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jaxlib-feedstock's Introduction

About jaxlib-feedstock

Feedstock license: BSD-3-Clause

Home: http://github.com/google/jax

Package license: Apache-2.0

Summary: Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

Development: http://github.com/google/jax

Current build status

Azure
VariantStatus
linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpython variant
linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpython variant
linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpython variant
linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpython variant
linux_64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.10.____cpython variant
linux_64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.9.____cpython variant
linux_64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.23python3.11.____cpython variant
linux_64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.26python3.12.____cpython variant
linux_aarch64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.10.____cpython variant
linux_aarch64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.22python3.9.____cpython variant
linux_aarch64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.23python3.11.____cpython variant
linux_aarch64_c_compiler_version12cuda_compilerNonecuda_compiler_versionNonecxx_compiler_version12numpy1.26python3.12.____cpython variant
osx_64_numpy1.22python3.10.____cpython variant
osx_64_numpy1.22python3.9.____cpython variant
osx_64_numpy1.23python3.11.____cpython variant
osx_64_numpy1.26python3.12.____cpython variant
osx_arm64_numpy1.22python3.10.____cpython variant
osx_arm64_numpy1.22python3.9.____cpython variant
osx_arm64_numpy1.23python3.11.____cpython variant
osx_arm64_numpy1.26python3.12.____cpython variant

Current release info

Name Downloads Version Platforms
Conda Recipe Conda Downloads Conda Version Conda Platforms

Installing jaxlib

Installing jaxlib from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, jaxlib can be installed with conda:

conda install jaxlib

or with mamba:

mamba install jaxlib

It is possible to list all of the versions of jaxlib available on your platform with conda:

conda search jaxlib --channel conda-forge

or with mamba:

mamba search jaxlib --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search jaxlib --channel conda-forge

# List packages depending on `jaxlib`:
mamba repoquery whoneeds jaxlib --channel conda-forge

# List dependencies of `jaxlib`:
mamba repoquery depends jaxlib --channel conda-forge

About conda-forge

Powered by NumFOCUS

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating jaxlib-feedstock

If you would like to improve the jaxlib recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/jaxlib-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

  • If the version of a package is not being increased, please add or increase the build/number.
  • If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

jaxlib-feedstock's People

Contributors

andlen avatar beckermr avatar conda-forge-admin avatar conda-forge-curator[bot] avatar ericmjl avatar github-actions[bot] avatar h-vetinari avatar hawkinsp avatar hmaarrfk avatar isuruf avatar maresb avatar ngam avatar ocefpaf avatar regro-cf-autotick-bot avatar xhochy avatar

Stargazers

avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar

Watchers

avatar avatar avatar avatar avatar avatar avatar

Forkers

regro-cf-autotick-bot ocefpaf andlen conda-forge-linter anacondarecipes xhochy maresb wolfv ngam hmaarrfk hawkinsp h-vetinari open-ce apmorton specter119 isuruf conda-forge-admin

jaxlib-feedstock's Issues

RFC proposal re cuda builds

Comment:

#97

we will likely be able to build most on the public CIs; we will also likely have some failures due to connections, memory, timeouts, etc.

Proposals:

  1. Adopt a policy to rerun (after merge) for failed builds twice to see if they could rebuild by chance. I assume the failures are gonna be somewhat random (i.e. not deterministic) within the cuda builds, so simply rerunning may fix stuff
  2. If rerunning twice (only twice, let's not keep rerunning) one of the maintainers will build locally and ask conda-forge/core to upload.

Let me know what you think.

How to test for LLVM errors

On the jax issue thread google/jax#5501, I commented that I had found a patch to locally build a functional jaxlib v0.1.71 on my M1 mac.

@xhochy asked (google/jax#5501 (comment)):

Any idea on how to trigger that error only using jaxlib? That would be nice as a test in the conda package of jaxlib to verify that everything is working (jax and jaxlib are built separately on conda-forge).

So I wanted to move that here so as not to add too much conda-forge specific discussion over there.

I think that the problem here (and the problem that the jax folks are facing) is that you can only reproduce this error on an arm64 machine, which I don't think we have access to, right? So while I'm confident that we can probably figure out how to cross-compile reliably for each release, it'll be hard to automatically test those releases until there is a CI service that offers that hardware. That being said, I'm happy to have a go at tracking down a jaxlib-only snippet that reproduces the error; hopefully later today.

unavailable for osx-arm64?

https://anaconda.org/conda-forge/jaxlib says osx-arm64, but when I try to install it in a clean environment:

PackagesNotFoundError: The following packages are not available from current channels:

  - jaxlib

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

What am I missing???

Issue:


Environment (conda list): 
$
(test) ~$ conda list
# packages in environment at /Users/ngam/Mambaforge/envs/test:
#
# Name                    Version                   Build  Channel
(test) ~$

Details about conda and system ( conda info ): 
(test) ~$ conda info

     active environment : test
    active env location : /Users/ngam/Mambaforge/envs/test
            shell level : 1
       user config file : /Users/ngam/.condarc
 populated config files : /Users/ngam/Mambaforge/.condarc
                          /Users/ngam/.condarc
          conda version : 4.11.0
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __osx=12.0.1=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/ngam/Mambaforge  (writable)
      conda av data dir : /Users/ngam/Mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/ngam/Mambaforge/pkgs
                          /Users/ngam/.conda/pkgs
       envs directories : /Users/ngam/Mambaforge/envs
                          /Users/ngam/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.11.0 requests/2.26.0 CPython/3.9.7 Darwin/21.1.0 OSX/12.0.1
                UID:GID : 501:20
             netrc file : None
           offline mode : False

(test) ~$

macOS arm64 build crashes with "Symbol not found"

Issue:

Thanks for your work with the macOS arm64 build @xhochy - I'm really looking forward to getting this to work!

On my new mac, when I create a fresh environment:

conda create -n jaxlib-test -c conda-forge python=3.9 jax jaxlib

and then import jax (or jaxlib.xla_client), it fails with the following ImportError:

Python 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:35:11) 
[Clang 11.1.0 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import jax
/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jax/lib/__init__.py:31: UserWarning: JAX on Mac ARM machines is experimental and minimally tested. Please see https://github.com/google/jax/issues/5501 in the event of problems.
  warnings.warn("JAX on Mac ARM machines is experimental and minimally tested. "
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jax/__init__.py", line 37, in <module>
    from . import config as _config_module
  File "/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jax/config.py", line 18, in <module>
    from jax._src.config import config
  File "/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jax/_src/config.py", line 27, in <module>
    from jax import lib
  File "/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jax/lib/__init__.py", line 73, in <module>
    from jaxlib import xla_client
  File "/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jaxlib/xla_client.py", line 31, in <module>
    from . import xla_extension as _xla
ImportError: dlopen(/opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jaxlib/xla_extension.so, 2): Symbol not found: __ZN3jax12_GLOBAL__N_121CompiledFunctionCache16kDefaultCapacityE
  Referenced from: /opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jaxlib/xla_extension.so
  Expected in: flat namespace
 in /opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test/lib/python3.9/site-packages/jaxlib/xla_extension.so

Do y'all have any thoughts or suggestions?


Environment (conda list): 
$ conda list
# packages in environment at /opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test:
#
# Name                    Version                   Build  Channel
absl-py                   0.13.0             pyhd8ed1ab_0    conda-forge
ca-certificates           2021.5.30            h4653dfc_0    conda-forge
jax                       0.2.19             pyhd8ed1ab_0    conda-forge
jaxlib                    0.1.69           py39h7f752ed_0    conda-forge
libblas                   3.9.0           11_osxarm64_openblas    conda-forge
libcblas                  3.9.0           11_osxarm64_openblas    conda-forge
libcxx                    12.0.1               h168391b_0    conda-forge
libgfortran               5.0.0.dev0      11_0_1_hf114ba7_23    conda-forge
libgfortran5              11.0.1.dev0         hf114ba7_23    conda-forge
liblapack                 3.9.0           11_osxarm64_openblas    conda-forge
libopenblas               0.3.17          openmp_h5dd58f0_1    conda-forge
llvm-openmp               12.0.1               hf3c4609_1    conda-forge
ncurses                   6.2                  h9aa5885_4    conda-forge
numpy                     1.21.2           py39h1f3b974_0    conda-forge
openssl                   1.1.1k               h3422bc3_1    conda-forge
opt_einsum                3.3.0              pyhd8ed1ab_1    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
python                    3.9.6           h54d631c_1_cpython    conda-forge
python-flatbuffers        2.0                pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
readline                  8.1                  hedafd6a_0    conda-forge
scipy                     1.7.0            py39h5060c3b_0    conda-forge
setuptools                57.4.0           py39h2804cbe_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.36.0               h72a2b83_0    conda-forge
tk                        8.6.11               he1e0b03_0    conda-forge
tzdata                    2021a                he74cb21_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.5                h642e427_1    conda-forge
zlib                      1.2.11            h31e879b_1009    conda-forge

Details about conda and system ( conda info ): 
$ conda info
     active environment : jaxlib-test
    active env location : /opt/homebrew/Caskroom/miniforge/base/envs/jaxlib-test
            shell level : 3
       user config file : /Users/dforemanmackey/.condarc
 populated config files : /opt/homebrew/Caskroom/miniforge/base/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.9.6.final.0
       virtual packages : __osx=11.5.2=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /opt/homebrew/Caskroom/miniforge/base  (writable)
      conda av data dir : /opt/homebrew/Caskroom/miniforge/base/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /opt/homebrew/Caskroom/miniforge/base/pkgs
                          /Users/dforemanmackey/.conda/pkgs
       envs directories : /opt/homebrew/Caskroom/miniforge/base/envs
                          /Users/dforemanmackey/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.6 Darwin/20.6.0 OSX/11.5.2
                UID:GID : 1185:20
             netrc file : None
           offline mode : False

Import errors from undefined symbols

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

For the past few days (I think since the 0.3.16 releases) I've had import errors when trying to import jax on Ubuntu 1. I have a reproduction in a repo where I've also done some tinkering. There are a few ways to trigger it, but the simplest is basically to import jax somewhere, which errors with a traceback like

>   from . import xla_extension as _xla
E   ImportError: /home/runner/micromamba-root/envs/jaxbug-test/lib/python3.10/site-packages/jaxlib/xla_extension.so: undefined symbol: _ZN4absl12lts_202206235MutexD1Ev

../../../micromamba-root/envs/jaxbug-test/lib/python3.10/site-packages/jaxlib/xla_client.py:25: ImportError

I haven't build XLA stuff myself so I'm not sure where to start looking. I couldn't find anything identical on the issue tracker; there's this from a bit ago but the user seems to be building from a commit between releases.

I thought it could have something to do with recent builds not being uploaded (0.3.16 is up for jax but not jaxlib, #136) but pinning both to 0.3.15 produced the same error. Unless I'm missing something while assuming that's all I need to bring in old builds, these don't seem intuitively related.

Anecdotally, I've also found

  • Imports work fine on the macos-latest image
  • The same or similar error happens with Python 3.9

Installed packages

# packages in environment at /home/runner/micromamba-root/envs/jaxbug-test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
absl-py                   1.2.0              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.6.15            ha878542_0    conda-forge
certifi                   2022.6.15       py310hff52083_0    conda-forge
cffi                      1.15.1          py310h255011f_0    conda-forge
charset-normalizer        2.1.0              pyhd8ed1ab_0    conda-forge
codecov                   2.1.11             pyhd3deb0d_0    conda-forge
coverage                  6.4.3           py310h5764c6d_0    conda-forge
cryptography              37.0.4          py310h597c629_0    conda-forge
etils                     0.7.1              pyhd8ed1ab_0    conda-forge
grpc-cpp                  1.46.4               h6fc47f4_3    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib_resources       5.9.0              pyhd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
jax                       0.3.15             pyhd8ed1ab_0    conda-forge
jaxbug                    0+untagged.15.g5dc1d2c          pypi_0    pypi
jaxlib                    0.3.15          cpu_py310he634034_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libabseil                 20211102.0      cxx17_h48a1fff_2    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_0    conda-forge
libprotobuf               3.20.1               h6239696_1    conda-forge
libsqlite                 3.39.2               h753d276_1    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libzlib                   1.2.12               h166bdaf_2    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
numpy                     1.23.2          py310h53a5b5f_0    conda-forge
openssl                   1.1.1q               h166bdaf_0    conda-forge
opt_einsum                3.3.0              pyhd8ed1ab_1    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0           py310hff52083_3    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1           py310hff52083_5    conda-forge
pytest                    7.1.2           py310hff52083_0    conda-forge
pytest-cov                3.0.0              pyhd8ed1ab_0    conda-forge
python                    3.10.5          h582c2e5_0_cpython    conda-forge
python_abi                3.10                    2_cp310    conda-forge
re2                       2022.06.01           h27087fc_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_0    conda-forge
scipy                     1.9.0           py310hdfbd76f_0    conda-forge
setuptools                65.0.1          py310hff52083_0    conda-forge
sqlite                    3.39.2               h4ff8645_1    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
tzdata                    2022c                h191b570_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zipp                      3.8.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h166bdaf_2    conda-forge

Environment info

Not in logs, but built from this environment file on Ubuntu 20.04 with mamba-org/provision-with-micromamba@main

Footnotes

  1. Specifically the ubuntu-latest image, which appears to be 20.04 ↩

Arm64 wheels are released!

Just leaving myself a note here.

It appears that macOS arm64 wheels are being built! 🎉

For reference, the file is hosted on pypi and can be downloaded here/

One thing of note, though, is that I didn't get it to work "out of the box".

Python 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:24:02) 
[Clang 11.1.0 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import jax.numpy as np
/Users/ericmjl/anaconda/envs/scratch/lib/python3.9/site-packages/jax/_src/lib/__init__.py:32: UserWarning: JAX on Mac ARM machines is experimental and minimally tested. Please see https://github.com/google/jax/issues/5501 in the event of problems.
  warnings.warn("JAX on Mac ARM machines is experimental and minimally tested. "
>>> a = np.arange(3)
WARNING:absl:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
'cyclone' is not a recognized processor for this target (ignoring processor)
LLVM ERROR: 64-bit code requested on a subtarget that doesn't support it!
[1]    68459 abort      python

rebuild due to updated tag upstream

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

The JAX team updated their tags post-release due to issues with NCCL. See more details here: google/jax#11265.

Their release procedure is to tag a preliminary release on GitHub and start testing, but the the actual release comes when the wheels are pushed to PyPI.

In v0.3.14, there was a substantial revision between the GitHub release after 7 days. This requires a rebuild on our end and we should mark our build as broken as it won't truly reflect the "release" version.

To avoid this issue in the future, we should only get our sources from PyPI.

Installed packages

n/a

Environment info

n/a

undefined symbol: PyVectorcall_Call (jax from pypi)

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

when i import jax
I got

Using /home/sunlinjun/.cache/torch_extensions/py36_cu102 as PyTorch extensions root...
Detected CUDA files, patching ldflags
Emitting ninja build file /home/sunlinjun/.cache/torch_extensions/py36_cu102/adam_upd_cuda/build.ninja...
Building extension module adam_upd_cuda...
Allowing ninja to set a default number of workers... (overridable by setting the environment variable MAX_JOBS=N)
ninja: no work to do.
Loading extension module adam_upd_cuda...
Traceback (most recent call last):
  File "run.py", line 24, in <module>
    import train_exp, train_imp
  File "/home/sunlinjun/Projects/PureCLIPNeRF/train_exp.py", line 23, in <module>
    from lib import utils, dvgo_exp
  File "/home/sunlinjun/Projects/PureCLIPNeRF/lib/dvgo_exp.py", line 12, in <module>
    from lib.jax_bkgd import augment
  File "/home/sunlinjun/Projects/PureCLIPNeRF/lib/jax_bkgd/augment.py", line 19, in <module>
    from lib.jax_bkgd import optvis
  File "/home/sunlinjun/Projects/PureCLIPNeRF/lib/jax_bkgd/optvis.py", line 22, in <module>
    import flax.linen as nn
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/flax/__init__.py", line 18, in <module>
    from . import core as core
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/flax/core/__init__.py", line 15, in <module>
    from .axes_scan import broadcast as broadcast
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/flax/core/axes_scan.py", line 19, in <module>
    import jax
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/jax/__init__.py", line 35, in <module>
    from jax import config as _config_module
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/jax/config.py", line 17, in <module>
    from jax._src.config import config  # noqa: F401
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/jax/_src/config.py", line 25, in <module>
    from jax._src import lib
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/jax/_src/lib/__init__.py", line 87, in <module>
    import jaxlib.xla_client as xla_client
  File "/home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/jaxlib/xla_client.py", line 26, in <module>
    from . import xla_extension as _xla
ImportError: /home/sunlinjun/.conda/envs/PureCLIPNeRF/lib/python3.8/site-packages/jaxlib/xla_extension.so: undefined symbol: PyVectorcall_Call

Installed packages

#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
_openmp_mutex             5.1                       1_gnu    defaults
absl-py                   1.4.0                    pypi_0    pypi
addict                    2.4.0                    pypi_0    pypi
blas                      1.0                         mkl    defaults
brotlipy                  0.7.0           py38h27cfd23_1003    defaults
bzip2                     1.0.8                h7b6447c_0    defaults
ca-certificates           2023.01.10           h06a4308_0    defaults
cachetools                5.3.0                    pypi_0    pypi
certifi                   2022.12.7        py38h06a4308_0    defaults
cffi                      1.15.1           py38h5eee18b_3    defaults
charset-normalizer        2.0.4              pyhd3eb1b0_0    defaults
chex                      0.1.7                    pypi_0    pypi
clip                      1.0                      pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
commonmark                0.9.1                    pypi_0    pypi
contourpy                 1.0.7                    pypi_0    pypi
cryptography              39.0.1           py38h9ce1e76_0    defaults
cudatoolkit               11.3.1               h2bc3f7f_2    defaults
cycler                    0.11.0                   pypi_0    pypi
dm-pix                    0.4.0                    pypi_0    pypi
dm-tree                   0.1.8                    pypi_0    pypi
einops                    0.6.0                    pypi_0    pypi
etils                     1.1.1                    pypi_0    pypi
ffmpeg                    4.3                  hf484d3e_0    pytorch
filelock                  3.10.7                   pypi_0    pypi
flatbuffers               2.0.7                    pypi_0    pypi
flax                      0.5.3                    pypi_0    pypi
flit-core                 3.8.0            py38h06a4308_0    defaults
fonttools                 4.39.2                   pypi_0    pypi
freetype                  2.12.1               h4a9f257_0    defaults
ftfy                      6.1.1                    pypi_0    pypi
giflib                    5.2.1                h5eee18b_3    defaults
gmp                       6.2.1                h295c915_3    defaults
gnutls                    3.6.15               he1e5248_0    defaults
google-auth               2.16.3                   pypi_0    pypi
google-auth-oauthlib      0.4.6                    pypi_0    pypi
grpcio                    1.53.0                   pypi_0    pypi
huggingface-hub           0.13.3                   pypi_0    pypi
idna                      3.4              py38h06a4308_0    defaults
imageio                   2.27.0                   pypi_0    pypi
imageio-ffmpeg            0.4.8                    pypi_0    pypi
importlib-metadata        6.1.0                    pypi_0    pypi
importlib-resources       5.12.0                   pypi_0    pypi
intel-openmp              2021.4.0          h06a4308_3561    defaults
jax                       0.4.6                    pypi_0    pypi
jaxlib                    0.4.6                    pypi_0    pypi
jpeg                      9e                   h5eee18b_1    defaults
kiwisolver                1.4.4                    pypi_0    pypi
lame                      3.100                h7b6447c_0    defaults
lcms2                     2.12                 h3be6417_0    defaults
ld_impl_linux-64          2.38                 h1181459_1    defaults
lerc                      3.0                  h295c915_0    defaults
libdeflate                1.17                 h5eee18b_0    defaults
libffi                    3.4.2                h6a678d5_6    defaults
libgcc-ng                 11.2.0               h1234567_1    defaults
libgomp                   11.2.0               h1234567_1    defaults
libiconv                  1.16                 h7f8727e_2    defaults
libidn2                   2.3.2                h7f8727e_0    defaults
libpng                    1.6.39               h5eee18b_0    defaults
libstdcxx-ng              11.2.0               h1234567_1    defaults
libtasn1                  4.16.0               h27cfd23_0    defaults
libtiff                   4.5.0                h6a678d5_2    defaults
libunistring              0.9.10               h27cfd23_0    defaults
libwebp                   1.2.4                h11a3e52_1    defaults
libwebp-base              1.2.4                h5eee18b_1    defaults
lpips                     0.1.4                    pypi_0    pypi
lz4-c                     1.9.4                h6a678d5_0    defaults
markdown                  3.4.3                    pypi_0    pypi
markupsafe                2.1.2                    pypi_0    pypi
matplotlib                3.7.1                    pypi_0    pypi
mkl                       2021.4.0           h06a4308_640    defaults
mkl-service               2.4.0            py38h7f8727e_0    defaults
mkl_fft                   1.3.1            py38hd3c417c_0    defaults
mkl_random                1.2.2            py38h51133e4_0    defaults
ml-dtypes                 0.0.4                    pypi_0    pypi
mmcv                      1.7.1                    pypi_0    pypi
msgpack                   1.0.5                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0    defaults
nettle                    3.7.3                hbbd107a_1    defaults
ninja                     1.11.1                   pypi_0    pypi
numpy                     1.23.5           py38h14f4228_0    defaults
numpy-base                1.23.5           py38h31eccc5_0    defaults
oauthlib                  3.2.2                    pypi_0    pypi
open-clip-torch           2.16.0                   pypi_0    pypi
opencv-python             4.7.0.72                 pypi_0    pypi
openh264                  2.1.1                h4ff587b_0    defaults
openssl                   1.1.1t               h7f8727e_0    defaults
opt-einsum                3.3.0                    pypi_0    pypi
optax                     0.1.4                    pypi_0    pypi
packaging                 23.0                     pypi_0    pypi
pillow                    9.4.0            py38h6a678d5_0    defaults
pip                       23.0.1           py38h06a4308_0    defaults
protobuf                  3.20.3                   pypi_0    pypi
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
pycparser                 2.21               pyhd3eb1b0_0    defaults
pygments                  2.14.0                   pypi_0    pypi
pyopenssl                 23.0.0           py38h06a4308_0    defaults
pyparsing                 3.0.9                    pypi_0    pypi
pysocks                   1.7.1            py38h06a4308_0    defaults
python                    3.8.16               h7a1cb2a_3    defaults
python-dateutil           2.8.2                    pypi_0    pypi
pytorch                   1.12.1          py3.8_cuda11.3_cudnn8.3.2_0    pytorch
pytorch-mutex             1.0                        cuda    pytorch
pytorch-scatter           2.1.0           py38_torch_1.12.0_cu113    pyg
pyyaml                    6.0                      pypi_0    pypi
readline                  8.2                  h5eee18b_0    defaults
regex                     2023.3.23                pypi_0    pypi
requests                  2.28.1           py38h06a4308_1    defaults
requests-oauthlib         1.3.1                    pypi_0    pypi
rich                      11.2.0                   pypi_0    pypi
rsa                       4.9                      pypi_0    pypi
scipy                     1.10.1                   pypi_0    pypi
sentencepiece             0.1.97                   pypi_0    pypi
setuptools                65.6.3           py38h06a4308_0    defaults
six                       1.16.0             pyhd3eb1b0_1    defaults
sqlite                    3.41.1               h5eee18b_0    defaults
tensorboard               2.12.0                   pypi_0    pypi
tensorboard-data-server   0.7.0                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorstore               0.1.33                   pypi_0    pypi
timm                      0.6.13                   pypi_0    pypi
tk                        8.6.12               h1ccaba5_0    defaults
toolz                     0.12.0                   pypi_0    pypi
torch-efficient-distloss  0.1.3                    pypi_0    pypi
torch-scatter             2.0.9                    pypi_0    pypi
torchaudio                0.12.1               py38_cu113    pytorch
torchvision               0.13.1               py38_cu113    pytorch
tqdm                      4.65.0                   pypi_0    pypi
typing_extensions         4.4.0            py38h06a4308_0    defaults
urllib3                   1.26.14          py38h06a4308_0    defaults
wcwidth                   0.2.6                    pypi_0    pypi
werkzeug                  2.2.3                    pypi_0    pypi
wheel                     0.38.4           py38h06a4308_0    defaults
xz                        5.2.10               h5eee18b_1    defaults
yapf                      0.32.0                   pypi_0    pypi
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.13               h5eee18b_0    defaults
zstd                      1.5.2                ha4553b6_0    defaults

Environment info

active environment : PureCLIPNeRF
    active env location : /home/sunlinjun/.conda/envs/PureCLIPNeRF
            shell level : 2
       user config file : /home/sunlinjun/.condarc
 populated config files : /home/sunlinjun/.condarc
          conda version : 4.10.1
    conda-build version : 3.21.4
         python version : 3.8.8.final.0
       virtual packages : __cuda=11.4=0
                          __linux=4.15.0=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /usr/local/anaconda3  (read only)
      conda av data dir : /usr/local/anaconda3/etc/conda
  conda av metadata url : https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
           channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/noarch
          package cache : /usr/local/anaconda3/pkgs
                          /home/sunlinjun/.conda/pkgs
       envs directories : /home/sunlinjun/.conda/envs
                          /usr/local/anaconda3/envs
               platform : linux-64
             user-agent : conda/4.10.1 requests/2.25.1 CPython/3.8.8 Linux/4.15.0-206-generic ubuntu/18.04.5 glibc/2.27
                UID:GID : 1010:1010
             netrc file : None
           offline mode : False

[Feature request]: Add support for Linux ARM64

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

According to https://anaconda.org/conda-forge/jaxlib the current supported OS+CPU architectures are:

  • Mac ARM64
  • Mac AMD64
  • Linux AMD64

I'd like to request adding Linux ARM64 to this list.

At the moment AlphaFold project cannot be used on Linux ARM64 due to a missing jaxlib+cuda Python wheel - google-deepmind/alphafold#528
Currently AlphaFold uses Pip3 to install jaxlib from https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
It would be nice if it could use conda-forge instead!

Installed packages

# packages in environment at /home/mgrigorov/devel/conda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                      51_gnu  
brotlipy                  0.7.0           py39hfd63f10_1002  
ca-certificates           2022.3.29            hd43f75c_1  
certifi                   2021.10.8        py39hd43f75c_2  
cffi                      1.15.0           py39h9a3cfec_1  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
colorama                  0.4.4              pyhd3eb1b0_0  
conda                     4.12.0           py39hd43f75c_0  
conda-content-trust       0.1.1              pyhd3eb1b0_0  
conda-package-handling    1.8.1            py39h2f4d8fa_0  
cryptography              36.0.0           py39h3d58568_0  
idna                      3.3                pyhd3eb1b0_0  
ld_impl_linux-aarch64     2.36.1               h0ab8de2_3  
libffi                    3.3                  h7c1a80f_2  
libgcc-ng                 10.2.0              h1234567_51  
libgomp                   10.2.0              h1234567_51  
libstdcxx-ng              10.2.0              h1234567_51  
ncurses                   6.3                  h2f4d8fa_2  
openssl                   1.1.1n               h2f4d8fa_0  
pip                       21.2.4           py39hd43f75c_0  
pycosat                   0.6.3            py39hfd63f10_2  
pycparser                 2.21               pyhd3eb1b0_0  
pyopenssl                 22.0.0             pyhd3eb1b0_0  
pysocks                   1.7.1            py39hd43f75c_0  
python                    3.9.12               hc137634_0  
readline                  8.1.2                h2f4d8fa_1  
requests                  2.27.1             pyhd3eb1b0_0  
ruamel_yaml               0.15.100         py39h2f4d8fa_0  
setuptools                61.2.0           py39hd43f75c_0  
six                       1.16.0             pyhd3eb1b0_1  
sqlite                    3.38.2               h6632b73_0  
tk                        8.6.11               h241ca14_0  
tqdm                      4.63.0             pyhd3eb1b0_0  
tzdata                    2022a                hda174b7_0  
urllib3                   1.26.8             pyhd3eb1b0_0  
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.5                hfd63f10_1  
yaml                      0.2.5                hfd63f10_0  
zlib                      1.2.12               h2f4d8fa_1

Environment info

active environment : None
       user config file : /home/mgrigorov/.condarc
 populated config files : 
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __linux=4.19.90=0
                          __glibc=2.28=0
                          __unix=0=0
                          __archspec=1=aarch64
       base environment : /home/mgrigorov/devel/conda  (writable)
      conda av data dir : /home/mgrigorov/devel/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-aarch64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-aarch64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/mgrigorov/devel/conda/pkgs
                          /home/mgrigorov/.conda/pkgs
       envs directories : /home/mgrigorov/devel/conda/envs
                          /home/mgrigorov/.conda/envs
               platform : linux-aarch64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/4.19.90-2207.4.0.0160.oe1.aarch64 openeuler/20.03 glibc/2.28
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

messed up 0.3.15 builds (should depend explicitly on abseil==*2022*)

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

... python3.10/site-packages/jaxlib/xla_extension.so: undefined symbol: _ZN4absl12lts_202206235MutexD1Ev

looks like we broke the build again with abseil stuff...

Installed packages

n/a
0.3.15 cuda

Environment info

n/a
0.3.15 cuda

import error

Issue:

I am seeing this issue on import

ImportError: dlopen(/Users/beckermr/miniconda3/envs/desy6/lib/python3.8/site-packages/jaxlib/xla_extension.so, 2): Symbol not found: __ZN3jax12_GLOBAL__N_121CompiledFunctionCache16kDefaultCapacityE
  Referenced from: /Users/beckermr/miniconda3/envs/desy6/lib/python3.8/site-packages/jaxlib/xla_extension.so
  Expected in: flat namespace
 in /Users/beckermr/miniconda3/envs/desy6/lib/python3.8/site-packages/jaxlib/xla_extension.so

Environment (conda list): 
$ conda list
# packages in environment at /Users/beckermr/miniconda3/envs/desy6:
#
# Name                    Version                   Build  Channel
absl-py                   0.15.0             pyhd8ed1ab_0    conda-forge
apipkg                    2.0.1              pyhd8ed1ab_0    conda-forge
appnope                   0.1.2            py38h50d1736_1    conda-forge
argon2-cffi               21.1.0           py38h96a0964_0    conda-forge
asteval                   0.9.23             pyhd8ed1ab_0    conda-forge
astropy                   4.3.1            py38hbe852b5_1    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
autoconf                  2.69            pl5321hc0e15e3_11    conda-forge
automake                  1.16.5          pl5321h694c41f_0    conda-forge
autopep8                  1.6.0              pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
blas-devel                3.9.0           12_osx64_openblas    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.0               he49afe7_0    conda-forge
bokeh                     2.4.1            py38h50d1736_1    conda-forge
brotlipy                  0.7.0           py38h96a0964_1001    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
c-compiler                1.3.0                h0d85af4_0    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                4.2.4              pyhd8ed1ab_0    conda-forge
cartopy                   0.20.1           py38hda056e9_2    conda-forge
cctools                   949.0.1             hd9211c8_21    conda-forge
cctools_osx-64            949.0.1             h6407bdd_21    conda-forge
certifi                   2021.10.8        py38h50d1736_1    conda-forge
cffi                      1.14.6           py38h1a44b6c_1    conda-forge
cfitsio                   3.470                h01dc385_7    conda-forge
chardet                   4.0.0            py38h50d1736_1    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
clang                     11.1.0               h694c41f_1    conda-forge
clang-11                  11.1.0          default_he082bbe_1    conda-forge
clang_osx-64              11.1.0               hb91bd55_3    conda-forge
clangxx                   11.1.0          default_he082bbe_1    conda-forge
clangxx_osx-64            11.1.0               h7e1b574_3    conda-forge
click                     8.0.3            py38h50d1736_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
compiler-rt               11.1.0               h654b07c_0    conda-forge
compiler-rt_osx-64        11.1.0               h8c5fa43_0    conda-forge
compilers                 1.3.0                h694c41f_0    conda-forge
coverage                  6.0.2            py38h96a0964_0    conda-forge
cryptography              35.0.0           py38h56c4533_1    conda-forge
curl                      7.79.1               hf45b732_1    conda-forge
cx_oracle                 8.2.1            py38h96a0964_0    conda-forge
cxx-compiler              1.3.0                h940c156_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.11.0           py38h96a0964_3    conda-forge
dask                      2021.10.0          pyhd8ed1ab_0    conda-forge
dask-core                 2021.10.0          pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               ha13b53f_2    conda-forge
debugpy                   1.4.1            py38ha048514_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
des-desmeds               0.9.12           py38h50d1736_0    conda-forge
des-easyaccess            1.4.7            py38h32f6830_3    conda-forge
des-pizza-cutter          0.4.8            py38h50d1736_0    conda-forge
des-pizza-cutter-metadetect 0.4.9            py38h50d1736_0    conda-forge
des-sxdes                 0.2.0              pyhd8ed1ab_0    conda-forge
des-y6utils               0.1.dev1+g0902119           dev_0    <develop>
distributed               2021.10.0        py38h50d1736_0    conda-forge
eigen                     3.4.0                h940c156_0    conda-forge
emcee                     3.1.1              pyh8a188c0_0    conda-forge
entrypoints               0.3             py38h32f6830_1002    conda-forge
ephem                     4.1              py38h96a0964_0    conda-forge
esutil                    0.6.8            py38h1f261ad_0    conda-forge
execnet                   1.9.0              pyhd8ed1ab_0    conda-forge
expat                     2.4.1                he49afe7_0    conda-forge
fancycompleter            0.9.1           py38h50d1736_1002    conda-forge
fftw                      3.3.10          nompi_h4024a70_101    conda-forge
fitsio                    1.1.5            py38hf771872_0    conda-forge
flake8                    3.9.2              pyhd8ed1ab_0    conda-forge
flaky                     3.7.0              pyh9f0ad1d_0    conda-forge
fortran-compiler          1.3.0                h6818c3e_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fsspec                    2021.10.1          pyhd8ed1ab_0    conda-forge
future                    0.18.2           py38h50d1736_3    conda-forge
galsim                    2.3.3            py38hb3169c0_0    conda-forge
geos                      3.10.0               he49afe7_0    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
gfortran                  9.3.0               h768ea0c_14    conda-forge
gfortran_impl_osx-64      9.3.0               h9cc0e5e_23    conda-forge
gfortran_osx-64           9.3.0               h18f7dce_14    conda-forge
glib                      2.70.0               hcf210ce_1    conda-forge
glib-tools                2.70.0               hcf210ce_1    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
gnureadline               8.0.0            py38h4d0b108_1    conda-forge
h5py                      3.4.0           nompi_py38h9f21798_101    conda-forge
hdf5                      1.12.1          nompi_h2f0ef1a_101    conda-forge
healpy                    1.15.0           py38hf54a6e8_2    conda-forge
healsparse                1.4.0              pyhd8ed1ab_0    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
hexalattice               1.1.0              pyh59e0f4d_0    conda-forge
hilbertcurve              2.0.5              pyhd8ed1ab_0    conda-forge
icu                       68.2                 he49afe7_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
iminuit                   2.8.4            py38ha048514_0    conda-forge
importlib-metadata        4.8.1            py38h50d1736_0    conda-forge
importlib_metadata        4.8.1                hd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
ipdb                      0.13.9             pyhd8ed1ab_0    conda-forge
ipykernel                 6.4.2            py38h5fd9f69_0    conda-forge
ipython                   7.28.0           py38h5fd9f69_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jax                       0.2.24             pyhd8ed1ab_0    conda-forge
jaxlib                    0.1.73           py38h25821e9_0    conda-forge
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.0           py38h50d1736_2    conda-forge
jinja2                    3.0.2              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   hbcb3906_0    conda-forge
jsonschema                4.1.2              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py38h50d1736_6    conda-forge
jupyter_client            7.0.6              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_contrib_core      0.3.3                      py_2    conda-forge
jupyter_contrib_nbextensions 0.5.1            py38h32f6830_1    conda-forge
jupyter_core              4.9.1            py38h50d1736_0    conda-forge
jupyter_highlight_selected_word 0.2.0           py38h50d1736_1002    conda-forge
jupyter_latex_envs        1.4.6           py38h50d1736_1001    conda-forge
jupyter_nbextensions_configurator 0.4.1            py38h50d1736_2    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.3.2            py38h12bbefe_0    conda-forge
krb5                      1.19.2               hcfbf3a7_2    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
ld64                      530                 hd2e7500_21    conda-forge
ld64_osx-64               530                 he8994da_21    conda-forge
ldid                      2.1.2                h6a69015_3    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           12_osx64_openblas    conda-forge
libcblas                  3.9.0           12_osx64_openblas    conda-forge
libclang                  11.1.0          default_he082bbe_1    conda-forge
libclang-cpp11.1          11.1.0          default_he082bbe_1    conda-forge
libcurl                   7.79.1               hf45b732_1    conda-forge
libcxx                    12.0.1               habf9029_0    conda-forge
libdeflate                1.8                  h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                he49afe7_4    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran-devel_osx-64  9.3.0               h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.70.0               hf1fb8c0_1    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           12_osx64_openblas    conda-forge
liblapacke                3.9.0           12_osx64_openblas    conda-forge
libllvm10                 10.0.1               h009f743_3    conda-forge
libllvm11                 11.1.0               hd011deb_2    conda-forge
libllvm8                  8.0.1                h770b8ee_0    conda-forge
libllvm9                  9.0.1           default_h2671707_4    conda-forge
libnghttp2                1.43.0               h6f36284_1    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libpq                     13.3                 hea3049e_1    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libssh2                   1.10.0               h52ee1ee_2    conda-forge
libtiff                   4.3.0                hd146c10_2    conda-forge
libtool                   2.4.6             he49afe7_1008    conda-forge
libwebp-base              1.2.1                h0d85af4_0    conda-forge
libxml2                   2.9.12               h93ec3fd_0    conda-forge
libxslt                   1.1.33               h5739fc3_2    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
llvm-openmp               12.0.1               hda6cdc1_1    conda-forge
llvm-tools                11.1.0               hd011deb_2    conda-forge
llvmlite                  0.36.0           py38h872f124_0    conda-forge
lmfit                     1.0.3              pyhd8ed1ab_0    conda-forge
locket                    0.2.0                      py_2    conda-forge
loky                      3.0.0              pyhd8ed1ab_0    conda-forge
lsstdesc.coord            1.2.2            py38h12bbefe_0    conda-forge
lxml                      4.6.3            py38h6ea4786_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
m4                        1.4.18            haf1e3a3_1001    conda-forge
markupsafe                2.0.1            py38h96a0964_0    conda-forge
matplotlib                3.4.3            py38h50d1736_1    conda-forge
matplotlib-base           3.4.3            py38hc7d2367_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
meds                      0.9.14           py38h0793694_0    conda-forge
metadetect                0.3.11             pyhd8ed1ab_1    conda-forge
mistune                   0.8.4           py38h96a0964_1004    conda-forge
mock                      4.0.3            py38h50d1736_1    conda-forge
more-itertools            8.10.0             pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpi4py                    3.1.1            py38h1087cf1_0    conda-forge
msgpack-python            1.0.2            py38h12bbefe_1    conda-forge
mysql-common              8.0.27               h694c41f_1    conda-forge
mysql-libs                8.0.27               h115446f_1    conda-forge
nb_conda_kernels          2.3.1            py38h50d1736_0    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 6.2.0            py38h50d1736_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
ngmix                     2.0.3                     dev_0    <develop>
nose                      1.3.7           py38h32f6830_1004    conda-forge
notebook                  6.4.5              pyha770c72_0    conda-forge
nspr                      4.32                 hcd9eead_0    conda-forge
nss                       3.71                 h31e2bf1_0    conda-forge
numba                     0.53.1           py38h5b9a75a_1    conda-forge
numexpr                   2.7.3            py38ha53d530_0    conda-forge
numpy                     1.21.3           py38h49b9922_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openblas                  0.3.18          openmp_h12da7db_0    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openmpi                   4.1.1                hd3cd54c_0    conda-forge
openssl                   1.1.1l               h0d85af4_0    conda-forge
opt_einsum                3.3.0              pyhd8ed1ab_1    conda-forge
oracle-instant-client     19.8.0.0.0           h694c41f_1    conda-forge
packaging                 21.2               pyhd8ed1ab_1    conda-forge
pandas                    1.3.4            py38ha53d530_0    conda-forge
pandoc                    2.15                 h0d85af4_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
partd                     1.2.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
perl                      5.32.1          1_h0d85af4_perl5    conda-forge
pexpect                   4.8.0            py38h32f6830_1    conda-forge
pickleshare               0.7.5           py38h32f6830_1002    conda-forge
piff                      1.1.0            py38h50d1736_2    conda-forge
pillow                    8.3.2            py38hee640a0_0    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
pixmappy                  1.0.0              pyh9f0ad1d_0    conda-forge
pizza-cutter-sims         0.1.0                     dev_0    <develop>
pluggy                    1.0.0            py38h50d1736_1    conda-forge
proj                      8.1.1                h1512c50_2    conda-forge
prometheus_client         0.12.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.21             pyha770c72_0    conda-forge
prompt_toolkit            3.0.21               hd8ed1ab_0    conda-forge
proplot                   0.9.5              pyhd8ed1ab_0    conda-forge
psfex                     0.4.1            py38hc7193ba_2    conda-forge
psutil                    5.8.0            py38h96a0964_1    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
py                        1.10.0             pyhd3deb0d_0    conda-forge
pybind11                  2.8.1            py38h12bbefe_0    conda-forge
pybind11-global           2.8.1            py38h12bbefe_0    conda-forge
pycodestyle               2.7.0              pyhd8ed1ab_0    conda-forge
pycodestyle-magic         0.5                      pypi_0    pypi
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyerfa                    2.0.0            py38h0793694_0    conda-forge
pyflakes                  2.3.1              pyhd8ed1ab_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 21.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyhd8ed1ab_1    conda-forge
pyproj                    3.2.1            py38h665cf17_2    conda-forge
pyqt                      5.12.3           py38h50d1736_7    conda-forge
pyqt-impl                 5.12.3           py38h721a93c_7    conda-forge
pyqt5-sip                 4.19.18          py38h5745d40_7    conda-forge
pyqtchart                 5.12             py38h721a93c_7    conda-forge
pyqtwebengine             5.12.1           py38h721a93c_7    conda-forge
pyrepl                    0.9.0            py38h96a0964_3    conda-forge
pyrsistent                0.17.3           py38h96a0964_2    conda-forge
pyshp                     2.1.3              pyh44b312d_0    conda-forge
pysocks                   1.7.1            py38h50d1736_3    conda-forge
pytables                  3.6.1            py38h5215406_4    conda-forge
pytest                    6.2.5            py38h50d1736_0    conda-forge
pytest-cov                3.0.0              pyhd8ed1ab_0    conda-forge
pytest-forked             1.3.0              pyhd3deb0d_0    conda-forge
pytest-runner             5.3.1              pyhd8ed1ab_0    conda-forge
pytest-xdist              2.4.0              pyhd8ed1ab_0    conda-forge
python                    3.8.12          h17280f6_2_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-flatbuffers        2.0                pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h96a0964_0    conda-forge
pyzmq                     22.3.0           py38hd3b92b6_0    conda-forge
qt                        5.12.9               h126340a_4    conda-forge
qtconsole                 5.1.1              pyhd8ed1ab_0    conda-forge
qtpy                      1.11.2             pyhd8ed1ab_0    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
schwimmbad                0.3.2            py38h50d1736_0    conda-forge
scikit-learn              1.0.1            py38h1021539_1    conda-forge
scipy                     1.7.1            py38hd329d04_0    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
sep                       1.2.0            py38h0793694_0    conda-forge
setuptools                58.3.0           py38h50d1736_0    conda-forge
setuptools-scm            6.3.2              pyhd8ed1ab_0    conda-forge
setuptools_scm            6.3.2                hd8ed1ab_0    conda-forge
setuptools_scm_git_archive 1.1                        py_0    conda-forge
shapely                   1.8.0            py38h3d97504_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
sqlite                    3.36.0               h23a322b_2    conda-forge
statsmodels               0.13.0           py38hbe852b5_0    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
termcolor                 1.1.0                      py_2    conda-forge
terminado                 0.12.1           py38h50d1736_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.0.0              pyh8a188c0_0    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     1.2.2              pyhd8ed1ab_0    conda-forge
toolz                     0.11.1                     py_0    conda-forge
tornado                   6.1              py38h96a0964_1    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
treecorr                  4.2.6            py38hffa2396_0    conda-forge
treegp                    0.6.0              pyhd8ed1ab_0    conda-forge
typing_extensions         3.10.0.2           pyha770c72_0    conda-forge
uncertainties             3.1.6              pyhd8ed1ab_0    conda-forge
unzip                     6.0                  hbcf498f_2    conda-forge
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.5.2            py38h50d1736_0    conda-forge
wmctrl                    0.4                pyhd8ed1ab_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
yaml                      0.2.5                haf1e3a3_0    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zict                      2.0.0                      py_0    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge
zstd                      1.5.0                h582d3a0_0    conda-forge

Details about conda and system ( conda info ): 
$ conda info

     active environment : desy6
    active env location : /Users/beckermr/miniconda3/envs/desy6
            shell level : 2
       user config file : /Users/beckermr/.condarc
 populated config files : /Users/beckermr/.condarc
          conda version : 4.10.3
    conda-build version : 3.21.4
         python version : 3.8.12.final.0
       virtual packages : __osx=10.14.6=0
                          __unix=0=0
                          __archspec=1=skylake
       base environment : /Users/beckermr/miniconda3  (writable)
      conda av data dir : /Users/beckermr/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/beckermr/miniconda3/pkgs
                          /Users/beckermr/.conda/pkgs
       envs directories : /Users/beckermr/miniconda3/envs
                          /Users/beckermr/.conda/envs
               platform : osx-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.8.12 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 501:20
             netrc file : /Users/beckermr/.netrc
           offline mode : False

JAX with GPU support

It would be a huge benefit if the JAX condaforge package would come precompiled for GPU and automatically install the necessary packages for GPU support. From my understanding, cudnn and cudatoolkit from the TF 2.2 package should work and if nvcc is needed, it's available in cudatoolkit-dev. This would remove the requirement for a system-wide CUDA installation and allow usage in isolated environments. Would probably also be hugely beneficial for Windows users who want to use JAX on GPU.

Thanks to all!

figure out a better run constraint for jax

Right now the jax run constraint is simply >={{ version }}. I've gotten reports of installation issues when jax gets too far ahead of jaxlib. Maybe we should pin to x.x or somethibg?

Setting jaxlib dependecy in a recipe?

Comment:

I am trying to make a bioconda recipe for (ColabFold)[https://github.com/sokrypton/ColabFold].
This recipe needs to be in bioconda, since we depend on multiple other bioconda packages.

How would I set a dependency on jaxlib with cuda inside another recipe?

I tried adding - jaxlib ==*=*cuda* to the run section, which did not work.
I also tried - jaxlib and - __cuda # [cuda_compiler_version != "None"] in the run section, which also does not work.

Is there any other recipe already that depends on jaxlib with cuda that I can use as a template?

cancel extra ci runs

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

The CI "rerun failed runs" produces extra unnecessary runs. Could someone from core please cancel the unnecessary reruns? Thanks

cc @conda-forge/core

Previously (like three months ago), @isuruf caught this issue and cancelled these runs and I thought the issue was fixed. Apparently it is not. Here's the link where I see three runs: https://dev.azure.com/conda-forge/feedstock-builds/_build?definitionId=7112&_a=summary. Please cancel two of them. (Keep the oldest.)

Thanks!

Installed packages

n/a

Environment info

n/a

packages are not being uploaded

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

@conda-forge/core could you please help me? The latest two pushes to main didn't result in uploading the packages. Something is wrong. I rerendered to no avail. Thanks!

@beckermr maybe?

xref:

Installed packages

n/a

Environment info

n/a

Jaxlib not compatible with the latest Pyarrow

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

I have discovered that jaxlib prevents installing the latest Pyarrow.

I am not able to create a Conda environment with jax and pyarrow>=14.0. I see that it's because of the pinned libgrpc version (>=1.58.1, <1.59.0a0)

google/jax#19792

Installed packages

pyarrow, python3.11, jax

Environment info

mamba create -n lala python=3.11 jax pyarrow=15 --dry-run

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