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Remove a vestigial print statement introduced in #8570
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* Don't overwrite suid/sgid bits when setting permissions
* add tests for permission setting
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Add fixes to support multiple installs and dependents using a subset
of IntelPackage functionality.
* Update IntelPackage to only return scalapack libraries if the root
spec depends on MPI: scalapack requires MPI to be mentioned as a
dependency in the DAG. Package builds using intel-mkl for its
blas/lapack implementations but not for scalapack were failing to
build.
Ideally it would be possible to ask if any of the packages in the
DAG are actually requesting the scalapack functionality provided by
the IntelPackage and only return scalapack libs in that case, but
that is not easily done at this time.
Fixes #11314
Fixes #11289
* set HOME when the intel silent installer is run. This prevents the
installer from using the ~/intel directory (which can cause
conflicts for multiple installs of the same IntelPackage)
Fixes #9713
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Use new `module` function instead of `get_module_cmd`
Previously, Spack relied on either examining the bash `module()` function or using the `which` command to find the underlying executable for modules. More complicated module systems do not allow for the sort of simple analysis we were doing (see #6451).
Spack now uses the `module` function directly and copies environment changes from the resulting subprocess back into Spack. This should provide a future-proof implementation for changes to the logic underlying the module system on various HPC systems.
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The license text is now expected to match almost exactly (not
accounting for formatting in different file types (e.g. rst vs.
bash script vs. python)
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Don't arbitrarily reset PWD and OLDPWD when sourcing, as well as other
session-specific IDs
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Add two functions to the EnvironmentModifications object to help
users sanitize environment variables in their package definitions:
* deprioritize_system_paths: this keeps system paths in the
environment variable but moves them to the end.
* prune_duplicate_paths: remove any duplicate paths from the
variable
This includes testing for the new functions as well as for
(previously-untested) old convenience functions for environment
variable manipulation.
This also adds special handling for bash functions so they
will be defined when the exported environment file is sourced.
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Fixes #11335
Update the Spack compiler wrappers to add the headerpad_max_install_names
linker flag on MacOS. This allows the install_name_tool to rewrite
the RPATH entry of the binary to be longer if needed. This is
primarily useful for creating and distributing binary caches of
packages (i.e. using the "spack buildcache" command); binary caches
created on MacOS before this commit may not successfully relocate
(if the target root path is larger).
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* Added a function that concretizes specs together
* Specs concretized together are copied instead of being referenced
This makes the specs different objects and removes any reference to the
fake root package that is needed currently for concretization.
* Factored creating a repository for concretization into its own function
* Added a test on overlapping dependencies
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head > trunk > 9999 (#1983)
* 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
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* _valid_tokens list is missing a needed comma
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- Add link to container image, as well as a description of VMs
- Update slide link to point to latest RIKEN tutorial
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- `spack edit` previously used `spack.util.executable` `Executable` objects,
and didn't `exec` the editor like you'd expect it to
- This meant that Spack was still running while your editor was, and
stdout/stdin were being set up in weird ways
- e.g. on macOS, if you call `spack edit` with `EDITOR` set to the
builtin `emacs` command, then type `Ctrl-g`, the whole thing dies with
a `==> Error: Keyboard interrupt`
- Fix all this by changing spack.util.editor to use `os.execv` instead of
Spack's `Executable` object
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* Fix detection of LLVM-enabled PGI compilers
* Add unit tests for LLVM-enabled PGI compiler version detection
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Also add constructor to NoLibrariesError which can either take an
error message (like other SpackErrors) or a name and prefix (in
which case the error message is constructed).
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PR #10758 made a slight change to find_versions_of_archive() which included
archive_url in the search process. While this fixed `spack create` and
`spack checksum` missing command-line arguments, it caused `spack
install` to prefer those URLs over those it found in the scrape process.
As a result, the package url was treated as a list_url causing all R
packages to stop fetching once the package was updated on CRAN.
This patch is more selective about including the archive_url in the
remote versions, explicitly overriding it with matching versions found
by the scraper.
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f242f5f8 changed the format strings but maintained backwards
compatibility in all cases except one: The list of valid tokens for
the module naming schemes was not updated properly to contain both
the new and old styles for compilers and package names.
This PR re-adds the old tokens into the list of valid tokens.
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#11152 added documentation for #8772 but some details were based on
an earlier implementation that had changed by the time #8772 was
merged. In particular, #11152 mentioned that upstream Spack instances
were configured in config.yaml, when in fact they should be placed in
a separate upstreams.yaml config file; this PR updates the
documentation accordingly.
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fixes #11159
The 'namespace' argument to both Repo and RepoPath were used to set the
"super namespace". Currently it seems to be vestigial as the only
"super namespace" allowed for packages is 'spack.pkg' since 39c9bbf
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* Make a separate CDash report for each package installed
Previously, we generated a single CDash report ("build") for the complete results
of running a `spack install` command. Now we create a separate CDash build for
each package that was installed.
This commit also changes some of the tests related to CDash reporting.
Now only one of the tests exercises the code path of uploading to a
(nonexistent) CDash server. The rest of the related tests write their reports
to disk without trying to upload them.
* Don't report errors to CDash for successful packages
Convert errors detected by our log scraper into warnings when the package
being installed reports that it was successful.
* Report a maximum of 50 errors/warnings to CDash
This is in line with what CTest does. The idea is that if you have more than
50 errors/warnings you probably aren't going to read through them all anyway.
This change reduces the amount of data that we need to transfer and store.
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* Update spec format to simpler syntax, maintain backwards compatibility
* Switch to new spec.format method throughout internals
* update package files for new format strings
* documentation and minor code cleanup. removed nonsensical variant sigils
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Fixes #11070 #11010
Spack attempts to intercede on behalf of all compiler invocations for
a build. This involves adding its wrappers to PATH. Cray systems
include a "ftn" executable and Spack was only redirecting this call
when the Spec was built with cce. This updates the compiler wrappers
to add "ftn" in all cases.
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The default (implied) behavior for all environments, as of ea1de6b,
is that an environment will maintain a view in a location of its
choosing. ea1de6b explicitly recorded all three possible states of
maintaining a view:
1. Maintain a view, and let the environment decide where to put it
(default)
2. Maintain a view, and let the user decide
3. Don't maintain a view
This commit updates the config writer so that for case [1], nothing
will be written to the config.yaml. This will not change any existing
behavior, it just serves to keep the config more compact.
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Compilers are treated separately from other dependencies in Spack.
#10761 added the option to automatically install compilers when a
package specifies using a compiler that is not available in Spack.
However, this did not work correctly for dependency packages (it
would only build a compiler for the root of an install DAG). This
commit enables the building of compilers for dependency packages.
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Environments are nowm by default, created with views. When activated, if an environment includes a view, this view will be added to `PATH`, `CPATH`, and other shell variables to expose the Spack environment in the user's shell.
Example:
```
spack env create e1 #by default this will maintain a view in the directory Spack maintains for the env
spack env create e1 --with-view=/abs/path/to/anywhere
spack env create e1 --without-view
```
The `spack.yaml` manifest file now looks like this:
```
spack:
specs:
- python
view: true #or false, or a string
```
These commands can be used to control the view configuration for the active environment, without hand-editing the `spack.yaml` file:
```
spack env view enable
spack env view envable /abs/path/to/anywhere
spack env view disable
```
Views are automatically updated when specs are installed to an environment. A view only maintains one copy of any package. An environment may refer to a package multiple times, in particular if it appears as a dependency. This PR establishes a prioritization for which environment specs are added to views: a spec has higher priority if it was concretized first. This does not necessarily exactly match the order in which specs were added, for example, given `X->Z` and `Y->Z'`:
```
spack env activate e1
spack add X
spack install Y # immediately concretizes and installs Y and Z'
spack install # concretizes X and Z
```
In this case `Z'` will be favored over `Z`.
Specs in the environment must be concrete and installed to be added to the view, so there is another minor ordering effect: by default the view maintained for the environment ignores file conflicts between packages. If packages are not installed in order, and there are file conflicts, then the version chosen depends on the order.
Both ordering issues are avoided if `spack install`/`spack add` and `spack install <spec>` are not mixed.
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Add documentation for the Spack chain feature added in #8772
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* intel: consolidate libs() in the base class
* white space
* flake8
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When providing a track, the cdash reporter will format the stamp
itself, as it has always done, and register the build during the
package installation process. When providing a stamp, it should
first be formatted as cdash expects, and then cdash will be sure
to report results to same build id which was registered manually
elsewhere.
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* Update Spec.prefix to have special case for 'None' in database path; regression test
* Update in database reader rather than spec
* Change assertion to conditional + raise
* Added test for concrete check in Spec.prefix
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The module_parsing test checks whether the module function is available
by looking for the string 'not found'. If the user has set a different
locale, the test can assume that the module function is available when
it actually is not.
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Directory layouts using ${NAMESPACE} were broken. This addresses that
and adds a test to prevent regression.
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* Split get_compiler_version into two functions:
get_compiler_version_output runs the compiler with the relevant
option to print the version; extract_version_from_output determines
the version by examining this output. This makes it easier to test
the customized version detection for each compiler. Users can
customize this by overriding the following:
* version_argument: this is the argument that tells the compiler to
print its version. It assumes that the compiler will report its
version if invoked with a single option (like "--version")
* version_regex: the regular expression used to extract the version
from the compiler argument. This assumes that a regular
expression is sufficient to extract the version, and that the
version can be extracted from a single capture group (Spack uses
the first capture group)
* default_version: allows you to completely override all version
detection logic
* get_compiler_version_output: if getting the compiler to report
its version is more complex than invoking it with a single arg
* extract_version_from_output: if it is difficult to define a regex
that can be used to extract the version from the output
* Added tests for version detection of most compilers
* Removed redundant code from xl_r compiler class (by inheriting
from xl compiler definition)
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Replace the original implementation of the "memoized" decorator with
an implementation that exposes the docstring and arguments of the
wrapped function. This is achieved using functools.wraps.
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* add libs property to IntelMkl and IntelParallelStudio
* fix scalapack_libs when MPI is provided by intel-parallel-studio
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This provides a mechanism to implement a new Spack command in a
separate directory, and with a small configuration change point Spack
to the new command.
To register the command, the directory must be added to the
"extensions" section of config.yaml. The command directory name must
have the prefix "spack-", and have the following layout:
spack-X/
pytest.ini #optional, for testing
X/
cmd/
name-of-command1.py
name-of-command2.py
...
tests/ #optional
conftest.py
test_name-of-command1.py
templates/ #optional jinja templates, if needed
And in config.yaml:
config:
extensions:
- /path/to/spack-X
If the extension includes tests, you can run them via spack by adding
the --extension option, like "spack test --extension=X"
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* preserve the order in which patches are applied by packages (in spite of grouping them by 'when')
* add tests confirming patch order
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* 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)
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