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
Preferred targets were failing because we were looking them up by
Microarchitecture object, not by string.
- [x] Add a call to `str()` to fix target lookup.
- [x] Add a test to exercise this part of concretization.
- [x] Add documentation for setting `target` in `packages.yaml`
Spack can now:
- label ppc64, ppc64le, x86_64, etc. builds with specific
microarchitecture-specific names, like 'haswell', 'skylake' or
'icelake'.
- detect the host architecture of a machine from /proc/cpuinfo or similar
tools.
- Understand which microarchitectures are compatible with which (for
binary reuse)
- Understand which compiler flags are needed (for GCC, so far) to build
binaries for particular microarchitectures.
All of this is managed through a JSON file (microarchitectures.json) that
contains detailed auto-detection, compiler flag, and compatibility
information for specific microarchitecture targets. The `llnl.util.cpu`
module implements a library that allows detection and comparison of
microarchitectures based on the data in this file.
The `target` part of Spack specs is now essentially a Microarchitecture
object, and Specs' targets can be compared for compatibility as well.
This allows us to label optimized binary packages at a granularity that
enables them to be reused on compatible machines. Previously, we only
knew that a package was built for x86_64, NOT which x86_64 machines it
was usable on.
Currently this feature supports Intel, Power, and AMD chips. Support for
ARM is forthcoming.
Specifics:
- Add microarchitectures.json with descriptions of architectures
- Relaxed semantic of compiler's "target" attribute. Before this change
the semantic to check if a compiler could be viable for a given target
was exact match. This made sense as the finest granularity of targets
was architecture families. As now we can target micro-architectures,
this commit changes the semantic by interpreting as the architecture
family what is stored in the compiler's "target" attribute. A compiler
is then a viable choice if the target being concretized belongs to the
same family. Similarly when a new compiler is detected the architecture
family is stored in the "target" attribute.
- Make Spack's `cc` compiler wrapper inject target-specific flags on the
command line
- Architecture concretization updated to use the same algorithm as
compiler concretization
- Micro-architecture features, vendor, generation etc. are included in
the package hash. Generic architectures, such as x86_64 or ppc64, are
still dumped using the name only.
- If the compiler for a target is not supported exit with an intelligible
error message. If the compiler support is unknown don't try to use
optimization flags.
- Support and define feature aliases (e.g., sse3 -> ssse3) in
microarchitectures.json and on Microarchitecture objects. Feature
aliases are defined in targets.json and map a name (the "alias") to a
list of rules that must be met for the test to be successful. The rules
that are available can be extended later using a decorator.
- Implement subset semantics for comparing microarchitectures (treat
microarchitectures as a partial order, i.e. (a < b), (a == b) and (b <
a) can all be false.
- Implement logic to automatically demote the default target if the
compiler being used is too old to optimize for it. Updated docs to make
this behavior explicit. This avoids surprising the user if the default
compiler is older than the host architecture.
This commit adds unit tests to verify the semantics of target ranges and
target lists in constraints. The implementation to allow target ranges
and lists is minimal and doesn't add any new type. A more careful
refactor that takes into account the type system might be due later.
Co-authored-by: Gregory Becker <becker33.llnl.gov>
- 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
Consolidate prefix calculation logic for intel packages into the
IntelPackage class.
Add documentation on installing Intel packages with Spack an
(alternatively) adding them as external packages in Spack.
Functional updates:
- `python` now creates a copy of the `python` binaries when it is added
to a view
- Python extensions (packages which subclass `PythonPackage`) rewrite
their shebang lines to refer to python in the view
- Python packages in the same namespace will not generate conflicts if
both have `...lib/site-packages/namespace-example/__init__.py`
- These `__init__` files will also remain when removing any package in
the namespace until the last package in the namespace is removed
Generally (Updated 2/16):
- Any package can define `add_files_to_view` to customize how it is added
to a view (and at the moment custom definitions are included for
`python` and `PythonPackage`)
- Likewise any package can define `remove_files_from_view` to customize
which files are removed (e.g. you don't always want to remove the
namespace `__init__`)
- Any package can define `view_file_conflicts` to customize what it
considers a merge conflict
- Global activations are handled like views (where the view root is the
spec prefix of the extendee)
- Benefit: filesystem-management aspects of activating extensions are
now placed in views (e.g. now one can hardlink a global activation)
- Benefit: overriding `Package.activate` is more straightforward (see
`Python.activate`)
- Complication: extension packages which have special-purpose logic
*only* when activated outside of the extendee prefix must check for
this in their `add_files_to_view` method (see `PythonPackage`)
- `LinkTree` is refactored to have separate methods for copying a
directory structure and for copying files (since it was found that
generally packages may want to alter how files are copied but still
wanted to copy directories in the same way)
TODOs (updated 2/20):
- [x] additional testing (there is some unit testing added at this point
but more would be useful)
- [x] refactor or reorganize `LinkTree` methods: currently there is a
separate set of methods for replicating just the directory structure
without the files, and a set for replicating everything
- [x] Right now external views (i.e. those not used for global
activations) call `view.add_extension`, but global activations do not
to avoid some extra work that goes into maintaining external views. I'm
not sure if addressing that needs to be done here but I'd like to
clarify it in the comments (UPDATE: for now I have added a TODO and in
my opinion this can be merged now and the refactor handled later)
- [x] Several method descriptions (e.g. for `Package.activate`) are out
of date and reference a distinction between global activations and
views, they need to be updated
- [x] Update aspell package activations
- spack.util.lock behaves the same as llnl.util.lock, but Lock._lock and
Lock._unlock do nothing.
- can be disabled with a control variable.
- configuration options can enable/disable locking:
- `locks` option in spack configuration controls whether Spack will use filesystem locks or not.
- `-l` and `-L` command-line options can force-disable or force-enable locking.
- Spack will check for group- and world-writability before disabling
locks, and it will not allow a group- or world-writable instance to
have locks disabled.
- update documentation
- Add a `spack gpg` subcommand in anticipation of signed binaries.
- GPG keys are stored in var/spack/gpg, and the spack gpg command manages them.
- Docs are included on the command.
* Fixed parser to eliminate need for escape quotes. TODO: Fix double call to shlex, fix spaces in spec __str__
* Fixed double shlex
* cleanup
* rebased on develop
* Fixed parsing for multiple specs; broken since #360
* Revoked elimination of the `-` sigil in the syntax, and added it back into tests
* flake8
* more flake8
* Cleaned up dead code and added comments to parsing code
* bugfix for spaces in arguments; new bug found in testing
* Added unit tests for kv pairs in parsing/lexing
* Even more flake8
* ... yet another flake8
* Allow multiple specs in install
* unfathomable levels of flake8
* Updated documentation to match parser fix
* Allow compiler wrapper to modify environment
This adds the ability to set environment variables in the compiler
wrappers. These are specified as part of the compilers.yaml config.
The user may also specify RPATHs in compilers.yaml that should be
added.
* Minor doc tweak
* module file support: major rework of docs
* module file support: fixed issues found by @adamjstewart
- list or enumeration should not be indented
- use console instead of bash or csh in things that are not scripts
- other typos
* module file support: fixed other issues found by @adamjstewart
- tables should not be indented
- substitute lines with pyobject to import an entire function
- get help output running commands
- typos
* module file support: fixes according to review comments
- @citibeth moved `spack module loads` after `spack load`
- @glennpj tried to clarify installation table + changes to language
- @tgamblin Removed top level section and moved the whole thing into the reference manual
* module file support: moved directive before spack module loads
* Fix various documentation bugs
* Keep long option names, but don't include in Command Index
* Use long option name
* Explicitly designate sections to be listed in the Command Index
* Consistent menu bar titles
* Transferred pending changes from efischer/develop
* 1. Rewrite of "Getting Started": everything you need to set up Spack, even on old/ornery systems. This is not a reference manual section; items covered here are covered more systematically elsewhere in the manual. Some sections were moved here from elsewhere.
2. Beginning to write three methods of application developer support. Two methods were moved from elsewhere.
* Edits...
* Moved sections in preparation for additional text to be added from old efischer/docs branch.
* Moved 2 more sections.
* Avoid accid
* Applied proofreading edits from @adamjstewart
* Fixed non-standard section characters.
* Moved section on profiling to the developer's guide.
* Still working on Spack workflows...
* Finished draft of packaging_guide.rst
* Renamed sample projects.
* Updates to docstrings
* Added documentation to resolve#638 (content taken from #846)
* Added section on resolving inconsistent run dependencies. Addresses #645
* Showed how to build Python extensions only compatible with certain versions of Python.
* Added examples of getting the right behavior from depends_on(). See #1035
* Added section on Intel compilers and their GCC masquerading feature. Addresses #638, #1687.
* Fixed formatting
* Added fixes to filesystem views. Added a caveats section to ``spack setup``.
* Updated section on Intel compiler configuration because compiler flags currently do not work (see #1687)
* Defined trusted downloads, and updated text based on them. (See #1696)
* Added workflow to deal with buggy upstream software. See #1683
* Added proper separation between Spack Docs vs. Reference Manual
* Renamed spack_workflows to workflows. Resolves a conflict with the .gitignore file.
* Removed repeated section.
* Created new "Vendor Specific Compiler Configuration" section and organized existing Intel section into it. Added new PGI and NAG sections; but they need to be expanded / rewritten based on the existing text plus research through Spack issues on GitHub.
* Fixed text on `spack load --dependencies` to conform to reality. See #1662
* Added patching as option for upstream bugfixes.
* Added section on using licensed compilers.
* Added section on non-downloadable tarballs.
* Wrote sections on NAG and PGI. Arranged compilers in alphabetical order.
* Fix indent.
* Fixed typos.
* Clarified dependency types.
* Applied edits from Adam J. Stewart. Spellchecked workflows and getting_started.
* Removed spurious header
* Fixed Sphinx errors
* Fixed erroneous symbol in docstring.
* Fix many typos and formatting problems.
* Spacing changes
* Added section on fixing Git problems. See #1779
* Fixed signature of install() method.
* Addressed system packages in greater detail. See #1794#1795
* Fixed typos
* Fixed quotes
* Duplicate section on Spack profiling removed from configuration.rst. It had earlier been moved to developer_guide.rst, where it fits better.
* Minor edits
- Tweak supported platform language.
- Various small changes to the new getting started guide.
* Fixed bug with quotes.
This list was not formatted correctly on [the ReadTheDocs site](http://software.llnl.gov/spack/basic_usage.html#specs-dependencies).
I'm not a .rst expert, but I think that it was improperly indented.
The example includes an `arch=...` string but *arch* is not listed in the valid compiler flag specifiers or architecture specifiers. Should it be, or is it considered an "optional variant specifier?
Updating how to use compilers.yaml on Cray as well as setting up
external packages. Also includes what needs to be set up for usage on
Cray and explains what needs to be done to get Spack properly working.
Also explain the architecture spec and what it does.
