Rare problem with numpy and dedalus

[Andrei Igoshev]

Dear All,

I use Dedalus 3 and run essentially the same code on multiple machines. Recently I tried to install Dedalus on new HPC university facility. Example problems from Dedalus web-site ran fine, but my code showed the following error:

Traceback (most recent call last):

  File "/mnt/nfs/home/nai77/two_fluids/anelastic_MHD.py", line 172, in <module>

    solver = problem.build_solver(timestepper)

             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/problems.py", line 98, in build_solver

    return self.solver_class(self, *args, **kw)

           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/solvers.py", line 565, in __init__

    self.build_matrices(self.subproblems, ['M', 'L'])

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/solvers.py", line 131, in build_matrices

    subsystems.build_subproblem_matrices(self, subproblems, matrices)

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/subsystems.py", line 81, in build_subproblem_matrices

    subproblem.build_matrices(matrices)

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/subsystems.py", line 520, in build_matrices

    eqn_blocks = eqn[name].expression_matrices(subproblem=self, vars=vars, ncc_cutoff=solver.ncc_cutoff, max_ncc_terms=solver.max_ncc_terms)

                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/arithmetic.py", line 190, in expression_matrices

    arg_matrices = arg.expression_matrices(subproblem, vars, **kw)

                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/operators.py", line 778, in expression_matrices

    operator_mat = self.subproblem_matrix(subproblem)

                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/operators.py", line 3195, in subproblem_matrix

    matrix = self._wrap_radial_matrix(regindex_in, regindex_out, ell, return_zeros=False)

             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/operators.py", line 3219, in _wrap_radial_matrix

    return self.radial_matrix(regindex_in, regindex_out, ell)

           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/mnt/nfs/home/nai77/venv/dedalus/lib/python3.11/site-packages/dedalus/core/basis.py", line 4776, in radial_matrix

    matrix[0, 0] = unit_amplitude

    ~~~~~~^^^^^^

ValueError: setting an array element with a sequence.

Exactly the same code runs fine on my own laptop and another HPC. I have successfully solved this problem by downgrading numpy to version 2.2.1.

Best regards,

Andrei Igoshev

[Keaton Burns]

Hi Andrei,

This should be fixed with the latest commit on the main branch of Dedalus. Could you try a source build from that with the newer version of numpy on your cluster? If that works I’ll release a new patch update to conda/pip.

Thanks,

-Keaton

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[Andrei Igoshev]

Dear Keaton,

Thank you very much for your fast reply.

I have installed Dedalus using:

git clone -b master https://github.com/DedalusProject/dedalus
cd dedalus
CC=mpicc pip3 install --no-cache --no-build-isolation .

Simulations starts, but I got the following warning:

/mnt/nfs/home/nai77/venv1/dedalus/lib/python3.11/site-packages/scipy/sparse/_construct.py:543: FutureWarning: Input has data type int64, but the output has been cast to float64.  In the future, the output data type will match the input. To avoid this warning, set the `dtype` parameter to `None` to have the output dtype match the input, or set it to the desired output data type.

Note: In Python 3.11, this warning can be generated by a call of scipy.sparse.diags(), but the code indicated in the warning message will refer to an internal call of scipy.sparse.diags_array(). If that happens, check your code for the use of diags().

  A = diags_array(diagonals, offsets=offsets, shape=shape, dtype=dtype)

2026-01-13 16:14:57,888 subsystems 0/4 INFO :: Building subproblem matrices 1/17 (~6%) Elapsed: 0s, Remaining: 7s, Rate: 2.4e+00/s

/mnt/nfs/home/nai77/venv1/dedalus/lib/python3.11/site-packages/scipy/sparse/_construct.py:543: FutureWarning: Input has data type int64, but the output has been cast to float64.  In the future, the output data type will match the input. To avoid this warning, set the `dtype` parameter to `None` to have the output dtype match the input, or set it to the desired output data type.

Note: In Python 3.11, this warning can be generated by a call of scipy.sparse.diags(), but the code indicated in the warning message will refer to an internal call of scipy.sparse.diags_array(). If that happens, check your code for the use of diags().

  A = diags_array(diagonals, offsets=offsets, shape=shape, dtype=dtype)

/mnt/nfs/home/nai77/venv1/dedalus/lib/python3.11/site-packages/scipy/sparse/_construct.py:543: FutureWarning: Input has data type int64, but the output has been cast to float64.  In the future, the output data type will match the input. To avoid this warning, set the `dtype` parameter to `None` to have the output dtype match the input, or set it to the desired output data type.

Note: In Python 3.11, this warning can be generated by a call of scipy.sparse.diags(), but the code indicated in the warning message will refer to an internal call of scipy.sparse.diags_array(). If that happens, check your code for the use of diags().

  A = diags_array(diagonals, offsets=offsets, shape=shape, dtype=dtype)

/mnt/nfs/home/nai77/venv1/dedalus/lib/python3.11/site-packages/scipy/sparse/_construct.py:543: FutureWarning: Input has data type int64, but the output has been cast to float64.  In the future, the output data type will match the input. To avoid this warning, set the `dtype` parameter to `None` to have the output dtype match the input, or set it to the desired output data type.

Note: In Python 3.11, this warning can be generated by a call of scipy.sparse.diags(), but the code indicated in the warning message will refer to an internal call of scipy.sparse.diags_array(). If that happens, check your code for the use of diags().

  A = diags_array(diagonals, offsets=offsets, shape=shape, dtype=dtype)



Best regards,

Andrei Igoshev

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[Manohar Teja]

Hi,

I just want to mention that I see a similar error as well, but originating from the subsystems.py file. See the warning below:

/home/e6a/mk737.e6a/miniforge3/envs/dedalus3/lib/python3.12/site-packages/dedalus/core/subsystems.py:548: FutureWarning: Input has data type int64, but the output has been cast to float64.  In the future, the output data type will match the input. To avoid this warning, set the `dtype` parameter to `None` to have the output dtype match the input, or set it to the desired output data type.
  valid_var = sparse.diags(np.concatenate([v.ravel() for v in valid_var], dtype=int)).tocsr()
2026-01-14 17:30:46,088 subsystems 0/64 INFO :: Building subproblem matrices 1/4 (~25%) Elapsed: 0s, Remaining: 0s, Rate: 3.1e+01/s

Any update on why this is happening and how can this be fixed? 

[Manohar Teja]

Hi,

I am facing similar problem but with subsystems.py (see warning message below). Any updates on how to fix this?

/home/e6a/mk737.e6a/miniforge3/envs/dedalus3/lib/python3.12/site-packages/dedalus/core/subsystems.py:548: FutureWarning: Input has data type int64, but the output has been cast to float64.  In the future, the output data type will match the input. To avoid this warning, set the `dtype` parameter to `None` to have the output dtype match the input, or set it to the desired output data type.

  valid_var = sparse.diags(np.concatenate([v.ravel() for v in valid_var], dtype=int)).tocsr()

2026-01-14 17:30:46,088 subsystems 0/64 INFO :: Building subproblem matrices 1/4 (~25%) Elapsed: 0s, Remaining: 0s, Rate: 3.1e+01/s

Regards

Manohar

CGAFD, Univ of Exeter

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