def test_Hexmesh3(self):
# Hexagonal mesh
#
# 1---2---7
# /5\0/1\6/7\
# 6---0---3---8
# \4/3\2/9\8/
# 5---4---9
#
# Divided 2 ways
# Calling order is: elements, verticies, edge list
# element type, number parts
edgecut, epart, npart = metis.partMeshNodal(10, 10,\
[0, 2, 1,\
0, 3, 2,\
0, 4, 3,\
0, 5, 4,\
0, 6, 5,\
0, 1, 6,\
3, 2, 7,\
3, 7, 8,\
3, 8, 9,\
3, 9, 4],\
1,\
3,)
#print edgecut
#print epart
#print npart
if sys.platform == 'win32':
epart_expected = array([2, 0, 2, 2, 1, 1, 0, 0, 0, 0], 'i')
npart_expected = array([2, 1, 0, 0, 2, 1, 1, 0, 2, 0], 'i')
self.assert_(edgecut == 12)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
elif sys.platform == 'darwin':
epart_expected = array([0, 2, 2, 2, 1, 0, 0, 1, 1, 2], 'i')
npart_expected = array([2, 0, 0, 1, 2, 1, 2, 0, 1, 2], 'i')
self.assert_(edgecut == 13)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
else:
epart_expected = array([0, 0, 0, 1, 2, 2, 2, 2, 1, 1], 'i')
npart_expected = array([0, 2, 0, 2, 1, 1, 2, 2, 0, 1], 'i')
self.assert_(edgecut == 14)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
def test_Hexmesh2(self):
# Hexagonal mesh
#
# 1---2
# / \ / \
# 6---0---3
# \ / \ /
# 5---4
#
# Divided 2 ways
# Calling order is: elements, verticies, edge list
# element type, number parts
edgecut, epart, npart = metis.partMeshNodal(6, 7,\
[0, 2, 1,\
0, 3, 2,\
0, 4, 3,\
0, 5, 4,\
0, 6, 5,\
0, 1, 6],\
1,\
2,)
#print edgecut
#print epart
#print npart
#print sys.platform
if sys.platform == 'win32':
epart_expected = array([1, 1, 1, 1, 1, 1], 'i')
npart_expected = array([1, 1, 1, 1, 1, 1, 1], 'i')
self.assert_(edgecut == 0)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
elif sys.platform == 'darwin':
epart_expected = array([1, 1, 1, 1, 1, 1], 'i')
npart_expected = array([1, 1, 1, 1, 1, 1, 1], 'i')
self.assert_(edgecut == 0)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
else:
epart_expected = array([1, 0, 0, 0, 1, 1], 'i')
npart_expected = array([0, 1, 1, 0, 0, 0, 1], 'i')
self.assert_(edgecut == 5)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
def test_Hexmesh3(self):
# Hexagonal mesh
#
# 1---2---7
# /5\0/1\6/7\
# 6---0---3---8
# \4/3\2/9\8/
# 5---4---9
#
# Divided 2 ways
# Calling order is: elements, verticies, edge list
# element type, number parts
edgecut, epart, npart = metis.partMeshNodal(10, 10,\
[0, 2, 1,\
0, 3, 2,\
0, 4, 3,\
0, 5, 4,\
0, 6, 5,\
0, 1, 6,\
3, 2, 7,\
3, 7, 8,\
3, 8, 9,\
3, 9, 4],\
1,\
3,)
#print edgecut
#print epart
#print npart
if sys.platform == 'win32':
epart_expected = array([2, 0, 2, 2, 1, 1, 0, 0, 0, 0], 'i')
npart_expected = array([2, 1, 0, 0, 2, 1, 1, 0, 2, 0], 'i')
self.assert_(edgecut == 12)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
else:
epart_expected = array([0, 0, 0, 1, 2, 2, 2, 2, 1, 1], 'i')
npart_expected = array([0, 2, 0, 2, 1, 1, 2, 2, 0, 1], 'i')
self.assert_(edgecut == 14)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
def test_Hexmesh2(self):
# Hexagonal mesh
#
# 1---2
# / \ / \
# 6---0---3
# \ / \ /
# 5---4
#
# Divided 2 ways
# Calling order is: elements, verticies, edge list
# element type, number parts
edgecut, epart, npart = metis.partMeshNodal(6, 7,\
[0, 2, 1,\
0, 3, 2,\
0, 4, 3,\
0, 5, 4,\
0, 6, 5,\
0, 1, 6],\
1,\
2,)
#print edgecut
#print epart
#print npart
if sys.platform == 'win32':
epart_expected = array([1, 1, 1, 1, 1, 1], 'i')
npart_expected = array([1, 1, 1, 1, 1, 1, 1], 'i')
self.assert_(edgecut == 0)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
else:
epart_expected = array([1, 0, 0, 0, 1, 1], 'i')
npart_expected = array([0, 1, 1, 0, 0, 0, 1], 'i')
self.assert_(edgecut == 5)
assert allclose(epart, epart_expected)
assert allclose(npart, npart_expected)
def pmesh_divide_metis_helper(domain, n_procs):
# Initialise the lists
# List, indexed by processor of # triangles.
#triangles_per_proc = []
# List of lists, indexed by processor of vertex numbers
#tri_list = []
# Serial to Parallel and Parallel to Serial Triangle index maps
tri_index = {}
r_tri_index = {} # reverse tri index, parallel to serial triangle index mapping
# Prepare variables for the metis call
n_tri = len(domain.triangles)
if n_procs != 1: #Because metis chokes on it...
n_vert = domain.get_number_of_nodes()
t_list = domain.triangles.copy()
t_list = num.reshape(t_list, (-1,))
# The 1 here is for triangular mesh elements.
# FIXME: Should update to Metis 5
edgecut, epart, npart = partMeshNodal(n_tri, n_vert, t_list, 1, n_procs)
# print edgecut
# print npart
#print epart
del edgecut
del npart
# Sometimes (usu. on x86_64), partMeshNodal returns an array of zero
# dimensional arrays. Correct this.
if type(epart[0]) == num.ndarray:
epart_new = num.zeros(len(epart), num.int)
epart_new[:] = epart[:][0]
# for i in xrange(len(epart)):
# epart_new[i] = epart[i][0]
epart = epart_new
del epart_new
triangles_per_proc = num.bincount(epart)
msg = "Metis created a partition where at least one submesh has no triangles. "
msg += "Try using a smaller number of mpi processes."
assert num.all(triangles_per_proc>0), msg
proc_sum = num.zeros(n_procs+1,num.int)
proc_sum[1:] = num.cumsum(triangles_per_proc)
epart_order = num.argsort(epart, kind='mergesort')
new_triangles = domain.triangles[epart_order]
#new_r_tri_index_flat = num.zeros((n_tri,3), num.int)
new_tri_index = num.zeros((n_tri,2), num.int)
for i in xrange(n_procs):
ids = num.arange(proc_sum[i],proc_sum[i+1])
eids = epart_order[ids]
nrange = num.reshape(num.arange(triangles_per_proc[i]), (-1,1))
nones = num.ones_like(nrange)
#print ids.shape
#print nrange.shape
new_tri_index[eids] = num.concatenate((i*nones, nrange), axis = 1)
#new_r_tri_index_flat[ids] = num.concatenate((i*nones, nrange, num.reshape(eids, (-1,1))), axis = 1)
if verbose:
from pprint import pprint
print 'epart'
pprint(epart)
print 'new_tri_index'
pprint(new_tri_index)
#print 50*'='
new_boundary = {}
for b in domain.boundary:
t = new_tri_index[b[0]]
#print t
new_boundary[proc_sum[t[0]]+t[1], b[1]] = domain.boundary[b]
#quantities = reorder(domain.quantities, tri_index, proc_sum)
new_quantities = reorder_new(domain.quantities, epart_order, proc_sum)
else:
new_boundary = domain.boundary.copy()
triangles_per_proc = [n_tri]
new_triangles = domain.triangles.copy()
new_tri_index = []
epart_order = []
# This is essentially the same as a chunk of code from reorder.
new_quantities = {}
for k in domain.quantities:
new_quantities[k] = num.zeros((n_tri, 3), num.float)
for i in range(n_tri):
new_quantities[k][i] = domain.quantities[k].vertex_values[i]
# Extract the node list
new_nodes = domain.get_nodes().copy()
return new_nodes, new_triangles, new_boundary, triangles_per_proc, new_quantities, new_tri_index, epart_order
def pmesh_divide_metis_helper(domain, n_procs):
# Initialise the lists
# List, indexed by processor of # triangles.
#triangles_per_proc = []
# List of lists, indexed by processor of vertex numbers
#tri_list = []
# Serial to Parallel and Parallel to Serial Triangle index maps
tri_index = {}
r_tri_index = {
} # reverse tri index, parallel to serial triangle index mapping
# Prepare variables for the metis call
n_tri = len(domain.triangles)
if n_procs != 1: #Because metis chokes on it...
n_vert = domain.get_number_of_nodes()
t_list = domain.triangles.copy()
t_list = num.reshape(t_list, (-1, ))
# The 1 here is for triangular mesh elements.
# FIXME: Should update to Metis 5
edgecut, epart, npart = partMeshNodal(n_tri, n_vert, t_list, 1,
n_procs)
# print edgecut
# print npart
#print epart
del edgecut
del npart
# Sometimes (usu. on x86_64), partMeshNodal returns an array of zero
# dimensional arrays. Correct this.
if type(epart[0]) == num.ndarray:
epart_new = num.zeros(len(epart), num.int)
epart_new[:] = epart[:][0]
# for i in xrange(len(epart)):
# epart_new[i] = epart[i][0]
epart = epart_new
del epart_new
triangles_per_proc = num.bincount(epart)
msg = "Metis created a partition where at least one submesh has no triangles. "
msg += "Try using a smaller number of mpi processes."
assert num.all(triangles_per_proc > 0), msg
proc_sum = num.zeros(n_procs + 1, num.int)
proc_sum[1:] = num.cumsum(triangles_per_proc)
epart_order = num.argsort(epart, kind='mergesort')
new_triangles = domain.triangles[epart_order]
#new_r_tri_index_flat = num.zeros((n_tri,3), num.int)
new_tri_index = num.zeros((n_tri, 2), num.int)
for i in xrange(n_procs):
ids = num.arange(proc_sum[i], proc_sum[i + 1])
eids = epart_order[ids]
nrange = num.reshape(num.arange(triangles_per_proc[i]), (-1, 1))
nones = num.ones_like(nrange)
#print ids.shape
#print nrange.shape
new_tri_index[eids] = num.concatenate((i * nones, nrange), axis=1)
#new_r_tri_index_flat[ids] = num.concatenate((i*nones, nrange, num.reshape(eids, (-1,1))), axis = 1)
if verbose:
from pprint import pprint
print 'epart'
pprint(epart)
print 'new_tri_index'
pprint(new_tri_index)
#print 50*'='
new_boundary = {}
for b in domain.boundary:
t = new_tri_index[b[0]]
#print t
new_boundary[proc_sum[t[0]] + t[1], b[1]] = domain.boundary[b]
#quantities = reorder(domain.quantities, tri_index, proc_sum)
new_quantities = reorder_new(domain.quantities, epart_order, proc_sum)
else:
new_boundary = domain.boundary.copy()
triangles_per_proc = [n_tri]
new_triangles = domain.triangles.copy()
new_tri_index = []
epart_order = []
# This is essentially the same as a chunk of code from reorder.
new_quantities = {}
for k in domain.quantities:
new_quantities[k] = num.zeros((n_tri, 3), num.float)
for i in range(n_tri):
new_quantities[k][i] = domain.quantities[k].vertex_values[i]
# Extract the node list
new_nodes = domain.get_nodes().copy()
return new_nodes, new_triangles, new_boundary, triangles_per_proc, new_quantities, new_tri_index, epart_order
