inciter::Discretization class
#include <src/Inciter/Discretization.hpp>

Discretization Charm++ chare array holding common functinoality to all discretization schemes.

Public static functions

static void registerReducers(): Configure Charm++ reduction types.

Constructors, destructors, conversion operators

Discretization(CkMigrateMessage* m) explicit: Migrate constructor.

Public functions

auto Discretization(std::size_t meshid, const CProxy_Transporter& transporter, const tk::CProxy_MeshWriter& meshwriter, const tk::UnsMesh::CoordMap& coordmap, const tk::UnsMesh::Chunk& el, const std::map<int, std::unordered_set<std::size_t>>& nodeCommMap, int nc) -> Discretization_SDAG_CODE explicit: Constructor.
void resizePostAMR(const tk::UnsMesh::Chunk& chunk, const tk::UnsMesh::Coords& coord, const std::unordered_map<int, std::unordered_set<std::size_t>>& nodeCommMap, const std::set<std::size_t>& removedNodes): Resize mesh data structures after mesh refinement.
void startvol(): Get ready for (re-)computing/communicating nodal volumes.
void vol(): Sum mesh volumes to nodes, start communicating them on chare-boundaries.
void setRefiner(const CProxy_Refiner& ref): Set Refiner Charm++ proxy.
void comvol(int c, const std::vector<std::size_t>& gid, const std::vector<tk::real>& nodevol): Collect nodal volumes across chare boundaries.
void totalvol(): Sum mesh volumes and contribute own mesh volume to total volume.
void stat(tk::real mesh_volume): Compute mesh cell statistics.
auto deastart() -> bool: Decide whether to start the deactivation procedure in this time step.
auto deactivate() const -> bool: Decide whether to run deactivation procedure in this time step.
void deactivated(int n): Receive deactivation report.
auto lb() const -> bool: Decide whether to do load balancing this time step.
void boxvol(): Compute total box IC volume.

Charm++ pack/unpack serializer member functions

std::size_t m_npoin: Total number of mesh points (across all meshes)
std::size_t m_meshid: Mesh ID.
int m_nchare: Total number of Discretization chares.
uint64_t m_it: Iteration count.
uint64_t m_itr
uint64_t m_itf
std::size_t m_initial: Flag that is nonzero during setup and zero during time stepping.
tk::real m_t: Physical time.
tk::real m_lastDumpTime: Physics time at last field output.
tk::real m_physFieldFloor: Recent floor of physics time divided by field output interval time.
tk::real m_physHistFloor: Recent floor of physics time divided by history output interval time.
tk::real m_physIntegFloor: Recent floor of physics time divided by integral output interval time.
std::vector<tk::real> m_rangeFieldFloor: Recent floors of physics time divided by field output time for ranges.
std::vector<tk::real> m_rangeHistFloor: Recent floors of physics time divided by history output time for ranges.
std::vector<tk::real> m_rangeIntegFloor: Recent floors of physics time divided by integral output time for ranges.
tk::real m_dt: Physical time step size.
tk::real m_dtn: Physical time step size at the previous time step.
std::size_t m_nvol: Number of chares from which we received nodal volume contributions on chare boundaries.
std::vector<std::unordered_set<std::size_t>> m_boxnodes: List of nodes at which box user ICs are set for each IC box.
CProxy_Transporter m_transporter: Transporter proxy.
tk::CProxy_MeshWriter m_meshwriter: Mesh writer proxy.
CProxy_Refiner m_refiner: Mesh refiner proxy.
tk::UnsMesh::Chunk m_el: Elements of the mesh chunk we operate on.
std::vector<std::size_t>& m_inpoel: Alias to element connectivity.
std::vector<std::size_t>& m_gid: Alias to global node IDs of owned elements.
std::unordered_map<std::size_t, std::size_t>& m_lid: Alias to local node ids associated to the global ones of owned elements.
tk::UnsMesh::Coords m_coord: Mesh point coordinates.
std::unordered_map<int, std::unordered_set<std::size_t>> m_nodeCommMap: Global mesh node IDs bordering the mesh chunk held by fellow Discretization chares associated to their chare IDs.
tk::real m_meshvol: Total mesh volume.
std::vector<tk::real> m_v
std::vector<tk::real> m_vol
std::unordered_map<std::size_t, tk::real> m_volc
std::unordered_map<int, std::unordered_map<std::size_t, tk::real>> m_cvolc
tk::real m_boxvol: Volume of user-defined box IC.
tk::Timer m_timer: Timer measuring a time step.
int m_refined: 1 if mesh was refined in a time step, 0 if it was not
Clock::time_point m_prevstatus: Time point storing clock state at status()
int m_nrestart: Number of times restarted.
std::vector<HistData> m_histdata: Data at history point locations.
tk::real m_res: Current residual (during convergence to steady state)
tk::real m_res0: Residual at previous ETA calcuation (during convergence to steady state)
tk::real m_res1: Residual at next ETA calcuation (during convergence to steady state)
int m_dea: Numberf of deactived chares.
int m_deastarted: Flag: 1 if deactivation procedure has started.
std::size_t m_pit: Numberf of recent pressure solve iterations taken.
std::size_t m_mit: Numberf of recent momentum/transport solve iterations taken.
void pup(PUP::er& p) override: Pack/Unpack serialize member function.
void operator|(PUP::er& p, Discretization& i): Pack/Unpack serialize operator|.

Accessors

auto Coord() const -> const tk::UnsMesh::Coords&
auto Coord() -> tk::UnsMesh::Coords&: Coordinates accessor as reference.
auto Gid() const -> const std::vector<std::size_t>&: Global ids accessors as const-ref.
auto Lid() const -> const std::unordered_map<std::size_t, std::size_t>&: Local ids accessors as const-ref.
auto Inpoel() const -> const std::vector<std::size_t>&: Tetrahedron element connectivity (with local ids) accessors as const-ref.
auto Chunk() const -> const tk::UnsMesh::Chunk&: Mesh chunk accessor as const-ref.
auto meshvol() const -> tk::real: Total mesh volume accessor.
auto V() const -> const std::vector<tk::real>&: Nodal mesh volume accessors const-ref.
auto Vol() const -> const std::vector<tk::real>&: Nodal mesh volumes at current time step accessors as const-ref.
auto Cvolc() const -> const std::unordered_map<int, std::unordered_map<std::size_t, tk::real>>&: Access chare-volume contributions per chare per chare-boundary node.
auto nchare() const -> int: Access number of chares.
void Initial(std::size_t i)
auto Initial() const -> bool
auto Hist() const -> const std::vector<HistData>&: History points data accessor as const-ref.
auto Boxvol() -> tk::real&: Box volume accessor.
auto MeshId() const -> std::size_t: Mesh ID accessor.
auto Dt() const -> tk::real: Time step size accessor.
auto Dtn() const -> tk::real: Time step size at previous time step accessor.
auto T() const -> tk::real: Physical time accessor.
auto It() const -> uint64_t: Iteration count accessor.
auto Itr() -> uint64_t&: Non-const-ref refinement iteration count accessor.
auto Itf() -> uint64_t&: Non-const-ref field-output iteration count accessor.
auto Nrestart() -> int&: Non-const-ref number of restarts accessor.
auto Timer() const -> const tk::Timer&: Timer accessor as const-ref.
auto Timer() -> tk::Timer&: Timer accessor as non-const-ref.
auto refined() const -> int: Accessor to flag indicating if the mesh was refined as a value.
auto refined() -> int&: Accessor to flag indicating if the mesh was refined as non-const-ref.
auto Tr() const -> const CProxy_Transporter&: Transporter proxy accessor as const-ref.
auto Tr() -> CProxy_Transporter&: Transporter proxy accessor as non-const-ref.
auto Ref() const -> Refiner*: Access bound Refiner class pointer.
auto NodeCommMap() const -> const std::unordered_map<int, std::unordered_set<std::size_t>>&: Node communication map accessor as const-ref.
auto BoxNodes() const -> const std::vector<std::unordered_set<std::size_t>>&: IC boxnodes accessor.
void setdt(tk::real newdt): Set time step size.
void next(): Prepare for next step.
void status(): Otput one-liner status report.
auto histfilename(const std::string& id, std::streamsize precision) -> std::string: Construct history output filename.
void histheader(std::vector<std::string>&& names): Output headers for time history files (one for each point)
void history(std::vector<std::vector<tk::real>>&& data): Output time history for a time step.
void write(const std::vector<std::size_t>& inpoel, const tk::UnsMesh::Coords& coord, const std::map<int, std::vector<std::size_t>>& bface, const std::map<int, std::vector<std::size_t>>& bnode, const std::vector<std::size_t>& triinpoel, const std::vector<std::string>& elemfieldnames, const std::vector<std::string>& nodefieldnames, const std::vector<std::string>& elemsurfnames, const std::vector<std::string>& nodesurfnames, const std::vector<std::vector<tk::real>>& elemfields, const std::vector<std::vector<tk::real>>& nodefields, const std::vector<std::vector<tk::real>>& elemsurfs, const std::vector<std::vector<tk::real>>& nodesurfs, CkCallback c): Output mesh and fields data (solution dump) to file(s)
void grindZero(): Zero grind-timer.
auto restarted(int nrestart) -> bool: Detect if just returned from a checkpoint and if so, zero timers.
void remap(const std::unordered_map<std::size_t, std::size_t>& map): Remap mesh data due to new local ids.
auto fielditer() const -> bool: Decide if field output iteration count interval is hit.
auto fieldtime() const -> bool: Decide if field output physics time interval is hit.
auto fieldrange() const -> bool: Decide if physics time falls into a field output time range.
auto histiter() const -> bool: Decide if history output iteration count interval is hit.
auto histtime() const -> bool: Decide if history output physics time interval is hit.
auto histrange() const -> bool: Decide if physics time falls into a history output time range.
auto integiter() const -> bool: Decide if integral output iteration count interval is hit.
auto integtime() const -> bool: Decide if integral output physics time interval is hit.
auto integrange() const -> bool: Decide if physics time falls into a integral output time range.
auto finished() const -> bool: Decide if this is the last time step.
void residual(tk::real r): Update residual (during convergence to steady state)
void pit(std::size_t it): Update number of pressure linear solve iterations taken.
void mit(std::size_t it): Update number of momentum/transport linear solve iterations taken.
void npoin(std::size_t n): Set number of mesh points (across all meshes)

Function documentation

static void inciter::Discretization::registerReducers()

Configure Charm++ reduction types.

Since this is a [initnode] routine, see the .ci file, the Charm++ runtime system executes the routine exactly once on every logical node early on in the Charm++ init sequence. Must be static as it is called without an object. See also: Section "Initializations at Program Startup" at in the Charm++ manual http://charm.cs.illinois.edu/manuals/html/charm++/manual.html.

Discretization_SDAG_CODE inciter::Discretization::Discretization(std::size_t meshid, const CProxy_Transporter& transporter, const tk::CProxy_MeshWriter& meshwriter, const tk::UnsMesh::CoordMap& coordmap, const tk::UnsMesh::Chunk& el, const std::map<int, std::unordered_set<std::size_t>>& nodeCommMap, int nc) explicit

Constructor.

Parameters
meshid in	Mesh ID
transporter in	Host (Transporter) proxy
meshwriter in	Mesh writer proxy
coordmap in	Coordinates of mesh nodes and their global IDs
el in	Elements of the mesh chunk we operate on
nodeCommMap in	Node lists associated to chare IDs bordering the mesh chunk we operate on
nc in	Total number of Discretization chares

void inciter::Discretization::resizePostAMR(const tk::UnsMesh::Chunk& chunk, const tk::UnsMesh::Coords& coord, const std::unordered_map<int, std::unordered_set<std::size_t>>& nodeCommMap, const std::set<std::size_t>& removedNodes)

Resize mesh data structures after mesh refinement.

Parameters
chunk in	New mesh chunk (connectivity and global<->local id maps)
coord in	New mesh node coordinates
nodeCommMap in	New node communication map
removedNodes in	Newly removed mesh node local ids

void inciter::Discretization::setRefiner(const CProxy_Refiner& ref)

Set Refiner Charm++ proxy.

Parameters
ref in	Incoming refiner proxy to store

void inciter::Discretization::comvol(int c, const std::vector<std::size_t>& gid, const std::vector<tk::real>& nodevol)

Collect nodal volumes across chare boundaries.

Parameters
c in	Sender chare id
gid in	Global mesh node IDs at which we receive volume contributions
nodevol in	Partial sums of nodal volume contributions to chare-boundary nodes

void inciter::Discretization::stat(tk::real mesh_volume)

Compute mesh cell statistics.

Parameters
mesh_volume in	Total mesh volume

bool inciter::Discretization::deastart()

Decide whether to start the deactivation procedure in this time step.

Returns	True to start the deactivation prcedure in this time step

bool inciter::Discretization::deactivate() const

Decide whether to run deactivation procedure in this time step.

Returns	True to run deactivation prcedure in this time step

void inciter::Discretization::deactivated(int n)

Receive deactivation report.

Parameters
n in	Sum of deactivated chares

bool inciter::Discretization::lb() const

Decide whether to do load balancing this time step.

Returns	True to do load balancing in this time step

void inciter::Discretization::pup(PUP::er& p) override

Pack/Unpack serialize member function.

Parameters
p in/out	Charm++'s PUP::er serializer object reference

void inciter::Discretization::operator|(PUP::er& p, Discretization& i)

Pack/Unpack serialize operator|.

Parameters
p in/out	Charm++'s PUP::er serializer object reference
i in/out	Discretization object reference

const tk::UnsMesh::Coords& inciter::Discretization::Coord() const

Coordinates accessor as const-ref

void inciter::Discretization::Initial(std::size_t i)

Parameters
i in	Value to put in 'initial'

Set 'initial' flag

bool inciter::Discretization::Initial() const

Returns	True during setup, false durign time stepping

Query 'initial' flag

void inciter::Discretization::setdt(tk::real newdt)

Set time step size.

Parameters
newdt in	Size of the new time step

std::string inciter::Discretization::histfilename(const std::string& id, std::streamsize precision)

Construct history output filename.

Parameters
id in	History point id
precision in	Floating point precision to use for output
Returns	History file name

void inciter::Discretization::histheader(std::vector<std::string>&& names)

Output headers for time history files (one for each point)

Parameters
names in	History output variable names

void inciter::Discretization::history(std::vector<std::vector<tk::real>>&& data)

Output time history for a time step.

Parameters
data in	Time history data for all variables and equations integrated

void inciter::Discretization::write(const std::vector<std::size_t>& inpoel, const tk::UnsMesh::Coords& coord, const std::map<int, std::vector<std::size_t>>& bface, const std::map<int, std::vector<std::size_t>>& bnode, const std::vector<std::size_t>& triinpoel, const std::vector<std::string>& elemfieldnames, const std::vector<std::string>& nodefieldnames, const std::vector<std::string>& elemsurfnames, const std::vector<std::string>& nodesurfnames, const std::vector<std::vector<tk::real>>& elemfields, const std::vector<std::vector<tk::real>>& nodefields, const std::vector<std::vector<tk::real>>& elemsurfs, const std::vector<std::vector<tk::real>>& nodesurfs, CkCallback c)

Output mesh and fields data (solution dump) to file(s)

Parameters
inpoel in	Mesh connectivity for the mesh chunk to be written
coord in	Node coordinates of the mesh chunk to be written
bface in	Map of boundary-face lists mapped to corresponding side set ids for this mesh chunk
bnode in	Map of boundary-node lists mapped to corresponding side set ids for this mesh chunk
triinpoel in	Interconnectivity of points and boundary-face in this mesh chunk
elemfieldnames in	Names of element fields to be output to file
nodefieldnames in	Names of node fields to be output to file
elemsurfnames in	Names of elem surface fields to be output to file
nodesurfnames in	Names of node surface fields to be output to file
elemfields in	Field data in mesh elements to output to file
nodefields in	Field data in mesh nodes to output to file
elemsurfs in	Surface field data in mesh elements to output to file
nodesurfs in	Surface field data in mesh nodes to output to file
c in	Function to continue with after the write

Since m_meshwriter is a Charm++ chare group, it never migrates and an instance is guaranteed on every PE. We index the first PE on every logical compute node. In Charm++'s non-SMP mode, a node is the same as a PE, so the index is the same as CkMyPe(). In SMP mode the index is the first PE on every logical node. In non-SMP mode this yields one or more output files per PE with zero or non-zero virtualization, respectively. If there are multiple chares on a PE, the writes are serialized per PE, since only a single entry method call can be executed at any given time. In SMP mode, still the same number of files are output (one per chare), but the output is serialized through the first PE of each compute node. In SMP mode, channeling multiple files via a single PE on each node is required by NetCDF and HDF5, as well as ExodusII, since none of these libraries are thread-safe.

bool inciter::Discretization::restarted(int nrestart)

Detect if just returned from a checkpoint and if so, zero timers.

Parameters
nrestart in	Number of times restarted
Returns	True if restart detected

void inciter::Discretization::remap(const std::unordered_map<std::size_t, std::size_t>& map)

Remap mesh data due to new local ids.

Parameters
map in	Mapping of old->new local ids

bool inciter::Discretization::fielditer() const

Decide if field output iteration count interval is hit.

Returns	True if field output iteration count interval is hit

bool inciter::Discretization::fieldtime() const

Decide if field output physics time interval is hit.

Returns	True if field output physics time interval is hit

bool inciter::Discretization::fieldrange() const

Decide if physics time falls into a field output time range.

Returns	True if physics time falls into a field output time range

bool inciter::Discretization::histiter() const

Decide if history output iteration count interval is hit.

Returns	True if history output iteration count interval is hit

bool inciter::Discretization::histtime() const

Decide if history output physics time interval is hit.

Returns	True if history output physics time interval is hit

bool inciter::Discretization::histrange() const

Decide if physics time falls into a history output time range.

Returns	True if physics time falls into a history output time range

bool inciter::Discretization::integiter() const

Decide if integral output iteration count interval is hit.

Returns	True if integral output iteration count interval is hit

bool inciter::Discretization::integtime() const

Decide if integral output physics time interval is hit.

Returns	True if integral output physics time interval is hit

bool inciter::Discretization::integrange() const

Decide if physics time falls into a integral output time range.

Returns	True if physics time falls into a integral output time range

bool inciter::Discretization::finished() const

Decide if this is the last time step.

Returns	True if this is the last time step

void inciter::Discretization::residual(tk::real r)

Update residual (during convergence to steady state)

Parameters
r in	Current residual

void inciter::Discretization::pit(std::size_t it)

Update number of pressure linear solve iterations taken.

Parameters
it in	Number of pressure linear solve iterations taken

void inciter::Discretization::mit(std::size_t it)

Update number of momentum/transport linear solve iterations taken.

Parameters
it in	Number of momentum/transport linear solve iterations taken

void inciter::Discretization::npoin(std::size_t n)

Set number of mesh points (across all meshes)

Parameters
n in	Number of mesh points

Variable documentation

uint64_t inciter::Discretization::m_itr

Iteration count with mesh refinement

Used as the restart sequence number {RS} in saving output in an ExodusII sequence

uint64_t inciter::Discretization::m_itf

Field output iteration count without mesh refinement

Counts the number of field outputs to file during two time steps with mesh efinement

tk::UnsMesh::Chunk inciter::Discretization::m_el

Elements of the mesh chunk we operate on.

Initialized by the constructor. The first vector is the element connectivity (local IDs), the second vector is the global node IDs of owned elements, while the third one is a map of global->local node IDs.

std::vector<tk::real> inciter::Discretization::m_v

Nodal mesh volumes

This is the volume of the mesh associated to nodes of owned elements (sum of surrounding cell volumes / 4) without contributions from other chares on chare-boundaries

std::vector<tk::real> inciter::Discretization::m_vol

Volume of nodes

This is the volume of the mesh associated to nodes of owned elements (sum of surrounding cell volumes / 4) with contributions from other chares on chare-boundaries

std::unordered_map<std::size_t, tk::real> inciter::Discretization::m_volc

Receive buffer for volume of nodes (with global node id as key)

This is a communication buffer used to compute the volume of the mesh associated to nodes of owned elements (sum of surrounding cell volumes / 4) with contributions from other chares on chare-boundaries.

std::unordered_map<int, std::unordered_map<std::size_t, tk::real>> inciter::Discretization::m_cvolc

Chare-volume contributions per chare per chare-boundary node

Outer key: chare id, value: local node id and node volume