
+ const int nral = NRAL(ftype);
+
+ for (int i = 0; i < il.size(); i += 1 + nral)
+ {
+ // ia[0] is the interaction type, ia[1, ...] the atom indices
+ const int* ia = il.iatoms.data() + i;
+ // Extract the global atom index of the first atom in this interaction
+ const int a0 = globalAtomIndices[ia[1]];
+ /* Check if this interaction is in
+ * the currently checked molblock.
+ */
+ if (atomRange.isInRange(a0))
+ {
+ // The molecule index in the list of this molecule type
+ const int moleculeIndex = (a0 - atomRange.begin()) / numAtomsPerMolecule;
+ const int atomOffset = (a0 - atomRange.begin()) - moleculeIndex * numAtomsPerMolecule;
+ const int globalAtomStartInMolecule = atomRange.begin() + moleculeIndex * numAtomsPerMolecule;
+ int j_mol = ril.index[atomOffset];
+ bool found = false;
+ while (j_mol < ril.index[atomOffset + 1] && !found)
+ {
+ const int j = moleculeIndex * nril_mol + j_mol;
+ const int ftype_j = ril.il[j_mol];
+ /* Here we need to check if this interaction has
+ * not already been assigned, since we could have
+ * multiply defined interactions.
+ */
+ if (ftype == ftype_j && ia[0] == ril.il[j_mol + 1] && isAssigned[j] == 0)
+ {
+ /* Check the atoms */
+ found = true;
+ for (int a = 0; a < nral; a++)
+ {
+ if (globalAtomIndices[ia[1 + a]]
+ != globalAtomStartInMolecule + ril.il[j_mol + 2 + a])
+ {
+ found = false;
+ }
+ }
+ if (found)
+ {
+ isAssigned[j] = 1;
+ }
+ }
+ j_mol += 2 + nral_rt(ftype_j);
+ }
+ if (!found)
+ {
+ gmx_incons("Some interactions seem to be assigned multiple times");
+ }
+ }
+ }
+}
+
+/*! \brief Help print error output when interactions are missing in a molblock
+ *
+ * \note This function needs to be called on all ranks (contains a global summation)
+ */
+static std::string printMissingInteractionsMolblock(t_commrec* cr,
+ const gmx_reverse_top_t& rt,
+ const char* moltypename,
+ const reverse_ilist_t& ril,
+ const gmx::Range<int>& atomRange,
+ const int numAtomsPerMolecule,
+ const int numMolecules,
+ const InteractionDefinitions& idef)
+{
+ const int nril_mol = ril.index[numAtomsPerMolecule];
+ std::vector<int> isAssigned(numMolecules * nril_mol, 0);
+ gmx::StringOutputStream stream;
+ gmx::TextWriter log(&stream);
+
+ for (int ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (dd_check_ftype(ftype, rt.options()))
+ {
+ flagInteractionsForType(
+ ftype, idef.il[ftype], ril, atomRange, numAtomsPerMolecule, cr->dd->globalAtomIndices, isAssigned);
+ }
+ }
+
+ gmx_sumi(isAssigned.size(), isAssigned.data(), cr);
+
+ const int numMissingToPrint = 10;
+ int i = 0;
+ for (int mol = 0; mol < numMolecules; mol++)
+ {
+ int j_mol = 0;
+ while (j_mol < nril_mol)
+ {
+ int ftype = ril.il[j_mol];
+ int nral = NRAL(ftype);
+ int j = mol * nril_mol + j_mol;
+ if (isAssigned[j] == 0 && !(interaction_function[ftype].flags & IF_VSITE))
+ {
+ if (DDMASTER(cr->dd))
+ {
+ if (i == 0)
+ {
+ log.writeLineFormatted("Molecule type '%s'", moltypename);
+ log.writeLineFormatted(
+ "the first %d missing interactions, except for exclusions:",
+ numMissingToPrint);
+ }
+ log.writeStringFormatted("%20s atoms", interaction_function[ftype].longname);
+ int a = 0;
+ for (; a < nral; a++)
+ {
+ log.writeStringFormatted("%5d", ril.il[j_mol + 2 + a] + 1);
+ }
+ while (a < 4)
+ {
+ log.writeString(" ");
+ a++;
+ }
+ log.writeString(" global");
+ for (int a = 0; a < nral; a++)
+ {
+ log.writeStringFormatted("%6d",
+ atomRange.begin() + mol * numAtomsPerMolecule
+ + ril.il[j_mol + 2 + a] + 1);
+ }
+ log.ensureLineBreak();
+ }
+ i++;
+ if (i >= numMissingToPrint)
+ {
+ break;
+ }
+ }
+ j_mol += 2 + nral_rt(ftype);
+ }
+ }
+
+ return stream.toString();
+}
+
+/*! \brief Help print error output when interactions are missing */
+static void printMissingInteractionsAtoms(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ const gmx_mtop_t& mtop,
+ const InteractionDefinitions& idef)
+{
+ const gmx_reverse_top_t& rt = *cr->dd->reverse_top;
+
+ /* Print the atoms in the missing interactions per molblock */
+ int a_end = 0;
+ for (const gmx_molblock_t& molb : mtop.molblock)
+ {
+ const gmx_moltype_t& moltype = mtop.moltype[molb.type];
+ const int a_start = a_end;
+ a_end = a_start + molb.nmol * moltype.atoms.nr;
+ const gmx::Range<int> atomRange(a_start, a_end);
+
+ auto warning = printMissingInteractionsMolblock(
+ cr,
+ rt,
+ *(moltype.name),
+ cr->dd->reverse_top->interactionListForMoleculeType(molb.type),
+ atomRange,
+ moltype.atoms.nr,
+ molb.nmol,
+ idef);
+
+ GMX_LOG(mdlog.warning).appendText(warning);
+ }
+}
+
+/*! \brief Print error output when interactions are missing */
+[[noreturn]] static 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,
+ ArrayRef<const RVec> x,
+ const matrix box)
+{
+ int cl[F_NRE];
+ gmx_domdec_t* dd = cr->dd;
+
+ GMX_LOG(mdlog.warning)
+ .appendText(
+ "Not all bonded interactions have been properly assigned to the domain "
+ "decomposition cells");
+
+ const int ndiff_tot = numBondedInteractionsOverAllDomains
+ - dd->reverse_top->expectedNumGlobalBondedInteractions();
+
+ for (int ftype = 0; ftype < F_NRE; ftype++)
+ {
+ const int nral = NRAL(ftype);
+ cl[ftype] = top_local->idef.il[ftype].size() / (1 + nral);
+ }
+
+ gmx_sumi(F_NRE, cl, cr);
+
+ if (DDMASTER(dd))
+ {
+ GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
+ int rest_global = dd->reverse_top->expectedNumGlobalBondedInteractions();
+ int rest = numBondedInteractionsOverAllDomains;
+ for (int ftype = 0; ftype < F_NRE; ftype++)
+ {
+ /* In the reverse and local top all constraints are merged
+ * into F_CONSTR. So in the if statement we skip F_CONSTRNC
+ * and add these constraints when doing F_CONSTR.
+ */
+ if (dd_check_ftype(ftype, dd->reverse_top->options()) && ftype != F_CONSTRNC)
+ {
+ int n = gmx_mtop_ftype_count(top_global, ftype);
+ if (ftype == F_CONSTR)
+ {
+ n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
+ }
+ int ndiff = cl[ftype] - n;
+ if (ndiff != 0)
+ {
+ GMX_LOG(mdlog.warning)
+ .appendTextFormatted("%20s of %6d missing %6d",
+ interaction_function[ftype].longname,
+ n,
+ -ndiff);
+ }
+ rest_global -= n;
+ rest -= cl[ftype];
+ }
+ }
+
+ int ndiff = rest - rest_global;
+ if (ndiff != 0)
+ {
+ GMX_LOG(mdlog.warning).appendTextFormatted("%20s of %6d missing %6d", "exclusions", rest_global, -ndiff);
+ }
+ }
+
+ printMissingInteractionsAtoms(mdlog, cr, top_global, top_local->idef);
+ write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr, -1, as_rvec_array(x.data()), box);
+
+ std::string errorMessage;
+
+ if (ndiff_tot > 0)
+ {
+ errorMessage =
+ "One or more interactions were assigned to multiple domains of the domain "
+ "decompostion. Please report this bug.";
+ }
+ else
+ {
+ errorMessage = gmx::formatString(
+ "%d of the %d bonded interactions could not be calculated because some atoms "
+ "involved moved further apart than the multi-body cut-off distance (%g nm) or the "
+ "two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds "
+ "also see option -ddcheck",
+ -ndiff_tot,
+ dd->reverse_top->expectedNumGlobalBondedInteractions(),
+ dd_cutoff_multibody(dd),
+ dd_cutoff_twobody(dd));
+ }
+ gmx_fatal_collective(FARGS, cr->mpi_comm_mygroup, MASTER(cr), "%s", errorMessage.c_str());
+}
+
+
+void scheduleCheckOfLocalTopology(gmx_domdec_t* dd, const int numBondedInteractionsToReduce)
+{
+ dd->localTopologyChecker->numBondedInteractionsToReduce = numBondedInteractionsToReduce;
+ // 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->localTopologyChecker->shouldCheckNumberOfBondedInteractions = true;
+ // Clear the old global value, which is now invalid
+ dd->localTopologyChecker->numBondedInteractionsOverAllDomains.reset();
+}
+
+bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd)
+{
+ return dd.localTopologyChecker->shouldCheckNumberOfBondedInteractions;
+}
+
+int numBondedInteractions(const gmx_domdec_t& dd)
+{
+ return dd.localTopologyChecker->numBondedInteractionsToReduce;
+}
+
+void setNumberOfBondedInteractionsOverAllDomains(gmx_domdec_t* dd, int newValue)
+{
+ GMX_RELEASE_ASSERT(!dd->localTopologyChecker->numBondedInteractionsOverAllDomains.has_value(),
+ "Cannot set number of bonded interactions because it is already set");
+ dd->localTopologyChecker->numBondedInteractionsOverAllDomains.emplace(newValue);
+}
+
+void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t* top_local,
+ ArrayRef<const 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->localTopologyChecker->shouldCheckNumberOfBondedInteractions)
+ {
+ GMX_RELEASE_ASSERT(cr->dd->localTopologyChecker->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->localTopologyChecker->numBondedInteractionsOverAllDomains.value()
+ != cr->dd->reverse_top->expectedNumGlobalBondedInteractions())
+ {
+ dd_print_missing_interactions(
+ mdlog,
+ cr,
+ cr->dd->localTopologyChecker->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->localTopologyChecker->shouldCheckNumberOfBondedInteractions = false;
+ }
+}
#include <optional>
+#include "gromacs/math/vectypes.h"
+
+struct gmx_domdec_t;
+struct gmx_localtop_t;
+struct gmx_mtop_t;
+struct t_commrec;
+struct t_inputrec;
+
+namespace gmx
+{
+class MDLogger;
+template<typename>
+class ArrayRef;
+enum class DDBondedChecking : bool;
+} // namespace gmx
+
namespace gmx
{
struct LocalTopologyChecker
{
+public:
/*! \brief Data to help check local topology construction
*
* Partitioning could incorrectly miss a bonded interaction.
} // namespace gmx
+//! Set that the local topology should be checked via observables reduction
+void scheduleCheckOfLocalTopology(gmx_domdec_t* dd, int numBondedInteractionsToReduce);
+
+/*! \brief Return whether the total bonded interaction count across
+ * domains should be checked in observables reduction. */
+bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd);
+
+//! Return the number of bonded interactions in this domain.
+int numBondedInteractions(const gmx_domdec_t& dd);
+
+/*! \brief Set total bonded interaction count across domains. */
+void setNumberOfBondedInteractionsOverAllDomains(gmx_domdec_t* dd, int newValue);
+
+/*! \brief Check whether bonded interactions are missing from the reverse topology
+ * produced by domain decomposition.
+ *
+ * Must only be called when DD is active.
+ *
+ * \param[in] mdlog Logger
+ * \param[in] cr Communication object
+ * \param[in] top_global Global topology for the error message
+ * \param[in] top_local Local topology for the error message
+ * \param[in] x Position vector for the error message
+ * \param[in] box Box matrix for the error message
+ */
+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);
+
#endif
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/domdec/localatomsetmanager.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/domdec/mdsetup.h"
#include "gromacs/domdec/nsgrid.h"
#include "gromacs/ewald/pme_pp.h"
std::unique_ptr<Impl> impl_;
};
+/*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
+int nral_rt(int ftype);
+
+/*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
+bool dd_check_ftype(int ftype, const ReverseTopOptions& rtOptions);
+
#endif
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/gmxlib/network.h"
GMX_RELEASE_ASSERT(DOMAINDECOMP(cr),
"No need to check number of bonded interactions when not using domain "
"decomposition");
- setNumberOfBondedInteractionsOverAllDomains(*cr->dd, gmx::roundToInt(nb));
+ setNumberOfBondedInteractionsOverAllDomains(cr->dd, gmx::roundToInt(nb));
}
if (!sig.empty())
#include <algorithm>
#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/gpuhaloexchange.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/domdec/mdsetup.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/domdec/mdsetup.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/domdec/mdsetup.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "computeglobalselement.h"
#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff