An error appeared when I tried to install the recommended compiler using command "spack ${scope_args} install gcc"

[DefeatAI]

Your name

Yibo Zhao

Your affiliation

University of Minnesota

What happened? What did you expect to happen?

The following error appeared when I tried to install the recommended compiler using command "spack ${scope_args} install gcc"

(base) zpan@acl62 [~/AerosolRecovery] % spack ${scope_args} install gcc
==> Error: GCClassic/spack/packages.yaml:27: Additional properties are not allowed ('compiler' was unexpected)

Then I tried to delete the lines including "compiler: [[email protected]]" contained in the "packages.yaml"

It seemed to work, but then another error appeared as below,

"==> Installing re2c-3.0-n6fkyitoujjxfoyoanwoxxtbglws6al5 [8/9]
==> No binary for re2c-3.0-n6fkyitoujjxfoyoanwoxxtbglws6al5 found: installing from source
==> Error: FetchError: All fetchers failed for spack-stage-re2c-3.0-n6fkyitoujjxfoyoanwoxxtbglws6al5
        https://mirror.spack.io/_source-cache/archive/b3/b3babbbb1461e13fe22c630a40c43885efcfbbbb585830c6f4c0d791cf82ba0b.tar.xz: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
    https://github.com/skvadrik/re2c/releases/download/3.0/re2c-3.0.tar.xz: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
==> Warning: Skipping build of clingo-bootstrap-spack-zdraelqnmaiebssvxme3ls6bxnkx4fuw since re2c-3.0-n6fkyitoujjxfoyoanwoxxtbglws6al5 failed
==> Error: cannot bootstrap the "clingo" Python module from spec "clingo-bootstrap@spack+python %gcc platform=linux target=x86_64" due to the following failures:
github-actions-v0.6 raised FetchCacheError: FetchIndexError: Could not fetch manifest from https://ghcr.io/v2/spack/bootstrap-buildcache-v1/manifests/index.spack, due to: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
github-actions-v0.5 raised RuntimeError: The binary index is empty
spack-install raised InstallError: Terminating after first install failure: FetchError: All fetchers failed for spack-stage-re2c-3.0-n6fkyitoujjxfoyoanwoxxtbglws6al5
        https://mirror.spack.io/_source-cache/archive/b3/b3babbbb1461e13fe22c630a40c43885efcfbbbb585830c6f4c0d791cf82ba0b.tar.xz: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
    https://github.com/skvadrik/re2c/releases/download/3.0/re2c-3.0.tar.xz: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
Run `spack --debug ...` for more detailed errors

I'm currently having trouble with installing the environment files necessary to start the simulation. Would you be able to assist me with resolving this issue?

Thank you very much for your help!

What are the steps to reproduce the bug?

model=GCClassic               # Use this if you will be working with GEOS-Chem Classic
model=GCHP                    # Use this if you will be working with GCHP
model=HEMCO                   # Use this if you will be working with HEMCO standalone

scope_dir="${model}/spack"    # Folder where customized YAML files are stored

scope_args="-C ${scope_dir}"  # Tell spack to for custom YAML files in scope_dir

git clone --recurse-submodules https://github.com/geoschem/${model}.git

spack ${scope_args} install gcc     # Install GNU Compiler Collection

Please attach any relevant configuration and log files.

No response

What GEOS-Chem version were you using?

newest

What environment were you running GEOS-Chem on?

Local cluster

What compiler and version were you using?

xx

Will you be addressing this bug yourself?

Yes, but I will need some help

In what configuration were you running GEOS-Chem?

GCClassic

What simulation were you running?

Aerosol

As what resolution were you running GEOS-Chem?

4x5

What meterology fields did you use?

MERRA-2

Additional information

No response

[yantosca]

Thanks for writing @DefeatAI and thanks for your patience.

It looks like the issue may have been an expired certificate at the source website.

==> Error: FetchError: All fetchers failed for spack-stage-re2c-3.0-n6fkyitoujjxfoyoanwoxxtbglws6al5
        https://mirror.spack.io/_source-cache/archive/b3/b3babbbb1461e13fe22c630a40c43885efcfbbbb585830c6f4c0d791cf82ba0b.tar.xz: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
    https://github.com/skvadrik/re2c/releases/download/3.0/re2c-3.0.tar.xz: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>

I would try issuing the same spack commands again just to make sure that the issue still persists. If it does, please open an issue on the Spack issue tracker (https://github.com/spack/spack/issues). Fixing this type of issue lies outside of the purview of the GCST.