The RunttimeContext is an example specific class to store the run specific input data, MOAB datastructures used during the run and provides other utility functions to profile operations etc. More...

Collaboration diagram for RuntimeContext:

Public Member Functions
	RuntimeContext (MPI_Comm comm=MPI_COMM_WORLD)
	Constructor: allocate MOAB interface and communicator, and initialize other data members with some default values. More...

	~RuntimeContext ()
	Destructor: deallocate MOAB interface and communicator. More...

void	ParseCLOptions (int argc, char *argv[])
	Parse the runtime command line options. More...

void	timer_push (const std::string &operation)
	Measure and start the timer to profile a task. More...

void	timer_pop (const int nruns=1)
	Stop the timer and store the elapsed duration. More...

double	last_elapsed () const
	Return the last elapsed time. More...

moab::ErrorCode	load_file (bool load_ghosts=false)
	Load a MOAB supported file (h5m or nc format) from disk representing an MPAS mesh. More...

moab::ErrorCode	create_sv_tags (moab::Tag &tagScalar, moab::Tag &tagVector, moab::Range &entities)
	Create scalar and vector tags in the MOAB mesh instance. More...

double	evaluate_function (double lon, double lat, int type=1, double multiplier=1.0) const
	Evaluate some closed-form Spherical Harmonic functions with an optional multiplier term. More...

Public Attributes
int	dimension { 2 }

std::string	input_filename
	dimension of the problem More...

std::string	output_filename
	input file name (nc format) More...

int	ghost_layers { 3 }
	output file name (h5m format) More...

std::string	scalar_tagname
	number of ghost layers More...

std::string	vector_tagname
	scalar tag name More...

int	vector_length { 3 }
	vector tag name More...

int	num_max_exchange { 10 }
	length of the vector tag components More...

bool	debug_output { false }
	total number of exchange iterations More...

int	proc_id { 1 }
	write debug output information? More...

int	num_procs { 1 }
	process identifier More...

double	last_counter { 0.0 }
	total number of processes More...

moab::Core	moab_interface
	last time counter between push/pop timer More...

moab::ParallelComm *	parallel_communicator

moab::EntityHandle	fileset { 0 }

moab::EntityHandle	partnset { 0 }

Private Member Functions
std::vector< double >	compute_centroids (const moab::Range &entities) const
	Compute the centroids of elements in 2D lat/lon space. More...

Private Attributes
moab::CpuTimer	mTimer

double	mTimerOps { 0.0 }

std::string	mOpName

Detailed Description

The RunttimeContext is an example specific class to store the run specific input data, MOAB datastructures used during the run and provides other utility functions to profile operations etc.

Definition at line 77 of file ExchangeHalos.cpp.

Constructor & Destructor Documentation

◆ RuntimeContext()

RuntimeContext::RuntimeContext ( MPI_Comm comm = MPI_COMM_WORLD )

explicit

Constructor: allocate MOAB interface and communicator, and initialize other data members with some default values.

Implementation details ///.

Definition at line 331 of file ExchangeHalos.cpp.

  : input_filename( std::string( MESH_DIR ) + std::string( "/io/mpasx1.642.t.2.nc" ) ),
  output_filename( "exchangeHalos_output.h5m" ), scalar_tagname( "scalar_variable" ),
  vector_tagname( "vector_variable" )
 {
  // Create sets for the mesh and partition. Then pass these to the load_file functions to populate the mesh.
  runchk_cont( moab_interface.create_meshset( moab::MESHSET_SET, fileset ), "Creating root set failed" );
  runchk_cont( moab_interface.create_meshset( moab::MESHSET_SET, partnset ), "Creating partition set failed" );
  
  // Create the parallel communicator object with the partition handle associated with MOAB
  parallel_communicator = moab::ParallelComm::get_pcomm( &moab_interface, partnset, &comm );
  
  proc_id = parallel_communicator->rank();
  num_procs = parallel_communicator->size();
 }

References moab::Core::create_meshset(), fileset, moab::ParallelComm::get_pcomm(), MESHSET_SET, moab_interface, num_procs, parallel_communicator, partnset, proc_id, moab::ParallelComm::rank(), runchk_cont, and moab::ParallelComm::size().

◆ ~RuntimeContext()

RuntimeContext::~RuntimeContext ( )

Destructor: deallocate MOAB interface and communicator.

Definition at line 347 of file ExchangeHalos.cpp.

 {
  delete parallel_communicator;
 }

References parallel_communicator.

Member Function Documentation

◆ compute_centroids()

std::vector< double > RuntimeContext::compute_centroids ( const moab::Range & entities ) const

private

Compute the centroids of elements in 2D lat/lon space.

Parameters

entities Entities to compute centroids

Returns: Vector of centroids (as lat/lon)

Definition at line 506 of file ExchangeHalos.cpp.

 {
  double node[3];
  std::vector< double > eCentroids( entities.size() * 2 ); // [lon, lat]
  size_t offset = 0;
  for( auto entity : entities )
  {
  // Get the element coordinates (centroid) on the real mesh
  runchk_cont( moab_interface.get_coords( &entity, 1, node ), "Getting entity coordinates failed" );
  
  // scale by magnitude so that element is on unit sphere
  double magnitude = std::sqrt( node[0] * node[0] + node[1] * node[1] + node[2] * node[2] );
  node[0] /= magnitude;
  node[1] /= magnitude;
  node[2] /= magnitude;
  
  // compute the spherical transformation onto unit sphere
  eCentroids[offset] = atan2( node[1], node[0] );
  if( eCentroids[offset] < 0.0 ) eCentroids[offset] += 2.0 * M_PI;
  eCentroids[offset + 1] = asin( node[2] );
  
  offset += 2; // increment the offset
  }
  // return centroid list for elements
  return eCentroids;
 }

References entities, moab::Core::get_coords(), moab_interface, and runchk_cont.

Referenced by create_sv_tags().

◆ create_sv_tags()

moab::ErrorCode RuntimeContext::create_sv_tags	(	moab::Tag &	tagScalar,
		moab::Tag &	tagVector,
		moab::Range &	entities
	)

Create scalar and vector tags in the MOAB mesh instance.

Parameters

tagScalar	Tag reference to the scalar field
tagVector	Tag reference to the vector field
entities	Entities on which both the scalar and vector fields are defined

Returns: Error code if any (else MB_SUCCESS)

Definition at line 408 of file ExchangeHalos.cpp.

 {
  // Get element (centroid) coordinates so that we can evaluate some arbitrary data
  std::vector< double > entCoords = compute_centroids( entities ); // [entities * [lon, lat]]
  
  if( proc_id == 0 ) std::cout << "> Getting scalar tag handle " << scalar_tagname << "..." << std::endl;
  double defSTagValue = -1.0;
  bool createdTScalar = false;
  // Get or create the scalar tag: default name = "scalar_variable"
  // Type: double, Components: 1, Layout: Dense (all entities potentially), Default: -1.0
  runchk( moab_interface.tag_get_handle( scalar_tagname.c_str(), 1, moab::MB_TYPE_DOUBLE, tagScalar,
  moab::MB_TAG_CREAT | moab::MB_TAG_DENSE, &defSTagValue, &createdTScalar ),
  "Retrieving scalar tag handle failed" );
  
  // we expect to create a new tag -- fail if Tag already exists since we do not want to overwrite data
  assert( createdTScalar );
  // set the data for scalar tag with an analytical Spherical Harmonic function
  {
  std::vector< double > tagValues( entities.size(), -1.0 );
  std::generate( tagValues.begin(), tagValues.end(), [=, &entCoords]() {
  static int index = 0;
  const int offset = index++ * 2;
  return evaluate_function( entCoords[offset], entCoords[offset + 1] );
  } );
  // Set local scalar tag data for exchange
  runchk( moab_interface.tag_set_data( tagScalar, entities, tagValues.data() ),
  "Setting scalar tag data failed" );
  }
  
  if( proc_id == 0 ) std::cout << "> Getting vector tag handle " << vector_tagname << "..." << std::endl;
  std::vector< double > defVTagValue( vector_length, -1.0 );
  bool createdTVector = false;
  // Get or create the scalar tag: default name = "vector_variable"
  // Type: double, Components: vector_length, Layout: Dense (all entities potentially), Default: [-1.0,..]
  runchk( moab_interface.tag_get_handle( vector_tagname.c_str(), vector_length, moab::MB_TYPE_DOUBLE, tagVector,
  moab::MB_TAG_CREAT | moab::MB_TAG_DENSE, defVTagValue.data(),
  &createdTVector ),
  "Retrieving vector tag handle failed" );
  
  // we expect to create a new tag -- fail if Tag already exists since we do not want to overwrite data
  assert( createdTVector );
  // set the data for vector tag with an analytical Spherical Harmonic function
  // with an optional scaling for each component; just to make it look different :-)
  {
  const int veclength = vector_length;
  std::vector< double > tagValues( entities.size() * veclength, -1.0 );
  std::generate( tagValues.begin(), tagValues.end(), [=, &entCoords]() {
  static int index = 0;
  const int offset = ( index++ / veclength ) * 2;
  return this->evaluate_function( entCoords[offset], entCoords[offset + 1], 2, ( index % veclength + 1.0 ) );
  } );
  // Set local tag data for exchange
  runchk( moab_interface.tag_set_data( tagVector, entities, tagValues.data() ),
  "Setting vector tag data failed" );
  }
  
  return moab::MB_SUCCESS;
 }

References compute_centroids(), entities, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_DOUBLE, moab_interface, proc_id, runchk, scalar_tagname, moab::Core::tag_get_handle(), moab::Core::tag_set_data(), vector_length, and vector_tagname.

◆ evaluate_function()

double RuntimeContext::evaluate_function	(	double	lon,
		double	lat,
		int	type = `1`,
		double	multiplier = `1.0`
	)		const

inline

Evaluate some closed-form Spherical Harmonic functions with an optional multiplier term.

Parameters

lon	Longitude in lat-lon space
lat	Latitude in lat-lon space
type	Function type
multiplier	Optional multiplier to scale value (default=1.0)

Returns: value of the evaluated function

Definition at line 142 of file ExchangeHalos.cpp.

  {
  switch( type )
  {
  case 1:
  return ( 2.0 + std::pow( sin( 2.0 * lat ), 16.0 ) * cos( 16.0 * lon ) ) * multiplier;
  default:
  return ( 2.0 + cos( lon ) * cos( lon ) * cos( 2.0 * lat ) ) * multiplier;
  }
  }

◆ last_elapsed()

double RuntimeContext::last_elapsed ( ) const

inline

Return the last elapsed time.

Returns: last_counter from timer_pop was called

Definition at line 403 of file ExchangeHalos.cpp.

 {
  return last_counter;
 }

References last_counter.

◆ load_file()

moab::ErrorCode RuntimeContext::load_file ( bool load_ghosts = false )

Load a MOAB supported file (h5m or nc format) from disk representing an MPAS mesh.

Parameters

load_ghosts Optional boolean to specify whether to load ghosts when reading the file (only relevant for h5m)

Returns: Error code if any (else MB_SUCCESS)

Parallel Read options: PARALLEL = type {READ_PART} : Read on all tasks PARTITION_METHOD = RCBZOLTAN : Use Zoltan partitioner to compute an online partition and redistribute on the fly PARTITION = PARALLEL_PARTITION : Partition as you read based on part information stored in h5m file PARALLEL_RESOLVE_SHARED_ENTS : Communicate to all processors to get the shared adjacencies consistently in parallel PARALLEL_GHOSTS : a.b.c : a = 2 - highest dimension of entities (2D in this case) : b = 1 - dimension of entities to calculate adjacencies (vertex=0, edges=1) : c = 3 - number of ghost layers needed (3 in this case)

Definition at line 467 of file ExchangeHalos.cpp.

 {
  /// Parallel Read options:
  /// PARALLEL = type {READ_PART} : Read on all tasks
  /// PARTITION_METHOD = RCBZOLTAN : Use Zoltan partitioner to compute an online partition and redistribute on the
  /// fly PARTITION = PARALLEL_PARTITION : Partition as you read based on part information stored in h5m file
  /// PARALLEL_RESOLVE_SHARED_ENTS : Communicate to all processors to get the shared adjacencies
  /// consistently in parallel
  /// PARALLEL_GHOSTS : a.b.c
  /// : a = 2 - highest dimension of entities (2D in this case)
  /// : b = 1 - dimension of entities to calculate adjacencies (vertex=0, edges=1)
  /// : c = 3 - number of ghost layers needed (3 in this case)
  std::string read_options = "DEBUG_IO=0;";
  std::string::size_type idx = input_filename.rfind( '.' );
  if( num_procs > 1 && idx != std::string::npos )
  {
  std::string extension = input_filename.substr( idx + 1 );
  if( !extension.compare( "nc" ) )
  // PARTITION_METHOD= [RCBZOLTAN, TRIVIAL]
  read_options += "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;"
  "PARALLEL_RESOLVE_SHARED_ENTS;NO_EDGES;NO_MIXED_ELEMENTS;VARIABLE=;";
  else if( !extension.compare( "h5m" ) )
  read_options +=
  "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;"
  "PARALLEL_RESOLVE_SHARED_ENTS;" +
  ( load_ghosts ? "PARALLEL_THIN_GHOST_LAYER;PARALLEL_GHOSTS=2.1." + std::to_string( ghost_layers ) + ";"
  : "" );
  else
  {
  std::cout << "Error unsupported file type (only h5m and nc) for this example: " << input_filename
  << std::endl;
  return moab::MB_UNSUPPORTED_OPERATION;
  }
  }
  
  // Load the file from disk with given read options in parallel and associate all entities to fileset
  return moab_interface.load_file( input_filename.c_str(), &fileset, read_options.c_str() );
 }

References fileset, ghost_layers, input_filename, moab::Core::load_file(), MB_UNSUPPORTED_OPERATION, moab_interface, and num_procs.

◆ ParseCLOptions()

void RuntimeContext::ParseCLOptions	(	int	argc,
		char *	argv[]
	)

Parse the runtime command line options.

Parameters

argc	- number of command line arguments
argv	- command line arguments as string list

Definition at line 352 of file ExchangeHalos.cpp.

 {
  ProgOptions opts;
  // Input mesh
  opts.addOpt< std::string >( "input", "Input mesh filename to load in parallel. Default=data/default_mesh_holes.h5m",
  &input_filename );
  // Output mesh
  opts.addOpt< void >( "debug", "Should we write output file? Default=false", &debug_output );
  opts.addOpt< std::string >( "output",
  "Output mesh filename for verification (use --debug). Default=exchangeHalos_output.h5m",
  &output_filename );
  // Dimension of the input mesh
  // Vector tag length
  opts.addOpt< int >( "vtaglength", "Size of vector components per each entity. Default=3", &vector_length );
  // Number of halo (ghost) regions
  opts.addOpt< int >( "nghosts", "Number of ghost layers (halos) to exchange. Default=3", &ghost_layers );
  // Number of times to perform the halo exchange for timing
  opts.addOpt< int >( "nexchanges", "Number of ghost-halo exchange iterations to perform. Default=10",
  &num_max_exchange );
  
  opts.parseCommandLine( argc, argv );
 }

References ProgOptions::addOpt(), debug_output, ghost_layers, input_filename, num_max_exchange, output_filename, ProgOptions::parseCommandLine(), and vector_length.

◆ timer_pop()

void RuntimeContext::timer_pop ( const int nruns = 1 )

Stop the timer and store the elapsed duration.

Parameters

nruns Optional argument used to average the measured time

Definition at line 381 of file ExchangeHalos.cpp.

 {
  double locElapsed = mTimer.time_since_birth() - mTimerOps;
  double avgElapsed = 0;
  double maxElapsed = 0;
  MPI_Reduce( &locElapsed, &maxElapsed, 1, MPI_DOUBLE, MPI_MAX, 0, parallel_communicator->comm() );
  MPI_Reduce( &locElapsed, &avgElapsed, 1, MPI_DOUBLE, MPI_SUM, 0, parallel_communicator->comm() );
  if( proc_id == 0 )
  {
  avgElapsed /= num_procs;
  if( nruns > 1 )
  std::cout << "[LOG] Time taken to " << mOpName.c_str() << ", averaged over " << nruns
  << " runs : max = " << maxElapsed / nruns << ", avg = " << avgElapsed / nruns << "\n";
  else
  std::cout << "[LOG] Time taken to " << mOpName.c_str() << " : max = " << maxElapsed
  << ", avg = " << avgElapsed << "\n";
  
  last_counter = maxElapsed / nruns;
  }
  mOpName.clear();
 }

References moab::ParallelComm::comm(), last_counter, mOpName, mTimer, mTimerOps, num_procs, parallel_communicator, proc_id, and moab::CpuTimer::time_since_birth().

◆ timer_push()

void RuntimeContext::timer_push ( const std::string & operation )

inline

Measure and start the timer to profile a task.

Parameters

operation String name of the task being measured

Definition at line 375 of file ExchangeHalos.cpp.

 {
  mTimerOps = mTimer.time_since_birth();
  mOpName = operation;
 }

References mOpName, mTimer, mTimerOps, and moab::CpuTimer::time_since_birth().

Member Data Documentation

◆ debug_output

bool RuntimeContext::debug_output { false }

total number of exchange iterations

Definition at line 88 of file ExchangeHalos.cpp.

Referenced by ParseCLOptions().

◆ dimension

int RuntimeContext::dimension { 2 }

Definition at line 80 of file ExchangeHalos.cpp.

◆ fileset

moab::EntityHandle RuntimeContext::fileset { 0 }

Definition at line 96 of file ExchangeHalos.cpp.

Referenced by load_file(), and RuntimeContext().

◆ ghost_layers

int RuntimeContext::ghost_layers { 3 }

output file name (h5m format)

Definition at line 83 of file ExchangeHalos.cpp.

Referenced by load_file(), and ParseCLOptions().

◆ input_filename

std::string RuntimeContext::input_filename

dimension of the problem

Definition at line 81 of file ExchangeHalos.cpp.

Referenced by load_file(), and ParseCLOptions().

◆ last_counter

double RuntimeContext::last_counter { 0.0 }

total number of processes

Definition at line 91 of file ExchangeHalos.cpp.

Referenced by last_elapsed(), and timer_pop().

◆ moab_interface

moab::Core RuntimeContext::moab_interface

last time counter between push/pop timer

Definition at line 94 of file ExchangeHalos.cpp.

Referenced by compute_centroids(), create_sv_tags(), load_file(), and RuntimeContext().

◆ mOpName

std::string RuntimeContext::mOpName

private

Definition at line 161 of file ExchangeHalos.cpp.

Referenced by timer_pop(), and timer_push().

◆ mTimer

moab::CpuTimer RuntimeContext::mTimer

private

Definition at line 159 of file ExchangeHalos.cpp.

Referenced by timer_pop(), and timer_push().

◆ mTimerOps

double RuntimeContext::mTimerOps { 0.0 }

private

Definition at line 160 of file ExchangeHalos.cpp.

Referenced by timer_pop(), and timer_push().

◆ num_max_exchange

int RuntimeContext::num_max_exchange { 10 }

length of the vector tag components

Definition at line 87 of file ExchangeHalos.cpp.

Referenced by ParseCLOptions().

◆ num_procs

int RuntimeContext::num_procs { 1 }

process identifier

Definition at line 90 of file ExchangeHalos.cpp.

Referenced by load_file(), RuntimeContext(), and timer_pop().

◆ output_filename

std::string RuntimeContext::output_filename

input file name (nc format)

Definition at line 82 of file ExchangeHalos.cpp.

Referenced by ParseCLOptions().

◆ parallel_communicator

moab::ParallelComm* RuntimeContext::parallel_communicator

Definition at line 95 of file ExchangeHalos.cpp.

Referenced by RuntimeContext(), timer_pop(), and ~RuntimeContext().

◆ partnset

moab::EntityHandle RuntimeContext::partnset { 0 }

Definition at line 96 of file ExchangeHalos.cpp.

Referenced by RuntimeContext().

◆ proc_id

int RuntimeContext::proc_id { 1 }

write debug output information?

Definition at line 89 of file ExchangeHalos.cpp.

Referenced by create_sv_tags(), RuntimeContext(), and timer_pop().

◆ scalar_tagname

std::string RuntimeContext::scalar_tagname

number of ghost layers

Definition at line 84 of file ExchangeHalos.cpp.

Referenced by create_sv_tags().

◆ vector_length

int RuntimeContext::vector_length { 3 }

vector tag name

Definition at line 86 of file ExchangeHalos.cpp.

Referenced by create_sv_tags(), and ParseCLOptions().

◆ vector_tagname

std::string RuntimeContext::vector_tagname

scalar tag name

Definition at line 85 of file ExchangeHalos.cpp.

Referenced by create_sv_tags().

The documentation for this struct was generated from the following file:

ExchangeHalos.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RuntimeContext()

◆ ~RuntimeContext()

Member Function Documentation

◆ compute_centroids()

◆ create_sv_tags()

◆ evaluate_function()

◆ last_elapsed()

◆ load_file()

◆ ParseCLOptions()

◆ timer_pop()

◆ timer_push()

Member Data Documentation

◆ debug_output

◆ dimension

◆ fileset

◆ ghost_layers

◆ input_filename

◆ last_counter

◆ moab_interface

◆ mOpName

◆ mTimer

◆ mTimerOps

◆ num_max_exchange

◆ num_procs

◆ output_filename

◆ parallel_communicator

◆ partnset

◆ proc_id

◆ scalar_tagname

◆ vector_length

◆ vector_tagname