Python unable to find modules within a Singularity container created with guix pack

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7 participants
  • Josselin Poiret
  • Konrad Hinsen
  • Ludovic Courtès
  • Ludovic Courtès
  • Marek Felšöci
  • Maxim Cournoyer
  • Simon Tournier
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unassigned
Submitted by
Marek Felšöci
Severity
normal
M
M
Marek Felšöci wrote on 14 Jan 2022 15:20
(address . bug-guix@gnu.org)
67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk
Hello folks,

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

However, if I do,

`export PYTHONPATH=$GUIX_PYTHONPATH`

the numpy module IS 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.__main__; 'numpy' is a package and cannot be directly executed

Still, the sitecustomize error persists.

See the output of `guix describe` below (only the guix channel):

Pokolenie 3    14. január 2022 14:33:06    (sú?asné)
  guix 5c5d9e5
    vetva: master
    úprava: 5c5d9e5a3208fa51351c6ad8267eba3d96fa2232

Thanks,

Marek
L
L
Ludovic Courtès wrote on 14 Jan 2022 18:45
(name . Marek Felšöci)(address . marek@felsoci.sk)
87wnj22ouh.fsf@gnu.org
Hi Marek,

Marek Felšöci <marek@felsoci.sk> skribis:

Toggle quote (22 lines)
> 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:

Toggle snippet (16 lines)
$ 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__']

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:

Toggle snippet (16 lines)
$ 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

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

Toggle snippet (16 lines)
$ 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 a? 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

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:

Toggle snippet (10 lines)
$ 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']

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

Does that ring a bell, Maxim?

Thanks,
Ludo’.
L
L
Ludovic Courtès wrote on 4 Feb 2022 21:50
(name . Marek Felšöci)(address . marek@felsoci.sk)
87v8xumk41.fsf@gnu.org
Hello!

Ludovic Courtès <ludovic.courtes@inria.fr> skribis:

Toggle quote (4 lines)
>>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:

Some news! Here’s a recap of the IRC discussion earlier today:
‘sys.prefix’ looks like
/tmp/pack2/bin/../../zmv1alp7dzjd6hkc7l6fjz817n2mfzzw-python-3.9.9R.

‘sys.normpath’ does lexical dot-dot resolution (which is incorrect on
POSIX):


Thus, passing the prefix above to ‘sys.normpath’ leads “pack2” to be
erased.

Josselin mentioned “path_hooks” as a possible solution, though I’m not
sure what that means; could you explain? :-)

Thanks!

Ludo’.
J
J
Josselin Poiret wrote on 5 Feb 2022 23:28
87v8xt3q3s.fsf@jpoiret.xyz
Hello everyone,

After the IRC investigation, it turned out the use of abspath in
Lib/site.py was in fact the culprit. Replacing all its uses with
realpath and doing `./pre-inst-env guix pack -RR python python-numpy -S
/bin=bin -S /etc=etc` did in fact resolve the issue!

I've raised the issue upstream at [1]. The fix itself is pretty simple,
but it's theoretically a breaking change, so we'll see how Python
maintainers want to move forward with it. We could backport this fix
for the next core-updates cycle, whether or not it gets accepted
upstream, and we will also need to modify sitecustomize.py as well to
call os.path.realpath on python_site.

Best,
--
Josselin Poiret
J
L
L
Ludovic Courtès wrote on 7 Mar 2022 09:25
(name . Josselin Poiret)(address . dev@jpoiret.xyz)
877d9641ab.fsf@gnu.org
Hi Josselin,

Josselin Poiret <dev@jpoiret.xyz> skribis:

Toggle quote (14 lines)
> After the IRC investigation, it turned out the use of abspath in
> Lib/site.py was in fact the culprit. Replacing all its uses with
> realpath and doing `./pre-inst-env guix pack -RR python python-numpy -S
> /bin=bin -S /etc=etc` did in fact resolve the issue!
>
> I've raised the issue upstream at [1]. The fix itself is pretty simple,
> but it's theoretically a breaking change, so we'll see how Python
> maintainers want to move forward with it. We could backport this fix
> for the next core-updates cycle, whether or not it gets accepted
> upstream, and we will also need to modify sitecustomize.py as well to
> call os.path.realpath on python_site.

> [1] https://bugs.python.org/issue46653

Thanks for the investigation and for reporting it upstream!

Is there a workaround we could apply locally, ideally one that does not
lead to a world rebuild?

Ludo’.
J
J
Josselin Poiret wrote on 2 Feb 2023 15:44
(name . Ludovic Courtès)(address . ludo@gnu.org)
87v8kkw2i1.fsf@jpoiret.xyz
Hi Ludo,

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (5 lines)
> Thanks for the investigation and for reporting it upstream!
>
> Is there a workaround we could apply locally, ideally one that does not
> lead to a world rebuild?

So, upstream hasn't replied at all to the above proposal. How do we move
forward? I have a patch that still applies on Python 3.9.9 that we can
put into core-updates. Would that be fine?

Best,
--
Josselin Poiret
M
M
Maxim Cournoyer wrote on 2 Feb 2023 16:40
(name . Josselin Poiret)(address . dev@jpoiret.xyz)
87tu04oz26.fsf@gmail.com
Hi Josselin,

Josselin Poiret <dev@jpoiret.xyz> writes:

Toggle quote (13 lines)
> Hi Ludo,
>
> Ludovic Courtès <ludo@gnu.org> writes:
>
>> Thanks for the investigation and for reporting it upstream!
>>
>> Is there a workaround we could apply locally, ideally one that does not
>> lead to a world rebuild?
>
> So, upstream hasn't replied at all to the above proposal. How do we move
> forward? I have a patch that still applies on Python 3.9.9 that we can
> put into core-updates. Would that be fine?

I haven't revisited that patch, but if you are confident it wouldn't
break anything in the Python world, core-updates would be a fine place,
yes.

--
Thanks,
Maxim
S
S
Simon Tournier wrote on 6 Feb 2023 18:34
87sffiiton.fsf@gmail.com
Hi,

On jeu., 02 févr. 2023 at 10:40, Maxim Cournoyer <maxim.cournoyer@gmail.com> wrote:

Toggle quote (8 lines)
>> So, upstream hasn't replied at all to the above proposal. How do we move
>> forward? I have a patch that still applies on Python 3.9.9 that we can
>> put into core-updates. Would that be fine?
>
> I haven't revisited that patch, but if you are confident it wouldn't
> break anything in the Python world, core-updates would be a fine place,
> yes.

Maybe for testing this change, you could create one Python interpreter
variant containing the patch. Then using ’package-with-explicit-python’
package transformation from (guix build-system python) we could build
Python packages and check if it correctly fixes and also incrementally
check if nothing break. It would avoid a full world rebuild.


Cheers,
simon
K
K
Konrad Hinsen wrote on 4 Jan 2024 13:35
Re: Python unable to find modules within a Singularity container created with guix pack
(address . 53258@debbugs.gnu.org)
m1v889jmy7.fsf@fastmail.net
Hi everyone,

I found this issue while investigating a related one (the error
message). It looks like the core problem discussed here has been solved
in the meantime:

Singularity> python3 -m numpy
Error in sitecustomize; set PYTHONVERBOSE for traceback:
ValueError: '/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages' is not in list
/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/python3: No module named numpy.__main__; 'numpy' is a package and cannot be directly executed

This error message is to be expected, and NumPy can be imported:

Singularity> python3
Error in sitecustomize; set PYTHONVERBOSE for traceback:
ValueError: '/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages' is not in list
Python 3.10.7 (main, Jan 1 1970, 00:00:01) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>>

What remains is the error message, which comes from a bug in Guix'
sitecustomize.py. It compares a raw path (sys.prefix) with paths that
have been normalized (os.path.normpath). That comparison fails if
sys.prefix contains "../", as it does when run from a Singularity
container. I will submit a patch for this.

Cheers,
Konrad
K
K
Konrad Hinsen wrote on 4 Jan 2024 14:01
(address . 53258@debbugs.gnu.org)
m1plyhjlrh.fsf@fastmail.net
Konrad Hinsen <konrad.hinsen@fastmail.net> writes:

Toggle quote (2 lines)
> I will submit a patch for this.


Cheers,
Konrad
K
M
M
Maxim Cournoyer wrote on 21 Jan 2024 19:31
Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack
(name . Konrad Hinsen)(address . konrad.hinsen@fastmail.net)(address . 53258-done@debbugs.gnu.org)
87r0ia8rnt.fsf@gmail.com
Hi Konrad,

Konrad Hinsen <konrad.hinsen@fastmail.net> writes:

Toggle quote (9 lines)
> Konrad Hinsen <konrad.hinsen@fastmail.net> writes:
>
>> Patch at https://issues.guix.gnu.org/68241
>
> If you want to test it without rebuilding tons of packages, here is a
> version that grafts a patched Python onto the existing ones (as substitutes):
>
> https://codeberg.org/khinsen/guix/src/branch/graft-fix-python-sitecustomize

I've applied your patch to core-updates. I trust that it fixed this
issue based on your own testing.

Closing; we can always reopen if we find it didn't fix every use cases
or create a fresh issue.

--
Thanks,
Maxim
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