bug#53258: Python unable to find modules within a Singularity container created with guix pack

[Ludovic Courtès]

Hi Marek,

Marek Felšöci <marek@felsoci.sk> skribis:

> Recently, I have come around this issue. I created a Singularity
> container using the following `guix pack` command:
>
> `guix pack -f squashfs bash coreutils python python-numpy`
>
> Then, I run a bash shell within the container:
>
> `singularity exec test.gz.squashfs bash`
>
> Now, if I want to use numpy,
>
> `python3 -m numpy`
>
> it gives me the following error and the numpy module IS NOT found:
>
> Error in sitecustomize; set PYTHONVERBOSE for traceback:
> ValueError:
> '/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages'
>  
> is not in list
> /gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/python3: No
> module named numpy

I can kinda reproduce via a relocatable pack (relocatable packs and
Singularity packs have in common that they use relative symlinks in
their profile, to allow for relocation):

  guix pack -RR python python-numpy -S /bin=bin -S /etc=etc

Then I unpack the thing:

  mkdir /tmp/pack; cd /tmp/pack; tar xf /gnu/store/…-pack.tar.gz

And from there I use the same trick as in
‘tests/guix-pack-relocatable.sh’ to “hide” /gnu/store:

--8<---------------cut here---------------start------------->8---
$ unshare -mrf sh -c 'mount -t tmpfs -o ro none /gnu/store; . 
/tmp/pack/etc/profile; echo $GUIX_PYTHONPATH ; /tmp/pack/bin/python3 '
/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-packages
Python 3.9.6 (default, Jan  1 1970, 00:00:01) 
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
>>> import os
>>> os.listdir("/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-packages")
['setuptools-56.0.0.dist-info', 'distutils-precedence.pth', '_distutils_hack', 
'setuptools', 'pip-21.1.3.dist-info', 'sitecustomize.py', 'README.txt', 'pip', 
'numpy-1.20.3-py3.9.egg-info', 'numpy', 'pkg_resources', '__pycache__']
>>> os.listdir("/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-packages/numpy")
['__init__.pyi', 'doc', 'matlib.py', 'ctypeslib.pyi', 'linalg', 'ctypeslib.py', 
'compat', 'typing', '__init__.pxd', 'lib', 'char.pyi', 'version.py', 
'__config__.py', 'core', '_distributor_init.py', 'distutils', 'tests', 
'emath.pyi', '_pytesttester.py', 'fft', '__init__.cython-30.pxd', 
'conftest.py', '__init__.py', 'py.typed', '_globals.py', 'rec.pyi', 'testing', 
'LICENSE.txt', 'polynomial', 'f2py', 'matrixlib', 'random', 'ma', 'dual.py', 
'setup.py', '__pycache__']
--8<---------------cut here---------------end--------------->8---

So in this case ‘GUIX_PYTHONPATH’ is correctly set, but it looks as
though ‘sitecustomize.py’ wasn’t loaded.  (I don’t get the “Error in
sitecustomize” message that Marek sees though, weird!)

>From Marek’s message, it would seem that somewhere file names are
constructed by appending “..”.  Given Unix’s weird dot-dot semantics,
relative symlinks could be interfering:

--8<---------------cut here---------------start------------->8---
$ ls -l 
/tmp/pack/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-packages/
totalo 48
lrwxrwxrwx 1 ludo users 102 Jan  1  1970 _distutils_hack -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/_distutils_hack
lrwxrwxrwx 1 ludo users 111 Jan  1  1970 distutils-precedence.pth -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/distutils-precedence.pth
lrwxrwxrwx 1 ludo users  99 Jan  1  1970 numpy -> 
../../../../mlccgh05bf8cdinq0ilpvpdmsspq36pv-python-numpy-1.20.3R/lib/python3.9/site-packages/numpy
lrwxrwxrwx 1 ludo users 121 Jan  1  1970 numpy-1.20.3-py3.9.egg-info -> 
../../../../mlccgh05bf8cdinq0ilpvpdmsspq36pv-python-numpy-1.20.3R/lib/python3.9/site-packages/numpy-1.20.3-py3.9.egg-info
lrwxrwxrwx 1 ludo users  90 Jan  1  1970 pip -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/pip
lrwxrwxrwx 1 ludo users 107 Jan  1  1970 pip-21.1.3.dist-info -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/pip-21.1.3.dist-info
lrwxrwxrwx 1 ludo users 100 Jan  1  1970 pkg_resources -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/pkg_resources
lrwxrwxrwx 1 ludo users  98 Jan  1  1970 __pycache__ -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/__pycache__
lrwxrwxrwx 1 ludo users  97 Jan  1  1970 README.txt -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/README.txt
lrwxrwxrwx 1 ludo users  97 Jan  1  1970 setuptools -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/setuptools
lrwxrwxrwx 1 ludo users 114 Jan  1  1970 setuptools-56.0.0.dist-info -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/setuptools-56.0.0.dist-info
lrwxrwxrwx 1 ludo users 103 Jan  1  1970 sitecustomize.py -> 
../../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/sitecustomize.py
--8<---------------cut here---------------end--------------->8---

Now look below how dot-dot resolution whereas “lexical” dot-dot
resolution dose the right thing:

--8<---------------cut here---------------start------------->8---
$ ls -l 
/tmp/pack/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages
ls: ne eblas atingi 
'/tmp/pack/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages':
 Dosiero aŭ dosierujo ne ekzistas
$ ls -l 
/tmp/pack/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages
totalo 40
dr-xr-xr-x 3 ludo users 4096 Jan  1  1970 _distutils_hack/
-r--r--r-- 1 ludo users  152 Jan  1  1970 distutils-precedence.pth
dr-xr-xr-x 5 ludo users 4096 Jan  1  1970 pip/
dr-xr-xr-x 2 ludo users 4096 Jan  1  1970 pip-21.1.3.dist-info/
dr-xr-xr-x 6 ludo users 4096 Jan  1  1970 pkg_resources/
dr-xr-xr-x 2 ludo users 4096 Jan  1  1970 __pycache__/
-r--r--r-- 1 ludo users  119 Jan  1  1970 README.txt
dr-xr-xr-x 7 ludo users 4096 Jan  1  1970 setuptools/
dr-xr-xr-x 2 ludo users 4096 Jan  1  1970 setuptools-56.0.0.dist-info/
-r--r--r-- 1 ludo users 2172 Jan  1  1970 sitecustomize.py
--8<---------------cut here---------------end--------------->8---

In Python’s ‘site.py’, the ‘addsitedir’ method indirectly calls
‘os.path.abspath’, not sure if that is at fault.

I also see that ‘sys.path’ is in fact completely bogus, with “pack”
missing from every directory name:

--8<---------------cut here---------------start------------->8---
$ unshare -mrf sh -c 'mount -t tmpfs -o ro none /gnu/store;  . 
/tmp/pack/etc/profile; echo $GUIX_PYTHONPATH ; /tmp/pack/bin/python3 '
/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-packages
Python 3.9.6 (default, Jan  1 1970, 00:00:01) 
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python39.zip', 
'/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9', 
'/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/lib-dynload',
 
'/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages']
--8<---------------cut here---------------end--------------->8---

So I think something somewhere is manipulating file names and gets
confused.

Does that ring a bell, Maxim?

Thanks,
Ludo’.