from jax._src.numpy.fft import ( How to deal with ImportError: cannot import name 'pytree' from 'jaxlib' of using jax? https://github.com/google/jax#installation, Running Jupyter with multiple Python and IPython paths, github.com/YukunXia/Carla_iLQR_MPC/issues/3, Improving time to first byte: Q&A with Dana Lawson of Netlify, What its like to be on the Python Steering Council (Ep. Beta Having a local module with the same name as an imported module. What is JAX? jax 0.3.22 . You signed in with another tab or window. Thanks for the colab. It appears that you are importing a much older jax version than you report in the question; jax.lib has not attempted to import pytree from jaxlib since version 0.2.8. I0621 08:53:06.984965 140132597880640 run_docker.py:255] File "/opt/conda/lib/python3.7/site-packages/haiku/_src/utils.py", line 24, in AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft', https://bytemeta.vip/repo/deepmind/alphafold/issues/515. It should be from jax.experimental import optix, Also if you want to use the GPU you need to modify the jaxlib install -> File "/home/conda1/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/experimental/maps.py", line 25, in I0621 08:53:06.984860 140132597880640 run_docker.py:255] from haiku._src import utils Find file. 8 comments danperazzo on May 22, 2021 completed on May 25, 2021 to join this conversation on GitHub . from haiku._src.data_structures import to_immutable_dict The text was updated successfully, but these errors were encountered: This is obviously hitting everyone at the moment, as made quite clear from @nfelt's good example and all of our CI failing. However, as jax and jaxlib don't do release candidates on either GitHub or PyPI, it would be great if someone in the know could comment if this is actually a regression or if there is a new release of jax that should be out in the very near future with some breaking API changes that are already reflected in jaxlib v0.1.58. --max_template_date=2022-06-20 Hi I imported through conda using: conda create -n scvi-env python=3.9 when importing in jupyter I use import scvi I get an import error with pytorch_lightning: ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' Full error message: ImportError Traceback (most recent call last) Cell In [3], line 1 I0621 08:53:04.709931 140132597880640 run_docker.py:113] Mounting /mnt/d/bdd/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir Already on GitHub? File "/home/conda1/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/lax/fft.py", line 144, in To see all available qualifiers, see our documentation. ---> 15 opt_state = opt.init(params) 13 @karlaarz yeah i found the solution for it jaxlib == 0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html and jax version= 0.2.14. To see all available qualifiers, see our documentation. To see all available qualifiers, see our documentation. The fix was: TF_CPP_MIN_LOG_LEVEL=0 CUDA_VISIBLE_DEVICES=0 python3 app.py --port 8080 --model_version mega_full Device 0 was the V100, device 1 was the 2080Ti. Note that the jax-releases address is necessary because this jaxlib version is no longer on PyPI due to its storage constraints. Please try enabling it if you encounter problems. I fixed it by doing this right after the install dependencies section: Though it feels so fragile. It appears that you are importing a much older jax version than you report in the question; jax.lib has not attempted to import pytree from jaxlib since version 0.2.8. This code works well on Colab. jaxlib [python-library] - Occam from .experimental.maps import soft_pmap Can you say more about the system you're using? jaxlib 0.3.24 (Nov 4, 2022)# Changes. the XLA compiler, the PJRT runtime, and a handful of handwritten kernels. AttributeError: module 'X' has no attribute 'Y' in Python jaxlib 0.3.10 , jax 0.3.23 , now I have the same issue, and I need your help,please!Thanks! 9419: Jax and Jaxlib versioning; 10657: Sequencing side-effects in JAX; 11830: `jax.remat` / `jax.checkpoint` new implementation; 12049: Type Annotation Roadmap for JAX; 14273: `shard_map` (`shmap`) for simple per-device code; 15856: `jax.extend`, an extensions module; Building on JAX; Notes. Have a question about this project? Edit: I think it also has to do with what Python (3.7 on TPU v2 and Colab, 3.8 on v3) version you're running and what TPU-version / accelerator-type. I tried this solution deepmind/alphafold#513 but still get same error. I0621 08:53:06.983701 140132597880640 run_docker.py:255] File "/app/alphafold/run_alphafold.py", line 37, in 7 comments . I0621 08:53:04.707824 140132597880640 run_docker.py:113] Mounting /mnt/d/bdd/uniref90 -> /mnt/uniref90_database_path PythonImportError: cannot import name - CSDN We read every piece of feedback, and take your input very seriously. Thanks for your answer and heads up. You switched accounts on another tab or window. You switched accounts on another tab or window. To see all available qualifiers, see our documentation. If this works for you, I will update the readme. Problems importing scvi [Windows] - scvi-tools - scverse I just released jax 0.2.8, which fixes the problem. I have jax and jaxlib with cuda installed on my computer running zorin os (Ubuntu 18), and I have had jax working for over a year and all of a sudden after doing some sudo updates, it no longer will work. return f(*args) . Have a question about this project? To see all available qualifiers, see our documentation. Connect and share knowledge within a single location that is structured and easy to search. jax.tree_util.Partial JAX documentation - Read the Docs and could you share the requirements? You switched accounts on another tab or window. I0621 08:53:06.985567 140132597880640 run_docker.py:255] File "/opt/conda/lib/python3.7/site-packages/jax/numpy/init.py", line 16, in You switched accounts on another tab or window. From your comments there, it sounds like you want to install a very old version of jax (0.1.68), and you're finding that a much newer version of jaxlib (0.1.67) is incompatible. This will allow you to give the file a name which you can then click on to open the blank file to edit it further. I0621 08:53:06.985467 140132597880640 run_docker.py:255] from .. import numpy as jnp I0621 08:53:04.708882 140132597880640 run_docker.py:113] Mounting /mnt/d/bdd/mgnify -> /mnt/mgnify_database_path I0621 08:53:06.986300 140132597880640 run_docker.py:255] from jax._src.lax.fft import ( to your account, Hello everyone, thank you for sharing this experiments for this wonderfull project! while trying to run alpha fold on wsl with the following command : docker/run_docker.py ImportError: cannot import name 'XXXXX' from 'XX' Perhaps try uninstalling and reinstalling jaxlib? Why are my film photos coming out so dark, even in bright sunlight? [jax2tf] Remove legacy bfloat16 conversion code. AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft' #515 Hi, while trying to run alpha fold on wsl with the following command : docker/run_docker.py --fasta_paths=test.faa --max_template_date=2022-06-20 --db_preset=reduced_dbs --model_preset=monomer --data_dir=/mnt/d/bdd/ my databases seemed to be ok : Already on GitHub? 2023 Python Software Foundation If you need to use jax 0.1.68, you'll probably need jaxlib somewhere around 0.1.50, which you can install this way: Note that the jax-releases address is necessary because th. API compatibility; Python and NumPy version support . Reverting to jaxlib 0.1.57 eliminates the error. cannot import name 'pytree' from 'jaxlib'. minimalistic ext4 filesystem without journal and other advanced features. privacy statement. pip install -q jaxlib==0.1.55+cuda110 -f https://storage.googleapis.com/jax-releases/jax_releases.html, Note that this command is for cuda 11.0 which is what colab is currently using. ImportError: cannot import name 'pytree' from 'jaxlib' - GitHub ImportError: cannot import name 'cusolver' from 'jaxlib' #7818 - GitHub Sign up for a free GitHub account to open an issue and contact its maintainers and the community. jax 0.3.23 (Oct 12, 2022)# Changes. AttributeError: module 'jaxlib.xla_extension' has no attribute from alphafold.model import data Well occasionally send you account related emails. jaxlib 0.1.50 works very well and the code is running. BSD 3-Clause "New" or "Revised" License. You switched accounts on another tab or window. 592), Stack Overflow at WeAreDevelopers World Congress in Berlin, Temporary policy: Generative AI (e.g., ChatGPT) is banned. AttributeError: 'Optimizer' object has no attribute 'init'. The most recent jaxlib CPU release (0.1.58), new to PyPI as of earlier today, leads to an ImportError at import jax (using jax 0.2.7) in a fresh venv on my machine: ImportError: cannot import name 'cusolver' from 'jaxlib'. AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'` The text was updated successfully, but these errors were encountered: 4 hibby50, cdmichaelb, leloch, and Larry-Schultz reacted with thumbs up emoji I0621 08:53:06.986621 140132597880640 run_docker.py:255] AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft', I tried to find what it means but got no result, Building from source JAX documentation - Read the Docs To see all available qualifiers, see our documentation. Proof that products of vector is a continuous function. Having an incorrect import statement. I0621 08:53:06.986495 140132597880640 run_docker.py:255] xla.backend_specific_translations['cpu'][fft_p] = pocketfft.pocketfft I0621 08:53:06.373428 140132597880640 run_docker.py:255] /sbin/ldconfig.real: /usr/lib/x86_64-linux-gnu/libcuda.so.1 is not a symbolic link The only Google search result that seems to mention something similar is this: https://bytemeta.vip/repo/deepmind/alphafold/issues/515. I0621 08:53:06.985076 140132597880640 run_docker.py:255] import jax --fasta_paths=test.faa jaxlib PyPI conda install To install this package run one of the following: conda install -c "conda-forge/label/broken" jaxlibconda install -c "conda-forge/label/cf202003" jaxlib By data scientists, for conda-forge 2023 Anaconda, Inc. All Rights Reserved. from .. import numpy as jnp I manually changed my Dockerfile to replicate the changes in #79 and this issue still happens on startup. This probably indicates that you are running pip install in a different environment than the one you're using to execute code. Hi everyone, I'm not able to import cusolver in any installable (>=0.1.60) version of jaxlib. Give feedback. JAX Quickstart JAX documentation - Read the Docs jaxlib pip package 0.1.58 regression: ImportError: cannot import name 'cusolver' from 'jaxlib', Avoid creating distributions when inferring value domain. We read every piece of feedback, and take your input very seriously. File "/home/datafiles/alphafold_data/alphafold/run_alphafold.py", line 33, in Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Already on GitHub? jaxlib-0.4.13-cp311-cp311-manylinux2014_x86_64.whl, jaxlib-0.4.13-cp311-cp311-macosx_11_0_arm64.whl, jaxlib-0.4.13-cp311-cp311-macosx_10_14_x86_64.whl, jaxlib-0.4.13-cp310-cp310-manylinux2014_x86_64.whl, jaxlib-0.4.13-cp310-cp310-macosx_11_0_arm64.whl, jaxlib-0.4.13-cp310-cp310-macosx_10_14_x86_64.whl, jaxlib-0.4.13-cp39-cp39-manylinux2014_x86_64.whl, jaxlib-0.4.13-cp39-cp39-macosx_11_0_arm64.whl, jaxlib-0.4.13-cp39-cp39-macosx_10_14_x86_64.whl, jaxlib-0.4.13-cp38-cp38-manylinux2014_x86_64.whl, jaxlib-0.4.13-cp38-cp38-macosx_11_0_arm64.whl, jaxlib-0.4.13-cp38-cp38-macosx_10_14_x86_64.whl. File "/home/conda1/anaconda3/envs/alphafold/lib/python3.8/site-packages/haiku/init.py", line 17, in from jax import lax AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft' Please help. Try using jax==0.2.1 yanked. all systems operational. File "./xxx/demo/demo.py", line 23, in < module > from predictor import FeatureExtractionDemo ImportError: cannot import name 'FeatureExtractionDemo' from 'predictor'. privacy statement. from haiku._src import utils File "/home/conda1/anaconda3/envs/alphafold/lib/python3.8/site-packages/haiku/data_structures.py", line 17, in I0621 08:53:06.984747 140132597880640 run_docker.py:255] File "/opt/conda/lib/python3.7/site-packages/haiku/_src/data_structures.py", line 30, in You switched accounts on another tab or window. You should update it using: pip install -U jaxlib We read every piece of feedback, and take your input very seriously. May I reveal my identity as an author during peer review? python - jaxlib - IT Sign up for a free GitHub account to open an issue and contact its maintainers and the community. in () I'm also using a TPU v2 setup and ran into this problem. By clicking Sign up for GitHub, you agree to our terms of service and yanked, 0.1.63 To see all available qualifiers, see our documentation. It can differentiate through loops, branches, recursion, and closures, and it can take derivatives of derivatives of derivatives.
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