When downloading from binary cache not only replace RPATHs to dependencies, but
also text references to dependencies.
Example:
`autoconf@2.69` contains a text reference to the executable of its dependency
`perl`:
```
$ grep perl-5 /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/autoconf-2.69-q3lo/bin/autoreconf
eval 'case $# in 0) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0";; *) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0" "$@";; esac'
```
These references need to be replace or any package using `autoreconf` will fail
as it cannot find the installed `perl`.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
"spack install" will not update the binary index if given a concrete
spec, which causes it to fall back to direct fetches when a simple
index update would have helped. For S3 buckets in particular, this
significantly and needlessly slows down the install process.
This commit alters the logic so that the binary index is updated
whenever a by-hash lookup fails. The lookup is attempted again with
the updated index before falling back to direct fetches. To avoid
updating too frequently (potentially once for each spec being
installed), BinaryCacheIndex.update now includes a "cooldown"
option, and when this option is enabled it will not update more
than once in a cooldown window (set in config.yaml).
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Add libpressio and dependencies; some of these packages are
maintained as forks of the original repositories and in those
cases the docstring mentions this.
* Add optional dependency in adios2 on libpressio
* cub package: set CUB_DIR environment variable for dependent
installations
* Clear R_HOME/R_ENVIRON before Spack installation (avoid sources
outside of Spack from affecting the installation in Spack)
* Rename dlib to dorian3d-dlib and update dependents; add new dlib
implementation. Pending an official policy on how to handle
packages with short names, reviewer unilaterally decided that
the rename was acceptable given that the new Spack dlib package
is referenced more widely (by orders of magnitude) than the
original
Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
When installing an individual spec `spack --only=package --cache-only /xyz`
from a buildcache, Spack currently issues tons of warnings about
missing build deps (and their deps) in the database.
This PR disables these warnings, since it's fine to have a spec without
its build deps in the db (they are just "missing").
Currently `traverse_dependencies` fixes deptypes to traverse once and
for all in the recursion, but this is incorrect, since deptypes depend
on the node (e.g. if it's a dependency and cache-only, don't follow
build type edges, even if the parent is build from sources and needs
build deps.)
Support spackbot rebuilding all specs from source when asked (with "rebuild everything")
- Allow overriding --prune-dag cli opt with env var
- Use job variable to optionally prevent rebuild jobs early exit behavior
- ci rebuild: Use new install argument to insist deps are always installed from binary, but
package is only installed from source.
- gitlab: fix bug w/ untouched pruning
- ci rebuild: install from hash rather than json file
- When doing a "rebuild everything" pipeline, make sure that each install job only consumes
binary dependencies from the mirror being populated by the current pipeline. This avoids
using, e.g. binaries from develop, when rebuilding everything on a PR.
- When running a pipeline to rebuild everything, do not die because we generated a hash on
the broken specs list. Instead only warn in that case.
- bugfix: Replace broken no-args tty.die() with sys.exit(1)
Print a message of the form
```
Fetch mm:ss. Build: mm:ss. Total: mm:ss
```
when installing from buildcache.
Previously this only happened for source builds.
Currently "spack ci generate" chooses the first matching entry in
gitlab-ci:mappings to fill attributes for a generated build-job,
requiring that the entire configuration matrix is listed out
explicitly. This unfortunately causes significant problems in
environments with large configuration spaces, for example the
environment in #31598 (spack.yaml) supports 5 operating systems,
3 architectures and 130 packages with explicit size requirements,
resulting in 1300 lines of configuration YAML.
This patch adds a configuraiton option to the gitlab-ci schema called
"match_behavior"; when it is set to "merge", all matching entries
are applied in order to the final build-job, allowing a few entries
to cover an entire matrix of configurations.
The default for "match_behavior" is "first", which behaves as before
this commit (only the runner attributes of the first match are used).
In addition, match entries may now include a "remove-attributes"
configuration, which allows matches to remove tags that have been
aggregated by prior matches. This only makes sense to use with
"match_behavior:merge". You can combine "runner-attributes" with
"remove-attributes" to effectively override prior tags.
When a pipeline generation job is automatically failed because it
generated jobs for specs known to be broken on develop, print better
information about the broken specs that were encountered. Include
at a minimum the hash and the url of the job whose failure caused it
to be put on the broken specs list in the first place.
* env depfile: allow deps only install
- Refactor `spack env depfile` to use a Jinja template, making it a bit
easier to follow as a human being.
- Add a layer of indirection in the generated Makefile through an
`<prefix>/.install-deps/<hash>` target, which allows one to specify
different options when installing dependencies. For example, only
verbose/debug mode on when installing some particular spec:
```
$ spack -e my_env env depfile -o Makefile --make-target-prefix example
$ make example/.install-deps/<hash> -j16
$ make example/.install/<hash> SPACK="spack -d" SPACK_INSTALL_FLAGS=--verbose -j16
```
This could be used to speed up `spack ci rebuild`:
- Parallel install of dependencies from buildcache
- Better readability of logs, e.g. reducing verbosity when installing
dependencies, and splitting logs into deps.log and current_spec.log
* Silence please!
* spack.compiler.Compiler: introduce prefix property
We currently don't really have something that gives the GCC install
path, which is used by many LLVM-based compilers (llvm, llvm-amdgpu,
nvhpc, ...) to fix the GCC toolchain once and for all.
This `prefix` property is dynamic in the sense that it queries the
compiler itself. This is necessary because it's not easy to deduce the
install path from the `cc` property (might be a symlink, might be a
filename like `gcc` which works by having the compiler load a module
that sets the PATH variable, might be a generic compiler wrapper based
on environment variables like on cray...).
With this property introduced, we can clean up some recipes that have
the logic repeated for GCC.
* intel-oneapi-compilers: set --gcc-sysroot to %gcc prefix
Caches used by repositories don't reference the global spack.repo.path instance
anymore, but get the repository they refer to during initialization.
Spec.virtual now use the index, and computation done to compute the index
use Repository.is_virtual_safe.
Code to construct mock packages and mock repository has been factored into
a unique MockRepositoryBuilder that is used throughout the codebase.
Add debug print for pushing and popping config scopes.
Changed spack.repo.use_repositories so that it can override or not previous repos
spack.repo.use_repositories updates spack.config.config according to the modifications done
Removed a peculiar behavior from spack.config.Configuration where push would always
bubble-up a scope named command_line if it existed
Resolves#31782
With this change, if a spec is concrete after parsing (e.g. spec.yaml
or /hash-based), then it is not disambiguated (a process which requires
(a) that the spec be installed and (b) that it be part of the
currently-active environment).
This commit allows you to:
* Diff specs from an environment regardless of whether they have
been installed (more useful for projection/matrix-based envs)
* Diff specs read from .yaml files which may or may not be entirely
different installations of Spack
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Docs: Getting Started Dependencies
Finally document what one needs to install to use Spack on
Linux and Mac :-)
With <3 for minimal container users and my colleagues with
their fancy Macs.
* Debian Update Packages: GCC, Python
- build-essential: includes gcc, g++ (thx Cory)
- Python: add python3-venv, python3-distutils (thx Pradyun)
* Add RHEL8 Dependencies
* filter_file: introduce argument 'start_at'
* autotools: extend patching of the libtool script
* autotools: refactor _patch_usr_bin_file
* autotools: improve readability of the filtering
* autotools: keep the modification time of the configure scripts
* autotools: do not try to patch directories
* autotools: explain libtool patching for posterity
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Remove `module-info mode load` condition that prevents auto-unloading when autoloading is enabled. It looks like this condition was added to work around an issue in environment-modules that is no longer necessary.
Add quotes to make is-loaded happy
When concurrent misc_cache provider index rebuilds happen, try to
rebuild it only once, so we don't exceed misc_cache lock timeout.
For example, when using `spack env depfile`, with no previous
misc_cache, running `make -f depfile -j8` could run at most 8 concurrent
`spack install` locking on misc_cache to rebuild the provider index. If
one rebuild takes 30s, before this fix, the "worst" lock could wait up
to 30s * 7, easily exceeding misc_cache lock timeout. Now, the "worst"
lock would take 30s * 1 + ~1s * 6.
Currently, module changes from `setup_dependent_package` are applied only to the module of the package class, but not to any parent classes' modules between the package class module and `spack.package_base`.
In this PR, we create a custom class to accumulate module changes, and apply those changes to each class that requires it. This design allows us to code for a single module, while applying the changes to multiple modules as needed under the hood, without requiring the user to reason about package inheritance.
* find/list: display package counts last
We have over 6,600 packages now, and `spack list` still displays the number of packages
before it lists them all. This is useless for large sets of results (e.g., with no args)
as the number has scrolled way off the screen before you can see it. The same is true
for `spack find` with large installations.
This PR changes `spack find` and `spack list` so that they display the package count
last.
* add some quick testing
Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
Allow environment variables and spack-specific path substitution variables (e.g. `$spack`) to be
used in the paths associated with develop specs, while maintaining the ability to keep those
paths relative to the environment rather than the working directory.
Install: Add use-buildcache option to install
* Allow differentiating between top level packages and dependencies when
determining whether to install from the cache or not.
* Add unit test for --use-buildcache
* Use metavar to display use-buildcache options.
* Update spack-completion
Make it possible to install the Clingo package on Windows; this
also provides a means to use Clingo with Spack on Windows.
This includes
* A new "winbison" package: Windows has a port of bison and flex where
the two packages are grouped together. Clingo dependencies have been
updated to use winbison on Windows and bison elsewhere (this avoids
complicating the existin bison/flex packages until we can add support
for implied virtuals).
* The CMake build system was incorrectly converting CMAKE_INSTALL_PREFIX
to POSIX format.
* The re2c package has been modified to use CMake on Windows; for now
this is done by overloading the configure/build/install methods to
perform CMake-appropriate operations; the package should be refactored
once support for multiple build systems in one Package is available.
This commit fixes#27027.
The root cause of the issue is that the `SPACK_OLD_PROMPT` variable
was evaluated in string interpolation regardless of whether the
guard condition above evaluates to true or false. This commit uses
the `eval` keyword to defer evaluation until the command is executed.
Co-authored-by: Alexander Hornburg <alexande@xilinx.com>
Spack currently depends on parsing filenames of downloaded files to
determine what type of archive they are and how to decompress them.
This commit adds a preliminary check based on magic numbers to
determine archive type (but falls back on name parsing if the
extension type cannot be determined).
As part of this work, this commit also enables decompression of
.tar.xz-compressed archives on Windows.
Include exception info related to url retrieval in debug messages
which otherwise would be swallowed. This is intended to be useful
for detecting if CA configuration interferes with downloads from
HTTPS links.
This fixes a bug where two installations that differ only by package hash will not show
up in `spack find`.
The bug arose because `_cmp_node` on `Spec` didn't include the package hash in its
yielded fields. So, any two `Spec` objects that were only different by package hash
would appear to be equal and would overwrite each other when inserted into the same
`dict`. Note that we could still *install* specs with different package hashes, and they
would appear in the database, but we code that needed to put them into data structures
that use `__hash__` would have issues.
This PR makes `Spec.__hash__` and `Spec.__eq__` include the `process_hash()`, and it
makes `Spec._cmp_node` include the package hash. All of these *should* include all
information in a spec so that we don't end up in a situation where we are blind to
particular field differences.
Eventually, we should unify the `_cmp_*` methods with `to_node_dict` so there aren't two
sources of truth, but this needs some thought, since the `_cmp_*` methods exist for
speed. We should benchmark whether it's really worth having two types of hashing now
that we use `json` instead of `yaml` for spec hashing.
- [x] Add `package_hash` to `Spec._cmp_node`
- [x] Add `package_hash` to `spack.solve.asp.spec_clauses` so that the `package_hash`
will show up in `spack diff`.
- [x] Add `package_hash` to the `process_hash` (which doesn't affect abstract specs
but will make concrete specs correct)
- [x] Make `_cmp_iter` report the dag_hash so that no two specs with different
process hashes will be considered equal.
53a7b49 created a reference error which broke `.libs` (and
`find_libraries`) for many packages. This fixes the reference
error and improves the testing for `find_libraries` by actually
checking the extension types of libraries that are retrieved by
the function.
* catch json schema errors and reraise as property of SpackError
* no need to catch subclass of given error
* Builtin json library for Python 2 uses more generic type
* Correct instantiation of SpackError (requires a string rather than an exception)
* Use exception chaining (where possible)
Add a post-install step which runs (only) on Windows to modify an
install prefix, adding symlinks to all dependency libraries.
Windows does not have the same concept of RPATHs as Linux, but when
resolving symbols will check the local directory for dependency
libraries; by placing a symlink to each dependency library in the
directory with the library that needs it, the package can then
use all Spack-built dependencies.
Note:
* This collects dependency libraries based on Package.rpath, which
includes only direct link dependencies
* There is no examination of libraries to check what dependencies
they require, so all libraries of dependencies are symlinked
into any directory of the package which contains libraries
* ci: restore coverage computation
* Mark "test_foreground_background" as xfail
* Mark "test_foreground_background_output" as xfail
* Make number of processes explicit, remove verbosity on linux
* Run coverage on just 3 Python jobs for linux
* Run coverage on just 3 Python jobs for linux
* Run coverage on just 2 Python jobs for linux
* Add back verbose, since before we didn't encounter the xdist internal error
* Reduce the workers to 2
* Try to use command line
* Fix a version cmp bug in asp.py
* Fix submodule bug for git refs
* Add branch in logic for submodules
* Fix git version comparisons
main does not satisfy git.foo=main
git.foo=main does satisfy main
* Add two no-op jobs named "all-prechecks" and "all"
These are a suggestion from @tgamblin, they are stable named markers we
can use from gitlab and possibly for required checks to make CI more
resilient to refactors changing the names of specific checks.
* Enable parallel testing using xdist for unit testing in CI
* Normalize tmp paths to deal with macos
* add -u flag compatibility to spack python
As of now, it is accepted and ignored. The usage with xdist, where it
is invoked specifically by `python -u spack python` which is then passed
`-u` by xdist is the entire reason for doing this. It should never be
used without explicitly passing -u to the executing python interpreter.
* use spack python in xdist to support python 2
When running on python2, spack has many import cycles unless started
through main. To allow that, this uses `spack python` as the
interpreter, leveraging the `-u` support so xdist doesn't error out when
it unconditionally requests unbuffered binary IO.
* Use shutil.move to account for tmpdir being in a separate filesystem sometimes
This patchset refactors our GitHub actions into a single top-level ci workflow that
invokes a series of reusable actions. The main goal of this is to be able to easily
control which tests run and in what order based on the success or failure of top-level
prechecks. Our previous workflows ran in three sets:
* nix tests: style and verification first, then linux and macos tests if successful
* windows tests: style and verification first, then linux and macos tests if successful
* bootstrap tests
As a result, the bootstrap tests ran even if the style failed, and style and verification
had to run on two different platforms despite running identical checks. I'm relatively
sure that's because of the limitation on dependencies between steps in the jobs.
Reusable workflows allow us to run the style, verification and now audit checks once,
then depending on the results, and the files changed, run the appropriate nix, windows
and bootstrap tests. While it saves only a few minutes by itself, this makes it easier to
refactor checks to subset tests without having to replicate tests or other workflow
components in the future.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Move the copying of the buildcache to a root job that runs after all the child
pipelines have finished, so that the operation can be coordinated across all
child pipelines to remove the possibility of race conditions during potentially
simlutandous copies. This lets us ensure the .spec.json.sig and .spack files
for any spec in the root mirror always come from the same child pipeline
mirror (though which pipeline is arbitrary). It also allows us to avoid copying
of duplicates, which we now do.
If you have an environment like
```
$ cat spack.yaml
spack:
specs: [openmpi@4.1.0+cuda]
```
this PR provides a new command `spack change` that you can use to adjust environment specs from the command line:
```
$ spack change openmpi~cuda
$ cat spack.yaml
spack:
specs: [openmpi@4.1.0~cuda]
```
in other words, this allows you to tweak the details of environment specs from the command line.
Notes:
* This is only allowed for environments that do not define matrices
* This is possible but not anticipated to be needed immediately
* If this were done, it should probably only be done for "named"/not-anonymous specs (i.e. we can change `openmpi+cuda` but not spec like `+cuda` or `@4.0.1~cuda`)
fixes#31484
Before this change if anything was matching an external
condition, it was considered "external" and thus something
to be "built".
This was happening in particular to external packages
that were re-read from the DB, which then couldn't be
reused, causing the problems shown in #31484.
This PR fixes the issue by excluding specs with a
"hash" from being considered "external"
* Test that users have a way to select a virtual
This ought to be solved by extending the "require"
attribute to virtual packages, so that one can:
```yaml
mpi:
require: 'multi-provider-mpi'
```
* Prevent conflicts to be enforced on specs that can be reused.
* Rename the "external_only" fact to "buildable_false", to better reflect its origin
* Preliminary support for include URLs in spack.yaml (environment) files
This commit adds support in environments for external configuration files obtained from a URL with a preference for grabbing raw text from GitHub and gitlab for efficient downloads of the relevant files. The URL can also be a link to a directory that contains multiple configuration files.
Remote configuration files are retrieved and cached for the environment. Configuration files with the same name will not be overwritten once cached.
Extend the semantics of package requirements to
allow using them also under a virtual package
attribute in packages.yaml
These requirements are enforced whenever that
virtual spec is present in the DAG.
Allow users to express default requirements in packages.yaml.
These requirements are overridden if more specific requirements
are present for a given package.
This support requires adding the '--tests' option to 'spack ci rebuild'.
Packages whose stand-alone tests are broken (in the CI environment) can
be configured in gitlab-ci to be skipped by adding them to
broken-tests-packages.
Highlights include:
- Restructured 'spack ci' help to provide better subcommand summaries;
- Ensured only one InstallError (i.e., installer's) rather than allowing
build_environment to have its own; and
- Refactored CI and CDash reporting to keep CDash-related properties and
behavior in a separate class.
This allows stand-alone tests from `spack ci` to run when the `--tests`
option is used. With `--tests`, stand-alone tests are run **after** a
**successful** (re)build of the package. Test results are collected
and report(able) using CDash.
This PR adds the following features:
- Adds `-t` and `--tests` to `spack ci rebuild` to run stand-alone tests;
- Adds `--fail-fast` to stop stand-alone tests after the first failure;
- Ensures a *single* `InstallError` across packages
(i.e., removes second class from build environment);
- Captures skipping tests for externals and uninstalled packages
(for CDash reporting);
- Copies test logs and outputs to the CI artifacts directory to facilitate
debugging;
- Parses stand-alone test results to report outputs from each `run_test` as
separate test parts (CDash reporting);
- Logs a test completion message to allow capture of timing of the last
`run_test` part;
- Adds the runner description to the CDash site to better distinguish entries
in CDash tables;
- Adds `gitlab-ci` `broken-tests-packages` to CI configuration to skip
stand-alone testing for packages with known issues;
- Changes `spack ci --help` so description of each subcommand is a single line;
- Changes `spack ci <subcommand> --help` to provide the full description of
each command (versus no description); and
- Ensures `junit` test log file ends in an `.xml` extension (versus default where
it does not).
Tasks:
- [x] Include the equivalent of the architecture information, or at least the host target, in the CDash output
- [x] Upload stand-alone test results files as `test` artifacts
- [x] Confirm tests are run in GitLab
- [x] Ensure CDash results are uploaded as artifacts
- [x] Resolve issues with CDash build-and test results appearing on same row of the table
- [x] Add unit tests as needed
- [x] Investigate why some (dependency) packages don't have test results (e.g., related from other pipelines)
- [x] Ensure proper parsing and reporting of skipped tests (as `not run`) .. post- #28701 merge
- [x] Restore the proper CDash URLand or mirror ONCE out-of-band testing completed
* modified list.py and added functionality for --tag
* Removed long and very long, shifted rest of code above return statement
* removed results variable
* added import statement at top
* added the line accidentally deleted
* added line accidentally deleted
* changed p.name to p, added line inside if statement
* line order switched
* [@spackbot] updating style on behalf of sparkyniner
* ran update completion command
* add tests
* Update lib/spack/spack/test/cmd/list.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of sparkyniner
* changed argument to mock_packages and moved code under filter by tag
* removed bad rebase code and added additional test
* [@spackbot] updating style on behalf of sparkyniner
* added line removed earlier
* added line removed earlier
* replaced function
* added more recommended changes
Co-authored-by: sairaj <sairaj@sairajs-MacBook-Pro.local>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Assertions without messages if/when hit create a blank error message for users.
This PR adds error messages to all assertions in asp.py even
if it seems unlikely they will ever be needed.
The argument is very likely a typo, and was meant to
be given to the fixture decorator. Since the value
being passed is the default, let's just remove it.
Ensure that build tools with module-level commands in spack use
the version built as part of their build graph if one exists.
This is now also required for mesa, scons, cmake and ctest, out
of graph versions of these tools in path will not be found unless
added as an external.
This bug appeared because a new version of rocprim needs cmake
3.16, while I have 3.14 in my path I had added an external for
cmake 3.20 to the dag, but 3.14 was still used to configure
rocprim causing it to fail. As far as I can tell, all the build
tools added in build_environment.py had this problem, despite the
fact that they should have been resolving these tools by name
with a path search and find the one in the dag that way. I'm
still investigating why the path searching and Executable logic
didn't do it, but this makes three of the build systems much more
explicit, and leaves only gmake and ninja as dependencies from
out in the system while ensuring the version in the dag is used
if there is one.
The additional sqlite version is to perturb the hash of python to
work around a relocation bug which will be fixed in a subsequent
PR.
* filesystem: use lstat in recursive mtime
When a `develop` path contains a dead symlink, the `os.stat` in the recursive `mtime` determination trips up over it.
Closes#32165.
`requirement_policy/3` is generated and may not be in Spack's inputs to Clingo.
Currently this is causing warnings like:
```
$ spack spec zlib
/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:510:3-43: info: atom does not occur in any rule head:
requirement_policy(Package,X,"one_of")
/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:517:3-43: info: atom does not occur in any rule head:
requirement_policy(Package,X,"one_of")
/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:523:3-43: info: atom does not occur in any rule head:
requirement_policy(Package,X,"any_of")
/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:534:3-43: info: atom does not occur in any rule head:
requirement_policy(Package,X,"any_of")
Input spec
--------------------------------
zlib
Concretized
--------------------------------
zlib@1.2.11%gcc@7.5.0+optimize+pic+shared arch=cray-sles15-haswell
```
- [x] Silence warning with `#defined requirement_policy/3`
Spack doesn't have an easy way to say something like "If I build
package X, then I *need* version Y":
* If you specify something on the command line, then you ensure
that the constraints are applied, but the package is always built
* Likewise if you `spack add X...`` to your environment, the
constraints are guaranteed to hold, but the environment always
builds the package
* You can add preferences to packages.yaml, but these are not
guaranteed to hold (Spack can choose other settings)
This commit adds a 'require' subsection to packages.yaml: the
specs added there are guaranteed to hold. The commit includes
documentation for the feature.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
All PRs are failing the docs build on account of an error with
pygments. These errors coincide with a new release of pygments
(2.13.0) and restricting to < 2.13 allows the doc tests to pass,
so this commit enforces that constraint for the docs build.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
A few attribute in packages are meant to be reserved for
Spack internal use. This audit checks packages to ensure none
of these attributes are overridden.
- [x] add additional audit check
This PR fixes the performance regression reported in #31985 and a few
other issues found while refactoring the spack mirror create command.
Modifications:
* (Primary) Do not require concretization for
`spack mirror create --all`
* Forbid using --versions-per-spec together with --all
* Fixed a few issues when reading specs from input file (specs were
not concretized, command would fail when trying to mirror
dependencies)
* Fix issue with default directory for spack mirror create not being
canonicalized
* Add more unit tests to poke spack mirror create
* Skip externals also when mirroring environments
* Changed slightly the wording for reporting (it was mentioning
"Successfully created" even in presence of errors)
* Fix issue with colify (was not called properly during error
reporting)
`LD_LIBRARY_PATH` can break system executables (e.g., when an enviornment is loaded) and isn't necessary thanks to `RPATH`s. Packages that require `LD_LIBRARY_PATH` can set this in `setup_run_environment`.
- [x] Prefix inspections no longer set `LD_LIBRARY_PATH` by default
- [x] Document changes and workarounds for people who want `LD_LIBRARY_PATH`
These changes make many packages build on nixos where nearly nothing
comes from /bin or /usr/bin (the only things in "system locations" are
/bin/sh and /usr/bin/env, all the rest is found through PATH).
Many configuration scripts hardcode /usr/bin/file instead of using the
one from PATH. This patches them to use file from PATH.
fixes#31736
Catch errors when concretizing specs and report them as
debug messages. The corresponding spec is skipped.
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Extracted two functions in cmd/install.py
* Extracted a function to perform installation from the active environment
* Rename a few functions, remove args from their arguments
* Rework conditional in install_from_active_environment to reduce nesting in the function
* Extract functions to parsespecs from cli and files
* Extract functions to getuser confirmation for overwrite
* Extract functions to install specs inside and outside environments
* Rename a couple of functions
* Fix outdated comment
* Add missing imports
* Split conditional to dedent one level
* Invert check and exit early to dedent one level when requiring user confirmation
The current use of git ref's as a version requires a search algorithm to pick the right matching version based on the tags in the git history of the package.
This is less than ideal for the use case where users already know the specific version they want the git ref to be associated with. This PR makes a new version syntax [package]@[ref]=[version] to allow the users to specify the exact hash they wish to use.
On some systems the shell in login mode wipes important parts of the
environment, such as PATH. This causes the build to fail since it can't
find `spack`.
For better robustness, don't use a login shell.
In a full CI job the final spack install is run in an environment formed by scripts running in this order:
export AWS_SECRET=... # 1. Load environment from GitLab project variables
source spack/share/spack/setup-env.sh # 2. Load Spack into the environment (PATH)
spack env activate -V concrete_env # 3. Activate the concrete environment
source /etc/profile # 4. Bash login shell (from -l)
spack install ...
Whereas when a user launches their own container with (docker|podman) run -it, they end up running spack install in an environment formed in this order:
source /etc/bash.bashrc # (not 4). Bash interactive shell (default with TTY)
export AWS_SECRET=... #~1. Manually load environment from GitLab project variables
source spack/share/spack/setup-env.sh # 2. Load Spack into the environment (PATH)
spack env activate -V concrete_env # 3. Activate the concrete environment
spack install ...
The big problem being that (4) has a completely different position and content (on Leap 15 and possibly other containers).
So in context, this PR removes (4) from the CI job case, leaving us with the simpler:
export AWS_SECRET=... # 1. Load environment from GitLab project variables
source spack/share/spack/setup-env.sh # 2. Load Spack into the environment (PATH)
spack env activate -V concrete_env # 3. Activate the concrete environment
spack install ...
* database: don't sort on return from query_local
* ASP-based solver: don't build the hash-lookup dictionary twice
Building this dictionary twice and traversing all the specs
might be time-consuming for large buildcaches.
This test relied on an old version of the `flake8_package` fixture that modified
the spack repository, but it doesn't do that anymore. There are other tests for
`changed_files()` that do a better job of mocking up a git repository with
changes, so we can just delete this one.
`spack style` tests were annoyingly brittle because we could not easily be
specific about which tools to run (we had to use `--no-black`, `--no-isort`,
`--no-flake8`, and `--no-mypy`). We should be able to specify what to run OR
what to skip.
Now you can run, e.g.:
spack style --tool black,flake8
or:
spack style --skip black,isort
- [x] Remove `--no-black`, `--no-isort`, `--no-flake8`, and `--no-mypy` args.
- [x] Add `--tool TOOL` argument.
- [x] Add `--skip TOOL` argument.
- [x] Allow either `--tool black --tool flake8` or `--tool black,flake8` syntax.
- [x] remove alignment spaces from tempaltes
- [x] replace single with double quotes
- [x] Makefile template now generates parsable code
(function body is `pass` instead of just a comment)
- [x] template checks now run black to check output
Previously we'd accept any version for bootstrapping black, but we need <= 21.
- [x] modify bootstrapping code to check black version before accepting an
executable from `PATH`.
- [x] add `.git-blame-ignore-revs` to ignore black reformatting
- [x] make `spack blame` respect `.git-blame-ignore-revs`
(even if the user hasn't configured git to do so)
Some of our tests rely on single vs. double quotes, and others rely on specific
line numbers in the source. These needed fixing after the switch to Black.
Black will automatically fix a lot of the exceptions we previously allowed for
directives, so we don't need them in our custom `flake8_formatter` anymore.
- [x] remove `E501` (long line) exceptions for directives from `flake8_formatter`,
as they won't help us now.
- [x] Refine exceptions for long URLs in the `flake8_formatter`.
- [x] Adjust the mock `flake8-package` to exhibit the exceptions we still allow.
- [x] Update style tests for new `flake8-package`.
- [x] Blacken style test.
Many noqa's in the code are no longer necessary now that the column limit is 99
characters. Others can easily be eliminated, and still more can just be made more
specific if they do not have to do with line length.
The only E501's still in the code are in the tests for `spack.util.path` and the tests
for `spack style`.
This adds necessary configuration for flake8 and black to work together.
This also sets the line length to 99, per the data here:
* https://github.com/spack/spack/pull/24718#issuecomment-876933636
Given the data and the spirit of black's 88-character limit, we set the limit to 99
characters for all of Spack, because:
* 99 is one less than 100, a nice round number, and all lines will fit in a
100-character wide terminal (even when the text editor puts a \ at EOL).
* 99 is just past the knee the file size curve for packages, and it means that packages
remain readable and not significantly longer than they are now.
* It doesn't seem to hurt core -- files in core might change length by a few percent but
seem like they'll be mostly the same as before -- just a bit more roomy.
- [x] set line length to 99
- [x] remove most exceptions from `.flake8` and add the ones black cares about
- [x] add `[tool.black]` to `pyproject.toml`
- [x] make `black` run if available in `spack style --fix`
Co-Authored-By: Tom Scogland <tscogland@llnl.gov>
In #31618 the idea was to determine the file extension heuristically by dropping query params etc from a url and then consider it as a file path. That broke for URLs that only have query params like http://example.com/?patch=x as it would result in empty string as basename. This PR reverts to the old behavior of saving files as ?patch=x in that case.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
* llvm: Use variant when clauses for many of the expressed conflicts
* llvm: Remove the shared variant as it wasn't really used
* llvm: Remove unnecessary deps and make explicit the ones that are
* llvm: Cleanup patch conditions
* pocl: Update for llvm cleanup
* unit-test: update unparse package hash with the updated llvm package
* llvm: Fix ppc long double patching and add clarifying comments
`self.archive_file` is (among others) a symlink to a tarball. `extension()` on a
symlink will result in no extension. This patch fixes the behavior introduced in
https://github.com/spack/spack/pull/31618.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
When
1. Spack installs libtool,
2. system libtool is installed too, and
3. system automake is used
Spack passes system automake's `-I <prefix>` flag to itself, even though
it's a default search path. This takes precedence over spack's libtool
prefix dir. This causes the wrong `libtool.m4` file to be used (since
system libtool is in the same prefix as system automake).
And that leads to error messages about incompatible libtool, something
something LT_INIT.
fixes#31627
spack.mirror.get_all_versions now uses the package class
instead of the package object in its implementation.
Ensure spec is concrete before staging for mirrors
Newer versions of botocore (>=1.23.47) support the full IOBase
interface, so the hacks added to supplement the missing attributes are
no longer needed. Conditionally disable the hacks if they appear to be
unnecessary based on the class hierarchy found at runtime.
* Add connection information to buildcache update command
Ensure that the s3 connection made when attempting to update the content
of a buildcache attempts to use the extra connection information
from the mirror creation.
* Add unique help for endpoint URL argument
Fix copy/paste error for endpoint URL help which was the same as
the access token
* Re-work URL checking for S3 mirrors
Due to the fact that nested bucket URLs would never match the string used
for checking that the mirror is the same, switch the check used.
Sort all mirror URLs by length to have the most specific cases first
and see if the desired URL "starts with" the mirror URL.
* Long line style fixes
Add execptions for long lines and fix other style errors
* Use format() function to rebuild URL
Use the format command to rebuild the url instead of crafing a
formatted string out of known values
* Add early exit for URL checking
When a valid mirror is found, break from the loop
For a long time the module configuration has had a few settings that use
`blacklist`/`whitelist` terminology. We've been asked by some of our users to replace
this with more inclusive language. In addition to being non-inclusive, `blacklist` and
`whitelist` are inconsistent with the rest of Spack, which uses `include` and `exclude`
for the same concepts.
- [x] Deprecate `blacklist`, `whitelist`, `blacklist_implicits` and `environment_blacklist`
in favor of `exclude`, `include`, `exclude_implicits` and `exclude_env_vars` in module
configuration, to be removed in Spack v0.20.
- [x] Print deprecation warnings if any of the deprecated names are in module config.
- [x] Update tests to test old and new names.
- [x] Update docs.
- [x] Update `spack config update` to fix this automatically, and include a note in the error
that you can use this command.
Python's built-in tarfile support doesn't address some general
cases of malformed tarfiles that are already handled by the system
'tar' utility; until these can be addressed, use that exclusively.
The goal of this PR is to make clearer where we need a package object in Spack as opposed to a package class.
We currently instantiate a lot of package objects when we could make do with a class. We should use the class
when we only need metadata, and we should only instantiate and us an instance of `PackageBase` at build time.
Modifications:
- [x] Remove the `spack.repo.get` convenience function (which was used in many places, and not really needed)
- [x] Use `spack.repo.path.get_pkg_class` wherever possible
- [x] Try to route most of the need for `spack.repo.path.get` through `Spec.package`
- [x] Introduce a non-data descriptor, that can be used as a decorator, to have "class level properties"
- [x] Refactor unit tests that had to be modified to reduce code duplication
- [x] `Spec.package` and `Repo.get` now require a concrete spec as input
- [x] Remove `RepoPath.all_packages` and `Repo.all_packages`
There's a race condition in `remove()` as the lockfile is removed after
releasing the lock, which is a problem when another process acquires a
write lock during deletion.
Also simplify life a bit in multiprocessing when a file is possibly
removed multiple times, which currently is an error on the second
deletion, so the proposed fix is to make remove(...) idempotent and not
error when deleting non-existing cache entries.
Don't tests for existence of lockfile, cause windows/linux behavior is different
Oversight in #31433, the non-phony `env` target was missing a file being
created for it, which can cause make to infinitely loop when including
multiple generated makefiles.
When no default editor is installed and no environment variable is set,
which_string would return None and this would be passed to os.execv
resulting in a TypeError. The message presented to the user would be:
Error: execv: path should be string, bytes or os.PathLike,
not NoneType
This change checks that which_string has returned successfully before
attempting to execute the result, resulting in a new error message:
Error: No text editor found! Please set the VISUAL and/or EDITOR
environment variable(s) to your preferred text editor.
It's not strictly necessary, but I've also changed try_exec to catch
all errors rather than just OSErrors. This would have provided slightly
more context for the original error message.
There were two choices: 1) remove '-p' from '-a' or 2) allow monkeypatching
the cleaning of the python cache since clean's test_function_calls isn't
supposed to be actually cleaning anything.
This commit supports the latter and adds a test case for `-p`.
Release branches and tags run protected pipelines, and we noticed
that those pipelines were generating all jobs in the stack, even
when the mirror contained all the built specs and an up to date
index. The problem was caused because the override mirror was
not present in spacks mirror configuration at the time when the
binary_distribution.update() method was called. This fixes that
by always adding the mirror override, if present, to the list of
configured mirrors.
* remove unhelpful comment
* Filter compiler duplicates while reading manifest
* more-specific version matching edited to use module-specific version (to avoid an issue where a user might add a compiler with the same version to the initial test configuration
* PythonPackage: add default libs/headers attributes
* Style fix
* libs and headers should be properties
* Check both platlib and include
* Fix variable reference
Building on #24639, this allows versions to be prefixed by `git.`. If a version begins `git.`, it is treated as a git ref, and handled as git commits are starting in the referenced PR.
An exception is made for versions that are `git.develop`, `git.main`, `git.master`, `git.head`, or `git.trunk`. Those are assumed to be greater than all other versions, as those prefixed strings are in other contexts.
This commit adds some changes which improve use of Spack-installed
oneAPI packages with Spack-generated modules, but not within Spack
(e.g. if you install some of these packages with Spack, then load
their associated modules to build other packages outside of Spack).
The majority of the PR diff is refactoring. The functional changes
are:
* intel-oneapi-mkl:
* setup_run_environment: update Intel compiler flags to RPATH the
mkl libs
* intel-oneapi-compilers: update the compiler configuration to RPATH
libraries installed by this package (note that Spack already handled
this when installing dependent packages with Spack, but this is
specifically to use the intel-oneapi-compilers package outside
of Spack). Specifically:
* inject_rpaths: this modifies the binaries installed as part of
the intel-oneapi-compilers package to RPATH libraries provided
by this package
* extend_config_flags: this instructs the compiler executables
provided by this package to RPATH those same libraries
Refactoring includes:
* intel-oneapi-compilers: in addition to the functional changes,
a large portion of this diff is reorganizing the creation of
resources/archives downloaded for the install
* The base oneAPI package renamed component_path, so several packages
changed as a result:
* intel-oneapi-dpl
* intel-oneapi-dnn
* extrae
* intel-oneapi-mpi:
* Perform file filtering in one pass rather than two
Allow `spack external find` (with no extra args) to proceed if the manifest file exists but
without sufficient permissions; in that case, print a warning. Also add a test for that behavior.
TODOs:
- [x] continue past any exception raised during manifest parsing as part of `spack external find`,
except for CTRL-C (and other errors that indicate immediate program termination)
- [x] Semi-unrelated but came up when discussing this with the user who reported this issue to
me: the manifest parser now accepts older schemas
See: https://github.com/spack/spack/issues/31191
fixes#30997
Instead of giving a penalty of 30 to all nodes when preferences
are not package specific, give a penalty of 100 to all targets
of a node where we have package specific preferences, if the target
is not explicitly preferred.
* Fixed a bug in the 'external find --all' command where the call failed
to find packages by both executable and library. The bug was that the
call `path.all_packages()` incorrectly turned the variable
`packages_to_check` into a generator rather than keeping it a list.
Thus the second call to `detection.by_library` had no work to do.
* Fixed the help message for the find external and compiler commands as
well as others that used the `scopes_metavar` field to define where
the results should be stored in configuration space. Specifically,
the fact that configuration could be added to the environment was not
mentioned in the help message.
