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.. role:: raw-html(raw)
:format: html
.. _c-spsolvers:
***********************
Sparse Linear Equations
***********************
In this section we describe routines for solving sparse sets of linear
equations.
A real symmetric or complex Hermitian sparse matrix is stored as an
:class:`spmatrix <cvxopt.spmatrix>` object ``X`` of size
(:math:`n`, :math:`n`) and an
additional character argument ``uplo`` with possible values :const:`'L'`
and :const:`'U'`. If ``uplo`` is :const:`'L'`, the lower triangular part
of ``X`` contains the lower triangular part of the symmetric or Hermitian
matrix, and the upper triangular matrix of ``X`` is ignored. If ``uplo``
is :const:`'U'`, the upper triangular part of ``X`` contains the upper
triangular part of the matrix, and the lower triangular matrix of ``X`` is
ignored.
A general sparse square matrix of order :math:`n` is represented by an
:class:`spmatrix` object of size (:math:`n`, :math:`n`).
Dense matrices, which appear as right-hand sides of equations, are
stored using the same conventions as in the BLAS and LAPACK modules.
.. _s-orderings:
Matrix Orderings
****************
CVXOPT includes an interface to the AMD library for computing approximate
minimum degree orderings of sparse matrices.
.. seealso::
* P. R. Amestoy, T. A. Davis, I. S. Duff, Algorithm 837: AMD, An
Approximate Minimum Degree Ordering Algorithm, ACM Transactions on
Mathematical Software, 30(3), 381-388, 2004.
.. function:: cvxopt.amd.order(A[, uplo = 'L'])
Computes the approximate mimimum degree ordering of a symmetric sparse
matrix :math:`A`. The ordering is returned as an integer dense matrix
with length equal to the order of :math:`A`. Its entries specify a
permutation that reduces fill-in during the Cholesky factorization.
More precisely, if ``p = order(A)`` , then ``A[p, p]`` has
sparser Cholesky factors than ``A``.
As an example we consider the matrix
.. math::
\left[ \begin{array}{rrrr}
10 & 0 & 3 & 0 \\
0 & 5 & 0 & -2 \\
3 & 0 & 5 & 0 \\
0 & -2 & 0 & 2
\end{array}\right].
>>> from cvxopt import spmatrix, amd
>>> A = spmatrix([10,3,5,-2,5,2], [0,2,1,2,2,3], [0,0,1,1,2,3])
>>> P = amd.order(A)
>>> print(P)
[ 1]
[ 0]
[ 2]
[ 3]
.. _s-umfpack:
General Linear Equations
************************
The module :mod:`cvxopt.umfpack` includes four functions for solving
sparse non-symmetric sets of linear equations. They call routines from
the UMFPACK library, with all control options set to the default values
described in the UMFPACK user guide.
.. seealso::
* T. A. Davis, Algorithm 832: UMFPACK -- an unsymmetric-pattern
multifrontal method with a column pre-ordering strategy, ACM
Transactions on Mathematical Software, 30(2), 196-199, 2004.
.. function:: cvxopt.umfpack.linsolve(A, B[, trans = 'N'])
Solves a sparse set of linear equations
.. math::
AX & = B \quad (\mathrm{trans} = \mathrm{'N'}), \\
A^TX & = B \quad (\mathrm{trans} = \mathrm{'T'}), \\
A^HX & = B \quad (\mathrm{trans} = \mathrm{'C'}),
where :math:`A` is a sparse matrix and :math:`B` is a dense matrix.
The arguments ``A`` and ``B`` must have the same type
(:const:`'d'` or :const:`'z'`) as ``A``. On exit ``B`` contains
the solution. Raises an :exc:`ArithmeticError` if the coefficient
matrix is singular.
In the following example we solve an equation with coefficient matrix
.. math::
:label: e-sp-Adef
A = \left[\begin{array}{rrrrr}
2 & 3 & 0 & 0 & 0 \\
3 & 0 & 4 & 0 & 6 \\
0 &-1 &-3 & 2 & 0 \\
0 & 0 & 1 & 0 & 0 \\
0 & 4 & 2 & 0 & 1
\end{array}\right].
>>> from cvxopt import spmatrix, matrix, umfpack
>>> V = [2, 3, 3, -1, 4, 4, -3, 1, 2, 2, 6, 1]
>>> I = [0, 1, 0, 2, 4, 1, 2, 3, 4, 2, 1, 4]
>>> J = [0, 0, 1, 1, 1, 2, 2, 2, 2, 3, 4, 4]
>>> A = spmatrix(V,I,J)
>>> B = matrix(1.0, (5,1))
>>> umfpack.linsolve(A,B)
>>> print(B)
[ 5.79e-01]
[-5.26e-02]
[ 1.00e+00]
[ 1.97e+00]
[-7.89e-01]
The function :func:`linsolve <cvxopt.umfpack.linsolve>` is
equivalent to the following three functions called in sequence.
.. function:: cvxopt.umfpack.symbolic(A)
Reorders the columns of ``A`` to reduce fill-in and performs a symbolic
LU factorization. ``A`` is a sparse, possibly rectangular, matrix.
Returns the symbolic factorization as an opaque C object that can be
passed on to :func:`numeric <cvxopt.umfpack.numeric>`.
.. function:: cvxopt.umfpack.numeric(A, F)
Performs a numeric LU factorization of a sparse, possibly rectangular,
matrix ``A``. The argument ``F`` is the symbolic factorization
computed by :func:`symbolic <cvxopt.umfpack.symbolic>`
applied to the matrix ``A``,
or another sparse matrix with the same sparsity pattern, dimensions,
and type. The numeric factorization is returned as an opaque C object
that that can be passed on to
:func:`solve <cvxopt.umfpack.solve>`. Raises an
:exc:`ArithmeticError` if the matrix is singular.
.. function:: cvxopt.umfpack.solve(A, F, B[, trans = 'N'])
Solves a set of linear equations
.. math::
AX & = B \quad (\mathrm{trans} = \mathrm{'N'}), \\
A^TX & = B \quad (\mathrm{trans} = \mathrm{'T'}), \\
A^HX & = B \quad (\mathrm{trans} = \mathrm{'C'}),
where :math:`A` is a sparse matrix and :math:`B` is a dense matrix.
The arguments ``A`` and ``B`` must have the same type. The argument
``F`` is a numeric factorization computed
by :func:`numeric <cvxopt.umfpack.numeric>`.
On exit ``B`` is overwritten by the
solution.
These separate functions are useful for solving several sets of linear
equations with the same coefficient matrix and different right-hand sides,
or with coefficient matrices that share the same sparsity pattern.
The symbolic factorization depends only on the sparsity pattern of
the matrix, and not on the numerical values of the nonzero coefficients.
The numerical factorization on the other hand depends on the sparsity
pattern of the matrix and on its the numerical values.
As an example, suppose :math:`A` is the matrix :eq:`e-sp-Adef` and
.. math::
B = \left[\begin{array}{rrrrr}
4 & 3 & 0 & 0 & 0 \\
3 & 0 & 4 & 0 & 6 \\
0 &-1 &-3 & 2 & 0 \\
0 & 0 & 1 & 0 & 0 \\
0 & 4 & 2 & 0 & 2
\end{array}\right],
which differs from :math:`A` in its first and last entries. The following
code computes
.. math::
\newcommand{\ones}{\mathbf 1}
x = A^{-T}B^{-1}A^{-1}\ones.
>>> from cvxopt import spmatrix, matrix, umfpack
>>> VA = [2, 3, 3, -1, 4, 4, -3, 1, 2, 2, 6, 1]
>>> VB = [4, 3, 3, -1, 4, 4, -3, 1, 2, 2, 6, 2]
>>> I = [0, 1, 0, 2, 4, 1, 2, 3, 4, 2, 1, 4]
>>> J = [0, 0, 1, 1, 1, 2, 2, 2, 2, 3, 4, 4]
>>> A = spmatrix(VA, I, J)
>>> B = spmatrix(VB, I, J)
>>> x = matrix(1.0, (5,1))
>>> Fs = umfpack.symbolic(A)
>>> FA = umfpack.numeric(A, Fs)
>>> FB = umfpack.numeric(B, Fs)
>>> umfpack.solve(A, FA, x)
>>> umfpack.solve(B, FB, x)
>>> umfpack.solve(A, FA, x, trans='T')
>>> print(x)
[ 5.81e-01]
[-2.37e-01]
[ 1.63e+00]
[ 8.07e+00]
[-1.31e-01]
.. _s-cholmod:
Positive Definite Linear Equations
**********************************
:mod:`cvxopt.cholmod` is an interface to the Cholesky factorization routines
of the CHOLMOD package. It includes functions for Cholesky factorization
of sparse positive definite matrices, and for solving sparse sets of linear
equations with positive definite matrices.
The routines can also be used for computing
:raw-html:`LDL<sup><small>T</small></sup>`
(or
:raw-html:`LDL<sup><small>H</small></sup>`
factorizations
of symmetric indefinite matrices (with :math:`L` unit lower-triangular and
:math:`D` diagonal and nonsingular) if such a factorization exists.
.. seealso::
* Y. Chen, T. A. Davis, W. W. Hager, S. Rajamanickam,
Algorithm 887: CHOLMOD, Supernodal Sparse Cholesky Factorization
and Update/Downdate, ACM Transactions on Mathematical Software,
35(3), 22:1-22:14, 2008.
.. function:: cvxopt.cholmod.linsolve(A, B[, p = None, uplo = 'L'])
Solves
.. math::
AX = B
with :math:`A` sparse and real symmetric or complex Hermitian.
``B`` is a dense matrix of the same type as ``A``. On exit it
is overwritten with the solution. The argument ``p`` is an integer
matrix with length equal to the order of :math:`A`, and specifies an
optional reordering.
See the comment on
:attr:`options['nmethods']` for details on which ordering is used
by CHOLMOD.
Raises an :exc:`ArithmeticError` if the factorization does not exist.
As an example, we solve
.. math::
:label: e-A-pd
\left[ \begin{array}{rrrr}
10 & 0 & 3 & 0 \\
0 & 5 & 0 & -2 \\
3 & 0 & 5 & 0 \\
0 & -2 & 0 & 2
\end{array}\right] X =
\left[ \begin{array}{cc}
0 & 4 \\ 1 & 5 \\ 2 & 6 \\ 3 & 7
\end{array} \right].
>>> from cvxopt import matrix, spmatrix, cholmod
>>> A = spmatrix([10, 3, 5, -2, 5, 2], [0, 2, 1, 3, 2, 3], [0, 0, 1, 1, 2, 3])
>>> X = matrix(range(8), (4,2), 'd')
>>> cholmod.linsolve(A,X)
>>> print(X)
[-1.46e-01 4.88e-02]
[ 1.33e+00 4.00e+00]
[ 4.88e-01 1.17e+00]
[ 2.83e+00 7.50e+00]
.. function:: cvxopt.cholmod.splinsolve(A, B[, p = None, uplo = 'L'])
Similar to :func:`linsolve <cvxopt.cholmod.linsolve>` except that
``B`` is an :class:`spmatrix <cvxopt.spmatrix>` and
that the solution is returned as an output argument (as a new
:class:`spmatrix`). ``B`` is not modified.
See the comment on
:attr:`options['nmethods']` for details on which ordering is used
by CHOLMOD.
The following code computes the inverse of the coefficient matrix
in :eq:`e-A-pd` as a sparse matrix.
>>> X = cholmod.splinsolve(A, spmatrix(1.0,range(4),range(4)))
>>> print(X)
[ 1.22e-01 0 -7.32e-02 0 ]
[ 0 3.33e-01 0 3.33e-01]
[-7.32e-02 0 2.44e-01 0 ]
[ 0 3.33e-01 0 8.33e-01]
The functions :func:`linsolve <cvxopt.cholmod.linsolve>` and
:func:`splinsolve <cvxopt.cholmod.splinsolve>` are equivalent to
:func:`symbolic <cvxopt.cholmod.symbolic>` and
:func:`numeric <cvxopt.cholmod.numeric>` called in sequence, followed by
:func:`solve <cvxopt.cholmod.solve>`, respectively,
:func:`spsolve <cvxopt.cholmod.spsolve>`.
.. function:: cvxopt.cholmod.symbolic(A[, p = None, uplo = 'L'])
Performs a symbolic analysis of a sparse real symmetric or
complex Hermitian matrix :math:`A` for one of the two factorizations:
.. math::
:label: e-chol-ll
PAP^T = LL^T, \qquad PAP^T = LL^H,
and
.. math::
:label: e-chol-ldl
PAP^T = LDL^T, \qquad PAP^T = LDL^H,
where :math:`P` is a permutation matrix, :math:`L` is lower triangular
(unit lower triangular in the second factorization), and :math:`D` is
nonsingular diagonal. The type of factorization depends on the value
of :attr:`options['supernodal']` (see below).
If ``uplo`` is :const:`'L'`, only the lower triangular part of ``A``
is accessed and the upper triangular part is ignored.
If ``uplo`` is :const:`'U'`, only the upper triangular part of ``A``
is accessed and the lower triangular part is ignored.
The symbolic factorization is returned as an opaque C object that
can be passed to :func:`numeric <cvxopt.cholmod.numeric>`.
See the comment on
:attr:`options['nmethods']` for details on which ordering is used
by CHOLMOD.
.. function:: cvxopt.cholmod.numeric(A, F)
Performs a numeric factorization of a sparse symmetric matrix
as :eq:`e-chol-ll` or :eq:`e-chol-ldl`. The argument ``F`` is the
symbolic factorization computed by
:func:`symbolic <cvxopt.cholmod.symbolic>` applied to
the matrix ``A``, or to another sparse matrix with the same sparsity
pattern and typecode, or by
:func:`numeric <cvxopt.cholmod.numeric>` applied to a matrix
with the same sparsity pattern and typecode as ``A``.
If ``F`` was created by a
:func:`symbolic <cvxopt.cholmod.symbolic>` with ``uplo``
equal
to :const:`'L'`, then only the lower triangular part of ``A`` is
accessed and the upper triangular part is ignored. If it was created
with ``uplo`` equal to :const:`'U'`, then only the upper triangular
part of ``A`` is accessed and the lower triangular part is ignored.
On successful exit, the factorization is stored in ``F``.
Raises an :exc:`ArithmeticError` if the factorization does not exist.
.. function:: cvxopt.cholmod.solve(F, B[, sys = 0])
Solves one of the following linear equations where ``B`` is a dense
matrix and ``F`` is the numeric factorization :eq:`e-chol-ll`
or :eq:`e-chol-ldl` computed by
:func:`numeric <cvxopt.cholmod.numeric>`.
``sys`` is an integer with values between 0 and 8.
+---------+--------------------+
| ``sys`` | equation |
+---------+--------------------+
| 0 | :math:`AX = B` |
+---------+--------------------+
| 1 | :math:`LDL^TX = B` |
+---------+--------------------+
| 2 | :math:`LDX = B` |
+---------+--------------------+
| 3 | :math:`DL^TX=B` |
+---------+--------------------+
| 4 | :math:`LX=B` |
+---------+--------------------+
| 5 | :math:`L^TX=B` |
+---------+--------------------+
| 6 | :math:`DX=B` |
+---------+--------------------+
| 7 | :math:`P^TX=B` |
+---------+--------------------+
| 8 | :math:`PX=B` |
+---------+--------------------+
(If ``F`` is a Cholesky factorization of the form :eq:`e-chol-ll`,
:math:`D` is an identity matrix in this table. If ``A`` is complex,
:math:`L^T` should be replaced by :math:`L^H`.)
The matrix ``B`` is a dense :const:`'d'` or :const:`'z'` matrix, with
the same type as ``A``. On exit it is overwritten by the solution.
.. function:: cvxopt.cholmod.spsolve(F, B[, sys = 0])
Similar to :func:`solve <cvxopt.cholmod.solve>`, except that ``B`` is
a class:`spmatrix`, and the solution is returned as an output argument
(as an :class:`spmatrix`). ``B`` must have the same typecode as ``A``.
For the same example as above:
>>> X = matrix(range(8), (4,2), 'd')
>>> F = cholmod.symbolic(A)
>>> cholmod.numeric(A, F)
>>> cholmod.solve(F, X)
>>> print(X)
[-1.46e-01 4.88e-02]
[ 1.33e+00 4.00e+00]
[ 4.88e-01 1.17e+00]
[ 2.83e+00 7.50e+00]
.. function:: cvxopt.cholmod.diag(F)
Returns the diagonal elements of the Cholesky factor :math:`L`
in :eq:`e-chol-ll`, as a dense matrix of the same type as ``A``.
Note that this only applies to Cholesky factorizations. The matrix
:math:`D` in an :raw-html:`LDL<sup><small>T</small></sup>`
factorization can be retrieved via :func:`solve <cvxopt.cholmod.solve>`
with ``sys`` equal to 6.
In the functions listed above, the default values of the control
parameters described in the CHOLMOD user guide are used, except for
:c:data:`Common.print` which is set to 0 instead of 3 and
:c:data:`Common.supernodal` which is set to 2 instead of 1.
These parameters (and a few others) can be modified by making an
entry in the dictionary :attr:`cholmod.options`.
The meaning of the options :attr:`options['supernodal']` and
:attr:`options['nmethods']` is summarized as follows (and described
in detail in the CHOLMOD user guide).
:attr:`options['supernodal']`
If equal to 0, a factorization :eq:`e-chol-ldl` is computed using a
simplicial algorithm. If equal to 2, a factorization :eq:`e-chol-ll`
is computed using a supernodal algorithm. If equal to 1, the most
efficient of the two factorizations is selected, based on the sparsity
pattern. Default: 2.
:attr:`options['nmethods']`
The default ordering used by the CHOLMOD is the ordering in the AMD
library, but depending on the value of :attr:`options['nmethods']`.
other orderings are also considered.
If ``nmethods`` is equal to 2, the ordering specified
by the user and the AMD ordering are compared, and the best of the two
orderings is used. If the user does not specify an ordering, the AMD
ordering is used.
If equal to 1, the user must specify an ordering, and the ordering
provided by the user is used.
If equal to 0, all available orderings are compared and the best
ordering is used. The available orderings include the AMD ordering,
the ordering specified by the user (if any), and possibly other
orderings if they are installed during the CHOLMOD installation.
Default: 0.
As an example that illustrates :func:`diag <cvxopt.cholmod.diag>` and the
use of :attr:`cholmod.options`, we compute the logarithm of the determinant
of the coefficient matrix in :eq:`e-A-pd` by two methods.
>>> import math
>>> from cvxopt.cholmod import options
>>> from cvxopt import log
>>> F = cholmod.symbolic(A)
>>> cholmod.numeric(A, F)
>>> print(2.0 * sum(log(cholmod.diag(F))))
5.50533153593
>>> options['supernodal'] = 0
>>> F = cholmod.symbolic(A)
>>> cholmod.numeric(A, F)
>>> Di = matrix(1.0, (4,1))
>>> cholmod.solve(F, Di, sys=6)
>>> print(-sum(log(Di)))
5.50533153593
Example: Covariance Selection
*****************************
This example illustrates the use of the routines for sparse Cholesky
factorization. We consider the problem
.. math::
:label: e-covsel
\newcommand{\Tr}{\mathop{\bf tr}}
\begin{array}{ll}
\mbox{minimize} & -\log\det K + \Tr(KY) \\
\mbox{subject to} & K_{ij}=0,\quad (i,j) \not \in S.
\end{array}
The optimization variable is a symmetric matrix :math:`K` of order
:math:`n` and the domain of the problem is the set of positive definite
matrices. The matrix :math:`Y` and the index set :math:`S` are given.
We assume that all the diagonal positions are included in :math:`S`.
This problem arises in maximum likelihood estimation of the covariance
matrix of a zero-mean normal distribution, with constraints
that specify that pairs of variables are conditionally independent.
We can express :math:`K` as
.. math::
\newcommand{\diag}{\mathop{\bf diag}}
K(x) = E_1\diag(x)E_2^T+E_2\diag(x)E_1^T
where :math:`x` are the nonzero elements in the lower triangular part of
:math:`K`, with the diagonal elements scaled by 1/2, and
.. math::
E_1 = \left[ \begin{array}{cccc}
e_{i_1} & e_{i_2} & \cdots & e_{i_q} \end{array}\right], \qquad
E_2 = \left[ \begin{array}{cccc}
e_{j_1} & e_{j_2} & \cdots & e_{j_q} \end{array}\right],
where (:math:`i_k`, :math:`j_k`) are the positions of the nonzero entries
in the lower-triangular part of :math:`K`. With this notation, we can
solve problem :eq:`e-covsel` by solving the unconstrained problem
.. math::
\newcommand{\Tr}{\mathop{\bf tr}}
\begin{array}{ll}
\mbox{minimize} & f(x) = -\log\det K(x) + \Tr(K(x)Y).
\end{array}
The code below implements Newton's method with a backtracking line search.
The gradient and Hessian of the objective function are given by
.. math::
\newcommand{\diag}{\mathop{\bf diag}}
\begin{split}
\nabla f(x)
& = 2 \diag( E_1^T (Y - K(x)^{-1}) E_2)) \\
& = 2\diag(Y_{IJ} - \left(K(x)^{-1}\right)_{IJ}) \\
\nabla^2 f(x)
& = 2 (E_1^T K(x)^{-1} E_1) \circ (E_2^T K(x)^{-1} E_2)
+ 2 (E_1^T K(x)^{-1} E_2) \circ (E_2^T K(x)^{-1} E_1) \\
& = 2 \left(K(x)^{-1}\right)_{II} \circ \left(K(x)^{-1}\right)_{JJ}
+ 2 \left(K(x)^{-1}\right)_{IJ} \circ
\left(K(x)^{-1}\right)_{JI},
\end{split}
where :math:`\circ` denotes Hadamard product.
::
from cvxopt import matrix, spmatrix, log, mul, blas, lapack, amd, cholmod
def covsel(Y):
"""
Returns the solution of
minimize -log det K + Tr(KY)
subject to K_{ij}=0, (i,j) not in indices listed in I,J.
Y is a symmetric sparse matrix with nonzero diagonal elements.
I = Y.I, J = Y.J.
"""
I, J = Y.I, Y.J
n, m = Y.size[0], len(I)
N = I + J*n # non-zero positions for one-argument indexing
D = [k for k in range(m) if I[k]==J[k]] # position of diagonal elements
# starting point: symmetric identity with nonzero pattern I,J
K = spmatrix(0.0, I, J)
K[::n+1] = 1.0
# Kn is used in the line search
Kn = spmatrix(0.0, I, J)
# symbolic factorization of K
F = cholmod.symbolic(K)
# Kinv will be the inverse of K
Kinv = matrix(0.0, (n,n))
for iters in range(100):
# numeric factorization of K
cholmod.numeric(K, F)
d = cholmod.diag(F)
# compute Kinv by solving K*X = I
Kinv[:] = 0.0
Kinv[::n+1] = 1.0
cholmod.solve(F, Kinv)
# solve Newton system
grad = 2*(Y.V - Kinv[N])
hess = 2*(mul(Kinv[I,J],Kinv[J,I]) + mul(Kinv[I,I],Kinv[J,J]))
v = -grad
lapack.posv(hess,v)
# stopping criterion
sqntdecr = -blas.dot(grad,v)
print("Newton decrement squared:%- 7.5e" %sqntdecr)
if (sqntdecr < 1e-12):
print("number of iterations: ", iters+1)
break
# line search
dx = +v
dx[D] *= 2 # scale the diagonal elems
f = -2.0 * sum(log(d)) # f = -log det K
s = 1
for lsiter in range(50):
Kn.V = K.V + s*dx
try:
cholmod.numeric(Kn, F)
except ArithmeticError:
s *= 0.5
else:
d = cholmod.diag(F)
fn = -2.0 * sum(log(d)) + 2*s*blas.dot(v,Y.V)
if (fn < f - 0.01*s*sqntdecr):
break
s *= 0.5
K.V = Kn.V
return K
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