Direct Solver: Recursive Skeletonization - #164

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

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

@alexfiklalexfikl changed the title Direct Solver: Direct Solver: Recursive SkeletonizationJun 30, 2022
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@inducer This should be ready for a look. It doesn't do much:

  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.

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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.

Comment threadpytential/linalg/cluster.py Outdated

Current level that is represented.

.. attribute:: nlevels

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Is this avoidable?

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Reworked this a while back, so not quite sure if your comment still applies?

Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py Outdated
# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:

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Is this two things rather than one?

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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.

Naming could still be better probably?

Comment threadtest/test_linalg_skeletonization.py
logger.info("\n%s", case)

run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)

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Update the test docstring to describe precisely what's being tested here.

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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef

Let me know if it's clear enough!

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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
"""Construct a parent map for :attr:`ClusterLevel.parent_map`."""

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Rephrase/rework? "All children in a bucket"?

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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?

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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?

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#225

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Pull request overview

This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.

Changes:

  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 5 comments.

Show a summary per file
FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.

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Comment threadpytential/linalg/cluster.py Outdated
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/skeletonization.py
Comment threadpytential/linalg/skeletonization.py
Comment threadpytential/linalg/cluster.py Outdated
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Direct Solver: Recursive Skeletonization - #164
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
Outdated


 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 5 comments.
Show a summary per file
FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Direct Solver: Recursive Skeletonization - #164
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
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 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
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FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Comment threadpytential/linalg/cluster.py
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Comment threadpytential/linalg/skeletonization.py
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Comment threadpytential/linalg/cluster.py
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Direct Solver: Recursive Skeletonization - #164
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
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 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
Reviewed changes
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FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
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 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 5 comments.
Show a summary per file
FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
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 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
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FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
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 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 5 comments.
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FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Attempting to break up the direct solver MR into smaller, more reviewable pieces. As a rundown
The code for this is mostly in the deprecated https://gitlab.tiker.net/inducer/pytential/-/merge_requests/137.
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@inducer This should be ready for a look. It doesn't do much:
  • adds a data structure to hold the hierarchical cluster info from boxtree.Tree and merge cluster indices.
  • adds some helper functions to do the recursive skeletonization + simple tests.
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Noticed a pending review. Figured it'd be better to submit it. :) Don't quite know how old this is.
Comment threadpytential/linalg/cluster.py
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 Current level that is represented.

 .. attribute:: nlevels
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Is this avoidable?
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Reworked this a while back, so not quite sure if your comment still applies?
Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/cluster.py
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# {{{ cluster tree

@dataclass(frozen=True)
class ClusterTreeLevel:
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Is this two things rather than one?
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Yeah, separated into a ClusterTree and ClusterLevel with a ClusterTree.levels() iterator to go through them for the recursive skeletonization.
Naming could still be better probably?
Comment threadtest/test_linalg_skeletonization.py
 logger.info("\n%s", case)

 run_skeletonize_by_proxy(actx, case, case.resolutions[0], visualize=visualize)
 dd = sym.DOFDescriptor(case.name, discr_stage=case.skel_discr_stage)
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Update the test docstring to describe precisely what's being tested here.
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Updated the blurb in
https://github.com/inducer/pytential/compare/f71a21b1a54791b02b35712225b9cfaca4be60cf..9a8db7ff410051a6b7d86cd8d5b934d02d094fef
Let me know if it's clear enough!
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Comment threadpytential/linalg/cluster.py


def make_cluster_parent_map(parent_ids: np.ndarray) -> np.ndarray:
 """Construct a parent map for :attr:`ClusterLevel.parent_map`."""
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Rephrase/rework? "All children in a bucket"?
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Rephrased and added some more context in https://github.com/inducer/pytential/compare/e9643cc480e53575274e4dc8e14d81d9b060f6b6..20fbc31a57c1a9a642abfa0a9b7a83ad81f1a1d5. Thoughts?
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@inducer I think inducer/ci-support@1475971 broke pylint (it's not finding the cython stuff anymore?). Any suggestion for a fix?
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#225
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Pull request overview
This PR advances the direct solver work by introducing hierarchical clustering infrastructure and wiring it into proxy-based skeletonization to enable recursive (multi-level) skeletonization, along with the associated test and documentation updates.
Changes:
  • Add a new pytential.linalg.cluster module providing cluster trees/levels, clustering helpers, and partition_by_nodes.
  • Extend skeletonization to produce richer results (including diagonal blocks) and add rec_skeletonize_by_proxy for multi-level skeletonization.
  • Update proxy and skeletonization tests (and docs) to match the new clustering/tree and neighbor-gathering APIs.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 5 comments.
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FileDescription
pytential/linalg/cluster.pyNew clustering module (cluster tree/levels, partitioning, visualization utilities).
pytential/linalg/skeletonization.pyAdds recursive skeletonization and augments skeletonization results/weighting/logging.
pytential/linalg/proxy.pyRemoves partition_by_nodes (moved to cluster module) and updates neighbor gathering API.
pytential/linalg/utils.pyDocuments/exports helper utilities used by skeletonization (make_flat_cluster_diag, interp_decomp).
test/extra_matrix_data.pyUpdates test fixtures to return (index, tree) and import partitioning from linalg.cluster.
test/test_linalg_cluster.pyNew tests for cluster tree construction and (un)clustering behavior.
test/test_linalg_proxy.pyAdapts tests to updated cluster index return type and neighbor gathering signature.
test/test_linalg_skeletonization.pyUpdates tests to exercise multilevel skeletonization flow.
test/test_matrix.pyAdapts callers to updated get_cluster_index / get_tgt_src_cluster_index return type.
doc/linalg.rstIncludes pytential.linalg.cluster in the linalg documentation.
doc/conf.pyAdds/adjusts intersphinx mappings for new referenced types.
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Comment threadpytential/linalg/cluster.py
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Comment threadpytential/linalg/cluster.py
Comment threadpytential/linalg/skeletonization.py
Comment threadpytential/linalg/skeletonization.py
Comment threadpytential/linalg/cluster.py
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