Conda pack does not work with Python 3.10 or 3.11 #244
Comments
luismarquezgft
added
the
type::bug
luismarquezgft
changed the title
|
Also observed on our HPC cluster using older versions of Anaconda |
|
I can't reproduce this issue. What happens when you run the following three lines? conda create -y -n python310 python=3.10 conda-pack # (you can also use mamba instead of conda here)
conda activate python310
conda-packThis works on Linux and macos for me. Based on the error message that you're getting, I suspect that you ran For example, when I do conda create -y -n python310pip python=3.10 conda-pack # (you can also use mamba instead of conda here)
conda activate python310pip
pip install 'pip<22.3.1'
conda-packI get which looks a lot like your error message. You seem to be using |
|
Hello Jan, Thank you for looking at this! I did not run any pip installs, and I did exactly the three lines you said. Note: I do not have conda-forge in my channels, so using just the default channel I end up with conda-pack 0.6.0. which throwns an error: $ cat ~/.condarc
channels:
- defaults
$ module --force purge
$ module load anaconda/2020.11-py38
$ conda create -y -n python310 python=3.10 conda-pack
[...]
conda-pack pkgs/main/noarch::conda-pack-0.6.0-pyhd3eb1b0_0
[...]
$ conda activate python310
$ conda-pack
Collecting packages...
CondaPackError:
Files managed by conda were found to have been deleted/overwritten in the
following packages:
- wheel 0.37.1:
lib/python3.1/site-packages/wheel-0.37.1-py3.9.egg-info/PKG-INFO
lib/python3.1/site-packages/wheel-0.37.1-py3.9.egg-info/SOURCES.txt
lib/python3.1/site-packages/wheel-0.37.1-py3.9.egg-info/dependency_links.txt
+ 20 others
- conda-pack 0.6.0:
lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/INSTALLER
lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/LICENSE.txt
lib/python3.1/site-packages/conda_pack-0.6.0.dist-info/METADATA
+ 19 others
This is usually due to `pip` uninstalling or clobbering conda managed files,
...As you can see, the pip warning is actually a red herring (note the But the problem is that I also see the same error with 0.7.0 from conda-forge: $ conda create -y -n python310forge -c conda-forge python=3.10 conda-pack
[...]
conda-pack conda-forge/noarch::conda-pack-0.7.0-pyh6c4a22f_0
[...]
$ conda activate python310forge
$ conda-pack
Collecting packages...
CondaPackError:
Files managed by conda were found to have been deleted/overwritten in the
following packages:
- setuptools 65.5.1:
lib/python3.1/site-packages/_distutils_hack/__init__.py
lib/python3.1/site-packages/_distutils_hack/override.py
lib/python3.1/site-packages/distutils-precedence.pth
...Again, there hasn't been any pip-ing, so the pip message is mistaken. And again the error messages shows Strangely, there is indeed this weird 3.1 symlink in the site packages: $ ls -ld ~/.conda/envs/cent7/2020.11-py38/python310forge/lib/python3.1
lrwxrwxrwx 1 lev itap 10 Dec 13 00:39 python3.1 -> python3.10/
drwxr-sr-x 36 lev itap 210 Dec 13 00:39 python3.10/I wonder if it's an artifact of a (somehwhat old) Anaconda? I did not get the error with conda-pack 0.7.0 when I used the latest downloaded Miniconda (with conda 4.12 as opposed to 4.9.2). OTOH, both conda versions create that 3.1 symlink, so somehow conda-pack is capable to trace thing in some circumstances? |
|
I can reproduce your issue with conda-pack 0.6.0 when pulling it from anaconda (but I don't think there's anything we can do about that). I can't reproduce your issue with conda-pack 0.7.0 from conda-forge. Can you please run and report the output from: You can also run conda-pack with The python3.1 symlink isn't necessarily an issue. It comes with python3.10 by default. Edit: I somehow missed your comment about the conda versions. Yes: I can reproduce your issue with |
|
Thank you Jan. This being a centralized installation on an HPC cluster, updating its version of conda is, let's say, a process. So having a functional workaround with For completeness sake, here's the report the commands you requested: $ module load anaconda/2020.11-py38
$ conda create -y -f -n python310forge -c conda-forge python=3.10 conda-pack
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.9.2
latest version: 22.11.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/lev/.conda/envs/cent7/2020.11-py38/python310forge
added / updated specs:
- conda-pack
- python=3.10
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
ca-certificates conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0
conda-pack conda-forge/noarch::conda-pack-0.7.0-pyh6c4a22f_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.39-hcc3a1bd_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libsqlite conda-forge/linux-64::libsqlite-3.40.0-h753d276_0
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libzlib conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
openssl conda-forge/linux-64::openssl-3.0.7-h0b41bf4_1
pip conda-forge/noarch::pip-22.3.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.10.8-h4a9ceb5_0_cpython
readline conda-forge/linux-64::readline-8.1.2-h0f457ee_0
setuptools conda-forge/noarch::setuptools-65.5.1-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
tzdata conda-forge/noarch::tzdata-2022g-h191b570_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate python310forge
#
# To deactivate an active environment, use
#
# $ conda deactivateThen $ conda activate python310forge
$ conda info
active environment : python310forge
active env location : /home/lev/.conda/envs/cent7/2020.11-py38/python310forge
shell level : 1
user config file : /home/lev/.condarc
populated config files : /home/lev/.condarc
conda version : 4.9.2
conda-build version : 3.20.5
python version : 3.8.5.final.0
virtual packages : __glibc=2.17=0
__unix=0=0
__archspec=1=x86_64
base environment : /apps/spack/bell/apps/anaconda/2020.11-py38-gcc-4.8.5-nhzhrm2 (read only)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /apps/spack/bell/apps/anaconda/2020.11-py38-gcc-4.8.5-nhzhrm2/pkgs
/home/lev/.conda/pkgs
envs directories : /home/lev/.conda/envs/cent7/2020.11-py38
/home/lev/.conda/envs
/apps/spack/bell/apps/anaconda/2020.11-py38-gcc-4.8.5-nhzhrm2/envs
platform : linux-64
user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Linux/3.10.0-1160.76.1.el7.x86_64 centos/7.9.2009 glibc/2.17
UID:GID : 27004:6751
netrc file : None
offline mode : False
$ conda list
# packages in environment at /home/lev/.conda/envs/cent7/2020.11-py38/python310forge:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
conda-pack 0.7.0 pyh6c4a22f_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
openssl 3.0.7 h0b41bf4_1 conda-forge
pip 22.3.1 pyhd8ed1ab_0 conda-forge
python 3.10.8 h4a9ceb5_0_cpython conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
setuptools 65.5.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022g h191b570_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forgeAnd $ conda-pack --version
conda-pack 0.7.0
$ conda-pack
Collecting packages...
CondaPackError:
Files managed by conda were found to have been deleted/overwritten in the
following packages:
- conda-pack 0.7.0:
lib/python3.1/site-packages/conda_pack-0.7.0.dist-info/INSTALLER
lib/python3.1/site-packages/conda_pack-0.7.0.dist-info/LICENSE.txt
lib/python3.1/site-packages/conda_pack-0.7.0.dist-info/METADATA
+ 19 others
- wheel 0.38.4:
lib/python3.1/site-packages/wheel-0.38.4-py3.11.egg-info/PKG-INFO
lib/python3.1/site-packages/wheel-0.38.4-py3.11.egg-info/SOURCES.txt
lib/python3.1/site-packages/wheel-0.38.4-py3.11.egg-info/dependency_links.txt
+ 21 others
- pip 22.3.1:
lib/python3.1/site-packages/pip-22.3.1-py3.11.egg-info/PKG-INFO
lib/python3.1/site-packages/pip-22.3.1-py3.11.egg-info/SOURCES.txt
lib/python3.1/site-packages/pip-22.3.1-py3.11.egg-info/dependency_links.txt
+ 498 others
- setuptools 65.5.1:
lib/python3.1/site-packages/_distutils_hack/__init__.py
lib/python3.1/site-packages/_distutils_hack/override.py
lib/python3.1/site-packages/distutils-precedence.pth
+ 238 others
This is usually due to `pip` uninstalling or clobbering conda managed files,
resulting in an inconsistent environment. Please check your environment for
conda/pip conflicts using `conda list`, and fix the environment by ensuring
only one version of each package is installed (conda preferred). |
|
It works. I was running Thank you very much for your help. This is the code (adapted from your example @jtilly): |
|
I do not think this is complete, though. With $ conda-pack --ignore-missing-files
Collecting packages...
Packing environment at '/home/lev/.conda/envs/cent7/2020.11-py38/python310forge' to 'python310forge.tar.gz'
[########################################] | 100% Completed | 8.4sHowever, I have received an error message upon unpacking: $ module load anaconda/2020.11-py38
$ mkdir $HOME/.conda/envs/cent7/2020.11-py38/XXX
$ tar -xf python310forge.tar.gz -C $HOME/.conda/envs/cent7/2020.11-py38/XXX
tar: lib/python3.1: Cannot create symlink to `python3.10': File exists
tar: Exiting with failure status due to previous errorsThe resulting environment activated and seemed to work, but the untaring error looks a bit scary, and it would definitely spook people. Looking into the tarball, it seems that there are a lot of lines with normal (note the symlink to a file inside python3.1 in addition to the python3.1 itself). And this is causing the error message, because upon unpacking the $ ls -ld ~/.conda/envs/cent7/2020.11-py38/*/lib/python3.1*
lrwxrwxrwx 1 lev itap 10 Dec 13 09:27 /home/lev/.conda/envs/cent7/2020.11-py38/python310forge/lib/python3.1 -> python3.10/
drwxr-sr-x 36 lev itap 210 Dec 13 09:27 /home/lev/.conda/envs/cent7/2020.11-py38/python310forge/lib/python3.10/
drwxr-sr-x 3 lev itap 3 Dec 13 10:18 /home/lev/.conda/envs/cent7/2020.11-py38/XXX/lib/python3.1/
drwxr-sr-x 36 lev itap 210 Dec 13 10:18 /home/lev/.conda/envs/cent7/2020.11-py38/XXX/lib/python3.10/(note how the original environment has a symlink, but the extracted one has two distinct directories) |
|
Hi @lgorenstein. I ran the customized Python backend in a Triton server (local docker), and it loaded successfully. Now we are trying to load it into a Kubernetes cluster. |
|
@luismarquezgft sure, I totally understand. I believe this symlink handling is a glitch in conda-pack - that's why I posted it here for @jtilly to look at. The |
|
But I am happy to spin it off as a separate issue, if that makes more sense for you, @jtilly |
|
@lgorenstein I don't think anybody will want to invest a lot of time into fixing this given that it works with more recent versions of conda. (That's correct, right?). It's my understanding that the lib/python3.1 symlink doesn't do much and can safely be removed from the environment. So you could just run conda-pack like this: Full example that I can run with conda=4.9.2: |
|
for anybody who is facing the same issue, you are using an old conda version, you need to upgrade conda. changelog: https://conda.io/projects/continuumio-conda/en/latest/release-notes.html#id73 conda 4.11.0 (2021-11-22)
conda 4.10.0 (2021-03-30)
|
|
Error still there with conda 23.5.2 (tested with the continuumio/miniconda3:23.5.2 docker container). |
Checklist
What happened?
This is a recurring issue. There's a problem with the parsing of the Python version, and conda pack maps Python 3.10 or 3.11 to Python 3.1.
Steps to reproduce
Conda Info
Conda Config
Conda list
Additional Context
No response
The text was updated successfully, but these errors were encountered: