Direct Solver: Skeletonization by alexfikl · Pull Request #30 · inducer/pytential

alexfikl · 2020-09-23T19:50:48Z

Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown

[Done] Add proxy generation (already in linalg.proxy).
[Current] Add single-level skeletonization.
[TODO] Add multi-level skeletonization.
[TODO] Add the actual multi-level direct solver.

Previously found https://gitlab.tiker.net/inducer/pytential/-/merge_requests/211.
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.

test/test_linalg_proxy.py

test/test_linalg_skeletonization.py

alexfikl · 2022-06-19T12:45:22Z

@inducer Gave this another read and it's looking very boring to me now (i.e. no big sketchy issues). It should be good to go!

inducer · 2022-06-29T23:48:12Z

LGTM, thanks! While I was reading, I saw various things I thought that would be nice to have, but generally nothing that I thought warranted holding this up. It's been long enough!

alexfikl · 2022-06-30T07:42:48Z

LGTM, thanks! While I was reading, I saw various things I thought that would be nice to have, but generally nothing that I thought warranted holding this up. It's been long enough!

@inducer Feel free to either leave the comments here or make an issue. I'll go through them with time!

inducer

Thanks for offering! Left a few notes based on my read yesterday.

inducer · 2022-06-30T19:49:31Z

pytential/linalg/utils.py

+
+# {{{ cluster matrix errors
+
+def cluster_skeletonization_error(


Add a docstring?

inducer · 2022-06-30T19:49:41Z

pytential/linalg/utils.py

+    return tgt_error, src_error
+
+
+def skeletonization_error(


Add a docstring?

inducer · 2022-06-30T19:50:40Z

pytential/linalg/skeletonization.py

@@ -0,0 +1,645 @@
+__copyright__ = "Copyright (C) 2018-2022 Alexandru Fikl"


In this file, it of then took me a while to understand the shape of ndarrays. Mentioning what it is when it's not already specified would help!

inducer · 2022-06-30T19:52:19Z

pytential/linalg/skeletonization.py

+    .. attribute:: L
+
+        A block diagonal :class:`~numpy.ndarray` object array.
+
+    .. attribute:: R
+
+        A block diagonal :class:`~numpy.ndarray` object array.


What's in the object array? What shape?

inducer · 2022-06-30T19:53:10Z

pytential/linalg/utils.py

+    """
+
+    import scipy.linalg.interpolative as sli    # pylint:disable=no-name-in-module
+    if rank is None:


Error if both rank and eps are specified?

inducer · 2022-06-30T19:53:24Z

pytential/linalg/utils.py

+# {{{ interpolative decomposition
+
+def interp_decomp(
+        A: np.ndarray, rank: Optional[int], eps: Optional[float],


inducer · 2022-06-30T19:53:54Z

test/test_linalg_skeletonization.py

+    replace(SKELETONIZE_TEST_CASES[0], op_type="double", knl_class_or_helmholtz_k=5),
+    ])
+def test_skeletonize_symbolic(actx_factory, case, visualize=False):
+    """Tests that the symbolic manipulations work for different kernels / IntGs."""


What does "work" mean?

inducer · 2022-06-30T19:54:39Z

test/test_linalg_skeletonization.py

+def test_skeletonize_by_proxy_convergence(
+        actx_factory, case, weighted=True,
+        visualize=False):
+    """Test single-level level skeletonization accuracy."""


Be more precise here.

inducer · 2022-06-30T19:55:51Z

pytential/linalg/skeletonization.py

@@ -0,0 +1,645 @@
+__copyright__ = "Copyright (C) 2018-2022 Alexandru Fikl"


Throughout this file, document the weighting schemes a bit better. I feel that might be hard to reverse-engineer later on.

alexfikl commented Sep 23, 2020

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alexfikl force-pushed the direct-solver-skeletonization branch from add8d42 to de75fa8 Compare March 4, 2021 22:18

Base automatically changed from master to main March 8, 2021 05:22

alexfikl marked this pull request as draft March 24, 2021 23:17

alexfikl force-pushed the direct-solver-skeletonization branch from 169c617 to 840e8ff Compare May 26, 2021 20:14

This was referenced Jun 3, 2021

Matrix evaluation updates #89

Merged

Improve proxy generator #90

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alexfikl force-pushed the direct-solver-skeletonization branch 4 times, most recently from eca3be7 to 2baf1f3 Compare June 10, 2021 14:57

alexfikl mentioned this pull request Jun 11, 2021

Import and update BlockIndexRanges from sumpy #92

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2 tasks

alexfikl force-pushed the direct-solver-skeletonization branch from 2baf1f3 to 72915ec Compare June 16, 2021 16:20

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alexfikl mentioned this pull request Jan 28, 2022

Misc ProxyGenerator changes #131

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alexfikl force-pushed the direct-solver-skeletonization branch from ff25741 to eaa5224 Compare February 5, 2022 02:07

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alexfikl force-pushed the direct-solver-skeletonization branch from 46813d8 to ffccac0 Compare April 18, 2022 00:42

alexfikl marked this pull request as ready for review April 18, 2022 01:12

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alexfikl mentioned this pull request May 8, 2022

Add mappers for direct solver #152

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inducer reviewed Jun 17, 2022

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alexfikl requested a review from inducer June 19, 2022 12:45

alexfikl force-pushed the direct-solver-skeletonization branch from 471a0c7 to 07f392e Compare June 24, 2022 06:54

alexfikl added 8 commits June 29, 2022 18:46

add skeletonization by interpolative decomposition

e520ed5

add docs for new mappers

4995be6

use proxy/neighbor vs farfield/nearfield naming

4356f70

proxy: also compute cluster radii for debugging

9eb8312

port test additions to dataclasses

5643b5c

remove duplicated symbolic skeletonization helpers

528df1b

add an assert to test_skeletonize_by_proxy_convergence

bd583a2

clean up additions to matrix evaluation

0e6e4f7

inducer force-pushed the direct-solver-skeletonization branch from 07f392e to 0e6e4f7 Compare June 29, 2022 23:46

inducer enabled auto-merge (rebase) June 29, 2022 23:48

inducer merged commit b29a492 into inducer:main Jun 30, 2022

alexfikl deleted the direct-solver-skeletonization branch June 30, 2022 07:34

alexfikl mentioned this pull request Jun 30, 2022

Direct Solver: Recursive Skeletonization #164

Open

inducer reviewed Jun 30, 2022

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alexfikl mentioned this pull request Jul 1, 2022

Address remaining comments from #30 #165

Merged

alexfikl mentioned this pull request Aug 4, 2022

Direct Solver: Multilevel Proxy-based Solver #174

Open


		# {{{ cluster matrix errors

		def cluster_skeletonization_error(

		@@ -0,0 +1,645 @@
		__copyright__ = "Copyright (C) 2018-2022 Alexandru Fikl"

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alexfikl commented Sep 23, 2020

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inducer commented Jun 29, 2022

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alexfikl commented Jun 19, 2022 •

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