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"body": "<div id=\"comment:0\"></div>\n\nThe problem is in the code which looks like the following\n\n```\ndef test1():\n K = QuadraticField(2)\n for _ in range(100):\n i = randint(2,3)\n j = randint(2,3)\n m = matrix(K, i, j, range(i*j))\n```\nIt causes the various matrix spaces to rebuilt almost each time! If we compare with\n\n```\ndef test2():\n K = QuadraticField(2)\n M = {(i,j): MatrixSpace(K,i,j) for i in range(2,4) for j in range(2,4)}\n for _ in range(100):\n i = randint(2,3)\n j = randint(2,3)\n m = M[i,j](range(i*j))\n```\nthen we got\n\n```\nsage: %timeit test1()\n10 loops, best of 3: 55 ms per loop\nsage: %timeit test2()\n100 loops, best of 3: 6.49 ms per loop\n```\n\nThis is one of the reasons why the creation of Polyhedron is so slow (see #18213). (This has now improved since the creation of the ticket)\n\nIn the branch we:\n- replace some old Cython code in `matrix_generic_dense` and `matrix0` and do some optimization\n- move the function `_get_matrix_class` in `MatrixSpace` out of the class (as it depends only on the base ring and the sparseness)\n- In the class `MatrixSpace` the argument `__matrix_class` is now `_matrix_class`. That way, it is possible in other part of Sage to optimize the creation of matrices by calling directly\n\n```\nsage: M = MatrixSpace(ZZ,3,2)\nsage: M._matrix_class([1,5,3,-1,2,3], coerce=False, copy=False)\n```\n- we simplify the main element constructor of matrix, namely `MatrixSpace.matrix` and gain a significant speedup.\n\nfollow up: #18258\n\nCC: @nathanncohen\n\nComponent: **linear algebra**\n\n_Issue created by migration from https://trac.sagemath.org/ticket/18231_\n\n",
"closed_at": "2022-02-25T10:34:15Z",
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"title": "constructing matrices is very slow",
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}The problem is in the code which looks like the following
def test1():
K = QuadraticField(2)
for _ in range(100):
i = randint(2,3)
j = randint(2,3)
m = matrix(K, i, j, range(i*j))
It causes the various matrix spaces to rebuilt almost each time! If we compare with
def test2():
K = QuadraticField(2)
M = {(i,j): MatrixSpace(K,i,j) for i in range(2,4) for j in range(2,4)}
for _ in range(100):
i = randint(2,3)
j = randint(2,3)
m = M[i,j](range(i*j))
then we got
sage: %timeit test1()
10 loops, best of 3: 55 ms per loop
sage: %timeit test2()
100 loops, best of 3: 6.49 ms per loop
This is one of the reasons why the creation of Polyhedron is so slow (see #18213). (This has now improved since the creation of the ticket)
In the branch we:
- replace some old Cython code in
matrix_generic_denseandmatrix0and do some optimization - move the function
_get_matrix_classinMatrixSpaceout of the class (as it depends only on the base ring and the sparseness) - In the class
MatrixSpacethe argument__matrix_classis now_matrix_class. That way, it is possible in other part of Sage to optimize the creation of matrices by calling directly
sage: M = MatrixSpace(ZZ,3,2)
sage: M._matrix_class([1,5,3,-1,2,3], coerce=False, copy=False)
- we simplify the main element constructor of matrix, namely
MatrixSpace.matrixand gain a significant speedup.
follow up: #18258
CC: @nathanncohen
Component: linear algebra
Issue created by migration from https://trac.sagemath.org/ticket/18231
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"body": "<div id=\"comment:1\" align=\"right\">comment:1</div>\n\nI only did some cleanup in `matrix_space.py` and `matrix_generic_dense.pyx`. And there is a substantial gain in speed! The tiny modification in #18213 to `NumberField.__cmp__` actually makes a much bigger difference.\n\nI did not solve the problem of the matrix space being rebuilt every time.\n\n---\nNew commits:\n<table><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/f6a87ed8ba412a58a9c8dd582ac716ac968fcf1b\"><code>f6a87ed</code></a></td><td><code>Trac 18231: better code in matrices</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/d834354d719c55a88018c8c7bb0d6ab94542d771\"><code>d834354</code></a></td><td><code>Trac 18231: move _get_matrix_class out of the class</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/d52a63da8ae80bb9be6d5e401568bb4cf4baef6c\"><code>d52a63d</code></a></td><td><code>Trac 18231: constructor + __matrix_class -> _matrix_class</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/ecd6e2743f973b05632edc688bd7a99c68e22ab8\"><code>ecd6e27</code></a></td><td><code>Trac 18231: removed unused import</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/a23d09c1d4420f0bef8271785225bd12d4ad05c1\"><code>a23d09c</code></a></td><td><code>Trac 18231: get rid of a one year old deprecation</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/6e9aab1a94f9df0cdca30ba026639d48b550e24c\"><code>6e9aab1</code></a></td><td><code>Trac 18231: remove a useless function</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/95c9dfe9d827b2b83bfa2eb76fcb5b44eb6726f3\"><code>95c9dfe</code></a></td><td><code>Trac 18231: set .__call__() as an alias of .matrix()</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/6dbf25e277f2e73c6a917c4d41872e370f65d56f\"><code>6dbf25e</code></a></td><td><code>Trac 18231: rewrite .matrix()</code></td></tr><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/c1c7034ed54c7493a7fedbf6fa9798f23946902c\"><code>c1c7034</code></a></td><td><code>Trac 18231: fix dict_to_list</code></td></tr></table>\n",
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I only did some cleanup in matrix_space.py and matrix_generic_dense.pyx. And there is a substantial gain in speed! The tiny modification in #18213 to NumberField.__cmp__ actually makes a much bigger difference.
I did not solve the problem of the matrix space being rebuilt every time.
New commits:
f6a87ed | Trac 18231: better code in matrices |
d834354 | Trac 18231: move _get_matrix_class out of the class |
d52a63d | Trac 18231: constructor + __matrix_class -> _matrix_class |
ecd6e27 | Trac 18231: removed unused import |
a23d09c | Trac 18231: get rid of a one year old deprecation |
6e9aab1 | Trac 18231: remove a useless function |
95c9dfe | Trac 18231: set .__call__() as an alias of .matrix() |
6dbf25e | Trac 18231: rewrite .matrix() |
c1c7034 | Trac 18231: fix dict_to_list |
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"body": "<div id=\"comment:2\"></div>\n\nBranch pushed to git repo; I updated commit sha1. New commits:\n<table><tr><td><a href=\"https://github.com/sagemath/sagetrac-mirror/commit/da310db9b3b4238121b1a1ad2c3d5e36a5e846b5\"><code>da310db</code></a></td><td><code>Trac 18231: typo</code></td></tr></table>\n",
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da310db | Trac 18231: typo |
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"body": "<div id=\"comment:3\" align=\"right\">comment:3</div>\n\nHello Vincent,\n\nIn this branch you create functions, remove others, and change a lot of code. There is still a lot of guessing to do on the reviewer's part.\n\nIt would be really cool if you could be more verbose about what you do. Really.\n\nI began to read the first commit, and I have several more specific questions:\n\n- You modify a function which takes a `MonoidElement` as input, which you immeditely cast with `cdef Matrix right = _right`. Either it is a matrix and it should not read `MonoidElement` in the first place, or it is not a `Matrix` and you cannot cast it?..\n\n- This is cool and everything to gain miliseconds, but that's not a good way to write public code\n\n ```\n - matrix.Matrix.__init__(self, parent)\n + # the four lines below avoid the following call\n + # matrix.Matrix.__init__(self, parent)\n + self._parent = parent\n + res._ncols = parent.ncols()\n + res._nrows = parent.nrows()\n + R = res._base_ring = parent.base_ring()\n ```\n If the main constructor does not do what you want ty to change it. What if somebody adds a new parameter to matrix? The code has to be copy/pasted in every single function that did not want to call `__init__`?\n\n- Why?\n\n ```\n \n cdef set_unsafe(self, Py_ssize_t i, Py_ssize_t j, value):\n - Py_DECREF(<object>PyList_GET_ITEM(self._entries, i*self._ncols + j))\n - Py_INCREF(value)\n - PyList_SET_ITEM(self._entries, i*self._ncols + j, value)\n + self._entries[i*self._ncols + j] = value\n \n cdef get_unsafe(self, Py_ssize_t i, Py_ssize_t j):\n - return <object>PyList_GET_ITEM(self._entries, i*self._ncols + j)\n + return self._entries[i*self._ncols + j]\n ```\n\nNathann",
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Hello Vincent,
In this branch you create functions, remove others, and change a lot of code. There is still a lot of guessing to do on the reviewer's part.
It would be really cool if you could be more verbose about what you do. Really.
I began to read the first commit, and I have several more specific questions:
-
You modify a function which takes a
MonoidElementas input, which you immeditely cast withcdef Matrix right = _right. Either it is a matrix and it should not readMonoidElementin the first place, or it is not aMatrixand you cannot cast it?.. -
This is cool and everything to gain miliseconds, but that's not a good way to write public code
- matrix.Matrix.__init__(self, parent) + # the four lines below avoid the following call + # matrix.Matrix.__init__(self, parent) + self._parent = parent + res._ncols = parent.ncols() + res._nrows = parent.nrows() + R = res._base_ring = parent.base_ring()If the main constructor does not do what you want ty to change it. What if somebody adds a new parameter to matrix? The code has to be copy/pasted in every single function that did not want to call
__init__? -
Why?
cdef set_unsafe(self, Py_ssize_t i, Py_ssize_t j, value): - Py_DECREF(<object>PyList_GET_ITEM(self._entries, i*self._ncols + j)) - Py_INCREF(value) - PyList_SET_ITEM(self._entries, i*self._ncols + j, value) + self._entries[i*self._ncols + j] = value cdef get_unsafe(self, Py_ssize_t i, Py_ssize_t j): - return <object>PyList_GET_ITEM(self._entries, i*self._ncols + j) + return self._entries[i*self._ncols + j]
Nathann
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"body": "Description changed:\n``````diff\n--- \n+++ \n@@ -29,3 +29,14 @@\n ```\n \n This is one of the reason why the creation of Polyhedron is so slow (see #18213).\n+\n+In the branch we:\n+- replace some old Cython code in `matrix_generic_dense` and `matrix0` and do some optimization\n+- move the function `_get_matrix_class` in `MatrixSpace` out of the class (as it depends only on the base ring and the sparseness)\n+- In the class `MatrixSpace` the argument `__matrix_class` is now `_matrix_class`. That way, it is possible in other part of Sage to optimize the creation of matrices by calling directly\n+\n+```\n+sage: M = MatrixSpace(ZZ,3,2)\n+sage: M._matrix_class([1,5,3,-1,2,3], coerce=False, copy=False)\n+```\n+- we simplify the main element constructor of matrix, namely `MatrixSpace.matrix` and gain a significant speedup.\n``````\n",
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---
+++
@@ -29,3 +29,14 @@
```
This is one of the reason why the creation of Polyhedron is so slow (see #18213).
+
+In the branch we:
+- replace some old Cython code in `matrix_generic_dense` and `matrix0` and do some optimization
+- move the function `_get_matrix_class` in `MatrixSpace` out of the class (as it depends only on the base ring and the sparseness)
+- In the class `MatrixSpace` the argument `__matrix_class` is now `_matrix_class`. That way, it is possible in other part of Sage to optimize the creation of matrices by calling directly
+
+```
+sage: M = MatrixSpace(ZZ,3,2)
+sage: M._matrix_class([1,5,3,-1,2,3], coerce=False, copy=False)
+```
+- we simplify the main element constructor of matrix, namely `MatrixSpace.matrix` and gain a significant speedup.archive/issue_events_256850.json:
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"body": "<div id=\"comment:4\" align=\"right\">comment:4</div>\n\nHello Nathann,\n\nThanks for having a look.\n\nReplying to [@nathanncohen](#comment%3A3):\n> In this branch you create functions, remove others, and change a lot of code. There is still a lot of guessing to do on the reviewer's part.\n>\n>\n\n> It would be really cool if you could be more verbose about what you do. Really.\n\nI made a big effort to separate the commit at least! It is now in the description of the ticket.\n\n> I began to read the first commit, and I have several more specific questions:\n> \n> - You modify a function which takes a `MonoidElement` as input, which you immeditely cast with `cdef Matrix right = _right`. Either it is a matrix and it should not read `MonoidElement` in the first place, or it is not a `Matrix` and you cannot cast it?..\n\nNo choice. This is a cdef function defined in `structure.element.Element` and you can not change the signature in children classes. I thought it was more readable this way.\n\n> - This is cool and everything to gain miliseconds, but that's not a good way to write public code\n> If the main constructor does not do what you want ty to change it. What if somebody adds a new parameter to matrix? The code has to be copy/pasted in every single function that did not want to call `__init__`?\n\nAll right. But then there is something wrong in the docstring of `matrix0.Matrix`\n\n```\n def __init__(...):\n ...\n Subclasses of ``Matrix`` can safely skip calling\n ``Matrix.__init__`` provided they take care of initializing these\n attributes themselves.\n ...\n```\n\n> - Why?\n\nAll this was just old Cython code at the time Cython was not able to understand `l[i]` when `l` is a `cdef list`.",
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Hello Nathann,
Thanks for having a look.
Replying to @nathanncohen:
In this branch you create functions, remove others, and change a lot of code. There is still a lot of guessing to do on the reviewer's part.
It would be really cool if you could be more verbose about what you do. Really.
I made a big effort to separate the commit at least! It is now in the description of the ticket.
I began to read the first commit, and I have several more specific questions:
- You modify a function which takes a
MonoidElementas input, which you immeditely cast withcdef Matrix right = _right. Either it is a matrix and it should not readMonoidElementin the first place, or it is not aMatrixand you cannot cast it?..
No choice. This is a cdef function defined in structure.element.Element and you can not change the signature in children classes. I thought it was more readable this way.
- This is cool and everything to gain miliseconds, but that's not a good way to write public code If the main constructor does not do what you want ty to change it. What if somebody adds a new parameter to matrix? The code has to be copy/pasted in every single function that did not want to call
__init__?
All right. But then there is something wrong in the docstring of matrix0.Matrix
def __init__(...):
...
Subclasses of ``Matrix`` can safely skip calling
``Matrix.__init__`` provided they take care of initializing these
attributes themselves.
...
- Why?
All this was just old Cython code at the time Cython was not able to understand l[i] when l is a cdef list.
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"body": "<div id=\"comment:7\" align=\"right\">comment:7</div>\n\nYoooooo !\n\n> I made a big effort to separate the commit at least! It is now in the description of the ticket.\n\nThanks\n\n> No choice. This is a cdef function defined in `structure.element.Element` and you can not change the signature in children classes. I thought it was more readable this way.\n\nOh, okay!\n\n> All right. But then there is something wrong in the docstring of `matrix0.Matrix`\n\nHmmmm.... Can you at least observe the difference? All that this `__init__` function does is precisely what you do. Can you measure this function call when your function copies lists around? `O_o`\n\n> All this was just old Cython code at the time Cython was not able to understand `l[i]` when `l` is a `cdef list`.\n\nOkay!\n\nNathann",
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Yoooooo !
I made a big effort to separate the commit at least! It is now in the description of the ticket.
Thanks
No choice. This is a cdef function defined in
structure.element.Elementand you can not change the signature in children classes. I thought it was more readable this way.
Oh, okay!
All right. But then there is something wrong in the docstring of
matrix0.Matrix
Hmmmm.... Can you at least observe the difference? All that this __init__ function does is precisely what you do. Can you measure this function call when your function copies lists around? O_o
All this was just old Cython code at the time Cython was not able to understand
l[i]whenlis acdef list.
Okay!
Nathann
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Okay, I give up. Sorry, I just don't know these classes enough, I barely ever used them, I would do a terrible job as a reviewer.
Nathann
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"body": "Description changed:\n``````diff\n--- \n+++ \n@@ -40,3 +40,5 @@\n sage: M._matrix_class([1,5,3,-1,2,3], coerce=False, copy=False)\n ```\n - we simplify the main element constructor of matrix, namely `MatrixSpace.matrix` and gain a significant speedup.\n+\n+follow up: #18258\n``````\n",
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---
+++
@@ -40,3 +40,5 @@
sage: M._matrix_class([1,5,3,-1,2,3], coerce=False, copy=False)
```
- we simplify the main element constructor of matrix, namely `MatrixSpace.matrix` and gain a significant speedup.
+
+follow up: #18258archive/issue_comments_249745.json:
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needs rebase, does not apply
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Whether to see if patchbot is happy.
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268cfc3 | Trac 18231: move _get_matrix_class out of the class |
66e5068 | Trac 18231: constructor + __matrix_class -> _matrix_class |
c9a82f2 | Trac 18231: removed unused import |
321d073 | Trac 18231: get rid of a one year old deprecation |
6111c37 | Trac 18231: remove a useless function |
cb6b82d | Trac 18231: set .__call__() as an alias of .matrix() |
2dd0d09 | Trac 18231: rewrite .matrix() |
00dd4ac | Trac 18231: fix dict_to_list |
07ba681 | Trac 18231: fix documentation |
742de47 | Trac 18231: fix doctests |
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"body": "<div id=\"comment:16\" align=\"right\">comment:16</div>\n\nI moved the first commit to another ticket (#19026).",
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I moved the first commit to another ticket (#19026).
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needs rebase
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"body": "Description changed:\n``````diff\n--- \n+++ \n@@ -28,7 +28,7 @@\n 100 loops, best of 3: 6.49 ms per loop\n ```\n \n-This is one of the reason why the creation of Polyhedron is so slow (see #18213).\n+This is one of the reasons why the creation of Polyhedron is so slow (see #18213). (This has now improved since the creation of the ticket)\n \n In the branch we:\n - replace some old Cython code in `matrix_generic_dense` and `matrix0` and do some optimization\n``````\n",
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---
+++
@@ -28,7 +28,7 @@
100 loops, best of 3: 6.49 ms per loop
```
-This is one of the reason why the creation of Polyhedron is so slow (see #18213).
+This is one of the reasons why the creation of Polyhedron is so slow (see #18213). (This has now improved since the creation of the ticket)
In the branch we:
- replace some old Cython code in `matrix_generic_dense` and `matrix0` and do some optimizationarchive/issue_comments_249756.json:
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"body": "<div id=\"comment:19\" align=\"right\">comment:19</div>\n\nOutdated, this was fixed in #24742.\n\n```\nsage: %timeit test1()\n3.91 ms \u00b1 47.3 \u00b5s per loop (mean \u00b1 std. dev. of 7 runs, 100 loops each)\nsage: %timeit test2()\n3.03 ms \u00b1 19.4 \u00b5s per loop (mean \u00b1 std. dev. of 7 runs, 100 loops each)\n```",
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Outdated, this was fixed in #24742.
sage: %timeit test1()
3.91 ms ± 47.3 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
sage: %timeit test2()
3.03 ms ± 19.4 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
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