DO NOT SQUASH Add PyOP2 to Firedrake repository by JDBetteridge · Pull Request #3817 · firedrakeproject/firedrake

JDBetteridge · 2024-10-22T15:34:13Z

Description

The big merge!

Closes #3877

Key changes introduced by this PR

PyOP2 is ingested into this repository (TSFC will be done later)
Existing tests are moved into a tests/firedrake subdirectory
Adds a pyproject.toml
pip install git+https://github.com/firedrakeproject/firedrake.git becomes a viable install method (subject to setting a number of environment variables). This ultimately will be our path to a Firedrake wheel.
Removes firedrake_configuration. The information is all accessible by inspecting PETSc variables.

Outstanding tasks

CI passing
Make sure that firedrake-install, firedrake-update, firedrake-status and firedrake-clean pass locally (these are not fully tested in the CI).
git rebase -i to try and keep a clean history.
Fix firedrake-zenodo as PyOP2 repo is going away.
Check manual for possible inaccuracies about install and Zenodo.

Following feedback

firedrake-update using an existing installation
firedrake-zenodo should be found

Future work

Also include TSFC in Firedrake repo (and put GEM and FInAT into FIAT).
pip install libsupermesh (nearly ready to go: JDBetteridge/pip install libsupermesh#10)

Make PETSc and petsc4py for CI use Firedrake not pip

actions: Build docs at end of successful test run

* Change requirements on loopy to point at the loopy sprint branch. * Replace lp.register_callable_kernel with lp.merge knl = lp.register_callable_kernel(knl, callee) is now knl = lp.merge([knl, callee]) . Reason given for loopy breaking back-compat: earlier they had a notion of a special "root_kernel" which only permitted one level of nesting loopy kernel calls and that was too restrictive. * Loopy callables: adapt to new API for registering. * Loopy Callables: register callables on a kernel not functions. * name is static property on SolveCallable and INVCallable * Loopy callables: register the callables rather than functions and remove the lookup functions. * Some progress * Loopy callables: Adapt API of with_types. * INVCallable has name "inverse" in loopy rep * Always pass a target when generating loopy kernels, otherwise we cannot merge them with wrapper kernels. * flake8 * Maybe generate call to inner kernel correctly Still doesn't work later. * Revert "Maybe generate call to inner kernel correctly" This reverts commit 009ca19f3fb133d53affeab53cd016c9b55620a9. * Revert "Revert "Maybe generate call to inner kernel correctly"" This reverts commit c85b60e6382b4762076b2744227fa5a6d903b830. * Remove dead code * rep2loopy: get name of callee kernel for matching the args. * Add missing code target * Maybe handle loopy argument access correctly dat.zero still doesn't work * Promote dats with shape (n,) to shape (n, 1) This enables sweeping indices to pick up a direct loop. * Set lang_version on all make_function calls * Fix disjoint arguments to C-string kernels * Resolve review comments * Rename function_args -> kernel_parameters * WIP Match args for all kernels in the callables table besides for LACallables? Why? * Only match args for callables that are CallableKernels. * Pin decorator Decorator version 5 changes the API in ways that break the argument type checking in PyOP2. We're therefore pinning on the version that works. * catch up with numpy type changes * Set within_inames_is_final on instructions * Squash numpy warning * Set strides on GlobalArgs * Caching: produce key for loop Programs. * Check if kernel is a loopy Program. * loopy.program.Program -> loopy.Program * Adapt to loopy interface changes. * Maintain loopy automatic reshaping (was in loopy) Everything in loopycompat.py file was in loopy/transform/callable.py but is removed in inducer/loopy#327. This commit maintains compatibility but should be phased out. * Fix loopy.program -> loopy.translation_unit * dont lint automatic reshaping (was in loopy) * Lint to pass flake8 * Fix loopy automatic reshaping (was in loopy) Changes were copied from an out of date branch by accident. * Fix type case error (recursively) This mirrors inducer/loopy#326 * ? Maybe fix the last dimension error mismatch. Not sure this will break things in other places. * Codegen: Don't merge indices of extent 1, so that the instructions are schedulable. This will fix e.g. the failure of tests/extrusion/test_steady_advection_2D_extr.py * Testing: Update loopy branch * Squashed commit of the following: commit 5a89bfc Author: Connor Ward <c.ward20@imperial.ac.uk> Date: Mon May 10 10:44:33 2021 +0100 Use Firedrake PETSc and petsc4py commit 948cb7d Author: David Ham <David.Ham@imperial.ac.uk> Date: Wed Apr 21 13:30:50 2021 +0100 Pin decorator Decorator version 5 changes the API in ways that break the argument type checking in PyOP2. We're therefore pinning on the version that works. commit 121c2a6 Author: David Ham <David.Ham@imperial.ac.uk> Date: Wed Apr 21 13:45:58 2021 +0100 catch up with numpy type changes * Revert "Squashed commit of the following:" This reverts commit bd1916142f883d6a4f0371ca6de2c344f0c7e78a. * Squashed commit of the following: commit 9a90c9f Merge: f1daf21 c8d7ff6 Author: Lawrence Mitchell <lawrence@wence.uk> Date: Tue May 11 12:07:33 2021 +0100 Merge pull request #618 from OP2/wence/fix/actions-doc-build actions: Build docs at end of successful test run commit c8d7ff6 Author: Lawrence Mitchell <lawrence@wence.uk> Date: Tue May 11 11:41:20 2021 +0100 actions: Build docs at end of successful test run commit f1daf21 Merge: d0cc348 5a89bfc Author: Lawrence Mitchell <lawrence@wence.uk> Date: Mon May 10 20:32:24 2021 +0100 Merge pull request #617 from connorjward/test-ci Make PETSc and petsc4py for CI use Firedrake not pip commit 5a89bfc Author: Connor Ward <c.ward20@imperial.ac.uk> Date: Mon May 10 10:44:33 2021 +0100 Use Firedrake PETSc and petsc4py commit 948cb7d Author: David Ham <David.Ham@imperial.ac.uk> Date: Wed Apr 21 13:30:50 2021 +0100 Pin decorator Decorator version 5 changes the API in ways that break the argument type checking in PyOP2. We're therefore pinning on the version that works. commit 121c2a6 Author: David Ham <David.Ham@imperial.ac.uk> Date: Wed Apr 21 13:45:58 2021 +0100 catch up with numpy type changes * Lint. * Jenkins * Make import global. * Drop package branches. Co-authored-by: Sophia Vorderwuelbecke <sv2518@ic.ac.uk> Co-authored-by: Lawrence Mitchell <lawrence@wence.uk> Co-authored-by: Connor Ward <c.ward20@imperial.ac.uk> Co-authored-by: David Ham <David.Ham@imperial.ac.uk> Co-authored-by: Kaushik Kulkarni <kaushikcfd@gmail.com>

Something like this will be necessary if we want general symmetry group stuff in the maps. It is also convenient if you want to stage in a permutation from the canonical FIAT order.

Instead of pattern matching on node names to determine whether nodes should be relabelled, just use a name generation scheme for everything. Now we have one less problem.

…versionning

Add PETSc decorator to compile

More loopy interface changes: arg_id_to_val -> arg_id_to_arg

…problem

* Add petsc_raises fixture to catch PETSc callback exceptions

* Fix assembly of Real matrices

* Refactor test_demos, avoid mpiexec invocation * Fix multigrid test, __main__ is not valid when importing

* Get value_shape from FunctionSpace * Define FunctionSpace.block_size as the number of dofs per node * sort_domains --------- Co-authored-by: ksagiyam <k.sagiyama@imperial.ac.uk>

* DO NOT MERGE * Test VOM with point variant * Update .github/workflows/build.yml * Test Regge point variant * add continuity test * Test H(curl div) element (#3843) * Test H(curl div) element * test Hu-Zhang * checkout ufl master branch * checkout master branches

Signed-off-by: Umberto Zerbinati <zerbinati@maths.ox.ac.uk> Co-authored-by: Umberto Zerbinati <zerbinati@maths.ox.ac.uk>

* Disk checkpointing managing start, pause and continue checkpointing. * AdjointDiskCheckpoint --------- Co-authored-by: David A. Ham <david.ham@imperial.ac.uk>

* Moves PyOP2 code into Firedrake repository. * Adds a pyproject.toml for Firedrake * Enables (with some caveats) one to `pip install firedrake`! * Adds a new pip workflow to make sure things work * Moves Firedrake tests into a `tests/firedrake` subdirectory.

…pyop2_tsfc

ksagiyam · 2024-11-25T15:33:50Z

I did a clean install using the branch. Wanted to test firedrake-zenodo, but I got the following:

>>> firedrake-zenodo -t "My paper title"
firedrake-zenodo: command not found

firedrake-update seems almost working, but I had to copy firedrake/scripts/firedrake-install to scripts/firedrake-install.

connorjward · 2024-11-25T15:51:45Z

I did a clean install using the branch. Wanted to test firedrake-zenodo, but I got the following:
>>> firedrake-zenodo -t "My paper title"
firedrake-zenodo: command not found

Thanks for noticing this. Will fix ASAP.

firedrake-update seems almost working, but I had to copy firedrake/scripts/firedrake-install to scripts/firedrake-install.

Specifically what failed? I thought I tried this and things worked.

ksagiyam · 2024-11-25T16:07:04Z

(firedrake) ksagiyam@ma-ksagiyam-2:~/cpython/test/firedrake/src/firedrake$ firedrake-update 
/home/ksagiyam/cpython/test/firedrake/bin/firedrake-update:20: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pkg_resources.extern.packaging.version import Version, InvalidVersion
Running /home/ksagiyam/cpython/test/firedrake/bin/firedrake-update
BLAS config is {}
Configuration saved to /home/ksagiyam/cpython/test/firedrake/.configuration.json
Updating the git repository for firedrake
Creating firedrake-update script.
Traceback (most recent call last):
  File "/home/ksagiyam/cpython/test/firedrake/bin/firedrake-update", line 1902, in <module>
    build_update_script()
  File "/home/ksagiyam/cpython/test/firedrake/bin/firedrake-update", line 1407, in build_update_script
    with open("firedrake/scripts/firedrake-install", "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'firedrake/scripts/firedrake-install'

connorjward · 2024-11-25T16:10:13Z

(firedrake) ksagiyam@ma-ksagiyam-2:~/cpython/test/firedrake/src/firedrake$ firedrake-update 
/home/ksagiyam/cpython/test/firedrake/bin/firedrake-update:20: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pkg_resources.extern.packaging.version import Version, InvalidVersion
Running /home/ksagiyam/cpython/test/firedrake/bin/firedrake-update
BLAS config is {}
Configuration saved to /home/ksagiyam/cpython/test/firedrake/.configuration.json
Updating the git repository for firedrake
Creating firedrake-update script.
Traceback (most recent call last):
  File "/home/ksagiyam/cpython/test/firedrake/bin/firedrake-update", line 1902, in <module>
    build_update_script()
  File "/home/ksagiyam/cpython/test/firedrake/bin/firedrake-update", line 1407, in build_update_script
    with open("firedrake/scripts/firedrake-install", "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'firedrake/scripts/firedrake-install'

But that's not what I have... https://github.com/firedrakeproject/firedrake/pull/3817/files#diff-e86a30193cf50f52a86c9839c05da17a3f06c2ff5d082571efc52644f7f79771L1407-R1400

Strange. I think that running firedrake-update is pulling the current master version of the script.

ksagiyam · 2024-11-25T16:22:56Z

To be clear, I installed current master, checked out this PR branch, and then ran firedrake-update. I think in this case bin/firedrake-update tries to pull from scripts/firedrake-update (

firedrake/scripts/firedrake-install

Line 1407 in b783253

with open("firedrake/scripts/firedrake-install", "r") as f:

), but it does not exist in the new firedrake structure.

connorjward · 2024-11-25T16:26:32Z

To be clear, I installed current master, checked out this PR branch, and then ran firedrake-update. I think in this case bin/firedrake-update tries to pull from scripts/firedrake-update (

firedrake/scripts/firedrake-install

Line 1407 in b783253

with open("firedrake/scripts/firedrake-install", "r") as f:

), but it does not exist in the new firedrake structure.

Ah I see. This is a case I had not (and certainly should have) considered.

connorjward and others added 30 commits May 10, 2021 17:21

Use Firedrake PETSc and petsc4py

5a89bfc

Merge pull request #617 from connorjward/test-ci

f1daf21

Make PETSc and petsc4py for CI use Firedrake not pip

actions: Build docs at end of successful test run

c8d7ff6

Merge pull request #618 from OP2/wence/fix/actions-doc-build

9a90c9f

actions: Build docs at end of successful test run

add standard set operations

afe4ad4

codegen/api: New PermutedMap class corresponding to map o permutation

ded8578

Something like this will be necessary if we want general symmetry group stuff in the maps. It is also convenient if you want to stage in a permutation from the canonical FIAT order.

codegen: No more regular expressions in node renaming

dfeec40

Instead of pattern matching on node names to determine whether nodes should be relabelled, just use a name generation scheme for everything. Now we have one less problem.

tests: Squash numpy deprecation warnings

a257d1d

Merge remote-tracking branch 'origin/master' into DataCarrier-object-…

07a47b3

…versionning

Add PETSc decorator to compile

1e74cea

add standard set operations

2781213

Merge branch 'fs_filter' of github.com:OP2/PyOP2 into fs_filter

855ec95

Add some missing DataCarrier inits

29973b1

Merge pull request #623 from OP2/connorjward/time-compilation

c45a751

Add PETSc decorator to compile

Merge remote-tracking branch 'origin/master' into fs_filter

bb27936

More loopy interface changes: arg_id_to_val -> arg_id_to_arg

e56d26f

Add recreate to Arg

f057908

Recreate method of Arg

3442f06

Fix cache problem

92184de

Fix cache problem

e9b73ab

Fix cache problem

f24478a

Requirements: update loopy fork.

b28bf14

Merge pull request #627 from OP2/new-loopy-master

781201c

More loopy interface changes: arg_id_to_val -> arg_id_to_arg

Merge remote-tracking branch 'origin/master' into Melina97/fix_cache_…

760dbe7

…problem

Updated changes

899a543

Don't use a parloop when not needed

70c4b39

added subset case for copy

58f89ef

@dham

2460b37

Don't use a parloop when not needed

3ddc70a

connorjward and others added 11 commits November 25, 2024 10:49

Fixes for updated PETSc (#3853)

c9d3922

* Add petsc_raises fixture to catch PETSc callback exceptions

function space: fix collapse (#3861)

654bb27

Fix assembly of Real matrices (#3846)

6fe96de

* Fix assembly of Real matrices

ngsPETSc "stable" release is coming ! (#3857)

bb8f6e1

Parallel test improvements (#3865)

dff63f8

* Refactor test_demos, avoid mpiexec invocation * Fix multigrid test, __main__ is not valid when importing

Get value_shape from FunctionSpace (#3862)

cf46e77

* Get value_shape from FunctionSpace * Define FunctionSpace.block_size as the number of dofs per node * sort_domains --------- Co-authored-by: ksagiyam <k.sagiyama@imperial.ac.uk>

Actually install ngsPETSc using pip (#3873)

f222dc5

Signed-off-by: Umberto Zerbinati <zerbinati@maths.ox.ac.uk> Co-authored-by: Umberto Zerbinati <zerbinati@maths.ox.ac.uk>

Disk checkpointing (#3812)

8f45d26

* Disk checkpointing managing start, pause and continue checkpointing. * AdjointDiskCheckpoint --------- Co-authored-by: David A. Ham <david.ham@imperial.ac.uk>

test: add test for 0**{min_value, max_value} (#3855)

6bb9a9f

connorjward force-pushed the JDBetteridge/merge_pyop2_tsfc branch from 463eb23 to 1bceac4 Compare November 25, 2024 10:55

Merge remote-tracking branch 'origin/master' into JDBetteridge/merge_…

ccec788

…pyop2_tsfc

connorjward mentioned this pull request Nov 25, 2024

Revert "Hack dataclass'd function_interface to avoid breaking Firedrake" inducer/loopy#886

Merged

Use correct link to get firedrake-install script

c72810a

ksagiyam reviewed Nov 25, 2024

View reviewed changes

Comment thread firedrake/scripts/firedrake_clean.py Outdated

Fix firedrake-zenodo and firedrake-clean

8bcb96f

connorjward force-pushed the JDBetteridge/merge_pyop2_tsfc branch from 01273f3 to 8bcb96f Compare November 25, 2024 16:23

connorjward added 2 commits November 25, 2024 16:34

Revert firedrake-install location, to avoid breaking firedrake-update

867337f

Do not specify numpy>=2 and tweak install instructions

74a3f85

dham merged commit dab79d3 into master Nov 27, 2024

dham deleted the JDBetteridge/merge_pyop2_tsfc branch November 27, 2024 16:10

vojtamolda mentioned this pull request Dec 5, 2024

Compatibility fix for Firedrake 2024-12 Docker image IvanYashchuk/firedrake-ts#24

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DO NOT SQUASH Add PyOP2 to Firedrake repository#3817

DO NOT SQUASH Add PyOP2 to Firedrake repository#3817
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JDBetteridge commented Oct 22, 2024 •

edited by connorjward

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Description

Key changes introduced by this PR

Outstanding tasks

Following feedback

Future work

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ksagiyam commented Nov 25, 2024

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connorjward commented Nov 25, 2024

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ksagiyam commented Nov 25, 2024

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JDBetteridge commented Oct 22, 2024 •

edited by connorjward

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