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Add command for reading JSON-based DB description (now with more tests) (#29652)

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This is an amended version of https://github.com/spack/spack/pull/24894 (reverted in https://github.com/spack/spack/pull/29603). https://github.com/spack/spack/pull/24894
broke all instances of `spack external find` (namely when it is invoked without arguments/options)
because it was mandating the presence of a file which most systems would not have.
This allows `spack external find` to proceed if that file is not present and adds tests for this.

- [x] Add a test which confirms that `spack external find` successfully reads a manifest file
      if present in the default manifest path

--- Original commit message ---

Adds `spack external read-cray-manifest`, which reads a json file that describes a
set of package DAGs. The parsed results are stored directly in the database. A user
can see these installed specs with `spack find` (like any installed spec). The easiest
way to use them right now as dependencies is to run
`spack spec ... ^/hash-of-external-package`.

Changes include:

* `spack external read-cray-manifest --file <path/to/file>` will add all specs described
  in the file to Spack's installation DB and will also install described compilers to the
  compilers configuration (the expected format of the file is described in this PR as well including examples of the file)
* Database records now may include an "origin" (the command added in this PR
  registers the origin as "external-db"). In the future, it is assumed users may want
  to be able to treat installs registered with this command differently (e.g. they may
  want to uninstall all specs added with this command)
* Hash properties are now always preserved when copying specs if the source spec
  is concrete
  * I don't think the hashes of installed-and-concrete specs should change and this
    was the easiest way to handle that
  * also specs that are concrete preserve their `.normal` property when copied
    (external specs may mention compilers that are not registered, and without this
    change they would fail in `normalize` when calling `validate_or_raise`)
  * it might be this should only be the case if the spec was installed

- [x] Improve testing
- [x] Specifically mark DB records added with this command (so that users can do
      something like "uninstall all packages added with `spack read-external-db`)
  * This is now possible with `spack uninstall --all --origin=external-db` (this will
    remove all specs added from manifest files)
- [x] Strip variants that are listed in json entries but don't actually exist for the package
This commit is contained in:
Peter Scheibel 2022-04-28 10:56:26 -07:00 committed by GitHub
parent 6a9df34abd
commit bb43308c44
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
18 changed files with 811 additions and 55 deletions
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91
lib/spack/spack/cmd/external.py
View file

@ -5,6 +5,7 @@
from __future__ import print_function
import argparse
import os
import sys
import llnl.util.tty as tty
@ -13,6 +14,7 @@
import spack
import spack.cmd
import spack.cmd.common.arguments
import spack.cray_manifest as cray_manifest
import spack.detection
import spack.error
import spack.util.environment
@ -55,8 +57,40 @@ def setup_parser(subparser):
'list', help='list detectable packages, by repository and name'
)
read_cray_manifest = sp.add_parser(
'read-cray-manifest', help=(
"consume a Spack-compatible description of externally-installed "
"packages, including dependency relationships"
)
)
read_cray_manifest.add_argument(
'--file', default=None,
help="specify a location other than the default")
read_cray_manifest.add_argument(
'--directory', default=None,
help="specify a directory storing a group of manifest files")
read_cray_manifest.add_argument(
'--dry-run', action='store_true', default=False,
help="don't modify DB with files that are read")
read_cray_manifest.add_argument(
'--fail-on-error', action='store_true',
help=("if a manifest file cannot be parsed, fail and report the "
"full stack trace")
)
def external_find(args):
if args.all or not (args.tags or args.packages):
# If the user calls 'spack external find' with no arguments, and
# this system has a description of installed packages, then we should
# consume it automatically.
try:
_collect_and_consume_cray_manifest_files()
except NoManifestFileError:
# It's fine to not find any manifest file if we are doing the
# search implicitly (i.e. as part of 'spack external find')
pass
# If the user didn't specify anything, search for build tools by default
if not args.tags and not args.all and not args.packages:
args.tags = ['core-packages', 'build-tools']
@ -106,6 +140,56 @@ def external_find(args):
tty.msg('No new external packages detected')
def external_read_cray_manifest(args):
_collect_and_consume_cray_manifest_files(
manifest_file=args.file,
manifest_directory=args.directory,
dry_run=args.dry_run,
fail_on_error=args.fail_on_error
)
def _collect_and_consume_cray_manifest_files(
manifest_file=None, manifest_directory=None, dry_run=False,
fail_on_error=False):
manifest_files = []
if manifest_file:
manifest_files.append(manifest_file)
manifest_dirs = []
if manifest_directory:
manifest_dirs.append(manifest_directory)
if os.path.isdir(cray_manifest.default_path):
tty.debug(
"Cray manifest path {0} exists: collecting all files to read."
.format(cray_manifest.default_path))
manifest_dirs.append(cray_manifest.default_path)
else:
tty.debug("Default Cray manifest directory {0} does not exist."
.format(cray_manifest.default_path))
for directory in manifest_dirs:
for fname in os.listdir(directory):
manifest_files.append(os.path.join(directory, fname))
if not manifest_files:
raise NoManifestFileError(
"--file/--directory not specified, and no manifest found at {0}"
.format(cray_manifest.default_path))
for path in manifest_files:
try:
cray_manifest.read(path, not dry_run)
except (spack.compilers.UnknownCompilerError, spack.error.SpackError) as e:
if fail_on_error:
raise
else:
tty.warn("Failure reading manifest file: {0}"
"\n\t{1}".format(path, str(e)))
def external_list(args):
# Trigger a read of all packages, might take a long time.
list(spack.repo.path.all_packages())
@ -117,5 +201,10 @@ def external_list(args):
def external(parser, args):
action = {'find': external_find, 'list': external_list}
action = {'find': external_find, 'list': external_list,
'read-cray-manifest': external_read_cray_manifest}
action[args.external_command](args)
class NoManifestFileError(spack.error.SpackError):
pass

14
lib/spack/spack/cmd/uninstall.py
View file

@ -62,9 +62,14 @@ def setup_parser(subparser):
'-a', '--all', action='store_true', dest='all',
help="remove ALL installed packages that match each supplied spec"
)
subparser.add_argument(
'--origin', dest='origin',
help="only remove DB records with the specified origin"
)
def find_matching_specs(env, specs, allow_multiple_matches=False, force=False):
def find_matching_specs(env, specs, allow_multiple_matches=False, force=False,
origin=None):
"""Returns a list of specs matching the not necessarily
concretized specs given from cli
@ -85,8 +90,8 @@ def find_matching_specs(env, specs, allow_multiple_matches=False, force=False):
has_errors = False
for spec in specs:
install_query = [InstallStatuses.INSTALLED, InstallStatuses.DEPRECATED]
matching = spack.store.db.query_local(spec, hashes=hashes,
installed=install_query)
matching = spack.store.db.query_local(
spec, hashes=hashes, installed=install_query, origin=origin)
# For each spec provided, make sure it refers to only one package.
# Fail and ask user to be unambiguous if it doesn't
if not allow_multiple_matches and len(matching) > 1:
@ -240,7 +245,8 @@ def do_uninstall(env, specs, force):
def get_uninstall_list(args, specs, env):
# Gets the list of installed specs that match the ones give via cli
# args.all takes care of the case where '-a' is given in the cli
uninstall_list = find_matching_specs(env, specs, args.all, args.force)
uninstall_list = find_matching_specs(env, specs, args.all, args.force,
args.origin)
# Takes care of '-R'
active_dpts, inactive_dpts = installed_dependents(uninstall_list, env)

10
lib/spack/spack/compilers/__init__.py
View file

@ -495,7 +495,8 @@ def get_compiler_duplicates(compiler_spec, arch_spec):
@llnl.util.lang.memoized
def class_for_compiler_name(compiler_name):
"""Given a compiler module name, get the corresponding Compiler class."""
assert supported(compiler_name)
if not supported(compiler_name):
raise UnknownCompilerError(compiler_name)
# Hack to be able to call the compiler `apple-clang` while still
# using a valid python name for the module
@ -788,6 +789,13 @@ def __init__(self):
"Spack could not find any compilers!")
class UnknownCompilerError(spack.error.SpackError):
def __init__(self, compiler_name):
super(UnknownCompilerError, self).__init__(
"Spack doesn't support the requested compiler: {0}"
.format(compiler_name))
class NoCompilerForSpecError(spack.error.SpackError):
def __init__(self, compiler_spec, target):
super(NoCompilerForSpecError, self).__init__(

165
lib/spack/spack/cray_manifest.py Normal file
View file

@ -0,0 +1,165 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import json
import jsonschema
import six
import llnl.util.tty as tty
import spack.cmd
import spack.hash_types as hash_types
from spack.schema.cray_manifest import schema as manifest_schema
#: Cray systems can store a Spack-compatible description of system
#: packages here.
default_path = '/opt/cray/pe/cpe-descriptive-manifest/'
def compiler_from_entry(entry):
compiler_name = entry['name']
paths = entry['executables']
version = entry['version']
arch = entry['arch']
operating_system = arch['os']
target = arch['target']
compiler_cls = spack.compilers.class_for_compiler_name(compiler_name)
spec = spack.spec.CompilerSpec(compiler_cls.name, version)
paths = [paths.get(x, None) for x in ('cc', 'cxx', 'f77', 'fc')]
return compiler_cls(
spec, operating_system, target, paths
)
def spec_from_entry(entry):
arch_str = ""
if 'arch' in entry:
arch_format = "arch={platform}-{os}-{target}"
arch_str = arch_format.format(
platform=entry['arch']['platform'],
os=entry['arch']['platform_os'],
target=entry['arch']['target']['name']
)
compiler_str = ""
if 'compiler' in entry:
compiler_format = "%{name}@{version}"
compiler_str = compiler_format.format(
name=entry['compiler']['name'],
version=entry['compiler']['version']
)
spec_format = "{name}@{version} {compiler} {arch}"
spec_str = spec_format.format(
name=entry['name'],
version=entry['version'],
compiler=compiler_str,
arch=arch_str
)
package = spack.repo.get(entry['name'])
if 'parameters' in entry:
variant_strs = list()
for name, value in entry['parameters'].items():
# TODO: also ensure that the variant value is valid?
if not (name in package.variants):
tty.debug("Omitting variant {0} for entry {1}/{2}"
.format(name, entry['name'], entry['hash'][:7]))
continue
# Value could be a list (of strings), boolean, or string
if isinstance(value, six.string_types):
variant_strs.append('{0}={1}'.format(name, value))
else:
try:
iter(value)
variant_strs.append(
'{0}={1}'.format(name, ','.join(value)))
continue
except TypeError:
# Not an iterable
pass
# At this point not a string or collection, check for boolean
if value in [True, False]:
bool_symbol = '+' if value else '~'
variant_strs.append('{0}{1}'.format(bool_symbol, name))
else:
raise ValueError(
"Unexpected value for {0} ({1}): {2}".format(
name, str(type(value)), str(value)
)
)
spec_str += ' ' + ' '.join(variant_strs)
spec, = spack.cmd.parse_specs(spec_str.split())
for ht in [hash_types.dag_hash, hash_types.build_hash,
hash_types.full_hash]:
setattr(spec, ht.attr, entry['hash'])
spec._concrete = True
spec._hashes_final = True
spec.external_path = entry['prefix']
spec.origin = 'external-db'
spack.spec.Spec.ensure_valid_variants(spec)
return spec
def entries_to_specs(entries):
spec_dict = {}
for entry in entries:
try:
spec = spec_from_entry(entry)
spec_dict[spec._hash] = spec
except spack.repo.UnknownPackageError:
tty.debug("Omitting package {0}: no corresponding repo package"
.format(entry['name']))
except spack.error.SpackError:
raise
except Exception:
tty.warn("Could not parse entry: " + str(entry))
for entry in filter(lambda x: 'dependencies' in x, entries):
dependencies = entry['dependencies']
for name, properties in dependencies.items():
dep_hash = properties['hash']
deptypes = properties['type']
if dep_hash in spec_dict:
if entry['hash'] not in spec_dict:
continue
parent_spec = spec_dict[entry['hash']]
dep_spec = spec_dict[dep_hash]
parent_spec._add_dependency(dep_spec, deptypes)
return spec_dict
def read(path, apply_updates):
with open(path, 'r') as json_file:
json_data = json.load(json_file)
jsonschema.validate(json_data, manifest_schema)
specs = entries_to_specs(json_data['specs'])
tty.debug("{0}: {1} specs read from manifest".format(
path,
str(len(specs))))
compilers = list()
if 'compilers' in json_data:
compilers.extend(compiler_from_entry(x)
for x in json_data['compilers'])
tty.debug("{0}: {1} compilers read from manifest".format(
path,
str(len(compilers))))
if apply_updates and compilers:
spack.compilers.add_compilers_to_config(
compilers, init_config=False)
if apply_updates:
for spec in specs.values():
spack.store.db.add(spec, directory_layout=None)

13
lib/spack/spack/database.py
View file

@ -187,6 +187,7 @@ def __init__(
installation_time=None,
deprecated_for=None,
in_buildcache=False,
origin=None
):
self.spec = spec
self.path = str(path) if path else None
@ -196,6 +197,7 @@ def __init__(
self.installation_time = installation_time or _now()
self.deprecated_for = deprecated_for
self.in_buildcache = in_buildcache
self.origin = origin
def install_type_matches(self, installed):
installed = InstallStatuses.canonicalize(installed)
@ -217,6 +219,9 @@ def to_dict(self, include_fields=default_install_record_fields):
else:
rec_dict.update({field_name: getattr(self, field_name)})
if self.origin:
rec_dict['origin'] = self.origin
return rec_dict
@classmethod
@ -1131,6 +1136,10 @@ def _add(
'explicit': explicit,
'installation_time': installation_time
}
# Commands other than 'spack install' may add specs to the DB,
# we can record the source of an installed Spec with 'origin'
if hasattr(spec, 'origin'):
extra_args['origin'] = spec.origin
self._data[key] = InstallRecord(
new_spec, path, installed, ref_count=0, **extra_args
)
@ -1462,6 +1471,7 @@ def _query(
end_date=None,
hashes=None,
in_buildcache=any,
origin=None
):
"""Run a query on the database."""
@ -1490,6 +1500,9 @@ def _query(
if hashes is not None and rec.spec.dag_hash() not in hashes:
continue
if origin and not (origin == rec.origin):
continue
if not rec.install_type_matches(installed):
continue

8
lib/spack/spack/rewiring.py
View file

@ -95,7 +95,8 @@ def rewire_node(spec, explicit):
spec.prefix)
relocate.relocate_text_bin(binaries=bins_to_relocate,
prefixes=prefix_to_prefix)
# copy package into place (shutil.copytree)
# Copy package into place, except for spec.json (because spec.json
# describes the old spec and not the new spliced spec).
shutil.copytree(os.path.join(tempdir, spec.dag_hash()), spec.prefix,
ignore=shutil.ignore_patterns('spec.json',
'install_manifest.json'))
@ -104,7 +105,10 @@ def rewire_node(spec, explicit):
spec.build_spec.prefix,
spec.prefix)
shutil.rmtree(tempdir)
# handle all metadata changes; don't copy over spec.json file in .spack/
# Above, we did not copy spec.json: instead, here we write the new
# (spliced) spec into spec.json, without this, Database.add would fail on
# the next line (because it checks the spec.json in the prefix against the
# spec being added to look for mismatches)
spack.store.layout.write_spec(spec, spack.store.layout.spec_file_path(spec))
# add to database, not sure about explicit
spack.store.db.add(spec, spack.store.layout, explicit=explicit)

131
lib/spack/spack/schema/cray_manifest.py Normal file
View file

@ -0,0 +1,131 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
"""Schema for Cray descriptive manifest: this describes a set of
installed packages on the system and also specifies dependency
relationships between them (so this provides more information than
external entries in packages configuration).
This does not specify a configuration - it is an input format
that is consumed and transformed into Spack DB records.
"""
schema = {
"$schema": "http://json-schema.org/schema#",
"title": "CPE manifest schema",
"type": "object",
"additionalProperties": False,
"properties": {
"_meta": {
"type": "object",
"additionalProperties": False,
"properties": {
"file-type": {"type": "string", "minLength": 1},
"cpe-version": {"type": "string", "minLength": 1},
"system-type": {"type": "string", "minLength": 1},
"schema-version": {"type": "string", "minLength": 1},
}
},
"compilers": {
"type": "array",
"items": {
"type": "object",
"additionalProperties": False,
"properties": {
"name": {"type": "string", "minLength": 1},
"version": {"type": "string", "minLength": 1},
"prefix": {"type": "string", "minLength": 1},
"executables": {
"type": "object",
"additionalProperties": False,
"properties": {
"cc": {"type": "string", "minLength": 1},
"cxx": {"type": "string", "minLength": 1},
"fc": {"type": "string", "minLength": 1}
}
},
"arch": {
"type": "object",
"required": ["os", "target"],
"additionalProperties": False,
"properties": {
"os": {"type": "string", "minLength": 1},
"target": {"type": "string", "minLength": 1}
}
}
}
}
},
"specs": {
"type": "array",
"items": {
"type": "object",
"required": [
"name",
"version",
"arch",
"compiler",
"prefix",
"hash"],
"additionalProperties": False,
"properties": {
"name": {"type": "string", "minLength": 1},
"version": {"type": "string", "minLength": 1},
"arch": {
"type": "object",
"required": ["platform", "platform_os", "target"],
"additioanlProperties": False,
"properties": {
"platform": {"type": "string", "minLength": 1},
"platform_os": {"type": "string", "minLength": 1},
"target": {
"type": "object",
"additionalProperties": False,
"required": ["name"],
"properties": {
"name": {"type": "string", "minLength": 1}
}
}
}
},
"compiler": {
"type": "object",
"required": ["name", "version"],
"additionalProperties": False,
"properties": {
"name": {"type": "string", "minLength": 1},
"version": {"type": "string", "minLength": 1}
}
},
"dependencies": {
"type": "object",
"patternProperties": {
"\\w[\\w-]*": {
"type": "object",
"required": ["hash"],
"additionalProperties": False,
"properties": {
"hash": {"type": "string", "minLength": 1},
"type": {
"type": "array",
"items": {
"type": "string", "minLength": 1}
}
}
}
}
},
"prefix": {
"type": "string", "minLength": 1},
"rpm": {"type": "string", "minLength": 1},
"hash": {"type": "string", "minLength": 1},
"parameters": {
"type": "object",
}
}
}
}
}
}

9
lib/spack/spack/solver/asp.py
View file

@ -1526,9 +1526,12 @@ def generate_possible_compilers(self, specs):
continue
if strict and s.compiler not in cspecs:
raise spack.concretize.UnavailableCompilerVersionError(
s.compiler
)
if not s.concrete:
raise spack.concretize.UnavailableCompilerVersionError(
s.compiler
)
# Allow unknown compilers to exist if the associated spec
# is already built
else:
cspecs.add(s.compiler)
self.gen.fact(fn.allow_compiler(

56
lib/spack/spack/spec.py
View file

@ -2943,7 +2943,7 @@ def concretized(self, tests=False):
if a list of names activate them for the packages in the list,
if True activate 'test' dependencies for all packages.
"""
clone = self.copy(caches=True)
clone = self.copy()
clone.concretize(tests=tests)
return clone
@ -3242,8 +3242,8 @@ def normalize(self, force=False, tests=False, user_spec_deps=None):
"Attempting to normalize anonymous spec")
# Set _normal and _concrete to False when forced
if force:
self._mark_concrete(False)
if force and not self._concrete:
self._normal = False
if self._normal:
return False
@ -3712,7 +3712,7 @@ def patches(self):
return patches
def _dup(self, other, deps=True, cleardeps=True, caches=None):
def _dup(self, other, deps=True, cleardeps=True):
"""Copy the spec other into self. This is an overwriting
copy. It does not copy any dependents (parents), but by default
copies dependencies.
@ -3727,10 +3727,6 @@ def _dup(self, other, deps=True, cleardeps=True, caches=None):
cleardeps (bool): if True clears the dependencies of ``self``,
before possibly copying the dependencies of ``other`` onto
``self``
caches (bool or None): preserve cached fields such as
``_normal``, ``_hash``, and ``_dunder_hash``. By
default this is ``False`` if DAG structure would be
changed by the copy, ``True`` if it's an exact copy.
Returns:
True if ``self`` changed because of the copy operation,
@ -3781,12 +3777,6 @@ def _dup(self, other, deps=True, cleardeps=True, caches=None):
self.extra_attributes = other.extra_attributes
self.namespace = other.namespace
# Cached fields are results of expensive operations.
# If we preserved the original structure, we can copy them
# safely. If not, they need to be recomputed.
if caches is None:
caches = (deps is True or deps == dp.all_deptypes)
# If we copy dependencies, preserve DAG structure in the new spec
if deps:
# If caller restricted deptypes to be copied, adjust that here.
@ -3794,29 +3784,31 @@ def _dup(self, other, deps=True, cleardeps=True, caches=None):
deptypes = dp.all_deptypes
if isinstance(deps, (tuple, list)):
deptypes = deps
self._dup_deps(other, deptypes, caches)
self._dup_deps(other, deptypes)
self._concrete = other._concrete
self._hashes_final = other._hashes_final
if caches:
if self._concrete:
self._hash = other._hash
self._build_hash = other._build_hash
self._dunder_hash = other._dunder_hash
self._normal = other._normal
self._normal = True
self._full_hash = other._full_hash
self._package_hash = other._package_hash
else:
self._hash = None
self._build_hash = None
self._dunder_hash = None
# Note, we could use other._normal if we are copying all deps, but
# always set it False here to avoid the complexity of checking
self._normal = False
self._full_hash = None
self._package_hash = None
return changed
def _dup_deps(self, other, deptypes, caches):
def _dup_deps(self, other, deptypes):
def spid(spec):
return id(spec)
@ -3827,11 +3819,11 @@ def spid(spec):
if spid(edge.parent) not in new_specs:
new_specs[spid(edge.parent)] = edge.parent.copy(
deps=False, caches=caches
deps=False
)
if spid(edge.spec) not in new_specs:
new_specs[spid(edge.spec)] = edge.spec.copy(deps=False, caches=caches)
new_specs[spid(edge.spec)] = edge.spec.copy(deps=False)
new_specs[spid(edge.parent)].add_dependency_edge(
new_specs[spid(edge.spec)], edge.deptypes
@ -4709,16 +4701,16 @@ def from_self(name, transitive):
return False
return True
self_nodes = dict((s.name, s.copy(deps=False, caches=True))
self_nodes = dict((s.name, s.copy(deps=False))
for s in self.traverse(root=True)
if from_self(s.name, transitive))
if transitive:
other_nodes = dict((s.name, s.copy(deps=False, caches=True))
other_nodes = dict((s.name, s.copy(deps=False))
for s in other.traverse(root=True))
else:
# NOTE: Does not fully validate providers; loader races possible
other_nodes = dict((s.name, s.copy(deps=False, caches=True))
other_nodes = dict((s.name, s.copy(deps=False))
for s in other.traverse(root=True)
if s is other or s.name not in self)
@ -4751,23 +4743,12 @@ def from_self(name, transitive):
for dep in ret.traverse(root=True, order='post'):
opposite = other_nodes if dep.name in self_nodes else self_nodes
if any(name in dep for name in opposite.keys()):
# Record whether hashes are already cached
# So we don't try to compute a hash from insufficient
# provenance later
has_build_hash = getattr(dep, ht.build_hash.name, None)
has_full_hash = getattr(dep, ht.full_hash.name, None)
# package hash cannot be affected by splice
dep.clear_cached_hashes(ignore=['package_hash'])
# Since this is a concrete spec, we want to make sure hashes
# are cached writing specs only writes cached hashes in case
# the spec is too old to have full provenance for these hashes,
# so we can't rely on doing it at write time.
if has_build_hash:
_ = dep.build_hash()
if has_full_hash:
_ = dep.full_hash()
dep.build_hash()
dep.full_hash()
dep.dag_hash()
return nodes[self.name]
@ -4779,6 +4760,7 @@ def clear_cached_hashes(self, ignore=()):
if h.attr not in ignore:
if hasattr(self, h.attr):
setattr(self, h.attr, None)
self._dunder_hash = None
def __hash__(self):
# If the spec is concrete, we leverage the DAG hash and just use

42
lib/spack/spack/test/cmd/external.py
View file

@ -167,6 +167,48 @@ def test_find_external_cmd_full_repo(
assert {'spec': 'find-externals1@1.foo', 'prefix': prefix} in pkg_externals
def test_find_external_no_manifest(
mutable_config, working_env, mock_executable, mutable_mock_repo,
_platform_executables, monkeypatch):
"""The user runs 'spack external find'; the default path for storing
manifest files does not exist. Ensure that the command does not
fail.
"""
monkeypatch.setenv('PATH', '')
monkeypatch.setattr(spack.cray_manifest, 'default_path',
os.path.join('a', 'path', 'that', 'doesnt', 'exist'))
external('find')
def test_find_external_empty_default_manifest_dir(
mutable_config, working_env, mock_executable, mutable_mock_repo,
_platform_executables, tmpdir, monkeypatch):
"""The user runs 'spack external find'; the default path for storing
manifest files exists but is empty. Ensure that the command does not
fail.
"""
empty_manifest_dir = str(tmpdir.mkdir('manifest_dir'))
monkeypatch.setenv('PATH', '')
monkeypatch.setattr(spack.cray_manifest, 'default_path',
empty_manifest_dir)
external('find')
def test_find_external_nonempty_default_manifest_dir(
mutable_database, mutable_mock_repo,
_platform_executables, tmpdir, monkeypatch,
directory_with_manifest):
"""The user runs 'spack external find'; the default manifest directory
contains a manifest file. Ensure that the specs are read.
"""
monkeypatch.setenv('PATH', '')
monkeypatch.setattr(spack.cray_manifest, 'default_path',
str(directory_with_manifest))
external('find')
specs = spack.store.db.query('hwloc')
assert any(x.dag_hash() == 'hwlocfakehashaaa' for x in specs)
def test_find_external_merge(mutable_config, mutable_mock_repo):
"""Check that 'spack find external' doesn't overwrite an existing spec
entry in packages.yaml.

27
lib/spack/spack/test/conftest.py
View file

@ -43,6 +43,7 @@
import spack.stage
import spack.store
import spack.subprocess_context
import spack.test.cray_manifest
import spack.util.executable
import spack.util.gpg
import spack.util.spack_yaml as syaml
@ -809,7 +810,16 @@ def database(mock_store, mock_packages, config):
@pytest.fixture(scope='function')
def mutable_database(database, _store_dir_and_cache):
def database_mutable_config(mock_store, mock_packages, mutable_config,
monkeypatch):
"""This activates the mock store, packages, AND config."""
with spack.store.use_store(str(mock_store)) as store:
yield store.db
store.db.last_seen_verifier = ''
@pytest.fixture(scope='function')
def mutable_database(database_mutable_config, _store_dir_and_cache):
"""Writeable version of the fixture, restored to its initial state
after each test.
"""
@ -817,7 +827,7 @@ def mutable_database(database, _store_dir_and_cache):
store_path, store_cache = _store_dir_and_cache
store_path.join('.spack-db').chmod(mode=0o755, rec=1)
yield database
yield database_mutable_config
# Restore the initial state by copying the content of the cache back into
# the store and making the database read-only
@ -1635,6 +1645,19 @@ def brand_new_binary_cache():
spack.binary_distribution._binary_index)
@pytest.fixture
def directory_with_manifest(tmpdir):
"""Create a manifest file in a directory. Used by 'spack external'.
"""
with tmpdir.as_cwd():
test_db_fname = 'external-db.json'
with open(test_db_fname, 'w') as db_file:
json.dump(spack.test.cray_manifest.create_manifest_content(),
db_file)
yield str(tmpdir)
@pytest.fixture()
def noncyclical_dir_structure(tmpdir):
"""

247
lib/spack/spack/test/cray_manifest.py Normal file
View file

@ -0,0 +1,247 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import json
import pytest
import spack
import spack.cray_manifest as cray_manifest
from spack.cray_manifest import compiler_from_entry, entries_to_specs
example_x_json_str = """\
{
"name": "packagex",
"hash": "hash-of-x",
"prefix": "/path/to/packagex-install/",
"version": "1.0",
"arch": {
"platform": "linux",
"platform_os": "centos8",
"target": {
"name": "haswell"
}
},
"compiler": {
"name": "gcc",
"version": "10.2.0"
},
"dependencies": {
"packagey": {
"hash": "hash-of-y",
"type": ["link"]
}
},
"parameters": {
"precision": ["double", "float"]
}
}
"""
example_compiler_entry = """\
{
"name": "gcc",
"prefix": "/path/to/compiler/",
"version": "7.5.0",
"arch": {
"os": "centos8",
"target": "x86_64"
},
"executables": {
"cc": "/path/to/compiler/cc",
"cxx": "/path/to/compiler/cxx",
"fc": "/path/to/compiler/fc"
}
}
"""
class JsonSpecEntry(object):
def __init__(self, name, hash, prefix, version, arch, compiler,
dependencies, parameters):
self.name = name
self.hash = hash
self.prefix = prefix
self.version = version
self.arch = arch
self.compiler = compiler
self.dependencies = dependencies
self.parameters = parameters
def to_dict(self):
return {
'name': self.name,
'hash': self.hash,
'prefix': self.prefix,
'version': self.version,
'arch': self.arch,
'compiler': self.compiler,
'dependencies': self.dependencies,
'parameters': self.parameters
}
def as_dependency(self, deptypes):
return (self.name,
{'hash': self.hash,
'type': list(deptypes)})
class JsonArchEntry(object):
def __init__(self, platform, os, target):
self.platform = platform
self.os = os
self.target = target
def to_dict(self):
return {
'platform': self.platform,
'platform_os': self.os,
'target': {
'name': self.target
}
}
class JsonCompilerEntry(object):
def __init__(self, name, version):
self.name = name
self.version = version
def to_dict(self):
return {
'name': self.name,
'version': self.version
}
_common_arch = JsonArchEntry(
platform='linux',
os='centos8',
target='haswell'
).to_dict()
_common_compiler = JsonCompilerEntry(
name='gcc',
version='10.2.0'
).to_dict()
def test_compatibility():
"""Make sure that JsonSpecEntry outputs the expected JSON structure
by comparing it with JSON parsed from an example string. This
ensures that the testing objects like JsonSpecEntry produce the
same JSON structure as the expected file format.
"""
y = JsonSpecEntry(
name='packagey',
hash='hash-of-y',
prefix='/path/to/packagey-install/',
version='1.0',
arch=_common_arch,
compiler=_common_compiler,
dependencies={},
parameters={}
)
x = JsonSpecEntry(
name='packagex',
hash='hash-of-x',
prefix='/path/to/packagex-install/',
version='1.0',
arch=_common_arch,
compiler=_common_compiler,
dependencies=dict([y.as_dependency(deptypes=['link'])]),
parameters={'precision': ['double', 'float']}
)
x_from_entry = x.to_dict()
x_from_str = json.loads(example_x_json_str)
assert x_from_entry == x_from_str
def test_compiler_from_entry():
compiler_data = json.loads(example_compiler_entry)
compiler_from_entry(compiler_data)
def generate_openmpi_entries():
"""Generate two example JSON entries that refer to an OpenMPI
installation and a hwloc dependency.
"""
# The hashes need to be padded with 'a' at the end to align with 8-byte
# boundaries (for base-32 decoding)
hwloc = JsonSpecEntry(
name='hwloc',
hash='hwlocfakehashaaa',
prefix='/path/to/hwloc-install/',
version='2.0.3',
arch=_common_arch,
compiler=_common_compiler,
dependencies={},
parameters={}
)
# This includes a variant which is guaranteed not to appear in the
# OpenMPI package: we need to make sure we can use such package
# descriptions.
openmpi = JsonSpecEntry(
name='openmpi',
hash='openmpifakehasha',
prefix='/path/to/openmpi-install/',
version='4.1.0',
arch=_common_arch,
compiler=_common_compiler,
dependencies=dict([hwloc.as_dependency(deptypes=['link'])]),
parameters={
'internal-hwloc': False,
'fabrics': ['psm'],
'missing_variant': True
}
)
return [openmpi, hwloc]
def test_spec_conversion():
"""Given JSON entries, check that we can form a set of Specs
including dependency references.
"""
entries = list(x.to_dict() for x in generate_openmpi_entries())
specs = entries_to_specs(entries)
openmpi_spec, = list(x for x in specs.values() if x.name == 'openmpi')
assert openmpi_spec['hwloc']
def create_manifest_content():
return {
'specs': list(x.to_dict() for x in generate_openmpi_entries()),
'compilers': []
}
def test_read_cray_manifest(
tmpdir, mutable_config, mock_packages, mutable_database):
"""Check that (a) we can read the cray manifest and add it to the Spack
Database and (b) we can concretize specs based on that.
"""
if spack.config.get('config:concretizer') == 'clingo':
pytest.skip("The ASP-based concretizer is currently picky about "
" OS matching and will fail.")
with tmpdir.as_cwd():
test_db_fname = 'external-db.json'
with open(test_db_fname, 'w') as db_file:
json.dump(create_manifest_content(), db_file)
cray_manifest.read(test_db_fname, True)
query_specs = spack.store.db.query('openmpi')
assert any(x.dag_hash() == 'openmpifakehasha' for x in query_specs)
concretized_specs = spack.cmd.parse_specs(
'depends-on-openmpi %gcc@4.5.0 arch=test-redhat6-x86_64'
' ^/openmpifakehasha'.split(),
concretize=True)
assert concretized_specs[0]['hwloc'].dag_hash() == 'hwlocfakehashaaa'

2
lib/spack/spack/test/rewiring.py
View file

@ -23,7 +23,7 @@
@pytest.mark.requires_executables(*args)
@pytest.mark.parametrize('transitive', [True, False])
def test_rewire(mock_fetch, install_mockery, transitive):
def test_rewire_db(mock_fetch, install_mockery, transitive):
"""Tests basic rewiring without binary executables."""
spec = Spec('splice-t^splice-h~foo').concretized()
dep = Spec('splice-h+foo').concretized()

2
lib/spack/spack/test/spec_dag.py
View file

@ -602,8 +602,6 @@ def test_copy_normalized(self):
assert orig == copy
assert orig.eq_dag(copy)
assert orig._normal == copy._normal
assert orig._concrete == copy._concrete
# ensure no shared nodes bt/w orig and copy.
orig_ids = set(id(s) for s in orig.traverse())

8
share/spack/spack-completion.bash
View file

@ -1017,7 +1017,7 @@ _spack_external() {
then
SPACK_COMPREPLY="-h --help"
else
SPACK_COMPREPLY="find list"
SPACK_COMPREPLY="find list read-cray-manifest"
fi
}
@ -1034,6 +1034,10 @@ _spack_external_list() {
SPACK_COMPREPLY="-h --help"
}
_spack_external_read_cray_manifest() {
SPACK_COMPREPLY="-h --help --file --directory --dry-run --fail-on-error"
}
_spack_fetch() {
if $list_options
then
@ -1791,7 +1795,7 @@ _spack_undevelop() {
_spack_uninstall() {
if $list_options
then
SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all"
SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all --origin"
else
_installed_packages
fi

16
var/spack/repos/builtin.mock/packages/depends-on-openmpi/package.py Normal file
View file

@ -0,0 +1,16 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class DependsOnOpenmpi(Package):
"""For testing concretization of packages that use
`spack external read-cray-manifest`"""
depends_on('openmpi')
version('1.0')
version('0.9')

10
var/spack/repos/builtin.mock/packages/hwloc/package.py Normal file
View file

@ -0,0 +1,10 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Hwloc(Package):
version('2.0.3')

15
var/spack/repos/builtin.mock/packages/openmpi/package.py Normal file
View file

@ -0,0 +1,15 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Openmpi(Package):
version('4.1.1')
variant('internal-hwloc', default=False)
variant('fabrics', values=any_combination_of('psm', 'mxm'))
depends_on('hwloc', when="~internal-hwloc")