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Cannot import cell2location: Failed in nopython mode pipeline (step: native lowering) #142
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Hi @98xy We have just updated cell2location to the latest scvi-tools version (0.15.3+). Please try re-creating a clean conda environment. The error you observe looks like umap installation version issues. Given that cell2location passes GitHub tests, the problem with UMAP can be specific to your platform. |
Hi @vitkl |
Hi again
This error comes from package version mismatch. Maybe your conda environments don't work correctly.
Do you use `export PYTHONNOUSERSITE="someletters"` as described in the installation section? Maybe you need to add this every time you open the terminal, before activating the conda environment, before creating the conda environment. I have to do that on our compute cluster.
…On Sun, 17 Apr 2022, 09:38 Yin Xu, ***@***.***> wrote:
Hi @98xy <https://github.com/98xy>
We have just updated cell2location to the latest scvi-tools version
(0.15.3+). Please try re-creating a clean conda environment. The error you
observe looks like umap installation version issues. Given that
cell2location passes GitHub tests, the problem with UMAP can be specific to
your platform.
Hi @vitkl <https://github.com/vitkl>
Thanks for your help! I have re-created a clean conda environment but the
error is still exist.
—
Reply to this email directly, view it on GitHub
<#142 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AFMFTV6WUE3Y4ZT7FEGFTKLVFPEW5ANCNFSM5S4NY2DQ>
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You are receiving this because you were mentioned.Message ID:
***@***.***>
|
Hi again:
Thanks very much for your help! After `export PYTHONNOUSERSITE="someletters"`, this error removed.
And sorry to disturb you again, another mistake comes now… Could you give me some advice for solving it? Thanks sincerely again!
AttributeError: module 'jaxlib.xla_extension' has no attribute 'CpuDevice'
# details :
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Input In [2], in <cell line: 14>() 11 import matplotlib.pyplot as plt 12 import matplotlib as mpl ---> 14 import cell2location 15 import scvi 17 from matplotlib import rcParams File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/__init__.py:5, in <module> 2 from pyro.distributions.transforms import SoftplusTransform 3 from torch.distributions import biject_to, transform_to ----> 5 from .run_c2l import run_cell2location 6 from .run_colocation import run_colocation 7 from .run_regression import run_regression File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/run_c2l.py:18, in <module> 15 import scipy 16 import theano ---> 18 import cell2location.models as models 19 import cell2location.plt as c2lpl 20 from cell2location.cluster_averages import compute_cluster_averages, select_features File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/models/__init__.py:1, in <module> ----> 1 from ._cell2location_model import Cell2location 2 from ._cell2location_module import ( 3 LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel, 4 ) 5 from .downstream import CoLocatedGroupsSklearnNMF File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/cell2location/models/_cell2location_model.py:10, in <module> 8 from pyro import clear_param_store 9 from pyro.nn import PyroModule ---> 10 from scvi import REGISTRY_KEYS 11 from scvi.data import AnnDataManager 12 from scvi.data.fields import ( 13 CategoricalJointObsField, 14 CategoricalObsField, (...) 17 NumericalObsField, 18 ) File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/scvi/__init__.py:10, in <module> 7 from ._settings import settings 9 # this import needs to come after prior imports to prevent circular import ---> 10 from . import data, model, external, utils 12 # python-poetry/poetry#2366 (comment) 13 # python-poetry/poetry#144 (comment) 14 try: File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/scvi/model/__init__.py:6, in <module> 4 from ._condscvi import CondSCVI 5 from ._destvi import DestVI ----> 6 from ._jaxscvi import JaxSCVI 7 from ._linear_scvi import LinearSCVI 8 from ._multivi import MULTIVI File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/scvi/model/_jaxscvi.py:7, in <module> 5 import jax.numpy as jnp 6 import numpy as np ----> 7 import optax 8 import pandas as pd 9 import tqdm File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/optax/__init__.py:17, in <module> 1 # Copyright 2019 DeepMind Technologies Limited. All Rights Reserved. 2 # 3 # Licensed under the Apache License, Version 2.0 (the "License"); (...) 13 # limitations under the License. 14 # ============================================================================== 15 """Optax: composable gradient processing and optimization, in JAX.""" ---> 17 from optax import experimental 18 from optax._src.alias import adabelief 19 from optax._src.alias import adafactor File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/optax/experimental/__init__.py:20, in <module> 1 # Copyright 2021 DeepMind Technologies Limited. All Rights Reserved. 2 # 3 # Licensed under the Apache License, Version 2.0 (the "License"); (...) 13 # limitations under the License. 14 # ============================================================================== 15 """Experimental features in Optax. 16 17 Features may be removed or modified at any time. 18 """ ---> 20 from optax._src.experimental.complex_valued import split_real_and_imaginary 21 from optax._src.experimental.complex_valued import SplitRealAndImaginaryState File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/optax/_src/experimental/complex_valued.py:32, in <module> 15 """Complex-valued optimization. 16 17 When using `split_real_and_imaginary` to wrap an optimizer, we split the complex (...) 27 See details at google-deepmind/optax#196 28 """ 30 from typing import NamedTuple, Union ---> 32 import chex 33 import jax 34 import jax.numpy as jnp File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/chex/__init__.py:17, in <module> 1 # Copyright 2020 DeepMind Technologies Limited. All Rights Reserved. 2 # 3 # Licensed under the Apache License, Version 2.0 (the "License"); (...) 13 # limitations under the License. 14 # ============================================================================== 15 """Chex: Testing made fun, in JAX!""" ---> 17 from chex._src.asserts import assert_axis_dimension 18 from chex._src.asserts import assert_axis_dimension_comparator 19 from chex._src.asserts import assert_axis_dimension_gt File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/chex/_src/asserts.py:26, in <module> 23 import unittest 24 from unittest import mock ---> 26 from chex._src import asserts_internal as _ai 27 from chex._src import pytypes 28 import jax File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/chex/_src/asserts_internal.py:32, in <module> 29 from typing import Any, Sequence, Union, Callable, Optional, Set, Tuple, Type 31 from absl import logging ---> 32 from chex._src import pytypes 33 import jax 34 import jax.numpy as jnp File /data/xy/anaconda3/envs/cell2loc_env/lib/python3.9/site-packages/chex/_src/pytypes.py:40, in <module> 37 PyTreeDef = type(jax.tree_structure(None)) 38 Shape = Tuple[int, ...] ---> 40 CpuDevice = jax.lib.xla_extension.CpuDevice 41 GpuDevice = jax.lib.xla_extension.GpuDevice 42 TpuDevice = jax.lib.xla_extension.TpuDevice AttributeError: module 'jaxlib.xla_extension' has no attribute 'CpuDevice'
…------------------ 原始邮件 ------------------
发件人: "BayraktarLab/cell2location" ***@***.***>;
发送时间: 2022年4月17日(星期天) 下午5:47
***@***.***>;
***@***.******@***.***>;
主题: Re: [BayraktarLab/cell2location] Cannot import cell2location: Failed in nopython mode pipeline (step: native lowering) (Issue #142)
Hi again
This error comes from package version mismatch. Maybe your conda
environments don't work correctly.
Do you use `export PYTHONNOUSERSITE="someletters"` as described in the
installation section? Maybe you need to add this every time you open
terminal, before activating conda environment, before creating conda
environment. I have to do that our compute cluster.
On Sun, 17 Apr 2022, 09:38 Yin Xu, ***@***.***> wrote:
> Hi @98xy <https://github.com/98xy>
>
> We have just updated cell2location to the latest scvi-tools version
> (0.15.3+). Please try re-creating a clean conda environment. The error you
> observe looks like umap installation version issues. Given that
> cell2location passes GitHub tests, the problem with UMAP can be specific to
> your platform.
>
> Hi @vitkl <https://github.com/vitkl>
> Thanks for your help! I have re-created a clean conda environment but the
> error is still exist.
>
> —
> Reply to this email directly, view it on GitHub
> <#142 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AFMFTV6WUE3Y4ZT7FEGFTKLVFPEW5ANCNFSM5S4NY2DQ>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you were mentioned.Message ID: ***@***.***>
|
This is a temporary error with JAX (scvi-tools dependency) - as discussed here: #144 I think you can solve this by installing older jax and jaxlib:
|
Thanks sincerely again for your help! The error has been solved now :)
…------------------ 原始邮件 ------------------
发件人: "BayraktarLab/cell2location" ***@***.***>;
发送时间: 2022年4月17日(星期天) 晚上6:38
***@***.***>;
***@***.******@***.***>;
主题: Re: [BayraktarLab/cell2location] Cannot import cell2location: Failed in nopython mode pipeline (step: native lowering) (Issue #142)
This is a temporary error with JAX (scvi-tools dependency) - as discussed here: #144
I think you can solve this by installing oldex jax and jaxlib:
pip install jax>=0.3,<=0.3.6 jaxlib>=0.1.65,<=0.3.5
—
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You are receiving this because you were mentioned.Message ID: ***@***.***>
|
This does not seem to be a problem anymore (JAX fixed this). If you see similar issues with JAX in the future - could be good to try installing the previous version or wait for a few days until the bug is fixed. |
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Minimal code sample (that we can run without your data, using public data)
This issue came up quite suddenly and it worked normally before. No library-related changes have been made.
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