Source code for spack.database

# 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)

"""Spack's installation tracking database.

The database serves two purposes:

  1. It implements a cache on top of a potentially very large Spack
     directory hierarchy, speeding up many operations that would
     otherwise require filesystem access.

  2. It will allow us to track external installations as well as lost
     packages and their dependencies.

Prior to the implementation of this store, a directory layout served
as the authoritative database of packages in Spack.  This module
provides a cache and a sanity checking mechanism for what is in the
filesystem.
"""

import contextlib
import datetime
import os
import socket
import sys
import time
from typing import Dict  # novm

import six

try:
    import uuid

    _use_uuid = True
except ImportError:
    _use_uuid = False
    pass

import llnl.util.filesystem as fs
import llnl.util.lang as lang
import llnl.util.tty as tty

import spack.hash_types as ht
import spack.repo
import spack.spec
import spack.store
import spack.util.lock as lk
import spack.util.spack_json as sjson
from spack.directory_layout import DirectoryLayoutError
from spack.error import SpackError
from spack.filesystem_view import YamlFilesystemView
from spack.util.crypto import bit_length
from spack.version import Version

# TODO: Provide an API automatically retyring a build after detecting and
# TODO: clearing a failure.

# DB goes in this directory underneath the root
_db_dirname = ".spack-db"

# DB version.  This is stuck in the DB file to track changes in format.
# Increment by one when the database format changes.
# Versions before 5 were not integers.
_db_version = Version("6")

# For any version combinations here, skip reindex when upgrading.
# Reindexing can take considerable time and is not always necessary.
_skip_reindex = [
    # reindexing takes a significant amount of time, and there's
    # no reason to do it from DB version 0.9.3 to version 5. The
    # only difference is that v5 can contain "deprecated_for"
    # fields.  So, skip the reindex for this transition. The new
    # version is saved to disk the first time the DB is written.
    (Version("0.9.3"), Version("5")),
    (Version("5"), Version("6")),
]

# Default timeout for spack database locks in seconds or None (no timeout).
# A balance needs to be struck between quick turnaround for parallel installs
# (to avoid excess delays) and waiting long enough when the system is busy
# (to ensure the database is updated).
_db_lock_timeout = 120

# Default timeout for spack package locks in seconds or None (no timeout).
# A balance needs to be struck between quick turnaround for parallel installs
# (to avoid excess delays when performing a parallel installation) and waiting
# long enough for the next possible spec to install (to avoid excessive
# checking of the last high priority package) or holding on to a lock (to
# ensure a failed install is properly tracked).
_pkg_lock_timeout = None

# Types of dependencies tracked by the database
# We store by DAG hash, so we track the dependencies that the DAG hash includes.
_tracked_deps = ht.dag_hash.deptype

# Default list of fields written for each install record
default_install_record_fields = [
    "spec",
    "ref_count",
    "path",
    "installed",
    "explicit",
    "installation_time",
    "deprecated_for",
]


def _now():
    """Returns the time since the epoch"""
    return time.time()


def _autospec(function):
    """Decorator that automatically converts the argument of a single-arg
    function to a Spec."""

    def converter(self, spec_like, *args, **kwargs):
        if not isinstance(spec_like, spack.spec.Spec):
            spec_like = spack.spec.Spec(spec_like)
        return function(self, spec_like, *args, **kwargs)

    return converter


[docs]class InstallStatus(str): pass
[docs]class InstallStatuses(object): INSTALLED = InstallStatus("installed") DEPRECATED = InstallStatus("deprecated") MISSING = InstallStatus("missing")
[docs] @classmethod def canonicalize(cls, query_arg): if query_arg is True: return [cls.INSTALLED] elif query_arg is False: return [cls.MISSING] elif query_arg is any: return [cls.INSTALLED, cls.DEPRECATED, cls.MISSING] elif isinstance(query_arg, InstallStatus): return [query_arg] else: try: # Try block catches if it is not an iterable at all if any(type(x) != InstallStatus for x in query_arg): raise TypeError except TypeError: raise TypeError( "installation query must be `any`, boolean, " "InstallStatus, or iterable of InstallStatus" ) return query_arg
[docs]class InstallRecord(object): """A record represents one installation in the DB. The record keeps track of the spec for the installation, its install path, AND whether or not it is installed. We need the installed flag in case a user either: a) blew away a directory, or b) used spack uninstall -f to get rid of it If, in either case, the package was removed but others still depend on it, we still need to track its spec, so we don't actually remove from the database until a spec has no installed dependents left. Args: spec (spack.spec.Spec): spec tracked by the install record path (str): path where the spec has been installed installed (bool): whether or not the spec is currently installed ref_count (int): number of specs that depend on this one explicit (bool or None): whether or not this spec was explicitly installed, or pulled-in as a dependency of something else installation_time (datetime.datetime or None): time of the installation """ def __init__( self, spec, path, installed, ref_count=0, explicit=False, installation_time=None, deprecated_for=None, in_buildcache=False, origin=None, ): self.spec = spec self.path = str(path) if path else None self.installed = bool(installed) self.ref_count = ref_count self.explicit = explicit self.installation_time = installation_time or _now() self.deprecated_for = deprecated_for self.in_buildcache = in_buildcache self.origin = origin
[docs] def install_type_matches(self, installed): installed = InstallStatuses.canonicalize(installed) if self.installed: return InstallStatuses.INSTALLED in installed elif self.deprecated_for: return InstallStatuses.DEPRECATED in installed else: return InstallStatuses.MISSING in installed
[docs] def to_dict(self, include_fields=default_install_record_fields): rec_dict = {} for field_name in include_fields: if field_name == "spec": rec_dict.update({"spec": self.spec.node_dict_with_hashes()}) elif field_name == "deprecated_for" and self.deprecated_for: rec_dict.update({"deprecated_for": self.deprecated_for}) else: rec_dict.update({field_name: getattr(self, field_name)}) if self.origin: rec_dict["origin"] = self.origin return rec_dict
[docs] @classmethod def from_dict(cls, spec, dictionary): d = dict(dictionary.items()) d.pop("spec", None) # Old databases may have "None" for path for externals if "path" not in d or d["path"] == "None": d["path"] = None if "installed" not in d: d["installed"] = False return InstallRecord(spec, **d)
[docs]class ForbiddenLockError(SpackError): """Raised when an upstream DB attempts to acquire a lock"""
[docs]class ForbiddenLock(object): def __getattribute__(self, name): raise ForbiddenLockError("Cannot access attribute '{0}' of lock".format(name))
_query_docstring = """ Args: query_spec: queries iterate through specs in the database and return those that satisfy the supplied ``query_spec``. If query_spec is `any`, This will match all specs in the database. If it is a spec, we'll evaluate ``spec.satisfies(query_spec)`` known (bool or None): Specs that are "known" are those for which Spack can locate a ``package.py`` file -- i.e., Spack "knows" how to install them. Specs that are unknown may represent packages that existed in a previous version of Spack, but have since either changed their name or been removed installed (bool or InstallStatus or typing.Iterable or None): if ``True``, includes only installed specs in the search; if ``False`` only missing specs, and if ``any``, all specs in database. If an InstallStatus or iterable of InstallStatus, returns specs whose install status (installed, deprecated, or missing) matches (one of) the InstallStatus. (default: True) explicit (bool or None): A spec that was installed following a specific user request is marked as explicit. If instead it was pulled-in as a dependency of a user requested spec it's considered implicit. start_date (datetime.datetime or None): filters the query discarding specs that have been installed before ``start_date``. end_date (datetime.datetime or None): filters the query discarding specs that have been installed after ``end_date``. hashes (typing.Container): list or set of hashes that we can use to restrict the search in_buildcache (bool or None): Specs that are marked in this database as part of an associated binary cache are ``in_buildcache``. All other specs are not. This field is used for querying mirror indices. Default is ``any``. Returns: list of specs that match the query """
[docs]class Database(object): """Per-process lock objects for each install prefix.""" _prefix_locks = {} # type: Dict[str, lk.Lock] """Per-process failure (lock) objects for each install prefix.""" _prefix_failures = {} # type: Dict[str, lk.Lock] def __init__( self, root, db_dir=None, upstream_dbs=None, is_upstream=False, enable_transaction_locking=True, record_fields=default_install_record_fields, ): """Create a Database for Spack installations under ``root``. A Database is a cache of Specs data from ``$prefix/spec.yaml`` files in Spack installation directories. By default, Database files (data and lock files) are stored under ``root/.spack-db``, which is created if it does not exist. This is the ``db_dir``. The Database will attempt to read an ``index.json`` file in ``db_dir``. If that does not exist, it will create a database when needed by scanning the entire Database root for ``spec.yaml`` files according to Spack's ``DirectoryLayout``. Caller may optionally provide a custom ``db_dir`` parameter where data will be stored. This is intended to be used for testing the Database class. This class supports writing buildcache index files, in which case certain fields are not needed in each install record, and no transaction locking is required. To use this feature, provide ``enable_transaction_locking=False``, and specify a list of needed fields in ``record_fields``. """ self.root = root # If the db_dir is not provided, default to within the db root. self._db_dir = db_dir or os.path.join(self.root, _db_dirname) # Set up layout of database files within the db dir self._index_path = os.path.join(self._db_dir, "index.json") self._verifier_path = os.path.join(self._db_dir, "index_verifier") self._lock_path = os.path.join(self._db_dir, "lock") # This is for other classes to use to lock prefix directories. self.prefix_lock_path = os.path.join(self._db_dir, "prefix_lock") # Ensure a persistent location for dealing with parallel installation # failures (e.g., across near-concurrent processes). self._failure_dir = os.path.join(self._db_dir, "failures") # Support special locks for handling parallel installation failures # of a spec. self.prefix_fail_path = os.path.join(self._db_dir, "prefix_failures") # Create needed directories and files if not is_upstream and not os.path.exists(self._db_dir): fs.mkdirp(self._db_dir) if not is_upstream and not os.path.exists(self._failure_dir): fs.mkdirp(self._failure_dir) self.is_upstream = is_upstream self.last_seen_verifier = "" # Failed write transactions (interrupted by exceptions) will alert # _write. When that happens, we set this flag to indicate that # future read/write transactions should re-read the DB. Normally it # would make more sense to resolve this at the end of the transaction # but typically a failed transaction will terminate the running # instance of Spack and we don't want to incur an extra read in that # case, so we defer the cleanup to when we begin the next transaction self._state_is_inconsistent = False # initialize rest of state. self.db_lock_timeout = spack.config.get("config:db_lock_timeout") or _db_lock_timeout self.package_lock_timeout = ( spack.config.get("config:package_lock_timeout") or _pkg_lock_timeout ) tty.debug("DATABASE LOCK TIMEOUT: {0}s".format(str(self.db_lock_timeout))) timeout_format_str = ( "{0}s".format(str(self.package_lock_timeout)) if self.package_lock_timeout else "No timeout" ) tty.debug("PACKAGE LOCK TIMEOUT: {0}".format(str(timeout_format_str))) if self.is_upstream: self.lock = ForbiddenLock() else: self.lock = lk.Lock( self._lock_path, default_timeout=self.db_lock_timeout, desc="database" ) self._data = {} # For every installed spec we keep track of its install prefix, so that # we can answer the simple query whether a given path is already taken # before installing a different spec. self._installed_prefixes = set() self.upstream_dbs = list(upstream_dbs) if upstream_dbs else [] # whether there was an error at the start of a read transaction self._error = None # For testing: if this is true, an exception is thrown when missing # dependencies are detected (rather than just printing a warning # message) self._fail_when_missing_deps = False if enable_transaction_locking: self._write_transaction_impl = lk.WriteTransaction self._read_transaction_impl = lk.ReadTransaction else: self._write_transaction_impl = lang.nullcontext self._read_transaction_impl = lang.nullcontext self._record_fields = record_fields
[docs] def write_transaction(self): """Get a write lock context manager for use in a `with` block.""" return self._write_transaction_impl(self.lock, acquire=self._read, release=self._write)
[docs] def read_transaction(self): """Get a read lock context manager for use in a `with` block.""" return self._read_transaction_impl(self.lock, acquire=self._read)
def _failed_spec_path(self, spec): """Return the path to the spec's failure file, which may not exist.""" if not spec.concrete: raise ValueError("Concrete spec required for failure path for {0}".format(spec.name)) return os.path.join(self._failure_dir, "{0}-{1}".format(spec.name, spec.dag_hash()))
[docs] def clear_all_failures(self): """Force remove install failure tracking files.""" tty.debug("Releasing prefix failure locks") for pkg_id in list(self._prefix_failures.keys()): lock = self._prefix_failures.pop(pkg_id, None) if lock: lock.release_write() # Remove all failure markings (aka files) tty.debug("Removing prefix failure tracking files") for fail_mark in os.listdir(self._failure_dir): try: os.remove(os.path.join(self._failure_dir, fail_mark)) except OSError as exc: tty.warn( "Unable to remove failure marking file {0}: {1}".format(fail_mark, str(exc)) )
[docs] def clear_failure(self, spec, force=False): """ Remove any persistent and cached failure tracking for the spec. see `mark_failed()`. Args: spec (spack.spec.Spec): the spec whose failure indicators are being removed force (bool): True if the failure information should be cleared when a prefix failure lock exists for the file or False if the failure should not be cleared (e.g., it may be associated with a concurrent build) """ failure_locked = self.prefix_failure_locked(spec) if failure_locked and not force: tty.msg("Retaining failure marking for {0} due to lock".format(spec.name)) return if failure_locked: tty.warn("Removing failure marking despite lock for {0}".format(spec.name)) lock = self._prefix_failures.pop(spec.prefix, None) if lock: lock.release_write() if self.prefix_failure_marked(spec): try: path = self._failed_spec_path(spec) tty.debug("Removing failure marking for {0}".format(spec.name)) os.remove(path) except OSError as err: tty.warn( "Unable to remove failure marking for {0} ({1}): {2}".format( spec.name, path, str(err) ) )
[docs] def mark_failed(self, spec): """ Mark a spec as failing to install. Prefix failure marking takes the form of a byte range lock on the nth byte of a file for coordinating between concurrent parallel build processes and a persistent file, named with the full hash and containing the spec, in a subdirectory of the database to enable persistence across overlapping but separate related build processes. The failure lock file, ``spack.store.db.prefix_failures``, lives alongside the install DB. ``n`` is the sys.maxsize-bit prefix of the associated DAG hash to make the likelihood of collision very low with no cleanup required. """ # Dump the spec to the failure file for (manual) debugging purposes path = self._failed_spec_path(spec) with open(path, "w") as f: spec.to_json(f) # Also ensure a failure lock is taken to prevent cleanup removal # of failure status information during a concurrent parallel build. err = "Unable to mark {0.name} as failed." prefix = spec.prefix if prefix not in self._prefix_failures: mark = lk.Lock( self.prefix_fail_path, start=spec.dag_hash_bit_prefix(bit_length(sys.maxsize)), length=1, default_timeout=self.package_lock_timeout, desc=spec.name, ) try: mark.acquire_write() except lk.LockTimeoutError: # Unlikely that another process failed to install at the same # time but log it anyway. tty.debug( "PID {0} failed to mark install failure for {1}".format(os.getpid(), spec.name) ) tty.warn(err.format(spec)) # Whether we or another process marked it as a failure, track it # as such locally. self._prefix_failures[prefix] = mark return self._prefix_failures[prefix]
[docs] def prefix_failed(self, spec): """Return True if the prefix (installation) is marked as failed.""" # The failure was detected in this process. if spec.prefix in self._prefix_failures: return True # The failure was detected by a concurrent process (e.g., an srun), # which is expected to be holding a write lock if that is the case. if self.prefix_failure_locked(spec): return True # Determine if the spec may have been marked as failed by a separate # spack build process running concurrently. return self.prefix_failure_marked(spec)
[docs] def prefix_failure_locked(self, spec): """Return True if a process has a failure lock on the spec.""" check = lk.Lock( self.prefix_fail_path, start=spec.dag_hash_bit_prefix(bit_length(sys.maxsize)), length=1, default_timeout=self.package_lock_timeout, desc=spec.name, ) return check.is_write_locked()
[docs] def prefix_failure_marked(self, spec): """Determine if the spec has a persistent failure marking.""" return os.path.exists(self._failed_spec_path(spec))
[docs] def prefix_lock(self, spec, timeout=None): """Get a lock on a particular spec's installation directory. NOTE: The installation directory **does not** need to exist. Prefix lock is a byte range lock on the nth byte of a file. The lock file is ``spack.store.db.prefix_lock`` -- the DB tells us what to call it and it lives alongside the install DB. n is the sys.maxsize-bit prefix of the DAG hash. This makes likelihood of collision is very low AND it gives us readers-writer lock semantics with just a single lockfile, so no cleanup required. """ timeout = timeout or self.package_lock_timeout prefix = spec.prefix if prefix not in self._prefix_locks: self._prefix_locks[prefix] = lk.Lock( self.prefix_lock_path, start=spec.dag_hash_bit_prefix(bit_length(sys.maxsize)), length=1, default_timeout=timeout, desc=spec.name, ) elif timeout != self._prefix_locks[prefix].default_timeout: self._prefix_locks[prefix].default_timeout = timeout return self._prefix_locks[prefix]
[docs] @contextlib.contextmanager def prefix_read_lock(self, spec): prefix_lock = self.prefix_lock(spec) prefix_lock.acquire_read() try: yield self except lk.LockError: # This addresses the case where a nested lock attempt fails inside # of this context manager raise except (Exception, KeyboardInterrupt): prefix_lock.release_read() raise else: prefix_lock.release_read()
[docs] @contextlib.contextmanager def prefix_write_lock(self, spec): prefix_lock = self.prefix_lock(spec) prefix_lock.acquire_write() try: yield self except lk.LockError: # This addresses the case where a nested lock attempt fails inside # of this context manager raise except (Exception, KeyboardInterrupt): prefix_lock.release_write() raise else: prefix_lock.release_write()
def _write_to_file(self, stream): """Write out the database in JSON format to the stream passed as argument. This function does not do any locking or transactions. """ # map from per-spec hash code to installation record. installs = dict( (k, v.to_dict(include_fields=self._record_fields)) for k, v in self._data.items() ) # database includes installation list and version. # NOTE: this DB version does not handle multiple installs of # the same spec well. If there are 2 identical specs with # different paths, it can't differentiate. # TODO: fix this before we support multiple install locations. database = { "database": { # TODO: move this to a top-level _meta section if we ever # TODO: bump the DB version to 7 "version": str(_db_version), # dictionary of installation records, keyed by DAG hash "installs": installs, } } try: sjson.dump(database, stream) except (TypeError, ValueError) as e: raise sjson.SpackJSONError("error writing JSON database:", str(e)) def _read_spec_from_dict(self, hash_key, installs, hash=ht.dag_hash): """Recursively construct a spec from a hash in a YAML database. Does not do any locking. """ spec_dict = installs[hash_key]["spec"] # Install records don't include hash with spec, so we add it in here # to ensure it is read properly. if "name" not in spec_dict.keys(): # old format, can't update format here for name in spec_dict: spec_dict[name]["hash"] = hash_key else: # new format, already a singleton spec_dict[hash.name] = hash_key # Build spec from dict first. spec = spack.spec.Spec.from_node_dict(spec_dict) return spec
[docs] def db_for_spec_hash(self, hash_key): with self.read_transaction(): if hash_key in self._data: return self for db in self.upstream_dbs: if hash_key in db._data: return db
[docs] def query_by_spec_hash(self, hash_key, data=None): """Get a spec for hash, and whether it's installed upstream. Return: (tuple): (bool, optional InstallRecord): bool tells us whether the spec is installed upstream. Its InstallRecord is also returned if it's installed at all; otherwise None. """ if data and hash_key in data: return False, data[hash_key] if not data: with self.read_transaction(): if hash_key in self._data: return False, self._data[hash_key] for db in self.upstream_dbs: if hash_key in db._data: return True, db._data[hash_key] return False, None
def _assign_dependencies(self, hash_key, installs, data): # Add dependencies from other records in the install DB to # form a full spec. spec = data[hash_key].spec spec_node_dict = installs[hash_key]["spec"] if "name" not in spec_node_dict: # old format spec_node_dict = spec_node_dict[spec.name] if "dependencies" in spec_node_dict: yaml_deps = spec_node_dict["dependencies"] for dname, dhash, dtypes, _ in spack.spec.Spec.read_yaml_dep_specs(yaml_deps): # It is important that we always check upstream installations # in the same order, and that we always check the local # installation first: if a downstream Spack installs a package # then dependents in that installation could be using it. # If a hash is installed locally and upstream, there isn't # enough information to determine which one a local package # depends on, so the convention ensures that this isn't an # issue. upstream, record = self.query_by_spec_hash(dhash, data=data) child = record.spec if record else None if not child: msg = "Missing dependency not in database: " "%s needs %s-%s" % ( spec.cformat("{name}{/hash:7}"), dname, dhash[:7], ) if self._fail_when_missing_deps: raise MissingDependenciesError(msg) tty.warn(msg) continue spec._add_dependency(child, dtypes) def _read_from_file(self, filename): """Fill database from file, do not maintain old data. Translate the spec portions from node-dict form to spec form. Does not do any locking. """ try: with open(filename, "r") as f: fdata = sjson.load(f) except Exception as e: raise six.raise_from( CorruptDatabaseError("error parsing database:", str(e)), e, ) if fdata is None: return def check(cond, msg): if not cond: raise CorruptDatabaseError("Spack database is corrupt: %s" % msg, self._index_path) check("database" in fdata, "no 'database' attribute in JSON DB.") # High-level file checks db = fdata["database"] check("installs" in db, "no 'installs' in JSON DB.") check("version" in db, "no 'version' in JSON DB.") installs = db["installs"] # TODO: better version checking semantics. version = Version(db["version"]) if version > _db_version: raise InvalidDatabaseVersionError(_db_version, version) elif version < _db_version: if not any(old == version and new == _db_version for old, new in _skip_reindex): tty.warn( "Spack database version changed from %s to %s. Upgrading." % (version, _db_version) ) self.reindex(spack.store.layout) installs = dict( (k, v.to_dict(include_fields=self._record_fields)) for k, v in self._data.items() ) def invalid_record(hash_key, error): msg = "Invalid record in Spack database: " "hash: %s, cause: %s: %s" msg %= (hash_key, type(error).__name__, str(error)) raise CorruptDatabaseError(msg, self._index_path) # Build up the database in three passes: # # 1. Read in all specs without dependencies. # 2. Hook dependencies up among specs. # 3. Mark all specs concrete. # # The database is built up so that ALL specs in it share nodes # (i.e., its specs are a true Merkle DAG, unlike most specs.) # Pass 1: Iterate through database and build specs w/o dependencies data = {} installed_prefixes = set() for hash_key, rec in installs.items(): try: # This constructs a spec DAG from the list of all installs spec = self._read_spec_from_dict(hash_key, installs) # Insert the brand new spec in the database. Each # spec has its own copies of its dependency specs. # TODO: would a more immmutable spec implementation simplify # this? data[hash_key] = InstallRecord.from_dict(spec, rec) if not spec.external and "installed" in rec and rec["installed"]: installed_prefixes.add(rec["path"]) except Exception as e: invalid_record(hash_key, e) # Pass 2: Assign dependencies once all specs are created. for hash_key in data: try: self._assign_dependencies(hash_key, installs, data) except MissingDependenciesError: raise except Exception as e: invalid_record(hash_key, e) # Pass 3: Mark all specs concrete. Specs representing real # installations must be explicitly marked. # We do this *after* all dependencies are connected because if we # do it *while* we're constructing specs,it causes hashes to be # cached prematurely. for hash_key, rec in data.items(): rec.spec._mark_root_concrete() self._data = data self._installed_prefixes = installed_prefixes
[docs] def reindex(self, directory_layout): """Build database index from scratch based on a directory layout. Locks the DB if it isn't locked already. """ if self.is_upstream: raise UpstreamDatabaseLockingError("Cannot reindex an upstream database") # Special transaction to avoid recursive reindex calls and to # ignore errors if we need to rebuild a corrupt database. def _read_suppress_error(): try: if os.path.isfile(self._index_path): self._read_from_file(self._index_path) except CorruptDatabaseError as e: self._error = e self._data = {} self._installed_prefixes = set() transaction = lk.WriteTransaction( self.lock, acquire=_read_suppress_error, release=self._write ) with transaction: if self._error: tty.warn("Spack database was corrupt. Will rebuild. Error was:", str(self._error)) self._error = None old_data = self._data old_installed_prefixes = self._installed_prefixes try: self._construct_from_directory_layout(directory_layout, old_data) except BaseException: # If anything explodes, restore old data, skip write. self._data = old_data self._installed_prefixes = old_installed_prefixes raise
def _construct_entry_from_directory_layout( self, directory_layout, old_data, spec, deprecator=None ): # Try to recover explicit value from old DB, but # default it to True if DB was corrupt. This is # just to be conservative in case a command like # "autoremove" is run by the user after a reindex. tty.debug("RECONSTRUCTING FROM SPEC.YAML: {0}".format(spec)) explicit = True inst_time = os.stat(spec.prefix).st_ctime if old_data is not None: old_info = old_data.get(spec.dag_hash()) if old_info is not None: explicit = old_info.explicit inst_time = old_info.installation_time extra_args = {"explicit": explicit, "installation_time": inst_time} self._add(spec, directory_layout, **extra_args) if deprecator: self._deprecate(spec, deprecator) def _construct_from_directory_layout(self, directory_layout, old_data): # Read first the `spec.yaml` files in the prefixes. They should be # considered authoritative with respect to DB reindexing, as # entries in the DB may be corrupted in a way that still makes # them readable. If we considered DB entries authoritative # instead, we would perpetuate errors over a reindex. with directory_layout.disable_upstream_check(): # Initialize data in the reconstructed DB self._data = {} self._installed_prefixes = set() # Start inspecting the installed prefixes processed_specs = set() for spec in directory_layout.all_specs(): self._construct_entry_from_directory_layout(directory_layout, old_data, spec) processed_specs.add(spec) for spec, deprecator in directory_layout.all_deprecated_specs(): self._construct_entry_from_directory_layout( directory_layout, old_data, spec, deprecator ) processed_specs.add(spec) for key, entry in old_data.items(): # We already took care of this spec using # `spec.yaml` from its prefix. if entry.spec in processed_specs: msg = "SKIPPING RECONSTRUCTION FROM OLD DB: {0}" msg += " [already reconstructed from spec.yaml]" tty.debug(msg.format(entry.spec)) continue # If we arrived here it very likely means that # we have external specs that are not dependencies # of other specs. This may be the case for externally # installed compilers or externally installed # applications. tty.debug("RECONSTRUCTING FROM OLD DB: {0}".format(entry.spec)) try: layout = None if entry.spec.external else spack.store.layout kwargs = { "spec": entry.spec, "directory_layout": layout, "explicit": entry.explicit, "installation_time": entry.installation_time, } self._add(**kwargs) processed_specs.add(entry.spec) except Exception as e: # Something went wrong, so the spec was not restored # from old data tty.debug(e) self._check_ref_counts() def _check_ref_counts(self): """Ensure consistency of reference counts in the DB. Raise an AssertionError if something is amiss. Does no locking. """ counts = {} for key, rec in self._data.items(): counts.setdefault(key, 0) for dep in rec.spec.dependencies(deptype=_tracked_deps): dep_key = dep.dag_hash() counts.setdefault(dep_key, 0) counts[dep_key] += 1 if rec.deprecated_for: counts.setdefault(rec.deprecated_for, 0) counts[rec.deprecated_for] += 1 for rec in self._data.values(): key = rec.spec.dag_hash() expected = counts[key] found = rec.ref_count if not expected == found: raise AssertionError( "Invalid ref_count: %s: %d (expected %d), in DB %s" % (key, found, expected, self._index_path) ) def _write(self, type, value, traceback): """Write the in-memory database index to its file path. This is a helper function called by the WriteTransaction context manager. If there is an exception while the write lock is active, nothing will be written to the database file, but the in-memory database *may* be left in an inconsistent state. It will be consistent after the start of the next transaction, when it read from disk again. This routine does no locking. """ # Do not write if exceptions were raised if type is not None: # A failure interrupted a transaction, so we should record that # the Database is now in an inconsistent state: we should # restore it in the next transaction self._state_is_inconsistent = True return temp_file = self._index_path + (".%s.%s.temp" % (socket.getfqdn(), os.getpid())) # Write a temporary database file them move it into place try: with open(temp_file, "w") as f: self._write_to_file(f) fs.rename(temp_file, self._index_path) if _use_uuid: with open(self._verifier_path, "w") as f: new_verifier = str(uuid.uuid4()) f.write(new_verifier) self.last_seen_verifier = new_verifier except BaseException as e: tty.debug(e) # Clean up temp file if something goes wrong. if os.path.exists(temp_file): os.remove(temp_file) raise def _read(self): """Re-read Database from the data in the set location. This does no locking.""" if os.path.isfile(self._index_path): current_verifier = "" if _use_uuid: try: with open(self._verifier_path, "r") as f: current_verifier = f.read() except BaseException: pass if (current_verifier != self.last_seen_verifier) or (current_verifier == ""): self.last_seen_verifier = current_verifier # Read from file if a database exists self._read_from_file(self._index_path) elif self._state_is_inconsistent: self._read_from_file(self._index_path) self._state_is_inconsistent = False return elif self.is_upstream: tty.warn("upstream not found: {0}".format(self._index_path)) def _add(self, spec, directory_layout=None, explicit=False, installation_time=None): """Add an install record for this spec to the database. Assumes spec is installed in ``layout.path_for_spec(spec)``. Also ensures dependencies are present and updated in the DB as either installed or missing. Args: spec: spec to be added directory_layout: layout of the spec installation **kwargs: explicit Possible values: True, False, any A spec that was installed following a specific user request is marked as explicit. If instead it was pulled-in as a dependency of a user requested spec it's considered implicit. installation_time Date and time of installation """ if not spec.concrete: raise NonConcreteSpecAddError("Specs added to DB must be concrete.") key = spec.dag_hash() spec_pkg_hash = spec._package_hash upstream, record = self.query_by_spec_hash(key) if upstream: return # Retrieve optional arguments installation_time = installation_time or _now() for dep in spec.dependencies(deptype=_tracked_deps): dkey = dep.dag_hash() if dkey not in self._data: extra_args = {"explicit": False, "installation_time": installation_time} self._add(dep, directory_layout, **extra_args) # Make sure the directory layout agrees whether the spec is installed if not spec.external and directory_layout: path = directory_layout.path_for_spec(spec) installed = False try: directory_layout.ensure_installed(spec) installed = True self._installed_prefixes.add(path) except DirectoryLayoutError as e: msg = ( "{0} is being {1} in the database with prefix {2}, " "but this directory does not contain an installation of " "the spec, due to: {3}" ) action = "updated" if key in self._data else "registered" tty.warn(msg.format(spec.short_spec, action, path, str(e))) elif spec.external_path: path = spec.external_path installed = True else: path = None installed = True if key not in self._data: # Create a new install record with no deps initially. new_spec = spec.copy(deps=False) extra_args = {"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) # Connect dependencies from the DB to the new copy. for dep in spec.edges_to_dependencies(deptype=_tracked_deps): dkey = dep.spec.dag_hash() upstream, record = self.query_by_spec_hash(dkey) new_spec._add_dependency(record.spec, dep.deptypes) if not upstream: record.ref_count += 1 # Mark concrete once everything is built, and preserve # the original hashes of concrete specs. new_spec._mark_concrete() new_spec._hash = key new_spec._package_hash = spec_pkg_hash else: # It is already in the database self._data[key].installed = installed self._data[key].installation_time = _now() self._data[key].explicit = explicit
[docs] @_autospec def add(self, spec, directory_layout, explicit=False): """Add spec at path to database, locking and reading DB to sync. ``add()`` will lock and read from the DB on disk. """ # TODO: ensure that spec is concrete? # Entire add is transactional. with self.write_transaction(): self._add(spec, directory_layout, explicit=explicit)
def _get_matching_spec_key(self, spec, **kwargs): """Get the exact spec OR get a single spec that matches.""" key = spec.dag_hash() upstream, record = self.query_by_spec_hash(key) if not record: match = self.query_one(spec, **kwargs) if match: return match.dag_hash() raise KeyError("No such spec in database! %s" % spec) return key
[docs] @_autospec def get_record(self, spec, **kwargs): key = self._get_matching_spec_key(spec, **kwargs) upstream, record = self.query_by_spec_hash(key) return record
def _decrement_ref_count(self, spec): key = spec.dag_hash() if key not in self._data: # TODO: print something here? DB is corrupt, but # not much we can do. return rec = self._data[key] rec.ref_count -= 1 if rec.ref_count == 0 and not rec.installed: del self._data[key] for dep in spec.dependencies(deptype=_tracked_deps): self._decrement_ref_count(dep) def _increment_ref_count(self, spec): key = spec.dag_hash() if key not in self._data: return rec = self._data[key] rec.ref_count += 1 def _remove(self, spec): """Non-locking version of remove(); does real work.""" key = self._get_matching_spec_key(spec) rec = self._data[key] # This install prefix is now free for other specs to use, even if the # spec is only marked uninstalled. if not rec.spec.external and rec.installed: self._installed_prefixes.remove(rec.path) if rec.ref_count > 0: rec.installed = False return rec.spec del self._data[key] # Remove any reference to this node from dependencies and # decrement the reference count rec.spec.detach(deptype=_tracked_deps) for dep in rec.spec.dependencies(deptype=_tracked_deps): self._decrement_ref_count(dep) if rec.deprecated_for: new_spec = self._data[rec.deprecated_for].spec self._decrement_ref_count(new_spec) # Returns the concrete spec so we know it in the case where a # query spec was passed in. return rec.spec
[docs] @_autospec def remove(self, spec): """Removes a spec from the database. To be called on uninstall. Reads the database, then: 1. Marks the spec as not installed. 2. Removes the spec if it has no more dependents. 3. If removed, recursively updates dependencies' ref counts and removes them if they are no longer needed. """ # Take a lock around the entire removal. with self.write_transaction(): return self._remove(spec)
[docs] def deprecator(self, spec): """Return the spec that the given spec is deprecated for, or None""" with self.read_transaction(): spec_key = self._get_matching_spec_key(spec) spec_rec = self._data[spec_key] if spec_rec.deprecated_for: return self._data[spec_rec.deprecated_for].spec else: return None
[docs] def specs_deprecated_by(self, spec): """Return all specs deprecated in favor of the given spec""" with self.read_transaction(): return [ rec.spec for rec in self._data.values() if rec.deprecated_for == spec.dag_hash() ]
def _deprecate(self, spec, deprecator): spec_key = self._get_matching_spec_key(spec) spec_rec = self._data[spec_key] deprecator_key = self._get_matching_spec_key(deprecator) self._increment_ref_count(deprecator) # If spec was already deprecated, update old deprecator's ref count if spec_rec.deprecated_for: old_repl_rec = self._data[spec_rec.deprecated_for] self._decrement_ref_count(old_repl_rec.spec) spec_rec.deprecated_for = deprecator_key spec_rec.installed = False self._data[spec_key] = spec_rec
[docs] @_autospec def mark(self, spec, key, value): """Mark an arbitrary record on a spec.""" with self.write_transaction(): return self._mark(spec, key, value)
def _mark(self, spec, key, value): record = self._data[self._get_matching_spec_key(spec)] setattr(record, key, value)
[docs] @_autospec def deprecate(self, spec, deprecator): """Marks a spec as deprecated in favor of its deprecator""" with self.write_transaction(): return self._deprecate(spec, deprecator)
[docs] @_autospec def installed_relatives(self, spec, direction="children", transitive=True, deptype="all"): """Return installed specs related to this one.""" if direction not in ("parents", "children"): raise ValueError("Invalid direction: %s" % direction) relatives = set() for spec in self.query(spec): if transitive: to_add = spec.traverse(direction=direction, root=False, deptype=deptype) elif direction == "parents": to_add = spec.dependents(deptype=deptype) else: # direction == 'children' to_add = spec.dependencies(deptype=deptype) for relative in to_add: hash_key = relative.dag_hash() upstream, record = self.query_by_spec_hash(hash_key) if not record: reltype = "Dependent" if direction == "parents" else "Dependency" msg = "Inconsistent state! %s %s of %s not in DB" % ( reltype, hash_key, spec.dag_hash(), ) if self._fail_when_missing_deps: raise MissingDependenciesError(msg) tty.warn(msg) continue if not record.installed: continue relatives.add(relative) return relatives
[docs] @_autospec def installed_extensions_for(self, extendee_spec): """ Return the specs of all packages that extend the given spec """ for spec in self.query(): if spec.package.extends(extendee_spec): yield spec.package
[docs] @_autospec def activated_extensions_for(self, extendee_spec, extensions_layout=None): """ Return the specs of all packages that extend the given spec """ if extensions_layout is None: view = YamlFilesystemView(extendee_spec.prefix, spack.store.layout) extensions_layout = view.extensions_layout for spec in self.query(): try: extensions_layout.check_activated(extendee_spec, spec) yield spec.package except spack.directory_layout.NoSuchExtensionError: continue
# TODO: conditional way to do this instead of catching exceptions def _get_by_hash_local(self, dag_hash, default=None, installed=any): # hash is a full hash and is in the data somewhere if dag_hash in self._data: rec = self._data[dag_hash] if rec.install_type_matches(installed): return [rec.spec] else: return default # check if hash is a prefix of some installed (or previously # installed) spec. matches = [ record.spec for h, record in self._data.items() if h.startswith(dag_hash) and record.install_type_matches(installed) ] if matches: return matches # nothing found return default
[docs] def get_by_hash_local(self, *args, **kwargs): """Look up a spec in *this DB* by DAG hash, or by a DAG hash prefix. Arguments: dag_hash (str): hash (or hash prefix) to look up default (object or None): default value to return if dag_hash is not in the DB (default: None) installed (bool or InstallStatus or typing.Iterable or None): if ``True``, includes only installed specs in the search; if ``False`` only missing specs, and if ``any``, all specs in database. If an InstallStatus or iterable of InstallStatus, returns specs whose install status (installed, deprecated, or missing) matches (one of) the InstallStatus. (default: any) ``installed`` defaults to ``any`` so that we can refer to any known hash. Note that ``query()`` and ``query_one()`` differ in that they only return installed specs by default. Returns: (list): a list of specs matching the hash or hash prefix """ with self.read_transaction(): return self._get_by_hash_local(*args, **kwargs)
[docs] def get_by_hash(self, dag_hash, default=None, installed=any): """Look up a spec by DAG hash, or by a DAG hash prefix. Arguments: dag_hash (str): hash (or hash prefix) to look up default (object or None): default value to return if dag_hash is not in the DB (default: None) installed (bool or InstallStatus or typing.Iterable or None): if ``True``, includes only installed specs in the search; if ``False`` only missing specs, and if ``any``, all specs in database. If an InstallStatus or iterable of InstallStatus, returns specs whose install status (installed, deprecated, or missing) matches (one of) the InstallStatus. (default: any) ``installed`` defaults to ``any`` so that we can refer to any known hash. Note that ``query()`` and ``query_one()`` differ in that they only return installed specs by default. Returns: (list): a list of specs matching the hash or hash prefix """ spec = self.get_by_hash_local(dag_hash, default=default, installed=installed) if spec is not None: return spec for upstream_db in self.upstream_dbs: spec = upstream_db._get_by_hash_local(dag_hash, default=default, installed=installed) if spec is not None: return spec return default
def _query( self, query_spec=any, known=any, installed=True, explicit=any, start_date=None, end_date=None, hashes=None, in_buildcache=any, origin=None, ): """Run a query on the database.""" # TODO: Specs are a lot like queries. Should there be a # TODO: wildcard spec object, and should specs have attributes # TODO: like installed and known that can be queried? Or are # TODO: these really special cases that only belong here? # Just look up concrete specs with hashes; no fancy search. if isinstance(query_spec, spack.spec.Spec) and query_spec.concrete: # TODO: handling of hashes restriction is not particularly elegant. hash_key = query_spec.dag_hash() if hash_key in self._data and (not hashes or hash_key in hashes): return [self._data[hash_key].spec] else: return [] # Abstract specs require more work -- currently we test # against everything. results = [] start_date = start_date or datetime.datetime.min end_date = end_date or datetime.datetime.max for key, rec in self._data.items(): 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 if in_buildcache is not any and rec.in_buildcache != in_buildcache: continue if explicit is not any and rec.explicit != explicit: continue if known is not any and spack.repo.path.exists(rec.spec.name) != known: continue if start_date or end_date: inst_date = datetime.datetime.fromtimestamp(rec.installation_time) if not (start_date < inst_date < end_date): continue if query_spec is any or rec.spec.satisfies(query_spec, strict=True): results.append(rec.spec) return results if _query.__doc__ is None: _query.__doc__ = "" _query.__doc__ += _query_docstring
[docs] def query_local(self, *args, **kwargs): """Query only the local Spack database. This function doesn't guarantee any sorting of the returned data for performance reason, since comparing specs for __lt__ may be an expensive operation. """ with self.read_transaction(): return self._query(*args, **kwargs)
if query_local.__doc__ is None: query_local.__doc__ = "" query_local.__doc__ += _query_docstring
[docs] def query(self, *args, **kwargs): """Query the Spack database including all upstream databases.""" upstream_results = [] for upstream_db in self.upstream_dbs: # queries for upstream DBs need to *not* lock - we may not # have permissions to do this and the upstream DBs won't know about # us anyway (so e.g. they should never uninstall specs) upstream_results.extend(upstream_db._query(*args, **kwargs) or []) local_results = set(self.query_local(*args, **kwargs)) results = list(local_results) + list(x for x in upstream_results if x not in local_results) return sorted(results)
if query.__doc__ is None: query.__doc__ = "" query.__doc__ += _query_docstring
[docs] def query_one(self, query_spec, known=any, installed=True): """Query for exactly one spec that matches the query spec. Raises an assertion error if more than one spec matches the query. Returns None if no installed package matches. """ concrete_specs = self.query(query_spec, known=known, installed=installed) assert len(concrete_specs) <= 1 return concrete_specs[0] if concrete_specs else None
[docs] def missing(self, spec): key = spec.dag_hash() upstream, record = self.query_by_spec_hash(key) return record and not record.installed
[docs] def is_occupied_install_prefix(self, path): with self.read_transaction(): return path in self._installed_prefixes
@property def unused_specs(self): """Return all the specs that are currently installed but not needed at runtime to satisfy user's requests. Specs in the return list are those which are not either: 1. Installed on an explicit user request 2. Installed as a "run" or "link" dependency (even transitive) of a spec at point 1. """ needed, visited = set(), set() with self.read_transaction(): for key, rec in self._data.items(): if not rec.explicit: continue # recycle `visited` across calls to avoid redundantly traversing for spec in rec.spec.traverse(visited=visited, deptype=("link", "run")): needed.add(spec.dag_hash()) unused = [ rec.spec for key, rec in self._data.items() if key not in needed and rec.installed ] return unused
[docs] def update_explicit(self, spec, explicit): """ Update the spec's explicit state in the database. Args: spec (spack.spec.Spec): the spec whose install record is being updated explicit (bool): ``True`` if the package was requested explicitly by the user, ``False`` if it was pulled in as a dependency of an explicit package. """ rec = self.get_record(spec) if explicit != rec.explicit: with self.write_transaction(): message = "{s.name}@{s.version} : marking the package {0}" status = "explicit" if explicit else "implicit" tty.debug(message.format(status, s=spec)) rec.explicit = explicit
[docs]class UpstreamDatabaseLockingError(SpackError): """Raised when an operation would need to lock an upstream database"""
[docs]class CorruptDatabaseError(SpackError): """Raised when errors are found while reading the database."""
[docs]class NonConcreteSpecAddError(SpackError): """Raised when attemptint to add non-concrete spec to DB."""
[docs]class MissingDependenciesError(SpackError): """Raised when DB cannot find records for dependencies"""
[docs]class InvalidDatabaseVersionError(SpackError): def __init__(self, expected, found): super(InvalidDatabaseVersionError, self).__init__( "Expected database version %s but found version %s." % (expected, found), "`spack reindex` may fix this, or you may need a newer " "Spack version.", )