diff --git a/src/bvpy/boundary_conditions/dirichlet.py b/src/bvpy/boundary_conditions/dirichlet.py
index 7255301d6c23f571b5e24183ac6ed39252af2cd7..8440be53c1cc71b43cc44506deabc3442394361e 100644
--- a/src/bvpy/boundary_conditions/dirichlet.py
+++ b/src/bvpy/boundary_conditions/dirichlet.py
@@ -21,6 +21,7 @@
# -----------------------------------------------------------------------
import fenics as fe
from bvpy import logger
+from bvpy import MPI_COMM_WORLD
import numpy as np
from sympy import Symbol
@@ -98,10 +99,12 @@ class ConstantDirichlet(object):
dir = fe.DirichletBC(functionSpace.sub(self._subspace),
fe.Constant(self._val),
self._boundary(), method=self._method)
-
+
if not dir.get_boundary_values():
- logger.warning('No nodes are marked for this domain: '
- + str(self._boundary._string))
+ if (MPI_COMM_WORLD.Get_size() > 1) and (MPI_COMM_WORLD.Get_rank() == 0):
+ logger.warning('No nodes are marked for some domain (this can be normal when using MPI)')
+ elif MPI_COMM_WORLD.Get_size() == 1:
+ logger.warning('No nodes are marked for this domain: ' + str(self._boundary._string))
return dir
diff --git a/src/bvpy/domains/abstract.py b/src/bvpy/domains/abstract.py
index 21836c3e5b6fecdb63a3b6e2f96a8157360fdf9f..0260aa592bfd6a3f75a4a3231e841848ab603c80 100644
--- a/src/bvpy/domains/abstract.py
+++ b/src/bvpy/domains/abstract.py
@@ -19,6 +19,7 @@
# https://www.gnu.org/licenses/lgpl-3.0.en.html
#
# -----------------------------------------------------------------------
+import time
import gmsh
import sys
@@ -159,8 +160,23 @@ class AbstractDomain(ABC):
verbosity=verbosity, algorithm=algorithm)
AbstractDomain._domain_instances += 1
+
if AbstractDomain._domain_instances == 1:
- gmsh.initialize() # for all processes
+ # - Initialize GMSH and the temp dir necessary to store the mesh
+ gmsh.initialize() # required for all processes
+ self.set_verbosity(verbosity)
+ log.debug(f'Initialize GMSH for {MPI_COMM_WORLD.Get_rank()}')
+
+ if MPI_COMM_WORLD.Get_rank() == 0:
+ self._mesh_dir = tempfile.TemporaryDirectory() # keep reference to avoid suppression of temp folder
+ dir_name = self._mesh_dir.name
+ else:
+ dir_name = None
+
+ # Broadcast to other processes
+ self._dir_name = MPI_COMM_WORLD.bcast(dir_name, root=0)
+
+ log.debug(f'TempFile {self._dir_name} for {MPI_COMM_WORLD.Get_rank()}')
if clear:
gmsh.clear()
@@ -170,18 +186,7 @@ class AbstractDomain(ABC):
self._cell_size = cell_size
self._algorithm = algorithm
- if MPI_COMM_WORLD.Get_rank() == 0:
- # Creation of the temporary folder only for the process of rank 0
- self._mesh_dir = tempfile.TemporaryDirectory() # keep a reference to avoid suppression of the temp file
- dir_name = self._mesh_dir .name
- else:
- dir_name = None
-
- # Diffusion of the folder to the other processess
- self._dir_name = MPI_COMM_WORLD.bcast(dir_name, root=0)
-
self.set_cell_type(cell_type)
- self.set_verbosity(verbosity)
self.set_cell_size(cell_size)
self.set_meshing_algorithm(algorithm)
self.set_dim(dim)
@@ -206,14 +211,18 @@ class AbstractDomain(ABC):
"""
#self._mesh_dir.cleanup()
- if MPI_COMM_WORLD.Get_rank() == 0:
- # Remove the temporary folder and its content using process of rank 0
- if self._dir_name and os.path.isdir(self._dir_name):
+ if (MPI_COMM_WORLD.Get_rank() == 0) and hasattr(self, '_dir_name'):
+ if os.path.isdir(self._dir_name):
+ # Remove the temporary folder and its content using process of rank 0
+ log.debug(f'Clear temp file for {MPI_COMM_WORLD.Get_rank()} at {self._dir_name} instances')
shutil.rmtree(self._dir_name)
+
AbstractDomain._domain_instances -= 1
if AbstractDomain._domain_instances == 0:
gmsh.finalize() # for all processes
+ log.debug(
+ f'Finalize GMSH for {MPI_COMM_WORLD.Get_rank()}')
def __repr__(self):
"""Returns a short description of the considered domain.
@@ -487,10 +496,11 @@ class AbstractDomain(ABC):
# - Set default values for the domain & boundaries labels/name
has_bdata = False # flag to fill automatically labels to boundary
- sub_boundary_names = {0: 'boundary'} # default naming for the boundary
has_cdata = False # flag to fill automatically labels if needed
+ sub_boundary_names = {0: 'boundary'} # default naming for the boundary
sub_domain_names = {0: 'domain'} # default naming for the domain
+
### From GMSH to MESHIO
# Only the rank 0 process generate the gmsh mesh, convert it to MeshIO and save it as XDMF file.
# It will avoid duplicates
@@ -504,9 +514,9 @@ class AbstractDomain(ABC):
element_type, element_tags, _ = self.model.mesh.getElements(ele_dim) # get the entities of dimension `ele_dim`
N = len(element_tags[np.where(element_type == ELEMENT_GMSH_TYPES[self._cell_type])[0][0]]) # number of entities
- gmsh.write(self._dir_name+'/mesh.msh')
-
path = self._dir_name + '/mesh.msh'
+
+ gmsh.write(path)
mesh_io = mio.read(path, file_format='gmsh')
# - Get the coordinates of the vertices
@@ -573,7 +583,7 @@ class AbstractDomain(ABC):
sub_domain_names.update({lab: f'sub_domain_{i}'
for i, lab in enumerate(set(labels) - set(sub_domain_names))})
- mio.write(self._dir_name + '/' + 'mesh.xdmf',
+ mio.write(self._dir_name + '/mesh.xdmf',
mio.Mesh(points=mesh_io.points,
cells={self._cell_type:
mesh_io.cells_dict[self._cell_type]},
@@ -581,10 +591,11 @@ class AbstractDomain(ABC):
else:
log.debug(f"No labels found at the dimension {ele_dim}, use default.")
- mio.write(self._dir_name + '/' + 'mesh.xdmf',
+ mio.write(self._dir_name + '/mesh.xdmf',
mio.Mesh(points=mesh_io.points,
cells={self._cell_type:
mesh_io.cells_dict[self._cell_type]}))
+ log.debug(f"MeshIO Mesh was written at {self._dir_name + '/mesh.xdmf'}")
# - Extract physical properties (and possible names) for the boundaries (ele_dim - 1)
bnd_cell_type = [cell_type for cell_type, d in CELL_TYPE.items() if d == (ele_dim - 1)][0]
@@ -618,6 +629,7 @@ class AbstractDomain(ABC):
mesh_io.cells_dict[bnd_cell_type]},
cell_data={f"boundary": [labels]})
mio.xdmf.write(self._dir_name + '/mesh_boundary.xdmf', bnd_mesh)
+ log.debug(f"MeshIO Boundary was written at {self._dir_name + '/mesh_boundary.xdmf'}")
# Update state of other processes from rank 0 (labels and sub-domain names)
has_cdata = MPI_COMM_WORLD.bcast(has_cdata, root=0)
@@ -636,7 +648,7 @@ class AbstractDomain(ABC):
mesh = fe.Mesh()
# Read the saved mesh
- with fe.XDMFFile(MPI_COMM_WORLD, self._dir_name + '/' + 'mesh.xdmf') as f:
+ with fe.XDMFFile(MPI_COMM_WORLD, self._dir_name + '/mesh.xdmf') as f:
f.read(mesh)
# Fill the cdata
@@ -681,9 +693,9 @@ class GmshProxy:
def __getattr__(self, name):
"""Redirige les appels de méthode vers factory si le rang est 0."""
def method(*args, **kwargs):
- log.debug(f'Call from {MPI_COMM_WORLD.Get_rank()} of the method {name}')
+ #log.debug(f'Call from {MPI_COMM_WORLD.Get_rank()} of the method {name}')
if MPI_COMM_WORLD.Get_rank() == 0:
- log.debug(f'Ok for {MPI_COMM_WORLD.Get_rank()} of the method {name}')
+ #log.debug(f'Ok for {MPI_COMM_WORLD.Get_rank()} of the method {name}')
return getattr(self._factory, name)(*args, **kwargs)
else:
log.debug(f'NO for {MPI_COMM_WORLD.Get_rank()} of the method {method}')
diff --git a/src/bvpy/solvers/nonlinear.py b/src/bvpy/solvers/nonlinear.py
index b136475409c446211c4080961cb21d9253413389..d42e9cf68ddc4c77a37b84d6f61d487a7a41ce74 100644
--- a/src/bvpy/solvers/nonlinear.py
+++ b/src/bvpy/solvers/nonlinear.py
@@ -221,26 +221,28 @@ class NonLinearSolver():
of the performed computation.
"""
if self._type == 'petsc':
- logger.info(' Backend : petsc')
- logger.info(' Linear Solver : '
- + str(self._solver.parameters['linear_solver']))
- logger.info(' Preconditioner: '
- + str(self._solver.parameters['preconditioner']))
- logger.info(f" atol: {self._solver.parameters['absolute_tolerance']}")
- logger.info(f" rtol: {self._solver.parameters['relative_tolerance']}")
- logger.info(' Size : '
- + str(self._u.function_space().dim()))
- logger.info(' Solving NonLinearProblem ...')
+ if MPI_COMM_WORLD.Get_rank() == 0:
+ logger.info(' Backend : petsc')
+ logger.info(' Linear Solver : '
+ + str(self._solver.parameters['linear_solver']))
+ logger.info(' Preconditioner: '
+ + str(self._solver.parameters['preconditioner']))
+ logger.info(f" atol: {self._solver.parameters['absolute_tolerance']}")
+ logger.info(f" rtol: {self._solver.parameters['relative_tolerance']}")
+ logger.info(' Size : '
+ + str(self._u.function_space().dim()))
+ logger.info(' Solving NonLinearProblem ...')
start = time.time()
self._solver.solve(self._problem, self._u.vector())
end = time.time()
residuals = self._snes.getConvergenceHistory()[0]
-
- logger.info(' ... Done [' + str(end - start) + ' s]')
conv = self._snes.getConvergedReason()
- logger.info(' Iterations : ' + str(len(residuals)))
- logger.info(' Resiudal : ' + str(residuals[-1]))
+
+ if MPI_COMM_WORLD.Get_rank() == 0:
+ logger.info(' ... Done [' + str(end - start) + ' s]')
+ logger.info(' Iterations : ' + str(len(residuals)))
+ logger.info(' Resiudal : ' + str(residuals[-1]))
return residuals
\ No newline at end of file