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2021-03-30Fix clearing cache of InternalConfigScope (#22609)Harmen Stoppels3-38/+47
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-03-29move binary indices are stored into the misc_cache (#22500)Danny McClanahan2-13/+20
Remote buildcache indices need to be stored in a place that does not require writing to the Spack prefix. Move them from the install_tree to the misc_cache.
2021-03-29bugfix for active when pkg is already active error (#22587)Cyrus Harrison1-2/+7
* bugfix for active when pkg is already active error Co-authored-by: Greg Becker <becker33@llnl.gov>
2021-03-29Externals are preferred even when they have non-default variant valuesMassimiliano Culpo3-1/+33
fixes #22596 Variants which are specified in an external spec are not scored negatively if they encode a non-default value.
2021-03-29Enforce uniqueness of the version_weight atom per nodeMassimiliano Culpo4-7/+32
fixes #22565 This change enforces the uniqueness of the version_weight atom per node(Package) in the DAG. It does so by applying FTSE and adding an extra layer of indirection with the possible_version_weight/2 atom. Before this change it may have happened that for the same node two different version_weight/2 were in the answer set, each of which referred to a different spec with the same version, and their weights would sum up. This lead to unexpected result like preferring to build a new version of an external if the external version was older.
2021-03-29Make stage use concrete specs from environment (#22320)Harmen Stoppels2-1/+121
* Make stage use concrete specs from environment Same as in https://github.com/spack/spack/pull/21642, the idea is that we want to easily stage a package that fails to build in a complex environment. Instead of making the user create a spec by hand (basically transforming all the rules in the environment manifest into a spec, defying the purpose of the environment...), use the provided spec as a filter for the already concretized specs. This also speeds up things, cause we don't have to reconcretize.
2021-03-29Add "spack [cd|location] --source-dir" (#22321)Harmen Stoppels2-56/+80
2021-03-26clingo: modify recipe for bootstrapping (#22354)Massimiliano Culpo2-12/+57
* clingo: modify recipe for bootstrapping Modifications: - clingo builds with shared Python only if ^python+shared - avoid building the clingo app for bootstrapping - don't link to libpython when bootstrapping * Remove option that breaks on linux * Give more hints for the current Python * Disable CLINGO_BUILD_PY_SHARED for bootstrapping * bootstrapping: try to detect the current python from std library This is much faster than calling external executables * Fix compatibility with Python 2.6 * Give hints on which compiler and OS to use when bootstrapping This change hints which compiler to use for bootstrapping clingo (either GCC or Apple Clang on MacOS). On Cray platforms it also hints to build for the frontend system, where software is meant to be installed. * Use spec_for_current_python to constrain module requirement
2021-03-26ASP-based solver: model disjoint sets for multivalued variants (#22534)Massimiliano Culpo3-2/+49
* ASP-based solver: avoid adding values to variants when they're set fixes #22533 fixes #21911 Added a rule that prevents any value to slip in a variant when the variant is set explicitly. This is relevant for multi-valued variants, in particular for those that have disjoint sets of values. * Ensure disjoint sets have a clear semantics for external packages
2021-03-26Make SingleFileScope able to repopulate the cache after clearing it (#22559)Massimiliano Culpo2-16/+47
fixes #22547 SingleFileScope was not able to repopulate its cache before this change. This was affecting the configuration seen by environments using clingo bootstrapped from sources, since the bootstrapping operation involved a few cache invalidation for config files.
2021-03-24Add doc for mirror of env (#22525)Frédéric Simonis1-0/+21
2021-03-23Add stdcxx_libs for PGI and Cray compilers (#22491)Sergey Kosukhin3-0/+12
2021-03-23bootstrap: account for platform specific configuration scopes (#22489)Massimiliano Culpo1-7/+18
This change accounts for platform specific configuration scopes, like ~/.spack/linux, during bootstrapping. These scopes were previously not accounted for and that was causing issues e.g. when searching for compilers.
2021-03-22Oneapi packages: update URLs, environment management, and dependencies (#22202)Robert Cohn4-36/+185
* Replace URL computation in base IntelOneApiPackage class with defining URLs in component packages (this is expected to be simpler for now) * Add component_dir property that all oneAPI component packages must define. This property names a directory that should exist after installation completes (useful for making sure the install was successful) and also defines the search location for the component's environment update script. * Add needed dependencies for components (e.g. intel-oneapi-dnn requires intel-oneapi-tbb). The compilers provided by intel-oneapi-compilers need some components under certain circumstances (e.g. when enabling SYCL support) but these were omitted since the libraries should only be linked when a dependent package requests that feature * Remove individual setup_run_environment implementations and use IntelOneApiPackage superclass method which sources vars.sh (located in a subdirectory of component_dir) * Add documentation for IntelOneApiPackge build system Co-authored-by: Vasily Danilin <vasily.danilin@yandex.ru>
2021-03-22use link/run deps only to compare extensions (#22396)Greg Becker1-2/+2
2021-03-21Document cli syntax for environment scopes (#20344)Greg Becker2-4/+18
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-03-18Fix broken spack -c flag (#22361)Harmen Stoppels1-1/+1
2021-03-18archspec: update to latest version (#22357)Massimiliano Culpo2-2/+45
2021-03-18Tab to spaces (#22362)Harmen Stoppels1-2/+2
2021-03-17Fix indentation compiler wrapper issue (#22352)Harmen Stoppels1-1/+1
2021-03-17aocc: add support for v3.0 compilers (#22219)AMD Toolchain Support3-0/+29
A mitigation of a known issue that affects v3.0 is added, see https://developer.amd.com/wp-content/resources/AOCC-3.0-Install-Guide.pdf
2021-03-17spack location: bugfix for out of source build dirs (#22348)Harmen Stoppels1-1/+13
2021-03-16fix weird failure in variant values (#22328)Danny McClanahan1-1/+14
2021-03-16containerize: fix typo in documentation (#22331)Wouter Deconinck1-1/+1
Before this fix, `spack containerize` complains that `centos/7` is invalid (should have been `centos:7`)
2021-03-16Speed-up CI by reorganizing tests (#22247)Massimiliano Culpo6-12/+18
* unit tests: mark slow tests as "maybeslow" This commit also removes the "network" marker and marks every "network" test as "maybeslow". Tests marked as db are maintained, but they're not slow anymore. * GA: require style tests to pass before running unit-tests * GA: make MacOS unit tests fail fast * GA: move all unit tests into the same workflow, run style tests as a prerequisite All the unit tests have been moved into the same workflow so that a single run of the dorny/paths-filter action can be used to ask for coverage based on the files that have been changed in a PR. The basic idea is that for PRs that introduce only changes to packages coverage is not necessary, this resulting in a faster execution of the tests. Also, for package only PRs slow unit tests are skipped. Finally, MacOS and linux unit tests are now conditional on style tests passing meaning that e.g. we won't waste a MacOS worker if we know that the PR has flake8 issues. * Addressed review comments * Skipping slow tests on MacOS for package only recipes * QA: make tests on changes correct before merging
2021-03-16bugfix: allow imposed constraints to be overridden in special casesTodd Gamblin1-6/+16
In most cases, we want condition_holds(ID) to imply any imposed constraints associated with the ID. However, the dependency relationship in Spack is special because it's "extra" conditional -- a dependency *condition* may hold, but we have decided that externals will not have dependencies, so we need a way to avoid having imposed constraints appear for nodes that don't exist. This introduces a new rule that says that constraints are imposed *unless* we define `do_not_impose(ID)`. This allows rules like dependencies, which rely on more than just spec conditions, to cancel imposed constraints. We add one special case for this: dependencies of externals.
2021-03-16bugfix: do not generate dep conditions when no dependencyTodd Gamblin1-10/+15
We only consider test dependencies some of the time. Some packages are *only* test dependencies. Spack's algorithm was previously generating dependency conditions that could hold, *even* if there was no potential dependency type. - [x] change asp.py so that this can't happen -- we now only generate dependency types for possible dependencies.
2021-03-16concretizer: unify logic for spec conditionalsTodd Gamblin3-183/+119
This builds on #20638 by unifying all the places in the concretizer where things are conditional on specs. Previously, we duplicated a common spec conditional pattern for dependencies, virtual providers, conflicts, and externals. That was introduced in #20423 and refined in #20507, and roughly looked as follows. Given some directives in a package like: ```python depends_on("foo@1.0+bar", when="@2.0+variant") provides("mpi@2:", when="@1.9:") ``` We handled the `@2.0+variant` and `@1.9:` parts by generating generated `dependency_condition()`, `required_dependency_condition()`, and `imposed_dependency_condition()` facts to trigger rules like this: ```prolog dependency_conditions_hold(ID, Parent, Dependency) :- attr(Name, Arg1) : required_dependency_condition(ID, Name, Arg1); attr(Name, Arg1, Arg2) : required_dependency_condition(ID, Name, Arg1, Arg2); attr(Name, Arg1, Arg2, Arg3) : required_dependency_condition(ID, Name, Arg1, Arg2, Arg3); dependency_condition(ID, Parent, Dependency); node(Parent). ``` And we handled `foo@1.0+bar` and `mpi@2:` parts ("imposed constraints") like this: ```prolog attr(Name, Arg1, Arg2) :- dependency_conditions_hold(ID, Package, Dependency), imposed_dependency_condition(ID, Name, Arg1, Arg2). attr(Name, Arg1, Arg2, Arg3) :- dependency_conditions_hold(ID, Package, Dependency), imposed_dependency_condition(ID, Name, Arg1, Arg2, Arg3). ``` These rules were repeated with different input predicates for requirements (e.g., `required_dependency_condition`) and imposed constraints (e.g., `imposed_dependency_condition`) throughout `concretize.lp`. In #20638 it got to be a bit confusing, because we used the same `dependency_condition_holds` predicate to impose constraints on conditional dependencies and virtual providers. So, even though the pattern was repeated, some of the conditional rules were conjoined in a weird way. Instead of repeating this pattern everywhere, we now have *one* set of consolidated rules for conditions: ```prolog condition_holds(ID) :- condition(ID); attr(Name, A1) : condition_requirement(ID, Name, A1); attr(Name, A1, A2) : condition_requirement(ID, Name, A1, A2); attr(Name, A1, A2, A3) : condition_requirement(ID, Name, A1, A2, A3). attr(Name, A1) :- condition_holds(ID), imposed_constraint(ID, Name, A1). attr(Name, A1, A2) :- condition_holds(ID), imposed_constraint(ID, Name, A1, A2). attr(Name, A1, A2, A3) :- condition_holds(ID), imposed_constraint(ID, Name, A1, A2, A3). ``` this allows us to use `condition(ID)` and `condition_holds(ID)` to encapsulate the conditional logic on specs in all the scenarios where we need it. Instead of defining predicates for the requirements and imposed constraints, we generate the condition inputs with generic facts, and define predicates to associate the condition ID with a particular scenario. So, now, the generated facts for a condition look like this: ```prolog condition(121). condition_requirement(121,"node","cairo"). condition_requirement(121,"variant_value","cairo","fc","True"). imposed_constraint(121,"version_satisfies","fontconfig","2.10.91:"). dependency_condition(121,"cairo","fontconfig"). dependency_type(121,"build"). dependency_type(121,"link"). ``` The requirements and imposed constraints are generic, and we associate them with their meaning via the id. Here, `dependency_condition(121, "cairo", "fontconfig")` tells us that condition 121 has to do with the dependency of `cairo` on `fontconfig`, and the conditional dependency rules just become: ```prolog dependency_holds(Package, Dependency, Type) :- dependency_condition(ID, Package, Dependency), dependency_type(ID, Type), condition_holds(ID). ``` Dependencies, virtuals, conflicts, and externals all now use similar patterns, and the logic for generating condition facts is common to all of them on the python side, as well. The more specific routines like `package_dependencies_rules` just call `self.condition(...)` to get an id and generate requirements and imposed constraints, then they generate their extra facts with the returned id, like this: ```python def package_dependencies_rules(self, pkg, tests): """Translate 'depends_on' directives into ASP logic.""" for _, conditions in sorted(pkg.dependencies.items()): for cond, dep in sorted(conditions.items()): condition_id = self.condition(cond, dep.spec, pkg.name) # create a condition and get its id self.gen.fact(fn.dependency_condition( # associate specifics about the dependency w/the id condition_id, pkg.name, dep.spec.name )) # etc. ``` - [x] unify generation and logic for conditions - [x] use unified logic for dependencies - [x] use unified logic for virtuals - [x] use unified logic for conflicts - [x] use unified logic for externals LocalWords: concretizer mpi attr Arg concretize lp cairo fc fontconfig LocalWords: virtuals def pkg cond dep fn refactor github py
2021-03-15Expand relative dev paths in environment files (#22045)Harmen Stoppels6-19/+138
* Rewrite relative dev_spec paths internally to absolute paths in case of relocation of the environment file * Test relative paths for dev_path in environments * Add a --keep-relative flag to spack env create This ensures that relative paths of develop paths are not expanded to absolute paths when initializing the environment in a different location from the spack.yaml init file.
2021-03-15Propagate --test= for environments (#22040)Harmen Stoppels7-27/+125
* Propagate --test= for environments * Improve help comment for spack concretize --test flag * Add tests for --test with environments
2021-03-15Fix use of quotes in Python build system (#22279)Adam J. Stewart1-1/+1
2021-03-14do not validate variants of concrete specs in solver setup (#22272)Vanessasaurus1-10/+11
Currently, regardless of a spec being concrete or not, we validate its variants in `spec_clauses` (part of `SpackSolverSetup`). This PR skips the check if the spec is concrete. The reason we want to do this is so that the solver setup class (really, `spec_clauses`) can be used for cases when we just want the logic statements / facts (is that what they are called?) and we don't need to re-validate an already concrete spec. We can't change existing concrete specs, and we have to be able to handle them *even if they violate constraints in the current spack*. This happens in practice if we are doing the validation for a spec produced by a different spack install. Signed-off-by: vsoch <vsoch@users.noreply.github.com>
2021-03-13adding spack -c to set one off config arguments (#22251)Vanessasaurus5-72/+132
This pull request will add the ability for a user to add a configuration argument on the fly, on the command line, e.g.,: ```bash $ spack -c config:install_tree:root:/path/to/config.yaml -c packages:all:compiler:[gcc] list --help ``` The above command doesn't do anything (I'm just getting help for list) but you can imagine having another root of packages, and updating it on the fly for a command (something I'd like to do in the near future!) I've moved the logic for config_add that used to be in spack/cmd/config.py into spack/config.py proper, and now both the main.py (where spack commands live) and spack/cmd/config.py use these functions. I only needed spack config add, so I didn't move the others. We can move the others if there are also needed in multiple places.
2021-03-12bugfix: ensure spack test list still works (#22203)Tamara Dahlgren2-2/+25
Was getting the following error: ``` $ spack test list ==> Error: issubclass() arg 1 must be a class ``` This PR adds a check in `has_test_method` (in case it is re-used elsewhere such as #22097) and ensures a class is passed to the method from `spack test list`.
2021-03-10Pipelines: Fix issue that allowed failing jobs to pass (#22199)Scott Wittenburg1-1/+3
This is a workaround for an issue with how "spack install" is invoked from within "spack ci rebuild". The fact that we don't get an exception or even the actual returncode when using the object returned by spack.util.executable.which('spack') to install the target spec means we get no indication of failures about the install command itself. Instead we rely on the subsequent buildcache creation failure to fail the job.
2021-03-08Fix `spack graph` when deptypes are filtered (#22121)Harmen Stoppels3-8/+16
2021-03-08Add `--vanilla` flag to r build system (#22166)Glenn Johnson1-0/+1
Unlike the other commands of the `R CMD` interface, the `INSTALL` command will read `Renviron` files. This can potentially break builds of r- packages, depending on what is set in the `Renviron` file. This PR adds the `--vanilla` flag to ensure that neither `Rprofile` nor `Renviron` files are read during Spack builds of r- packages.
2021-03-07spack python: add --path option (#22006)Todd Gamblin2-0/+13
This adds a `--path` option to `spack python` that shows the `python` interpreter that Spack is using. e.g.: ```console $ spack python --path /Users/gamblin2/src/spack/var/spack/environments/default/.spack-env/view/bin/python ``` This is useful for debugging, and we can ask users to run it to understand what python Spack is picking up via preferences in `bin/spack` and via the `SPACK_PYTHON` environment variable introduced in #21222.
2021-03-07add `spack test list --all` (#22032)Todd Gamblin2-5/+38
`spack test list` will show you which *installed* packages can be tested but it won't show you which packages have tests. - [x] add `spack test list --all` to show which packages have test methods - [x] update `has_test_method()` to handle package instances *and* package classes.
2021-03-05Improve R package creation (#21861)Glenn Johnson3-6/+125
* Improve R package creation This PR adds the `list_url` attribute to CRAN R packages when using `spack create`. It also adds the `git` attribute to R Bioconductor packages upon creation. * Switch over to using cran/bioc attributes The cran/bioc entries are set to have the '=' line up with homepage entry, but homepage does not need to exist in the package file. If it does not, that could affect the alignment. * Do not have to split bioc * Edit R package documentation Explain Bioconductor packages and add `cran` and `bioc` attributes. * Update lib/spack/docs/build_systems/rpackage.rst Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update lib/spack/docs/build_systems/rpackage.rst Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Simplify the cran attribute The version can be faked so that the cran attribute is simply equal to the CRAN package name. * Edit the docs to reflect new `cran` attribute format * Use the first element of self.versions() for url Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-03-04Allow relative paths in config files (relative to file dirname) (#21996)Greg Becker2-8/+63
This allows users to use relative paths for mirrors and repos and other things that may be part of a Spack environment. There are two ways to do it. 1. Relative to the file ```yaml spack: repos: - local_dir/my_repository ``` Which will refer to a repository like this in the directory where `spack.yaml` lives: ``` env/ spack.yaml <-- the config file above local_dir/ my_repository/ <-- this repository repo.yaml packages/ ``` 2. Relative to the environment ```yaml spack: repos: - $env/local_dir/my_repository ``` Both of these would refer to the same directory, but they differ for included files. For example, if you had this layout: ``` env/ spack.yaml repository/ includes/ repos.yaml repository/ ``` And this `spack.yaml`: ```yaml spack: include: includes/repos.yaml ``` Then, these two `repos.yaml` files are functionally different: ```yaml repos: - $env/repository # refers to env/repository/ above repos: - repository # refers to env/includes/repository/ above ``` The $env variable will not be evaluated if there is no active environment. This generally means that it should not be used outside of an environment's spack.yaml file. However, if other aspects of your workflow guarantee that there is always an active environment, it may be used in other config scopes.
2021-03-03Bootstrap clingo from sources (#21446)Massimiliano Culpo10-19/+348
* Allow the bootstrapping of clingo from sources Allow python builds with system python as external for MacOS * Ensure consistent configuration when bootstrapping clingo This commit uses context managers to ensure we can bootstrap clingo using a consistent configuration regardless of the use case being managed. * Github actions: test clingo with bootstrapping from sources * Add command to inspect and clean the bootstrap store Prevent users to set the install tree root to the bootstrap store * clingo: documented how to bootstrap from sources Co-authored-by: Gregory Becker <becker33@llnl.gov>
2021-03-02Assert the use of the patch directive with a non-existing file will fail ↵Adam J. Stewart1-6/+22
(#21524)
2021-02-27Raise InstallError if any explicit specs is skipped (#21980)Tamara Dahlgren4-11/+32
2021-02-26Compilers: make oneapi ifx version_regex tolerant to wrappers (#21742)e4s-21.02Gregory Lee1-1/+1
If a user creates a wrapper for the ifx binary called ifx_orig, this causes the ifx --version command to produce: $ ifx --version ifx_orig (IFORT) 2021.1 Beta 20201113 Copyright (C) 1985-2020 Intel Corporation. All rights reserved. The regex for ifx currently expects the output to begin with "ifx (IFORT)..." so the wrapper would not be detected as ifx. This PR removes the need for the static "ifx" string which allows wrappers to be detected as ifx. In general, the Intel compiler regexes do not include the invoked executable name (i.e., ifort, icc, icx, etc.), so this is not expected to cause any issues.
2021-02-26make `spack fetch` work with environments (#19166)Andreas Baumbach4-20/+117
* make `spack fetch` work with environments * previously: `spack fetch` required the explicit statement of the specs to be fetched, even when in an environment * now: if there is no spec(s) provided to `spack fetch` we check if an environment is active and if yes we fetch all uninstalled specs.
2021-02-25typo fix (#21967)Greg Becker1-1/+1
2021-02-25Old concretizer: prevent unexpected propagation of external config (#20976)Michael Kuron2-0/+31
When using an external package with the old concretizer, all dependencies of that external package were severed. This was not performed bidirectionally though, so for an external package W with a dependency on Z, if some other package Y depended on Z, Z could still pull properties (e.g. compiler) from W since it was not severed as a parent dependency. This performs the severing bidirectionally, and adds tests to confirm expected behavior when using config from DAG-adjacent packages during concretization.
2021-02-24Config prefer upstream (#21487)Paul Ferrell3-2/+138
This allows for quickly configuring a spack install/env to use upstream packages by default. This is particularly important when upstreaming from a set of officially supported spack installs on a production cluster. By configuring such that package preferences match the upstream, you ensure maximal reuse of existing package installations.
2021-02-23Gitlab fix pr workflow (#21786)Scott Wittenburg1-1/+2
Fixes for gitlab pipelines * Remove accidentally retained testing branch name * Generate pipeline w/out debug mode * Make jobs interruptible for auto-cancel pending * Work around concretization conflicts