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ArpackError on cpu with recent installs #82

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sjfleming opened this issue Feb 10, 2025 · 0 comments
Open

ArpackError on cpu with recent installs #82

sjfleming opened this issue Feb 10, 2025 · 0 comments

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@sjfleming
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sjfleming commented Feb 10, 2025 •
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Great package, thanks! I have had great success with pymde in the past.

Recently, I am getting some funny business during installation of pymde. For example, on a Mac (or Linux I think):

(base) $ conda create -n test python=3.10
(base) $ conda activate test
(test) $ pip install -U pymde
Successfully installed MarkupSafe-3.0.2 certifi-2025.1.31 charset-normalizer-3.4.1 contourpy-1.3.1 cycler-0.12.1 filelock-3.17.0 fonttools-4.56.0 fsspec-2025.2.0 idna-3.10 jinja2-3.1.5 joblib-1.4.2 kiwisolver-1.4.8 llvmlite-0.44.0 matplotlib-3.10.0 mpmath-1.3.0 networkx-3.4.2 numba-0.61.0 numpy-2.1.3 packaging-24.2 pillow-11.1.0 pymde-0.1.18 pynndescent-0.5.13 pyparsing-3.2.1 python-dateutil-2.9.0.post0 requests-2.32.3 scikit-learn-1.6.1 scipy-1.15.1 six-1.17.0 sympy-1.13.1 threadpoolctl-3.5.0 torch-2.6.0 torchvision-0.21.0 typing-extensions-4.12.2 urllib3-2.3.0

running this (in a jupyter notebook via vscode)

import pymde

mnist = pymde.datasets.MNIST()
embedding = pymde.preserve_neighbors(mnist.data, embedding_dim=2, verbose=True).embed()
pymde.plot(embedding, color_by=mnist.attributes['digits'])

results in

ValueError                                Traceback (most recent call last)
Cell In[3], [line 1](vscode-notebook-cell:?execution_count=3&line=1)
----> [1](vscode-notebook-cell:?execution_count=3&line=1) import pymde
      [3](vscode-notebook-cell:?execution_count=3&line=3) mnist = pymde.datasets.MNIST()
      [4](vscode-notebook-cell:?execution_count=3&line=4) embedding = pymde.preserve_neighbors(mnist.data, embedding_dim=2, verbose=True).embed()

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/__init__.py:7
      [3](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/__init__.py:3) from pymde.problem import MDE
      [5](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/__init__.py:5) from pymde.constraints import Centered, Anchored, Standardized
----> [7](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/__init__.py:7) from pymde import datasets
      [9](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/__init__.py:9) from pymde.preprocess.graph import Graph
     [11](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/__init__.py:11) from pymde.util import all_edges

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/datasets.py:19
     [16](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/datasets.py:16) import os
     [18](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/datasets.py:18) import numpy as np
---> [19](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/datasets.py:19) from pymde.preprocess.graph import Graph
     [20](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/datasets.py:20) from pymde.problem import LOGGER
     [21](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/datasets.py:21) import scipy.sparse as sp

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/__init__.py:5
      [2](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/__init__.py:2) from pymde.preprocess.preprocess import deduplicate_edges, sample_edges
      [3](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/__init__.py:3) from pymde.preprocess.preprocess import scale
----> [5](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/__init__.py:5) from pymde.preprocess.generic import distances, k_nearest_neighbors
      [7](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/__init__.py:7) from . import graph
      [8](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/__init__.py:8) from .graph import Graph

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/generic.py:5
      [2](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/generic.py:2) import scipy.sparse as sp
      [3](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/generic.py:3) import torch
----> [5](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/generic.py:5) from pymde.preprocess import data_matrix
      [6](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/generic.py:6) from pymde.preprocess import graph
      [9](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/generic.py:9) def _is_data_matrix(data):

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/data_matrix.py:6
      [3](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/data_matrix.py:3) import torch
      [5](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/data_matrix.py:5) from pymde import problem
----> [6](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/data_matrix.py:6) from pymde.preprocess.graph import Graph
      [7](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/data_matrix.py:7) from pymde.preprocess.preprocess import sample_edges
      [8](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/data_matrix.py:8) from pymde import util

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/graph.py:12
     [10](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/graph.py:10) from pymde import util
     [11](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/graph.py:11) from pymde.functions import penalties, losses
---> [12](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/graph.py:12) from pymde.preprocess import _graph
     [15](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/graph.py:15) __this_module = sys.modules[__name__]
     [18](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/preprocess/graph.py:18) LOGGER = problem.LOGGER

File pymde/preprocess/_graph.pyx:1, in init pymde.preprocess._graph()

ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

this is an error I've seen before in the context of numpy version incompatibilities.

If I run

(test) $ pip install numpy==1.26.4

then the above ValueError resolves.

However, a new error arises, which several of my colleagues have seen in different contexts, on Ubuntu linux in particular:

again I run

import pymde

mnist = pymde.datasets.MNIST()
embedding = pymde.preserve_neighbors(mnist.data, embedding_dim=2, verbose=True).embed()
pymde.plot(embedding, color_by=mnist.attributes['digits'])

and now I see

Feb 10 04:40:21 PM: Loading cached dataset.
Feb 10 04:40:21 PM: Computing 15-nearest neighbors, with max_distance=None
Mon Feb 10 16:40:21 2025 Building RP forest with 21 trees
Mon Feb 10 16:40:22 2025 NN descent for 16 iterations
	 1  [/](https://file+.vscode-resource.vscode-cdn.net/)  16
	 2  [/](https://file+.vscode-resource.vscode-cdn.net/)  16
	 3  [/](https://file+.vscode-resource.vscode-cdn.net/)  16
	 4  [/](https://file+.vscode-resource.vscode-cdn.net/)  16
	Stopping threshold met -- exiting after 4 iterations
Feb 10 04:40:24 PM: Computing quadratic initialization.

ArpackError                               Traceback (most recent call last)
Cell In[1], [line 4](vscode-notebook-cell:?execution_count=1&line=4)
      [1](vscode-notebook-cell:?execution_count=1&line=1) import pymde
      [3](vscode-notebook-cell:?execution_count=1&line=3) mnist = pymde.datasets.MNIST()
----> [4](vscode-notebook-cell:?execution_count=1&line=4) embedding = pymde.preserve_neighbors(mnist.data, embedding_dim=2, verbose=True).embed()
      [5](vscode-notebook-cell:?execution_count=1&line=5) pymde.plot(embedding, color_by=mnist.attributes['digits'])

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:367, in preserve_neighbors(data, embedding_dim, attractive_penalty, repulsive_penalty, constraint, n_neighbors, repulsive_fraction, max_distance, init, device, verbose)
    [365](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:365) # use cg + torch when using GPU
    [366](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:366) cg = device == "cuda"
--> [367](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:367) X_init = quadratic.spectral(
    [368](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:368)     n,
    [369](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:369)     embedding_dim,
    [370](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:370)     edges,
    [371](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:371)     weights,
    [372](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:372)     max_iter=1000,
    [373](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:373)     device=device,
    [374](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:374)     cg=cg,
    [375](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:375) )
    [376](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:376) if not isinstance(
    [377](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:377)     constraint, (constraints._Centered, constraints._Standardized)
    [378](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:378) ):
    [379](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/recipes.py:379)     constraint.project_onto_constraint(X_init, inplace=True)

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:174, in spectral(n_items, embedding_dim, edges, weights, cg, max_iter, device)
    [172](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:172) use_scipy = not cg
    [173](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:173) L = _laplacian(n_items, embedding_dim, edges, weights, use_scipy=use_scipy)
--> [174](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:174) emb = _spectral(L, embedding_dim, cg=cg, device=device, max_iter=max_iter)
    [175](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:175) if use_scipy:
    [176](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:176)     emb -= emb.mean(axis=0)

File ~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:85, in _spectral(L, m, cg, max_iter, edges, weights, warm_start, device)
     [83](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:83) if not cg:
     [84](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:84)     num_lanczos_vectors = max(2 * k + 1, int(np.sqrt(L.shape[0])))
---> [85](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:85)     eigenvalues, eigenvectors = scipy.sparse.linalg.eigsh(
     [86](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:86)         L,
     [87](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:87)         k,
     [88](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:88)         which="SM",
     [89](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:89)         ncv=num_lanczos_vectors,
     [90](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:90)         tol=1e-4,
     [91](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:91)         v0=np.ones(L.shape[0]),
     [92](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:92)         maxiter=L.shape[0] * 5,
     [93](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:93)     )
     [94](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:94)     order = np.argsort(eigenvalues)[1:k]
     [95](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/pymde/quadratic.py:95) else:

File ~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:1696, in eigsh(A, k, M, sigma, which, v0, ncv, maxiter, tol, return_eigenvectors, Minv, OPinv, mode)
   [1694](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:1694) with _ARPACK_LOCK:
   [1695](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:1695)     while not params.converged:
-> [1696](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:1696)         params.iterate()
   [1698](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:1698)     return params.extract(return_eigenvectors)

File ~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:578, in _SymmetricArpackParams.iterate(self)
    [576](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:576)     self._raise_no_convergence()
    [577](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:577) else:
--> [578](https://file+.vscode-resource.vscode-cdn.net/Users/sfleming/Documents/Projects/cellarium_gpt/mehrtash_inference/~/miniconda3/envs/test/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py:578)     raise ArpackError(self.info, infodict=self.iterate_infodict)

ArpackError: ARPACK error -9: Starting vector is zero.

This error I have not figured out how to solve (without changing the device to cuda).
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