def read(self, debug, interpolate):
"""
Read finite-element mesh and store in Sieve mesh object.
@returns PETSc mesh object containing finite-element mesh
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Reading finite-element mesh")
# Set flags
self.debug(debug)
self.interpolate(interpolate)
# Initialize coordinate system
if self.coordsys is None:
raise ValueError, "Coordinate system for mesh is unknown."
from pylith.mpi.Communicator import petsc_comm_world
from pylith.topology.Mesh import Mesh
mesh = Mesh(dim=self.coordsys.spaceDim(), comm=petsc_comm_world())
mesh.coordsys(self.coordsys)
# Read mesh
ModuleMeshIO.read(self, mesh)
return mesh
def read(self, debug, interpolate):
"""
Read finite-element mesh and store in Sieve mesh object.
@returns PETSc mesh object containing finite-element mesh
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Reading finite-element mesh")
# Set flags
self.debug(debug)
self.interpolate(interpolate)
# Initialize coordinate system
if self.coordsys is None:
raise ValueError, "Coordinate system for mesh is unknown."
from pylith.mpi.Communicator import petsc_comm_world
from pylith.topology.Mesh import Mesh
mesh = Mesh(dim=self.coordsys.spaceDim(), comm=petsc_comm_world())
mesh.coordsys(self.coordsys)
# Read mesh
ModuleMeshIO.read(self, mesh)
return mesh
def create(self, normalizer, faults=None):
"""
Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
# Read mesh
mesh = self.reader.read(self.debug, self.interpolate)
if self.debug:
mesh.view()
# Reorder mesh
if self.reorderMesh:
logEvent2 = "%sreorder" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent2)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Reordering cells and vertices.")
from pylith.topology.ReverseCuthillMcKee import ReverseCuthillMcKee
ordering = ReverseCuthillMcKee()
ordering.reorder(mesh)
self._eventLogger.eventEnd(logEvent2)
# Adjust topology
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Adjusting topology.")
self._adjustTopology(mesh, faults)
# Distribute mesh
if comm.size > 1:
if 0 == comm.rank:
self._info.log("Distributing mesh.")
mesh = self.distributor.distribute(mesh, normalizer)
if self.debug:
mesh.view()
mesh.memLoggingStage = "DistributedMesh"
# Refine mesh (if necessary)
newMesh = self.refiner.refine(mesh)
if not newMesh == mesh:
mesh.cleanup()
newMesh.memLoggingStage = "RefinedMesh"
# Can't reorder mesh again, because we do not have routine to
# unmix normal and hybrid cells.
# Nondimensionalize mesh (coordinates of vertices).
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(newMesh, normalizer)
self._eventLogger.eventEnd(logEvent)
return newMesh
def create(self, normalizer, faults=None):
"""
Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
# Read mesh
mesh = self.reader.read(self.debug, self.interpolate)
if self.debug:
mesh.view()
# Reorder mesh
if self.reorderMesh:
logEvent2 = "%sreorder" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent2)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Reordering cells and vertices.")
from pylith.topology.ReverseCuthillMcKee import ReverseCuthillMcKee
ordering = ReverseCuthillMcKee()
ordering.reorder(mesh)
self._eventLogger.eventEnd(logEvent2)
# Adjust topology
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Adjusting topology.")
self._adjustTopology(mesh, faults)
# Distribute mesh
if comm.size > 1:
if 0 == comm.rank:
self._info.log("Distributing mesh.")
mesh = self.distributor.distribute(mesh, normalizer)
if self.debug:
mesh.view()
mesh.memLoggingStage = "DistributedMesh"
# Refine mesh (if necessary)
newMesh = self.refiner.refine(mesh)
if not newMesh == mesh:
mesh.cleanup()
newMesh.memLoggingStage = "RefinedMesh"
# Can't reorder mesh again, because we do not have routine to
# unmix normal and hybrid cells.
# Nondimensionalize mesh (coordinates of vertices).
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(newMesh, normalizer)
self._eventLogger.eventEnd(logEvent)
return newMesh
def finalize(self):
"""Finalize PETSc.
"""
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if 0 == comm.rank:
self._info.log("Finalizing PETSc.")
petsc.finalize()
return
def finalize(self):
"""
Finalize PETSc.
"""
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if 0 == comm.rank:
self._info.log("Finalizing PETSc.")
petsc.finalize()
return
def initialize(self):
"""Initialize PETSc.
"""
import sys
args = [sys.executable]
options = self._getOptions()
if len(options) > 0:
for arg in options:
args.append(arg)
petsc.initialize(args)
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if 0 == comm.rank:
self._info.log("Initialized PETSc.")
return
def initialize(self):
"""
Initialize PETSc.
"""
import sys
args = [sys.executable]
options = self._getOptions()
if len(options) > 0:
for arg in options:
args.append(arg)
petsc.initialize(args)
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if 0 == comm.rank:
self._info.log("Initialized PETSc.")
return
def _showStatus(self, stage):
import sys
from pylith.utils.profiling import resourceUsageString
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if comm.rank == 0:
print "\n----------------------------------------------------------------------"
print "STAGE: %s" % stage
print "----------------------------------------------------------------------"
for irank in xrange(comm.size):
comm.barrier()
if comm.rank == irank:
print "\nPROCESSOR %d" % comm.rank
print "\nStatus from ps: %s\n" % resourceUsageString()
self.logger.show()
sys.stdout.flush()
comm.barrier()
return
def refine(self, mesh):
"""Refine mesh.
"""
self._setupLogging()
logEvent = "%srefine" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if 0 == comm.rank:
self._info.log("Refining mesh using uniform refinement.")
from .Mesh import Mesh
newMesh = Mesh()
newMesh.debug(mesh.debug())
newMesh.setCoordSys(mesh.getCoordSys())
ModuleRefineUniform.refine(self, newMesh, mesh, self.levels)
mesh.cleanup()
self._eventLogger.eventEnd(logEvent)
return newMesh
def refine(self, mesh):
"""
Refine mesh.
"""
self._setupLogging()
logEvent = "%srefine" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if 0 == comm.rank:
self._info.log("Refining mesh using uniform refinement.")
from Mesh import Mesh
newMesh = Mesh()
newMesh.debug(mesh.debug())
newMesh.coordsys(mesh.coordsys())
ModuleRefineUniform.refine(self, newMesh, mesh, self.levels)
mesh.cleanup()
self._eventLogger.eventEnd(logEvent)
return newMesh
def _runTest(self):
"""
Run test.
"""
#filenameIn = "data/tet4.exo"
#filenameIn = "tri3_200m_gradient.exo"
filenameIn = "tet4_150m.exo"
from pylith.perf.MemoryLogger import MemoryLogger
self.logger = MemoryLogger()
self.logger._configure()
from pylith.utils.petsc import MemoryLogger
sieveLogger = MemoryLogger.singleton()
from pylith.topology.topology import MeshOps_numMaterialCells
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
self._showStatus("Before reading mesh")
# ------------------------------------------------------------
# Read mesh
from pylith.meshio.MeshIOCubit import MeshIOCubit
io = MeshIOCubit()
io.inventory.filename = filenameIn
io.inventory.useNames = False
io._configure()
from pylith.materials.ElasticIsotropic3D import ElasticIsotropic3D
material = ElasticIsotropic3D()
material.inventory.label = "Elastic material"
material.inventory.id = 1
material._configure()
mesh = io.read(debug=False, interpolate=False)
self.logger.logMesh(mesh.memLoggingStage, mesh)
material.ncells = MeshOps_numMaterialCells(mesh, material.id())
self.logger.logMaterial(mesh.memLoggingStage, material)
self._showStatus("After reading mesh")
# ------------------------------------------------------------
# Reorder mesh
from pylith.topology.ReverseCuthillMcKee import ReverseCuthillMcKee
ordering = ReverseCuthillMcKee()
ordering.reorder(mesh)
# Expect no memory allocation
self.logger.memory["MeshReordering"] = 0
self._showStatus("After reordering mesh")
# ------------------------------------------------------------
# Distribute mesh
if comm.size > 1:
from pylith.topology.Distributor import Distributor
from spatialdata.units.Nondimensional import Nondimensional
distributor = Distributor()
normalizer = Nondimensional()
dmesh = distributor.distribute(mesh, normalizer)
dmesh.memLoggingStage = "DistributedMesh"
self.logger.logMesh(mesh.memLoggingStage, mesh)
material.ncells = MeshOps_numMaterialCells(mesh, material.id())
self.logger.logMaterial(mesh.memLoggingStage, material)
self.logger.logMesh(dmesh.memLoggingStage, dmesh)
material.ncells = MeshOps_numMaterialCells(dmesh, material.id())
self.logger.logMaterial(dmesh.memLoggingStage, material)
self._showStatus("After distributing mesh")
mesh = dmesh
if False: # Refine mesh (if necessary)
from pylith.topology.RefineUniform import RefineUniform
refiner = RefineUniform()
rmesh = refiner.refine(mesh)
rmesh.memLoggingStage = "RefinedMesh"
print "Unrefined mesh logging stage",mesh.memLoggingStage
self.logger.logMesh(mesh.memLoggingStage, mesh)
material.ncells = MeshOps_numMaterialCells(mesh, material.id())
self.logger.logMaterial(mesh.memLoggingStage, material)
self.logger.logMesh(rmesh.memLoggingStage, rmesh)
material.ncells = MeshOps_numMaterialCells(rmesh, material.id())
self.logger.logMaterial(rmesh.memLoggingStage, material)
self._showStatus("After refining mesh")
return