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"""Unit tests for the Matrix interface"""
# Copyright (C) 2011-2014 Garth N. Wells
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# DOLFIN is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
#
# Modified by Anders Logg 2011
# Modified by Mikael Mortensen 2011
# Modified by Jan Blechta 2013
import pytest
from dolfin import *
from dolfin_utils.test import *
# TODO: Reuse this fixture setup code between matrix and vector tests:
# Lists of backends supporting or not supporting FooMatrix::data()
# access
data_backends = []
no_data_backends = [("PETSc", ""), ("Tpetra", "")]
# Add serial only backends
if MPI.size(MPI.comm_world) == 1:
# TODO: What about "Dense" and "Sparse"? The sub_backend wasn't
# used in the old test.
data_backends += [("Eigen", "")]
# Remove backends we haven't built with
data_backends = [b for b in data_backends if has_linear_algebra_backend(b[0])]
no_data_backends = [b for b in no_data_backends if has_linear_algebra_backend(b[0])]
any_backends = data_backends + no_data_backends
# Fixtures setting up and resetting the global linear algebra backend
# for a list of backends
any_backend = set_parameters_fixture("linear_algebra_backend", any_backends,
lambda x: x[0])
data_backend = set_parameters_fixture("linear_algebra_backend", data_backends,
lambda x: x[0])
no_data_backend = set_parameters_fixture("linear_algebra_backend",
no_data_backends, lambda x: x[0])
# With and without explicit backend choice
use_backend = true_false_fixture
class TestMatrixForAnyBackend:
def assemble_matrices(self, use_backend=False, keep_diagonal=False):
" Assemble a pair of matrices, one (square) MxM and one MxN"
mesh = UnitSquareMesh(21, 23)
V = FunctionSpace(mesh, "Lagrange", 2)
W = FunctionSpace(mesh, "Lagrange", 1)
v = TestFunction(V)
u = TrialFunction(V)
s = TrialFunction(W)
# Forms
a = dot(grad(u), grad(v))*ds
b = v*s*dx
if use_backend:
backend = globals()[self.backend + self.sub_backend + 'Factory'].instance()
else:
backend = None
# Build square matrix with some 'empty' diagonals
A = assemble(a, backend=backend, keep_diagonal=keep_diagonal)
# Build non-square matrix
B = assemble(b, backend=backend, keep_diagonal=keep_diagonal)
return A, B
def test_basic_la_operations(self, use_backend, any_backend):
# Hack to make old tests work in new framework. The original
# setup was a bit exoteric...
# TODO: Removing use of self in this class will make it
# clearer what happens in this test.
self.backend, self.sub_backend = any_backend
from numpy import ndarray, array, ones, sum
A, B = self.assemble_matrices(use_backend)
unit_norm = A.norm('frobenius')
def wrong_getitem(type):
if type == 0:
A["0,1"]
elif type == 1:
A[0]
elif type == 2:
A[0, 0, 0]
# Test wrong getitem
with pytest.raises(TypeError):
wrong_getitem(0)
with pytest.raises(TypeError):
wrong_getitem(1)
with pytest.raises(TypeError):
wrong_getitem(2)
# Test __imul__ operator
A *= 2
assert round(A.norm('frobenius') - 2*unit_norm, 7) == 0
# Test __idiv__ operator
A /= 2
assert round(A.norm('frobenius') - unit_norm, 7) == 0
# Test __mul__ operator
C = 4*A
assert round(C.norm('frobenius') - 4*unit_norm, 7) == 0
# Test __iadd__ operator
A += C
assert round(A.norm('frobenius') - 5*unit_norm, 7) == 0
# Test __isub__ operator
A -= C
assert round(A.norm('frobenius') - unit_norm, 7) == 0
# Test __mul__ and __add__ operator
D = (C+A)*0.2
assert round(D.norm('frobenius') - unit_norm, 7) == 0
# Test __div__ and __sub__ operator
F = (C-A)/3
assert round(F.norm('frobenius') - unit_norm, 7) == 0
# Test axpy
A.axpy(10,C,True)
assert round(A.norm('frobenius') - 41*unit_norm, 7) == 0
# Test expected size of rectangular array
assert A.size(0) == B.size(0)
assert B.size(1) == 528
# Test setitem/getitem
#A[5,5] = 15
#assert A[5,5] == 15
@skip_in_parallel
def test_numpy_array(self, use_backend, any_backend):
self.backend, self.sub_backend = any_backend
from numpy import ndarray, array, ones, sum
# Assemble matrices
A, B = self.assemble_matrices(use_backend)
# Test to NumPy array
A2 = A.array()
assert isinstance(A2,ndarray)
assert A2.shape == (2021, 2021)
assert round(sqrt(sum(A2**2)) - A.norm('frobenius'), 7) == 0
if self.backend == 'Eigen':
try:
import scipy.sparse
import numpy.linalg
A = as_backend_type(A)
A3 = A.sparray()
assert isinstance(A3, scipy.sparse.csr_matrix)
assert round(numpy.linalg.norm(A3.todense() - A2) - 0.0, 7) == 0
row, col, val = A.data()
A_scipy = scipy.sparse.csr_matrix((val, col, row))
assert round(numpy.linalg.norm(A_scipy.todense(), 'fro') \
- A.norm("frobenius"), 7) == 0.0
except ImportError:
pass
def test_create_empty_matrix(self, any_backend):
A = Matrix()
assert A.size(0) == 0
assert A.size(1) == 0
info(A)
info(A, True)
def test_copy_empty_matrix(self, any_backend):
A = Matrix()
B = Matrix(A)
assert B.size(0) == 0
assert B.size(1) == 0
def test_copy_matrix(self, any_backend):
A0, B0 = self.assemble_matrices()
A1 = Matrix(A0)
assert A0.size(0) == A1.size(0)
assert A0.size(1) == A1.size(1)
assert A0.norm("frobenius") == A1.norm("frobenius")
B1 = Matrix(B0)
assert B0.size(0) == B1.size(0)
assert B0.size(1) == B1.size(1)
assert round(B0.norm("frobenius") - B1.norm("frobenius"), 7) == 0
def test_ident_zeros(self, use_backend, any_backend):
self.backend, self.sub_backend = any_backend
# Check that PETScMatrix::ident_zeros() rethrows PETSc error
if self.backend[0:5] == "PETSc":
try:
from petsc4py import PETSc
except ImportError:
# Can't detect PETSc version. Skip the test.
pass
else:
petsc_version = PETSc.Sys.getVersion()
if petsc_version[0:2] == (3, 7) and petsc_version[2] >= 6:
# Skip the test. PETSc 3.7.(>=6) is doing the diagonal
# check only in debug mode so that DOLFIN might not
# rethrow the error. Fixed in
# https://bitbucket.org/petsc/petsc/commits/a21198abcdd10db88d217ac122e897fcbe3179cd
pass
else:
# NOTE: Throw try-except-else,if blocks above and do the
# test everytime when PETSc requirement is bumped
# to 3.8
A, B = self.assemble_matrices(use_backend=use_backend)
with pytest.raises(RuntimeError):
A.ident_zeros()
# Assemble matrix A with diagonal entries
A, B = self.assemble_matrices(use_backend=use_backend,
keep_diagonal=True)
# Find zero rows
zero_rows = []
for i in range(A.local_range(0)[0], A.local_range(0)[1]):
row = A.getrow(i)[1]
if sum(abs(row)) < DOLFIN_EPS:
zero_rows.append(i)
# Set zero rows to (0,...,0, 1, 0,...,0)
A.ident_zeros()
# Check it
for i in zero_rows:
cols = A.getrow(i)[0]
row = A.getrow(i)[1]
for j in range(cols.size + 1):
if i == cols[j]:
assert round(row[j] - 1.0, 7) == 0
break
assert j < cols.size
assert round(sum(abs(row)) - 1.0, 7) == 0
@skip_in_parallel
def test_ident(self, use_backend, any_backend):
self.backend, self.sub_backend = any_backend
if self.backend == 'Tpetra':
pytest.skip()
A, B = self.assemble_matrices(use_backend)
N, M = A.size(0), A.size(1)
# Make sure rows are not identity from before
import numpy
ROWS = [2, 4]
for row in ROWS:
block = numpy.array([[42.0]], dtype=float)
A.set(block, numpy.array([row], dtype=numpy.intc),
numpy.array([row], dtype=numpy.intc))
A.apply("insert")
def check_row(A, row, idented):
cols, vals = A.getrow(row)
i = list(cols).index(row)
if idented:
assert vals[i] == 1
vals[i] = 0
for c in cols:
if c != row:
assert (vals == 0).all()
else:
assert vals[i] == 42.0
for row in ROWS:
check_row(A, row, False)
A.ident(numpy.array(ROWS, dtype=numpy.intc))
A.apply("insert")
for row in ROWS:
check_row(A, row, True)
def test_setting_getting_diagonal(self, use_backend, any_backend):
self.backend, self.sub_backend = any_backend
mesh = UnitSquareMesh(21, 23)
V = FunctionSpace(mesh, "Lagrange", 2)
v = TestFunction(V)
u = TrialFunction(V)
w = Function(V)
if use_backend:
backend = globals()[self.backend + self.sub_backend + 'Factory'].instance()
else:
backend = None
B = assemble(u*v*dx(), backend=backend, keep_diagonal=True)
b = assemble(action(u*v*dx(), Constant(1)))
A = B.copy()
A.zero()
A.set_diagonal(b)
resultsA = Vector()
resultsB = Vector()
A.init_vector(resultsA, 1)
B.init_vector(resultsB, 1)
ones = b.copy()
ones[:] = 1.0
A.mult(ones, resultsA)
B.mult(ones, resultsB)
assert round(resultsA.norm("l2") - resultsB.norm("l2"), 7) == 0
A.get_diagonal(w.vector())
w.vector()[:] -= b
assert round(w.vector().norm("l2"), 14) == 0
@skip_in_parallel
def test_get_set(self, use_backend, any_backend):
self.backend, self.sub_backend = any_backend
if self.backend == 'Tpetra':
pytest.skip()
A, B = self.assemble_matrices(use_backend)
N, M = A.size(0), A.size(1)
import numpy
rows = numpy.array([1, 2], dtype=numpy.intc)
cols = numpy.array([1, 2], dtype=numpy.intc)
block_in = numpy.ones((2, 2), dtype=float) * 42
Anp0 = A.array()
assert (Anp0[1:3,1:3] != block_in).any()
A.set(block_in, rows, cols)
A.apply("insert")
Anp1 = A.array()
assert (Anp1[1:3,1:3] == block_in).all()
block_out = numpy.zeros_like(block_in)
A.get(block_out, rows, cols)
assert (block_out == block_in).all()
# def test_create_from_sparsity_pattern(self):
# def test_size(self):
# def test_local_range(self):
# def test_zero(self):
# def test_apply(self):
# def test_str(self):
# def test_resize(self):
# Test the access of the raw data through pointers
# This is only available for the Eigen backend
def test_matrix_data(self, use_backend, data_backend):
""" Test for ordinary Matrix"""
self.backend, self.sub_backend = data_backend
A, B = self.assemble_matrices(use_backend)
A = as_backend_type(A)
B = as_backend_type(B)
array = A.array()
rows, cols, values = A.data()
i = 0
for row in range(A.size(0)):
for col in range(rows[row], rows[row+1]):
assert array[row, cols[col]] == values[i]
i += 1
# Test for as_backend_typeed Matrix
A = as_backend_type(A)
rows, cols, values = A.data()
for row in range(A.size(0)):
for k in range(rows[row], rows[row+1]):
assert array[row,cols[k]] == values[k]
def test_matrix_nnz(self, any_backend):
A, B = self.assemble_matrices()
assert A.nnz() == 2992
assert B.nnz() == 9398
A, B = self.assemble_matrices(keep_diagonal=True)
assert A.nnz() == 4589
# NOTE: Following should never be tested because diagonal is not
# invariant w.r.t. different row and column dof reordering!
#assert B.nnz() == ??
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