During CI testing: Unable to dlopen(cxxpath) in parent! cannot open shared object file: File name too long #2455
Description
Bug Description
The build-documentation continuous integration run at https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/5180345336 failed when running sphinx with the log:
Running Sphinx v5.0.2
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 206 source files that are out of date
updating environment: [new config] 206 added, 0 changed, 0 removed
reading sources... [ 0%] contents
reading sources... [ 0%] latex-api
reading sources... [ 1%] latex-rmg
reading sources... [ 1%] reference/arkane/common
ERROR: Unable to dlopen(cxxpath) in parent!
Message: /usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rdkit/../../../libstdc++.so.6nts a live Julia runtime.
Note: Use `LibJulia` to fully control the initialization of
the Julia runtime.
Parameters
==========
init_julia : bool
If True, try to initialize the Julia runtime. If this code is
being called from inside an already running Julia, the flag should
be passed as False so the interpreter isn't re-initialized.
Note that it is safe to call this class constructor twice in the
same process with `init_julia` set to True, as a global reference
is kept to avoid re-initializing it. The purpose of the flag is
only to manage situations when Julia was initialized from outside
this code.
runtime : str
Custom Julia binary, e.g. "/usr/local/bin/julia" or "julia-1.0.0".
debug : bool
If True, print some debugging information to STDERR
: cannot open shared object file: File name too long
Error: Process completed with exit code 1.
I can't see what has changed to cause it, so I am attempting to just restart the job and see what happens.
and shortly after that, this build-and-test job failed in a similar way
https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/5180282876/jobs/9334261409#step:9:39
run make test-unittests
make test-unittests
shell: /usr/bin/bash -l {0}
env:
RMG_DATABASE_BRANCH: main
INPUT_RUN_POST: true
CONDA: /usr/share/miniconda3
CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
PYTHONPATH: /home/runner/work/RMG-Py/RMG-Py/RMG-Py:
nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
ERROR: Unable to dlopen(cxxpath) in parent!
Message: /usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/scipy/sparse/../../../../libstdc++.so.6 Julia runtime.
Note: Use `LibJulia` to fully control the initialization of
the Julia runtime.
Parameters
==========
init_julia : bool
If True, try to initialize the Julia runtime. If this code is
being called from inside an already running Julia, the flag should
be passed as False so the interpreter isn't re-initialized.
Note that it is safe to call this class constructor twice in the
same process with `init_julia` set to True, as a global reference
is kept to avoid re-initializing it. The purpose of the flag is
only to manage situations when Julia was initialized from outside
this code.
runtime : str
Custom Julia binary, e.g. "/usr/local/bin/julia" or "julia-1.0.0".
debug : bool
If True, print some debugging information to STDERR
: cannot open shared object file: File name too long
make: *** [Makefile:64: test-unittests] Error 1
Error: Process completed with exit code 2.
How To Reproduce
Opened a pull request. The CI failed.
Installation Information
Describe your installation method and system information.
- OS: The documentation test CI runs on Ubuntu-latest
- Installation method: from source (via CI)
- RMG version information: latest (running on CI)
Additional Context
It looks a bit like
scipy/scipy#18626
and
conda-forge/scipy-feedstock#238