We spoke briefly at SC22 regarding a bug I encountered using e4s that "netcdf" was an UnknownPackage. I have since investigated further, and can confirm that there is no package in either my repo or spack.builtin which contains the text depends_on("netcdf or depends_on('netcdf` by grepping for the matching string.
I then searched for this in the spack cache indicies .json files and the only entries I found for this package were the ones from e4s. Removing these references as well as those to zeromq (also no longer in spack). as well as those packages with namespace olcf finally enabled me to build my packages using the e4s binary mirror.
I would appreciate if you or someone from your team could investigate further and purge these packages and namespaces not distributed with upstream spack.
I've attached a Dockerfile that reproduces this issue.
root@a28489caffc1:/app# spack --debug install libpressio
==> [2022-11-23-11:05:28.663631] Imported install from built-in commands
==> [2022-11-23-11:05:28.664453] Reading config from file /app/etc/spack/defaults/config.yaml
==> [2022-11-23-11:05:28.673422] Skipping nonexistent config path /app/etc/spack/defaults/linux/config.yaml
==> [2022-11-23-11:05:28.673456] Skipping nonexistent config path /etc/spack/config.yaml
==> [2022-11-23-11:05:28.673475] Skipping nonexistent config path /etc/spack/linux/config.yaml
==> [2022-11-23-11:05:28.673492] Skipping nonexistent config path /app/etc/spack/config.yaml
==> [2022-11-23-11:05:28.673507] Skipping nonexistent config path /app/etc/spack/linux/config.yaml
==> [2022-11-23-11:05:28.673523] Skipping nonexistent config path /root/.spack/config.yaml
==> [2022-11-23-11:05:28.673538] Skipping nonexistent config path /root/.spack/linux/config.yaml
==> [2022-11-23-11:05:28.673806] Imported install from built-in commands
==> [2022-11-23-11:05:28.674180] Reading config from file /app/etc/spack/defaults/bootstrap.yaml
==> [2022-11-23-11:05:28.677256] Skipping nonexistent config path /app/etc/spack/defaults/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.677288] Skipping nonexistent config path /etc/spack/bootstrap.yaml
==> [2022-11-23-11:05:28.677307] Skipping nonexistent config path /etc/spack/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.677323] Skipping nonexistent config path /app/etc/spack/bootstrap.yaml
==> [2022-11-23-11:05:28.677339] Skipping nonexistent config path /app/etc/spack/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.677360] Skipping nonexistent config path /root/.spack/bootstrap.yaml
==> [2022-11-23-11:05:28.677382] Skipping nonexistent config path /root/.spack/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.680656] Reading config from file /app/etc/spack/defaults/repos.yaml
==> [2022-11-23-11:05:28.681430] Skipping nonexistent config path /app/etc/spack/defaults/linux/repos.yaml
==> [2022-11-23-11:05:28.681460] Skipping nonexistent config path /etc/spack/repos.yaml
==> [2022-11-23-11:05:28.681478] Skipping nonexistent config path /etc/spack/linux/repos.yaml
==> [2022-11-23-11:05:28.681494] Skipping nonexistent config path /app/etc/spack/repos.yaml
==> [2022-11-23-11:05:28.681514] Skipping nonexistent config path /app/etc/spack/linux/repos.yaml
==> [2022-11-23-11:05:28.681542] Reading config from file /root/.spack/repos.yaml
==> [2022-11-23-11:05:28.681937] Skipping nonexistent config path /root/.spack/linux/repos.yaml
==> [2022-11-23-11:05:28.683041] Skipping nonexistent config path /app/etc/spack/defaults/upstreams.yaml
==> [2022-11-23-11:05:28.683069] Skipping nonexistent config path /app/etc/spack/defaults/linux/upstreams.yaml
==> [2022-11-23-11:05:28.683091] Skipping nonexistent config path /etc/spack/upstreams.yaml
==> [2022-11-23-11:05:28.683106] Skipping nonexistent config path /etc/spack/linux/upstreams.yaml
==> [2022-11-23-11:05:28.683121] Skipping nonexistent config path /app/etc/spack/upstreams.yaml
==> [2022-11-23-11:05:28.683136] Skipping nonexistent config path /app/etc/spack/linux/upstreams.yaml
==> [2022-11-23-11:05:28.683151] Skipping nonexistent config path /root/.spack/upstreams.yaml
==> [2022-11-23-11:05:28.683165] Skipping nonexistent config path /root/.spack/linux/upstreams.yaml
==> [2022-11-23-11:05:28.683460] Reading config from file /app/etc/spack/defaults/config.yaml
==> [2022-11-23-11:05:28.692187] Skipping nonexistent config path /app/etc/spack/defaults/linux/config.yaml
==> [2022-11-23-11:05:28.692226] Skipping nonexistent config path /etc/spack/config.yaml
==> [2022-11-23-11:05:28.692247] Skipping nonexistent config path /etc/spack/linux/config.yaml
==> [2022-11-23-11:05:28.692266] Skipping nonexistent config path /app/etc/spack/config.yaml
==> [2022-11-23-11:05:28.692288] Skipping nonexistent config path /app/etc/spack/linux/config.yaml
==> [2022-11-23-11:05:28.692310] Skipping nonexistent config path /root/.spack/config.yaml
==> [2022-11-23-11:05:28.692331] Skipping nonexistent config path /root/.spack/linux/config.yaml
==> [2022-11-23-11:05:28.692384] DATABASE LOCK TIMEOUT: 3s
==> [2022-11-23-11:05:28.692401] PACKAGE LOCK TIMEOUT: No timeout
==> [2022-11-23-11:05:28.693291] Reading config from file /app/etc/spack/defaults/bootstrap.yaml
==> [2022-11-23-11:05:28.695978] Skipping nonexistent config path /app/etc/spack/defaults/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.696009] Skipping nonexistent config path /etc/spack/bootstrap.yaml
==> [2022-11-23-11:05:28.696029] Skipping nonexistent config path /etc/spack/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.696045] Skipping nonexistent config path /app/etc/spack/bootstrap.yaml
==> [2022-11-23-11:05:28.696063] Skipping nonexistent config path /app/etc/spack/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.696086] Skipping nonexistent config path /root/.spack/bootstrap.yaml
==> [2022-11-23-11:05:28.696107] Skipping nonexistent config path /root/.spack/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.696823] DATABASE LOCK TIMEOUT: 3s
==> [2022-11-23-11:05:28.696841] PACKAGE LOCK TIMEOUT: No timeout
==> [2022-11-23-11:05:28.696877] [BOOTSTRAP CONFIG SCOPE] name=_builtin
==> [2022-11-23-11:05:28.697675] [BOOTSTRAP CONFIG SCOPE] name=defaults, path=/app/etc/spack/defaults
==> [2022-11-23-11:05:28.697694] [BOOTSTRAP CONFIG SCOPE] name=defaults/linux, path=/app/etc/spack/defaults/linux
==> [2022-11-23-11:05:28.697712] [BOOTSTRAP CONFIG SCOPE] name=bootstrap, path=/root/.spack/bootstrap/config
==> [2022-11-23-11:05:28.697729] [BOOTSTRAP CONFIG SCOPE] name=bootstrap/linux, path=/root/.spack/bootstrap/config/linux
==> [2022-11-23-11:05:28.697878] Skipping nonexistent config path /app/etc/spack/defaults/compilers.yaml
==> [2022-11-23-11:05:28.697901] Skipping nonexistent config path /app/etc/spack/defaults/linux/compilers.yaml
==> [2022-11-23-11:05:28.697925] Skipping nonexistent config path /root/.spack/bootstrap/config/compilers.yaml
==> [2022-11-23-11:05:28.697971] Reading config from file /root/.spack/bootstrap/config/linux/compilers.yaml
==> [2022-11-23-11:05:28.711576] [BOOTSTRAP ROOT SPEC] clingo-bootstrap@spack+python %gcc target=x86_64
==> [2022-11-23-11:05:28.711608] [BOOTSTRAP MODULE clingo] Try importing from Python
==> [2022-11-23-11:05:28.711750] Reading config from file /app/etc/spack/defaults/bootstrap.yaml
==> [2022-11-23-11:05:28.714621] Skipping nonexistent config path /app/etc/spack/defaults/linux/bootstrap.yaml
==> [2022-11-23-11:05:28.714670] Skipping nonexistent config path /root/.spack/bootstrap/config/bootstrap.yaml
==> [2022-11-23-11:05:28.751943] Reading config from file /app/etc/spack/defaults/config.yaml
==> [2022-11-23-11:05:28.760582] Skipping nonexistent config path /app/etc/spack/defaults/linux/config.yaml
==> [2022-11-23-11:05:28.760625] Skipping nonexistent config path /root/.spack/bootstrap/config/config.yaml
==> [2022-11-23-11:05:28.825166] Reading config from file /app/etc/spack/defaults/packages.yaml
==> [2022-11-23-11:05:28.838399] Skipping nonexistent config path /app/etc/spack/defaults/linux/packages.yaml
==> [2022-11-23-11:05:28.838441] Skipping nonexistent config path /root/.spack/bootstrap/config/packages.yaml
==> [2022-11-23-11:05:28.838461] Skipping nonexistent config path /root/.spack/bootstrap/config/linux/packages.yaml
==> [2022-11-23-11:05:28.873536] [BOOTSTRAP MODULE clingo] The installed spec "clingo-bootstrap@spack+python %gcc target=x86_64 ^[email protected]/ba5ijauisd3uuixtmactc36vps7yfsrl" provides the "clingo" Python module
==> [2022-11-23-11:05:28.873790] Reading config from file /app/etc/spack/defaults/concretizer.yaml
==> [2022-11-23-11:05:28.875929] Skipping nonexistent config path /app/etc/spack/defaults/linux/concretizer.yaml
==> [2022-11-23-11:05:28.875962] Skipping nonexistent config path /etc/spack/concretizer.yaml
==> [2022-11-23-11:05:28.875981] Skipping nonexistent config path /etc/spack/linux/concretizer.yaml
==> [2022-11-23-11:05:28.875997] Skipping nonexistent config path /app/etc/spack/concretizer.yaml
==> [2022-11-23-11:05:28.876011] Skipping nonexistent config path /app/etc/spack/linux/concretizer.yaml
==> [2022-11-23-11:05:28.876026] Skipping nonexistent config path /root/.spack/concretizer.yaml
==> [2022-11-23-11:05:28.876040] Skipping nonexistent config path /root/.spack/linux/concretizer.yaml
==> [2022-11-23-11:05:28.876095] Reading config from file /app/etc/spack/defaults/repos.yaml
==> [2022-11-23-11:05:28.876888] Skipping nonexistent config path /app/etc/spack/defaults/linux/repos.yaml
==> [2022-11-23-11:05:28.876917] Skipping nonexistent config path /etc/spack/repos.yaml
==> [2022-11-23-11:05:28.876942] Skipping nonexistent config path /etc/spack/linux/repos.yaml
==> [2022-11-23-11:05:28.876964] Skipping nonexistent config path /app/etc/spack/repos.yaml
==> [2022-11-23-11:05:28.876986] Skipping nonexistent config path /app/etc/spack/linux/repos.yaml
==> [2022-11-23-11:05:28.877013] Reading config from file /root/.spack/repos.yaml
==> [2022-11-23-11:05:28.877402] Skipping nonexistent config path /root/.spack/linux/repos.yaml
==> [2022-11-23-11:05:28.901018] Reading config from file /app/etc/spack/defaults/config.yaml
==> [2022-11-23-11:05:28.909504] Skipping nonexistent config path /app/etc/spack/defaults/linux/config.yaml
==> [2022-11-23-11:05:28.909539] Skipping nonexistent config path /etc/spack/config.yaml
==> [2022-11-23-11:05:28.909557] Skipping nonexistent config path /etc/spack/linux/config.yaml
==> [2022-11-23-11:05:28.909572] Skipping nonexistent config path /app/etc/spack/config.yaml
==> [2022-11-23-11:05:28.909586] Skipping nonexistent config path /app/etc/spack/linux/config.yaml
==> [2022-11-23-11:05:28.909601] Skipping nonexistent config path /root/.spack/config.yaml
==> [2022-11-23-11:05:28.909615] Skipping nonexistent config path /root/.spack/linux/config.yaml
==> [2022-11-23-11:05:28.930415] Reading config from file /app/etc/spack/defaults/packages.yaml
==> [2022-11-23-11:05:28.943868] Skipping nonexistent config path /app/etc/spack/defaults/linux/packages.yaml
==> [2022-11-23-11:05:28.943906] Skipping nonexistent config path /etc/spack/packages.yaml
==> [2022-11-23-11:05:28.943925] Skipping nonexistent config path /etc/spack/linux/packages.yaml
==> [2022-11-23-11:05:28.943941] Skipping nonexistent config path /app/etc/spack/packages.yaml
==> [2022-11-23-11:05:28.943955] Skipping nonexistent config path /app/etc/spack/linux/packages.yaml
==> [2022-11-23-11:05:28.943970] Skipping nonexistent config path /root/.spack/packages.yaml
==> [2022-11-23-11:05:28.943984] Skipping nonexistent config path /root/.spack/linux/packages.yaml
==> [2022-11-23-11:05:28.945589] Reading config from file /app/etc/spack/defaults/mirrors.yaml
==> [2022-11-23-11:05:28.946156] Skipping nonexistent config path /app/etc/spack/defaults/linux/mirrors.yaml
==> [2022-11-23-11:05:28.946184] Skipping nonexistent config path /etc/spack/mirrors.yaml
==> [2022-11-23-11:05:28.946203] Skipping nonexistent config path /etc/spack/linux/mirrors.yaml
==> [2022-11-23-11:05:28.946218] Skipping nonexistent config path /app/etc/spack/mirrors.yaml
==> [2022-11-23-11:05:28.946233] Skipping nonexistent config path /app/etc/spack/linux/mirrors.yaml
==> [2022-11-23-11:05:28.946252] Reading config from file /root/.spack/mirrors.yaml
==> [2022-11-23-11:05:28.948626] Skipping nonexistent config path /root/.spack/linux/mirrors.yaml
==> [2022-11-23-11:05:28.948963] Checking existence of https://cache.e4s.io/build_cache/index.json
==> [2022-11-23-11:05:29.819905] Cached index for https://cache.e4s.io already up to date
==> [2022-11-23-11:05:29.820586] Checking existence of https://mirror.spack.io/build_cache/index.json
==> [2022-11-23-11:05:30.037778] Failure reading URL: Download failed: HTTP Error 404: Not Found
==> [2022-11-23-11:05:30.040313] DATABASE LOCK TIMEOUT: 3s
==> [2022-11-23-11:05:30.040418] PACKAGE LOCK TIMEOUT: No timeout
==> [2022-11-23-11:05:44.764705] Skipping nonexistent config path /app/etc/spack/defaults/compilers.yaml
==> [2022-11-23-11:05:44.764754] Skipping nonexistent config path /app/etc/spack/defaults/linux/compilers.yaml
==> [2022-11-23-11:05:44.764779] Skipping nonexistent config path /etc/spack/compilers.yaml
==> [2022-11-23-11:05:44.764799] Skipping nonexistent config path /etc/spack/linux/compilers.yaml
==> [2022-11-23-11:05:44.764821] Skipping nonexistent config path /app/etc/spack/compilers.yaml
==> [2022-11-23-11:05:44.764840] Skipping nonexistent config path /app/etc/spack/linux/compilers.yaml
==> [2022-11-23-11:05:44.764860] Skipping nonexistent config path /root/.spack/compilers.yaml
==> [2022-11-23-11:05:44.764887] Reading config from file /root/.spack/linux/compilers.yaml
==> [2022-11-23-11:05:58.698251] UnknownPackageError: Package '[email protected]%[email protected]~dap~hdf4+mpi~parallel-netcdf+pic+shared maxdims=1024 maxvars=8192 arch=linux-centos8-x86_64 ^[email protected]%[email protected]~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe patches=b61e2f0 arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]~python arch=linux-centos8-x86_64 ^[email protected]%[email protected]+hydra+pci+romio~slurm~verbs~wrapperrpath device=ch3 netmod=tcp pmi=pmi arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos8-x86_64' not found.
You may need to run 'spack clean -m'.
==> [2022-11-23-11:05:58.698360] UnknownPackageError: Package '[email protected]%[email protected]~dap~hdf4+mpi~parallel-netcdf+pic+shared maxdims=1024 maxvars=8192 arch=linux-centos8-x86_64 ^[email protected]%[email protected]~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe patches=b61e2f0 arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]~python arch=linux-centos8-x86_64 ^[email protected]%[email protected]+hydra+pci+romio~slurm~verbs~wrapperrpath device=ch3 netmod=tcp pmi=pmi arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos8-x86_64' not found.
You may need to run 'spack clean -m'.
==> [2022-11-23-11:05:58.698387] Error: Package '[email protected]%[email protected]~dap~hdf4+mpi~parallel-netcdf+pic+shared maxdims=1024 maxvars=8192 arch=linux-centos8-x86_64 ^[email protected]%[email protected]~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe patches=b61e2f0 arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]~python arch=linux-centos8-x86_64 ^[email protected]%[email protected]+hydra+pci+romio~slurm~verbs~wrapperrpath device=ch3 netmod=tcp pmi=pmi arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos8-x86_64' not found.
You may need to run 'spack clean -m'.
Traceback (most recent call last):
File "/app/lib/spack/spack/repo.py", line 1232, in get_pkg_class
module = importlib.import_module(fullname)
File "/usr/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 973, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'spack.pkg.builtin.netcdf'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/spack/spack/repo.py", line 1043, in get
package_class = self.get_pkg_class(spec.name)
File "/app/lib/spack/spack/repo.py", line 1234, in get_pkg_class
raise UnknownPackageError(pkg_name)
spack.repo.UnknownPackageError: Package 'netcdf' not found.
You may need to run 'spack clean -m'.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/spack/spack/main.py", line 1000, in main
return _main(argv)
File "/app/lib/spack/spack/main.py", line 955, in _main
return finish_parse_and_run(parser, cmd_name, env_format_error)
File "/app/lib/spack/spack/main.py", line 983, in finish_parse_and_run
return _invoke_command(command, parser, args, unknown)
File "/app/lib/spack/spack/main.py", line 632, in _invoke_command
return_val = command(parser, args)
File "/app/lib/spack/spack/cmd/install.py", line 531, in install
abstract_specs, concrete_specs = specs_from_cli(args, install_kwargs, reporter)
File "/app/lib/spack/spack/cmd/install.py", line 447, in specs_from_cli
concrete_specs = spack.cmd.parse_specs(
File "/app/lib/spack/spack/cmd/__init__.py", line 227, in parse_specs
spec.concretize(tests=tests) # implies normalize
File "/app/lib/spack/spack/spec.py", line 2978, in concretize
self._new_concretize(tests)
File "/app/lib/spack/spack/spec.py", line 2953, in _new_concretize
result = solver.solve([self], tests=tests)
File "/app/lib/spack/spack/solver/asp.py", line 2435, in solve
result, _, _ = self.driver.solve(setup, specs, reuse=reusable_specs, output=output)
File "/app/lib/spack/spack/solver/asp.py", line 625, in solve
setup.setup(self, specs, reuse=reuse)
File "/app/lib/spack/spack/solver/asp.py", line 1989, in setup
self._facts_from_concrete_spec(reusable_spec, possible)
File "/app/lib/spack/spack/solver/asp.py", line 1897, in _facts_from_concrete_spec
self.impose(h, spec, body=True)
File "/app/lib/spack/spack/solver/asp.py", line 1090, in impose
imposed_constraints = self.spec_clauses(imposed_spec, body=body, required_from=name)
File "/app/lib/spack/spack/solver/asp.py", line 1313, in spec_clauses
clauses = self._spec_clauses(*args, **kwargs)
File "/app/lib/spack/spack/solver/asp.py", line 1478, in _spec_clauses
for virtual in dep.package.virtuals_provided:
File "/app/lib/spack/spack/spec.py", line 1638, in package
self._package = spack.repo.path.get(self)
File "/app/lib/spack/spack/repo.py", line 849, in get
return self.repo_for_pkg(spec).get(spec)
File "/app/lib/spack/spack/repo.py", line 1045, in get
raise UnknownPackageError(str(spec))
spack.repo.UnknownPackageError: Package '[email protected]%[email protected]~dap~hdf4+mpi~parallel-netcdf+pic+shared maxdims=1024 maxvars=8192 arch=linux-centos8-x86_64 ^[email protected]%[email protected]~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe patches=b61e2f0 arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]~python arch=linux-centos8-x86_64 ^[email protected]%[email protected]+hydra+pci+romio~slurm~verbs~wrapperrpath device=ch3 netmod=tcp pmi=pmi arch=linux-centos8-x86_64 ^[email protected]%[email protected] arch=linux-centos8-x86_64 ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos8-x86_64' not found.
You may need to run 'spack clean -m'.
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