Spack BootStrap Status fails due to path #38233
Description
Steps to reproduce
On Ubuntu 22.04, I am able to use Spack with no issues to install various packages. However, when I try to confine the Spack application inside a snap running Ubuntu Core 22 I am unable to to run the spack bootstrap status command.
# Clone Spack Snap Repo
git clone https://github.com/dvdgomez/spack-snap.git
# Build Snap
snapcraft
# Install locally built snap
sudo snap install spack_0.20.0_amd64.snap --dangerous
# Run command
spack bootstrap status
Error message
My current workaround patch is to change the failing search path from '/snap/spack/x1/usr/sbin', '/snap/spack/x1/usr/bin', '/snap/spack/x1/bin', '/usr/sbin', '/usr/bin', '/sbin', '/bin', '/usr/games' -> '/snap/spack/x1/usr/sbin', '/snap/spack/x1/usr/bin', '/snap/spack/x1/bin' and that works fine. Maybe there is a way for it to silently ignore the rest of the path.
$ spack --debug --stacktrace bootstrap status
lib/spack/spack/cmd/__init__.py:123 ==> [2023-06-07-10:53:38.874656] Imported bootstrap from built-in commands
lib/spack/spack/cmd/__init__.py:123 ==> [2023-06-07-10:53:38.876897] Imported bootstrap from built-in commands
Spack v0.20.0 - [email protected]
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.877797] Reading config from file /snap/spack/x1/spack/etc/spack/defaults/bootstrap.yaml
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.883935] Reading config from file /snap/spack/x1/spack/etc/spack/defaults/config.yaml
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.898723] Reading config from file /home/dave/snap/spack/common/config.yaml
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.916174] Reading config from file /snap/spack/x1/spack/etc/spack/defaults/repos.yaml
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.919483] Reading config from file /snap/spack/x1/spack/etc/spack/defaults/config.yaml
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.943055] Reading config from file /home/dave/snap/spack/common/config.yaml
lib/spack/spack/database.py:391 ==> [2023-06-07-10:53:38.955921] DATABASE LOCK TIMEOUT: 60s
lib/spack/spack/database.py:397 ==> [2023-06-07-10:53:38.956057] PACKAGE LOCK TIMEOUT: No timeout
lib/spack/spack/database.py:391 ==> [2023-06-07-10:53:38.956575] DATABASE LOCK TIMEOUT: 60s
lib/spack/spack/database.py:397 ==> [2023-06-07-10:53:38.956698] PACKAGE LOCK TIMEOUT: No timeout
lib/spack/spack/bootstrap/config.py:125 ==> [2023-06-07-10:53:38.956816] [BOOTSTRAP CONFIG SCOPE] name=_builtin
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.957142] Reading config from file /snap/spack/x1/spack/etc/spack/defaults/bootstrap.yaml
lib/spack/spack/bootstrap/config.py:138 ==> [2023-06-07-10:53:38.961860] [BOOTSTRAP CONFIG SCOPE] name=defaults, path=/snap/spack/x1/spack/etc/spack/defaults
lib/spack/spack/bootstrap/config.py:139 ==> [2023-06-07-10:53:38.961973] [BOOTSTRAP CONFIG SCOPE] name=defaults/linux, path=/snap/spack/x1/spack/etc/spack/defaults/linux
lib/spack/spack/bootstrap/config.py:138 ==> [2023-06-07-10:53:38.962077] [BOOTSTRAP CONFIG SCOPE] name=bootstrap, path=/home/dave/snap/spack/x1/.spack/bootstrap/config
lib/spack/spack/bootstrap/config.py:139 ==> [2023-06-07-10:53:38.962171] [BOOTSTRAP CONFIG SCOPE] name=bootstrap/linux, path=/home/dave/snap/spack/x1/.spack/bootstrap/config/linux
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.966181] Reading config from file /snap/spack/x1/spack/etc/spack/defaults/config.yaml
lib/spack/spack/config.py:996 ==> [2023-06-07-10:53:38.979742] Reading config from file /home/dave/snap/spack/common/config.yaml
Traceback (most recent call last):
File "/snap/spack/x1/spack/lib/spack/llnl/util/lang.py", line 193, in _memoized_function
return func.cache[key]
KeyError: ('/snap/spack/x1/usr/sbin', '/snap/spack/x1/usr/bin', '/snap/spack/x1/bin', '/usr/sbin', '/usr/bin', '/sbin', '/bin', '/usr/games')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/snap/spack/x1/spack/bin/spack", line 54, in <module>
sys.exit(main())
File "/snap/spack/x1/spack/lib/spack/spack_installable/main.py", line 37, in main
sys.exit(spack.main.main(argv))
File "/snap/spack/x1/spack/lib/spack/spack/main.py", line 1018, in main
return _main(argv)
File "/snap/spack/x1/spack/lib/spack/spack/main.py", line 973, in _main
return finish_parse_and_run(parser, cmd_name, env_format_error)
File "/snap/spack/x1/spack/lib/spack/spack/main.py", line 1001, in finish_parse_and_run
return _invoke_command(command, parser, args, unknown)
File "/snap/spack/x1/spack/lib/spack/spack/main.py", line 650, in _invoke_command
return_val = command(parser, args)
File "/snap/spack/x1/spack/lib/spack/spack/cmd/bootstrap.py", line 468, in bootstrap
callbacks[args.subcommand](args)
File "/snap/spack/x1/spack/lib/spack/spack/cmd/bootstrap.py", line 316, in _status
with spack.bootstrap.ensure_bootstrap_configuration():
File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
return next(self.gen)
File "/snap/spack/x1/spack/lib/spack/spack/bootstrap/config.py", line 105, in ensure_bootstrap_configuration
with _ensure_bootstrap_configuration():
File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
return next(self.gen)
File "/snap/spack/x1/spack/lib/spack/spack/bootstrap/config.py", line 167, in _ensure_bootstrap_configuration
_add_compilers_if_missing()
File "/snap/spack/x1/spack/lib/spack/spack/bootstrap/config.py", line 145, in _add_compilers_if_missing
if not spack.compilers.compilers_for_arch(arch):
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 362, in compilers_for_arch
config = all_compilers_config(scope)
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 210, in all_compilers_config
_cache_config_file = get_compiler_config(scope, init_config)
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 130, in get_compiler_config
init_compiler_config()
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 117, in init_compiler_config
compilers = find_compilers()
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 242, in find_compilers
arguments.extend(arguments_to_detect_version_fn(o, search_paths))
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 651, in arguments_to_detect_version_fn
return fn(paths)
File "/snap/spack/x1/spack/lib/spack/spack/compilers/__init__.py", line 628, in _default
files_to_be_tested = fs.files_in(*search_paths)
File "/snap/spack/x1/spack/lib/spack/spack/util/path.py", line 198, in path_filter_caller
return func(*args, **kwargs)
File "/snap/spack/x1/spack/lib/spack/llnl/util/lang.py", line 195, in _memoized_function
ret = func(*args, **kwargs)
File "/snap/spack/x1/spack/lib/spack/llnl/util/filesystem.py", line 2520, in files_in
lambda x: os.path.isfile(x[1]), [(f, os.path.join(d, f)) for f in os.listdir(d)]
PermissionError: [Errno 13] Permission denied: '/usr/sbin'Information on your system
$ spack debug report
* **Spack:** 0.20.0
* **Python:** 3.10.6
* **Platform:** linux-ubuntu_core22-zen3
* **Concretizer:** clingocompilers.yaml
compilers:
- compiler:
spec: [email protected]
paths:
cc: /snap/spack/x1/usr/bin/gcc-11
cxx: /snap/spack/x1/usr/bin/g++-11
f77: /snap/spack/x1/usr/bin/gfortran
fc: /snap/spack/x1/usr/bin/gfortran
flags: {}
operating_system: ubuntu_core22
target: x86_64
modules: []
environment:
prepend_path:
LD_LIBRARY_PATH: /snap/spack/x1/usr/lib/x86_64-linux-gnu
extra_rpaths: []General information
- I have run
spack debug reportand reported the version of Spack/Python/Platform - I have searched the issues of this repo and believe this is not a duplicate
- I have run the failing commands in debug mode and reported the output
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