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Clingo bootstrap doesn't work on Gentoo #24928

Closed
#25138
Closed
Clingo bootstrap doesn't work on Gentoo#24928
#25138
Assignees
alalazo
Labels
bugSomething isn't workingimpact-medium
@robertu94

Description

@robertu94
robertu94
opened on Jul 16, 2021

Gentoo has a python launcher to support it's slot system that gets used that seems to break clingo's bootstrap. Specifically, it uses https://github.com/mgorny/python-exec. The "real" pythons are installed to

/usr/lib/python-exec/python3.8/python
/usr/lib/python-exec/python3.9/python

I tried to override this by providing an external python with a path to the "real" python that doesn't use the wrapper, but that didn't work either. I'm at a loss at how to work around this.

Steps to reproduce the issue

spack env create -d .
spack env activate
# modify spack.yaml to set conretizer to clingo
spack install zlib
...

Error Message

[runderwood@voyager z-checker2]$ spack --debug --stacktrace install zlib
lib/spack/spack/cmd/__init__.py:121 ==> [2021-07-16-11:13:21.836383] Imported install from built-in commands
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:21.840660] Reading config file /home/runderwood/git/play/z-checker2/spack.yaml
lib/spack/spack/cmd/__init__.py:121 ==> [2021-07-16-11:13:21.842890] Imported install from built-in commands
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:21.846059] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/bootstrap.yaml
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:21.849286] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/config.yaml
lib/spack/spack/database.py:371 ==> [2021-07-16-11:13:21.867635] DATABASE LOCK TIMEOUT: 3s
lib/spack/spack/database.py:375 ==> [2021-07-16-11:13:21.867820] PACKAGE LOCK TIMEOUT: No timeout
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:21.868322] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/bootstrap.yaml
lib/spack/spack/database.py:371 ==> [2021-07-16-11:13:21.870098] DATABASE LOCK TIMEOUT: 3s
lib/spack/spack/database.py:375 ==> [2021-07-16-11:13:21.870261] PACKAGE LOCK TIMEOUT: No timeout
lib/spack/spack/bootstrap.py:201 ==> [2021-07-16-11:13:21.870435] [BOOTSTRAP CONFIG SCOPE] name=_builtin
lib/spack/spack/bootstrap.py:213 ==> [2021-07-16-11:13:21.870835] [BOOTSTRAP CONFIG SCOPE] name=defaults, path=/home/runderwood/git/contrib/spack/etc/spack/defaults
lib/spack/spack/bootstrap.py:214 ==> [2021-07-16-11:13:21.870988] [BOOTSTRAP CONFIG SCOPE] name=defaults/linux, path=/home/runderwood/git/contrib/spack/etc/spack/defaults/linux
lib/spack/spack/bootstrap.py:213 ==> [2021-07-16-11:13:21.871151] [BOOTSTRAP CONFIG SCOPE] name=system, path=/etc/spack
lib/spack/spack/bootstrap.py:214 ==> [2021-07-16-11:13:21.871330] [BOOTSTRAP CONFIG SCOPE] name=system/linux, path=/etc/spack/linux
lib/spack/spack/bootstrap.py:213 ==> [2021-07-16-11:13:21.871649] [BOOTSTRAP CONFIG SCOPE] name=site, path=/home/runderwood/git/contrib/spack/etc/spack
lib/spack/spack/bootstrap.py:214 ==> [2021-07-16-11:13:21.871871] [BOOTSTRAP CONFIG SCOPE] name=site/linux, path=/home/runderwood/git/contrib/spack/etc/spack/linux
lib/spack/spack/bootstrap.py:213 ==> [2021-07-16-11:13:21.872074] [BOOTSTRAP CONFIG SCOPE] name=user, path=/home/runderwood/.spack
lib/spack/spack/bootstrap.py:214 ==> [2021-07-16-11:13:21.872231] [BOOTSTRAP CONFIG SCOPE] name=user/linux, path=/home/runderwood/.spack/linux
lib/spack/spack/bootstrap.py:268 ==> [2021-07-16-11:13:21.876701] [BOOTSTRAP ROOT SPEC] clingo: clingo-bootstrap@spack+python %gcc target=x86_64
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:21.877895] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/config.yaml
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.941592] diffutils applying constraint iconv
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.952648] ncurses applying constraint pkgconfig
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.954302] readline applying constraint ncurses
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.956690] gdbm applying constraint readline
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.960950] bzip2 applying constraint diffutils
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.963320] perl applying constraint gdbm
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.964517] perl applying constraint berkeley-db
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.965639] perl applying constraint bzip2+shared
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.966716] perl applying constraint zlib+shared
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.967988] bison applying constraint diffutils
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.970728] bison applying constraint m4
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.973103] bison applying constraint perl
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.974835] python applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.976131] python applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.978049] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.979282] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.980793] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:21.981883] clingo-bootstrap applying constraint python
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:21.983878] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/packages.yaml
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:22.023630] Reading config file /home/runderwood/.spack/packages.yaml
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.057308] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.058938] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.059929] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.060875] clingo-bootstrap applying constraint python
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.061438] python applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.066315] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.067270] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.068254] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.069135] clingo-bootstrap applying constraint python
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.069690] python applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.073763] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.074641] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.075545] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.076333] clingo-bootstrap applying constraint python
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:22.080690] Reading config file /home/runderwood/.spack/linux/compilers.yaml
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.133970] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.135174] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.136343] clingo-bootstrap applying constraint [email protected]:
lib/spack/spack/spec.py:2813 ==> [2021-07-16-11:13:22.137266] clingo-bootstrap applying constraint python
lib/spack/spack/spec.py:2488 ==> [2021-07-16-11:13:22.146638] Ordered hashes [cmake]: cmake/23/b48396c0e4f61756248156b6cebe9bc0d7a22228639b47b5aa77c9330588ce88
lib/spack/spack/spec.py:2488 ==> [2021-07-16-11:13:22.146861] Ordered hashes [python]: python/6/0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:22.215956] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/config.yaml
lib/spack/spack/installer.py:1406 ==> [2021-07-16-11:13:22.268842] Initializing the build queue from the build requests
lib/spack/spack/installer.py:1020 ==> [2021-07-16-11:13:22.269017] Initializing the build queue for clingo-bootstrap
lib/spack/spack/installer.py:2147 ==> [2021-07-16-11:13:22.270963] Processing dependencies for clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he: ('build', 'link', 'run')
lib/spack/spack/installer.py:1885 ==> [2021-07-16-11:13:22.271175] Pkg id bison-3.7.1-unkbbf6hnv22mtzfrokpalc3eat5rbwq has the following dependents:
lib/spack/spack/installer.py:1888 ==> [2021-07-16-11:13:22.271325] - clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/installer.py:1885 ==> [2021-07-16-11:13:22.284071] Pkg id cmake-3.19.7-n5hux5ukgvkn3crkk2n6tox4mu76fqlu has the following dependents:
lib/spack/spack/installer.py:1888 ==> [2021-07-16-11:13:22.284706] - clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/installer.py:1885 ==> [2021-07-16-11:13:22.298703] Pkg id python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y has the following dependents:
lib/spack/spack/installer.py:1888 ==> [2021-07-16-11:13:22.298897] - clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/installer.py:1885 ==> [2021-07-16-11:13:22.327835] Pkg id re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt has the following dependents:
lib/spack/spack/installer.py:1888 ==> [2021-07-16-11:13:22.328239] - clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/database.py:476 ==> [2021-07-16-11:13:22.341519] Removing failure marking for clingo-bootstrap
lib/spack/spack/installer.py:1885 ==> [2021-07-16-11:13:22.342036] Pkg id clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he has the following dependents:
lib/spack/spack/installer.py:1412 ==> [2021-07-16-11:13:22.343251] Ensure all dependencies know all dependents across specs
lib/spack/spack/installer.py:323 ==> [2021-07-16-11:13:22.345730] [email protected] : externally installed in /usr
lib/spack/spack/installer.py:329 ==> [2021-07-16-11:13:22.346118] [email protected] : already registered in DB
[+] /usr (external bison-3.7.1-unkbbf6hnv22mtzfrokpalc3eat5rbwq)
lib/spack/spack/installer.py:1384 ==> [2021-07-16-11:13:22.346419] Flagging bison-3.7.1-unkbbf6hnv22mtzfrokpalc3eat5rbwq as installed
lib/spack/spack/installer.py:1391 ==> [2021-07-16-11:13:22.346624] Removing bison-3.7.1-unkbbf6hnv22mtzfrokpalc3eat5rbwq from clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he's uninstalled dependencies.
lib/spack/spack/installer.py:1992 ==> [2021-07-16-11:13:22.346841] clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he: Removed bison-3.7.1-unkbbf6hnv22mtzfrokpalc3eat5rbwq from uninstalled deps list: {'python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y', 're2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt', 'cmake-3.19.7-n5hux5ukgvkn3crkk2n6tox4mu76fqlu'}
lib/spack/spack/installer.py:323 ==> [2021-07-16-11:13:22.347078] [email protected] : externally installed in /usr
lib/spack/spack/installer.py:329 ==> [2021-07-16-11:13:22.347224] [email protected] : already registered in DB
[+] /usr (external cmake-3.19.7-n5hux5ukgvkn3crkk2n6tox4mu76fqlu)
lib/spack/spack/installer.py:1384 ==> [2021-07-16-11:13:22.347487] Flagging cmake-3.19.7-n5hux5ukgvkn3crkk2n6tox4mu76fqlu as installed
lib/spack/spack/installer.py:1391 ==> [2021-07-16-11:13:22.347634] Removing cmake-3.19.7-n5hux5ukgvkn3crkk2n6tox4mu76fqlu from clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he's uninstalled dependencies.
lib/spack/spack/installer.py:1992 ==> [2021-07-16-11:13:22.347820] clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he: Removed cmake-3.19.7-n5hux5ukgvkn3crkk2n6tox4mu76fqlu from uninstalled deps list: {'python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y', 're2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt'}
lib/spack/spack/installer.py:323 ==> [2021-07-16-11:13:22.348046] [email protected] : externally installed in /usr/lib/python-exec
lib/spack/spack/installer.py:329 ==> [2021-07-16-11:13:22.348194] [email protected] : already registered in DB
[+] /usr/lib/python-exec (external python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y)
lib/spack/spack/installer.py:1384 ==> [2021-07-16-11:13:22.348385] Flagging python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y as installed
lib/spack/spack/installer.py:1391 ==> [2021-07-16-11:13:22.348550] Removing python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y from clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he's uninstalled dependencies.
lib/spack/spack/installer.py:1992 ==> [2021-07-16-11:13:22.348738] clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he: Removed python-3.9-cwu7hmf6jfwszsbpphpomv7drbfvh32y from uninstalled deps list: {'re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt'}
lib/spack/spack/installer.py:966 ==> [2021-07-16-11:13:22.349895] Acquiring a write lock on re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt with timeout 1e-09
lib/spack/spack/installer.py:1384 ==> [2021-07-16-11:13:22.350705] Flagging re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt as installed
lib/spack/spack/installer.py:1391 ==> [2021-07-16-11:13:22.350855] Removing re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt from clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he's uninstalled dependencies.
lib/spack/spack/installer.py:1992 ==> [2021-07-16-11:13:22.351023] clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he: Removed re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt from uninstalled deps list: set()
lib/spack/spack/stage.py:327 ==> [2021-07-16-11:13:22.352034] Creating stage lock spack-stage-re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt
lib/spack/spack/installer.py:982 ==> [2021-07-16-11:13:22.352241] Downgrading to a read lock on re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt with timeout 1e-09
[+] /home/runderwood/.spack/bootstrap/store/linux-gentoo2-x86_64/gcc-10.3.0/re2c-1.2.1-d4ai3o6hw7aw6lkcnc4nuj24zlrmxtgt
lib/spack/spack/installer.py:966 ==> [2021-07-16-11:13:22.352729] Acquiring a write lock on clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he with timeout 1e-09
lib/spack/spack/installer.py:1126 ==> [2021-07-16-11:13:22.354616] Installing clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/installer.py:394 ==> [2021-07-16-11:13:22.354771] Searching for binary cache of clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/config.py:989 ==> [2021-07-16-11:13:22.355315] Reading config file /home/runderwood/git/contrib/spack/etc/spack/defaults/mirrors.yaml
lib/spack/spack/binary_distribution.py:1430 ==> [2021-07-16-11:13:22.745648] Did not find linux-gentoo2-x86_64-gcc-10.3.0-clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he.spec.yaml on https://mirror.spack.io/build_cache/linux-gentoo2-x86_64-gcc-10.3.0-clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he.spec.yaml
  Download failed: HTTP Error 404: Not Found
lib/spack/spack/installer.py:282 ==> [2021-07-16-11:13:22.746939] No binary for clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he found: installing from source
lib/spack/spack/util/executable.py:190 ==> [2021-07-16-11:13:22.823209] '/usr/bin/git' 'describe' '--tags' '--match' 'v*'
lib/spack/spack/compilers/__init__.py:741 ==> [2021-07-16-11:13:22.954372] [TOOLCHAIN] MATCH Gcc
lib/spack/spack/build_environment.py:365 ==> [2021-07-16-11:13:22.956773] Adding compiler bin/ paths: /home/runderwood/git/contrib/spack/lib/spack/env /home/runderwood/git/contrib/spack/lib/spack/env/case-insensitive /home/runderwood/git/contrib/spack/lib/spack/env/gcc
lib/spack/spack/stage.py:327 ==> [2021-07-16-11:13:22.967005] Creating stage lock spack-stage-clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/error.py:54 ==> [2021-07-16-11:13:22.969505] Error: RuntimeError: Unable to locate python command in /usr/lib/python-exec/bin

/home/runderwood/git/contrib/spack/var/spack/repos/builtin/packages/python/package.py:660, in command:
        657                return Executable(path)
        658        else:
        659            msg = 'Unable to locate {0} command in {1}'
  >>    660            raise RuntimeError(msg.format(self.name, self.prefix.bin))


Traceback (most recent call last):
  File "/home/runderwood/git/contrib/spack/lib/spack/spack/build_environment.py", line 1011, in _setup_pkg_and_run
    setup_package(pkg, dirty=kwargs.get('dirty', False),
  File "/home/runderwood/git/contrib/spack/lib/spack/spack/build_environment.py", line 768, in setup_package
    set_wrapper_variables(pkg, env)
  File "/home/runderwood/git/contrib/spack/lib/spack/spack/build_environment.py", line 424, in set_wrapper_variables
    update_compiler_args_for_dep(dspec)
  File "/home/runderwood/git/contrib/spack/lib/spack/spack/build_environment.py", line 403, in update_compiler_args_for_dep
    dep_link_dirs.extend(query.libs.directories)
  File "/home/runderwood/git/contrib/spack/lib/spack/spack/spec.py", line 949, in __get__
    value = f()
  File "/home/runderwood/git/contrib/spack/lib/spack/spack/spec.py", line 938, in <lambda>
    callbacks_chain.append(lambda: getattr(pkg, self.attribute_name))
  File "/home/runderwood/git/contrib/spack/var/spack/repos/builtin/packages/python/package.py", line 777, in libs
  File "/home/runderwood/git/contrib/spack/var/spack/repos/builtin/packages/python/package.py", line 695, in get_config_var
  File "/home/runderwood/git/contrib/spack/var/spack/repos/builtin/packages/python/package.py", line 661, in command
RuntimeError: Unable to locate python command in /usr/lib/python-exec/bin
lib/spack/spack/installer.py:1336 ==> [2021-07-16-11:13:22.970121] Flagging clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he as failed: RuntimeError: Unable to locate python command in /usr/lib/python-exec/bin
lib/spack/spack/stage.py:327 ==> [2021-07-16-11:13:22.972865] Creating stage lock spack-stage-clingo-bootstrap-spack-rygx3hggm5itz37tbf2wptnhggikt2he
lib/spack/spack/cmd/install.py:397 ==> [2021-07-16-11:13:22.973130] ChildError: RuntimeError: Unable to locate python command in /usr/lib/python-exec/bin
lib/spack/spack/main.py:777 ==> [2021-07-16-11:13:22.973268] ChildError: RuntimeError: Unable to locate python command in /usr/lib/python-exec/bin

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  • [x ] I have run spack debug report and reported the version of Spack/Python/Platform
[runderwood@voyager z-checker2]$ spack debug report
* **Spack:** 0.16.2-3541-64f31c4579
* **Python:** 3.9.5
* **Platform:** linux-gentoo2-skylake
* **Concretizer:** clingo
  • 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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