Add default methods `toarray` and `tosparse` to `LinearOperator` #368

mateomarin97 · 2023-12-12T12:03:38Z

The default toarray and tosparse functions have been added to linearoperator.
Also, parallel tests for these functions have been written.

A special case of the toarray function is toarray_1d implemented in PR #538

psydac/linalg/basic.py

… _tosparse_array, that contains the functionality to get both the sparse matrix and the full matrix

…ide the main for loop that kept allocating memory unecessarily

yguclu · 2024-10-09T14:50:03Z

@mateomarin97 We see that you have made changes to the code after Elena's questions, but it is not clear what exactly they are for. Could you please answer explicitly?

mateomarin97 · 2024-10-09T14:59:43Z

@mateomarin97 We see that you have made changes to the code after Elena's questions, but it is not clear what exactly they are for. Could you please answer explicitly?

Hello. The changes were just aesthetic. I made the code more readable by implementing the suggestions Elena mentioned. The only thing stopping this function from being ready is that for the sparse matrix case, I could not write a Pyccel kernel to replace the for loop that appends the new matrices entries since Pyccel did not support Python lists.

As the code stands it works but it is too slow due to this problem.

mateomarin97 · 2024-10-09T15:30:25Z

@mateomarin97 We see that you have made changes to the code after Elena's questions, but it is not clear what exactly they are for. Could you please answer explicitly?

Hello. The changes were just aesthetic. I made the code more readable by implementing the suggestions Elena mentioned. The only thing stopping this function from being ready is that for the sparse matrix case, I could not write a Pyccel kernel to replace the for loop that appends the new matrices entries since Pyccel did not support Python lists.

As the code stands it works but it is too slow due to this problem.

Now that I think about it I am fairly certain I have a newer version of this branch that I did not push. I will push it later.

e-moral-sanchez

For clarity and to avoid repetition, I would group the lines within a bunch of if BoS =='b' elif ...

psydac/linalg/basic.py

psydac/linalg/tests/toarray_parallel.py

Erased unnecessary file.

Add multigrid modules

yguclu · 2025-11-27T10:03:30Z

@kvrigor The unit tests fail when uploading the coverage report to Codacy. Do you see anything wrong with our current configuration?

yguclu · 2025-11-27T11:39:42Z

@kvrigor The unit tests fail when uploading the coverage report to Codacy. Do you see anything wrong with our current configuration?

I think I have understood the issue now. It is due to the fact that this PR originates from a forked repository which does not have a proper Codacy token.

e-moral-sanchez · 2025-12-04T10:35:46Z

psydac/linalg/basic.py

+
+        Parameters
+        ----------
+        out : numpy.ndarray, optional


In principle out could also be scipy.sparse.csr.csr_matrix , no? If we don't allow it, then we should add it in the function docstrings.

psydac/linalg/basic.py

e-moral-sanchez · 2025-12-04T10:47:35Z

psydac/linalg/basic.py

+        ----------
+        out : numpy.ndarray, optional
+            If given, the output will be written in-place into this array.
+        is_sparse : bool, optional


I would rename is_sparse as return_sparse

e-moral-sanchez · 2025-12-04T10:54:19Z

psydac/linalg/basic.py

+
+        Returns
+        -------
+        out : numpy.ndarray or scipy.sparse.csr.csr_matrix


In this method there is no variable called out

e-moral-sanchez · 2025-12-04T11:02:21Z

psydac/linalg/kernels/toarray_kernels.py

+    for i0 in range(itterables2[0][0],itterables2[0][1]):
+        if(tmp2[pds[0]+counter0] != 0):
+            row = i0
+            out[spoint2list+row,col] = tmp2[pds[0]+counter0]


isn't the ghost region formed by "pads*shifts"? so here (and in the other kernels) you would need

out[spoint2list+row,col] = tmp2[pds[0]*mld[0]+counter0]

where mld is from V.cart.shifts

e-moral-sanchez · 2025-12-04T12:11:20Z

psydac/linalg/tests/test_tosparse_parallel.py

+    N1arrloc = N1P.tosparse().toarray()
+    #We get the global matrix of the PowerLinearOperator
+    N1arr = np.zeros(np.shape(N1arrloc), dtype=dtype) 
+    comm.Allreduce(N1arrloc, N1arr, op=MPI.SUM)


We don't need to assemble the dense matrix. We can call Allreduce on the indices and data vectors of the sparse matrix.

e-moral-sanchez · 2025-12-04T12:12:38Z

psydac/linalg/tests/test_toarray_parallel.py

+
+    assert isinstance(N1P, PowerLinearOperator)
+    assert isinstance(N1P.domain, StencilVectorSpace)
+    compare_arrays(N1P.dot(v0), np.matmul(N1arr,v0arr), rank)


I have the same comments as in test_tosparse_parallel.py. Since we assemble the dense matrices, we should compare the arrays directly instead of the dot product with a vector.

e-moral-sanchez · 2025-12-04T12:25:04Z

psydac/linalg/tests/test_toarray.py

+    Bpow = B**3
+    Bpowarr = Bpow.toarray()
+    assert isinstance(Bpow, PowerLinearOperator)
+    assert np.array_equal(np.matmul(Bpowarr,vbarr),Bpow.dot(vb).toarray())


I have the same comments as in test_toarray_parallel.py. Since we assemble the dense matrices, we should compare the arrays directly instead of the dot product with a vector.

e-moral-sanchez · 2025-12-04T12:26:32Z

psydac/linalg/tests/test_toarray.py

+@pytest.mark.parametrize('p1', p1array)
+@pytest.mark.parametrize('p2', p2array)
+
+def test_square_block_basic(n1, n2, p1, p2, P1=False, P2=False):


the name of the test could be more descriptive, for instance: test_toarray_powerlinearoperator_block

e-moral-sanchez · 2025-12-04T12:34:22Z

psydac/linalg/tests/test_toarray.py

+    assert isinstance(Sinv, InverseLinearOperator)
+
+    Itest = np.matmul(A1,Sinvarr)
+    assert np.allclose(Itest, np.eye(np.size(Itest[0])),atol= 10**(-5))


Why would Itest be the identity? Isn't A1 different than S?

mateomarin97 added 2 commits December 6, 2023 16:48

To array and to sparse are ready

fe29b51

Cleaned the comments

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e-moral-sanchez requested changes Dec 12, 2023

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mateomarin97 added 6 commits December 12, 2023 16:55

Implemented some of the suggested changes

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Merge branch 'devel' into devel

0ed812a

Reduced the amount of code by writing and additional private function…

f5de4d3

… _tosparse_array, that contains the functionality to get both the sparse matrix and the full matrix

Merge branch 'devel' of github.com:mateomarin97/psydac into devel

a7b55c5

Optimized the toarray_sparse function by removing toarray() calls ins…

484365a

…ide the main for loop that kept allocating memory unecessarily

Added pyccel kernels for construction of dense matrices.

db79c17

mateomarin97 added 2 commits December 28, 2024 15:41

Parallel tests

4f1a218

Merge branch 'devel' into devel

beb1b70

e-moral-sanchez requested changes Feb 5, 2025

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Nathan and others added 2 commits March 17, 2025 15:26

Made the requested clean up of the code.

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Merge branch 'devel' into devel

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e-moral-sanchez requested changes Mar 17, 2025

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mateomarin97 and others added 4 commits March 19, 2025 12:46

Delete psydac/linalg/tests/toarray_parallel.py

9b8dda1

Erased unnecessary file.

Create multigrid.py

cb86549

Add multigrid modules

Merge remote-tracking branch 'upstream/devel' into devel

34720fb

Merge branch 'devel' into devel

c6cbe92

yguclu mentioned this pull request Nov 25, 2025

Add LST preconditioner #538

Merged

yguclu added 7 commits November 26, 2025 15:16

Merge branch 'devel' into devel

047d703

Use typing.TypeVar in toarray_kernels.py

cfced7a

Clean up toarray test files

f2dc22b

Clean up test_tosparse_parallel.py

9d0f418

Add missing newlines at end of files

47ab655

Remove unused empty module psydac.linalg.multigrid

5cb5a72

Clean up psydac/linalg/basic.py

2459a73

yguclu added 2 commits November 26, 2025 17:42

Further clean up psydac/linalg/basic.py

3766611

Further clean up psydac/linalg/basic.py

612ae7c

yguclu changed the title ~~To array and to sparse functions are ready for linearoperator~~ Add default implementations to methods toarray and tosparse of LinearOperator Nov 26, 2025

yguclu changed the title ~~Add default implementations to methods toarray and tosparse of LinearOperator~~ Add default methods LinearOperator.toarray and tosparse Nov 26, 2025

yguclu added the Next Release Must be in next release label Nov 26, 2025

yguclu changed the title ~~Add default methods LinearOperator.toarray and tosparse~~ Add default methods toarray and tosparse to LinearOperator Nov 26, 2025

yguclu requested a review from e-moral-sanchez November 26, 2025 17:12

yguclu and others added 2 commits November 27, 2025 16:10

Merge branch 'devel' into devel

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Merge branch 'devel' into devel

d867ec1

e-moral-sanchez requested changes Dec 4, 2025

View reviewed changes

yguclu removed the Next Release Must be in next release label Dec 10, 2025

Add default methods toarray and tosparse to LinearOperator #368

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Add default methods `toarray` and `tosparse` to `LinearOperator` #368

Add default methods `toarray` and `tosparse` to `LinearOperator` #368

mateomarin97 commented Dec 12, 2023 •

edited by yguclu

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