The YAML config for paths and modules of external packages has
changed: the new format allows a single spec to load multiple
modules. Spack will automatically convert from the old format
when reading the configs (the updates do not add new essential
properties, so this change in Spack is backwards-compatible).
With this update, Spack cannot modify existing configs/environments
without updating them (e.g. “spack config add” will fail if the
configuration is in a format that predates this PR). The user is
prompted to do this explicitly and commands are provided. All
config scopes can be updated at once. Each environment must be
updated one at a time.
* Buildcache:
* Try mocking an install of quux, corge and garply using prebuilt binaries
* Put patchelf install after ccache restore
* Add script to install patchelf from source so it can be used on Ubuntu:Trusty which does not have a patchelf pat package. The script will skip building on macOS
* Remove mirror at end of bindist test
* Add patchelf to Ubuntu build env
* Revert mock patchelf package to allow other tests to run.
* Remove depends_on('patchelf', type='build') relying instead on
* Test fixture to ensure patchelf is available.
* Call g++ command to build libraries directly during test build
* Flake8
* Install patchelf in before_install stage using apt unless on Trusty where a build is done.
* Add some symbolic links between packages
* Flake8
* Flake8:
* Update mock packages to write their own source files
* Create the stage because spec search does not create it any longer
* updates after change of list command arguments
* cleanup after merge
* flake8
Because of the way abstract variants are implemented, the following
spec matrix does not work as intended:
```
matrix:
- [foo]
- [bar=a, bar=b]
exclude:
- bar=a
```
because abstract variants always satisfy any variant of the same
name, regardless of values.
This PR converts abstract variants to whatever their appropriate
type is before running satisfaction checks for the excludes clause
in a matrix.
fixes#16841
This change also adds a code path through the spack ci pipelines
infrastructure which supports PR testing on the Spack repository.
Gitlab pipelines run as a result of a PR (either creation or pushing
to a PR branch) will only verify that the packages in the environment
build without error. When the PR branch is merged to develop,
another pipeline will run which results in the generated binaries
getting pushed to the binary mirror.
Add a `spack external find` command that tries to populate
`packages.yaml` with external packages from the user's `$PATH`. This
focuses on finding build dependencies. Currently, support has only been
added for `cmake`.
For a package to be discoverable with `spack external find`, it must define:
* an `executables` class attribute containing a list of
regular expressions that match executable names.
* a `determine_spec_details(prefix, specs_in_prefix)` method
Spack will call `determine_spec_details()` once for each prefix where
executables are found, passing in the path to the prefix and the path to
all found executables. The package is responsible for invoking the
executables and figuring out what type of installation(s) are in the
prefix, and returning one or more specs (each with version, variants or
whatever else the user decides to include in the spec).
The found specs and prefixes will be added to the user's `packages.yaml`
file. Providing the `--not-buildable` option will mark all generated
entries in `packages.yaml` as `buildable: False`
Update compiler config with bootstrapped compiler when it was already installed and added config defaults to code so mutable_config test fixture works.
* SourceForge: Mirror Mixin
Add a mixing class for direct `CNAME`s to sourceforge mirrors.
Since the main gateway servers are often down, this could reduce
timeouts and fetch errors for sourceforge.net hosted software.
* SourceForge: unspectacular mirror replacement
add mirrors to all sourceforge packages with trivial
download logic.
tested fetch of latest version of each of these packages
with various mirrors before committing.
* SourceForge: xz
the author homepage is chronocially overrun and this is the offical
upload with many mirrors.
Add a 'define_from_variant` helper function to CMake-based Spack
packages to convert package variants into CMake arguments. For
example:
args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF'))
can be replaced with:
args.append(self.define_from_variant('foo'))
The following conversions are handled automatically:
* Flag variants will be converted to CMake booleans
* Multivalued variants will be converted to semicolon-separated strings
* Other variant values are converted to CMake string arguments
This also adds a 'define' helper method to convert any variable to
a CMake argument. It has the same conversion rules as
'define_from_variant' (but operates directly on values rather than
requiring the user to supply the name of a package variant).
PR #15212 added a new connect_timeout option that can be overridden
using fetch_options but had to specified per-version. This adds a new
per-package variable that can be used to override fetch_options for
all versions in the package. This includes connect_timeout as well
as 'cookie' (e.g. for the jdk package).
Packages can combine package-level fetch_options with per-version
fetch_options, in which case the version fetch_options completely
override the package-level fetch_options.
This commit includes tests for the added behavior.
* add --skip-unstable-versions option to 'spack mirror create' which skips sources/resource for packages if their version is not stable (i.e. if they are the head of a git branch rather than a fixed commit)
* '--skip-unstable-versions' should skip all VCS sources/resources, not just those which are not cachable
The hashing logic looks for function calls that are Spack directives.
It expects that when a Spack directive is used that it is referenced
directly by name, and that the directive function is not itself
retrieved by calling another function. When the hashing logic
encountered a function call where the function was determined
dynamically, it would fail (attempting to access a name attribute
that does not happen to exist in this case).
This updates the hashing logic to filter out function calls where the
function is determined dynamically when looking for uses of Spack
directives.
Fixes#9394Closes#13217.
## Background
Spack provides the ability to enable/disable parallel builds through two options: package `parallel` and configuration `build_jobs`. This PR changes the algorithm to allow multiple, simultaneous processes to coordinate the installation of the same spec (and specs with overlapping dependencies.).
The `parallel` (boolean) property sets the default for its package though the value can be overridden in the `install` method.
Spack's current parallel builds are limited to build tools supporting `jobs` arguments (e.g., `Makefiles`). The number of jobs actually used is calculated as`min(config:build_jobs, # cores, 16)`, which can be overridden in the package or on the command line (i.e., `spack install -j <# jobs>`).
This PR adds support for distributed (single- and multi-node) parallel builds. The goals of this work include improving the efficiency of installing packages with many dependencies and reducing the repetition associated with concurrent installations of (dependency) packages.
## Approach
### File System Locks
Coordination between concurrent installs of overlapping packages to a Spack instance is accomplished through bottom-up dependency DAG processing and file system locks. The runs can be a combination of interactive and batch processes affecting the same file system. Exclusive prefix locks are required to install a package while shared prefix locks are required to check if the package is installed.
Failures are communicated through a separate exclusive prefix failure lock, for concurrent processes, combined with a persistent store, for separate, related build processes. The resulting file contains the failing spec to facilitate manual debugging.
### Priority Queue
Management of dependency builds changed from reliance on recursion to use of a priority queue where the priority of a spec is based on the number of its remaining uninstalled dependencies.
Using a queue required a change to dependency build exception handling with the most visible issue being that the `install` method *must* install something in the prefix. Consequently, packages can no longer get away with an install method consisting of `pass`, for example.
## Caveats
- This still only parallelizes a single-rooted build. Multi-rooted installs (e.g., for environments) are TBD in a future PR.
Tasks:
- [x] Adjust package lock timeout to correspond to value used in the demo
- [x] Adjust database lock timeout to reduce contention on startup of concurrent
`spack install <spec>` calls
- [x] Replace (test) package's `install: pass` methods with file creation since post-install
`sanity_check_prefix` will otherwise error out with `Install failed .. Nothing was installed!`
- [x] Resolve remaining existing test failures
- [x] Respond to alalazo's initial feedback
- [x] Remove `bin/demo-locks.py`
- [x] Add new tests to address new coverage issues
- [x] Replace built-in package's `def install(..): pass` to "install" something
(i.e., only `apple-libunwind`)
- [x] Increase code coverage
Fixes#10019
If multiple instances of a package were installed in a single
instance of Spack, and they differed in terms of dependencies, then
"spack find" would not distinguish specs based on their dependencies.
For example if two instances of X were installed, one with Y and one
with Z, then "spack find X ^Y" would display both instances of X.
Users can now list mirrors of the main url in packages.
- [x] Instead of just a single `url` attribute, users can provide a list (`urls`) in the package, and these will be tried by in order by the fetch strategy.
- [x] To handle one of the most common mirror cases, define a `GNUMirrorPackage` mixin to handle all the standard GNU mirrors. GNU packages can set `gnu_mirror_path` to define the path within a mirror, and the mixin handles setting up all the requisite GNU mirror URLs.
- [x] update all GNU packages in `builtin` to use the `GNUMirrorPackage` mixin.
- Add an optional argument so that `possible_dependencies()` will report
missing dependencies.
- Add a test to ensure it works.
- Ignore missing dependencies in `possible_dependencies()` by default.
* when constructing package hash, default to including a method in the content hash if we can't determine whether it would be included by examining the AST
* add a test for updated content-hash calculations
* refactor content hash tests to eliminate repeated lines
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions
* add mixed version checks to version comparison tests
Rename the `spack diy` command to `spack dev-build` to make the use case clearer.
The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing. Developers do not notice it, partly because of the obscure name.
The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds.
To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well.
The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought.
This PR ensures that environment activation sets all environment variables set by the equivalent `module load` operations, except that the spec prefixes are "rebased" to the view associated with the environment.
Currently, Spack blindly adds paths relative to the environment view root to the user environment on activation. Issue #12731 points out ways in which this behavior is insufficient.
This PR changes that behavior to use the `setup_run_environment` logic for each package to augment the prefix inspections (as in Spack's modulefile generation logic) to ensure that all necessary variables are set to make use of the packages in the environment.
See #12731 for details on the previous problems in behavior.
This PR also updates the `ViewDescriptor` object in `spack.environment` to have a `__contains__` method. This allows for checks like `if spec in self.default_view`. The `__contains__` operator for `ViewDescriptor` objects checks whether the spec satisfies the filters of the View descriptor, not whether the spec is already linked into the underlying `FilesystemView` object.
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.
A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.
* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
- Fix trailing whitespace missed by the bug described in #12755.
- Fix other style issues that have crept in over time (this can happen
when flake8 adds new checks with new versions)
This adds a special package type to Spack which is used to aggregate
a set of packages that a user might commonly install together; it
does not include any source code itself and does not require a
download URL like other Spack packages. It may include an 'install'
method to generate scripts, and Spack will run post-install hooks
(including module generation).
* Add new BundlePackage type
* Update the Xsdk package to be a BundlePackage and remove the
'install' method (previously it had a noop install method)
* "spack create --template" now takes "bundle" as an option
* Rename cmd_create_repo fixture to "mock_test_repo" and relocate it
to shared pytest fixtures
* Add unit tests for BundlePackage behavior
- We don't currently make enough use of the maintainers field on
packages, though we could use it to assign reviews.
- add a command that allows maintainers to be queried
- can ask who is maintaining a package or packages
- can ask what packages users are maintaining
- can list all maintained or unmaintained packages
- add tests for the command
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
support nameless specs. We don't need it anymore because now we can
write Spec() for a spec that will match anything, and satisfies()
semantics work properly for anonymous specs.
- Delete `parse_anonymous_spec()` and replace its uses with simple calls
to the Spec() constructor.
- make then handling of when='...' specs in directives more consistent.
- clean up Spec.__contains__()
- refactor directives and tests slightly to accommodate the change.
This PR implements several refactors requested in #11373, specifically:
- Config scopes are used to handle builtin defaults, command line overrides
and package overrides (`parallel=False`)
- `Package.make_jobs` attribute has been removed; `make_jobs` remains
as a module-scope variable in the build environment.
- The use of the argument `-j` has been rationalized across commands
- move '-j'/'--jobs' argument into `spack.cmd.common.arguments`
- Add unit tests to check that setting parallel jobs works as expected
- add new test to ensure that build job setting is isolated to each build
- Fix packages that used `Package.make_jobs` (i.e. `bazel`)
* extend Version class so that 2.0 > 1.develop > 1.1
* add concretization tests, with preferences and preferred version.
* add master, head, trunk as develop-like versions, develop > master > head > trunk
* update documentation on version comparison
* initial work to make use of an 'upstream' spack installation: this uses the DB of the upstream installation to check if a package is installed
* need to query upstream dbs when adding new record to local db
* prevent reindexing upstream DBs
* set prefix on specs read from DB based on path stored in install record
* check that Spack does not install packages that are recorded as installed in an upstream db
* externals do not add their path to install records - need to use 'external_path' to get path of upstream externals
* views need to check for upstream installations when linking metadata
* package and spec now calculate upstream installation properties on-demand themselves rather than depending on concretization to set these properties up-front. The added tests for upstream installations don't work with this new strategy so they need to be updated
* only refresh modules for local specs (not those in upstream packages); optionally generate local module files for packages installed upstream
* when a user tries to locate a module file for a package installed upstream, tell them to use the upstream spack instance to locate it
* support recursive upstream databases (allow upstream databases to use their own upstream databases)
* separate upstream config into separate file with its own schema; each entry now also includes a name
* metadata_dir is no longer customizable on a per-instance basis for YamlDirectoryLayout
* treat metadata_dir as an instance variable but dont set it from kwargs; this follows several other hardcoded variables which must be consistent between upstream and downstream DBs. Also update DirectoryLayout.metadata_path to work entirely with Spec.prefix, since Spec.prefix is set from the DB when available (so metadata_path was duplicating that logic)
Allow customizing views with Spec-formatted directory structure
Allow views to specify projections that are more complicated than
merging every package into a single shared prefix. This will allow
sites to configure a view for the way they want to present packages
to their users; for example this can be used to create a prefix for
each package but omit the DAG hash from the path.
This includes a new YAML format file for specifying the simplified
prefix for a spec in a view. This configuration allows the use of
different prefix formats for different specs (i.e. specs depending
on MPI can include the MPI implementation in the prefix).
Documentation on usage of the view projection configuration is
included.
Depending on the projection configuration, paths are not guaranteed
to be unique and it may not be possible to add multiple installs of
a package to a view.
This enforces conventions that allow for correct handling of
multi-valued variants where specifying no value is an option,
and adds convenience functionality for specifying multi-valued
variants with conflicting sets of values. This also adds a notion
of "feature values" for variants, which are those that are understood
by the build system (e.g. those that would appear as configure
options). In more detail:
* Add documentation on variants to the packaging guide
* Forbid usage of '' or None as a possible variant value, in
particular as a default. To indicate choosing no value, the user
must explicitly define an option like 'none'. Without this,
multi-valued variants with default set to None were not parsable
from the command line (Fixes#6314)
* Add "disjoint_sets" function to support the declaration of
multi-valued variants with conflicting sets of options. For example
a variant "foo" with possible values "a", "b", and "c" where "c"
is exclusive of the other values ("foo=a,b" and "foo=c" are
valid but "foo=a,c" is not).
* Add "any_combination_of" function to support the declaration of
multi-valued variants where it is valid to choose none of the
values. This automatically defines "none" as an option (exclusive
with all other choices); this value does not appear when iterating
over the variant's values, for example in "with_or_without" (which
constructs autotools option strings from variant values).
* The "disjoint_sets" and "any_combination_of" methods return an
object which tracks the possible values. It is also possible to
indicate that some of these values do not correspond to options
understood by the package's build system, such that methods like
"with_or_without" will not define options for those values (this
occurs automatically for "none")
* Add documentation for usage of new functions for specifying
multi-valued variants
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
- dependency patching test didn't attempt to apply patches; just to see
whether they were on the spec.
- it applies the patch now and verifies that that patch was applied.
