Tests for test_lensing[classy] and test_lensing_lite[classy] fail

[emilymmoser]

After installing SOLikeT and running "pytest -v ." as specified in the documentation, the tests for test_lensing.py and test_lensing_lite.py fail from the same failed installation of CLASS.

The error message indicates that the version for gcc is too low, needing to be newer than 6.4. The entire error message is copied below:

'''
theory = 'classy'

    @pytest.mark.parametrize("theory", ["camb", "classy"])
    def test_lensing(theory):
>       model, test_point = get_demo_lensing_model(theory)

soliket/tests/test_lensing.py:87: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
soliket/tests/test_lensing.py:64: in get_demo_lensing_model
    install(info, path=packages_path, skip_global=True)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

infos = ({'likelihood': {'soliket.LensingLikelihood': {'stop_at_error': True}}, 'params': {'H0': {'prior': {'max': 100, 'min':...{'prior': {'max': 1.2, 'min': 0.8}}}, 'theory': {'classy': {'extra_args': {'output': 'lCl, tCl'}, 'path': 'global'}}},)
kwargs = {'path': '/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages', 'skip_global': True}
debug = None, path = '/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages'
abspath = '/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages'
kwargs_install = {'code': True, 'data': True, 'force': False, 'no_progress_bars': None}
what = 'data', spath = '/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages/data'
failed_components = ['theory:classy'], skip_keywords_arg = set(), skip_keywords_env = set()
skip_keywords = set()

    def install(*infos, **kwargs):
        debug = kwargs.get("debug")
        # noinspection PyUnresolvedReferences
        if not log.root.handlers:
            logger_setup(debug=debug)
        path = kwargs.get("path")
        if not path:
            path = resolve_packages_path(infos)
        if not path:
            raise LoggedError(
                log, "No 'path' argument given, and none could be found in input infos "
                     "(as %r), the %r env variable or the config file. "
                     "Maybe specify one via a command line argument '-%s [...]'?",
                "packages_path", packages_path_env, packages_path_arg[0])
        abspath = os.path.abspath(path)
        log.info("Installing external packages at '%s'", abspath)
        kwargs_install = {"force": kwargs.get("force", False),
                          "no_progress_bars": kwargs.get("no_progress_bars")}
        for what in (code_path, data_path):
            kwargs_install[what] = kwargs.get(what, True)
            spath = os.path.join(abspath, what)
            if kwargs_install[what] and not os.path.exists(spath):
                try:
                    os.makedirs(spath)
                except OSError:
                    raise LoggedError(
                        log, "Could not create the desired installation folder '%s'", spath)
        failed_components = []
        skip_keywords_arg = set(kwargs.get("skip", []) or [])
        # NB: if passed with quotes as `--skip "a b"`, it's interpreted as a single key
        skip_keywords_arg = set(chain(*[word.split() for word in skip_keywords_arg]))
        skip_keywords_env = set(
            os.environ.get(install_skip_env, "").replace(",", " ").lower().split())
        skip_keywords = skip_keywords_arg.union(skip_keywords_env)
        used_components, components_infos = get_used_components(*infos, return_infos=True)
        for kind, components in used_components.items():
            for component in components:
                print()
                print(create_banner(kind + ":" + component,
                                    symbol=_banner_symbol, length=_banner_length), end="")
                print()
                if _skip_helper(component.lower(), skip_keywords, skip_keywords_env, log):
                    continue
                info = components_infos[component]
                if isinstance(info, str) or "external" in info:
                    log.warning("Component '%s' is a custom function. "
                                "Nothing to do.", component)
                    continue
                try:
                    class_name = (info or {}).get("class")
                    if class_name:
                        log.info("Class to be installed for this component: %r", class_name)
                    imported_class = get_resolved_class(
                        component, kind=kind, component_path=info.pop("python_path", None),
                        class_name=class_name)
                except ImportError as excpt:
                    log.error("Component '%s' not recognized. [%s].", component, excpt)
                    failed_components += ["%s:%s" % (kind, component)]
                    continue
                else:
                    if _skip_helper(imported_class.__name__.lower(), skip_keywords,
                                    skip_keywords_env, log):
                        continue
                is_compatible = getattr(imported_class, "is_compatible", lambda: True)()
                if not is_compatible:
                    log.info(
                        "Skipping %r because it is not compatible with your OS.", component)
                    continue
                log.info("Checking if dependencies have already been installed...")
                is_installed = getattr(imported_class, "is_installed", None)
                if is_installed is None:
                    log.info("%s.%s is a fully built-in component: nothing to do.",
                             kind, imported_class.__name__)
                    continue
                install_path = abspath
                get_path = getattr(imported_class, "get_path", None)
                if get_path:
                    install_path = get_path(install_path)
                has_been_installed = False
                with NoLogging(None if debug else logging.ERROR):
                    if kwargs.get("skip_global"):
                        has_been_installed = is_installed(path="global", **kwargs_install)
                    if not has_been_installed:
                        has_been_installed = is_installed(path=install_path, **kwargs_install)
                if has_been_installed:
                    log.info("External dependencies for this component already installed.")
                    if kwargs.get("test", False):
                        continue
                    if kwargs_install["force"] and not kwargs.get("skip_global"):
                        log.info("Forcing re-installation, as requested.")
                    else:
                        log.info("Doing nothing.")
                        continue
                else:
                    log.info("Check found no existing installation")
                    if not debug:
                        log.info(
                            "(If you expected this to be already installed, re-run "
                            "`cobaya-install` with --debug to get more verbose output.)")
                    if kwargs.get("test", False):
                        continue
                    log.info("Installing...")
                try:
                    install_this = getattr(imported_class, "install", None)
                    success = install_this(path=abspath, **kwargs_install)
                except KeyboardInterrupt:
                    raise
                except:
                    traceback.print_exception(*sys.exc_info(), file=sys.stdout)
                    log.error("An unknown error occurred. Delete the external packages "
                              "folder %r and try again. "
                              "Please, notify the developers if this error persists.",
                              abspath)
                    success = False
                if success:
                    log.info("Successfully installed! Let's check it...")
                else:
                    log.error("Installation failed! Look at the error messages above. "
                              "Solve them and try again, or, if you are unable to solve, "
                              "install the packages required by this component manually.")
                    failed_components += ["%s:%s" % (kind, component)]
                    continue
                # test installation
                with NoLogging(None if debug else logging.ERROR):
                    successfully_installed = is_installed(path=install_path, check=False,
                                                          **kwargs_install)
                if not successfully_installed:
                    log.error("Installation apparently worked, "
                              "but the subsequent installation test failed! "
                              "Look at the error messages above, or re-run with --debug "
                              "for more more verbose output. "
                              "Try to solve the issues and try again, or, if you are unable "
                              "to solve them, install the packages required by this "
                              "component manually.")
                    failed_components += ["%s:%s" % (kind, component)]
                else:
                    log.info("Installation check successful.")
        print()
        print(create_banner(" * Summary * ",
                            symbol=_banner_symbol, length=_banner_length), end="")
        print()
        if failed_components:
            bullet = "\n - "
            raise LoggedError(
                log, "The installation (or installation test) of some component(s) has "
                     "failed: %s\nCheck output of the installer of each component above "
                     "for precise error info.\n",
>               bullet + bullet.join(failed_components))
E           cobaya.log.LoggedError: The installation (or installation test) of some component(s) has failed: 
E            - theory:classy
E           Check output of the installer of each component above for precise error info.

../../.local/lib/python3.6/site-packages/cobaya/install.py:196: LoggedError
--------------------------------------- Captured stdout call ----------------------------------------
 2022-03-01 15:37:29,071 [install] Installing external packages at '/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages'

================================================================================
theory:classy
================================================================================

 2022-03-01 15:37:29,076 [install] Checking if dependencies have already been installed...
 2022-03-01 15:37:29,078 [install] Check found no existing installation
 2022-03-01 15:37:29,078 [install] (If you expected this to be already installed, re-run `cobaya-install` with --debug to get more verbose output.)
 2022-03-01 15:37:29,078 [install] Installing...
 2022-03-01 15:37:29,078 [classy] Installing pre-requisites...
Collecting cython
  Downloading Cython-0.29.28-py2.py3-none-any.whl (983 kB)
Installing collected packages: cython
Successfully installed cython-0.29.28
 2022-03-01 15:37:34,464 [classy] Downloading classy...
 2022-03-01 15:37:37,982 [classy] Downloaded filename class_public-2.9.3.tar.gz
 2022-03-01 15:37:38,177 [classy] class_public v2.9.3 downloaded and decompressed correctly.
 2022-03-01 15:37:38,251 [classy] *ERROR* Your gcc version is too low! CLASS would probably compile, but it would leak memory when running a chain. Please use a gcc version newer than 6.4. You can still compile CLASS by hand, maybe changing the compiler in the Makefile. CLASS has been downloaded into '/private/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages/code/classy'
 2022-03-01 15:37:38,252 [install] *ERROR* Installation failed! Look at the error messages above. Solve them and try again, or, if you are unable to solve, install the packages required by this component manually.

================================================================================
likelihood:soliket.LensingLikelihood
================================================================================

 2022-03-01 15:37:38,253 [install] Checking if dependencies have already been installed...
 2022-03-01 15:37:38,254 [install] External dependencies for this component already installed.
 2022-03-01 15:37:38,254 [install] Doing nothing.

================================================================================
* Summary * 
================================================================================

 2022-03-01 15:37:38,254 [install] *ERROR* The installation (or installation test) of some component(s) has failed: 
 - theory:classy
Check output of the installer of each component above for precise error info.

--------------------------------------- Captured stderr call ----------------------------------------
3.31MiB [00:02, 1.16MiB/s]
----------------------------------------- Captured log call -----------------------------------------
INFO     install:install.py:64 Installing external packages at '/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages'
INFO     install:install.py:117 Checking if dependencies have already been installed...
INFO     install:install.py:143 Check found no existing installation
INFO     install:install.py:146 (If you expected this to be already installed, re-run `cobaya-install` with --debug to get more verbose output.)
INFO     install:install.py:150 Installing...
INFO     classy:classy.py:573 Installing pre-requisites...
INFO     classy:classy.py:578 Downloading classy...
INFO     classy:install.py:242 Downloaded filename class_public-2.9.3.tar.gz
INFO     classy:install.py:292 class_public v2.9.3 downloaded and decompressed correctly.
ERROR    classy:classy.py:595 Your gcc version is too low! CLASS would probably compile, but it would leak memory when running a chain. Please use a gcc version newer than 6.4. You can still compile CLASS by hand, maybe changing the compiler in the Makefile. CLASS has been downloaded into '/private/var/folders/15/lt28zrgs54nbr15_scf2bjtm0000gn/T/lensing_packages/code/classy'
ERROR    install:install.py:166 Installation failed! Look at the error messages above. Solve them and try again, or, if you are unable to solve, install the packages required by this component manually.
INFO     install:install.py:117 Checking if dependencies have already been installed...
INFO     install:install.py:134 External dependencies for this component already installed.
INFO     install:install.py:140 Doing nothing.
ERROR    install:log.py:35 The installation (or installation test) of some component(s) has failed: 
 - theory:classy
Check output of the installer of each component above for precise error info.
_______________________________________ test_lensing[classy] ________________________________________

theory = 'classy'

    @pytest.mark.parametrize("theory", ["camb", "classy"])
    def test_lensing(theory):
>       model = get_demo_lensing_model(theory)

soliket/tests/test_lensing_lite.py:61: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
soliket/tests/test_lensing_lite.py:55: in get_demo_lensing_model
    model = get_model(info)
../../.local/lib/python3.6/site-packages/cobaya/model.py:1189: in get_model
    stop_at_error=info.get("stop_at_error", False))
../../.local/lib/python3.6/site-packages/cobaya/model.py:150: in __init__
    timing=timing)
../../.local/lib/python3.6/site-packages/cobaya/theory.py:397: in __init__
    info, packages_path=packages_path, timing=timing, name=name))
../../.local/lib/python3.6/site-packages/cobaya/theory.py:67: in __init__
    standalone=standalone)
../../.local/lib/python3.6/site-packages/cobaya/component.py:95: in __init__
    self.initialize()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = classy

    def initialize(self):
        """Importing CLASS from the correct path, if given, and if not, globally."""
        # Allow global import if no direct path specification
        allow_global = not self.path
        if not self.path and self.packages_path:
            self.path = self.get_path(self.packages_path)
        self.classy_module = self.is_installed(path=self.path, allow_global=allow_global,
                                               check=False)
        if not self.classy_module:
            raise NotInstalledError(
>               self.log, "Could not find CLASS. Check error message above.")
E           cobaya.install.NotInstalledError: Could not find CLASS. Check error message above.

../../.local/lib/python3.6/site-packages/cobaya/theories/classy/classy.py:186: NotInstalledError
--------------------------------------- Captured stdout call ----------------------------------------
 2022-03-01 15:37:41,379 [classy] Importing *global* CLASS.
 2022-03-01 15:37:41,381 [classy] *ERROR* Could not import global CLASS installation. Specify a Cobaya or CLASS installation path, or install the CLASS Python interface globally with 'cd /path/to/class/python/ ; python setup.py install'
 2022-03-01 15:37:41,381 [classy] *ERROR* Could not find CLASS. Check error message above.
----------------------------------------- Captured log call -----------------------------------------
INFO     classy:classy.py:545 Importing *global* CLASS.
ERROR    classy:classy.py:558 Could not import global CLASS installation. Specify a Cobaya or CLASS installation path, or install the CLASS Python interface globally with 'cd /path/to/class/python/ ; python setup.py install'
ERROR    classy:log.py:35 Could not find CLASS. Check error message above.
====================================== short test summary info ======================================
FAILED soliket/tests/test_lensing.py::test_lensing[classy] - cobaya.log.LoggedError: The installat...
FAILED soliket/tests/test_lensing_lite.py::test_lensing[classy] - cobaya.install.NotInstalledError...
'''

[mgerbino]

Ciao Emily, thanks! Is this happening on your own laptop/cluster or in the remote cluster used to run unit tests?

[emilymmoser]

Hi Martina, sorry for the delay I didn't see the notification- this was on my own laptop.

[itrharrison]

Looking at the above, this seems to be being generated by the cobaya install script when it tries to install classy.

I think you have probably two options:

• Update your gcc version, as it suggests (6.5 dates from 2018, so this seems reasonable) and if you can on your system
• Manually install classy yourself (by whatever means necessary... such as an older version, although that won't be ideal), following e.g. the instructions here

[emilymmoser]

I tried updating my gcc to version 11.2 and I run into the same error messages. After installing classy with pip these tests pass, so the issue appears to be that cobaya is not finding the correct version of gcc when trying to install classy