Sage ImportError: canot load Singular library

[Jaco Van Tonder]

I am running Fedora 36 (had the same issue in Fedora 35) on a Lenovo IdeaPad. After installing sage using dnf I tried running it but it failed due to: "ImportError: cannot load Singular library from libSingular.so (b'libSingular.so: cannot open shared object file: No such file or directory')". The full error report is:

Error in sys.excepthook:
Traceback (most recent call last):
  File "/usr/lib64/python3.10/pathlib.py", line 1303, in is_dir
    return S_ISDIR(self.stat().st_mode)
AttributeError: 'str' object has no attribute 'stat'

Original exception was:
Traceback (most recent call last):
  File "/usr/lib64/sagemath/local/bin/sage-ipython", line 15, in <module>
    app.initialize()
  File "/home/jacovantonder/.local/lib/python3.10/site-packages/traitlets/config/application.py", line 88, in inner
    return method(app, *args, **kwargs)
  File "/usr/lib/python3.10/site-packages/IPython/terminal/ipapp.py", line 276, in initialize
    self.init_shell()
  File "/usr/lib64/python3.10/site-packages/sage/repl/interpreter.py", line 789, in init_shell
    self.shell.extension_manager.load_extension(SAGE_EXTENSION)
  File "/usr/lib/python3.10/site-packages/IPython/core/extensions.py", line 76, in load_extension
    return self._load_extension(module_str)
  File "/usr/lib/python3.10/site-packages/IPython/core/extensions.py", line 99, in _load_extension
    if self._call_load_ipython_extension(mod):
  File "/usr/lib/python3.10/site-packages/IPython/core/extensions.py", line 151, in _call_load_ipython_extension
    mod.load_ipython_extension(self.shell)
  File "/usr/lib64/python3.10/site-packages/sage/repl/__init__.py", line 5, in load_ipython_extension
    sage.repl.ipython_extension.load_ipython_extension(*args)
  File "/usr/lib64/python3.10/site-packages/sage/repl/ipython_extension.py", line 617, in wrapper
    result = func(*args, **kwargs)
  File "/usr/lib64/python3.10/site-packages/sage/repl/ipython_extension.py", line 630, in load_ipython_extension
    SageCustomizations(shell=ip)
  File "/usr/lib64/python3.10/site-packages/sage/repl/ipython_extension.py", line 434, in __init__
    import sage.all # until sage's import hell is fixed
  File "/usr/lib64/python3.10/site-packages/sage/all.py", line 131, in <module>
    from sage.rings.all      import *
  File "/usr/lib64/python3.10/site-packages/sage/rings/all.py", line 87, in <module>
    from .qqbar import (AlgebraicRealField, AA,
  File "/usr/lib64/python3.10/site-packages/sage/rings/qqbar.py", line 2810, in <module>
    QQxy = QQ['x', 'y']
  File "sage/structure/parent.pyx", line 1276, in sage.structure.parent.Parent.__getitem__
  File "/usr/lib64/python3.10/site-packages/sage/categories/rings.py", line 1177, in __getitem__
    return PolynomialRing(self, elts)
  File "/usr/lib64/python3.10/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py", line 647, in PolynomialRing
    return _multi_variate(base_ring, names, **kwds)
  File "/usr/lib64/python3.10/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py", line 775, in _multi_variate
    from sage.rings.polynomial.multi_polynomial_libsingular import MPolynomialRing_libsingular
  File "sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 1, in init sage.rings.polynomial.multi_polynomial_libsingular
  File "sage/libs/singular/singular.pyx", line 1558, in init sage.libs.singular.singular
  File "sage/libs/singular/singular.pyx", line 1532, in sage.libs.singular.singular.init_libsingular
ImportError: cannot load Singular library from libSingular.so (b'libSingular.so: cannot open shared object file: No such file or directory')

I've had issues with installing sage with conda as well. Not being able to get the kernel to connect in Jupyter.

[Vegard Lima]

Hi,

what does this command say?
$ rpm -q Singular-libs
On fedora 35 I get:
Singular-libs-4.2.0p3-1.fc35.x86_64

And my output from this
$ ldd /usr/lib64/python3.10/site-packages/sage/libs/singular/singular.cpython*
contains a line
libSingular-4.2.0.so =>
/usr/lib64/sagemath/local/lib/libSingular-4.2.0.so
(0x00007f7cc833b000)

Does singular.console() work (or maybe sage doesn't start from the
console at all?)
sage: singular_console()

Cheers,
Vegard

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[Matthias Koeppe]

Report Fedora packaging bugs to Fedora

[Francesco Buscemi]

Hello there; any news? I'm getting exactly the same errors...

[Vegard Lima]

Hi,

there should be a fix for this in updates-testing for Fedora 36:
$ sudo dnf update sagemath --enablerepo=updates-testing

You might have to do this first:
$ sudo dnf erase sagemath-doc-en

Cheers,
Vegard

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[Dima Pasechnik]

On Fri, Jun 10, 2022 at 12:50 PM 'Alan Stafford' via sage-support
<sage-s...@googlegroups.com> wrote:
>
> sudo cd /
> sudo rm -r *.*

I don't think this is an appropriate joke to post here.

We might have to start screening your posts...

Dima

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[Jaco Van Tonder]

Hi Vegard,

This fixes the Singular library load problem but I now have another problem. When I try to load the sage kernel on Jupyter Lab it can't connect:

[I 2022-06-14 12:24:36.977 ServerApp] Kernel started: 7081cbfd-e5e1-4168-b1e4-cac56170523f
/home/jacovantonder/anaconda3/bin/python3: Error while finding module specification for 'sage.repl.ipython_kernel' (ModuleNotFoundError: No module named 'sage')
[I 2022-06-14 12:24:39.978 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (1/5), new random ports
/home/jacovantonder/anaconda3/bin/python3: Error while finding module specification for 'sage.repl.ipython_kernel' (ModuleNotFoundError: No module named 'sage')
[I 2022-06-14 12:24:42.989 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (2/5), new random ports
/home/jacovantonder/anaconda3/bin/python3: Error while finding module specification for 'sage.repl.ipython_kernel' (ModuleNotFoundError: No module named 'sage')
[I 2022-06-14 12:24:46.000 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (3/5), new random ports
/home/jacovantonder/anaconda3/bin/python3: Error while finding module specification for 'sage.repl.ipython_kernel' (ModuleNotFoundError: No module named 'sage')
[I 2022-06-14 12:24:49.008 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (4/5), new random ports
/home/jacovantonder/anaconda3/bin/python3: Error while finding module specification for 'sage.repl.ipython_kernel' (ModuleNotFoundError: No module named 'sage')
[W 2022-06-14 12:24:49.285 ServerApp] 404 GET /api/kernels/ed469bfa-69f5-4462-9fc6-ac5089e55f07?1655173488778 (127.0.0.1): Kernel does not exist: ed469bfa-69f5-4462-9fc6-ac5089e55f07
[W 2022-06-14 12:24:49.286 ServerApp] Kernel does not exist: ed469bfa-69f5-4462-9fc6-ac5089e55f07
[W 2022-06-14 12:24:49.286 ServerApp] 404 GET /api/kernels/ed469bfa-69f5-4462-9fc6-ac5089e55f07?1655173488778 (127.0.0.1) 1.81ms referer=http://localhost:8888/lab/tree/%E3%83%89%E3%82%AD%E3%83%A5%E3%83%A1%E3%83%B3%E3%83%88/Brilliant/Neural%20Networks/Untitled.ipynb
[W 2022-06-14 12:24:52.020 ServerApp] AsyncIOLoopKernelRestarter: restart failed
[W 2022-06-14 12:24:52.020 ServerApp] Kernel 7081cbfd-e5e1-4168-b1e4-cac56170523f died, removing from map.

[Vegard Lima]

Hi,

On Tue, Jun 14, 2022 at 4:30 AM Jaco Van Tonder
<jacovant...@gmail.com> wrote:
> This fixes the Singular library load problem but I now have another problem. When I try to load the sage kernel on Jupyter Lab it can't connect:
>
> [I 2022-06-14 12:24:36.977 ServerApp] Kernel started: 7081cbfd-e5e1-4168-b1e4-cac56170523f
> /home/jacovantonder/anaconda3/bin/python3: Error while finding module specification for 'sage.repl.ipython_kernel' (ModuleNotFoundError: No module named 'sage')

My guess would be that anaconda's python3 cannot see
the system installation of the sage packages.

I've only used jupyter-notebook from the "python3-notebook" fedora package.
Have not tried Jupyter Lab, but maybe this could be useful:
https://www.redhat.com/sysadmin/install-jupyterlab-linux

Cheers,
--
Vegard