Success!
sage: G = graphs.GridGraph([100,100])
sage: L = G.laplacian_matrix()
sage: L
10000 x 10000 sparse matrix over Integer Ring
sage: sage: time M = L[1:9999]
CPU times: user 21.98 s, sys: 0.01 s, total: 21.99 s
Wall time: 22.93 s
sage: sage: time N = L._delete_row_(0)
CPU times: user 0.01 s, sys: 0.00 s, total: 0.01 s
Wall time: 0.01 s
sage: sage: timeit('N = L._delete_row_(0)')
25 loops, best of 3: 10.9 ms per loop
I am travelling for the next several days but will follow up on this
soon.
Thanks a lot!
On Jun 2, 10:12 pm, William Stein <wst...@gmail.com> wrote:
> On Tue, Jun 2, 2009 at 10:10 PM, davidp <dav...@reed.edu> wrote:
>
> > I might be going down the wrong path, but is seems like I would want
> > to add a
>
> > copy_mpz_vector_init
>
> > function to vector_integer_sparse_c.pxi that would make a copy of an
> > mpz_vector. Is that overkill?
>
> That sounds like a good idea to me.
>
> William
>
>
>
>
>
> > My first idea was to use add_mpz_vector_init(sum, v, w, mul), which
> > sets sum equal to v + mul*w, but let mul = 0. However
> > add_mpz_vector_init returns the zero vector when mul = 0 !
>
> > Dave
>
> > On Jun 2, 9:06 pm, William Stein <wst...@gmail.com> wrote:
> >> On Tue, Jun 2, 2009 at 8:45 PM, davidp <dav...@reed.edu> wrote:
>
> >> > I can't figure out how to create a new sparse matrix (see below).
>
> >> > Sorry,
> >> > Dave
>
> >> You can make a new matrix with the analogous parent but a different
> >> shape using the new_matrix method.
>
> >> sage: a = random_matrix(ZZ,3,4,sparse=True)
> >> sage: a.new_matrix(2,4)
> >> [0 0 0 0]
> >> [0 0 0 0]
>
> >> In your cython code you would write something like
>
> >> cdef Matrix_integer_sparse M = a.new_matrix(2,4)
>
> >> William
>
> >> > M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> >> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> >> > sparse=True), None, None, None)
>
> >> > -------------------
> >> > ...
> >> > def _delete_row_(self, Py_ssize_t row_number):
> >> > cdef Py_ssize_t i
> >> > cdef mpz_vector* self_row, *M_row
> >> > cdef Matrix_integer_sparse M
>
> >> > M = Matrix_integer_sparse.__new__(Matrix_integer_sparse,
> >> > sage.matrix.matrix_space.MatrixSpace(ZZ, self._nrows-1, self._ncols,
> >> > sparse=True), None, None, None)
>
> >> > ^
> >> > ------------------------------------------------------------
>
> >> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> >> > matrix_integer_sparse.pyx:221:101: Compiler crash in
> >> > AnalyseExpressionsTransform
>
> >> > ModuleNode.body = StatListNode(matrix_integer_sparse.pyx:23:0)
> >> > StatListNode.stats[13] = StatListNode(matrix_integer_sparse.pyx:43:5)
> >> > StatListNode.stats[0] = CClassDefNode(matrix_integer_sparse.pyx:43:5,
> >> > as_name = u'Matrix_integer_sparse',
> >> > base_class_module = u'matrix_sparse',
> >> > base_class_name = u'Matrix_sparse',
> >> > class_name = u'Matrix_integer_sparse',
> >> > module_name = '',
> >> > visibility = 'private')
> >> > CClassDefNode.body = StatListNode(matrix_integer_sparse.pyx:55:4)
> >> > StatListNode.stats[9] = DefNode(matrix_integer_sparse.pyx:216:4,
> >> > name = u'_delete_row_',
> >> > num_required_args = 2,
> >> > reqd_kw_flags_cname = '0')
> >> > File 'Nodes.py', line 360, in analyse_expressions: StatListNode
> >> > (matrix_integer_sparse.pyx:217:8)
> >> > File 'Nodes.py', line 2835, in analyse_expressions:
> >> > SingleAssignmentNode(matrix_integer_sparse.pyx:221:41)
> >> > File 'Nodes.py', line 2928, in analyse_types: SingleAssignmentNode
> >> > (matrix_integer_sparse.pyx:221:41)
> >> > File 'ExprNodes.py', line 2281, in analyse_types: SimpleCallNode
> >> > (matrix_integer_sparse.pyx:221:41)
> >> > File 'ExprNodes.py', line 3105, in analyse_types: TupleNode
> >> > (matrix_integer_sparse.pyx:221:41,
> >> > is_sequence_constructor = 1)
> >> > File 'ExprNodes.py', line 2972, in analyse_types: TupleNode
> >> > (matrix_integer_sparse.pyx:221:41,
> >> > is_sequence_constructor = 1)
> >> > File 'ExprNodes.py', line 2522, in analyse_types: GeneralCallNode
> >> > (matrix_integer_sparse.pyx:221:101)
>
> >> > Compiler crash traceback from this point on:
> >> > File "/usr/local/sage-devel/local/lib/python2.5/site-packages/Cython/
> >> > Compiler/ExprNodes.py", line 2532, in analyse_types
> >> > if hasattr(self.function, 'entry') and not
> >> > self.function.entry.as_variable:
> >> > AttributeError: 'NoneType' object has no attribute 'as_variable'
> >> > Error running command, failed with status 256.
> >> > sage: There was an error installing modified sage library code.
>
> >> > On Jun 2, 7:28 pm, William Stein <wst...@gmail.com> wrote:
> >> >> On Tue, Jun 2, 2009 at 7:22 PM, davidp <dav...@reed.edu> wrote:
>
> >> >> > I tried adding a delete_row method to matrix_integer_sparse.pyx but
> >> >> > stopped after getting the error message:
>
> >> >> Just def your method -- do not cpdef it. You can still use Cython
> >> >> code in a cpdef's method and it will be just as fast.
>
> >> >> Make sure that your "delete row" method returns a *new* matrix by the
> >> >> way...
>
> >> >> William
>
> >> >> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >> > Error converting Pyrex file to C:
> >> >> > ------------------------------------------------------------
> >> >> > ...
> >> >> > add_mpz_vector_init(&M._matrix[i], &self._matrix[i], &
> >> >> > (<Matrix_integer_sparse>right)._matrix[i], mul)
> >> >> > mpz_clear(mul)
> >> >> > return M
>
> >> >> > # added by David Perkinson
> >> >> > cpdef ModuleElement _delete_row_(self, Py_ssize_t row_number):
> >> >> > ^
> >> >> > ------------------------------------------------------------
>
> >> >> > /usr/local/sage-devel/devel/sage-devel/sage/matrix/
> >> >> > matrix_integer_sparse.pyx:216:10: C method '_delete_row_' not
> >> >> > previously declared in definition part of extension type
> >> >> > Error running command, failed with status 256.
> >> >> > sage: There was an error installing modified sage library code.
>
> >> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> >> >> > I might have to actually read the Cython documentation!
>
> >> >> > Dave
>
> >> >> > On Jun 2, 5:43 pm, Jason Grout <jason-s...@creativetrax.com> wrote:
> >> >> >> William Stein wrote:
> >> >> >> > On Mon, Jun 1, 2009 at 5:16 PM, davidp <dav...@reed.edu> wrote:
> >> >> >> >> Is there a fast way to create a submatrix?
>
> >> >> >> >> -------------------------------------------------
>
> >> >> >> >> sage: version()
> >> >> >> >> 'Sage Version 4.0.alpha0, Release Date: 2009-05-15'
> >> >> >> >> sage: G = graphs.GridGraph([100,100])
> >> >> >> >> sage: L = G.laplacian_matrix()
> >> >> >> >> sage: L
> >> >> >> >> 10000 x 10000 sparse matrix over Integer Ring
> >> >> >> >> sage: time M = L[1:9999,1:9999]
> >> >> >> >> CPU times: user 24.93 s, sys: 0.04 s, total: 24.97 s
> >> >> >> >> Wall time: 25.27 s
>
> >> >> >> >> ----------------------------------------------------
>
> >> >> >> >> I am just interested in deleting a single row and column of the
> >> >> >> >> matrix
> >> >> >> >> (not necessarily the first).
>
> >> >> >> >> Thanks,
>
> >> >> >> > There is no fast way to do that right now. One could easily add
> >> >> >> > code
> >> >> >> > to SAGE_ROOT/devel/sage/sage/matrix/matrix_integer_sparse.pyx that
> >> >> >> > would provide blazingly fast deletion of a row, and reasonably fast
> >> >> >> > deletion of a column. Of course it would be better to implement
> >> >> >> > arbitrary slicing in some optimized way in
> >> >> >> > matrix_integer_sparse.pyx.
> >> >> >> > I hope somebody does so.
>
> >> >> >> Just looking at the generic code, it seems that it goes through each
> >> >> >> and
> >> >> >> every index position in the slice, setting the new matrix entry to
> >> >> >> the
> >> >> >> old one. This is obviously the wrong thing to do for sparse
> >> >> >> matrices,
> >> >> >> and can likely trivially be made faster. I think all you may have
> >> >> >> to do
> >> >> >> is override the matrix_from_rows_and_columns for sparse matrices.
>
> >> >> >> Jason
>
> >> >> --
> >> >> William Stein
> >> >> Associate Professor of Mathematics
> >> >> University of Washingtonhttp://wstein.org
>
> >> --
> >> William Stein
> >> Associate Professor of Mathematics
> >> University of Washingtonhttp://wstein.org
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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