Spatial domain decomposition (for parallelization over MPI)

Collaboration diagram for Spatial domain decomposition (for parallelization over MPI):

Description

Manages the decomposition of the simulation volume over MPI ranks to try to distribute work evenly with minimal communication overheads.

Todo:

Get domdec stuff out of mdtypes/commrec.h

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Classes
class	gmx::LocalAtomSet
	A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator. More...
class	gmx::LocalAtomSetManager
	Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...

Files
file	atomdistribution.h
	Declares the AtomDistribution struct.
file	box.cpp
	This file defines functions used by the domdec module for (bounding) box and pbc information generation.
file	box.h
	This file declares functions used by the domdec module for (bounding) box and pbc information generation.
file	builder.h
	This file declares a builder class for the manager of domain decomposition.
file	cellsizes.h
	Declares DD cell-size related functions.
file	collect.h
	Declares functions to collect state data to the master rank.
file	computemultibodycutoffs.cpp
	This file defines functions used by the domdec module while managing the construction, use and error checking for topologies local to a DD rank.
file	computemultibodycutoffs.h
	This file declares the function for computing the required cutoff distance for inter-domain multi-body interactions, when those exist.
file	distribute.h
	Declares the atom distribution function.
file	dlb.cpp
	This file implements functions to interact with the dynamic load balancing machinery.
file	dlb.h
	This file declares functions to interact with the dynamic load balancing machinery.
file	dlbtiming.h
	This file declares functions for timing the load imbalance due to domain decomposition.
file	domdec.h
	This file declares functions for mdrun to call to manage the details of its domain decomposition.
file	domdec_constraints.cpp
	This file implements functions for domdec to use while managing inter-atomic constraints.
file	domdec_constraints.h
	This file declares functions for domdec to use while managing inter-atomic constraints.
file	domdec_internal.h
	Declares implementation functions and types for the domain decomposition module.
file	domdec_network.cpp
	This file defines functions for (mostly) the domdec module to use MPI functionality.
file	domdec_network.h
	This file declares functions for (mostly) the domdec module to use MPI functionality.
file	domdec_setup.cpp
	This file defines functions used by the domdec module in its initial setup phase.
file	domdec_setup.h
	Declares functions for choosing the DD grid setup.
file	domdec_specatomcomm.cpp
	This file implements functions for domdec to use while managing inter-atomic constraints.
file	domdec_specatomcomm.h
	This file declares functions for domdec to use while managing communication of atoms required for special purposes.
file	domdec_struct.h
	Declares structures related to domain decomposition.
file	domdec_vsite.cpp
	This file implements functions for domdec to use while managing inter-atomic constraints.
file	domdec_vsite.h
	This file declares functions for domdec to use while managing virtual sites.
file	dump.cpp
	This file definees functions for DD to write PDB files e.g. when reporting problems.
file	dump.h
	This file declares functions for DD to write PDB files e.g. when reporting problems.
file	ga2la.cpp
	Implements functions for mapping from global to local atom indices.
file	ga2la.h
	Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined.
file	gpuhaloexchange.h
	Declaration of GPU halo exchange.
file	gpuhaloexchange_impl.cpp
	May be used to implement Domdec CUDA interfaces for non-GPU builds.
file	hashedmap.h
	Defines structures and functions for mapping from keys to entries indices using a hash table. The functions are performance critical and should be inlined.
file	localatomset.cpp
	Implements classes in LocalAtomSet.h.
file	localatomset.h
	Declares gmx::LocalAtomSet.
file	localatomsetdata.cpp
	Declares gmx::internal::LocalAtomSetDataData.
file	localatomsetdata.h
	Declares gmx::internal::LocalAtomSetData.
file	localatomsetmanager.cpp
	Implements classes in LocalAtomSetmanager.h.
file	localatomsetmanager.h
	Declares gmx::LocalAtomSetManager.
file	localtopology.cpp
	This file defines functions used by the domdec module while building topologies local to a domain.
file	localtopology.h
	This file makes declarations used for building the local topology.
file	localtopologychecker.cpp
	This file defines functions used by the domdec module while managing the construction, use and error checking for topologies local to a DD rank.
file	localtopologychecker.h
	This file declares functionality for checking whether local topologies describe all bonded interactions.
file	makebondedlinks.cpp
	Defines a function that makes the list of links between atoms connected by bonded interactions.
file	makebondedlinks.h
	Declares a function that makes the list of links between atoms connected by bonded interactions.
file	mdsetup.h
	Contains functions relevant to simulation setup in MD drivers.
file	options.h
	This file declares command-line options for mdrun related to domain decomposition.
file	partition.cpp
	This file defines functions for mdrun to call to make a new domain decomposition, and check it.
file	partition.h
	This file declares functions for mdrun to call to make a new domain decomposition, and check it.
file	redistribute.h
	Declares the atom redistribution function.
file	reversetopology.cpp
	This file defines functions used in making the reverse topology.
file	reversetopology.h
	This file makes declarations used for building the reverse topology.
file	haloexchange_mpi.cpp
	Tests for the halo exchange.
file	hashedmap.cpp
	Tests for the HashedMap class.
file	localatomsetmanager.cpp
	Tests for general functionality in gmx::LocalAtomSetManager and gmx::LocalAtomSet, which is only accesible through the manager.
file	utility.cpp
	Declares utility functions used in the domain decomposition module.
file	utility.h
	Declares utility functions used in the domain decomposition module.