* update cairo for new meson build system
* update patch range. remove old conflict
* style
* update pango to reflect the changes in cairo
* refine depends
* style
* add lzo depends
* add +shared
* non self-referential variant requireme
* style
* Move +shared variant back to just autotools as meson automatically handles it
* clarify patch when=
* update based on reviews. switch from conflicts to requires to enforce variant synchronization
* refine conflicts and requires
* better group build deps together
* comment for meson build lower version bound
* clarifying comments
* clarify version ranges, enforce build_system with version ranges
* style
* cairo: no need to require for build_systems
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Up to now, Spack was allowing all build-tools that
may appear in the DAG to have 2 max_dupes.
This is not needed in practice for most of them,
and adding them out of caution just increases
grounding and concretization time.
This PR makes the value of max_dupes configurable
per package, and sets only a few known packages to
2 max_dupes by default.
In case user needs different values, they can
tune the configuration for their use case.
On macOS, prefix_a/file and prefix_b/FILE map to the same file view/file or view/FILE.
This commit ensures that we test whether a view is created on a case insensitive filesystem and handle projection conflicts accordingly.
With this change spec["pkg"] searches only direct dependencies and transitive link/run
dependencies, ordered by depth. This avoids situations where we pick up unwanted
deps of build/test deps.
To reach those, you need to do spec["build_dep"]["pkg"] explicitly.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
meson's `dependency` function often uses pkg-config to locate a dependency, and may even fall back to cmake. The former case is very common, and since packagers often forget to add the tiny pkgconfig package as a build dep, we do it for them.
Currently this is hardcoded to the same value as listed in the class
definition. If one ever overrides this attribute, such as:
```
packages:
openblas:
package_attributes:
libraries = [ 'libopenblaso64', ]
```
this patch will make sure that override also in the
`spec['openblas'].libs()` call. (Which happens in `hypre`, likely
others).
( see
https://spack.readthedocs.io/en/latest/packages_yaml.html#assigning-package-attributes
)
Thanks to becker33 for debugging help in Slack
* Name of zlib's library differs on Windows; also account for name
differing when building +shared
* `zlib`'s `.libs` implementation was searching for the runtime
libraries (the .dlls) and should be searching for link-time libs
* pandoramonitoring: add v3.6.0; pandorapfa: add v4.11.2
Remove variables that are not being used in pandorasdk. Use the C++ standard
from ROOT when possible and pass -Wno-error to override the -Werror that will
typically fail with a new standard. Add a cxxstd variant for pandorasdk
* Fix style
* Update var/spack/repos/builtin/packages/pandorasdk/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Fix style
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* h5hut: Remove H5_USE_110_API for newer versions
* h5hut: style reformat and add maintainer
* h5hut: correct version syntax for <v2.x.x
* h5hut: Bump default version to 2.0.0rc7 and remove older rc candidates
* Update var/spack/repos/builtin/packages/h5hut/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
---------
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
cray-mpich now has a rocm variant. You can use gtl_lib in the
flag_handler like so:
```python
def flag_handler(self, name, flags):
wrapper_flags = []
environment_flags = []
build_system_flags = []
if self.spec.satisfies("+rocm"):
if self.spec.satisfies("^cray-mpich"):
gtl_lib = self.spec["cray-mpich"].package.gtl_lib
build_system_flags.extend(gtl_lib.get(name) or [])
# hipcc is not wrapped, we need to pass the flags via the
# build system.
build_system_flags.extend(flags)
return (wrapper_flags, environment_flags, build_system_flags)
```
---------
Co-authored-by: Richard Berger <rberger@lanl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Richard Berger <richard.berger@outlook.com>
* postgresql: add version 17.2
* postgresql: install flex, bison and perl when building versions 17 and up
* postgresql: do not install perl by default when building versions 17 and up
This PR is effectively a breaking change extracted from #45189, which removes
support for spec["mpi"] if spec itself is openmpi / mpich that could provide mpi;
from the Spec instance we don't have any parent it provides it to,
hence it's a KeyError.
* g4vg: add develop version
* celeritas: add develop version
* Fix style
* REVERTME: move celeritas changes to another branch
* Get full repo
* remove unneeded variable
Currently, a few packages using kokkos rely on
kokkos itself monkeypatching its own spec to
provide some attribute.
In this commit we change this attribute to be
defined on the package, and never be monkeypatched.
Currently, when we setup the ASP problem for `clingo`, we don't take into account the configuration. This results in setting up ASP problems that are larger than necessary, with possibly redundant information, and higher concretization times.
This PR tries to improve things by adding an opt-in feature that computes the _possible dependencies_ of a solve taking also into account the current configuration, and avoids adding possible dependencies that we are certain can't be in the final solution.
The feature can be activated with:
```yaml
concretizer:
static_analysis: true
```
Examples of simple rules to discard dependencies are:
- Dependencies that are not buildable, and for which no binary is present (e.g. `cray-mpich` etc. on non Cray systems)
- Dependencies that are not for the current platform (e.g. `msmpi` on non Windows platforms)
- Conditional dependencies that cannot be activated, because of some user requirement (e.g. `cuda` etc. if the user requires `~cuda` in configuration)
- Virtual providers that cannot be used, because of a requirement on a virtual
The speed-up these rules seem to give depends on the use case at hand, but if the configuration is updated properly, they are noticeable.
Since in cases where there is no rule to exclude packages upfront, reuse is active, and this option is activated, it's possible to see some minor slow down, the feature has been added as opt-in, so it's turned off by default.
* Bump up the version for rocm-6.3.2 release
* rocm-openmp-extras update and style correction
* Updating mivisionx, omniperf, rccl & rocprofiler-systems
* Updating hipsparselt & rocm-opencl
* rocprofiler-systems on gcc-13 and rvs commit instead of patch
* Updated rocjpeg & rocm-examples for 6.3.2
* ROCPROFSYS_BUILD_DYNINST & DYNINST_BUILD_TBB are required only with gcc-13
---------
Co-authored-by: afzpatel <122491982+afzpatel@users.noreply.github.com>
Current location is within the Spack prefix, which causes builds to
pollute VCS with stage artifacts and generally inflates the Spack
install prefix.
This PR moves it to the user cache location now that we can
consistently support paths with spaces on Windows.
With CFLAGS, the code path in the amdfftw build system will bypass the logic around AMD_ARCH.
---------
Co-authored-by: vijay kallesh <Vijay-teekinavar.Kallesh@amd.com>
* salt: Add v0.3.0 of SALT
This version contains important bug fixes for building and parsing
projects containing Fortran
* salt: Be more explicit about dependency types
- llvm+clang+flang is needed at build, link and runtime for the
correct operation of SALT
- Testing with llvm@master ( llvm > 19.x ) shows that SALT is
currently incompatible with the latest llvm API so an updated salt
will be required when LLVM 20 is released
`relocate_links` warns when the target is absolute and not matched by
any prefix from the prefix to prefix map.
This can lead to false positives, cause the prefix to prefix map does
not contain trivial/identity entries whenever a package is installed to
its original location.
Since relocate_links is the odd one out there (we don't warn about
similar issues with rpaths, etc), just remove the warning.
Codecov needs to see the token secret when uploading, so we have to
add this line to the workflow YAML:
```yaml
with:
token: ${{ secrets.CODECOV_TOKEN }}
```
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Remove variable from cmake.py
#48775 left a dangling variable that was not caught in CI but by the eyes of @haampie. Restructure variable to local method.
* [@spackbot] updating style on behalf of psakievich
* Update cmake.py
* Update lib/spack/spack/build_systems/cmake.py
* Update lib/spack/spack/build_systems/cmake.py
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
* Fix upcxx problem with a template argument list is expected after a name prefixed by the template keyword
* Revert "Fix upcxx problem with a template argument list is expected after a name prefixed by the template keyword"
This reverts commit faf9b8ce85.
* Apply workaround for oneAPI compiler
* style problem resolved
* use spec.satisfies syntax
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Add ruff configuration to `pyproject.toml`.
This allows `ruff format` in the Spack repository to format all the files we care about,
with our line length of 99, the exceptions we already put in place, and excluding things
we don't auto-format, like vendored dependencies.
Right now it'll reformat 175 or so files, but only slightly, in places where `ruff` differs from
`black`. For the most part I like the ruff format decisions better than `black`, but none of
the changes seem too severe.
This does not change `spack style` -- I figure that can come later but this at least will
let people start playing with `ruff`.
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
These are some changes that `ruff check --fix` would make that the current
`spack style` also agrees with. Make the changes now so that the `ruff`
change is less disruptive.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
The import-check action now presents problematic import statements
introduced by the PR better.
The idea is roughly:
* Let (V₁, E₁) be the graph of modules as vertices and import statements
as edges before the change
* Let (V₂, E₂) be the graph after the code change, which is typically a small
perturbation of (V₁, E₁).
* X₁ = FAS(V₁, E₁) is the feedback arc set before (a minimal set of edges to
delete to make it acyclic)
* X₂ = FAS(V₂, E₂ ∖ X₁) is the feedback arc set after deletion of the minimal
set of edges that made the old graph acyclic.
* X₃ = FAS(V₂, E₂) is the feedback arc set after
Previously I displayed X₁ and X₃ and users had to diff themselves.
Now, I'm showing X₂, which is a small set, typically directly related to
code changes.
However, it can be that a small code change adding say 2 problematic imports
creates a completely different solution X₃ that only requires deletion of just 1
different import. In that case the user is informed that they can potentially do
less work.
So for PR #48784 the output is now:
> The overall number of problematic import statements increased by 1 from 31 to 32.
> This is likely a direct consequence of the following import statements:
>
> ```
> spack/config imports: spack.spec, spack.util.path, spack.util.remote_file_cache
> ```
>
> However, instead of removing 3 import statements, it is sufficient to remove only 1
> import statement from the following list:
>
> ```
> spack/concretize imports: spack.bootstrap, spack.solver.asp
> spack/environment imports: spack.bootstrap, spack.environment
> spack/fetch_strategy imports: spack.version.git_ref_lookup
> spack/install_test imports: spack.build_environment, spack.package_base
> spack/modules imports: spack.modules
> spack/platforms imports: spack.config
> spack/relocate imports: spack.bootstrap
> spack/repo imports: spack.package_base, spack.patch, spack.tag
> spack/spec imports: spack.binary_distribution, spack.compiler, spack.compilers, spack.concretize, spack.environment, spack.hash_types, spack.provider_index, spack.repo, spack.spec_parser, spack.store, spack.traverse, spack.variant, spack.version.git_ref_lookup
> spack/subprocess_context imports: spack.environment
> spack/util/gpg imports: spack.bootstrap
> spack/util/package_hash imports: spack.package_base
> spack/util/path imports: spack.config, spack.environment
> spack/util/remote_file_cache imports: spack.util.web
> ```
from which the user can figure out that
`spack/util/remote_file_cache imports: spack.util.web` is the "bottleneck" now.
* Add versions 2 and 3 of py-sphinx-rtd-theme.
Allow for versions of py-sphinx greater than 6.
Fix the Python version for older versions that depend on distutils.
Get the py-docutils dependency from the py-sphinx recipe.
* Depend purely on the py-docutils dependency in py-sphinx.
* More refined dependency versioning.
* Fixed versioning for py-sphinx and py-docutils.
Currently, environments created from manifest files with relative includes result in broken
references to config files.
This PR modifies `spack env create` to create local copies in the new environment of any local
config files from relative paths in the environment manifest passed as an init file.
This PR does not change the behavior if the include is an absolute path or if the include is from
a relative path outside the environment directory, but it does warn about missing relative includes if
they are inside the environment directory.
Includes regression test and short blurb in docs.
* Added salt variant to tau
* Update package.py
* [@spackbot] updating style on behalf of wspear
---------
Co-authored-by: wspear <wspear@users.noreply.github.com>
* Create SALT package.py
Added a package for the SALT Source AnaLysis Toolkit
@zbeekman
* [@spackbot] updating style on behalf of wspear
* Update package.py
Line wrap
---------
Co-authored-by: wspear <wspear@users.noreply.github.com>
* py-mdit-py-plugins: Add new versions 0.3.5, 0.4.2
Signed-off-by: Jonathon Anderson <anderson.jonathonm@gmail.com>
* py-myst-parser: Add new versions 0.19.0 to 4.0.0
Signed-off-by: Jonathon Anderson <anderson.jonathonm@gmail.com>
* hpctoolkit: Add +docs variant and manpages
This commit unconditionally enables manpages for the HPCToolkit tools.
The new `+docs` variant enables additional documentation, specifically
the user's manual. Both require new build-time dependencies.
Signed-off-by: Jonathon Anderson <anderson.jonathonm@gmail.com>
---------
Signed-off-by: Jonathon Anderson <anderson.jonathonm@gmail.com>
* package api: drop wildcard re-export
To ensure package repos are forward/backward compatibility with Spack,
we should explicitly export all symbols we want to expose in the public
package API, and drop `from spack.something import *` because
removal/addition to the public API will go unnoticed.
Also `llnl.util.filesystem` has some methods that shouldn't be exposed
in the package API, so better to enumerate a subset explicitly.
* remove flatten_dependencies / install_dependency_symlinks
* JAX: add v0.4.34
* Disable search for clang
* Update CUDA flags
* Add py-jax 0.4.33, comment out until py-jaxlib 0.4.33 is also released
* Fix GCC build
* Try TF_NVCC_CLANG
* py-jax: add v0.4.34
* jax no longer has separate tags for jaxlib
* Install compiled wheel
* Join path before glob
* Wheel is in spack stage, not tmp path
* Add 0.4.35
* Add newer versions
* Build system has been refactored yet again
* Drop clang
* Fix build with source tarball, rocm support
* Support GCC
* Remove clang-specific compiler flags
* enable_cuda flag was removed
* Fix logic
* py-jax: add v0.4.38
* Add patch to fix GCC support
* Patch no longer needed
* Skip patching, directly pass flags
* New flags
* Remove unused import
* Patch changed
* Use older version of patch
* Newer patch
* Add CUDA symlink
* Symlink more directories
* Recursive symlink
* Import function
* Recursive search
* Undo cuda changes
* Add v0.5.0
* I quit
* Improve definition of a few placeholder packages
These packages are placeholders for vendor provided software,
that is not buildable, and should be declared as external.
* ibm-java: remove package, as asked by maintainer
Regressed in #47126
Spack was not interpreting mirrors using relative path with respect to the
metadata directory.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* test_no_matching_compiler_specs: does not need mock_low_high_config,
since mutable_config is already used at class level
* bindist.py: setup a configuration that doesn't super-impose builtin.mock
over builtin
* builder.py: use a mock configuration for the tests
This commit adds version 6.8.0 of GeoModel. As far as I can tell from
the change notes, there are no changes required to the build
configuration or dependencies.
This adds a new configuration section called `env_vars:` that can be set in an environment.
It looks very similar to the existing `environment:` section that can be added to `modules.yaml`,
but it is global for an entire spack environment. It's called `env_vars:` to deconflate it with spack
environments (the term was too overloaded).
The syntax looks like this:
```yaml
spack:
specs:
- cmake%gcc
env_vars:
set:
ENVAR_SET_IN_ENV_LOAD: "True"
```
Any of our standard environment modifications can be added to the `env_vars` section, e.g.
`prepend_path:`, `unset:`, `append_path:`, etc. Operations in `env_vars:` are performed
on `spack env activate` and undone on `spack env deactivate`.
* Reduce the size of outputted go built binaries
* Remove unused import from go package
* go: remove comment from setup dependents build env
* Add back missing imports after rebase
* Backward compat with Python 3.9 for socket.timeout
* Forward compat with Python [unknown] as HTTPResponse.geturl is deprecated
* Catch timeout etc from .read()
* Some minor simplifications: json.load(...) takes file object in binary mode.
* Fix CDash code which does error handling wrong: non-2XX responses raise.
The conflict is too strict and prevents usable combinations from being
concretized. Some packages depend on pika, but do not include pika
headers in HIP device code files, and can thus be compiled even with the
bad combination of HIP and GCC versions.
* py-awkward: add dependency on py-importlib-metadata and py-fsspec
* Implement suggested constraint and dependency type changes
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
On macOS you cannot unconditionally pass `-rpath`, it can conflict with
`-r`.
mpicc is not the place to inject rpaths to compiler runtime
libraries. That's up to the compiler's config files (spec files in gcc,
config files in llvm).
Also remove some patches that are redundant in newer versions of
openmpi.
Should be sufficient to set CONFIG_SITE to /dev/null before running configure to
prevent any config site file to be loaded, which currently causes non-determinism in builds.
Setting the variable CONFIG_SITE prevents configure files to check $prefix/share/config.site,
$prefix/etc/config.site, $ac_default_prefix/share/config.site, $ac_default_prefix/etc/config.site
so we don't have to patch a block of code.
* Address quoting issue that casuses dev_paths containing @ symbols to parse as versions
* Fix additional location were dev_path was imporperly constructed
The dev_path must be quoted to avoid parsing issues when
paths contain '@' symbols. Also add tests to catch
regression of this behavior
* Format to fix line length
* fix failing tests
* Fix whitespace error
* Add binary_compatibility fixture to test
* Change string formatting to avoid multiline f string
* Update lib/spack/spack/test/concretization/core.py
* Add tmate debug session
* Revert "Add tmate debug session"
This reverts commit 24e2f77e3c.
* Move test and refactor to use env methods
* Update lib/spack/spack/test/cmd/develop.py
---------
Co-authored-by: psakievich <psakiev@sandia.gov>
Since macOS 15 `ld -single_module` warns with a deprecation message,
which makes configure scripts believe the flag is unsupported. That
in turn triggers a code path where `archive_cmds` is set to
```
$CC -r -keep_private_externs -nostdlib ... -dynamiclib
```
instead of just
```
$CC -dynamiclib ...
```
This code path was meant to trigger only on ancient macOS <= 14.4 where
libtool had to add `-single_module`, which is the default since macos
14.4, and is now apparently deprecated because the flag is a no-op for
more than 15 years.
The wrong `archive_cmds` causes actual problems combined with a bug in
OpenMPI's compiler wrapper (`CC=mpicc`), which appends `-rpath` flags,
which cause an error when combined with the `-r` flag added by the
autotools.
Spack's compiler wrapper doesn't do this, but it's likely there are
other compiler wrappers out there that are not aware that `-r` and
`-rpath` cannot be combined.
The fix is to change defaults: `lt_cv_apple_cc_single_mod=yes`.
* BF+ENH: Add wxwidgets 3.2.6 and py-wxpython 4.2.2
Improves compat with newer Python (>3.9) and numpy.
Fix error during configure step (even on at least some older
versions) by including 'pkgconfig' as a build dep so gtk+ is found.
* BF: Make wxpython use spack built wxwidgets instead of rebuilding
* Update var/spack/repos/builtin/packages/py-wxpython/package.py
Avoid using too new version of py-setuptools as license file format is currently not compatible.
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* for config: let `syaml_dict` inherit from `dict` instead of `OrderedDict`. `syaml_dict` now only exists as a mutable wrapper for yaml related metadata.
* for spec serialization / hashing: use `dict` directly
This is possible since we only support cpython 3.6+ in which dicts are ordered.
This improves performance of hash computation a bit. For a larger spec I'm getting 9.22ms instead of 11.9ms, so 22.5% reduction in runtime.
* OSError.errno apparently is int | None, but already part of __str__ anyway so drop
* fix disambiguate_spec_from_hashes
* List[Spec].sort() complains, ignore it
* fix typing of KnownCompiler, and use it in asp.py
Adds packages for the Arkouda server (`arkouda`) and Arkouda python client (`py-arkouda`).
Arkouda server and client are divided into separate packages to allow for them to be
installed independently of one another.
Future work remains to add a `+dev` variant to `py-arkouda`, but that will require additional
supporting packages made available through spack (e.g. for `py-pytest-env`
Modifications:
* Fix a severe bug where a spliced spec has the same hash as the original build spec
* Removed CacheManager in favor of install_mockery. The latter sets up a temporary store, and removes it at the end
of the test.
* Deleted a couple of helper functions e.g. _has_dependencies
* Checked that SolverException is raised, rather than Exception (more specific)
* Extended, and renamed the splicing_setup fixture (now called install_specs)
* Added more specific assertions in each test
One test is currently flaky, due to some instability when sorting multiple specs. It's currently marked xfail
The methods spack.spec.Spec.concretize and spack.spec.Spec.concretized
are deprecated in favor of spack.concretize.concretize_one.
This will resolve a circular dependency between the spack.spec and
spack.concretize in the next Spack release.
* add python bindings variant to chapel
* fix chpl_home, update chapel frontend rpath in venv
* fix chpl frontend shared lib rpath hack
* patch chapel env var line length limit
* patch chapel python shared lib location by chapel version
* unhack chpl frontend lib rpath
* fix postinstall main version number file path
* update chapel version number to 2.3
* use chapel releases instead of source tarballs, remove dead code
* Chapel 2.3 adds support for LLVM 19
* Bundled LLVM always requires CMake 3.20:
* Apply 2.3 patch for LLVM include search path
Fixes build errors for `chapel@2.3+rocm` of the form:
```
compiler/llvm/llvmDebug.cpp:174:9: error: cannot convert 'const char*' to 'llvm::dwarf::MemorySpace'
compiler/llvm/llvmDebug.cpp:254:15: error: cannot convert 'const char*' to 'llvm::dwarf::MemorySpace'
```
* fix style
* Fix misreporting of test_hello failures
`test_part` was aliasing the enclosing test name, leading to confusing and incorrect reporting on test failure.
* Ensure `libxml2` optional dep of `hwloc` is also added to `PKG_CONFIG_PATH` in the run env
* patch chplCheck for GPU + multilocale configs, install docs
* Adjust patch for checkChplInstall
* Ensure `CHPL_DEVELOPER` is unset for `~developer`
---------
Co-authored-by: Dan Bonachea <dobonachea@lbl.gov>
* Improve support using external modules with zsh
Spack integrates with external modules by launching a python subprocess
to scrape the path from the module command. In zsh, subshells do not
inheret functions defined in the parent shell (only environment
variables). This breaks the module function in module_cmd.py.
As a workaround, source the module commands using $MODULESHOME prior to
running the module command.
* Fix formatting
* Fix flake error
* Add guard around sourcing module file
* Add improved unit testing to module src command
* Correct style
* Another attempt at style
* formatting again
* formatting again
---------
Co-authored-by: psakievich <psakiev@sandia.gov>
* bdsim: update to point to the new location in github and add 1.7.7
* Remove the C++ standard patch
* Remove the cmake_args and add a comment instead
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
`spack find` and other commands that read the DB will fail if the databse is in a
read-only location, because `FailureTracker` and `Database` can try to create their
parent directories when they are constructed, even if the DB root is read-only.
Instead, we should only write to the filesystem when needed.
- [x] don't create parent directories in constructors
- [x] have write operations create parents if needed
- [x] in tests, `chmod` databases to be read-only unless absolutely needed.
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Adding the PACE library to the LAMMPS build
* Adding the PACE library for ML-PACE in LAMMPS
---------
Co-authored-by: Richard Berger <rberger@lanl.gov>
* Add py-protobuf@4.24.4 (needed for py-cylc-flow@8.3.6).
* Add py-cylc-flow@8.3.6 and enable png output when creating graphs
by requesting variant pangocairo for graphviz dependency.
* Add corresponding versions of py-metomi-rose@2.3.2,
py-cylc-rose@1.4.2, py-cylc-uiserver@1.4.2.
* Add myself as maintainer to all the cylc-related packages.
This PR allows using the subscript notation directly on packages. The
intent is to reduce the boilerplate needed to retrieve package
properties from nodes other than root.
New year, new versions of the ACTS dependencies. This time, we have a
new version of detray, a new version of algebra plugins, as well as a
new version of ACTS itself.
* Add type-hints to `spack.util.executable.Executable`
* Add type-hint to input
* Use overload, and remove assertions at calling sites
* Bump mypy to v1.11.2 (working locally), Python to 3.13
* root: Restrict patch range
* root: Set minimum gcc version for cxxstd=20
* root: fix gcc range when cxxstd 20
Co-authored-by: Paul Gessinger <hello@paulgessinger.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* add parse tool, json, and load json
bug fix
add variants and conflictions for g4tendl
* correct format
* correct format
* update version mapping
* remove 1.0
* Update var/spack/repos/builtin/packages/geant4-data/package.py
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
* add options
* depends on it
* fix typo
---------
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
* e4s cray rhel ci stack: re-enable and update for new cpe, should fix cray libsci issue
* only run e4s-cray-rhel stack
* Mkae Autotools build_system point at correct build_directory
* remove selective enable of cray-rhel stacks
* restore SPACK_CI_DISABLE_STACKS
* use dot prefix to hide cray-sles jobs instead of comment-out
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
* edm4hep: Add lower clang version bounds
EDM4hep 0.99.1 introduced usage of consteval. While this is technically
supported in clang versions below 17, the implementation seems to be
incomplete and fail compilation of EDM4hep 0.99.1 and up.
* Update var/spack/repos/builtin/packages/edm4hep/package.py
Co-authored-by: Thomas Madlener <thomas.madlener@desy.de>
---------
Co-authored-by: Thomas Madlener <thomas.madlener@desy.de>
* py-py-spy: add 0.4.0
* py-py-spy: port from Package to CargoPackage
* CargoPackage: respect make_jobs
* rust: respect make_jobs during build and install
* spack style
* CargoBuilder: fix make_jobs syntax
* CargoBuilder: don't write to $HOME, use stage dir
* rivet: add version 3.1.11 with some back-port fixes
Some back-ported fixes from the 4.x series. Most importantly the
possibility to build against HepMC 3.3.0.
* yoda: Add version 1.9.11
* Add a conflict with hepmc=2
* Unify hepmc@3.3.0 conflicts into one statement
* Remove conflict and update conditional hepmc variant
* Use caret to signify conflict with dependency
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Make conflict and msg more specific
* Add dedicated version dependency to yoda
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* gromacs: remove dependency on Fortran
Fortran was removed from GROMACS core since 4.6. There are a few contrib
files around, but they are not built anyway.
Also fix a couple typos.
* [@spackbot] updating style on behalf of al42and
---------
Co-authored-by: al42and <al42and@users.noreply.github.com>
* zoltan: Ignore errors about incompatible pointer type with gcc@14
In gcc 14 -Werror=incompatible-pointer-types is now the default.
Silence it until it gets fixed in zoltan upstream.
* zoltan: Fix linking error when built with ifx
* mpich: gather in a single place env modifications needed by mpich derivatives
MPICH, and its derivatives, share a lot of copy/paste code to setup the
environment during the different stages of the package life-cycle.
This commit gathers the common modifications in a single place (a mixin class),
living in the Mpich package, and makes derivatives import, and reuse, it.
* Fix docs for Python < 3.13
* openloops: Add cmodel to user config file to override setting added in 2.1.2.
* openloops: Change cmodel from small to large following author recommendation.
A few changes to tarball creation (for build caches):
- do not run file to distinguish binary from text
- file is slow, even when running it in a batched fashion -- it usually reads all bytes and has slow logic to categorize specific types
- we don't need a highly detailed file categorization; a crude categorization of elf, mach-o, text suffices.
detecting elf and mach-o is straightforward and cheap
- detecting utf-8 (and with that ascii) is highly accurate: false positive rate decays exponentially as file size increases. Further it's not only the most common encoding, but the most common file type in package prefixes.
iso-8859-1 is cheaply (but heuristically) detected too, and sufficiently accurate after binaries and utf-8 files are classified earlier
- remove file as a dependency of Spack in general, which makes Spack itself easier to install
- detect file type and need to relocate as part of creating the tarball, which is more cache friendly and thus faster
mpicxx_shared_libraries seems a relic of #1550, and is
not currently used by any builtin package.
Thus, cleanup the recipes, and avoid monkey-patching
spec objects.
Python >= 3.13 does not have the crypt variant anymore. Still no matter
if the test for crypt succeeds (which it can on Fedora providing its own
crypt module for Python 3.13) or fails, it will add +crypt or ~crypt,
which both fail because the variant only exists until Python 3.12.
Co-authored-by: Richard Berger <rberger@lanl.gov>
* silo: variant python needs python
* Dependency to Python did not resolve the "Python.h" header not being found
Added the -I path to Python header to the compiler.
Having silo depend on python was not sufficient to get the path to python.
Maybe there is a smarter way to do that, but this one works.
* Update var/spack/repos/builtin/packages/silo/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/silo/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/silo/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* thepeg: Correctly specify rivet version for dependency
* herwig3: Add latest version 7.3.0
* thepeg: Make sure to have consistent hepmc version
rivet and thepeg need to have the same hepmc version otherwise things
will not compile
* libzip links with external libs found on host feelpp/spack#6
* add maintainers
* fix style
* use multi-build system
/cc @wdconinc
* fix style
* rm space and rename variant bz2 to bzip2
/cc @wdconinc
* fix variant name for bzip2
* zstd is supported in libzip@:1.8
* fix style
* fix style
* fix style
* rm deprecated version and versions that cannot be found easily
use only cmake from now on
* fix style
* fix style
* use variant when option for zstd
* Update var/spack/repos/builtin/packages/libzip/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* fix style
/cc @wdconinc
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
`kcov` was removed in Ubuntu 24.04, and it is no longer
installable via `apt` in our CI images. Instal it via
Linuxbrew instead, at least until it comes back to Ubuntu.
`subversion` is also not installed on ubuntu 24 by default,
so we have to install it manually.
- [x] Add linuxbrew to linux tests
- [x] Install `kcov` with brew
- [x] Install subversion with `apt`
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Fix silent error when reporting builds to CDash
CDash has a 191 char maximum for build names. When this
is exceeded, CDash silently fails to correctly process the
reported XML. This truncates CDash build names to 190 chars
and emits a warning indicating it is doing so to prevent
such errors from occuring.
* test/reporters.py: add unittest for buildname len issue
* test/reporters.py: rename cdash buildname test
* ci/common.py: fix syntax causing breaking test
It appears that the CDash reporter is expecting a string
as the buildname.
* Update lib/spack/spack/reporters/cdash.py
Fix warning message to reflect actual issue.
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* ci/common.py: fix function call to actually call function
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: psakievich <psakiev@sandia.gov>
* py-typer: add version 0.15.1 and "standard" optional dependencies
* py-typer: remove variant that only exists in source, not sdist. Remove trailing .0 from versions.
* Improve variant robustness for dd4hep and edm4hep
Now variants won't be "false" if there's a typo.
* Use libs instead of manual prefix paths
* Improve cmake for another hep package
* Fix variant use and style
* Use directories for ODD
* r-rlas is a dependency for r-lidr
* new package r-lidr w/ suggests to address masking issues
* fixed flake8 issues and added maintainers
* removed boost import statement for flake sake
* Score-P: Replace with-or-without, document options that are not currently explicitly mapped in package for mpi and shmem.
* trim long lines
---------
Co-authored-by: wrwilliams <wrwilliams@users.noreply.github.com>
Improve our typing by updating some todo locations in the code to use
`Literal` instead of a simple `str`.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Fix issue reported by some users regarding some build dependencies.
* Remove invalid configure-time flag that was recently introduced.
Signed-off-by: Samuel K. Gutierrez <samuel@lanl.gov>
There are still more fix ups required for the missing libs to work as
expected in CI. Dropping the error requirement in favor of moving to a
log scraping method until we can verify all package issues have been
addressed correctly.
* Set the "build_jobs" on concretization/generate for CI
build_jobs also controls the concretization pool size. Set this
in the config section for CI generate.
This config is overwritten by build_job CI using the SPACK_BUILD_JOBS
environment variable. This implicitly will drop the default build
CPU request on all "default" grouped build jobs from (max) 16 to 8.
* Add default allocations for build jobs
* Add common jobs and concretize args to ci generate and rebuild
* CI: Specify parallel concretize and build jobs via argument
* Increase power and cray concretization limits
Lowering limits for these stacks creates timeout
* Increase default pool size to 8
intermittent timeouts with 4 CPU
* Add reduced requests for windows for now
This turns some variant-specific methods for dealing with when-keyed dictionaries into
more generic versions, in preparation for conditional version definitions.
`_by_name`, `_names`, etc. are replaced with generic methods for transforming
when-keyed dictionaries:
* `_by_subkey()`
* `_subkeys()`
* `_num_definitions()`
* `_definitions()`
* `_remove_overridden_defs()`
And the variant accessors are refactored to use these methods underneath.
To do this, types like `WhenDict` had to be generified, and some `TypeVars`
were added for sortable keys and values.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
We are using more and more typing features in Spack, and without features like
protocols, typing core is becoming harder and harder.
I think it's worth vendoring `typing_extensions` for this. It will get us a number of
useful capabilities:
* `Literal`
* `TypedDict`
* `Protocol`
among others.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
This commit adds a config option `config:shared_linking:missing_library_policy:error/warn/ignore` which will cause installation errors or warnings when ELF executables or libraries need shared libraries which cannot be resolved from RPATH search paths. The default is to ignore.
This is a safeguard against accidentally linking to system libraries instead of Spack libraries. It makes it more likely that build cache installs work on different machines. It works only at the level of libraries, not at the level of symbols. Some system dependencies are allowed (e.g. kernel and libc).
Packages can (but are discouraged to) set `unresolved_libraries` to a list of patterns of sonames/library names that are know to be unresolvable in RPATHs. In the future this could be made more fine-grained in a non-breaking way by allowing a dictionary of patterns `lib => [deps]`.
Extracted #45189
Common test setup has been extracted in fixtures. Some matrix
dimensions moved from being "compiler" to be "targets".
Use --fake install for packages in test.
The `_normal` attribute on specs is no longer used and has no meaning.
It's left over from part of the original concretizer.
The `concrete` constructor argument is also not used by any part of core.
- [x] remove `_normal` attribute from `Spec`
- [x] remove `concrete` argument from `Spec.__init__`
- [x] remove unused `check_diamond_normalized_dag` function in tests
- [x] simplify `Spec` constructor and docstrings
I tried to add typing to `Spec` here, but it creates a huge number of type issues
because *most* things on `Spec` are optional. We probably need separate `Spec` and
`ConcreteSpec` classes before attempting that.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* nim: fix deps, deprecate and patch old versions
* Fix runtime dependencies for produced binaries:
- Add -rpaths pointing at dependencies to
std wrapper modules
- Set version constraints for OpenSSL
- Added SQLite3 variant for <2.0
* Parallelize build with make
* Deprecate 1.0.10 due to CVEs
* Deprecate 1.9.3 as it's an old development version
* Backport patch for CVE-2021-21372 to <1.2.10/<1.4.4,
CVE-2021-21374 to 1.4.2 and CVE-2021-46872 to 1.4.*
* Avoid empty low ranges that include devel
* Add previously missing CVE comment
* Keep "link" type for dynamic libraries for MSVC
* Omit "run" type for library dependencies
* Disable SQLite variant by default
* Fix version ranges
Had assumed they were exclusive, but they're inclusive
* Correct version range for sqlite variant
Difference doesn't matter outside of development versions
* Move patches to use GitHub URLs instead of files
* Retry CI
* append ?full_index=1
Previously the pip setup would delete the visitmodule during the install
step. This was fixed by forcing the pip setup to only run once before
the dependents are created.
Add missing encoding=utf-8 to various open calls. This makes
files like spec.json, spack.yaml, spack.lock, config.yaml etc locale
independent w.r.t. text encoding. In practice this is not often an
issue since Python 3.7, where the C locale is promoted to
C.UTF-8. But it's better to enforce UTF-8 explicitly, since there is
no guarantee text files are written in the right encoding.
Also avoid opening in text mode if it can be avoided.
* `f.tell` on a `TextIOWrapper` does not return the offset in bytes, but
an opaque integer that can only be used for `f.seek` on the same
object. Spack assumes it's a byte offset.
* Do not open in a locale dependent way, but assume utf-8 (and allow
users to override that)
* Use tempfile to generate a backup/temporary file in a safe way
* Comparison between None and str is valid and on purpose.
Follow-up to #47956
* Rename `token.py` -> `tokenize.py`
* Rename `parser.py` -> `spec_parser.py`
* Move common code related to iterating over tokens into `tokenize.py`
* Add "unexpected character token" (i.e. `.`) to `SpecTokens` by default instead of having a separate tokenizer / regex.
* Python: deprecate 3.8
* Remove preference for EOL Python versions
* Explicitly deprecate things requiring EOL Python
* More deprecations
* deprecate old versions of slepc, py-petsc4py, py-slepc4py in sync with old versions of petsc
---------
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
The use of `^` in `depends_on` directives has never been allowed, since
the dawn of Spack.
Up to now, we used to have an audit to catch this kind of issue, mainly
because in that way we could easily collect all issues and report them
to packagers at once.
Due to implementation details, this audit doesn't work if a dependency
without a `^` is followed by the same dependency with a `^`.
This PR makes this pattern an error, which will be reported eagerly, and
removes the corresponding audit. It also fixes a package using the wrong
idiom.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
So far, the ESMF package recipe in spack assumes that the spack
compilers clang and apple-clang are using gfortran as the Fortran
compiler. But with the latest improvements to the LLVM compilers,
we need to also support clang with flang.
Reorganize the pipeline generation aspect of the ci module,
mostly to separate the representation, generation, and
pruning of pipeline graphs from platform-specific output
formatting.
Introduce a pipeline generation registry to support generating
pipelines for other platforms, though gitlab is still the only
supported format currently.
Fix a long-existing bug in pipeline pruning where only direct
dependencies were added to any nodes dependency list.
* Set the "build_jobs" on concretization/generate for CI
build_jobs also controls the concretization pool size. Set this
in the config section for CI generate.
This config is overwritten by build_job CI using the SPACK_BUILD_JOBS
environment variable. This implicitly will drop the default build
CPU request on all "default" grouped build jobs from (max) 16 to 8.
* Add default allocations for build jobs
* Add common jobs and concretize args to ci generate and rebuild
* CI: Specify parallel concretize and build jobs via argument
* Increase power and cray concretization limits
Lowering limits for these stacks creates timeout
* py-nbclassic: add v1.1
* py-nbclassic: reduce explicit dependencies for v1.1.0
Having all the 'excess' packages listed did not break anything, as
they were needed for `py-jupyter-server` (pulled in via `py-notebook-shim`)
anyway, but the change makes it more clear on why things are being pulled in.
* acts dependencies: new versions as of 2024/12/08
This commit includes a new version of ACTS, as well as new versions of
the ACTS algebra plugins, covfie, detray, and geomodel.
* Fixes
* covfie: depends_on cmake@3.21: when @0.11:
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Add py-param@2.1.1
* Add py-panel@1.5.2
* Add py-bokeh@3.5.2
* New package py-datashader
* New package py-geoviews
* New package py-holoviews
* WIP: new package py-uxarray
* New package py-antimeridian
* New package py-dask-expr
* New package py-spatialpandas
* New package py-hvplot
* Add dependency on py-dask-expr for 'py-dask@2024.3: +dataframe'
* Added all dependencies for py-uxarray; still having problems with py-dask +dataframe / py-dask-expr
* Fix style errors in many packages
* Clean up comments and fix style errors in var/spack/repos/builtin/packages/py-dask-expr/package.py
* In var/spack/repos/builtin/packages/py-dask/package.py: since 2023.8, the dataframe variant requires the array variant
* Fix style errors in py-uxarray package
- [x] Clean up arguments on the `resource` directive.
- [x] Add type annotations
- [x] Add `resource` to type annotations on `PackageBase`
- [x] Fix up `resource` docstrings
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Some of the class-level annotations were wrong, and some were missing. Annotate all the
functions here and fix the class properties to match what's actually happening.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
The first argument to each Spack directive is not a `PackageBase` instance but a
`PackageBase` class object, so fix the type annotations to reflect this.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
`Optional` shouldn't be part of `PatchesType` -- it's clearer to specify `Optional` it
in the methods that need their arguments to be optional.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* update py-numl and py-nugraph recipes
this commit adds the develop branch as a valid option for each of these two packages. in order to enable this, package tarballs are now retrieved from the github source repository instead of pypi, and their checksums and the build system have been updated accordingly.
* rename versions "develop" -> "main" to be consistent with branch name
* nim: add latest versions
In addition:
- Create separate build and install phases.
- Remove koch nimble call as it's redundant with koch tools.
- Install all additional tools bundled with Nim instead of only Nimble.
* Fix 1.6 version
* nim: add devel
In addition:
- Fix build accessing user config/cache
* Bump Kokkos and Kokkos-kernels to 4.5.00
* petsc@:3.22 add a conflict with this new version of kokkos
* Update kokkos/kokkos-kernel dependency
---------
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
the nis module was removed in python 3.13
we had it default to ~nis
no package requires +nis
required dependencies for +nis were missing
so better to remove the nis module entirely.
* acts dependencies: new versions as of 2024/11/25
This commit adds a new version of detray and two new versions of vecmem.
* acts dependencies: new versions as of 2024/12/02
This commit adds version 38 of ACTS and a new version of detray.
In preparation for adding `when=` to `version()`, I'm cleaning up the types in
`version_types` and making sure the methods here pass `mypy` checks. This started as an
attempt to use `ConcreteVersion` outside of `spack.version` and grew into a larger type
refactor.
The hierarchy now looks like this:
* `VersionType`
* `ConcreteVersion`
* `StandardVersion`
* `GitVersion`
* `ClosedOpenRange`
* `VersionList`
Note that the top-level thing can't easily be `Version` as that is a method and it
returns only `ConcreteVersion` right now. I *could* do something fancy with `__new__` to
make `Version` a synonym for the `ConcreteVersion` constructor, which would allow it to
be used as a type. I could also do something similar with `VersionRange` but not sure if
it's worth it just to make these into types.
There are still some places where I think `GitVersion` might not be handled properly,
but I have not attempted to fix those here.
- [x] Add a top-level `VersionType` class that all version types extend from
- [x] Define and document common methods and rich comparisons on `VersionType`
- [x] Replace complicated `Union` types with `VersionType` and `ConcreteVersion` as needed
- [x] Annotate most methods (skipping `__getitem__` and friends as the typing is a pain)
- [x] Fix up the `VersionList` constructor a bit
- [x] Add cases to methods that weren't handling all `VersionType`s
- [x] Rework some places to clarify typing for `mypy`
- [x] Simplify / optimize _next_version
- [x] Make StandardVersion.string a property to enable lazy comparison
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
This visitor accepts the sub-dag of all nodes and unique edges that have
deptype X directly from given roots, or deptype Y transitively for any
of the roots.
LLVM can be a transitive link dependency of hip through gl's dependency mesa, which uses it for software rendering.
In this case make sure llvm-amdgpu is found with find_package(LLVM) and
find_package(Clang) by setting LLVM_ROOT and Clang_ROOT.
That makes the patch of find_package's HINTS redundant, so remove that.
It did not work anyways, because CMAKE_PREFIX_PATH has higher precedence
than HINTS.
Explcitly sets the CMake variables Faodel_INCLUDE_DIRS and Faodel_LIBRARY_DIRS when +faodel.
This seems to be needed for recent versions of seacas (seacas@2021-04-02:), but should be safe
to do for all versions.
For Faodel_INCLUDE_DIRS, it looks like Faodel has header files under $(Faodel_Prefix)/include/faodel,
but seacas is not including the "faodel" part in #includes. So add both $(Faodel_Prefix)/include
and $(Foadel_Prefix)/include/faodel
Co-authored-by: payerle <payerle@users.noreply.github.com>
* c/c++ flags should have been modified for all 2023.x.y versions, but
upper bound was too low
* Fortran flags should have been modified for all 2024.x.y versions, but
likewise the upper bound was too low
* gromacs: announce deprecation policy and start to implement
* Style it up
* [@spackbot] updating style on behalf of mabraham
* Bump versions used in CI
---------
Co-authored-by: mabraham <mabraham@users.noreply.github.com>
Permit configuring GROMACS with support for mdrun to trace its timing
regions by calling the ITT API. This permits tools like VTune and
unitrace to augment their analysis with GROMACS-specific annotation.
external googletest breaks dependents because they end up with
ITK_LIBRARIES set to `GTest::GTest;GTest::Main`, which then end up
literally in a nonsensical link line `-lGTest::GtTest`.
the vendored googletest produces a cmake config file where
`ITKGoogleTest_LIBRARIES` is empty.
* gromacs: oneapi does not always require gcc
* Support intel_provided_gcc only with %intel classic compiler
Require gcc only when needed with %intel
* New approach depending on gcc-runtime directly
* Update var/spack/repos/builtin/packages/gromacs/package.py
Co-authored-by: Christoph Junghans <christoph.junghans@gmail.com>
---------
Co-authored-by: Christoph Junghans <christoph.junghans@gmail.com>
* Visit: Add new versions 3.4.0 and 3.4.1
* Adios2: Restrict python, 3.11 doesn't not work for older Adios2
* VisIt: Set the VTK_VERSION for @3.4:
Older versions of VTK used the VTK_{MAJOR, MINOR}_VERSION variables for
VTK detection. VisIt >= 3.4 uses the full string VTK_VERSION.
* CI: Don't build llvm-amdgpu for non-HIP stack
* VisIt: v3.4.1 handles newer Adios2 correctly
* Visit: Add missing links in HDF5, set correct VTK version configuration parameter
* VisIt: Add py-pip requirement and patch visit with configuration changes
* HDF5 symlinks move when inside of callback
* VisIt ninja install fails with python module. Using make does not
* VisIt 3.4 has a high minimum cmake requirement
* HDF5: Early return when not mpi for mpi symlinks
* HDF5: Use platform agnostic method for creating legacy compatible MPI symlinks
* Fix VISIT_VTK_VERSION handling for 8.2.1a hack
* This extends PR #47285 to properly include some of the required version constrains of cgal 6 incl C++ standard. It also adds the new no-gmp backend as a variant.
* fix style
* disable cgal@6 +demo variant as the demos require qt6 which is not in spack
* disable the gmp variant until clarity on how its supposed to work is provided. bound shared and header_only variants to relevant versions
* Fix missing msvc compiler limit, fix variant left in
* Add more comments. Better describe the gmp variant. Remove testing code
* fix style
The default build of clang on darwin couldn't actually build anything
because of a lack of a sysroot built in. Also several compilation
errors finding the system libc++ cropped up, much like those in GCC, and
have been fixed.
* packages: Update 'yambo'
* add call to 'resource' method to download Ydriver and iotk during fetch instead of during build
* air-gapped installation could be performed since version 5.2.1
* add versions 5.2.3 and 5.2.4
* remove some inexistant configure options for versions "@5:"
* add a sanity_check on 'bin/yambo'
The gni libfabric provider works on some Cray systems, but not all. For
example, Slingshot-based machines use a different libfabric provider
(cxi). Therefore libfabric/gni should not be a dependency when using
Cray PMI.
* celeritas: remove deprecated versions through 0.3
* celeritas: deprecate old versions
* celeritas: add c++20 option
* Propagate vecgeom CUDA requirements
* Remove outdated conflicts and format it
Automatic splicing say `Spec` grow a `__len__` method but it's only used
in one place and it's not clear the semantics are useful elsewhere. It also
runs the risk of Specs one day being confused for other types of containers.
Rather than introduce a new function for one algorithm, let's use a more
specific method in the splice code.
- [x] Use topological ordering in `_resolve_automatic_splices` instead of
sorting by node count
- [x] delete `Spec.__len__()` and `Spec.__bool__()`
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Greg Becker <becker33@llnl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
`spack spec` output has looked like this for a while:
```console
> spack spec /v5fn6xo /wd2p2v7
Input spec
--------------------------------
- /v5fn6xo
Concretized
--------------------------------
[+] openssl@3.3.1%apple-clang@16.0.0~docs+shared build_system=generic certs=mozilla arch=darwin-sequoia-m1
[+] ^ca-certificates-mozilla@2023-05-30%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
...
Input spec
--------------------------------
- /wd2p2v7
Concretized
--------------------------------
[+] py-six@1.16.0%apple-clang@16.0.0 build_system=python_pip arch=darwin-sequoia-m1
[+] ^py-pip@23.1.2%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
```
But the input spec is right there on the CLI, and it doesn't add anything to the output.
Also, since #44843, specs concretized in the CLI line can be unified, so it makes sense
to display them as we did in #44489 -- as one multi-root tree instead of as multiple
single-root trees.
With this PR, concretize output now looks like this:
```console
> spack spec /v5fn6xo /wd2p2v7
[+] openssl@3.3.1%apple-clang@16.0.0~docs+shared build_system=generic certs=mozilla arch=darwin-sequoia-m1
[+] ^ca-certificates-mozilla@2023-05-30%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[+] ^gmake@4.4.1%apple-clang@16.0.0~guile build_system=generic arch=darwin-sequoia-m1
[+] ^perl@5.40.0%apple-clang@16.0.0+cpanm+opcode+open+shared+threads build_system=generic arch=darwin-sequoia-m1
[+] ^berkeley-db@18.1.40%apple-clang@16.0.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=darwin-sequoia-m1
[+] ^bzip2@1.0.8%apple-clang@16.0.0~debug~pic+shared build_system=generic arch=darwin-sequoia-m1
[+] ^diffutils@3.10%apple-clang@16.0.0 build_system=autotools arch=darwin-sequoia-m1
[+] ^libiconv@1.17%apple-clang@16.0.0 build_system=autotools libs=shared,static arch=darwin-sequoia-m1
[+] ^gdbm@1.23%apple-clang@16.0.0 build_system=autotools arch=darwin-sequoia-m1
[+] ^readline@8.2%apple-clang@16.0.0 build_system=autotools patches=bbf97f1 arch=darwin-sequoia-m1
[+] ^ncurses@6.5%apple-clang@16.0.0~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=darwin-sequoia-m1
[+] ^pkgconf@2.2.0%apple-clang@16.0.0 build_system=autotools arch=darwin-sequoia-m1
[+] ^zlib-ng@2.2.1%apple-clang@16.0.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=darwin-sequoia-m1
[+] ^gnuconfig@2022-09-17%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[+] py-six@1.16.0%apple-clang@16.0.0 build_system=python_pip arch=darwin-sequoia-m1
[+] ^py-pip@23.1.2%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[+] ^py-setuptools@69.2.0%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[-] ^py-wheel@0.41.2%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
...
```
With no input spec displayed -- just the concretization output shown as one consolidated
tree and multiple roots.
- [x] remove "Input Spec" section and "Concretized" header from `spack spec` output
- [x] print concretized specs as one BFS tree instead of multiple
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
This PR provides complementary 2 features:
1. An augmentation to the package language to express ABI compatibility relationships among packages.
2. An extension to the concretizer that can synthesize splices between ABI compatible packages.
1. The `can_splice` directive and ABI compatibility
We augment the package language with a single directive: `can_splice`. Here is an example of a package `Foo` exercising the `can_splice` directive:
class Foo(Package):
version("1.0")
version("1.1")
variant("compat", default=True)
variant("json", default=False)
variant("pic", default=False)
can_splice("foo@1.0", when="@1.1")
can_splice("bar@1.0", when="@1.0+compat")
can_splice("baz@1.0+compat", when="@1.0+compat", match_variants="*")
can_splice("quux@1.0", when=@1.1~compat", match_variants="json")
Explanations of the uses of each directive:
- `can_splice("foo@1.0", when="@1.1")`: If `foo@1.0` is the dependency of an already installed spec and `foo@1.1` could be a valid dependency for the parent spec, then `foo@1.1` can be spliced in for `foo@1.0` in the parent spec.
- `can_splice("bar@1.0", when="@1.0+compat")`: If `bar@1.0` is the dependency of an already installed spec and `foo@1.0+compat` could be a valid dependency for the parent spec, then `foo@1.0+compat` can be spliced in for `bar@1.0+compat` in the parent spec
- `can_splice("baz@1.0", when="@1.0+compat", match_variants="*")`: If `baz@1.0+compat` is the dependency of an already installed spec and `foo@1.0+compat` could be a valid dependency for the parent spec, then `foo@1.0+compat` can be spliced in for `baz@1.0+compat` in the parent spec, provided that they have the same value for all other variants (regardless of what those values are).
- `can_splice("quux@1.0", when=@1.1~compat", match_variants="json")`:If `quux@1.0` is the dependency of an already installed spec and `foo@1.1~compat` could be a valid dependency for the parent spec, then `foo@1.0~compat` can be spliced in for `quux@1.0` in the parent spec, provided that they have the same value for their `json` variant.
2. Augmenting the solver to synthesize splices
### Changes to the hash encoding in `asp.py`
Previously, when including concrete specs in the solve, they would have the following form:
installed_hash("foo", "xxxyyy")
imposed_constraint("xxxyyy", "foo", "attr1", ...)
imposed_constraint("xxxyyy", "foo", "attr2", ...)
% etc.
Concrete specs now have the following form:
installed_hash("foo", "xxxyyy")
hash_attr("xxxyyy", "foo", "attr1", ...)
hash_attr("xxxyyy", "foo", "attr2", ...)
This transformation allows us to control which constraints are imposed when we select a hash, to facilitate the splicing of dependencies.
2.1 Compiling `can_splice` directives in `asp.py`
Consider the concrete spec:
foo@2.72%gcc@11.4 arch=linux-ubuntu22.04-icelake build_system=autotools ^bar ...
It will emit the following facts for reuse (below is a subset)
installed_hash("foo", "xxxyyy")
hash_attr("xxxyyy", "hash", "foo", "xxxyyy")
hash_attr("xxxyyy", "version", "foo", "2.72")
hash_attr("xxxyyy", "node_os", "ubuntu22.04")
hash_attr("xxxyyy", "hash", "bar", "zzzqqq")
hash_attr("xxxyyy", "depends_on", "foo", "bar", "link")
Rules that derive abi_splice_conditions_hold will be generated from
use of the `can_splice` directive. They will have the following form:
can_splice("foo@1.0.0+a", when="@1.0.1+a", match_variants=["b"]) --->
abi_splice_conditions_hold(0, node(SID, "foo"), "foo", BaseHash) :-
installed_hash("foo", BaseHash),
attr("node", node(SID, SpliceName)),
attr("node_version_satisfies", node(SID, "foo"), "1.0.1"),
hash_attr("hash", "node_version_satisfies", "foo", "1.0.1"),
attr("variant_value", node(SID, "foo"), "a", "True"),
hash_attr("hash", "variant_value", "foo", "a", "True"),
attr("variant_value", node(SID, "foo"), "b", VariVar0),
hash_attr("hash", "variant_value", "foo", "b", VariVar0).
2.2 Synthesizing splices in `concretize.lp` and `splices.lp`
The ASP solver generates "splice_at_hash" attrs to indicate that a particular node has a splice in one of its immediate dependencies.
Splices can be introduced in the dependencies of concrete specs when `splices.lp` is conditionally loaded (based on the config option `concretizer:splice:True`.
2.3 Constructing spliced specs in `asp.py`
The method `SpecBuilder._resolve_splices` implements a top-down memoized implementation of hybrid splicing. This is an optimization over the more general `Spec.splice`, since the solver gives a global view of exactly which specs can be shared, to ensure the minimal number of splicing operations.
Misc changes to facilitate configuration and benchmarking
- Added the method `Solver.solve_with_stats` to expose timers from the public interface for easier benchmarking
- Added the boolean config option `concretizer:splice` to conditionally load splicing behavior
Co-authored-by: Greg Becker <becker33@llnl.gov>
We added unification semantics for parsing specs from the CLI, but there are a couple
of special cases in which we can avoid calls to the concretizer for speed when the
specs can all be resolved by lookups.
- [x] special case 1: solving a single spec
- [x] special case 2: all specs are either concrete (come from a file) or have an abstract
hash. In this case if concretizer:unify:true we need an additional check to confirm
the specs are compatible.
- [x] add a parameterized test for unifying on the CI
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* libunwind: Add 1.7.2 and 1.8.1
* libunwind: Remove deprecated 1.1 version
* libunwind: Add newer *-stable branches: Remove 1.5-stable branch as well as cleanup.
* libunwind: Use GitHub url for all versions
* libunwind: Add conflict for PPC and 1.8.*
* libunwind: Add conflict for aarch64 and 1.8:
Build fails with
aarch64/Gos-linux.c: In function '_ULaarch64_local_resume':
aarch64/Gos-linux.c:147:1: error: x29 cannot be used in asm here
}
^
aarch64/Gos-linux.c:147:1: error: x29 cannot be used in asm here
make[2]: *** [Makefile:4795: aarch64/Los-linux.lo] Error 1
* added updated versions
* added pyhmmer
* updated infernal
* fix blast-plus for apple-clang
* fix py-biopython build on apple-clang
* remove erroneous biopython dep: build issue is with python 3.8, not biopython
* deepsig python 3.9: expanding unnecessary python restrictions
* add pyrodigal
* fix unnecessarily strict diamond version
* builds and updates: blast-plus indexing broken, still need to test db download and bakta pipeline
* builds and runs
* revert blast-plus changes: remove my personal hacks to get blast-plus to build
* fix the build error during compilation of rocdecode.was dependent on libva-devel packag
* address review comment
* address review changes.commit the changes
* Add two_level_namespace variant (default is disabled) for MacOS to enable building
executables and libraries with two level namespace enabled.
* Addressed reviewer comments.
* Moved two_level_namespace variant ahead of the patch that uses that variant to
get concretize to work properly.
* Removed extra print statements
* soqt: Add SoQt package
The geomodel package needs this if visualization is turned on.
* make qt versions explicit
* use virtual dependency for qt
* pr feedback
Remove myself as maintainer
Remove v1.6.0
Remove unused qt variant
This addresses part [1] of #46345#44713 introduced a bug where all non-spec query parameters like date
ranges, -x, etc. were ignored when an env was active.
This fixes that issue and adds tests for it.
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
`spack mirror add` and `set` now have flags `--oci-password-variable`, `--oci-password-variable`, `--s3-access-key-id-variable`, `--s3-access-key-secret-variable`, `--s3-access-token-variable`, which allows users to specify an environment variable in which a username or password is stored.
Storing plain text passwords in config files is considered deprecated.
The schema for mirrors.yaml has changed, notably the `access_pair` list is generally replaced with a dictionary of `{id: ..., secret_variable: ...}` or `{id_variable: ..., secret_variable: ...}`.
the py-oracledb package only has a single outdated version available in its recipe. this PR adds a much broader range of versions and their corresponding checksums.
* add more versions of py-oracledb
* update py-oracledb recipe
* add py-cython version dependencies
* tweak py-cython version dependencies
* remove older versions of py-oracledb
This filters any selected executable ending with `-ocl` from the list of executables being probed as candidate for external `llvm` installations.
I couldn't reproduce the entire issue, but with a simple script:
```
#!/bin/bash
touch foo.o
echo "clang version 10.0.0-4ubuntu1 "
echo "Target: x86_64-pc-linux-gnu"
echo "Thread model: posix"
echo "InstalledDir: /usr/bin"
exit 0
```
I noticed the executable was still probed:
```
$ spack -d compiler find /tmp/ocl
[ ... ]
==> [2024-11-11-08:38:41.933618] '/tmp/ocl/bin/clang-ocl' '--version'
```
and `foo.o` was left in the working directory. With this change, instead the executable is filtered out of the list on which we run `--version`, so `clang-ocl --version` is not run by Spack.
- [x] Get rid of a call to `parser.quote_if_needed()` during solver setup, which
introduces a circular import and also isn't necessary.
- [x] Rename `spack.variant.Value` to `spack.variant.ConditionalValue`, as it is *only*
used for conditional values. This makes it much easier to understand some of the
logic for variant definitions.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
`conditional()`, which defines conditional variant values, and the other ways to declare
variant values should probably be in a layer above `spack.variant`. This does the simple
thing and moves *just* `conditional()` to `spack.directives` to avoid a circular import.
We can revisit the public variant interface later, when we split packages from core.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* lua: add +pcfile support for @5.4: versions, without using a version-dependent patch
* lua: always generate pcfile, remove +pcfile variant from all packages
* lua: minor fixes
* rpm: minor fix
* Add 5.030 and remove the requirement to patch verilator, the problem has be fixed in this rev
* Update var/spack/repos/builtin/packages/verilator/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* benchmark: enable shared libraries by default
The existing behaviour of Google Benchmark yiels static objects which
are of little use for most projects. This PR changes the spec to use
dynamic libraries instead.
* Add shared variant
* librdkafka: added missing dependency on curl
This PR adds a missing dependency on curl in librdkafka.
* librdkafka: added dependency on openssl and zlib
* Added support for Codeplay AMD Plugin for Intel OneAPI Compilers
* [@spackbot] updating style on behalf of kaanolgu
* Adding 2025.0.0
* removed HOME and XDG_RUNTIME_DIR
* [@spackbot] updating style on behalf of kaanolgu
---------
Co-authored-by: Kaan Olgu <kaan.olgu@bristol.ac.uk>
No ROOT `builtin` should ever be set to true if possible, because that
builds an existing library that spack may not know about.
Furthermore, using `builtin_glew` forces the package to be on, even when
not building x/gl/aqua on macos. This causes build failures.
Caused by https://github.com/spack/spack/pull/45632#issuecomment-2276311748 .
Currently, if a package has a dependency from another repository and patches it,
generation of the patch cache will fail. Concretization succeeds if a fixed patch
cache is in place.
- [x] don't assume that patched dependencies are in the same repo when indexing
- [x] add some test fixtures to support multi-repo tests.
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* spack.compiler: cache output
* compute libc from the dynamic linker at most once per spack process
* wrap compiler cache entry in class, add type hints
* test compiler caching
* ensure tests do not populate user cache, and fix 2 tests
* avoid recursion: cache lookup -> compute key -> cflags -> real_version -> cache lookup
* allow compiler execution in test that depends on get_real_version
If a package `foo` doesn't implement `libs`, the default was to search recursively for `libfoo` whenever asking for `spec[foo].libs` (this also happens automatically if a package includes `foo` as a link dependency).
This can lead to some strange behavior:
1. A package that is normally used as a build dependency (e.g. `cmake` at one point) is referenced like
`depends_on(cmake)` which leads to a fully-recursive search for `libcmake` (this can take
"forever" when CMake is registered as an external with a prefix like `/usr`, particularly on NFS mounts).
2. A similar hang can occur if a package is registered as an external with an incorrect prefix
- [x] Update the default library search to stop after a maximum depth (by default, search
the root prefix and each directory in it, but no lower).
- [x]
The following is a list of known changes to `find` compared to `develop`:
1. Matching directories are no longer returned -- `find` consistently only finds non-dirs,
even at `max_depth`
2. Symlinked directories are followed (needed to support max_depth)
3. `find(..., "dir/*.txt")` is allowed, for finding files inside certain dirs. These "complex"
patterns are delegated to `glob`, like they are on `develop`.
4. `root` and `files` arguments both support generic sequences, and `root`
allows both `str` and `path` types. This allows us to specify multiple entry points to `find`.
---------
Co-authored-by: Peter Scheibel <scheibel1@llnl.gov>
This PR adds a sub-command to `spack env` (`track`) which allows users to add/link
anonymous environments into their installation as named environments. This allows
users to more easily track their installed packages and the environments they're
dependencies of. For example, with the addition of #41731 it's now easier to remove
all packages not required by any environments with,
```
spack gc -bE
```
#### Usage
```
spack env track /path/to/env
==> Linked environment in /path/to/env
==> You can activate this environment with:
==> spack env activate env
```
By default `track /path/to/env` will use the last directory in the path as the name of
the environment. However users may customize the name of the linked environment
with `-n | --name`. Shown below.
```
spack env track /path/to/env --name foo
==> Tracking environment in /path/to/env
==> You can activate this environment with:
==> spack env activate foo
```
When removing a linked environment, Spack will remove the link to the environment
but will keep the structure of the environment within the directory. This will allow
users to remove a linked environment from their installation without deleting it from
a shared repository.
There is a `spack env untrack` command that can be used to *only* untrack a tracked
environment -- it will fail if it is used on a managed environment. Users can also use
`spack env remove` to untrack an environment.
This allows users to continue to share environments in git repositories while also having
the dependencies of those environments be remembered by Spack.
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
You can now provide multiple roots to a single `find()` call and all of
them will be searched. The roots can overlap (e.g. can be parents of one
another).
This also adds a library function for taking a set of regular expression
patterns and creating a single OR expression (and that library function
is used in `find` to improve its performance).
Set command line scopes last in _main, so they are higher scopes
Restore the global configuration in a spawned process by inspecting
the result of ctx.get_start_method()
Add the ability to pass a mp.context to PackageInstallContext.
Add shell-tests to check overriding the configuration:
- Using both -c and -C from command line
- With and without an environment active
* edm4hep: Add json variant for newer versions
Explicit option has been added to EDM4hep so we now expose it via a
variant as well. We keep the old behavior where we unconditionally
depended on nlohmann-json and implicitly built JSON support if we could
detect it cmake stage
* Fix condition statement in when clause
* Use open version range to avoid fixing to single version
---------
Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
Variants can now be propagated from a dependent package to (transitive) dependencies,
even if the source or transitive dependencies have the propagated variants.
For example, here `zlib` doesn't have a `guile` variant, but `gmake` does:
```
$ spack spec zlib++guile
- zlib@1.3%gcc@12.2.0+optimize+pic+shared build_system=makefile arch=linux-rhel8-broadwell
- ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rhel8-broadwell
- ^gmake@4.4.1%gcc@12.2.0+guile build_system=generic arch=linux-rhel8-broadwell
```
Adding this property has some strange ramifications for `satisfies()`. In particular:
* The abstract specs `pkg++variant` and `pkg+variant` do not intersect, because `+variant`
implies that `pkg` *has* the variant, but `++variant` does not.
* This means that `spec.satisfies("++foo")` is `True` if:
* for concrete specs: `spec` and its dependencies all have `foo` set if it exists
* for abstract specs: no dependency of `spec` has `~foo` (i.e. no dependency contradicts `++foo`).
* This also means that `Spec("++foo").satisfies("+foo")` is `False` -- we only know after concretization.
The `satisfies()` semantics may be surprising, but this is the cost of introducing non-subset
semantics (which are more useful than proper subsets here).
- [x] Change checks for variants
- [x] Resolve conflicts
- [x] Add tests
- [x] Add documentation
---------
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* pythia8: Include patch for C++20 / Clang
Pythia8 vendors some FJCore sources that are as of Pythia8 312
incompatible with C++20 on clang. This adds a patch that makes it
compatible in these scenarios
* Add issue link
* rename setup_cxxstd function
* Remove an accidental printout
* Apply patch to all compilers, add lower bound
* `find(..., max_depth=...)` can be used to control how many directories at most to descend into below the starting point
* `find` now enters every unique (symlinked) directory once at the lowest depth
* `find` is now repeatable: it traverses the directory tree in a deterministic order
In the pure `ld` case, we weren't actually parsing `RPATH` arguments separately as we
do for `ccld`. Fix this by adding *another* nested case statement for raw `RPATH`
parsing.
There are now 3 places where we deal with `-rpath` and friends, but I don't see a great
way to unify them, as `-Wl,`, `-Xlinker`, and raw `-rpath` arguments are all ever so
slightly different.
Also, this Fixes ordering of assertions to make `pytest` diffs more intelligible.
The meaning of `+` and `-` in diffs changed in `pytest` 6.0 and the "preferred" order
for assertions became `assert actual == expected` instead of the other way around.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
`cc` divides most paths up into system paths, spack managed paths, and other paths.
This gets really repetitive and makes the code hard to read. Simplify the script
by adding some functions to do most of the redundant work for us.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
This PR has two small contributions:
- It adds another phase to the timer for concrectization, "construct_specs", to actually see the time the concretizer spends interpreting the `clingo` output to build the Python object for a concretized spec.
- It adds the method `Solver.solve_with_stats` to expose the timers that were already in the concretizer to the public solver API. `Solver.solve` just becomes a special case of `Solver.solve_with_stats` that throws away the timing output (which is what it was already doing).
These changes will make it easier to benchmark concretizer performance and provide a more complete picture of the time spent in the concretizer by including the time spent interpreting clingo output.
Currently, the `geant4-data` spec creates symlink to all of its
dependencies, and it does so by globbing their `share/` directories.
This works very well for the way Spack installs these, but it doesn't
work for anybody wanting to use e.g. the Geant4 data on CVMFS. See pull
request #47298. This commit changes the way the `geant4-data` spec
works. It no longer blindly globs directories and makes symlinks, but it
asks its dependencies specifically for the name of their data directory.
This should allow us to use Spack to use the CVMFS installations as
externals.
* zabbix: add v5.0.44, v6.0.34, v7.0.4 (fix CVEs)
* [@spackbot] updating style on behalf of wdconinc
* zabbix: use f-string
* zabbix: fix f-string quoting
* zabbix: use mysql-client
* @wdconic, this fixes the mysql client virtual for me
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
The idea is to go from most to least used: backward compat -> forward compat -> pinning on major or major.minor version -> pinning specific, concrete versions.
Further, the following
```python
# backward compatibility with Python
depends_on("python@3.8:")
depends_on("python@3.9:", when="@1.2:")
depends_on("python@3.10:", when="@1.4:")
# forward compatibility with Python
depends_on("python@:3.12", when="@:1.10")
depends_on("python@:3.13", when="@:1.12")
depends_on("python@:3.14")
```
is better than disjoint when ranges causing repetition of the rules on dependencies, and requiring frequent editing of existing lines after new releases are done:
```python
depends_on("python@3.8:3.12", when="@:1.1")
depends_on("python@3.9:3.12", when="@1.2:1.3")
depends_on("python@3.10:3.12", when="@1.4:1.10")
depends_on("python@3.10:3.13", when="@1.11:1.12")
depends_on("python@3.10:3.14", when="@1.13:")
When compiled without MPI support, a fake mpi header is autogenerated during configure/build. The header is missing one symbol in version 1.9.5. The problem has since been fixed upstream.
A simular problem does also occur for 1.9.4. Unfortunately, the patch does not work for 1.9.4 and I also don't know if further fixes would be required for 1.9.4. Therefore, only the newest version 1.9.5 is patched.
Update HDF5 version for develop branch to develop-2.0 to match the new
version in the develop branch.
Remove develop-1.16 as it has been decided to make next release HDF5 2.0.0.
This PR changes the semantic of == for spec so that:
hdf5++mpi == hdf5+mpi
won't hold true anymore. It also changes the constrain semantic, so that a
non-propagating variant always override a propagating variant. This means:
(hdf5++mpi).constrain(hdf5+mpi) -> hdf5+mpi
Before we had a very weird semantic, that was supposed to be tested by unit-tests:
(libelf++debug).constrain(libelf+debug+foo) -> libelf++debug++foo
This semantic has been dropped, as it was never really tested due to the == bug.
According to https://github.com/root-project/root/issues/7160, if
`-Dcocoa=ON` build must also be configured with `-Dopengl=ON`, since
otherwise the build encounters missing includes. This is/was a silent
failure in ROOT CMake, but I believe has been made an explicit failure
some time this year.
Currently, the schema reads:
from:
- type:
environment: path_or_name
but this can't be extended easily to other types, e.g. to buildcaches,
without duplicating the extension keys. Use instead:
from:
- type: environment
path: path_or_name
Currently, the `concretizer:unify:` config option only affects environments.
With this PR, it now affects any group of specs given to a command using the `parse_specs(*, concretize=True)` interface.
- [x] implementation in `parse_specs`
- [x] tests
- [x] ensure all commands that accept multiple specs and concretize use `parse_specs` interface
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* don't concretize in CI if changed packages are not in stacks
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Generate noop job when no specs to rebuild due to untouched pruning
* Add test to verify skipping generate creates a noop job
* Changed debug for early exit
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
This changes `Spec` serialization to include information about propagation for abstract specs.
This was previously not included in the JSON representation for abstract specs, and couldn't be
stored.
Now, there is a separate `propagate` dictionary alongside the `parameters` dictionary. This isn't
beautiful, but when we bump the spec version for Spack `v0.24`, we can clean up this and other
aspects of the schema.
* geant4: make downloading data dependency optional
This PR makes downloading the data repository of the Geant4 spec
optional by adding a sticky, default-enabled variant which controls the
dependency on `geant4-data`. This should not change the default
behaviour, but should allow users to choose whether or not they want the
data directory.
* Add comment
* Update env variable
* Generic docs
* Buildable false
- Merging sycl2020usm and sycl2020acc into sycl2020 and the submodel=acc/usm variant is introduced
- implementation is renamed to option
- impl ( fortran implementation options) renamed to foption
- sycl_compiler_implementation and thrust_backend
- stddata,stdindices,stdranges to a single std with std_submodel introduction
- std_use_tbb to be boolean; also changed model filtering algorithm to make sure that it only picks model names
- Modified comments to clear confusion with cuda_arch cc_ and sm_ prefix appends
- Deleted duplicate of cuda_arch definition from +omp
- CMAKE_CXX_COMPILER moved to be shared arg between all models except tbb and thrust
- Replaced sys.exit with InstallError and created a dictionary to simplify things and eliminate excess code lines doing same checks
- Replaced the -mcpu flags to -march since it is deprecated now
- Replaced platform.machine with spec.target
- Removing raja_backend, introducing openmp_flag,removing -march flags,clearing debugging print(), removing excess if ___ in self.spec.variants
- [FIX] Issue where Thrust couldn't find correct compiler (it requires nvcc)
- [FIX] Fortran unsupported check to match the full string
- [FIX] RAJA cuda_arch to be with sm_ not cc_
- dir= option is no longer needed for kokkos
- dir is no longer needed
- [omp] Adding clang support for nvidia offload
- SYCL2020 offload to nvidia GPU
- changing model dependency to be languages rather than build system
- removing hardcoded arch flags and replacing with archspec
- removing cpu_arch from acc model
---------
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Greg Becker <becker33@llnl.gov>
Co-authored-by: Kaan Olgu <kaan.olgu@bristol.ac.uk>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Introduce support for ArmPL and ACfL 24.10
This patch introduces the possibility of installing armpl-gcc
and acfl 24.10 through spack. It also addressed one issue observed
after PR https://github.com/spack/spack/pull/46594
* Fix Github action issues.
- Remove default URL
- Reinstate default OS for ACfL to RHEL.
Fixes an issue reported where `spack env depfile` + `make -j` would
non-deterministically refuse to mark all environment roots explicit.
`update_explicit` had the pattern
```python
rec = self._data[key]
with self.write_transaction():
rec.explicit = explicit
```
but `write_transaction` may reinitialize `self._data`, meaning that
mutating `rec` won't mutate `self._data`, and the changes won't be
persisted.
Instead, use `mark` which has a correct implementation.
Also avoids the essentially incorrect early return in `update_explicit`
which is a pattern I don't think belongs in database.py: it branches on
possibly stale data to realize there is nothing to change, but in reality
it requires a write transaction to know that for a fact, but that would
defeat the purpose. So, leave this optimization to the call site.
The already concrete specs in an environment are now among the reusable specs for the concretizer.
This includes concrete specs from all include_concrete environments.
In addition to this change to the default reuse, `environment` is added as a reuse type for
the concretizer config. This allows users to specify:
spack:
concretizer:
# Reuse from this environment (including included concrete) but not elsewhere
reuse:
from:
- type: environment
# or reuse from only my_env included environment
reuse:
from:
- type:
environment: my_env
# or reuse from everywhere
reuse: true
If reuse is specified from a specific environment, only specs from that environment will be reused.
If the reused environment is not specified via include_concrete, the concrete specs will be retried
at concretization time to be reused.
Signed-off-by: Ryan Krattiger <ryan.krattiger@kitware.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Currently the order in which hooks are run is arbitrary.
This can be fixed by sorted(list_modules(...)) but I think it is much
more clear to just have a static list.
Hooks are not extensible other than modifying Spack code, which
means it's unlikely people maintain custom hooks since they'd have
to fork Spack. And if they fork Spack, they might as well add an entry
to the list when they're continuously rebasing.
The idea is that `spack -e env add ./concrete-spec.json` would list the
full hash in the specs, so that (a) it's not ambiguous and (b) it could
in principle results in constant time lookup instead of linear time
substring match in large build caches.
* r-*: updates to latest versions
* r-*: add new dependencies
* r-proj: fix docstring line length
* r-list: add homepage
* r-*: add more dependencies
* r-rmpi: use virtual dependencies, conflict openmpi@5:
* r-cairo: require cairo +png; +pdf for some versions; cairo +fc when +ft
* r-proj: set LD_LIBRARY_PATH since rpath not respected
* Added packages to for intel-2025.0.0 release
* fix style
* pin mkl to 2024.2.2
until e4s can upgrade to 2025 compiler and ginkgo compatibility issue can be resolved.
---------
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Add a descriptor to have a class level constant
This descriptor helps intercept places where we set a value on instances.
It does not really behave like "const" in C-like languages, but is the
simplest implementation that might still be useful.
* Add a descriptor to deprecate properties/attributes of an object
This descriptor is used as a base class. Derived classes may implement a
factory to return an adaptor to the attribute being deprecated. The
descriptor can either warn, or raise an error, when usage of the deprecated
attribute is intercepted.
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
This adds the current latest version of py-uv. While working on this, I also
found that uv (including older versions) has a build dependency on cmake which
was not specified in the package, so I added it as a dependency.
I also found that on my machine, the build process had trouble finding cmake,
so I set the path to it explicitly as an environment variable.
* py-jupyter-core: set environment variables for extensions
* Changes committed by gh-spack-pr
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
Currently, `spack solve` has different spec selection semantics than `spack spec`.
`spack solve` currently does not allow specifying a single spec when an environment is active.
This PR modifies `spack solve` to inherit the interface from `spack spec`, and to use
the same spec selection logic. This will allow for better use of `spack solve --show opt`
for debugging.
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* gdk-pixbuf: delete old versions, make mesonpackage
goal is to get rid of `std_meson_args` global, but clean up package
while at it.
`setup_dependent_run_environment` was removed because it did not depend
on the dependent spec, and would result in repeated env variable
changes.
* atk: idem
* fix a dependent
* ML CI: Linux aarch64
* Add config files
* No aarch64 tag
* Don't specify image
* Use amazonlinux image
Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
* Update and require
* GCC is too old
* Fix some builds
* xgboost doesn't support old GCC + cuda
* Run on newer Ubuntu
* Remove mxnet
* Try aarch64 range
* Use main branch
* Conflict applies to all targets
* cuda only required when +cuda
* Use tagged version
* Comment out tf-estimator
* Add ROCm, use newer Ubuntu
* Remove ROCm
---------
Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
Originally, concretization failed if the splice config points to an invalid replacement.
This PR defers the check until we know the splice is needed, so that irrelevant splices
with bad config cannot stop concretization.
While I was at it, I improved an error message from an assert to a ValueError.
* Normalize Spack Win entrypoints
Currently Spack has multiple entrypoints on Windows that in addition to
differing from *nix implementations, differ from shell to shell on
Windows. This is a bit confusing for new users and in general
unnecessary.
This PR adds a normal setup script for the batch shell while preserving
the previous "click from file explorer for spack shell" behavior.
Additionally adds a shell title to both powershell and cmd letting users
know this is a Spack shell
* remove doskeys
#44588 we added logic to suppress deprecation warnings for the
Intel classic compilers. This depended on matching against
* The compiler names (looking for icc, icpc, ifort)
* The compiler version
When using an Intel compiler with fortran wrappers, the first check
always fails. To support using the fortran wrappers (in combination
with the classic Intel compilers), we remove the first check and
suppress if just the version matches. This works because:
* The newer compilers like icx can handle (ignore) the flags that
suppress deprecation warnings
* The Cray wrappers pass the underlying compiler version (e.g. they
report what icc would report)
* new openjdk variant to symlink system certificate
* new openjdk variant to symlink system certificate
* new openjdk variant to symlink system certificate
* new openjdk variant to symlink system certificate
* Update var/spack/repos/builtin/packages/openjdk/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
Connection objects are Python version, platform and multiprocessing
start method independent, so better to use those than a mix of plain
file descriptors and inadequate guesses in the child process whether it
was forked or not.
This also allows us to delete the now redundant MultiProcessFd class,
hopefully making things a bit easier to follow.
This allows the following
```python
cache.init_entry("my/cache")
with cache.read_transaction("my/cache") as f:
data = f.read() if f is not None else None
```
mirroring `write_transaction`, which returns a tuple `(old, new)` where
`old` is `None` if the cache file did not exist yet.
The alternative that requires less defensive programming on the call
site would be to create the "old" file upon first read, but I did not
want to think about how to safely atomically create the file, and it's
not unthinkable that an empty file is an invalid format (for instance
the call site may expect a json file, which requires at least {} bytes).
This PR is in response to a question in the `environments` slack channel (https://spackpm.slack.com/archives/CMHK7MF51/p1729200068557219) about inadequate CLI help/documentation for one specific subcommand.
This PR uses the approach I took for the descriptions and help for `spack test` subcommands. Namely, I use the first line of the relevant docstring as the description, which is shown per subcommand in `spack env -h`, and the entire docstring as the help. I then added, where it seemed appropriate, help. I also tweaked argument docstrings to tighten them up, make consistent with similar arguments elsewhere in the command, and elaborate when it seemed important. (The only subcommand I didn't touch is `loads`.)
For example, before:
```
$ spack env update -h
usage: spack env update [-hy] env
positional arguments:
env name or directory of the environment to activate
optional arguments:
-h, --help show this help message and exit
-y, --yes-to-all assume "yes" is the answer to every confirmation request
```
After the changes in this PR:
```
$ spack env update -h
usage: spack env update [-hy] env
update the environment manifest to the latest schema format
update the environment to the latest schema format, which may not be
readable by older versions of spack
a backup copy of the manifest is retained in case there is a need to revert
this operation
positional arguments:
env name or directory of the environment
optional arguments:
-h, --help show this help message and exit
-y, --yes-to-all assume "yes" is the answer to every confirmation request
```
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Commit aa0825d642 accidentally added a semicolon
to the ANSI escape sequence even if the color code was `None` or unknown, breaking the
bold, uncolored font-face. This PR restores the old behavior.
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Add type hints to all query* methods
* Inline docstrings
* Change defaults from `any` to `None` so they can be type hinted in old Python
* Pre-filter on given hashes instead of iterating over all db specs
* Fix a bug where the `--origin` option of uninstall had no effect
* Fix a bug where query args were not applied when searching by concrete spec
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Fixes a change in behavior/bug in
70412612c7, where partial environment
installs would mark the selected spec as explicitly installed, even if
it was not a root of the environment.
The desired behavior is that roots by definition are the to be
explicitly installed specs. The specs on the `spack -e ... install x`
command line are just filters for partial installs, so leave them
implicitly installed if they aren't roots.
ci: Remove deprecated logic from the ci module
Remove the following from the ci module, schema, and tests:
- deprecated ci stack and handling of old ci config
- deprecated mirror handling logic
- support for artifacts buildcache
- support for temporary storage url
* ParaView: Explicitly set the ENABLE_MPI on/off
* Disallow MPI in the DAG when ~mpi
* @5.13 uses 'remove_children', use pugixml@1.11:, See #47098
* cloud_pipelines/stacks/data-vis-sdk: paraview +raytracing: add +adios2 +fides
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
When building ParaView with ADIOS2 and allowing VTK-m to be
built, also build Fides. This reads ADIOS2 files with a
particular JSON schema, but it requires VTK-m to read data.
* Libmng: Restore Autotools system
CMake, when building its Qt gui, depends on Qt, which in turn, depends on libmng, a CMake based build. To avoid this obvious cyclic dependency, we re-introduce libmng's autotools build into Spack and require when building Qt as a CMake dependency, libmng is built with autotools
* Ensure autotools constraint is limited to non-Windows
* refactor qt-libmng relation from CMake
This commit remove all the uses of spec.compiler that
can be easily substituted by a more idiomatic approach,
e.g. using spec.satisfies or directives
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* py-sphinxcontrib-spelling: new package
* Dependency enchant: Add missing dep on pkgconfig
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
Both `multiprocessing.connection.Connection.__del__` and `io.IOBase.__del__` called `os.close` on the same file descriptor. As of Python 3.13, this is an explicit warning. Ensure we close once by usef `os.fdopen(..., closefd=False)`
* stacks: add a stack for devtools on darwin
After getting this whole mess building on darwin, let's keep it that
way, and maybe make it so we have some non-ML darwin binaries in spack
as well.
* reuse: false for devtools
* dtc: fix darwin dylib name and id
On mac the convention is `lib<name>.<num>.dylib`, while the makefile
creates a num suffixed one by default. The id in the file is also a
local name rather than rewritten to the full path, this fixes both
problems.
* node-js: make whereis more deterministic
* relocation(darwin): catch Mach-O load failure
The MachO library can throw an exception rather than return no headers,
this happened in an elf file in the test data of go-bootstrap. Trying
catching the exception and moving on for now. May also need to look
into why we're trying to rewrite an elf file.
* qemu: add darwin flags to clear out warnings
There's a build failure for qemu in CI, but it's invisible because of
the immense mass of warning output. Explicitly specify the target macos
version and remove the extraneous unknown-warning-option flag.
* dtc: libyaml is also a link dependency
libyaml is required at runtime to run the dtc binary, lack of it caused
the ci for qemu to fail when the library wasn't found.
fixes#47101
The bug was introduced in #33495, where `spack find was not updated,
and wasn't caught by unit tests.
Now a Database can accept a custom predicate to select the installation
records. A unit test is added to prevent regressions. The weird convention
of having `any` as a default value has been replaced by the more commonly
used `None`.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* root: fix variant detection for external
A few fixes (possibly non-exhaustive) to `spack external find root`
Several variants have had `when=` clauses added that need to be
propagated to determine_variants. The previously used
Version.satifies("") method also has been removed, it seems. It's
slightly cumbersome that there is no self.spec to use in
determine_variants, but comparisons using Version(version_str) work at least
* remove debug printout
* sccache: add new package
* sccache: add older versions and minimum rust versions
* sccache: add more minimum rust versions
* sccache: add sccache executable and tag as build-tools
* sccache: add dist-server
* sccache: add determine_version and determin_variants
* sccache: add sccache-dist executable
* sccache: fix style
* Update var/spack/repos/builtin/packages/sccache/package.py
* In case building very old sccache <= 5 is not needed with these older rust version is not needed, they can be omitted.
* sccache: drop older versions
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
* sccache: add openssl dependency
* sccache: openssl is a linux only dependency?
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
Older builds of Boost were failing on Windows because they were
adding --without-... flags for libraries that did not exist in those
versions. So:
* lib variants are updated with version range info (current range
info for libs is not comprehensive, but represents changes over the
last few minor versions up to 1.85)
* On Windows, --without-... options are omitted for libraries when they
don't exist for the version of boost being built. Non-Windows uses
a different approach, which was not affected because the new libraries
were not activated by default. It would benefit from similar attention
though to avoid potential future issues.
#44327 made sure to always run `set_package_py_globals` on all
packages before running `setup_dependent_package` for any package,
so that packages implementing the latter could depend on variables
like `spack_cc` being defined.
This ran into an undocumented dependency: `std_cmake_args` is set in
`set_package_py_globals` and makes use of `cmake_prefix_paths` (if it
is defined in the package); `py-torch`es implementation of
`cmake_prefix_paths` depends on a variable set by
`setup_dependent_package` (`python_platlib`).
This generally restores #44327, and corrects the resulting issue by
moving assignment of `std_cmake_args` to after both actions have been
run.
* py-clip-anytorch: new package
* py-clip-anytorch: ran black
py-langchain-core: ran black
py-pydantic: ran black
py-dalle2-pytorch: ran black
* [py-clip-anytorch] fixed license(checked_by)
* Apply suggestion from Wouter on fixing CI
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Alex C Leute <acl2809@rit.edu>
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* py-pytorch-warmup: new package
* py-clip-anytorch: ran black
py-langchain-core: ran black
py-pydantic: ran black
py-dalle2-pytorch: ran black
---------
Co-authored-by: Alex C Leute <acl2809@rit.edu>
Some unused methods in VTK-m resulted in compile errors. These were
not discovered because many compilers ignore unused methods in templated
classes, but the SYCL compiler for Aurora gave an error.
Turns out `os=...` of the spec and `MACOSX_DEPLOYMENT_TARGET` are kept
in sync, and the env variable is used to initialize
`CMAKE_MACOSX_DEPLOYMENT_TARGET`.
In bootstrap code we set the env variable, so these bits are redundant.
---------
Co-authored-by: haampie <haampie@users.noreply.github.com>
* Remove the implicit CORE-AVX512 since the CPU specific flags are added by the
compiler wrappers.
* Add `-i_use-path` to help `ifx` find `lld` even if `-gcc-name` is set in
`ifx.cfg`. This file is written by `intel-oneapi-compilers` package to find the
correct `gcc`. Not being able to find `ldd` is a bug in `ifx`. @rschon2 found
this workaround.
* e4s external rocm ci: upgrade to v6.2.1
* use ghcr.io/spack/spack/ubuntu22.04-runner-amd64-gcc-11.4-rocm6.2.1:2024.10.08
* magma +rocm: add entry for v6.2.1
Extrae normally separates the C and MPI fortran interception libs, but
for mixed C/Fortran applications a combined lib is needed.
Co-authored-by: fpanichi <fpanichi@amd.com>
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
* [ftgl] Restrict GCC 14+ patch to apply only to GCC 14+
The patch added by #46927 should only be applied where it is needed:
with GCC 11 it causes a compilation failure where none previously
existed.
* Fix the contraint for applying unsiged char patch to ^freetype@2.13.3:
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
The purpose of this CI job is to ensure that we
can use a modern clingo to concretize specs, if
e.g. it was installed in a virtual environment
with pip.
Since there is no need to re-test unrelated parts
of Spack, reduce the number of tests we run to just
concretize.py
* lua: update luarocks resource to 3.11.1
We have kept an older 3.8 for some time, but that now uses an incorrect
value for the deployment target for macos, causing builds for bundles to
succeed but in such a way that they can't be linked to applications by
`ld` but only loaded by dlopen. This fixes that, and also generally
updates the tool.
* lua-luajit-openresty: add new version fix LUA_PATH
Adds a newer version of openresty's luajor, and adds the slightly odd
extra share path they use that contains the `jit.*` modules. Without
that, things that use bytecode-saving and other jit routines (like
neovim) fail.
* lua-lpeg: fix lpeg build to work for neovim on OSX
Normally luarocks builds all lua libraries as bundles on macos, this
makes sense, but means they can't then be linked by LD into executables
the way neovim expects to do. I'm not sure how this ever worked, if it
did. This patch adds the appropriate variables to have luarocks build
the library as a shared librar, and subsequently fix the id with
install_name_tool (the built-in functionality for this does not
trigger).
This also adds a symlink from `liblpeg.dylib` to `lpeg.so` because
neovim will not build on macos without it. See corresponding upstream
pull request at https://github.com/neovim/neovim/pull/30749
Remove the constraint for concrete specs and simply take the
max(version) if a version is not given. This should default to the
highest infinity version which is also the logical best guess for
doing development.
* Remove concrete verision constriant for develop, set docs
* Add unit-test
* Update lib/spack/docs/environments.rst
Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
* Update lib/spack/spack/cmd/develop.py
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Consolidate env collection in cmd
* Style
---------
Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
Remove the `build-tools` tag of python, otherwise these types of
concretizations are possible:
```
py-root
^py-pip
^python@3.12
^python@3.13
```
So, a package would be configured with py-pip using python 3.12, but
installed for 3.13, which does not work.
* Add new version for master branch
Added new version for master branch. Also added additional functions to ensure tempo will actually run. Tempo assumes the stage directory sticks around and references numerous files and directory there. That has been corrected here only if using the master version. The LWA-10-2020 version will also have this problem but they may have additional setup in their compute/Spack environment to address this issue already so I did not modify anything when that's the version. Example of what happens in the LWA-10-17-2020 version regarding missing files is given below
user@cs:~/spack/bin$ tempo
more: cannot open /tempo.hlp: No such file or directory
* Updated to fix format errors
Flake8 check found errors. Fixed those formatting issues
* Additional format change
Removed redundant setup_dependent_run_environment missed in previous update
* Update url to use https: https is the usual transport and is needed to support checkout behind some firewalls
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
The CMake builder in Spack actually adds incorrect rpaths. They are
unfiltered and incorrectly ordered compared to what the compiler wrapper
adds.
There is no need to specify paths to dependencies in `CMAKE_INSTALL_RPATH`
because of two reasons:
1. CMake preserves "toolchain" rpaths, which includes the rpaths injected
by our compiler wrapper.
2. We use `CMAKE_INSTALL_RPATH_USE_LINK_PATH=ON`, so libraries we link
to are rpath'ed automatically.
However, CMake does not create install rpaths to directories in the package's
own install prefix, so we set `CMAKE_INSTALL_RPATH` to the educated guess
`<prefix>/{lib,lib64}`, but omit dependencies.
Some assertion are not testing DAG invariants, and they are passing only
because of the simple structure of the builtin.mock repository on develop.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* update versions of Neo4j and Redis deps
* deprecating older versions due to security vulnerabilities
* [@spackbot] updating style on behalf of kchilleri
* Update var/spack/repos/builtin/packages/redis/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* adding previous urls to use archives on project websites
* [@spackbot] updating style on behalf of kchilleri
* adding new required maven version
* label when to use specific maven versions
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Krishna Chilleri <krishnachilleri@lanl.gov>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Add versions 1.14.4-3, 1.14.5, develop-1.16, and update develop-1.15 to
develop-1.17.
* Remove unused list_url, list_depth, and style disapproved spaced in url
= "...
* One more style fix.
This PR allows users to configure explicit splicing replacement of an abstract spec in the concretizer.
concretizer:
splice:
explicit:
- target: mpi
replacement: mpich/abcdef
transitive: true
This config block would mean "for any spec that concretizes to use mpi, splice in mpich/abcdef in place of the mpi it would naturally concretize to use. See #20262, #26873, #27919, and #46382 for PRs enabling splicing in the Spec object. This PR will be the first place the splice method is used in a user-facing manner. See https://spack.readthedocs.io/en/latest/spack.html#spack.spec.Spec.splice for more information on splicing.
This will allow users to reuse generic public binaries while splicing in the performant local mpi implementation on their system.
In the config file, the target may be any abstract spec. The replacement must be a spec that includes an abstract hash `/abcdef`. The transitive key is optional, defaulting to true if left out.
Two important items to note:
1. When writing explicit splice config, the user is in charge of ensuring that the replacement specs they use are binary compatible with whatever targets they replace. In practice, this will likely require either specific knowledge of what packages will be installed by the user's workflow, or somewhat more specific abstract "target" specs for splicing, to ensure binary compatibility.
2. Explicit splices can cause the output of the concretizer not to satisfy the input. For example, using the config above and consider a package in a binary cache `hdf5/xyzabc` that depends on mvapich2. Then the command `spack install hdf5/xyzabc` will instead install the result of splicing `mpich/abcdef` into `hdf5/xyzabc` in place of whatever mvapich2 spec it previously depended on. When this occurs, a warning message is printed `Warning: explicit splice configuration has caused the the concretized spec {concrete_spec} not to satisfy the input spec {input_spec}".
Highlighted technical details of implementation:
1. This PR required modifying the installer to have two separate types of Tasks, `RewireTask` and `BuildTask`. Spliced specs are queued as `RewireTask` and standard specs are queued as `BuildTask`. Each spliced spec retains a pointer to its build_spec for provenance. If a RewireTask is dequeued and the associated `build_spec` is neither available in the install_tree nor from a binary cache, the RewireTask is requeued with a new dependency on a BuildTask for the build_spec, and BuildTasks are queued for the build spec and its dependencies.
2. Relocation is modified so that a spack binary can be simultaneously installed and rewired. This ensures that installing the build_spec is not necessary when splicing from a binary cache.
3. The splicing model is modified to more accurately represent build dependencies -- that is, spliced specs do not have build dependencies, as spliced specs are never built. Their build_specs retain the build dependencies, as they may be built as part of installing the spliced spec.
4. There were vestiges of the compiler bootstrapping logic that were not removed in #46237 because I asked alalazo to leave them in to avoid making the rebase for this PR harder than it needed to be. Those last remains are removed in this PR.
Co-authored-by: Nathan Hanford <hanford1@llnl.gov>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* cuda: Add 12.6.2
* Update cuda build system
- Remove gcc@6 conflict that was only a deprecation (probably has be added again with cuda@13)
- Update cuda_arch support by CUDA version
- Kepler support has ended with cuda@12
- Recently added 90a Hopper "experimental" features architecture was
missing the dependency on cuda@12:
adds the lima-vm project, in order to make that useful adds a newer
version of qemu so qemu VMs can work, and builds qemu with flags that
allow it to do things like give the VMs networking and virtfs
filesystems.
Also adds vde as a dependency of qemu.
* CMake: Improve incremental build speed.
CMake automatically embeds an updated configure step into make/ninja that will be called during the build phase. By default if a `CMakeCache.txt` file exists in the build directory CMake will use it and this + `spec.is_develop` is sufficient evidence of an incremental build.
This PR removes duplicate work/expense from CMake packages when using `spack develop`.
* Update cmake.py
* [@spackbot] updating style on behalf of psakievich
* Update cmake.py
meant self not spec...
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
* fix typo in variable name in hepmc3 variant
* set cxx standard to 14 when using protobuf
* add myself to hepmc3 maintainer list
* hepmc3: Applied suggestion of @acecbs for spec.satisfies("+protobuf") (agreed!)
Co-authored-by: Alec Scott <hi@alecbcs.com>
* hepmc3: cxx_standard for protobuf
only set cxx standard to meet protobuf minimum (14) if not also rootio variant as that sets the cxx standard to match the root public API standard requirements
* Environment.clear: ensure clearing is passed through to manifest
* test/cmd/env: make test_remove_commmand round-trip to disk
* cleanup vestigial variables
Some Windows Python installations may store the Python exe in Scripts/
rather than the base directory. Update `.command` to search in both
locations on Windows. On all systems, the search is now done
recursively from the search root: on Windows, that is the base install
directory, and on other systems it is bin/.
* Add libALL support
* cabana: also require ALL
* cabana: Bugfix: Fix spec for cmake>=3.26 to be @3.26: and HDF5 support requires MPI
* cabana: MPI requires C: Add depends_on("c", type="build", when="+mpi")
* cabana: +mpi requires C, but at least for some CMake versions, Cabana's enable of C is too late. Patch it.
* cabana: simplify disabling of find_package's for disabled options and improve comment
* cabana: +grid of 0.6.0 does not compile with gcc-13: It misses iostream includes
* cabana: +test requires googletest at build time: gtest is a linked library(not a plugin or tool)
* cabana: 0.6.0+cuda requires kokkos@3.7:, see https://github.com/ECP-copa/Cabana/releases
* cabana: As 0.6.0+grid does not support gcc-13 and newer, I think it's good to add 0.6.1 and 0.7.0?
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
* added py-evodiff and dependencies
* deleted the FIXME
* fixed style issues
* added versions for biotite dependencies; added hash to py-hatch-vcs
* added python version for py-hatch-cython
* updated biotraj dependencies
* - added versions for the packages and dependencies
- added more dependencies for py-hatch
- added rust versions
- added py-uv as a new package
* updated pacakges and their dependencies according to the PR review by @meyersbs
* typo fix for hatchling version; fix the minimum required setuptools version for evodiff
* added 1.9.0 and 1.7.0 userpath versions; required as a dependency
* added mlflow as a dependency
* changed biopython to an optional dependency according to review from @meyersbs; variant esmfold
* Updated Specs
- Pinned biotraj to 1:1 for py-biotite
- Added numpy and other dependencies for py-biotraj; they are dependent
on the versions
- Excluded py-mlflow as a dependency for package py-evodiff; missing
usage in
package.
- Removed versioned dependencies from py-fair-esm
- Added a version to py-packaging
- Added py-setuptools as a dependency in py-userpath
- Added sha256 as hashes for py-uv
* style changes
* Remove "modify_object_macholib"
According to documentation, this function is used when installing
Mach-O binaries on linux. The implementation seems questionable at
least, and the code seems to be never hit (Spack currently doesn't
support installing Mach-O binaries on linux).
* Fix relocation on macOS, when store projection changes
---------
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Enable tests for symlink-based views (this works with almost no
modifications to the view logic). View logic is not yet robust
for hardlink/junction-based views, so those are disabled for now
(both in the tests and as subcommands to `spack view`).
* add new darshan-runtime variants
- `lustre` variant enables instrumentation of Lustre files
* requires Lustre headers, so Lustre is a proper dependency
for this variant
- `log_path` variant allows setting of a centralized log directory
for Darshan logs (commonly used for facility deployments)
* when this variant is used, the `DARSHAN_LOG_DIR_PATH` env var
is no longer used to set the log file path
- `group_readable_logs` variant sets Darshan log permissions to
allow reads from users in the same group
* add mmap_logs variant to enable usage of mmap logs
Also adds support for Paraview and CMake to build with Qt support on
Windows.
The remaining edits are to enable building of Qt itself on Windows:
* Several packages needed to update `.libs` to properly locate
libraries on Windows
* Qt needed a patch to allow it to build using a Python with a space
in the path
* Some Qt dependencies had not been ported to Windows yet
(e.g. `harfbuzz` and `lcms`)
This PR does not provide a sufficient GL for Qt to use Qt Quick2, as
such Qt Quick2 is disabled on the Windows platform by this PR.
---------
Co-authored-by: Dan Lipsa <dan.lipsa@kitware.com>
* Bugfix/Installer: properly track task queueing
* Move ordinal() to llnl.string; change time to attempt
* Convert BuildTask to use kwargs (after pkg); convert STATUS_ to BuildStats enum
* BuildTask: instantiate with keyword only args after the request
* Installer: build request is required for initializing task
* Installer: only the initial BuildTask cannnot have status REMOVED
* Change queueing check
* ordinal(): simplify suffix determination [tgamblin]
* BuildStatus: ADDED -> QUEUED [becker33]
* BuildTask: clarify TypeError for 'installed' argument
* madgraph5amc: add v3.5.6, add a preferred version and remove urls
* Fix format
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
We run tests for more python versions on `develop` than we do for PRs, so codecov
project status is nearly always failing. There is about a 1% difference in max coverage
between `develop` tests and PR tests, so we should increase the project threshold to 2%
to allow for this difference.
The purpose of the project test on PRs is just to make sure that nothing done on the PR
massively affects coverage of code not covered by the PR. This is valuable, but rare. It
only really affects PRs that deal with test or coverage configuration.
- [x] change project coverage threshold from .2% to 2%
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Add v3.0.0 version for libfirefly package
* [@spackbot] updating style on behalf of tbhaxor
---------
Co-authored-by: tbhaxor <tbhaxor@users.noreply.github.com>
`spack gc` has so far been a global or environment-specific thing.
This adds the ability to restrict garbage collection to specific specs,
e.g. if you *just* want to get rid of all your unused python installations,
you could write:
```console
spack gc python
```
- [x] add `constraint` arg to `spack gc`
- [x] add a simple test
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Avoid that hdf5 searches all search paths for ZLIB.cmake config files (inluding /usr/lib), before it looks for zlib without cmake config files, which is how Spack installs it
* WarpX: 24.10
This updates WarpX and dependencies for the 24.10 release.
New features:
- EB runtime control: we can now compile with EB on by default,
because it is not an incompatible binary option anymore
- Catalyst2 support: AMReX/WarpX 24.09+ support Catalyst2 through
the existing Conduit bindings
* Fix Typo in Variant
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Improve Python Dep Version Ranges
* Add Missing `-DWarpX_CATALYST`
* AMReX: Missing CMake Options for Vis
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
This allows us to keep the workflow file tidier, and avoid
using indirections to perform platform specific operations.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* py-mpi4py: add v4.0.0
* sensei: update mpi4py dependency
build with py-mpi4py@4.0.0 due to fatal no such file or directory error
* petsc4py: update license, and remove C++/Fortran dependency
There was a bit of mystery surrounding the arguments for `_setup_pkg_and_run`. It passes
two file descriptors for handling the `gmake`'s job server in child processes, but they are
unsed in the method.
It turns out that there are good reasons to do this -- depending on the multiprocessing
backend, these file descriptors may be closed in the child if they're not passed
directly to it.
- [x] Document all args to `_setup_pkg_and_run`.
- [x] Document all arguments to `_setup_pkg_and_run`.
- [x] Add type hints for `_setup_pkg_and_run`.
- [x] Refactor exception handling in `_setup_pkg_and_run` so it's easier to add type
hints. `exc_info()` was problematic because it *can* return `None` (just not
in the context where it's used). `mypy` was too dumb to notice this.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* new builtin package: ambertools
* fixes for the style test
* yet more changes for the style test
* hope this is the last fix for the style test
* netlib-xblas is a dependency, it needs a depends_on("m4", type="build")
* ambertools: Add new setuptool dependency, limit python to <= 3.10 (does not build with 3.11+)
---------
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
We mostly use `spack style` and `spack style --fix`, but it's nice to also be able to
run plain old `black .` in the repo.
- [x] Fix includes and excludes `pyproject.toml` so that we *only* cover files we expect
to be blackened.
Note that `spack style` is still likely the better way to go, because it looks at `git
status` and tells black to only check files that changed from `develop`. `black` with
`pyproject.toml` won't do that. Of course, you can always manually specify which files
you want blackened.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* postgresql: Add icu4c dependency for versions 16+
* postgresql: make ICU an option
* postgresql: ICU variant only needed for v16+
* postgresql: Check for negated option
Check for negated option instead of negating the test
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
* [py-flash-attn] Add version 2.6.3
* Update dependencies according to the latest version
* Add max_jobs environmental variable to avoid oom error
---------
Co-authored-by: aurianer <8trash-can8@protonmail.ch>
* Revert "`cc`: ensure that RPATHs passed to linker are unique"
This reverts commit 2613a14c43.
* Revert "`cc`: simplify ordered list handling"
This reverts commit a76a48c42e.
Updated the terminology for the two types of environments to be
consistent with that used in the tutorial for the last three years.
Additionally:
* changed 'anonymous' to 'independent in environment command+test for consistency.
* Update package.py
Update to pull Totalview tar files from AWS instead of requiring the user to download ahead of time. Use new license type, RLM license. Only allow for installs of versions using the new license type. 2024.1 and 2024.2. User selects the platform with the version as it is down from the TotalView downloads website.
* Update package.py
Update to pass style test
* Update package.py
fixing syle
* Updating to pass style check
removing more spaces to pass style check
* final style fixes
fixing the last 2 style errors
* Typo
Typo correction to pass style check
* REmove new line
removing new line character
* Ran black to reformat
Ran black to clear errors
* Changing to use sha256
Updating to use sha256 checksums for all TotalView files.
* acts dependencies: new versions as of 2024/09/30
This commit adds new versions of acts, actsvg, and detray.
* Add vecmem version, patch detray version
#45205 already removed previous use of single letter packages
from unit tests, in view of reserving `c` as a language (see #45191).
Some use of them has been re-introduced accidentally in #46382, and
is making unit-tests fail in the feature branch #45189 since there
`c` is a virtual package.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Kokkos: adding some sanity checks
We can pretty much guarentee that if bin, include or lib directory
is missing, something is wrong. Additionally KokkosCore_config.h
and Kokkos_Core.hpp. I guess technically we could look for all
public headers at least but that seems a bit overkill as well?
* Kokkos Kernels: adding sanity checks
* Remove check for lib directory since it might end up being lib64
* Also remove lib from kokkos-kernels sanity check
* Add latest releases of Camp, RAJA, Umpire, CHAI and CARE
* Address review comments + blt requirement in Umpire
* CARE @develop & @main: Submodules -> False
* Changes in Umpire
* Changes in RAJA
* Changes in CHAI
* Changes in RAJA: prefer 'spec.satisfies' to 'in spec'
This is due to a non-equivalence in Spack with providers like mpi.
See e.g. https://github.com/spack/spack/pull/46126
* Changes in Umpire: prefer 'spec.satisfies' to 'in spec'
This is due to a non-equivalence in Spack with providers like mpi.
See e.g. https://github.com/spack/spack/pull/46126
* Changes in CARE:
Still need to update to CachedCMakePackage based on RADIUSS Spack Configs version
* Missing change in RAJA + changes in fmt
* Fix synta
* Changes in Camp
* Fix style
* CHAI: when ~raja, turn off RAJA in build system
* Fix: Ascent@0.9.3 does not support RAJA@2024.07.0
* Enforce same version constraint on Umpire as for RAJA
* Enforce preferred version of vtk-m in ascent 0.9.3
* Migrate CARE package to CachedCMakePackage
* Fix style in CARE package
* CARE: Apply changes for uniform implementation accross RADIUSS projects
* Caliper: move to CachedCMakePackage, from RADIUSS Spack Configs
* Adapt RAJA Perf to spack CI
* Activate CHAI, CARE and RAJAPerf in Spack CI
* Fixes and diffs with RADIUSS Spack Configs
* Caliper: fix
* Caliper : fix + RAJAPerf : style
* RAJAPerf: fixes
* Update maintainers
* raja-perf: fix license header
* raja-perf: Fix variant naming openmp_target -> omptarget
* raja-perf: style and blt dependency versions
* CARE: benchmark and examples off by default (like tests)
* CARE: fix missing variable
* Update var/spack/repos/builtin/packages/raja-perf/package.py
* CARE: fix branch name
* Revert changes in MFEM to pass CI
* Fix CXX17 condition in RAJA + add sycl option in RAJAPerf
---------
Co-authored-by: Rich Hornung <hornung1@llnl.gov>
* cbindgen: new package
* Attempting to add rust dependencies for cbindgen
* adding rust-toml min rust version
* Removing dependencies that don't install with cargo
* cleanup broken packages
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
On sysroot systems like gentoo prefix, as well as nix/guix, our "is
system path" logic is broken cause it's static.
Talking about "the system paths" is not helpful, we have to talk
about default search paths of the dynamic linker instead.
If glibc is recent enough, we can query the dynamic loader's default
search paths, which is a much more robust way to avoid registering
rpaths to system dirs, which can shadow Spack dirs.
This PR adds an **additional** filter on rpaths the compiler wrapper
adds, dropping rpaths that are default search paths. The PR **does
not** remove any of the original `is_system_path` code yet.
This fixes issues where build systems run just-built executables
linked against their *not-yet-installed libraries*, typically:
```
LD_LIBRARY_PATH=. ./exe
```
which happens in `perl`, `python`, and other non-cmake packages.
If a default path is rpath'ed, it takes precedence over
`LD_LIBRARY_PATH`, and a system library gets loaded instead
of the just-built library in the stage dir, breaking the build. If
default paths are not rpath'ed, then LD_LIBRARY_PATH takes
precedence, as is desired.
This PR additionally fixes an inconsistency in rpaths between
cmake and non-cmake packages. The cmake build system
computed rpaths by itself, but used a different order than
computed for the compiler wrapper. In fact it's not necessary
to compute rpaths at all, since we let cmake do that thanks to
`CMAKE_INSTALL_RPATH_USE_LINK_PATH`. This covers rpaths
for all dependencies. The only install rpaths we need to set are
`<install prefix>/{lib,lib64}`, which cmake unfortunately omits,
although it could also know these. Also, cmake does *not*
delete rpaths added by the toolchain (i.e. Spack's compiler
wrapper), so I don't think it should be controversial to simplify
things.
https://docs.sylabs.io/guides/main/admin-guide/configfiles.html#loop-devices
shared loop devices: This allows containers running the same image
to share a single loop device. This minimizes loop device usage and
helps optimize kernel cache usage.
Enabling this feature can be particularly useful for large MPI jobs.
The current `Spec.splice` model is very limited by the inability to splice specs that
contain multiple nodes with the same name. This is an artifact of the original
algorithm design predating the separate concretization of build dependencies,
which was the first feature to allow multiple specs in a DAG to share a name.
This PR provides a complete reimplementation of `Spec.splice` to avoid that
limitation. At the same time, the new algorithm ensures that build dependencies
for spliced specs are not changed, since the splice by definition cannot change
the build-time information of the spec. This is handled by splitting the dependency
edges and link/run edges into separate dependencies as needed.
Signed-off-by: Gregory Becker <becker33@llnl.gov>
* CI: Add documentation for adding new stacks and runners
* More docs for runner registration
---------
Co-authored-by: Zack Galbreath <zack.galbreath@kitware.com>
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
This PR shorten the string representation for concrete specs,
in order to make it more legible.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
macOS Sequoia's linker will complain if RPATHs on the CLI are specified more than once.
To avoid errors due to this, make `cc` only append unique RPATHs to the final args list.
This required a few improvements to the logic in `cc`:
1. List functions in `cc` didn't have any way to append unique elements to a list. Add a
`contains()` shell function that works like our other list functions. Use it to implement
an optional `"unique"` argument to `append()` and an `extend_unique()`. Use that to add
RPATHs to the `args_list`.
2. In the pure `ld` case, we weren't actually parsing `RPATH` arguments separately as we
do for `ccld`. Fix this by adding *another* nested case statement for raw `RPATH`
parsing. There are now 3 places where we deal with `-rpath` and friends, but I don't
see a great way to unify them, as `-Wl,`, `-Xlinker`, and raw `-rpath` arguments are
all ever so slightly different.
3. Fix ordering of assertions to make `pytest` diffs more intelligible. The meaning of
`+` and `-` in diffs changed in `pytest` 6.0 and the "preferred" order for assertions
became `assert actual == expected` instead of the other way around.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
`cc` divides most paths up into system paths, spack managed paths, and other paths.
This gets really repetitive and makes the code hard to read. Simplify the script
by adding some functions to do most of the redundant work for us.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* axom/stand-alone tests: build and run in test stage directory
* Removed unused glob
* axom/stand-alone tests: add example_stage_dir variable for clarity
SimpleFilesystemView was producing an error due to looking for a
<prefix>/lib/.spack folder. Also, view_destination had no effect and
wasn't called. Changed this by instead patching in the correct
installation prefix for dictionaries.
Since aspell is using the resolved path of the executable prefix, the
runtime environment variable ASPELL_CONF is set to correct the prefix
when in a view. With this change aspell can now find installed
dictionaries. Verified with:
aspell dump config
aspell dump dicts
* shorten version number validations per reviewer feedback
* rename set_lib_path per reviewer feedback
* Add E4S tag
* Set CHPL_CUDA_PATH to ensure Chapel installer finds the right package
* Update ROCm dependency for Chapel 2.2
* Fix llvm-amdgpu and CHPL_TARGET_* for llvm=bundled
* Ensure CHPL_TARGET_COMPILER is set to "llvm" when required (llvm=spack
or +cuda or +rocm).
* Ensure CHPL_TARGET_{CC,CXX} are only set when using llvm=spack or llvm=none
* Use hip.prefix to set CHPL_ROCM_PATH
Since we might not directly depend on llvm-amdgpu, thus it might
not appear in our spec
* limit m4 dependency to +gmp
* limit names of env vars created from variants
* Ensure that +cuda and +rocm variants are Sticky
The concretizer should never be permitted to select GPU support, because
it's only meaningful and functional when the appropriate hardware is actually
available, and the concretizer cannot reliably determine that.
Also: Chapel's GPU support includes alot of complicated dependencies
and constraints, so leaving that choice free to the concretizer leads to alot
of extraneous and confusing messages when failing to concretize a
non-GPU-enabled spec.
Co-authored-by: Dan Bonachea <dobonachea@lbl.gov>
Add pre-built sbcl for x86 and arm for various glibc versions, making
way for an actual sblc built from source.
Also switch to use set_env in a context manager over setting the
environment variable for the build environment. I hit an issue with the
build system due to this in the sbcl package, pre-empting the same issue
here.
* dla-future: Add DLAF_ prefix to LAPACK_LIBRARY CMake variable in newer versions
* dla-future: Use spec.satisfies to check version constraint for LAPACK_LIBRARY variable prefix
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
---------
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* py-sphinx-tabs: new version 3.4.5
* py-sphinx-design: new versions 0.5.0, 0.6.0, and 0.6.1
* py-requests: new version 2.32.3
* py-dnspython: new version 2.6.1
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* py-hatch-vcs: new version 0.4.0
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Python 3.12 removed the `distutils` module, which is being required
by the build process of LLVM <= 14: Conflict with it for +python.
Fix build to not pick host tools like an incompatible Python from host
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
gcc on ubuntu has fix-cortex-a53-843419 set by default - this causes linking
issues (symbol relocation errors) for tf, even when compiling for different
cpus.
If `add_padding()` is allowed to return a path with a trailing path
separator, it will get collapsed elsewhere in Spack. This can lead to
buildcache entries that have RPATHS that are too short to be replaced by
other users whose install root happens to be padded to the correct
length. Detect this and replace the trailing path separator with a
concrete path character.
Signed-off-by: Samuel E. Browne <sebrown@sandia.gov>
Also: set the build and install directories to the source directory
because the build system unfortunately expects the `src_ext` directory
to be under the current working directory when building the bundled
third-party libraries, even when the configure script is run from
another directory.
@scemama pointed out that 'make' just calls 'dune' which is already
parallel, so make itself should not have more than one job.
opam@:2.1 need 'make lib-ext' for cmdliner, above it's obsolete.
Co-authored-by: Bernhard Kaindl <bernhard.kaindl@cloud.com>
The detection logic for the prefix used in py-bind11 if broken for spack
resulting in an empty prefix. However, the package provides an escape
hatch in the form of `prefix_for_pc_file`. Use this escape hatch to
provide the correct path; spack will always know better than pybind11's
CMake.
Co-authored-by: Robert Underwood <runderwood@anl.gov>
We've seen `getfqdn()` cause slowdowns on macOS in CI when added elsewhere. It's also
called by database.py every time we write the DB file.
- [x] replace the call with a memoized version so that it is only called once per process.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
This PR introduces a new heuristic for the solver, which behaves better when
compilers are treated as nodes. Apparently, it performs better also on `develop`,
where compilers are still node attributes.
The new heuristic:
- Sets an initial priority for guessing a few attributes. The order is "nodes" (300),
"dependencies" (150), "virtual dependencies" (60), "version" and "variants" (30), and
"targets" and "compilers" (1). This initial priority decays over time during the solve, and
falls back to the defaults.
- By default, it considers most guessed facts as "false". For instance, by default a node
doesn't exist in the optimal answer set, or a version is not picked as a node version etc.
- There are certain conditions that override the default heuristic using the _priority_ of
a rule, which previously we didn't use. For instance, by default we guess that a
`attr("variant", Node, Variant, Value)` is false, but if we know that the node is already
in the answer set, and the value is the default one, then we guess it is true.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This includes a test_linux699 variant which "activates" a version
that pulls from a repository other than the official repository.
This version is required to work with Linux kernel version
6.9.9 or later. Future official `msr-safe` versions are expected
to support later Linux kernel versions.
* opendatadetector: Add an env variable pointing to the share directory
* Rename the new variable to OPENDATADETECTOR_DATA and use join_path
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
The `spack.target.Target` class is a weird entity, that is just needed to:
1. Sort microarchitectures in lists deterministically
2. Being able to use microarchitectures in hashed containers
This PR removes it, and uses `archspec.cpu.Microarchitecture` directly. To sort lists, we use a proper `key=` when needed. Being able to use `Microarchitecture` objects in sets is achieved by updating the external `archspec`.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Introduce the bufr_query library from NOAA-EMC (#461)
This PR adds in a new package.py script for the new bufr_query library from NOAA-EMC. This is being used by JEDI and other applications.
* Add explicit build dependency spec to the pybind11 depends_on spec
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Convert patch file to the URL form which pulls the changes from github.
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Added new version (0.0.3) and removed obsolete site-packages.patch file
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
While the existing getting started guide does in fact reference the
powershell support, it's a footnote and easily missed. This PR adds
explicit, upfront mentions of the powershell support. Additionally
this PR adds notes about some of the issues with certain components
of the spec syntax when using CMD.
If the spec is external, it has extra attributes. If not, we know
which names are used. In both cases we don't need to search again
for executables.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Removes `spack.package_base.PackageBase.do_{install,deprecate}` in favor of
`spack.installer.PackageInstaller.install` and `spack.installer.deprecate` resp.
That drops a dependency of `spack.package_base` on `spack.installer`, which is
necessary to get rid of circular dependencies in Spack.
Also change the signature of `PackageInstaller.__init__` from taking a dict as
positional argument, to an explicit list of keyword arguments.
Continuing the work started in #40326, his changes the structure
of Variant metadata on Packages from a single variant definition
per name with a list of `when` specs:
```
name: (Variant, [when_spec, ...])
```
to a Variant definition per `when_spec` per name:
```
when_spec: { name: Variant }
```
With this change, everything on a package *except* versions is
keyed by `when` spec. This:
1. makes things consistent, in that conditional things are (nearly)
all modeled in the same way; and
2. fixes an issue where we would lose information about multiple
variant definitions in a package (see #38302). We can now have,
e.g., different defaults for the same variant in different
versions of a package.
Some notes:
1. This required some pretty deep changes to the solver. Previously,
the solver's job was to select value(s) for a single variant definition
per name per package. Now, the solver needs to:
a. Determine which variant definition should be used for a given node,
which can depend on the node's version, compiler, target, other variants, etc.
b. Select valid value(s) for variants for each node based on the selected
variant definition.
When multiple variant definitions are enabled via their `when=` clause, we will
always prefer the *last* matching definition, by declaration order in packages. This
is implemented by adding a `precedence` to each variant at definition time, and we
ensure they are added to the solver in order of precedence.
This has the effect that variant definitions from derived classes are preferred over
definitions from superclasses, and the last definition within the same class sticks.
This matches python semantics. Some examples:
```python
class ROCmPackage(PackageBase):
variant("amdgpu_target", ..., when="+rocm")
class Hipblas(ROCmPackage):
variant("amdgpu_target", ...)
```
The global variant in `hipblas` will always supersede the `when="+rocm"` variant in
`ROCmPackage`. If `hipblas`'s variant was also conditional on `+rocm` (as it probably
should be), we would again filter out the definition from `ROCmPackage` because it
could never be activated. If you instead have:
```python
class ROCmPackage(PackageBase):
variant("amdgpu_target", ..., when="+rocm")
class Hipblas(ROCmPackage):
variant("amdgpu_target", ..., when="+rocm+foo")
```
The variant on `hipblas` will win for `+rocm+foo` but the one on `ROCmPackage` will
win with `rocm~foo`.
So, *if* we can statically determine if a variant is overridden, we filter it out.
This isn't strictly necessary, as the solver can handle many definitions fine, but
this reduces the complexity of the problem instance presented to `clingo`, and
simplifies output in `spack info` for derived packages. e.g., `spack info hipblas`
now shows only one definition of `amdgpu_target` where before it showed two, one of
which would never be used.
2. Nearly all access to the `variants` dictionary on packages has been refactored to
use the following class methods on `PackageBase`:
* `variant_names(cls) -> List[str]`: get all variant names for a package
* `has_variant(cls, name) -> bool`: whether a package has a variant with a given name
* `variant_definitions(cls, name: str) -> List[Tuple[Spec, Variant]]`: all definitions
of variant `name` that are possible, along with their `when` specs.
* `variant_items() -> `: iterate over `pkg.variants.items()`, with impossible variants
filtered out.
Consolidating to these methods seems to simplify the code a lot.
3. The solver does a lot more validation on variant values at setup time now. In
particular, it checks whether a variant value on a spec is valid given the other
constraints on that spec. This allowed us to remove the crufty logic in
`update_variant_validate`, which was needed because we previously didn't *know* after
a solve which variant definition had been used. Now, variant values from solves are
constructed strictly based on which variant definition was selected -- no more
heuristics.
4. The same prevalidation can now be done in package audits, and you can run:
```
spack audit packages --strict-variants
```
This turns up around 18 different places where a variant specification isn't valid
given the conditions on variant definitions in packages. I haven't fixed those here
but will open a separate PR to iterate on them. I plan to make strict checking the
defaults once all existing package issues are resolved. It's not clear to me that
strict checking should be the default for the prevalidation done at solve time.
There are a few other changes here that might be of interest:
1. The `generator` variant in `CMakePackage` is now only defined when `build_system=cmake`.
2. `spack info` has been updated to support the new metadata layout.
3. split out variant propagation into its own `.lp` file in the `solver` code.
4. Add better typing and clean up code for variant types in `variant.py`.
5. Add tests for new variant behavior.
Historically, every PR, push, etc. to Spack generates a bunch of jobs, each of which
uploads its coverage report to codecov independently. This means that we get annoying
partial coverage numbers when only a few of the jobs have finished, and frequently
codecov is bad at understanding when to merge reports for a given PR. The numbers of the
site can be weird as a result.
This restructures our coverage handling so that we do all the merging ourselves and
upload exactly one report per GitHub actions workflow. In practice, that means that
every push to every PR will get exactly one coverage report and exactly one coverage
number reported. I think this will at least partially restore peoples' faith in what
codecov is telling them, and it might even make codecov handle Spack a bit better, since
this reduces the report burden by ~7x.
- [x] test and audit jobs now upload artifacts for coverage
- [x] add a new job that downloads artifacts and merges coverage reports together
- [x] set `paths` section of `pyproject.toml` so that cross-platform clone locations are merged
- [x] upload to codecov once, at the end of the workflow
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* kokkos, kokkos-kernels, kokkos-nvcc-wrapper: add v4.4.01
* trilinos: update @[master,develop] dependency on kokkos
==> Error: InstallError: For Trilinos@[master,develop], ^kokkos version in spec must match version in Trilinos source code. Specify ^kokkos@4.4.01 for trilinos@[master,develop] instead of ^kokkos@4.4.00.
* petsc: configure requires rocm-core/rocm_version.h to detect ROCM_VERSION_MAJOR.ROCM_VERSION_MINOR.ROCM_VERSION_PATCH
* mfem: add dependency on rocprim (as needed via petsc dependency)
In file included from linalg/petsc.cpp:19:
In file included from linalg/linalg.hpp:65:
In file included from linalg/petsc.hpp:48:
In file included from /scratch/svcpetsc/spack.x/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/petsc-3.22.0-7dsxwizo24ycnqvwnsscupuh4i7yusrh/include/petscsystypes.h:530:
In file included from /scratch/svcpetsc/spack.x/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/rocthrust-6.1.2-ux5nmi4utw27oaqmz3sfjmhb6hyt5zed/include/thrust/complex.h:30:
/scratch/svcpetsc/spack.x/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.4.0/rocthrust-6.1.2-ux5nmi4utw27oaqmz3sfjmhb6hyt5zed/include/thrust/detail/type_traits.h:29:10: fatal error: 'rocprim/detail/match_result_type.hpp' file not found
29 | #include <rocprim/detail/match_result_type.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Update seacas package.py
Adding libcatalyst variant to seacas package
When seacas is installed with "seacas +libcatalyst"
then a dependency on the spack package "libcatalyst"
(which is catalyst api 2 from kitware) is added, and
the appropriage cmake variable for the catalyst TPL
is set. The mpi variant option in catalyst (i.e. build
with mpi or build without mpi) is passed on to
libcatalyst. The default of the libcatalyst variant
is false/off, so if seacas is installed without the
"+libcatalyst" in the spec it will behave exactly as
it did before the introduction of this variant.
* shortened line 202 to comply with < 100 characters per line style requirement
* py-httpx: New version
* [py-httpx] fix when for dependencies
* [py-httpx] organized dependencies
* [py-httpx] added version 0.27.2
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* Automated deployment to update package flux-sched 2024-09-05
* flux-sched: add back check for run environment
* flux-sched: add conflict for gcc and clang above 0.37.0
---------
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
autotools packages with a configure script should generate the libtool
executable, there's no point in `depends_on("libtool", type="build")`.
the libtool executable in `<libtool prefix>/bin/libtool` is configured
for the wrong toolchain (libtools %compiler instead of the package's
%compiler).
Some package link to `libltdl.so`, which is fine, but had a wrong
dependency type.
See https://github.com/spack/spack/pull/46314#discussion_r1752940332.
This further simplifies `cxxstd` variant handling in `acts` by removing superfluous
version constraints from dependencies for `geant4` and `root`.
The version constraints in the loop are redundant with the conditional variant
values here:
```python
_cxxstd_values = (
conditional("14", when="@:0.8.1"),
conditional("17", when="@:35"),
conditional("20", when="@24:"),
)
_cxxstd_common = {
"values": _cxxstd_values,
"multi": False,
"description": "Use the specified C++ standard when building.",
}
variant("cxxstd", default="17", when="@:35", **_cxxstd_common)
variant("cxxstd", default="20", when="@36:", **_cxxstd_common)
```
So we can simplify the dependencies in the loop to:
```python
for _cxxstd in _cxxstd_values:
for _v in _cxxstd:
depends_on(f"geant4 cxxstd={_v.value}", when=f"cxxstd={_v.value} +geant4")
depends_on(f"geant4 cxxstd={_v.value}", when=f"cxxstd={_v.value} +fatras_geant4")
depends_on(f"root cxxstd={_v.value}", when=f"cxxstd={_v.value} +tgeo")
```
And avoid the potential for impossible variant expressions.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Openmpi provider statements were changed in #46102. The package change
was fine in and of itself, but apparently one of our tests depends on
the precise constraints used in those statements. I updated the test
to remove the checks for constraints that were removed.
In #44425, we add stricter variant audits that catch expressions that can never match.
This fixes 13 packages that had this type of issue.
Most packages had lingering spec expressions from before conditional variants with
`when=` statements were added. For example:
* Given `conflicts("+a", when="~b")`, if the package has since added
`variant("a", when="+b")`, the conflict is no longer needed, because
`a` and `b` will never exist together.
* Similarly, two packages that depended on `py-torch` depended on
`py-torch~cuda~cudnn`, which can't match because the `cudnn` variant
doesn't exist when `cuda` is disabled. Note that neither `+foo` or `~foo`
match (intentionally) if the `foo` variant doesn't exist.
* Some packages referred to impossible version/variant combinations, e.g.,
`ceed@1.0.0+mfem~petsc` when the `petsc` variant only exist at version `2`
or higher.
Some of these correct real issues (e.g. the `py-torch` dependencies would have never
worked). Others simply declutter old code in packages by making all constraints
consistent with version and variant updates.
The only one of these that I think is not all that useful is the one for `acts`,
where looping over `cxxstd` versions and package versions ends up adding some
constraints that are impossible. The additional dependencies could never have
happened and the code is more complicated with the needed extra constriant.
I think *probably* the best thing to do in `acts` is to just not to use a loop
and to write out the constraints explicitly, but maybe the code is easier to
maintain as written.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* Update var/spack/repos/builtin/packages/fms/package.py: apply patch for fms@2023.03 to fix compiler options bug in cmake config, add variant shared and corresponding patch for fms@2024.02
* Fix fms package audit: use c9bba516ba.patch?full_index=1 instead of c9bba516ba.patch?full_index=1
* Update checksum of patch for fms@2023.03
* CUDA: support Grace Hopper 9.0a compute capability
* Fix other packages
* Add type annotations
* Support ancient Python versions
* isort
* spec -> self.spec
Co-authored-by: Andrew W Elble <aweits@rit.edu>
* [@spackbot] updating style on behalf of adamjstewart
---------
Co-authored-by: Andrew W Elble <aweits@rit.edu>
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
fixes#46295
A proper solution would be a tag directive that accumulates tags
with the ones defined in base classes.
For the time being, rewrite them explicitly.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Boost:Adjust bootstrapping/b2 options as needed for Windows (the
bootstrapping phase sufficiently differs between Windows/Unix
that it is handled entirely within its own branch).
* Boost: Paths in user-config.jam should be POSIX, including on Windows
* Python: `.libs` for the Python package should return link libraries
on Windows. The libraries are also stored in a different directory.
The option config:install_missing_compilers is currently buggy,
and has been for a while. Remove it, since it won't be needed
when compilers are treated as dependencies.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* fast-float: new package
* fast-float: add test dependency
* fast-float: fix doctest dependency type
* fast-float: convert deps to tuple
* fast-float: add v6.1.5 and v6.1.6
* fast-float: patch older versions to use find_package(doctest)
* py-your: new package
Spack package recipe for YOUR, Your Unified Reader. YOUR processes pulsar data in different formats.
Output below from spack install py-your
spack install py-your
==> Installing py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x [83/83]
==> No binary for py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x found: installing from source
==> Fetching https://github.com/thepetabyteproject/your/archive/refs/tags/0.6.7.tar.gz
==> No patches needed for py-your
==> py-your: Executing phase: 'install'
==> py-your: Successfully installed py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x
Stage: 1.43s. Install: 0.99s. Post-install: 0.12s. Total: 3.12s
* Removed setup_run_environment
After some testing, both spack load and module load for the package will include the bin directory generated by py-your as well as the path to the version of python the package was built with, without the need for the setup_run_environment function.
I removed that function (Although, like Tamara I thought it would be necessary based on other package setups I used as a basis for this package).
Note: I also updated the required version of py-astropy from py-astropy@4.0: to @py-astropy@6.1.0: In my test builds, the install was picking up version py-astropy@4.0.1.post1 and numpy1.26. However when I tried to run some of the code I was getting errors about py-astropy making numpy calls that are now removed. The newer version of py-astropy corrects these. Ideally this would be handled in the py-astropy package to make sure numpy isn't too new
* Changed software pull location
The original package pulled a tagged release version from GitHub. That tagged version was created in 2022 and has not been updated since. It no longer runs because newer versions of numpy have removed deprecation warnings for several of their calls. The main branch for this repository has addressed these numpy issues as well as some other important fixes but no new release has been generated. Because of this and the apparent minimal development that now appears to be going on, it is probably best to always pull from the main branch
* [@spackbot] updating style on behalf of aweaver1fandm
* py-your: Changed software pull location
1. Restored original URL and version (0.6.7) as requested
2. Updated py-numpy dependency versions to be constrained based on the version of your. Because of numpy deprecations related to your version 0.6.7 need to ensure that the numpy version used is not 1.24 or greater because the depracations were removed starting with that version
* gptune: new test API
* gptune: cleanup; finish API changes; separate unrelated test parts
* gptune: standalone test cleanup with timeout constraints
* gptune: ensure stand-alone test bash failures terminate; enable in CI
* gptune: add directory to terminate_bash_failures
* gptune/stand-alone tests: use satisifes for checking variants
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* Add numactl 2.0.16-2.0.18
* Create link-with-latomic-if-needed-v2.0.16.patch
Add a link to libatomic, if needed, for numactl v2.0.16.
* Add some missing patches to v2.0.16
* Create numactl-2.0.18-syscall-NR-ppc64.patch
In short, we need numactl to set __NR_set_mempolicy_home_node on ppc64, if it's not already defined.
* Apply a necessary patch for v2.0.18 on PPC64
* Add libatomic patch for v2.0.16
`spack reindex` relies on projections from configuration to locate
installed specs and prefixes. This is problematic because config can
change over time, and we have reasons to do so when turning compilers
into depedencies (removing `{compiler.name}-{compiler.version}` from
projections)
This commit makes reindex recursively search for .spack/ metadirs.
* py-httpcore: Added new version
* [py-httpcore]
- added version 0.18.0
- restructured dependencies as everything has a when and
type/when ordering was all over the place
* [py-httpcore] ordered dependencies in the order listed in v1.0.5 pyproject.toml
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
When a package is running `setup_dependent_package` on a parent, ensure
that module variables like `spack_cc` are available. This was often
true prior to this commit, but externals were an exception.
---------
Co-authored-by: John Parent <john.parent@kitware.com>
* New package: py-monai
* Fixed linked issues with py-monai
* [py-monai] removed extra line
* [py-monai]
- New version 1.3.2
- ran black
- update copyright
* [py-monai] added license
* [py-monai]
- moved build only dependencies
- specified newer python requirements for newer versions
---------
Co-authored-by: vehrc <vehrc@rit.edu>
* Replace if ... in spec with spec.satisfies in f* and g* packages
* gromacs: ^amdfftw -> ^[virtuals=fftw-api] amdfftw
* flamemaster: add virtuals lapack for the amdlibflame dependency
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Allow flags from different sources (compilers, `require:`, command-line
specs, and `depends_on`) to be merged together, and enforce a consistent
order among them.
The order is based on the sources, e.g. flags on specs from the command
line always come last. Some flag order consistency issues are fixed:
1. Flags from `compilers.yaml` and the command line were always intra- and
inter-source order consistent.
2. Flags from dependents and packages.yaml (introduced via `require:`)
were not: for `-a -b` from one source and `-c` from another, the final
result might rearrange `-a -b`, and would also be inconsistent in terms
of whether `-c` came before or after.
(1) is/was handled by going back to the original source, i.e., flags are
retrieved directly from the command line spec rather than the solver.
(2) is addressed by:
* Keeping track of grouped flags in the solver
* Keeping track of flag sources in the solver on a per-flag basis
The latter info is used in this PR to enforce DAG ordering on flags
applied from multiple dependents to the same package, e.g., for this
graph:
```
a
/|\
b | c
\|/
d
```
If `a`, `b`, and `c` impose flags on `d`, the combined flags on `d` will
contain the flags of `a`, `b`, and `c` -- in that order.
Conflicting flags are allowed (e.g. -O2 and -O3). `Spec.satisifes()` has
been updated such that X satisfies Y as long as X has *at least* all of
the flags that Y has. This is also true in the solver constraints.
`.satisfies` does not account for how order can change behavior (so
`-O2 -O3` can satisfy `-O3 -O2`); it is expected that this can be
addressed later (e.g. by prohibiting flag conflicts).
`Spec.constrain` and `.intersects` have been updated to be consistent
with this new definition of `.satisfies`.
Spack can now bootstrap two new dependencies on Windows: GnuPG, and file.
These dependencies are modeled as a separate package, and they install a cross-compiled binary.
Details on how they binaries are built are in https://github.com/spack/windows-bootstrap-resources
This PR adds py-pybind11 versions 2.13.0, 2.13.1, 2.13.2, 2.13.3, and
2.13.4. It also adds a new conflict between gcc 14 and pybind versions
up to and including 2.13.1.
* Allow deprecating more than one property in config
This internal change allows the customization of errors
and warnings to be printed when deprecating a property.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* fix
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Use a list comprehension for "issues"
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---------
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
fixes#40791
Currently stacks behave differently if used in unify:false
environments, which leads to inconsistencies during concretization.
For instance, we might have two abstract user specs that do not
intersect with each other map to the same concrete spec in the
environment. This is clearly wrong.
This PR removes the best effort expansion, so that user specs
are always applied strictly.
* gaudi: Specify boost components and add +fiber for v39
* gaudi: Limit fmt version to allow building master branch
* Make boost dependencies a bit more readable
* Remove patches for no longer existing versions
* Replace if ... in spec with spec.satisfies in d* and e* packages
* Use virtuals for different mpi implementations in esmf
* esmf: ^[virtuals=mpi] mpt
* extrae: ^[virtuals=mpi] intel-oneapi-mpi
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
This change aligns the build condition for parmetis with the
depends_on condition.
The current build condition of parmetis looks for "+parmetis" in
the spec which is not added by the depends_on as that adds
"^parmetis" instead.
* Adding addtional check for omptarget library for amdgpu in nvidia environment
* Avoiding registration of duplicate when built on cuda
* Adding hsa library path in LD_LIBRARY_PATH
* Correction in hsa prefix library path in LD_LIBRARY_PATH
==> Error: InstallError: For Trilinos@[master,develop], ^kokkos version in spec must match version in Trilinos source code. Specify ^kokkos@4.4.00 for trilinos@[master,develop] instead of ^kokkos@4.3.01.
* root: Add dependency on libglx
We have been trying to build the Acts package on MacOS, and in this
process we have been running into problems with the ROOT spec on that
operating system; the primary issue we are encountering is that the
compiler is unable to find the `GL/glx.h` header, which is part of glx.
It seems, therefore, that ROOT depends on libglx, but this is not
currently encoded in the spec. This commit ensures that ROOT depends on
the virtual libglx package when both the OpenCL and X11 variants are
enabled.
* Enable builtin glew on MacOS
* Allow `root+opengl+aqua~x` on macOS
dd4hep versions up to and including 1.27 had a conflict with root
versions starting from 6.31.1, as shown in
https://github.com/AIDASoft/DD4hep/issues/1210. This PR explicitly adds
that conflict to the spec.
* whizard: add a patch when using hepmc3 3.3.0 or newer
* whizard: comment with patch origin
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* podio: apply patch for gcc 14 builds
Podio versions after 0.17.0 but before 1.0.0 are broken when using gcc
14 because of a missing include, which is addressed in the podio pull
request at https://github.com/AIDASoft/podio/pull/600. This commit
patches pre-1.0.0 versions of Podio so they can be compiled with gcc 14,
which is important for building Acts.
* Style
* Style 2
* Fixes
* Add comment:
* Add sha256
This should help not selecting, by default, some niche implementation that are supposed to be externals.
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This PR simplifies the code doing external spec detection by removing
the `DetectedPackage` class. Now, functions accepting or returning lists
of `DetectedPackage`, will accept or return list of specs.
Performance doesn't seem to change if we use `Spec.__reduce__` instead
of `DetectionPackage.__reduce__`.
- Honor compiler extra_rpaths (this build bypasses spack wrappers,
so the RPATHs are added explicitly as CMake options)
- Use root_cmakelists_dir instead of adding it to the command line
- Add BLT as a dependency, allowing different versions outside of what
is in the tarball
- Put a copy of host-config in the stage directory: this allows
examination of the host-config when a build fails (before, the
host-config was just stored in the install directory, which is
deleted by default on a failed build)
* Add conflict between NVSHMEM and cuFFTMp for GROMACS package
These don't work in the same build configuration.
* [@spackbot] updating style on behalf of mabraham
* Update package.py
Also constrain NVSHMEM appropriately
* Update var/spack/repos/builtin/packages/gromacs/package.py
Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
* Update package.py
* [@spackbot] updating style on behalf of mabraham
* Update package.py
* Update package.py
* Update package.py
* [@spackbot] updating style on behalf of mabraham
---------
Co-authored-by: mabraham <mabraham@users.noreply.github.com>
Co-authored-by: Christoph Junghans <christoph.junghans@gmail.com>
Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
Change the signature of Spec.from_detection to set the
external prefix, and the external modules, if they are
present.
Delete "spack.package_prefs.spec_externals" since it
is unused.
This context manager was used to prevent detecting a platform
as "cray". Since now Cray machines are detected as linux, we can
remove the context manager.
This commit adds version 0.73.0 of the detray package. As this version
drops support for pre-C++20 standards, I had to update the `cxxstd`
variant logic.
Right now if you run `spack ci generate` you get a warning about CDash credentials even
if there's no CDash configuration specified. We should only warn if there was actually a
CDash config.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Source mirrors store entries by digest and add a human readable alias of the
form 'name-version'. If no digest is available, the alias is used as the primary
storage location.
Spack erroneously fetches by alias when the digest path does not exist. This is
problematic if `version(..., sha256=...)` changes in package.py, and the mirror
is populated with the old shasum. That would result in an error when a digest
is available, but in case of git versions with a modified commit sha, the wrong
sources would be fetched without error. With this PR, only the digest path is
used, not the alias, in case a digest is available. This is also a small performance
optimization, as the number of request is halved for mirrors that don't contain
the sources.
Further, for git sources the tag was used as a digest, but this is a moving
target. Only commit sha is used now.
Also whenever the alias already existed, Spack used to keep it in place when
updating the mirror cache, which means that aliases would always point to
outdated mirror entries whenever digests are modified. With this PR the alias
is moved in place.
Lastly, fix a recent regression where `Stage.disable_mirrors` disabled mirrors
but not the local download cache, which was the intention.
* VTK-m: Point to github mirror for source tarball
The gitlab.kitware.com source location seems to have intermittent
network issues. Switching the to mirror hosted at Github may alleviate
some of the timeouts.
* Update sha256 for GitHub tarballs
---------
Co-authored-by: Zack Galbreath <zack.galbreath@kitware.com>
* davix: add versions 0.8.2-0.8.7 and dependencies
This commit adds new versions 0.8.2-0.8.7 of the davix package, and it
also improves the handling of embedded packages. Davix will try to build
libcurl from its own embedded version of that code, which doesn't mesh
well with Spack's design philosophy, so I've changed the CMake
configuration to disallow the builtin libcurl and use a Spack dependency
instead. Up to version 0.8.7, RapidJSON was also builtin, but version
0.8.7 allows users to specify that they want to use a pre-installed
version of RapidJSON, so this commit also adds that as a dependency for
versions 0.8.7:.
* Fix old versions
* acts: add v36.0.0, v36.1.0 and fixes
This commit makes several changes to the Acts repository, namely:
1. It adds versions 36.0.0 and 36.1.0.
2. It adds the traccc plugin and related dependencies.
3. It updates the version requirements of some dependencies.
4. It adds the Geant4 module of GeoModel.
5. It updates the C++ standard requirement.
6. It adds a new variant determining the scalar type to use.
This commit supercedes #45851. Thanks @jmcarcell for the version
updates; I have added you as co-author.
Co-authored-by: Juan Miguel Carceller <22276694+jmcarcell@users.noreply.github.com>
* Updates
* alphabetic cmake args
---------
Co-authored-by: Juan Miguel Carceller <22276694+jmcarcell@users.noreply.github.com>
* Add missing MultiMethodMeta metaclass in builders
and remove the Python 2 fallback option in favor of hard errors to catch
similar issues going forward.
The fallback option can cause about 10K stat calls due to use of
`realpath` in the inspect module, depending on how deep Spack itself is
nested in the file system, which is ... undesirable.
* code shuffling to avoid circular import
* more reshuffling
* move reserved variant names into variants module
Currently, the llvm-amdgpu package doesn't compile on MacOS, but it is
also not marked as a conflict. This causes problems because it seems
that Spack is very happy to pull in llvm-amdgpu as the default package
to satisfy any virtual libllvm dependency, which can cause dependent
specs to fail to install on MacOS. This commit marks a conflict between
this llvm package and the Darwin platform.
* root: set +webgui~http conflict from @6.28.12:
Currently, the ROOT spec correctly identifies a conflict between +webgui
and ~http, but this conflict is marked as affecting @6.29.00: only. As a
matter of fact, ROOT 6.28.12 is also affected. This commit, therefore,
updates the when clause on the conflict to @6.28.12:.
* Remove when clause entirely
* oops
* Adds an MSBuild system + Builder to the icu4c package
* Adds custom install method as MSBuild system does not vendor an
install target
* The cxxstd variant is not supported on Windows (there are no config
options you use to tell the build system what cxx standard to
build against), so the variant definition was updated to occur
everywhere except Windows
Also, this commit defines the c/cxx..._flag properties of the MSVC
compiler (although they are not used by `icu4c` and not strictly
necessary to bundle with this PR).
This commit adds a dependency on GeoModel 4.6.0 when the GeoModel plugin
is enabled. Note that the dependency is upgraded to 6.3.0 in Acts
36.1.0, but that will need to be covered in #45851.
* geomodel: add versions 5.1.0-6.4.0
This PR adds new versions 5.1.0 through 6.4.0 of the geomodel package.
It also updates the CMake configuration to use the `define_from_variant`
mechanism and it adds me as a maintainer.
* Undo cmake change
The avx2 version can be downloaded from the ORCA [forum](https://orcaforum.kofo.mpg.de/app.php/dlext/?view=detail&df_id=214#).
The version is named `avx2-6.0.0` (as opposed to the more
natural-looking `6.0.0-avx2`) to avoid the avx2 version shadowing the
non-avx2 one. Definitely open for better suggestion.
* hsakmt-roct: new test API
* hsakmt-roct: minor change to check_install script variable name
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* parallel-netcdf: new test API
* parallel-netcdf: fix test args and tweak docstring and variables
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* WarpX: Python on pyAMReX
Long overdue update for WarpX: in 2024, we updated our Python
bindings to rely on the new pyAMReX package. This deprecates the old
`py-warpx` package and adds a new dependency and variant to WarpX.
Also deprecates old versions that we will not continue to support.
* Update Cloud/E4S Pipelines for WarpX
`py-warpx` is replaced by `warpx +python`
oneAPI does not support IPO/LTO: diable for `py-amrex` even though
pybind11 strongly encourages it.
* Add `+python` variant
* `esmf` package installs Python bindings when `+python` is set
Note: this does not inherit `PythonPackage`, which force an either/or
choice between the Makefile and Pip builder: it instantiates a
`PythonPipBuilder` as needed (when `+python` is set).
Paths over 260 characters in length are not handled by `shutil.rmtree`
unless they use the extended-length path syntax (using a prefix of
"\\?\").
This fixes an issue where stage cleaning fails when paths in a stage
exceed the normal 260-character limit.
This indicates that other parts of the codebase should be examined/
refactored to handle long paths.
* harfbuzz: enable freetype in MesonBuilder to facilitate depends_on("freetype")
* spack style fix
* freetype is defined as a depends_on(), so set as enabled in MesonBuilder rather than an option/flag/variant
* add back depends_on($lang) lines for new test api
* keep original order
Previously `spack buildcache push --only=package` errored in the OCI
case, but it's been requested that OCI can be used as pure storage w/o
the need for runnable container images.
This commit makes it so that
1. manifests refer only to runtime dependencies that were selected to be
pushed
2. failure to upload a blob among the selected specs does not prevent a
manifest/tag to be created for dependents: they just don't refer to
the missing blob as a layer/dependency
This fixes the following issues:
1. dependents of non-redistributable specs can now be pushed to oci
build caches without error
2. failure to upload one tarball does not cause cascading failures for
dependents whose tarballs do upload succesfully -- so it's better
best-effort behavior
3. for some people uploading with deps caused a massive amount of
fetches of their manifests (which certain registries count as a
download of an image, even though their layers are not fetched) --
being able to specify --only=package reduces the number of fetches.
Stage objects create mirrors ad-hoc from current config.
- There is no way to prevent mirrors from being used
- There is no way to restrict mirrors to source/binary, which is of
course context dependent.
- Stage is also used in build caches, where iterating over mirrors is
already implemented differently, and wouldn't work anyways cause it's
source only, and in particular it makes no sense for OCI build caches.
This commit:
1. Injects the sensible mirrors into the stage object from contexts
where it is relevant
2. Separates mirrors from cache, so that w/o mirrors download cache can
still be used
The test_foreground_background unit test has been marked
xfail for a while, meaning:
- Nobody looks at the results of the test
- It still runs every time
That test happens to hang frequently on some Apple M1 I have access to,
so here I mark it as skip.
Also went through other xfailing and skipped tests, and applied minor changes.
* Use absolute paths instead of https:// fake mirrors (this speed-up tests by avoiding requests)
* Add a fixture to gather in a single place code that is copy/pasted in a lot of tests
* General clean-up of tests and repeated code
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* hypre: get rid of depreciated run_test method
* hypre: use mkdirp directly
* hypre: use install() for ij for addition of permissions fix
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* parsec: old to new test API
* parsec: restore stand-alone test subparts; preliminary test build fixes
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* n2p2: convert from old to new test API
* n2p2: Enhance stand-alone testing checks to reduce unnecessary processing
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* stand-alone test API update: self.cache_extra_test_sources(...) -> cache_extra_test_sources(self, ...)
* superlu: switch to new cache_extra_test_sources API
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* Add options for sparse checkout in GitFetcher
Newer versions of git have a beta feature called sparse checkout
that allow users to check out a portion of a large repo.
This feature will be ideal for monolithic repo projects that want to
model their infrastructure via spack. This PR implements an addition
to the GitFetcher that allows users to add a `git_sparse_paths`
attribute to package classes or versions which will then use sparse
checkout on those directories/files for the package.
* Style
* Split git clone into multiple functions
* Add sparse-checkout impl
* Internalize src clone functions
* Docs
* Adding sparse clone test
* Add test for partial clone
* [@spackbot] updating style on behalf of psakievich
* Small fixes
* Restore default branch status
* Fix attributes for package
* Update lib/spack/docs/packaging_guide.rst
Co-authored-by: Matthew Mosby <44072882+mdmosby@users.noreply.github.com>
* Extend unit test to multiple git versions
* style
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
Co-authored-by: Matthew Mosby <44072882+mdmosby@users.noreply.github.com>
* Feature update py-fortranformat
Add more recent versions of py-fortranformat. The currently included release (0.2.5) is from 2014. I've added the latest point release of each of the major versions from the last 4 years.
* update homepage
* magma: old to new test API
* magma: simplify stand-alone test method/part docstrings/purposes
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* initial commit to enable asan in remaining rocm packages
* remove os import
* add rocm-opencl rocm-dbgapi rocm-debug-agent
* add libclang path to LD_LIBRARY_PATH
* enable asan for rocfft
* add f-string and add +asan dependencies for hip and rocm-opencl
* add conflicts for centos7/8 and rhel 9
When sending Repo and RepoPath over to a child process,
we go through a marshaling procedure with pickle. The
default behavior for these classes is highly inefficient,
as it serializes a lot of specs that can just be
reconstructed on the other end of the pipe.
Here we write optimized procedures to __reduce__ both
classes.
* raja: new test API
* raja: tweak test method names and docstrings
* raja: restore running tests under proper directory
* raja: cleanup skiptest message and example call
* raja: Tweak expected outputs to match current
* raja: test_views -> test_stencil_offset_layout
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* mptensor: Changed skiptest, test name, and added docstring
* mptensor: make stand-alone test method name and docstring more specific
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Add version 2.0.-2
* Newer version at the top
* [@spackbot] updating style on behalf of rahmans1
* py-htgettoken: reorder comments
* Use sha256sum instead of commit id for version 2.0-2 and above
---------
Co-authored-by: rahmans1 <rahmans1@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Extracted from #44419
This adds / modifies some external detection tests for compilers,
to reproduce cases that are currently tested in unit tests.
The unit tests will later be removed.
Extracted from #45638
When adding the "detectable" tag to a package class that has the
"tag" attribute inherited from a base class, we need to copy it to
avoid modifying the base class.
* kickoff attempt
* resource similar to fortran
* delete unused install_component_codeplay
* Adding conflict for versions <= 2022.2.1, moving install to package.py, adding sha256 for version 2024.2.1
* [@spackbot] updating style on behalf of kaanolgu
---------
Co-authored-by: Kaan Olgu <kaan.olgu@bristol.ac.uk>
"spack buildcache push" for partially installed environments pushes all it
can by default, and only dumps errors towards the end.
If --fail-fast is provided, error out before pushing anything if any
of the packages is uninstalled
oci build caches using parallel push now use futures to ensure pushing
goes in best-effort style.
* migraphx: Old to new test API
* migraphx: tweak name and docstring to be more descriptive
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* c: new test API
* gcc: provides('c')
* c: bugfix and simplification of the new stand-alone test method
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* fortran: new test API
* fortran: add provides to gcc package
* fortran: simplify stand-alone test processing
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* hypre-cmake: old to new test API
* hypre-cmake: update Makefile to use installed files
* hypre-cmake: make stand-alone test method name more specific
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
The old concretizer is still used to bootstrap clingo from source. If we switch to a DAG model
where compilers are treated as nodes, we need to either:
1. fix the old concretizer to support this (which is a lot of work and possibly research), or
2. bootstrap `clingo` without the old concretizer.
This PR takes the second approach and gets rid of the old concretizer code. To bootstrap
`clingo`, we store some concrete spec prototypes as JSON, select one according to the
coarse-grained system architecture, and tweak them according to the current host.
The old concretizer and related dead code are removed. In particular, this removes
`Spec.normalize()` and related methods, which were used in many unit-tests to set
up the test context. The tests have been updated not to use `normalize()`.
- [x] Bootstrap clingo concretization based on a JSON file
- [x] Bootstrap clingo *before* patchelf
- [x] Remove any use of the old concretizer, including:
* Remove only_clingo and only_original fixtures
* Remove _old_concretize and _new_concretize
* Remove _concretize_together_old
* Remove _concretize_together_new
* Remove any use of `SPACK_TEST_SOLVER`
* Simplify CI jobs
- [x] ensure bootstrapping `clingo` works on on Darwin and Windows
- [x] Raise an intelligible error when a compiler is missing
- [x] Ensure bootstrapping works on FreeBSD
- [x] remove normalize and related methods
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
`setup-env.sh` is meant to be sourced, not executed directly.
By revoking execution permissions, users who accidentally execute
the script will receive an error instead of seeing no effect.
* Remove execution permission from `setup-env.sh` and friends
* Don't make output file executable in `spack commands --update-completion`
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* On Windows it is built with CMake, however CMake is built against
libuv, so libuv must depend on cmake+ownlibs to short circuit the
circular dependency
* libuv currently fetches the -dist source distribution of libuv for
certain versions because those versions contain a pre-generated
./configure script. However those distributions have all CMake
files removed, so they cannot be used to build on Windows.
Because the source distributions are different, this means the
checksums are different, and necessitates an additional version
declaration for each version we want to support with CMake.
* Update available versions
* fix style
* Reduce added versions to just a single new version as per review
* fix style
* Set dependency versions in line with pyproject and setup.py
* add new interp variant
* add wheel as required
* Add variant description
* change +interp default, actually add packaging this time
Fixes#43494
Add a set of environment variables SPACK_ALWAYS_CFLAGS (etc.) that
are always applied by the compiler wrapper.
Unlike SPACK_CFLAGS, for example, these will also be applied to
version checks (both SPACK_CFLAGS and SPACK_ALWAYS_CFLAGS will be
applied to the other invocation modes like ccld etc.).
Using this new functionality, the classic Intel and oneAPI compilers
are updated to pass compiler flags that disable warning messages
when newer versions are invoked via their older binary names
(these warnings were also generated for version checks, hence the
need for a new wrapper variable).
---------
Co-authored-by: Peter Josef Scheibel <scheibel1@llnl.gov>
* namd:add compile options for ROCm
* Combine --rocm-prefix and its value in a single opts.extend call to ensure they remain ordered correctly and improve code robustness.
* Standardize the code and add ROCm conflicts
* add single_node_gpu conflict
---------
Co-authored-by: U-PALLAS\boudaoud <boudaoud@pc44.pallas.cines.fr>
When clang is installed I get `clang: Permission denied`.
Setting CLANG to the full path of clang fixes this.
Signed-off-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
Fixes error:
```txt
3 errors found in build log:
61 ==> xmlto: Executing phase: 'build'
62 ==> [2023-10-26-09:48:35.425903] 'make' '-j16' 'V=1'
63 make all-am
64 make[1]: Entering directory '/tmp/root/spack-stage/spack-stage-xmlto-0.0.28-huuygrp4qasytrezg774yavnnaxzgp2e/spack-src'
65 /bin/sh ./ylwrap xmlif/xmlif.l .c xmlif/xmlif.c -- /bin/sh /tmp/root/spack-stage/spack-stage-xmlto-0.0.28-huuygrp4qasytrezg774yavnnaxzgp2e/spack-src/missing flex
66 /tmp/root/spack-stage/spack-stage-xmlto-0.0.28-huuygrp4qasytrezg774yavnnaxzgp2e/spack-src/missing: line 81: flex: command not found
>> 67 WARNING: 'flex' is missing on your system.
68 You should only need it if you modified a '.l' file.
69 You may want to install the Fast Lexical Analyzer package:
70 <http://flex.sourceforge.net/>
>> 71 make[1]: *** [Makefile:757: xmlif/xmlif.c] Error 127
72 make[1]: Leaving directory '/tmp/root/spack-stage/spack-stage-xmlto-0.0.28-huuygrp4qasytrezg774yavnnaxzgp2e/spack-src'
>> 73 make: *** [Makefile:584: all] Error 2
```
For example: spack install py-pyqt5 or py-pyqt6 would install pylupdate5 pyrcc5 and
pyuic5 into in python-venv's install prefix.
Fix https://github.com/spack/spack/issues/45359
* [py-configspace] fix dependency on cython
* py-cython not needed starting from 1.0.0
* added py-configspace 1.0.0 and 1.0.1
* py-configspace: fix style
* added py-configspace version 1.1.0
* added py-configspace version 1.1.1
* py-configspace: two more versions and new maintainer
* py-configspace: fixed typo
* py-configspace: added version 1.1.4
* Allow spec queries by `namespace`
Spack specs have "namespaces" that indicate what package repository they come from, but
there has not been a way to use the spec syntax to match one.
You can say things like this:
```console
spack find builtin.zlib
spack find myrepo.zlib
```
But, because namespaces are written as a dot-separated prefix on the name, you can't say
"find me all specs in namespace myrepo". The syntax doesn't allow it.
This PR allows you to specify anonymous specs with namespaces on the CLI. Specifically
you can do queries like this:
```console
spack find namespace=builtin
spack find namespace=myrepo
```
You can use this anywhere else you use spec syntax, e.g. in a config file to separate
installations based on what repo they came from:
```yaml
spack:
config:
install_tree:
root: $spack/opt/spack
projections:
namespace=myrepo: "myrepo_special_path/{name}-{hash}"
namespace=builtin: "builtin/{name}-{hash}"
```
This PR adds a special `namespace_if_anonymous` attribute to specs, which returns the
`namespace` if the spec has no name, otherwise it returns `None`. This allows us to
print the namespace for anonymous specs but to continue hiding it for most views, as
we've done so far.
This is implemented as a special case, but it's one that already exists, along with
`platform`, `os`, `target`, etc. This also reserves existing special case names for
variants so that users cannot define them in their package files. This change is
potentially breaking, but I do not think it will be common. There are no builtin
packages with a variant called `namespace`, and defining `os`, `target`, or `platform`
as a variant would've likely caused other problems if they were already being used.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* format: allow spaces in format specifiers
Key-value pair format specifiers can now contain spaces in the key. This allows us to
add spaces to format strings that are *only* present when the attribute formatted is not
``None``. Instead of writing:
```
{arch=architecture}
```
and special casing `arch=` like a sigil in `Spec.format()`, we can now write:
```
{ arch=architecture}
```
And the space is *only* printed when `architecture` is not `None`. This allows us to
remove the special case in `Spec.format()` for `arch=`.
Previously the only `key=` prefix allowed in format specifiers was `arch=`, but this PR
removes that requirement, and the `key=` part of a key-value specifier can be any name.
It does *not* have to correspond to the formatted attribute.
- [x] modify `SPEC_FORMAT_RE` to allow arbitrary keys in key-value pairs.
- [x] remove special case for `arch=` from `Spec.format()`.
- [x] modify format strings using `{arch=architecture}` to use `{ arch=architecture}`
- [x] add more tests for formatting
This PR saves other more complex attributes like compiler flags and their spacing for later.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
VC toolset versions 144 and 143 are both associated with the platform
toolset 143; this deviates from prior version choices made by the
MSVC devs; add a special case to report platform toolset version
as 143 when VC toolset version is >= 143 (this will need revisiting
for later releases).
The setSet tool (removed in version 10) has an optional dependency on readline.
The build script will use the system readline if not provided by Spack.
* dd4hep: restrict to podio@0 to prevent failures with podio@1
* acts: restrict to podio@0 to prevent failures with podio@1
* dd4hep: close when range for podio
* acts: close when range for podio
* acts: fix when range for podio
* acts: close when range for podio
* acts,dd4hep: ensure main/master still depends on podio
* Fix +rocm variant, to ensure correct dependencies on ROCm packages
and use of AMD LLVM
* Add a +pshm variant for comm=gasnet to enable fast shared-memory
comms between co-locales
* Add logic to ensure we get the native CXI libfabric network provider
on Cray EX
* Expand dependency type for package modules to encompass runtime
dependencies
* Factor logic for setting (LD_)LIBRARY_PATH and PKG_CONFIG_PATH of
runtime dependencies
* Workaround issue #44746 that causes a transitive dependency on lua
to break SLURM
* Disable nonfunctional checkChplDoc test
* Annotate some variants as conditional, to improve spack info output
and reduce confusion
---------
Co-authored-by: Dan Bonachea <dobonachea@lbl.gov>
`apple-libuuid` includes types that aren't available in other `uuid`
providers; this cause issues in consuming packages (e.g., py-matplotlib)
that use SDKs like CarbonCore.framework when they attempt to use
`util-linux-uuid` as a `uuid` provider on Mac OS.
Tweak `util-linux-uuid` to indicate that it does not provide `uuid`
on Mac OS.
This was missed in #45394 because we don't run unit tests for package PRs, and
`test_all_virtual_packages_have_default_providers`, which would've caught it, is a unit
test, not an audit.
- [x] add a default provider for `wasi-sdk` in `etc/spack/defaults/packages.yaml` (which
we require for all virtuals)
- [x] rework `test_all_virtual_packages_have_default_providers` as an audit called
`_ensure_all_virtual_packages_have_default_providers`
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* pinentry: New API
* move code around
* added back version check
* Complete check_version refactor
* Honor original handling of guis (i.e., don't try if not there)
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* upgrade apptainer: security fix
apptainer 1.3.1 has a high severity security issue: CVE-2024-3727
Upgrade to 1.3.2 or preferably 1.3.3
* added comment for 1.3.1
---------
Co-authored-by: Walter de Jong <walter.dejong@surf.nl>
* intel-oneapi-compilers: update description with current compilers
* Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
* intel-oneapi-compilers: break docstring line
---------
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
* kokkos: new test API
* kokkos: added import llnl.util.lang as lang because earlier versions couldn't be installed without it
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* povray: new test API
* capture output and test name change
* povray: add v3.7.0.10, deprecate 3.7.0.8
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* umpire: old to new test format
* umpire: old to new test method and refactor
* indentation
* black reformat
* last minute syntax
* docstring and checks
* black format
* change test name
* method call correction
* Resolve problem with stand-alone tests (or examples) not loading library (Fixes#44960)
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* sz: new test API
* fix typo; check installed executable; conform to subpart naming convention
* skip tests early if not installed; remove unnecessary "_sz" from test part names
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Library names on Windows are not typically prefixed with lib; the default
`.libs` implementation accounts for this, but `netlib-lapack` has a
custom implementation of `.libs` that did not account for this.
The `Executable` class emits a warning when you pass quoted arguments to it:
```
> spack pkg grep '"namespace"'
==> Warning: Quotes in command arguments can confuse scripts like configure.
The following arguments may cause problems when executed:
"namespace"
Quotes aren't needed because spack doesn't use a shell. Consider removing them.
If multiple levels of quotation are required, use `ignore_quotes=True`.
```
This is to warn new package authors who aren't used to calling build commands in python.
It's not useful for `spack pkg grep`, where we really are passing args on the command
line, and if we pass a quoted string, we probably meant to.
- [x] make `ignore_quotes` an instance variable, not just an argument to ``__call__`
- [x] set `ignore_quotes` to `True` in `spack pkg grep`
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* package/linux-pam: dependencies
* Adding variants to linux-pam
* Updating linux-pam variants
* Fixing variants for linux-pam after testing
* clean up flag handling
* clean up terrible tabs
* cant use default_args for compiler dependencies
* Change selinux to off by default
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Adding new versions and compilation conflict for nodejs
* Update failed version for gcc14
* Updating conflicts notes for correctness/clarity/format
* Applying spack-ized versions of fix in https://github.com/nodejs/node/issues/52223 to adddress CI failures
* Update fix-old-glibc-random-headers.patch
* Update package.py
* Update fix-old-glibc-random-headers.patch
* Update fix-old-glibc-random-headers.patch
* Adding conflict for older glibc
* Fixing patch for older systems, need to undef
* Removing overly strict conflicts
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Several tests can be enabled on Windows with no changes to logic
(either the test logic or logic being tested)
* Test for `spack location` requires modification of the test logic,
but with a minor change can be enabled on Windows
using self.compiler.cc_pic_flag here results in these errors:
==> sqlite: Executing phase: 'install'
==> Error: AttributeError: 'AutotoolsBuilder' object has no attribute 'compiler'
change it to self.pkg.compiler.cc_pic_flag instead.
* imoroved-rdock: new test API
* Make test subpart names and or descriptions more accurate
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* e4s ci: enable some disabled specs
* comment out cp2k +cuda due to unsupported cuda_arch
* comment out dealii+cuda due to concretize error
* work through concretize errors
* e4s: comment out failing builds
* e4s stack: disabled non-building specs
* comment out failing specs
* comment out failing specs
* cleanup comments
* rust: rework external find to require both rustc and cargo
* rust: handle unable to parse version
* [@spackbot] updating style on behalf of wdconinc
* rust: not x or not y -> not (x and y)
Co-authored-by: Alec Scott <hi@alecbcs.com>
* rust: pick first rustc found
Co-authored-by: Alec Scott <hi@alecbcs.com>
* rust: list comprehensions
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Alec Scott <hi@alecbcs.com>
* libmesh: add missing v1.7.1 release
* libmesh: avoid pulling in petsc if only +mpi or +metis is given
* libmesh: add shared variant
Co-authored-by: rbberger <rbberger@users.noreply.github.com>
The "use_store" context manager is used to swap the value
of a global variable (spack.store.STORE), while keeping
another global variable consistent (spack.config.CONFIG).
When doing that it tries to evaluate the previous value
of the store, if that was not done already. This is wrong,
since the configuration might be in an "intermediate" state
that was never meant to trigger side effects.
Remove that operation, and add a unit test to
prevent regressions.
Add language dependencies `c`, `cxx`, and `fortran`.
These `depends_on` statements are auto-generated based on file extensions found
in source tarballs/zipfiles.
The `# generated` comment can be removed by package maintainers after
validating correctness.
* detray: new package
This commit adds the detray package, a detector description library for
HEP experiments that is designed to be GPU-friendly.
* Update var/spack/repos/builtin/packages/detray/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/detray/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* vasp: add new version 6.4.3 and rework package
* vasp: remove redundant cuda dep
* vasp: bump fftlib variant version restriction
* vasp: honor the still existing scalapack variant
---------
Signed-off-by: Shane Nehring <snehring@iastate.edu>
Since the the MetaPathFinder now owns a lazily constructed RepoPath object, we need to deserialize environments before the package that needs to be restored. Before we were relying on globals to be inconsistent in a way that let the entire process go.
The patch which enables icx/ifx compilers is only added for `wrf@4.4:`. This PR prints a useful message at concretization time instead of failing the installation later on.
Co-authored-by: stephenmsachs <stephenmsachs@users.noreply.github.com>
* slate: changed from old to new format
* make code tighter
* replace assert method
* SkipTest plus other cleanup
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* vecmem: add infrastructure for working with SYCL
The vecmem package uses an unorthodox build system where, instead of
expecting a SYCL-capable compiler in the `CXX` environment variable, it
expects one in `SYCLCXX`. It also needs the correct SYCL flags to be
set. This commit adds a custom build environment for the vecmem package
which allows it to be built in this way. I've also added an extra CMake
flag to ensure that the build system doesn't download any unwanted
dependencies.
* Update var/spack/repos/builtin/packages/vecmem/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
- Add explicit conflict on ppc64le for 12.5 and newer.
- Update/fix intel compiler conflict to reflect that intel@2021 is compatible
only since 11.4.1 and not since 11.1.1.
- Add intel compiler conflicts to reflect strict support matrix since
12.2.0.
As discussed in https://github.com/spack/spack/pull/44881#issuecomment-2218411735 a `spack install py-globus-cli` fails to concretize on an Ubuntu 22.04 under Windows WSL2 because of too strict of explicit dependencies.
Let's try to remove them here (since these are "just in case" and in all honesty should be handled by `py-globus-sdk` anyways).
* Now builds with latest fmt release (11.0.1)
* Missing array include in nem_spread
* Fix timestep conssitency check in file-per-rank case if one or more dbs have no timesteps.
If an external happens to be a provider of anything, the solver would
set its weight to 0, meaning that it is most preferred, even if
packages.yaml config disagrees.
That was done so that `spack external find mpich` would be sufficent to
pick it up as mpi provider.
That may have made sense for mpi specifically, but doesn't make sense
for other virtuals. For example `glibc` provides iconv, and is an
external by design, but it's better to use libiconv as a separate
package as a provider.
Therefore, drop this rule, and instead let users add config:
```
mpi:
require: [mpich]
```
or
```
mpi:
buildable: false
```
which is well-documented.
This change makes `spack external find --not-buildable` mark virtuals
provided by detected packages as non-buildable, so that it's sufficient
for users to let spack detect say mpich and have the concretizer pick it
up as mpi provider even when openmpi is "more preferred".
Consistently with ArmPL@24:, the include directory for acfl@24:
has changed to include. The change wants to update to this change
and distinguish the include path for releases previous to 24.04
and the future ones
* rocm-cmake: changed test format from old to new
* Rename cmake variable
* post-conflict resolution: remove remaining version check
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Added Release 0.0.4 and 0.0.5
* Changed requirement for gotcha
use gotcha 1.0.5 for 0.0.2 and 0.0.3
* Combine gotcha 1.0.7 for master and develop
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
in case of inheritance the static tags prop may be updated multiple
times, and it turns out builder classes magically inherit from
traditional package classes
While trying to build packages with the OneAPI compiler version 2024.1 I
ran into the following error, indicating that the compiler is unable to
find some necessary libraries:
```
/storage/Software/oneapi/2024.1/compiler/2024.1/bin/sycl-post-link: error
while loading shared libraries: libonnxruntime.1.12.22.721.so: cannot open
shared object file: No such file or directory
icpx: error: unable to execute command: No such file or directory
icpx: error: sycl-post-link command failed due to signal (use -v to see
invocation)
```
Indeed, `libonnxruntime.1.12.22.721.so` does come bundled with the
OneAPI compiler, but it is not available in the build environment by
default. In this commit, I update the custom environment created by
OneAPI to include the `lib/` directory in which these libraries reside
in the `LD_LIBRARY_PATH` environment variable.
In my enthusiasm to add dfelibs to Spack, I didn't realise that the
unit tests of dfelibs use Boost and, as such, Boost is required as a
testing dependency.
Originally if you had `x -> y -> z`, and an env with `x` in its speclist that is concretized but not installed, then `spack find -c y` would not show anything. This was intended: `spack find` has up-until-now only ever listed out installed specs (and `-c` was for adding a preamble section about roots).
This changes `spack find` so:
* `-c` makes it search through all concretized specs in the env (in a sense it is anticipated that a concretized environment would serve as a "speculative" DB and users may want to query it like they query the DB outside of envs)
* Adds a `-i/--install-status` option, equivalent to `-I` from `spack spec`
* Shows install status for either `-c` or `-i`
* As a side effect to prior point, `spack find -i` can now distinguish different installation states (upstream/external)
Examples:
```
$ spack find -r
==> In environment findtest
==> 1 root specs
- raja
==> 6 installed packages (not shown)
==> 12 concretized packages to be installed (not shown)
```
```
$ spack find
==> In environment findtest
==> 1 root specs
- raja
-- darwin-ventura-m1 / apple-clang@14.0.3 -----------------------
berkeley-db@18.1.40 bzip2@1.0.8 diffutils@3.10 gmake@4.4.1 gnuconfig@2022-09-17 libiconv@1.17
==> 6 installed packages
==> 12 concretized packages to be installed (show with `spack find -c`)
```
```
$ spack find -c
==> In environment findtest
==> 1 root specs
- raja
-- darwin-ventura-m1 / apple-clang@14.0.3 -----------------------
[+] berkeley-db@18.1.40 [+] bzip2@1.0.8 - cmake@3.29.4 [+] diffutils@3.10 [+] gmake@4.4.1 [+] libiconv@1.17 - nghttp2@1.62.0 - pkgconf@2.2.0 - readline@8.2
- blt@0.6.2 - camp@2024.02.1 - curl@8.7.1 - gdbm@1.23 [+] gnuconfig@2022-09-17 - ncurses@6.5 - perl@5.38.2 - raja@2024.02.2 - zlib-ng@2.1.6
==> 6 installed packages
==> 12 concretized packages to be installed
```
$ spack -E find
...
==> 82 installed packages
```
* Add py-datasets version 2.20.0
* Add dependency requirements for version 2.20 + refactor
* Add missing tqdm and requests versions and to install latest py-datasets
* Add missing python requirements for 2.8.0 and 2.20.0
Fix a bug where Spec.tree with cover=nodes reduces deptypes from all
in-edges, including from nodes not reachable from the root, which almost
always happens for concrete specs
`Spec.__getitem__` queries dependent edges, which almost always point to
nodes outside the sub-dag considered. It should only ever look at edges
being traversed.
When using a newer Clang for Kokkos than supported by a given CUDA version, the
CUDA compiler detection in Legion's CMake still needs to be passed
CMAKE_CUDA_FLAGS to pass the compiler check.
This modifies heuristic to decay to clingo default
over time. The hope is that this helps with specs
that have an optimal solution with a high penalty.
Let target and compiler heuristic decay too, do not
guess compiler
* dfelibs: new package
This commits adds the `dfelibs` package, which is an Acts project fork
of dfelibs.
* dfelibs: docstring typo
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Add MatrixSwitch package
Add libOMM package
Use libOMM as external in ELSI
Add include paths for all libraries
Fortran modules need one directory up (can't use libs.directories since they are just the include/ directories)
This addresses a few issues in the kentutils package:
- Issue #44372
- Cleaning up formattting and styles
- Removing old versions that are not avaialble anymore
- Removing newer versions that are also not available anymore
- The installer does not install the static libs
that are expected by packages that depend on kentutils
- There are conflicts and less-than-desirable dependencies
that can be addressed via variants
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Bumping up to ROCm 6.1.2
* Bump up rocmlir & amdsmi to 6.1.2
* Removing llvm dependency from amdsmi
* Removed redundant for loops and brought rocm-cmake in for loop
* Removing version check of deprecated versions
This adds spack.util.spack_yaml.anchorify, which takes a non-cyclic
dict/list structure, and replaces identical values with (back)
references to the first instance, so that yaml serialization will use
anchors.
`repr` is used to identify sub-dags, which in principle is quadratic
complexity in depth of the graph, but in practice the depth is O(1) so
this should not matter.
Then this is used in CI to reduce the size of generated YAML files to
30% of their original size.
* lammps: add new versions
* lammps: add directories for plugins
* lammps-example-plugin: new package
Example illustrating how to install a LAMMPS plugin, based on the
example part of the LAMMPS distribution.
If netlib-lapack is built with ~external-blas, it internally links
liblapack.so with libblas.so, meaning that whenever netlib-lapack is
used as a lapack provider, the package must also be a blas provider.
Conversely using netli-lapack as a blas provider does not imply that it
also must provide lapack, but nothing is lost disallowing that...
In practice people don't care about having their build dependencies reinstalled with say cflags=-O3 if that is what is set at the input spec, so restrict propagation to link/run deps only.
Also simplify the encoding in asp.
* Changed test method from old method to new method
* Corrected test name and added docstring
* Split test method into stand alone-tests
* Added SkipTest
* code refactor
* removed repeated code
* Remove exe from test part purpose
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Improve proj version selection to avoid too new of a proj with older api usage in vtk9
* Proj constraint range around 8.2.1
---------
Co-authored-by: John Parent <john.parent@kitware.com>
Fix the following on Windows:
* `spack load --list` (this printed 0 packages even if packages were
loaded)
* `spack unload <package>` (this said that the package is not loaded
even if it was)
Update unit tests for `spack load` to also run on Windows (specifically
for ".bat"). This involved refactoring a few tests to parameterize
based on whether the unit tests are being run on a Windows system
(and to account for batch syntax).
* Adding additional versions to plink2 and switching to tarballs to allow for better version detection in the future
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
The pcluster pipeline runs spack external find and autodetects the most ancient of zlib versions on the system: 1.2.7, release date May 3, 2012.
Turns out some packages require parts of the zlib api added within the last decade.
* update e4s stacks
* adios2 +rocm: disable kokkos due to spack issue #44832
* comment out mgard+cuda due to spack issue #44833
* comment out cabana, legion, arborx due to kokkos spack issue #44832
* comment out slepc, petsc due to petsc spack issue #44600
* comment out adios2+rocm due to kokkos rocm spack issue #44832
* comment out kokkos due to spack issue #44832
When we changed how to deal with errors in November,
we didn't realize that for an unconstrained choice
rule it is more important in the heuristic to guess
what is NOT in the answer set, since it will be the
majority of options.
Previously this was following automatically from what
was in the answer set, via `1 { ... } 1` cardinality
constraints.
Here we improve the heuristic and the solve time for specs.
* Patched CMakeLists.txt to find drm include at libdrm - archlinux
* Restricted usage patch to versions 34 onwards
* Update var/spack/repos/builtin/packages/rdma-core/libdrm.patch
---------
Co-authored-by: Mark Abraham <Mark.J.Abraham@gmail.com>
* Spglib: add version 2.4.0
* DLA-Future: fix +test option
* elsi
* elsi improvements
* [@spackbot] updating style on behalf of RMeli
* remove test variants
* fix ntpoly and and use externals as default
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
* py-multiqc: updating to @1.21, adding new dependency py-pyyaml-env
* Correcting dependencies
* Drop matplotlib depends_on() for versions of multiqc not included in package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
* Allow zlib to find external installations.
* Apply suggestions from code review
* Fixed the determine_version function to loop over all of the potential
libraries that could be installed by zlib.
---------
Co-authored-by: John W. Parent <45471568+johnwparent@users.noreply.github.com>
* Update hohqmesh and feq-parse versions
Update feq-parse homepage to new documentation page
Update feq-parse license to be consistent with 2.2.2 release
---------
Co-authored-by: fluidnumerics-joe <fluidnumerics-joe@users.noreply.github.com>
This commit adds new versions of actsvg. I have also taken the liberty
of adding myself a maintainer as I work actively on the ACTS project and
its dependencies, and would like to start keeping the Spack specs more
up to date.
* e4s external rocm ci: bump rocm stack to v6.1.1
* comment out exago+rocm due to issue with raja@0.14.0 see spack issue #44593
* comment out adios2+rocm due to spack issue #44594
* comment out petsc+rocm due to spack issue #44600
* comment out sundials+rocm due to spack issue #44601
* comment out slepc+rocm due to petsc spack issue #44600
* comment out tau+rocm due to spack issue #44659
* comment out ecp-data-vis-sdk due to spack issue #44745
* packages: register rocm-core as external
* re-enable tau due to issue #44659 having been resolved
* use latest ci image: ecpe4s/ubuntu22.04-runner-amd64-gcc-11.4-rocm6.1.1:2024.06.17
* comment out paraview due to spack issue #44745
* comment out ecp-data-vis-sdk +vtkm due to issue https://gitlab.spack.io/spack/spack/-/jobs/11632511
* Update for 2.0.1
* cloudpickle dependency is only 'run'
* Follow new formatting guidelines
* black wants trailing commas
* Simplified version ranges, as recommended by @tldahlgren
* vtk-m: Changed test method names and skipping non-applicable tests from old to new approach
-----
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* add cray detection taken from upcxx
* add CUDA/ROCm support
* add numerous pass-through options to Chapel build,
like gpu_mem_strategy, comm_substrate, etc.; all variants are
translated to analogous CHPL_* environment variables. As a side
effect, this defines a number of environment variables that are
not actually used by Chapel.
* Define LD_LIBRARY_PATH, LIBRARY_PATH, and PKG_CONFIG_PATH to
help programs built with Chapel properly locate needed runtime
dependencies
---------
Co-authored-by: bonachea <dobonachea@lbl.gov>
* Projsync needs curl
This fixes a proj compilation error from paraview
* tiff does not set TIFF_INCLUDE_DIR tested by proj
* TIFF patch exists for proj 9.2
* Add comments with location of proj patch
* Use TIFF patches for different cmake versions
* Use modules starting cmake 3.28 and variables before that
* Fix black style
* Simpler patches, add newer proj
* Remove duplicated flag
* Deprecate PROJ 4.8 and older
* Remove PRIVATE
* Deprecate PROJ 7.0.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Not sure why I had this here, as `/bin/sh` will find the first spack in `PATH` just like
`env`.
- [x] remove `/usr/bin/env` and avoid an extra process launch.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
* omega-h: reformatted from old test method to new test method
* omega-h: added proper output checking
--------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
The ``+cluster` variant requires there be an MPI family known in the
spec. When using externals it is easy to miss-configure this requirement
leading to a runtime exception which is not desirable. This converts the
exception to a package rule.
* xorg libs: new versions
* xorg pkgs: update homepage from cgit to gitlab
* xorgs pkgs: fix homepage since, yeah, I did edit those 122 files by hand...
* libxmu: don't need the .0 patch version here
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Fixed some issues with installation breaking due to mysql_client
* Remove debugging details
* Adding client_only to deps
* Adding client_only to variant and deps
* Undoingw client_only to variant and deps
* py-pyopengl: new simple package
* py-pyopengl: Fix typo in comment
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pyopengl: add variants and dependencies
* py-pyopengl: build from source and improve variants
* py-pyopengl: use corrected freeglut libs
* py-pyopengl: update copyright
* py-pyopengl: remove duplicate conflict clause
* py-pyopengl: change dependency to link
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Core change: logic for extracting RPATHs from modules may return
`None`: filter this out of the set of RPATHs that is auto-generated
* Core change: `CachedCMakePackage` no longer adds ldflags to
`CMAKE_STATIC_LINKER_FLAGS`: generally these flags are not appropriate
for static linking (e.g. invocation of `ar`)
* [mfem] Add version 4.7
* [mfem] Add variant for precision (single/double). Enforce consistency
for precision amongst mfem and hypre/petsc/mumps dependencies
* [mfem] Add cxxstd (and related constraints preventing use of
old cxxstd values for newer versions of some dependencies)
* [hypre] In line with prior point, added support for specifying
precision
* [petsc] Add config option to avoid error when building against
`superlu-dist+rocm`
* [hiop] add proper `raja`/`umpire`/`camp` version constraints for
`hiop` versions 0.3.99-0.4.x; require `+raja` for `+rocm`, and
add dependency on `hiprand` for `+rocm`
* [butterflypack, mfem, strumpack, suite-sparse] Require
`CRAYLIBS_{target-family}` env var to be defined
* [suite-sparse] versions `@7.4:` changed install location of headers:
add symlink from old location to new location
* [zlib-ng] Fix error where shared libs were not successfully built for
`%cce@17` (the build did not fail, but the finished `zlib-ng%cce@17`
install did not have shared libs)
* suite-sparse library path can be lib or lib64
* fixing style check error
* Adding the missing import os
* Style check error fix
* Updating patch for 6.1.0 with correct lib path
* Preserve higher weight for CLI git ref versions
Currently the concretizer fails if you reuse a git ref version
that has already been installed but modify the spec at all.
See #38484 for futher diagnosis
The issue here is that since there is no established provenance for
these versions the highest weight they are currently assigned is
that of prior install. Re-use checks then fail because the weight of
the version is identical to the solver.
Ironically, these versions are given the highest weights possible when
specified on the CLI for the first time. They should only appear in a
DAG if they are an exact match or if the user specifies them at the CLI.
Therefore it makes sense to preserve their higher ordering.
Getting this right is critical to moving all branch based versions to a pinned
git-ref in the future.
* [@spackbot] updating style on behalf of psakievich
* Update lib/spack/spack/solver/asp.py
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Add provenance specific to git ref installs
* Sensitvity to name that I could not track down
* Add regression test
* Adjust test
* Add prefer standard unit-test
* Style
* Add required mock
* Format and mark
* Make unit-test case reproduce CLI investigation
* Remove unnecessary mock package
* [@spackbot] updating style on behalf of psakievich
* Use already developed fixture
* Add zlib-ng to mocks again
* Remove accidental adds
* Remove maintainer
* [@spackbot] updating style on behalf of psakievich
* Rename test file
* [@spackbot] updating style on behalf of psakievich
* Remove unused imports
* Update tests
* [@spackbot] updating style on behalf of psakievich
* Style
* Update lib/spack/spack/test/concretize.py
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Update solver rule
* Duplicate installed rules for installed_git_version
* Revert "Duplicate installed rules for installed_git_version"
This reverts commit 17223fc8d1.
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
* libdistributed: renamed test to check_test
* libpressio-rmetric: renamed test method
* libpressio-tools: renamed test method
* Renamed build-time test methods for: libpressio-opt, libpressio-tthresh, opened
---------
Co-authored-by: Jackson Peter Lawrence <lawrence31@borax5.llnl.gov>
* Provide instructions for building a developmental version of lcov.
* style fix
* style fix
* Promote single version git URL to the package level.
* Formatting fix.
* verilator: Some environment varibles are no longer required
* Revert depends_on for flex back to the deafult case
* Use decorator, when, for setup_run_environment insdtead of if inside function
* libtiff: add v4.6.0 and default disable opengl (#44545)
* libtiff: Fix typo in CMake key
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* libtiff: Broader description of OpenGL variant
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* libtiff: reformat using spack style black recommendation
* libtiff: couple opengl flag with autotools
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
There hasn't been a release in almost a decade, and build failures with
GCC 14 were reported. I don't think it makes sense to patch it, since
the project moved over to `util-linux`, and Spack's default provider is
that package. Better to just get rid of it in the next Spack release.
* py-your: new package
Spack package recipe for YOUR, Your Unified Reader. YOUR processes pulsar data in different formats.
Output below from spack install py-your
spack install py-your
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/pcre-8.45-33dfhul
[+] /opt/apps/spack/libpciaccess-0.17-2qdxdjo
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/qhull-2020.2-klc7ewb
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/alsa-lib-1.2.3.2-a7icjdy
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/yasm-1.3.0-v4etmmm
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/unzip-6.0-mqftjtp
[+] /opt/apps/spack/libjpeg-turbo-3.0.0-vjvivme
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/libpng-1.6.39-kiuku4y
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/swig-4.0.2-fortran-z3sbnze
[+] /opt/apps/spack/binutils-2.42-vkjcvfr
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/hdf5-1.14.3-sbuiw6q
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/ffmpeg-6.1.1-2vhrbda
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/freetype-2.13.2-in4taxi
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/hwloc-2.9.1-fhoz6al
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/lua-5.3.6-47356ia
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/elfutils-0.190-uswzaiw
[+] /opt/apps/spack/py-pytz-2023.3-ojdlhrd
[+] /opt/apps/spack/py-cycler-0.11.0-b7mjvv7
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/llvm-14.0.6-3nosumn
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-six-1.16.0-iv6iv3q
[+] /opt/apps/spack/py-pybind11-2.12.0-5rvupjv
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-pyparsing-3.1.2-fq6imlt
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
[+] /opt/apps/spack/py-llvmlite-0.41.1-qom3l5h
[+] /opt/apps/spack/py-astropy-4.0.1.post1-xbojixg
[+] /opt/apps/spack/py-python-dateutil-2.8.2-kzdfskc
[+] /opt/apps/spack/py-numexpr-2.8.4-fc5xc5s
[+] /opt/apps/spack/py-h5py-3.11.0-y6drk3j
[+] /opt/apps/spack/py-tifffile-2023.8.30-oof4try
[+] /opt/apps/spack/py-pygments-2.16.1-stgrccl
[+] /opt/apps/spack/py-mdurl-0.1.2-nqk43ry
[+] /opt/apps/spack/py-scipy-1.13.0-vxjgfov
[+] /opt/apps/spack/py-contourpy-1.0.7-jg5lhss
[+] /opt/apps/spack/py-pillow-10.3.0-ijh2cju
[+] /opt/apps/spack/py-kiwisolver-1.4.5-vdh5sq5
[+] /opt/apps/spack/py-fonttools-4.39.4-x5ydbox
[+] /opt/apps/spack/py-bottleneck-1.3.7-ztsm4lg
[+] /opt/apps/spack/py-lazy-loader-0.4-k7hgvka
[+] /opt/apps/spack/py-numba-0.58.1-hzvrjwj
[+] /opt/apps/spack/py-markdown-it-py-3.0.0-l4p4qv5
[+] /opt/apps/spack/py-imageio-2.34.0-z5hu4yc
[+] /opt/apps/spack/py-matplotlib-3.8.4-azq2fzm
[+] /opt/apps/spack/py-pandas-1.5.3-p3gnh6t
[+] /opt/apps/spack/py-rich-13.4.2-okhgwwz
[+] /opt/apps/spack/py-networkx-3.1-b54br7r
[+] /opt/apps/spack/py-scikit-image-0.23.2-cvyzh3t
==> Installing py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x [83/83]
==> No binary for py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x found: installing from source
==> Fetching https://github.com/thepetabyteproject/your/archive/refs/tags/0.6.7.tar.gz
==> No patches needed for py-your
==> py-your: Executing phase: 'install'
==> py-your: Successfully installed py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x
Stage: 1.43s. Install: 0.99s. Post-install: 0.12s. Total: 3.12s
* Removed setup_run_environment
After some testing, both spack load and module load for the package will include the bin directory generated by py-your as well as the path to the version of python the package was built with, without the need for the setup_run_environment function.
I removed that function (Although, like Tamara I thought it would be necessary based on other package setups I used as a basis for this package).
Note: I also updated the required version of py-astropy from py-astropy@4.0: to @py-astropy@6.1.0: In my test builds, the install was picking up version py-astropy@4.0.1.post1 and numpy1.26. However when I tried to run some of the code I was getting errors about py-astropy making numpy calls that are now removed. The newer version of py-astropy corrects these. Ideally this would be handled in the py-astropy package to make sure numpy isn't too new
#40773 introduced python-venv, which improved build isolation and avoids issues with,
e.g., `ubuntu`'s system python modifying `sysconfig` to include a (very unwanted)
`local` directory within the default install layout.
This addresses a few cases where #40773 removed functionality, without harming the
default cases where we use `python-venv`.
Traditionally, *every* view with `python` in it was essentially a virtual environment,
because we would copy the `python` interpreter and `os.py` into every view when linking.
We now rely on `python-venv` to do that, but only when it's used (i.e. new builds) and
only for packages that have an `extends("python")` directive.
This again makes every view with `python` in it a virtual environment, but only
if we're not already using a package like `python-venv`. This uses a different
mechanism from before -- instead of using the `virtualenv` trick of copying `python`
into the prefix, we instead create a `pyvenv.cfg` like `venv` (the more modern way
to do it).
This fixes two things:
1. If you already had an environment before Spack `v0.22` that worked, it would
stop working without a reconcretize and rebuild in `v0.22`, because we no longer
copy the python interpreter on link. Adding `pyvenv.cfg` fixes this in a more
modern way, so old views will keep working.
2. If you have an env that only includes python packages that use `depends_on("python")`
instead of `extends("python")`, those packages will now be importable as before,
though they won't have the same level of build isolation you'd get with `extends`
and `python-venv`.
* views: avoid making client code deal with link functions
Users of views and ViewDescriptors shouldn't have to deal with link functions -- they
should just say what type of linking they want.
- [x] views take a link_type, not a link function
- [x] views work out the link function from the link type
- [x] view descriptors and commands now just tell the view what they want.
* python: simplify logic for avoiding pyvenv.cfg in copy views
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
In #30882, we made Spack ignore `-Werror` calls so that it could more easily build
projects that inject `-Werror` into their builds. We did this by translating them to
`-Wno-error` in the compiler wrapper. However, some compilers (like `nvhpc`) do not
support `-Wno-error`. We need to exclude them from this feature until they do.
- [x] make a property on `PackageBase` for `keep_werror` that knows not to use it for
`nvhpc`.
- [x] update property so that it keeps only the specific `-Werror=...` args for newer nvhpc's,
which support `-Wno-error` but not `-Wno-error=...`
---------
Co-authored-by: William Mou <william.mou1024@gmail.com>
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
When Spack concretizes environments, it prints every (newly concretized) root spec
individually with all of its dependencies. For most reasonably sized environments, this
is too much output. This is true for three commands:
* `spack concretize` when concretizing an environment with newly added specs
* `spack install` when installing an environment with newly added specs
* `spack spec` with no arguments in an environment
The output dates back to before we had unified environments or nicer spec traversal
routines, and we can improve it.
This PR makes environment concretization output analogous to what we do for regular
specs. Just like `spack spec` for a single spec, we show all root specs with no
indentation, so you can easily see the specs you explicitly requested. Dependencies are
shown:
1. With indentation according to their depth in a breadth-first traversal starting at
the roots;
2. Only once if they appear on paths from multiple roots
So, the default is now consistent with `spack spec` for one spec--it's `--cover=nodes`.
i.e., if there are 100 specs in your environment, you'll get 100 lines of output.
If you want to see more details, you can do that with `spack spec` using the arguments
you're already familiar with. For example, if you wanted to see dependency types and
*all* dependencies, you could use `spack spec -l --cover=edges`. Or you could add
deptypes and namespaces with, e.g. `spack spec -ltN`.
With no arguments in an environment, `spack spec` concretizes (if necessary) and shows
the concretized environment. If you run `spack concretize` *first*, inspecting the
environment repeatedly with `spack spec` will be fast, as everything is already in the
`spack.lock` file.
- [x] factor most logic of `Spec.tree()` out of `Spec` class into `spack.spec.tree()`,
which can take multiple specs as roots.
- [x] make `Spec.tree()` call `spack.spec.tree()`
- [x] `spack.environment.display_specs()` now uses `spack.spec.tree()`
- [x] Update `spack concretize`
- [x] Update `spack install`
- [x] Update `spack spec` to call `spack.spec.tree()` for environments.
- [x] Continue to output specs individually for `spack spec` when using
`--yaml` or `--json`
* Apply patch from upstream to allow vtk compilation with %gcc 12 and 14.
* Fixes#44331
* fix soec usage
* fix compiler version range
* Finalize version range, switch to .diff file
---------
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
* Now need to explicitly depend on libfabric for Cray EX
* Ensure build uses the selected CUDA and ROCm versions
* Correct spelling on `configure --with-ldflags`
* Patch a defect regarding `configure --with-ldflags`
* Default to Spack's copy of GASNet-EX, which is newer than embedded
e2fsprogs: adding version 1.47.0 and fuse2fs variant
fuse-overlayfs: adding version 1.13
squashfuse: adding version 0.5.1 and 0.5.2
e2fsprogs: fixing audit errors
apptainer: expanding deps to cover more versions, fix binary_path logic.
apptainer: add go version deps, fix e2fsprogs patch sums, rework dep paths
fuse-overlayfs: tightening up the libfuse dep
Signed-off-by: Shane Nehring <snehring@iastate.edu>
* util-macros: ensure url_for_version only used for older versions
* util-macros: use url.substitute_version after xz -> bz2
* util-macros: mv url_for_version down the file
`BuildcacheBootstrapper` uses `Spec.intersects` to match specs needed
for bootstrapping against the binary cache. The specs were not
sufficiently-detailed to prevent matching e.g. cached binaries for
Mac OS on Windows; this commit adds the platform to each requested
bootstrap spec to prevent that.
* initial commit for RoCm-6.1.1 release
* fix style issues
* update the version for rocmlir and rocm-cmake
* restrict the patch for 6.0.0 release
* fix build failure for hipsolver-6.1.1 release
* update the hipblaslt for rocm-6.1.1 release
* add the patch for hipsparselt for 6.1.1 rel
Remove support for `cray` as a separate platform.
Any platform previously detected as `cray` is now detected as `linux`.
Users who still need platform=cray have to stick to Spack 0.22
Fixes a bug in the concretizer where specs depending on a host
incompatible libc would be used. This bug triggers when nothing is
built.
In the case where everything is reused, there is no libc provider from
the perspective of the solver, there is only compatible_libc. This
commit ensures that we require a host compatible libc on any reused
spec, additionally to requiring compat with the chosen libc provider.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Patch to add hsa prefix/include path:wq
* Style check error fix
* The patch need to be applied to 2024.01.stable. ROCm 6.0 requires hpctoolkit 2024.01.1 or later
* Fixing style chec error
* Adding a py4j variant that requires Java via spack to avoid situations where a system doesn't have Java and py4j expects it
* Adding new versions of py-pyspark
* Adding a new variant to require java (via py4j) and clean up dependency handling
* Adding myself as a maintainer for py-pyspark and py-py4j
* Fix overlooked version bump in py4j
* Version bump to meet py-spark expectations
* Version bump to add latest compatibile version with pyspark
* Matching py-grpcio bump
* Adding variants and dependents for pyspark
* Adding runtime deps
* Changing default java requirement. I'm not sure this is the right call
* Changing py4j with java dependency handling
* Fix style
* Update package.py fix unnecessary f-strinh
* Make +java the default for both
* Fix nested deps
* Revert styles after default change
* Added new versions and GCC 14 compatbility conflicts
* Added new versions and compatibility conflicts for gcc 14
* Added new versions paired to arrow (for gcc14 compat)
* Update py-protobuf compiler conflict
* Update depends to match
See https://github.com/grpc/grpc/blob/master/src/python/grpcio_status/setup.py
* Updating dependencies and conflicts for py-googleapis-common-protos. Added new version to avoid future issues
* Remove upper bound version on py-protobuf and add default_args
* Adding new versions and updating dependencies back to versions 1.35.0
* Updating oldest numpy deps
* Fixing merge
* bit more cleaniness for var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py
* Adding latest matching version of py-grpcio and py-grpcio-status
* Update package.py
https://github.com/spack/spack/pull/44263#discussion_r1612317943
* Update dependencies
* Adding additional versions for dependent packages. Deprecated two versions: 1.16 is old, built for python ~3.6, and does not build for 3.8. 1.52.0 was removed from pypi
* Revert py-grpcio-tools changes. Will include in separate PR
* Adding patches and constraints to get 1.48 to build as it's a dependency that is called out for some other packages
* Updating to account for yanked packages for dependencies
* Fix style
* Update sha256 for py-grpcio v0.16.0 to reflect change
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* py-astropy: Add version 6.1
Added build info for version 6.1 in py-astropy. Requires a new additional package, astropy-iers-data which has been included as py-astropy-iers-data to match with spack's general naming conventions.
Below is the output of the spack install showing successful build fro version 6.1 and the new py-astropy-iers-data package
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/libyaml-0.2.5-fxathvq
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/pcre2-10.42-fu62kky
[+] /opt/apps/spack/libunistring-1.2-whrov3e
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/berkeley-db-18.1.40-jftva2u
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/libidn2-2.3.7-vnie4rz
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/perl-5.38.0-gzljgek
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/krb5-1.20.1-tqiapsx
[+] /opt/apps/spack/py-pyyaml-6.0-rju7jls
[+] /opt/apps/spack/py-tomli-2.0.1-eanxpu2
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/openssh-9.7p1-jxrkzso
[+] /opt/apps/spack/py-pyerfa-2.0.0.1-kyfazhs
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-typing-extensions-4.8.0-ujwbb6g
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
[+] /opt/apps/spack/git-2.45.1-tuc5jnb
[+] /opt/apps/spack/py-cython-3.0.0-zx62ssd
==> Installing py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj [52/55]
==> No binary for py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj found: installing from source
==> No patches needed for py-astropy-iers-data
==> py-astropy-iers-data: Executing phase: 'install'
==> py-astropy-iers-data: Successfully installed py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj
Stage: 1.74s. Install: 0.93s. Post-install: 0.52s. Total: 3.36s
[+] /opt/apps/spack/py-astropy-iers-data-main-ukchsfz
[+] /opt/apps/spack/py-extension-helpers-0.1-a5hmr6j
[+] /opt/apps/spack/py-setuptools-scm-8.0.4-qdhxchg
==> Installing py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo [55/55]
==> No binary for py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/astropy/astropy-6.1.0.tar.gz
==> Ran patch() for py-astropy
==> py-astropy: Executing phase: 'install'
==> Warning: Module file /opt/modulefiles/spack/Core/py-astropy/6.1.0.lua exists and will not be overwritten
==> py-astropy: Successfully installed py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo
Stage: 1.29s. Install: 1m 5.77s. Post-install: 0.60s. Total: 1m 7.94s
* Removed extra-whitespace
A blank line had white space, removed the white space
* Additional formatting changes for black
* Additional package updates
Based on previous recommendations updated py-astropy and py-astropy-iers-data packages. Also added a new version to py-pyerfa package to match the 6.1.0 dependencies better
Of importance in these updates, I did add pypi and version info to py-astropy-iers-data. Originally I had argued that this package updates quite frequently (on a weekly basis) and so it did not make sense to include pypi/versions and we should instead use the non-version git-repo structure based on the master branch. However, when I tried to build the package py-setuptools-scm errored out when trying to build the package:
/opt/apps/spack/py-setuptools-scm-8.0.4-ax2zqro/lib/python3.10/site-packages/setuptools_scm/git.py:163: UserWarning: "/tmp/root/spack-stage/spack-stage-py-astropy-iers-data-main-iw2mdzlukb37mkcbcozjjefjoefw2eyp/spack-src" is shallow and may cause errors
I believe this is due to the download file/stage directory not containing the version and instead including the branch. I changed the package to use versions instead and it worked just fine as shown below. In addition, when I had done some preliminary testing, the package installed fine using the non-version master branch. When I checked, that installation it used py-setuptools-scm@7.1 while in this installation run it used a much more recent 8.0.4 so it is possible that somewhere between scm7.1 and 8.0.04 something changed that caused this error to show up. Since the setuptools-scm package has something to do extracting package versions, I imagine it's some kind of mismatch issue
Output from build:
spack install py-astropy
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/berkeley-db-18.1.40-jftva2u
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/libunistring-1.2-whrov3e
[+] /opt/apps/spack/pcre2-10.42-fu62kky
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/libyaml-0.2.5-fxathvq
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/libidn2-2.3.7-vnie4rz
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/perl-5.38.0-gzljgek
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/krb5-1.20.1-tqiapsx
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/openssh-9.7p1-jxrkzso
[+] /opt/apps/spack/py-tomli-2.0.1-eanxpu2
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/git-2.45.1-zu6qkoc
[+] /opt/apps/spack/py-markupsafe-2.1.3-isgtki6
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
==> Installing py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a [49/57]
==> No binary for py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a found: installing from source
==> Fetching ac8a6fe91c.tar.gz
==> No patches needed for py-extension-helpers
==> py-extension-helpers: Executing phase: 'install'
==> py-extension-helpers: Successfully installed py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a
Stage: 0.37s. Install: 0.88s. Post-install: 0.52s. Total: 1.89s
[+] /opt/apps/spack/py-extension-helpers-0.1-a5hmr6j
==> Installing py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m [50/57]
==> No binary for py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m found: installing from source
==> Fetching 350b18f967.tar.gz
==> No patches needed for py-cython
==> py-cython: Executing phase: 'install'
==> py-cython: Successfully installed py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m
Stage: 1.07s. Install: 2m 49.80s. Post-install: 0.40s. Total: 2m 51.37s
[+] /opt/apps/spack/py-cython-3.0.0-zx62ssd
[+] /opt/apps/spack/py-jinja2-3.1.2-wacpq7j
[+] /opt/apps/spack/py-typing-extensions-4.8.0-ujwbb6g
[+] /opt/apps/spack/py-pyyaml-6.0-rju7jls
[+] /opt/apps/spack/py-setuptools-scm-8.0.4-ax2zqro
==> Installing py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6 [55/57]
==> No binary for py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6 found: installing from source
==> Using cached archive: /opt/spack/var/spack/cache/_source-cache/archive/7f/7fff3d3404ae8560533ac0e685db7acc02c4d8984faa4ac3d607096879fba2d1.tar.gz
==> No patches needed for py-astropy-iers-data
==> py-astropy-iers-data: Executing phase: 'install'
==> py-astropy-iers-data: Successfully installed py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6
Stage: 0.07s. Install: 1.21s. Post-install: 0.39s. Total: 1.88s
[+] /opt/apps/spack/py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6
==> Installing py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp [56/57]
==> No binary for py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/p/pyerfa/pyerfa-2.0.1.1.tar.gz
==> No patches needed for py-pyerfa
==> py-pyerfa: Executing phase: 'install'
==> py-pyerfa: Successfully installed py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp
Stage: 0.93s. Install: 17.72s. Post-install: 0.33s. Total: 19.15s
[+] /opt/apps/spack/py-pyerfa-2.0.1.1-pkokp6u
==> Installing py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs [57/57]
==> No binary for py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/astropy/astropy-6.1.0.tar.gz
==> Ran patch() for py-astropy
==> py-astropy: Executing phase: 'install'
==> py-astropy: Successfully installed py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs
Stage: 1.16s. Install: 1m 3.34s. Post-install: 1.05s. Total: 1m 5.77s
[+] /opt/apps/spack/py-astropy-6.1.0-5brbkjn
* Updated to match with black formatting
Change the installer to take `([pkg], args)` in the constructor instead
of `[(pkg, args)]`. The reason is that certain arguments are global
settings, and the new API ensures that those arguments cannot be
different across different "build requests".
The `explicit` install arg is now a list of hashes, and the installer is
no longer responsible for determining what package is installed
explicitly. This way environment installs can simply pass the list of
environment roots, without them necessarily being explicit build
requests. For example an env with two roots [a, b], where b depends on
a, would not always cause spack install to mark b as explicit.
Notice that `overwrite` already took a list of hashes, this makes
`explicit` consistent.
`package.do_install(explicit=True)` continues to take a boolean.
* legion: add pip dependency for build
pip is needed for the build when the Legion Python binding is enabled
* legion: add variants for gc logging and system OpenMP use
This also removes the `cmake_cxx_flags` variable from `cmake_args()`
because that variable had no effect.
* [@spackbot] updating style on behalf of mpokorny
* legion: use spec.satisfies() in cmake_args()
e.g, replace use of '"+foo" in spec' with 'spec.satisfies("+foo")'
* legion: avoid configuring with multiple "-DLegion_REDOP_COMPLEX=ON" arguments
In the previous version, when both '+redop_complex' and '+bindings'
was set, two instances of "-DLegion_REDOP_COMPLEX=ON" arguments were
generated for cmake configuration.
* legion: fix value of "Legion_OUTPUT_LEVEL" for configuration
the previous version had no effect on setting the configuration value
---------
Co-authored-by: mpokorny <mpokorny@users.noreply.github.com>
The windows wrappers for basic functions like `os.symlink`,
`os.readlink` and `os.path.islink` in the `llnl.util.symlink` module
have bugs, and trigger more file system operations on non-windows than
they should.
This commit just binds `llnl.util.symlink.symlink = os.symlink` etc so
built-in functions are used on non-windows
`spack clean <spec>` will now resolve specs based on the active environment if one is active.
If an env is active but no matching spec is found, this will fall back on fully concretizing.
Before this PR, if Spack could see a possibility to reuse a spec that
doesn't match a strong preference, it would do so. After the PR, a
strong preference would take precedence.
`glibc` and `musl` provide a basic implementation of `iconv` (`iconv`,
`iconv_open`, `iconv_close`), but in practice the installation may be
missing the character encoding methods to make them usable. On Fedora
for example, users need to
```yum install glibc-gconv-extra```
to get the character encodings that `gettext` requires during configure,
namely EUC-JP. Users may not have permissions to install the missing
parts of glibc.
Since Spack can install `libiconv`, it is simpler to use that by
default.
* Spglib: add version 2.4.0
* dla-future-fortran: new package version 0.1.0
* [@spackbot] updating style on behalf of RMeli
* apply suggestion and add maintainer
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
* [emacs] When installing on Mac OS, build and install the native
Emacs.app along with the standard executables.
* [emacs] Make the GUI build on Mac optional by adding "gui" variant
* Apply reviewer suggestion
Co-authored-by: Alec Scott <hi@alecbcs.com>
* Add emacs version 29.3
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
avoid calling `spec.target` when None.
When an external compiler package has an `os` set but no `target` set, Spack
currently falls into a codepath that calls `spec.target` (which itself calls
`spec.architecture.target.Microarchitecture`) when `spec.architecture.target`
is None, throwing an error.
e.g.
```
packages:
gcc:
externals:
- spec: gcc@12.3.1 os=rhel7
prefix: /usr
```
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* glew: rework dependency on gl
This simplifies the package and ensures a single gl implementation is
pulled in. Before we were adding direct dependencies, and those are
not unified through the virtual.
* mesa-demos: rework dependency on gl
This simplifies the package and ensures a single gl implementation is
pulled in. Before we were adding direct dependencies, and those are
not unified through the virtual.
* mesa-glu: rework dependency on gl
This simplifies the package and ensures a single gl implementation is
pulled in. Before we were adding direct dependencies, and those are
not unified through the virtual.
* paraview: fix dependency on glew
* mesa: group dependency on when("+glx")
* Add missing dependency on libxml2
* paraview: remove the "osmesa" and "egl" variant
Instead, enforce consistency using the "gl" virtual that allows
only one provider.
* visit: remove osmesa variant
* Disable paraview in the aws-isc stacks
* data-vis-sdk: rework constrains to enforce front-ends
* e4s-power: remove redundant paraview
* Pipelines: update osmesa variants
* trilinos-catalyst-ioss-adapter: make gl a run dependency
Starting from 24.04, armpl-gcc will only have three packages files: dev, rpm, and macOS.
Only one version for gcc is provided, so the changes in the code reflect that the tar provided
for gcc is only one rather than many.
* Remove mesa18 and libosmesa
mesa18 was introduced in #19528 as a way to maintain the old
autotools build of mesa separate from the new meson build.
We could add a second build system to mesa, but since mesa18 has
been deprecated for a long time, we'll just remove it.
libosmesa was used to multiplex the gl provider between mesa18
and mesa, and is thus unecessary. Remove it to reduce complexity
in the graphical stack.
* Remove references to mesa18 and libosmesa
* vtk: rework dependency on gl and osmesa
* memsurfer: rework dependency on vtk
* visit: minimal fix to avoid having both osmesa and glx
* Use hdf5::hdf5 on Windows from Paraview CMake
This patch is already applied on VTK 9 or greater.
* Add comments stating that vtk and paraview patches are the same and should be modified in concert.
This fixes a bug occurring when two root specs need to select
old versions, and these versions have the same penalty in the
optimization. This sometimes caused an older version to be
preferred to a more recent one.
The issue was the omission of `PackageNode` in the optimization
tuple.
* rayleigh: new package
* Update var/spack/repos/builtin/packages/rayleigh/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* split edit into three methods
* add comments to clarify use of configure
* rayleigh: copyright year
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Use correct path separator in get_all_package_diffs for all platforms.
Ensures correct package change computation on Windows when pruning unchanged specs in Gitlab CI
* Update, fix serenity & serenity-libint
Version 1.6.1 of `serenity` is added, some dependencies are made more
explicit, some options are improved or fixed.
The url of `serenity-libint` is fixed. The old url is not reachable
anymore.
* Use upstream patch, modify cmake patch
* Update var/spack/repos/builtin/packages/serenity/package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* heimdall: Astronomy software package. Requires dedisp and psrdada (included as part of this commit)
* Updated packages to align with Spack's style
Minor updates based on wdconinc's comments regarding Spack's style guide
* [@spackbot] updating style on behalf of aweaver1fandm
* Minor edits to fix copyright year and dedisp install
Fixed copyright year to be 2024 instead of 2023
Removed the overridden version of install and created a preinstall function to create the missing lib and inc directories, therefore allowing the default install to run
Here is output from the spack install of heimdall showing successful build with cuda. If necessary I do a spack clean and freshly install it
./spack install heimdall +cuda cuda_arch=86
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libiconv-1.17-enpmbhsi3kztebwmpclpub2afhlbr3gy
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/xz-5.4.1-pte76kujkezxb3laqse3o4sctlbygsaw
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/zlib-1.2.13-utlfo5ltxz5v5bckirn5v3amtbxjdvwh
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/bzip2-1.0.8-x6navz7ucgfnb5xq7aelqmgd4zxsz5bs
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libmd-1.0.4-ncomhrodpdul4dm64o6b7426fhmc2u64
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/ncurses-6.4-c77h34rooycbzapxjvc27sg5td5jiwyb
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/zstd-1.5.5-eporpybumydxveg5rwtfzysrsu4eqzcv
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libffi-3.4.4-vskntokaojclfqxjfzkbyirkeogddbpx
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libxcrypt-4.4.33-gtpn32p6mxztul3c3dxzqj7gvcyh555j
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/util-linux-uuid-2.38.1-g322a5peqjaad6gl5q64cdu4qo7kvw6o
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libxml2-2.10.3-pza3kz2mtbncbbeim6rejfqkgftnf4rz
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/openssl-1.1.1t-adbquvgg4qpc3vq6jynf44qzq3gfwrv5
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/pigz-2.7-e7mxj4ya2u4a6zb4hu64g7docujmkxeb
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/libbsd-0.11.7-wh4xleivbe7wndiqt5nsehzlfrccnjcg
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/readline-8.2-hhb647bwmbcj7iwpmtetbylninfm5rxf
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/cuda-11.7.1-osue2sx5rv7dgzhsmaemydpwhyribxng
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/tar-1.34-35f5gki2ycxmy5zd7zs5tsvp3xoszxum
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/expat-2.5.0-4gizyhhqklciuyrbyinq2tdggt73gds4
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/gdbm-1.23-w3uzihtubj2iwv6es55fis6nt2q5zwlr
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/sqlite-3.40.1-m4ntzvuupsnbtkdfbz7oqpbjdlaffp2a
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/dedisp-1.0-pq6r3jnyxq6jzoygz3fp2e6jc2ojpvap
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/gettext-0.21.1-hglzdeadmgkzjb76bmemt6dnulfkrpha
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/python-3.10.10-khu36qq4p2te7jf475ewr2h7egidekfl
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/psrdada-master-by4w6mrpcfnoihlhos2jcfo2roiyagaz
[+] /home/htony/spack/opt/spack/linux-ubuntu22.04-zen3/gcc-11.3.0/heimdall-1.0-ohtdnltuhhejysshcert25h6nmuvluqp
* [@spackbot] updating style on behalf of aweaver1fandm
Restrict the hpcrun-fmt.txt patch to :2022. It's fixed in the code
after that, and in recent develop, some code paths have moved causing
this patch to fail.
This fixes an issue where ghcr, gitlab and possibly other container registries paginate tags by default, which violates the OCI spec v1.0, but is common practice (the spec was broken itself). After this commit, you can create build cache indices of > 100 specs on ghcr.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* pythia8: prefer 8.310
* [@spackbot] updating style on behalf of wdconinc
* pythia8: filter_file to remove sed n
* Revert "[@spackbot] updating style on behalf of wdconinc"
This reverts commit e2a3decaffbd3f464d1bd992025e1812df49f088.
* Revert "pythia8: prefer 8.310"
This reverts commit 568cb056b87129085e245d9dbef1732ee1c6c0aa.
* [@spackbot] updating style on behalf of wdconinc
* pythia8: comment for fix
* pythia8: fix style
* pythia8: filter_file with raw string because of escaped pipe
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
The release tarballs are not available anymore which means autoconf, automake and libtool are always needed.
The NVHPC specific patches don't make sense anymore being that the patched files are not distributed in the new tar files.
Add support for Gitlab CI on Windows
This PR adds the config changes required to configure and execute
Gitlab pipelines running Windows builds on Windows runners using
the existing Gitlab CI infrastructure (and newly added Windows
infrastructure).
* Adds support for generating child pipelines dispatched to Windows runners
* Refactors the relevant pre-scripts, scripts, and post scripts to be compatible with Windows
* Adds Windows config section describing Windows jobs
* Adds VTK as Windows build stack (to be expanded later)
* Modifies proj to build on Windows
* Refactors Windows rpath symlinking to avoid system libs and externals
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
Co-authored-by: Mike VanDenburgh <michael.vandenburgh@kitware.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Symlinks on Windows can use longpath prefixes (\\?\); these are fine
in the context of win32 API interactions but break numerous facets of
Spack behavior that rely on string parsing/matching (archiving,
binary distributions, tarball extraction, view regen, etc).
Spack's internal readlink method (llnl.util.symlink.readlink)
gracefully handles this by removing the prefix and otherwise behaving
exactly as os.readlink does, so we should prefer that in all cases.
* py-matplotlib: qualify when to do a post install
Older versions of py-matplotlib don't seem to have some of the
files that the post install step is trying to install.
Looks like the files first appeared in 3.6.0 and later.
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
* Change install paths for older matplotlib
---------
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add maintainer and fix linting
* allow for fewer deps in archive
* use meson for archive packages
* Fix version spec and f-string
* fix blas dependency links
* Add new release to spack
* Fix checksums for latest release
* Update version of iperf3 from 3.6 to 3.16
Spack currently only explicitly has version 3.6 of the iPerf3 package
(out of ESnet / LBNL). This makes the default the latest version of 3.16,
and adds some other versions (found in some Linux distros, for possible
compatibility purposes).
* iperf3: update to 3.17; update 3.6 hash for new url
* protobuf: update hash for patch needed when="@3.4:3.21"
* Revert "protobuf: update hash for patch needed when="@3.4:3.21""
This reverts commit 4d168d0b27.
* initial commit to enable tensorflow-2.14 for spack built ROCm
* fix style errors
* modify hipcc patch
* updates for rocm 6.1
* updates for tf-rocm-enhanced 2.16
* fix styling
* fix styling
* add patch for 2.16
* add patch for 2.16
* Update var/spack/repos/builtin/packages/py-tensorflow/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update rocm enhanced version names
* changes for rocm-enhanced version name change
* fix styling
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix gromacs installation with SVE. Issue 44062
* [@spackbot] updating style on behalf of paolotricerri
* Remove `neoverse_n2` target
We have removed the neoverse_n2 target as its detection is more involved
compared to neoverse_v*.
Set MPI_C_COMPILER etc. env vars when building with fujitsu-mpi, which
override CMake logic. Without using these variables to explicitly
request the Fujitsu MPI wrappers, the builtin CMake logic is unwilling
to use these wrappers unless the Fujitsu compiler is used, but they
should be used for %clang as well.
This avoids patching CMake module files like in #16864, primarily to
avoid the possibility of altering behavior for specs that do not use
%fj or ^fujitsu-mpi.
* Add openfoam to aws-pcluster-neoverse_v1 stack
* Add more apps to aws-pcluster-x86_64_v4 stack
* Remove WRF while hdf5 cannot build in buildcache at the moment
* Update comment
* Add more apps for aws-pcluster-neoverse_v1 stack
* Remove apps that currently do not build
* Disable those packages that won't build
* Modify syntax such that correct cflags are used
* Changing syntax again to what works with other packages
* Fix overriding packages.yaml entry for gettext
* Use new `prefer` and `require:when` clauses to clarify intent
* Use newer spack version to install intel compiler
This removes the need for patches and makes sure the `prefer` directives in
`package.yaml` are understood.
* `prefer` not strong enough, need to set compilers
* Revert "Use newer spack version to install intel compiler"
This reverts commit ecb25a192c.
Cannot update the spack version to install intel compiler as this changes the
compiler hash but not the version. This leads to incompatible compiler paths. If
we update this spack version in the future make sure the compiler version also updates.
Tested-by: Stephen Sachs <stesachs@amazon.com>
* Remove `prefer` clause as it is not strong enough for our needs
This way we can safely go back to installing the intel compiler with an older
spack version.
* Prefer gcc or oneapi to build gettext
* Pin gettext version compatible with system glibc-headers
* relax gettext version requirement to enable later versions
* oneapi cannot build older gettext version
* octave: use pcre2 for @8:
* Add 'pcre2' variant to octave to control pcre vs. pcre2
* Update var/spack/repos/builtin/packages/octave/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: Alex Richert <alexander.richert@noaa.gov>
Co-authored-by: Alec Scott <hi@alecbcs.com>
Apparently urllib can throw a range of different exceptions:
1. HTTPError
2. URLError with e.reason set to the actual exception
3. TimeoutError from getresponse, which is not wrapped
* New package: qpdf
* Update var/spack/repos/builtin/packages/qpdf/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
* Fix format of cmake_args
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
* archive: relative links only
Ensure all links written into tarfiles generated from Spack prefixes do not contain symlinks pointing outside the prefix
* binary_distribution: limit extraction to prefix
Ensure files extracted from spackballs are not links pointing outside of the prefix
* Ensure rpaths are properly set on Windows
* hard error on extraction of absolute links
* refactor for non link-modifying approach
* Restore tarball extraction to original impl
* use custom readlink
* cleanup symlink module
* make lstrip
* flux-sched: set the version if the ver file is missing
problem: flux-sched needs a version, it normally gets this from a
release tarball or from git tags, but if using a source archive or a git
clone without tags the version is missing
solution: set the version through cmake based on the version spack sees
when the version file is missing
* Update var/spack/repos/builtin/packages/flux-sched/package.py
Co-authored-by: Alec Scott <hi@alecbcs.com>
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
Problem: the libsodium download endpoints are not reliable,
they fail multiple times a day for several of our automated
pipelines.
Solution: use the GitHub releases and branches.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
GCC C++ headers like cstdlib use `#include_next <stdlib.h>` to wrap libc
headers. We're using `-isystem` for libc, which puts those headers too
early in the search path. `-idirafter` fixes this so `include_next`
works.
* add darshan-3.4.5 packages, update URLs
* py-setuptools version switches for py-darshan
* more py-darshan test dependencies
* try a conditional importlib_resources dependency
Add the ability to include any number of (potentially nested) concrete environments, e.g.:
```yaml
spack:
specs: []
concretizer:
unify: true
include_concrete:
- /path/to/environment1
- /path/to/environment2
```
or, from the CLI:
```console
$ spack env create myenv
$ spack -e myenv add python
$ spack -e myenv concretize
$ spack env create --include-concrete myenv included_env
```
The contents of included concrete environments' spack.lock files are
included in the environment's lock file at creation time. Any changes
to included concrete environments are only reflected after the environment
is re-concretized from the re-concretized included environments.
- [x] Concretize included envs
- [x] Save concrete specs in memory by hash
- [x] Add included envs to combined env's lock file
- [x] Add test
- [x] Update documentation
Co-authored-by: Kayla Butler <<butler59@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.co
m>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Currently SPACK_COLOR=always is not respected in the build process on
macOS, because the global `_force_color` is re-evaluated in global scope
during module setup, where it is always `None`.
So, move global init bits from main.py to the module itself.
Some specs which were excluded from reuse,
are currently added back to the solve when
we traverse dependencies of other reusable
specs.
This fixes the issue by keeping track of what
we can explicitly reuse.
This commit adds a layer of indirection to improve build isolation with
and without external Python, as well as usability of environment views.
It adds `python-venv` as a dependency to all packages that `extends("python")`,
which has the following advantages:
1. Build isolation: only `PYTHONPATH` is considered in builds, not
user / system packages
2. Stable install layout: fixes the problem on Debian, RHEL and Fedora where
external / system python produces `bin/local` subdirs in Spack install prefixes.
3. Environment views are Python virtual environments (and if you add
`py-pip` things like `pip list` work)
Views work whether they're symlink, hardlink or copy type.
This commit additionally makes `spec["python"].command` return
`spec["python-venv"].command`. The rationale is that packages in repos we do
not own do not pass the underlying python to the build system, which could still
result in incorrectly computed install layouts.
Other attributes like `libs`, `headers` should be on `python` anyways and need no change.
Currently bootstrapping from source fails because clingo requires gnupg
requires clingo.
This commit stops eager bootstrapping. We don't need `patchelf` nor `gnupg`
generally. They're bootstrapped when needed.
This creates shared infrastructure for compiler packages to implement the
detailed search capabilities from the `spack compiler find` command for the
`spack external find` command.
After this commit, `spack compiler find` can be replaced with
`spack external find --tag compiler`, with the exception of mixed toolchains.
A named env cannot contain `.` and `/`.
So when a user runs `spack env create ./here` do not error but treat it
as `spack env create -d ./here`.
Also fix help string of `spack env create`, which seems to have been
copied from `activate` incorrectly.
Since reuse is the default now, `--reuse-deps` can be confusing, as it
technically does not imply roots are fresh.
So add `--fresh-roots`, which is also easier to discover when running
`spack concretize --fre<tab>`
* WIP NWChem with ARMCI-MPI and TCE optional
* rename armci-mpi to armcimpi
* add version for git
* add ARMCI-MPI support to NWChem package
EXTERNAL_ARMCI_PATH needs to be set to the ARMCI-MPI package install prefix.
I could not get it from spec["armcimpi"] but it worked to use the dependent build environment method to export a generic environmental variable to use instead.
* i suppose i can maintain NWChem as well
* check rejects option that dozens of packages use
i do not have time to fight with this nonsense
Run . share/spack/setup-env.sh
==> Error: armcimpi version 'master' has extra arguments: 'branch'
Valid arguments for a url fetcher are:
'url', 'sha256', 'md5', 'sha1', 'sha224', 'sha384', 'sha512', and 'checksum'
Error: Process completed with exit code 1.
* style
* ARMCI-MPI needs depends_on; the rest seems fixed
* fix ARMCI selection per review feedback from @zzzoom
https://github.com/spack/spack/pull/43883#discussion_r1585014147
* address reviewer feedback from @yizeyi18
https://github.com/spack/spack/pull/43883#discussion_r1587228084
elaborate on what +extratce does, in terms of the NWChem build environment variables,
some of which are documented on https://nwchemgit.github.io/TCE.html.
* style
* Update var/spack/repos/builtin/packages/nwchem/package.py
---------
Signed-off-by: Jeff Hammond <jeff.science@gmail.com>
Co-authored-by: Carlos Bederián <4043375+zzzoom@users.noreply.github.com>
* [TAU package] Update with +rocprofv2. Updated some tests.
pdated with +rocprofv2 flag. Only works with rocm-core >= 6.0.0
Can be tested with (Omnia):
spack install tau@master +rocm+rocprofv2 %gcc@11
Needs the last commit in our local repository, can be done by modifying the "git = " line, or waiting until the public one is updated.
In the case that tests cause issues when building TAU, there is the flag:
disable_tests = False
The rocm test is disabled by default, as the PR regarding tests loading dependencies is not solved (PR#43682).
* [@spackbot] updating style on behalf of jordialcaraz
---------
Co-authored-by: jordialcaraz <jordialcaraz@users.noreply.github.com>
* py-tensorflow: fix aarch64 build
* [@spackbot] updating style on behalf of aweits
* patch format
* change patch strategy, actually get the logic correct in
the patch
* only patch 2.16.1 onwards for aarch64
* __CUDACC__ not __NVCC__
* !(defined(__NVCC__) && defined(__CUDACC__))
---------
Co-authored-by: aweits <aweits@users.noreply.github.com>
We recently switched to using the new ReadTheDocs with "addons". That includes its own
analytics, which is nice, but we also want to continue using our GA4 analytics.
Adding GA4 is no longer supported by RTD, so we have to add it manually.
- [x] re-add the gtag to all pages, manually
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
PR #43701 is broken, preventing scorep from being installed. As explained in #43700 the issue is internal to scorep and can not be fixed in the package, at least by the method being attempted here.
Adds a pre-concretization check for the Windows SDK and WGL (Windows
GL) packages as non-buildable externals.
This is a redo of https://github.com/spack/spack/pull/43459, but makes
sure to modify the configuration scope outside of the bootstrap scope:
whichever is highest-precedence in the user's environment at the time
the concretization runs, which should either be an env scope or the
~ scope.
Adds pytest fixture mocking the check for WGL and WSDK as if they were
present.
This PR gives users finer control over which specs are reused during concretization.
The value of the `concretizer:reuse` config option now can take an object with the following properties:
- `roots`: true if reusing roots, false if reusing just dependencies
- `exclude`: list of constraints used to select reusable specs
- `include`: list of constraints used to select reusable specs
- `from`: allows to select the sources of reused specs
### Examples
#### Reuse only specs compiled with GCC
```yaml
concretizer:
reuse:
roots: true
include:
- "%gcc"
```
#### `openmpi` must be used from externals, and it must be the only external used
```yaml
concretizer:
reuse:
roots: true
from:
- type: local
exclude:
- "openmpi"
- type: buildcache
exclude:
- "openmpi"
- type: external
include:
- "openmpi"
```
With v2.10+, ADIOS added a campaign manager. This is auto-enabled
if SQLite3 is found.
Add explicit control for it now and disables it by default, to avoid
picking up system dependencies or bloating by default the ADIOS2
dependencies. Also, not yet fully mature to be used by default:
https://github.com/ornladios/ADIOS2/issues/4148
* pypi build of py-simpy
* [py-simpy] toml explicitly called out
* py-simpy: New version
* py-setuptools-scm: Added new version
* py-setuptools-scm: add url_for_version
Because versions @:7 have an underscore (setuptools_scm) in the URL, and
newer versions have a dash (setuptools-scm).
* py-setuptools-scm: fix flake8 line too long
* py-simpy: Fix hash
---------
Co-authored-by: Sid Pendelberry <sid@rit.edu>
Co-authored-by: Jen Herting <jen@herting.cc>
* PackageStillNeededError: add pkg that needs spec to exception msg
* PackageStillNeededError: f-string with short fmt and hash
* PackageStillNeededError: split long string
The old concretizer creates a cyclic graph when expanding virtuals for
`iconv`, which is a bug. This hack drops glibc and musl as possible
providers for `iconv` in the old concretizer to work around it.
* Added package to build Ollama
* Update package.py
Add license and documentation
* [@spackbot] updating style on behalf of teaguesterling
* We can now use OVERRIDE_GIT_DESCRIBE to set the version in DuckDB
* Update duckdb/package.py
- use f-string
- fix version specs to address inconsistencies
* Update package.py
Fix spec definitions further
* [@spackbot] updating style on behalf of teaguesterling
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
The "DOTNET_CLI_TELEMETRY_OPTOUT" environment variable should be defined when using the product, not when installing it (the installation phase is just extract the files anyway).
Also use `~` instead of `-` to check for the variant and fix the second argument for `env.set` which should also be a string.
Add debug log for external detection tests. The debug log
is used to print which test is being executed.
Skip version audit on Windows where appropriate
* Update package.py to osg 1.119 and igtf 1.128
* Remove unnecessary white space
* Add missing comma
* change url to use git and use commit hash from repository instead of ssh256sum of tar.gz
* [@spackbot] updating style on behalf of rahmans1
---------
Co-authored-by: rahmans1 <rahmans1@users.noreply.github.com>
* * Add initial tests-sos package
* Remove failing call of missing setup_compiler_environment from sos
package
* Add several variants for sos package
* [@spackbot] updating style on behalf of jack-morrison
We run `extend spack_flags_list SPACK_LDFLAGS` for `$mode in ld|ccld`.
That's problematic, cause `ccld` needs `-Wl,--flag` whereas `ld` needs
`--flag` directly. Only `-L` and `-l` are common to compiler & linker.
In all build systems `LDFLAGS` is for the compiler not the linker, cause
any linker flag `-x` can be passed as a compiler flag `-Wl,-x`, and there
are many compiler flags that affect the linker invocation, like `-fopenmp`,
`-fuse-ld=`, `-fsanitize=` etc.
So don't pass `LDFLAGS` to the linker directly.
This way users can set `ldflags: -Wl,--allow-shlib-undefined` in compilers.yaml
to work around an issue where the linker tries to resolve the `libcuda.so.1`
stub lib which cannot be located by design in `cuda`.
* Updates for rocm
Updated for rocm@6
Added conflict between rocprofiler and roctracer.
Request either +rocprofiler or +roctracer when +rocm. In this case, it automatically builds for one, instead of displaying the message.
Request +rocm when using either +rocprofiler or +roctracer. In this case, it automatically builds with +rocm, instead of displaying the message.
Disabled the tests. Will update them with the new test method.
* [@spackbot] updating style on behalf of jordialcaraz
---------
Co-authored-by: jordialcaraz <jordialcaraz@users.noreply.github.com>
Some packages can't be redistributed in source or binary form. We need an explicit way to say that in a package.
This adds a `redistribute()` directive so that package authors can write, e.g.:
```python
redistribute(source=False, binary=False)
```
You can also do this conditionally with `when=`, as with other directives, e.g.:
```python
# 12.0 and higher are proprietary
redistribute(source=False, binary=False, when="@12.0:")
# can't redistribute when we depend on some proprietary dependency
redistribute(source=False, binary=False, when="^proprietary-dependency")
```
To prevent Spack from adding either their sources or binaries to public mirrors and build caches. You can still unconditionally add things *if* you run either:
* `spack mirror create --private`
* `spack buildcache push --private`
But the default behavior for build caches is not to include non-redistributable packages in either mirrors or build caches. We have previously done this manually for our public buildcache, but with this we can start maintaining redistributability directly in packages.
Caveats: currently the default for `redistribute()` is `True` for both `source` and `binary`, and you can only set either of them to `False` via this directive.
- [x] add `redistribute()` directive
- [x] add `redistribute_source` and `redistribute_binary` class methods to `PackageBase`
- [x] add `--private` option to `spack mirror`
- [x] add `--private` option to `spack buildcache push`
- [x] test exclusion of packages from source mirror (both as a root and as a dependency)
- [x] test exclusion of packages from binary mirror (both as a root and as a dependency)
If there's no compiler we currently don't have any external libc for the solver.
This commit adds a fallback on libc from the current Python process, which works if it is dynamically linked.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
When looking at where we spend our time in solver setup, I noticed a fair bit of time is spent
in `Spec.format()`, and `Spec.format()` is a pretty old, slow, convoluted method.
This PR does a number of things:
- [x] Consolidate most of what was being done manually with a character loop and several
regexes into a single regex.
- [x] Precompile regexes where we keep them
- [x] Remove the `transform=` argument to `Spec.format()` which was only used in one
place in the code (modules) to uppercase env var names, but added a lot of complexity
- [x] Avoid escaping and colorizing specs unless necessary
- [x] Refactor a lot of the colorization logic to avoid unnecessary object construction
- [x] Add type hints and remove some spots in the code where we were using nonexistent
arguments to `format()`.
- [x] Add trivial cases to `__str__` in `VariantMap` and `VersionList` to avoid sorting
- [x] Avoid calling `isinstance()` in the main loop of `Spec.format()`
- [x] Don't bother constructing a `string` representation for the result of `_prev_version`
as it is only used for comparisons.
In my timings (on all the specs formatted in a solve of `hdf5`), this is over 2.67x faster than the
original `format()`, and it seems to reduce setup time by around a second (for `hdf5`).
The reverse provider lookup may have stale entries for deleted packages, which used to cause errors. It's hard to invalidate those cache entries, so this commit simply drops entries w/o invalidating the cache.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This commit differentiate linux from other platforms by
using libc compatibility as a criterion for deciding
which buildcaches / binaries can be reused. Other
platforms still use OS compatibility.
On linux a libc is injected by all compilers as an implicit
external, and the compatibility criterion is that a libc is
compatible with all other libcs with the same name and a
version that is lesser or equal.
Some concretization unit tests use libc when run on linux.
Some logic to detect what libc the c / cxx compilers use by default,
based on `-dynamic-linker`.
The function `compiler.default_libc()` returns a `Spec` of the form
`glibc@x.y` or `musl@x.y` with the `external_path` property set.
The idea is this can be injected as a dependency.
If we can't run the dynamic linker directly, fall back to `ldd` relative
to the prefix computed from `ld.so.`
In the future we may transform the database from a single JSON object to
a stream of JSON objects.
This paves the way for constant time writes and constant time rereads
when only O(1) changes are made. Currently both are linear time.
This commit gives just enough forward compat for Spack to produce a
friendly error when we would move to a stream of json objects, and a db
would look like this:
```json
{"database": {"version": "<something newer>"}}
```
* compiler wrapper: prioritize spack managed paths in search order
This commit partitions search paths of -L, -I (and -rpath) into three
groups, from highest priority to lowest:
1. Spack managed directories: these include absolute paths such as
stores and the stage dir, as well as all relative paths since they
are relative to a Spack owned dir
2. Non-system dirs: these are for externals that live in non-system
locations
3. System dirs: your typical `/usr/lib` etc.
It's very easy for Spack to known the prefixes it owns, it's much more
difficult to tell system dirs from non-system dirs. Before this commit
Spack tried to distinguish only system and non-system dirs, and failed
for very trivial cases like `/usr/lib/x/..` which comes up often, since
build systems sometimes copy search paths from `gcc -print-search-dirs`.
Potentially this implementation is even faster than the current state of
things, since a loop over paths is replaced with an eval'ed `case ...`.
* Trigger a pipeline
* Revert "Trigger a pipeline"
This reverts commit 5d7fa863de.
* remove redudant return statement
* Add conflicts for some blas implementations that don't build on
Windows (or with %msvc)
* Need to enclose CC/CXX variables in quotes in case those paths
have spaces, otherwise Meson runs into errors
* On Windows, Python dependencies now add <prefix>/Scripts to the
PATH (this is established as a standard in PEP 370)
* Later versions of oneAPI have moved, so update detection to find it
in both old and new location
* Remove reliance on ONEAPI_ROOT env variable when determining Fortran
compiler version for %msvc
* When finding a Fortran compiler for MSVC, there was logic enforcing
a maximum MSVC version for a given oneAPI Fortran version. This
mapping was out of date and excluding valid combinations, so has
been removed (the logic now just picks the latest available
oneAPI Fortran compiler for any given MSVC version).
On Windows, bootstrapping logic now searches for and adds the win-sdk
and wgl packages to the user's top scope as externals if they are not
present.
These packages are generally required to install most packages with
Spack on Windows, and are only available as externals, so it is
assumed that doing this automatically would be useful and avoid
a mandatory manual step for each new Spack instance.
Note this is the first case of bootstrapping logic modifying
configuration other than the bootstrap configuration.
* gxsview: compiles againts system qt and vtk on rhel8
* Update gxsview/package.py for blanks around operator
* Update gxsview/package.py import blank line
* Update gxsview/package.py for style
* Update gxsview/package.py checking vtk version
Score-P does not accept "--with-foo=yes", but only "--with-foo" or "--with-foo=some-valid-specific-choice-or-path". This keeps Spack from generating config flags that will cause Score-P to barf.
This adds some improvements to `spack find` output when in environments based
around some thoughts about what users want to know when they're in an env.
If you're working in an enviroment, you mostly care about:
* What are the roots
* Which ones are installed / not installed
* What's been added that still needs to be concretized
So, this PR adds a couple tweaks to display that information more clearly:
- [x] We now display install status next to every root. You can easily see
which are installed and which aren't.
- [x] When you run `spack find -l` in an env, the roots now show their concrete
hash (if they've been concretized). They previously would show `-------`
(b/c the root spec itself is abstract), but showing the concretized root's
hash is a lot more useful.
- [x] Newly added/unconcretized specs still show `-------`, which now makes more
sense, b/c they are not concretized.
- [x] There is a new option, `-r` / `--only-roots` to *only* show env roots if
you don't want to look at all the installed specs.
- [x] Roots in the installed spec list are now highlighted as bold. This is
actually an old feature from the first env implementation , but various
refactors had disabled it inadvertently.
Reduce incidence of spurious errors by:
* Ensuring we're passing the buffer by reference
* Get the correct short string size from Windows API instead of computing ourselves
* Ensure sufficient space for null terminator character
Add test for `windows_sfn`
Currently if you request pkg +example where example is a conditional
variant, and you have a pkg in the database for which the condition
did not hold (so no +example nor ~example), the solver would reuse it
regardless, not imposing +example.
The change rules out exactly one thing: variant_set without variant_value,
which in practice could only happen when not node_has_variant (i.e. when
under the current package.py rules the variant's when condition did not
trigger).
Add a "default" option that passes no option to configure. Existing
options changed in the MPICH 4.2.0 release, so update the package to
reflect those changes.
Currently, some of the tests in `spec_format` and `spec_semantics` fetch
the actual zlib repository when run, because they call `str()` on specs
like `zlib@foo/bar`, which at least currently requires a remote git clone
to resolve.
This doesn't change the behavior of git versions, but it uses our mock git
repo infrastructure and clones the `git-test` package instead of the *real*
URL from the mock `zlib` package.
This should speed up tests. We could probably refactor more so that the git
tests *all* use such a fixture, but the `checks` field that unfortunately
tightly couples the mock git repository and the `git_fetch` tests complicates
this. We could also consider *not* making `str()` resolve git versions, but
I did not dig into that here.
- [x] add a mock_git_test_package fixture that sets up a mock git repo *and*
monkeypatches the `git-test` package (like our git test packages do)
- [x] use fixture in `test_spec_format_path`
- [x] use fixture in `test_spec_format_path_posix`
- [x] use fixture in `test_spec_format_path_windows`
- [x] use fixture in `test_parse_single_spec`
Commit 330a9a7c9a aimed at preventing
generation of .cfg files when a given compiler does not exist
in the particular release. However the check does not
contain the full paths so it always fails resulting in empty
.cfg files. This commit fixes it.
* add new axom releases, sync changes between repos
* add new version of axom and add fallback depends for umpire/raja
* remove now redundant flags, add flags to cuda flags to flags output by cachedcmakepackage
Co-authored-by: white238 <white238@users.noreply.github.com>
* w3nco %oneapi cflags: append -Wno-error=implicit-function-declaration
* update flag for %apple-clang, %clang
* [@spackbot] updating style on behalf of eugeneswalker
Upon close inspection of clingo answer sets, in some cases we have "equivalent" (i.e. same hash for the concrete spec) duplicates that differ only because of virtual nodes that are added to the answer set, without any edge using them.
This commit adds a property `autopush` to mirrors. When true, every source build is immediately followed by a push to the build cache. This is useful in ephemeral environments such as CI / containers.
To enable autopush on existing build caches, use `spack mirror set --autopush <name>`. The same flag can be used in `spack mirror add`.
* Simplify config command and add BLAS/LAPACK location
* Use BLAS_ROOT and LAPACK_ROOT and disable use of system
package registry
* Adds location of BLAS_LIBRARIES and LAPACK_LIBRARIES to CMake
* Adds CMake variables to prevent picking up system installations
of BLAS/LAPACK. Fixes previous PR #43328 that was picking up
incorrect installations
* Adds versions 7.2.1
* libzip: add up to v1.10.1
- update homepage and change download url to GitHub
- change build system to CMake for releases starting with 1.4
* [@spackbot] updating style on behalf of aumuell
* libzip: fix urls
* [@spackbot] updating style on behalf of aumuell
* libzip: do not add versions from libzip.org
these are old, and urllib refuses to fetch them
* libzip: deprecate versions from libzip.org
urllib refuses to fetch them, only curl would work
---------
Co-authored-by: aumuell <aumuell@users.noreply.github.com>
* acts: new version 33.1.0
* actsvg: new version 0.4.41
* geomodel: new package
* [@spackbot] updating style on behalf of wdconinc
* acts: plugin_cmake_variant(geomodel)
* geomodel: with when(+visualization)
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Include recent change for Ubuntu
Select option -disable-no-pie-on-ubuntu for some Ubuntu systems
823971df01
* Added conflict for new variant
* Updated conflict version
* Added mention of Ubuntu to variant description
* Kokkos Kernels: adding missing TPLs and pre-conditions
Adding variants and dependencies for rocBLAS and rocSPARSE.
Also adding a "when=" close to the TPL variants that prevents
enabling the TPLs in versions of the library when it was not
yet available.
* Kokkos Kernels: remove comment for better format
* Kokkos Kernels: adding cusolver and rocsolver for at version 4.3.00
* Kokkos Ecosystem: updating packages for release 4.3.00
* Kokkos: adding arch for SG2042
* Removing sg2042 from spack_micro_arch_map
Removing it here and will work to add it in the proper generic spack location, likely: `spack/lib/spack/external/archspec/json/cpu/microarchitectures.json` ?
Allow reuse of specs that were built with compilers not in the current configuration. This means that specs from build caches don't need to have a matching compiler locally to be reused. Similarly when updating a distro. If a node needs to be built, only available compilers will be considered as candidates.
* add c++11 header to gold for compiler not defaulting to c++11
* glibc: add 2.39
* llvm: add 18.1.3
* fix#42314, remove cxx11 flag for llvm; should be controlled by cmake.
* modify patch
* llvm version
* add gmake version request
* yoda: new versions 1.9.9, 1.9.10, and 2.0.0
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
As in the original makefile "FFLAGS_PROMOTION = -fdefault-real-8
-fdefault-double-8" is only used when `precision=double`. This is the default
for the Spack package, so no change if `precision` is left unset.
* Generally use os.replace on Windows and Linux
* Windows behavior for os.replace differs when the destination exists
and is a symlink to a directory: on Linux the dst is replaced and
on Windows this fails - this PR makes Windows behave like Linux
(by deleting the dst before doing the rename unless src and dst
are the same)
* Nalu: updating Trilinos recipe a bit
Basic changes to build/install nalu properly using Spack.
Some more changes would be nice for instance adding an
option to build against Trilinos master or develop. Adding
a dependency on googletest to avoid the annoying build
failures in the unit-tests.
* Nalu: adding release 1.6.0
Nalu v1.6.0 can build cleanly against Trilinos 14.0.0 with the
proposed changes. The only other combo is master / master but
than one is "floating" as these branch evolve over time. When a
new Nalu comes out we might want to add another fixed version to
keep this recipes up to date!
the autotools build system does something funky which causes a link line
where gccs default link dirs are explicitly added and end up before the
-L from spack's libunwind, so that ultimately it links against system
libunwind.
the cmake build system does better.
* upgrade new versions
* style fix
* update jaxlib deps (not cuda and bazel yet)
* update jaxlib cuda versions
* update jaxlib cuda versions
* update jaxlib cuda versions
* chore: style fix
* Update package.py
* Update package.py
* fix: typo
* docs: add source for cuda version
* py-jaxlib 0.4.14 also doesn't build on ppc64le
* Add 0.4.26
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ParaView: Update version 5.12.0
Add 5.12.0 release
Update default to 5.12.0
* Add patch for building ParaView 5.12 with kits
* Drop VTKm from neoverse
* For avx build, the start address of values_ buffer in KernelParameters
is not a correct as it is computed based on 16-byte alignment.
* Style check error fix
* updating package.py for py-celery, py-kombu, py-amq
* added more py-kombu package versions
* fix copyrights and stype on py-kombu/package.py
* removed extra spaces
* added py-billiard 4.2.0 and added back the license('BSD-3-Clause')
* removed extra spaces in py-celery/package.py
* fixed py-amqp 2.4.0 sha; fixed py-celery's dependency of py-click (when version restrictions)
* more clean up on specifying version bounds
* Relax compiler and target mismatches
The mismatch occurs on an edge. Previously it was assigned
the parent priority, now it is assigned the child priority.
This should make reuse from buildcaches or store more likely,
since most mismatches will be counted with "reused" priority.
* Optimize version badness for runtimes at very low priority
We don't want to e.g. switch other attributes because we
cannot reuse an old installed runtime.
* Optimize runtime attributes at very low priority
This is such that the version of the runtime would
not influence whether we should reuse a spec.
Compiler mismatches are considered for runtimes,
to avoid situations where compiling foo%gcc@9
brings in gcc-runtime%gcc@13 if gcc@13 is among
the available compilers
* Exclude specs without runtimes from reuse
This should ensure that we do not reuse specs that
could be broken, as they expect the compiler to be
installed in a specific place.
The installer runs `get_dependent_ids`, which follows edges outside the
subdag that's being installed, so it returns a superset of the actual
dependents.
That's generally fine, except that it calls `s.package` on every
dependent, which triggers a package class to be instantiated, which is a
lot of work.
Instead, compute the package id from the spec, since that's all that's
used anyways and does not trigger *lots* of slow and redundant
instantiations of package objects.
If ONEAPI_ROOT is not set as an environment variable, the current approach will raise an error.
Instead we can compute the OneAPI_ROOT from the compiler paths like we do with vcvarsall.
The installation mechanism used on Linux to install py-pip (using pip
from the downloaded wheel to install the wheel) does not work on Windows.
This updates the installation of py-pip on Windows to download and
use a zipapp of a specific pip version in order to install the wheel
pip version that is requested.
`dpcpp` is deprecated by intel and has been superseded by `oneapi` compilers for a very long time.
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
* SEACAS: Update package.py to handle new SEACAS project name
The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.
The refactor also changes several:
"-DSome_CMAKE_Option:BOOL=ON"
to
define("Some_CMAKE_Option", True)
* SEACAS, EXODUSII: New version; deprecate older versions; better variant descriptions
* [@spackbot] updating style on behalf of gsjaardema
* Fix long lines reported by flake8
---------
Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>
* Add release 2.8.0
* Changing C compiler to hipcc
* Final release version
* Adding new cmake definition for rocm support
* Enabling rocm version support
* Update sha256
* Updating website URL
* Removing unnecessary C compiler spec
* Adding rocm-core dependency
* fixing rocm-core version
* fixing rocm-core version
* fixing style
* bugfix
* Add systemd
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* gobject-introspection: Correct glib versions
- The meson.build requirement that the glib version
is >= the gobject-introspective version is not in place
until v1.76.1.
- Prior to that, the requirement was glib >= 2.58.0.
- Bug introduced in acbf0d99c4, PR #42222.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* util-linux: add v2.39.3
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-natsort: add new versions
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: default systemd support to true
- Make the dependency sticky to force a failure
if systemd compilation fails, or force
the user to disable the option.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: Add initial multi-architecture support
- Restrict arch conflicts to 3.0.1
- Disable cpuid at configure time on non-x86_64 platforms.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: update docstrings
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-geopmdpy
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add geopm-runtime recipe
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
---------
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
This PR allows the user to specify a path to a custom cert file (or directory) in
Spack's config:
```yaml
# This is where custom certs for proxy/firewall are stored.
# It can be a path or environment variable. To match ssl env configuration
# the default is the environment variable SSL_CERT_FILE
ssl_certs: $SSL_CERT_FILE
```
`config:ssl_certs` can be a path to a file or a directory, or it can be and environment
variable that resolves to one of those. When it posts to something valid, Spack will
update the ssl context to include custom certs, and fetching via `urllib` and `curl`
will trust the provided certs.
This should resolve many issues with fetching behind corporate firewalls.
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
Co-authored-by: Alec Scott <alec@bcs.sh>
After #41373, where we stopped considering the source directory to be the stage for develop builds,
we resumed *deleting* the stage even after a successful build.
We don't want this for develop builds because developers need to iterate; we should keep the artifacts
unless they explicitly run `spack clean`.
Now:
- [x] Build artifacts for develop packages are not removed after a successful install
- [x] They are also not removed before an install starts, i.e. develop packages always
reuse prior artifacts, if available.
- [x] They can be deleted in any other context, e.g. by running `spack clean --stage`
Prior FleCSI releases relied on commits on the control-replication branch (cr)
of Legion. That branch has now been merged into master and is part of the
24.03.0 Legion release.
* (py-)onnx: new version 1.14.{0,1}, 1.15.0
Notes on `onnx`:
- The C++ standard was changed to 14 in 1.15, so no more filter_file is needed. (The C++ standard has since changed to 17 in master.)
Notes on `py-onnx`:
- `py-pybind11` was an unlisted requirement in CMakeLists.txt since 1.3 or so (before earliest spack package).
* py-onnx: depends_on pybind11 with type link, not run
* py-onnx: depends_on py-setuptools@64:
Users requested an option to filter between local/upstream results in `spack find` output.
```
# default behavior, same as without --install-tree argument
$ spack find --install-tree all
# show only local results
$ spack find --install-tree local
# show results from all upstreams
$ spack find --install-tree upstream
# show results from a particular upstream or the local install_tree
$ spack find --install-tree /path/to/install/tree/root
```
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
* sundials: add new version
* note previous default
* update when clause for removed options
---------
Co-authored-by: David J. Gardner <gardner48@llnl.gov>
* SEACAS: Update package.py to handle new SEACAS project name
The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.
The refactor also changes several:
"-DSome_CMAKE_Option:BOOL=ON"
to
define("Some_CMAKE_Option", True)
* exodusii -- refactor and bring up-to-date
* Add missed patch file
* [@spackbot] updating style on behalf of gsjaardema
* Apply seacas windows patch here also.
* Update url so old checksums valid; redo new checksums
---------
Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>
* Initial commit to bump rocprofiler-dev to 6.0 and add aqlprofile recipe
* bump to 6.0.2 and extracting binaries from deb pkg
* fixes for hpctoolkit build errors
* add yum and zyp aqlprofile packages
* fix style issues
* Allow compilers to function across compatible OS's
* Add documentation in the default yaml
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* py-libsonata: new package starting at 0.1.25
* align spack version with the git branch
* Fix min required versions / use spack packages instead of submodules
* Create devcontainer.json
* Ensure codespace can be setup for current branch
* fix: find compilers in site scope
* fix: use cloud_pipelines ubuntu20.04 image
* fix: spack config --scope site add
* fix: use develop, not develop-root mirror
This adds a dependency on pkg-config which in turn builds pkg-config
on pipelines using %onapi/%cce: update the pkg-config build to disable
specific warnings-as-errors from these compilers.
Co-authored-by: Reid Priedhorsky <1682574+reidpr@users.noreply.github.com>
* Add macos-14 as a runner (Apple M1)
* Mark a test xfail
We need to check later if this test needs modifications
on Apple Silicon chips.
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Co-authored-by: alalazo <alalazo@users.noreply.github.com>
* buildcache sync: manifest-glob with arbitrary destination
The current implementation of the --manifest-glob is a bit restrictive
requiring the destination to be known by the generation stage of CI.
This allows specifying an arbitrary destination mirror URL.
* Add unit test for buildcache sync with manifest
* Fix test and arguments for manifest-glob with override destination
* Add testing path for unused mirror argument
* Remove a few compilers from static test data
These compilers were used only in a bunch of tests, so
they are added only there.
* Remove clang@3.3 from unit test configuration
* Parametrize compilers.yaml
* Remove specially named gcc from static data
The compilers are used in two tests
* Remove apple-clang and macOS compilers from static data
The compiler was used only in multimethod tests
* Remove clang@3.5 (compiler seems to be unused)
* Remove gcc@4.4.0 (compiler seems to be unused)
* Exclude x86_64 tests on other architectures
* Mark two tests as for clingo only
* Update version syntax in compilers.yaml
* Parametrize tcl tests on architectures
* Parametrize lmod tests on architectures
* Substitute gcc@4.5.0 with gcc@4.8.0 so it can be used on aarch64
* Fix a few issues with aarch64 and unit-tests
It's now possible to add config on the command line with `spack -c <CONFIG_VARS> ...`, but the new `command_line` scope isn't reflected in the help output for `--scope`:
```bash
> spack help config
...
--scope {defaults,system,site,user}[/PLATFORM] or env:ENVIRONMENT
configuration scope to read/modify
...
```
This PR adds:
- A new runtime for `%oneapi` compilers, called `intel-oneapi-runtime`
- Information to both `gcc-runtime` and `intel-oneapi-runtime`, to ensure
that we don't mix compilers using different soname for either `libgfortran`
or `libifcore`
To do so, the following internal mechanisms have been implemented:
- Possibility to inject virtual dependencies from the `runtime_constraints`
callback on packages
Information has been added to `gcc-runtime` to provide the correct soname
under different conditions on its `%gcc`.
Rules injected into the solver looks like:
```prolog
% Add a dependency on 'gfortran@5' for nodes compiled with gcc@=13.2.0 and using the 'fortran' language
attr("dependency_holds", node(ID, Package), "gfortran", "link") :-
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
attr("virtual_node", node(RuntimeID, "gfortran")) :-
attr("depends_on", node(ID, Package), ProviderNode, "link"),
provider(ProviderNode, node(RuntimeID, "gfortran")),
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
attr("node_version_satisfies", node(RuntimeID, "gfortran"), "5") :-
attr("depends_on", node(ID, Package), ProviderNode, "link"),
provider(ProviderNode, node(RuntimeID, "gfortran")),
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
```
The default url couldn't be the one with v0.0.0-aws since spack was
replacing v0.0.0-aws with v<version_number> for example, deleting the
-aws suffix. I used the url_for_version method to specify this suffix.
This adds support for prereleases. Alpha, beta and release candidate
suffixes are ordered in the intuitive way:
```
1.2.0-alpha < 1.2.0-alpha.1 < 1.2.0-beta.2 < 1.2.0-rc.3 < 1.2.0 < 1.2.0-xyz
```
Alpha, beta and rc prereleases are defined as follows: split the version
string into components like before (on delimiters and string boundaries).
If there's a string component `alpha`, `beta` or `rc` followed by an optional
numeric component at the end, then the version is prerelease.
So `1.2.0-alpha.1 == 1.2.0alpha1 == 1.2.0.alpha1` are all the same, as usual.
The strings `alpha`, `beta` and `rc` are chosen because they match semver,
they are sufficiently long to be unambiguous, and and all contain at least
one non-hex character so distinguish them from shasum/digest type suffixes.
The comparison key is now stored as `(release_tuple, prerelease_tuple)`, so in
the above example:
```
((1,2,0),(ALPHA,)) < ((1,2,0),(ALPHA,1)) < ((1,2,0),(BETA,2)) < ((1,2,0),(RC,3)) < ((1,2,0),(FINAL,)) < ((1,2,0,"xyz"), (FINAL,))
```
The version ranges `@1.2.0:` and `@:1.1` do *not* include prereleases of
`1.2.0`.
So for packaging, if the `1.2.0alpha` and `1.2.0` versions have the same constraints on
dependencies, it's best to write
```python
depends_on("x@1:", when="@1.2.0alpha:")
```
However, `@1.2:` does include `1.2.0alpha`. This is because Spack considers
`1.2 < 1.2.0` as distinct versions, with `1.2 < 1.2.0alpha < 1.2.0` as a consequence.
Alternatively, the above `depends_on` statement can thus be written
```python
depends_on("x@1:", when="@1.2:")
```
which can be useful too. A short-hand to include prereleases, but you
can still be explicit to exclude the prerelease by specifying the patch version
number.
### Concretization
Concretization uses a different version order than `<`. Prereleases are ordered
between final releases and develop versions. That way, users should not
have to set `preferred=True` on every final release if they add just one
prerelease to a package. The concretizer is unlikely to pick a prerelease when
final releases are possible.
### Limitations
1. You can't express a range that includes all alpha release but excludes all beta
releases. Only alternative is good old repeated nines: `@:1.2.0alpha99`.
2. The Python ecosystem defaults to `a`, `b`, `rc` strings, so translation of Python versions to
Spack versions requires expansion to `alpha`, `beta`, `rc`. It's mildly annoying, because
this means we may need to compute URLs differently (not done in this commit).
### Hash
Care is taken not to break hashes of versions that do not have a prerelease
suffix.
Generate CI scripts as powershell on Windows. This is intended to
output exactly the same bash scripts as before on Linux.
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
As the cmake build is triggered by scikit build, the usual spack option
for enabling tests had no effect and the heavy test suite ran all the time.
Used https://github.com/scikit-build/cmake-python-distributions/issues/172#issuecomment-890322263
to implement how to pass options to the actual `cmake` build.
I also excluded some tests that failed for me on alma9 (gcc 11.4.1),
so the rest of the test suite can be run.
Enable OpenBLAS's built-in CPU capability detection and kernel selection.
This allows run-time selection of the "best" kernels for the running CPU, rather
than what is specified at build time. For example, it allows OpenBLAS to use
AVX512 kernels when running on ZEN4, and built targeting the "ZEN" architecture.
Co-authored-by: Branden Moore <branden.moore@amd.com>
* Changes to re-enable aws-pcluster pipelines
- Use compilers from pre-installed spack store such that compiler path relocation works when downloading from buildcache.
- Install gcc from hash so there is no risk of building gcc from source in pipleine.
- `packages.yam` files are now part of the pipelines.
- No more eternal `postinstall.sh`. The necessary steps are in `setup=pcluster.sh` and will be version controlled within this repo.
- Re-enable pipelines.
* Add and
* Debugging output & mv skylake -> skylake_avx512
* Explicilty check for packages
* Handle case with no intel compiler
* compatibility when using setup-pcluster.sh on a pre-installed cluster.
* Disable palace as parser cannot read require clause at the moment
* ifort cannot build superlu in buildcache
`ifort` is unable to handle such long file names as used when cmake compiles
test programs inside build cache.
* Fix spack commit for intel compiler installation
* Need to fetch other commits before using them
* fix style
* Add TODO
* Update packages.yaml to not use 'compiler:', 'target:' or 'provider:'
Synchronize with changes in https://github.com/spack/spack-configs/blob/main/AWS/parallelcluster/
* Use Intel compiler from later version (orig commit no longer found)
* Use envsubst to deal with quoted newlines
This is cleaner than the `eval` command used.
* Need to fetch tags for checkout on version number
* Intel compiler needs to be from version that has compatible DB
* Install intel compiler with commit that has DB ver 7
* Decouple the intel compiler installation from current commit
- Use a completely different spack installation such that this current pipeline
commit remains untouched.
- Make the script suceed even if the compiler installation fails (e.g. because
the Database version has been updated)
- Make the install targets fall back to gcc in case the compiler did not install
correctly.
* Use generic target for x86_64_vX
There is no way to provision a skylake/icelake/zen runner. They are all in the
same pools under x86_64_v3 and x86_64_v4.
* Find the intel compiler in the current spack installation
* Remove SPACK_TARGET_ARCH
* Fix virtual package index & use package.yaml for intel compiler
* Use only one stack & pipeline per generic architecture
* Fix yaml format
* Cleanup typos
* Include fix for ifx.cfg to get the right gcc toolchain when linking
* [removeme] Adding timeout to debug hang in make (palace)
* Revert "[removeme] Adding timeout to debug hang in make (palace)"
This reverts commit fee8a01580489a4ea364368459e9353b46d0d7e2.
* palace x86_64_v4 gets stuck when compiling try newer oneapi
* Update comment
* Use the latest container image
* Update gcc_hashes to match new container
* Use only one tag providing tags per extends call
Also removed an unnecessary tag.
* Move generic setup script out of individual stack
* Cleanup from last commit
* Enable checking signature for packages available on the container
* Remove commented packages / Add comment for palace
* Enable openmpi@5 which needs pmix>3
* don't look for intel compiler on aarch64
* py-python-lsp-server: add v1.10.0
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-wheel from package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Running a `spack-python` script like this:
```python
import spack
import multiprocessing
def echo(args):
print(args)
if __name__ == "__main__":
pool = multiprocessing.Pool(2)
pool.map(echo, range(10))
```
will fail in `develop` with an error like this:
```console
_pickle.PicklingError: Can't pickle <function echo at 0x104865820>: attribute lookup echo on __main__ failed
```
Python expects to be able to look up the method `echo` in `sys.path["__main__"]` in
subprocesses spawned by `multiprocessing`, but because we use `InteractiveConsole` to
run `spack python`, the executed file isn't considered to be the `__main__` module, and
lookups in subprocesses fail. We tried to fake this by setting `__name__` to `__main__`
in the `spack python` command, but that doesn't fix the fact that no `__main__` module
exists.
Another annoyance with `InteractiveConsole` is that `__file__` is not defined in the
main script scope, so you can't use it in your scripts.
We can use the [runpy.run_path()](https://docs.python.org/3/library/runpy.html#runpy.run_path) function,
which has been around since Python 3.2, to fix this.
- [x] Use `runpy` module to launch non-interactive `spack python` invocations
- [x] Only use `InteractiveConsole` for interactive `spack python`
Often in containers, the files we use to detect whether a cray system supports new features are not available.
Given that the cray containers only support the newer versions, and that these versions have been
around for a while at this point and few sites don't support them, this PR changes the logic for
detecting cray systems so that:
1. Don't even consider whether something is the `cray` platform if `opt/cray` is not in `MODULEPATH`
2. Only use the `cray` platform if we can read files in /opt/cray/pe and positively detect an older version
3. Otherwise, assume we're *not* on a cray (includes newer Cray PE's, which we treat as Linux)
Compilation with the old flags fails on PowerPC (power8le) due to syntax
errors in the output from the preprocessor. Compilation with the
extended set of flags works both on PowerPC and x86_64.
The correct set of flags was suggested from the berkeleygw developers:
https://groups.google.com/a/berkeleygw.org/g/help/c/ewi3RZgOyeE/m/jSIoe45PAgAJ
Uses spack-provided compiler prefix to call cpp when compiling berkeleygw with gcc.
Adds variants to turn off tests
Add variants for some missing TPL options
Add the variables required to build in ~shared
* Add pamgen to Trilinos as a variant to support SEACAS
This adds the ability to turn off and on pamgen as needed
through the variant interface for the Trilinos package.py.
Add changes for seacas package.py to build the appropriate
Trilinos variants.
Add zlib-api as depends_on instead of zlib directly for SEACAS
package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Add variant typescript for py-jupyter-server@:1, which then requires npm/node. Patch the build system for ~typescript so that it doesn't find any npm/node installations and attempts to build the typescript extension even though it shouldn't
* Fix formatting in var/spack/repos/builtin/packages/py-jupyter-server/package.py
* Constrain typescript variant to py-jupyter-server versions 1.10.2:1
* with when not needed if variant doesn't exist for other versions
This should fix issue #43192
Basically, had issue where a make variable was set to the output
of a shell function which included cd commands, and then the value
of that variable used as a makefile target.
The cd commands in the shell function caused assorted informational
messages (e.g. "Entering directory ...") which got included in the
return of the shell function, corrupting the value of the variable.
The presence of colons in the corrupted value caused make to issue
"multiple target" erros.
This fix adds --no-print-directory flags to the calls to the
make function in the package's build method, which resolves the
issue above.
It is admittedly a crude fix, and will remove *all* informational
messages re directory changes, thereby potentially making it more
difficult to diagnose/debug future issues building this package.
However, I do not see a way for to turn off these messages in a
more surgical manner.
* mgard: don't restrict protobuf version more than necessary
successfully built:
mgard@2022-11-18 ^protobuf@3.{4,21,25}
mgard@2023-01-10 ^protobuf@3.{4,25}
mgard@2023-03-31 ^protobuf@3.{4,25}
compile failures:
mgard@2022-11-18 ^protobuf@3.3
mgard@2023-01-10 ^protobuf@3.3
mgard@2023-03-31 ^protobuf@3.3
* mgard: add conflicts to address CI errors
* mgard: conflict between cuda and abseil@20240116.1
compiling mgard+cuda with gcc@12.3.0 and nvcc from cuda@12.3.0 against
protobuf pulling in abseil-cpp@20240116.1 results in the errors reported
here: https://github.com/abseil/abseil-cpp/issues/1629
* py-shacl: new version, update dependencies
Also updates the dependencies py-prettytable and py-rdflib.
* review comments
* Update var/spack/repos/builtin/packages/py-pyshacl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-poetry-core: add required 1.8.1
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`jinja2` can be a costly import, and right now it happens at startup every time we run
Spack. This slows down `spack --print-shell-vars` a bit, which is needed by `setup-env.*sh`.
Patch allowing Clingo to build with VS22 has landed both in Spack
and Clingo upstream, update Spack's bootstrap constraints to handle
this.
Additionally, properly scope the patch application in the clingo
package to handle upstream patch.
Currently (outside of this PR) when you `spack develop` a path, this path is treated as the staging
directory (this means that for example all build artifacts are placed in the develop path).
This PR creates a separate staging directory for all `spack develop`ed builds. It looks like
```
# the stage root
/the-stage-root-for-all-spack-builds/
spack-stage-<hash>
# Spack packages inheriting CMakePackage put their build artifacts here
spack-build-<hash>/
```
Unlike non-develop builds, there is no `spack-src` directory, `source_path` is the provided `dev_path`.
Instead, separately, in the `dev_path`, we have:
```
/dev/path/for/foo/
build-{arch}-<hash> -> /the-stage-root-for-all-spack-builds/spack-stage-<hash>/
```
The main benefit of this is that build artifacts for out-of-source builds that are relative to
`Stage.path` are easily identified (and you can delete them with `spack clean`).
Other behavior added here:
- [x] A symlink is made from the `dev_path` to the stage directory. This symlink name incorporates
spec details, so that multiple Spack environments that develop the same path will not conflict
with one another
- [x] `spack cd` and `spack location` have added a `-c` shorthand for `--source-dir`
Spack builds can still change the develop path (in particular to keep track of applied patches),
and for in-source builds, this doesn't change much (although logs would not be written into
the develop path). Packages inheriting from `CMakePackage` should get this benefit
automatically though.
Add current versions of the 17 and 18 releases
Stop making it nearly impossible to compose this correctly with code built with gcc
Build for compatibility by default like we do in every other llvm package
The `patch()` directive can now be invoked with `reverse=True` to apply a patch in reverse.
This is useful for reverting commits that caused errors in projects, even if only the forward
patch is available, e.g. via a GitHub commit patch URL.
`patch(..., reverse=True)` runs `patch -R` behind the scenes. This is a POSIX option so we
can expect it to be available on the `patch` command.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
set the FC variable to the MPI Fortran compiler and also set the F90 variable
to the same compiler for versions 9.8 and up. FC needs to be set because the
configure script still uses FC.
* unmaintained packages: add new versions
* Fix parallel and numactl
* Revert numactl changes
* rollback lua-sol2 version
* Update alluxio version format
* py-psyclone and py-fparser new releases added
* py-fparser: add missing releases for py-psyclone
* py-psyclone: actioned @adamjstewart comments
* py-psyclone: removed py-pytest-pylint
* py-pytest-pylint: added package @ latest version
* py-pytest-pylint: reformatted
* Update var/spack/repos/builtin/packages/py-psyclone/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pytest-pylint: added build deps and runtime dep versions
* py-pytest-pylint: removed version from setuptools
* py-psyclone: add py-pytest-pylint test dep and alphabetize deps
* Update var/spack/repos/builtin/packages/py-pytest-pylint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-psyclone: deps ordered
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
fixes#43097
Before this PR the behavior of mixins used together with
builders was to mask completely the callbacks defined from
the class coming later in the MRO.
Here we fix the behavior by accumulating all callbacks,
and de-duplicating them later.
* package/qgis: add new version
* improve Qsci.pro
* improve
* fix undefined symbol qsciprinter error
* add import test
* fix bug
* add version 3.36
* [@spackbot] updating style on behalf of Sinan81
* fix long line
* only run import test when +python
* first attempt at stand-alone test
* add TODO
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Sinan81 <Sinan@world>
* proj: correct CMake arg for shared build with proj older than 7.0.0
* Actually use new CMake arg
* Update var/spack/repos/builtin/packages/proj/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This adds Spack packages for these Perl distributons:
- Bio::DB::EUtilities and its dependencies:
- Bio::ASN1::EntrezGene
- Bio::Cluster
- Bio::Variation
* Properly specify Curl builder interface for static vs shared curl
with NMake system to ensure all built curls export expected
symbols.
* Symlinks curl library build artifact to more idiomatic name for
FindCurl.cmake implementations and other NMake consumers.
* Deprecating py-pylint@2.3 as it cannot build with python@3.8:
* Style fix
* Removed versions because can't build with python@3.7
---------
Co-authored-by: Gava, Francesco <francesco.gava@mclaren.com>
* py_cheap_repr: add initial package.py
* Update var/spack/repos/builtin/packages/py-cheap-repr/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cheap-repr: use pypi link instead
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Added new versions @1.5.1 and @1.4.1 (sfcgal moved from github to gitlab)
Placed restrictions on what versions of cgal are supported for different
cfcgal versions. These restrictions are based on what was found in the
version history at https://gitlab.com/sfcgal/SFCGAL/-/blob/v1.5.1/NEWS?ref_type=tags
as well as the CMakeLists.txt for different versions.
@1.4 and @1.5 seem to require a specific version of cgal based on CMakeLists.txt
Earlier versions (@1.3.8:1.3.10) claim to support cgal@4.3: (but Spack recipe
claims did not work until @4.7, so sticking with that as minimum). CMakeList.txt
suggests they support cgal@5 as well, but version history suggests otherwise.
* Expanding the duckdb package to fix the version number (required for external extensions to work) being pulled from git and have variants for the built-in extensions at build-time. This also changes the build system from CMakePackage to Makefile package (as advised from upstream).
* - Reorganized and cleaned up variants
- Updated the patch to work for 0.10.0+
- Removed (or made non-default) some unecessary variants
- Added ninja as the default generator
- Set up some shared library dependencies;
* enable tensorflow-2.11 support for ROCm
* add latest sha for mesa and limit the patches to older version.similar
changes in #37910 to enable gitlab-ci pass
* address review commemts
Remove dependency on `importlib_metadata` and `pkg_resources`, which can be problematic if the version in PYTHONPATH is incompatible with the interpreter Spack is running under.
* Kokkos Kernels: adding missing TPLs and pre-conditions
Adding variants and dependencies for rocBLAS and rocSPARSE.
Also adding a "when=" close to the TPL variants that prevents
enabling the TPLs in versions of the library when it was not
yet available.
* Kokkos Kernels: remove comment for better format
* Kokkos Kernels: fix issue with unpacking wrong number of args
After changing the tpls dictionary we need to update the unpacking
logic to catch the right number of outputs out of it!
* Kokkos Kernels: updating doc string for tpls var and using f-string
Improving comment a bit and switching to f-string for more readability.
When setup to do more testing will try to use f-string in the CMake
options generation part of the package.
* Style change
* sst-core now effectively depends on ncurses
* use --with-curses
* sst-core: update comment about ncurses
* should have curses for build, link, and run
Closes#43052.
Maybe moving the argument to the `find` subcommand is a good idea, but I
just wanted to get the docs fix out.
Co-authored-by: Patrice Peterson <patrice.peterson@itz.uni-halle.de>
This PR adds the ability to load spack extensions through `importlib.metadata` entry
points, in addition to the regular configuration variable.
It requires Python 3.8 or greater to be properly supported.
#42878 adds a post install filter of the netCDFConfig.cmake file
that replaces a valid CMake target on Windows with an invalid one.
Don't do this replacement on Windows.
* Updates for migraphx 6.0.0 & 6.0.2
* Style check error and audit check error fix
* Adding patch for half-include-directory
* The parameter GPU_TARGETS is used from 5.7 in migraphx
* Adding rocmlir dependency in migraphx and 6.0 updates in rocmlir
* Applying upcoming changes to make CK JIT optional and enable
compilation on Windows in order to build without ck dependency
* mpfr: missing dependency for version 4.0.1
mpfr 4.0.1 (like 4.0.2) needs autoconf-archive where it takes the
AX_PHREAD macro from
* autoconf-archive is also required for mpfr@4.0.0
New changes have been made to nvptx-tools that address dropping support
for sm_30 in later CUDA versions (12.0+).
Also refactor gcc to make nvptx-tools a dependency instead of a resource.
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Adds CHI::Driver::Memcached.
Modified perl-chi to make the tests work. Testing modules in perl-chi
were not loaded when testing CHI::Driver::Memcached, so added the "run"
type to these.
* ASP-based solver: improve reusing nodes with gcc-runtime
This PR skips emitting dependency constraints on "gcc-runtime",
for concrete specs that are considered for reuse.
Instead, an appropriate version of gcc-runtime is recomputed
considering also the concrete nodes from reused specs.
This ensures that root nodes in a DAG have always a runtime
that is at a version greater or equal than their dependencies.
* Add unit-test for view with multiple runtimes
* Select latest version of runtimes in views
* Construct result keeping track of latest
* Keep ordering stable, just in case
1) support for version @3.0
Unfortunately, download seems to require registration now
so using manual_download mechanism for @3:
2) copying from hdf-eos5 patch from @vanderwb to enable
use of Spack compiler wrappers instead of h4cc
3) Patching an issue in hdf-eos2 configure script. The
script will test for jpeg, libz libraries, succeed and
append HAVE_LIBJPEG=1, etc to confdefs.h, and then abort
because HAVE_LIBJPEG not set in running environment.
4) Add some LDFLAGS to build environment. Otherwise
seems to fail to build test script due to rpc dependence
in HDF4.
Adds Net::Server::SS::PreFork and its dependencies.
Installed OK with build-time tests. Added dependencies:
- Server::Starter
- Net::Server
- HTTP::Server::Simple
Adds Catalyst::Action::RenderView and its dependencies.
Installed OK with build-time tests. Added dependencies:
- Catalyst::Action::RenderView
- Catalyst::Action::RenderView
- Catalyst::Action::RenderView
* package/imagemagick add new version, improve
* confimed that build fails when libsm is missing on linux
---------
Co-authored-by: Sinan81 <Sinan@world>
* perl-chi and deps: new packages
Adds CHI and its dependencies.
Installed OK with build-time tests. Added dependencies:
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
* Add license
* legion: Add 23.09.0 and 23.12.0, remove control_replication.
The branch control_replication has been merged to master and should no
longer be used.
* flecsi: Switch to Legion master branch.
Legion control_replication has been merged to master.
* Fix Legion 23.09.0 and 23.12.0 build for ROCm 6.
* Add ncvis and opengl option for wxwidgets
* Style fixes for ncvis
* Replace in with satisfies for opengl constraint
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
* when built with cmake, libogg does not build with a shared libary by default. This resolves that
* spack style fixes
* Clean up imports
* enforce +pic when +shared
* Execute `args.help` after setting main options so that extension commands will show with `spack -h`
---------
Co-authored-by: psakievich <psakiev@sandia.gov>
* Update package.py
1. add one compiler type named 'musl'
2. add a variant name 'multilib'
3. add a variant name 'cmodel'
* Added one compiler type named 'musl'.
Added a variant named 'multilib'.
Added a variant named 'cmodel'.
Added several versions.
* aarch64 is not supported.
The deps were added in #40945 to make it work on macOS 11, because the
old configure scripts only detect macOS 10. Apparently people reported the
autoreconf script caused issues, later fixed in #41057. However, also
with that fix, things are incorrect, cause people now report:
```
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.7
libtool: and run autoconf again.
```
HOWEVER, all this is unnecessary, because the underlying issue was
already fixed long ago, it's just that it regressed at some point, but
it's back in place since #41205.
This adds Readonly::XS. Since this module can not be used by itself, the
Spack package comes with a test override. This anticipates that the perl
builder will one day have a generic standalone module usage test.
This should fix issue #40780
We explicitly cast self.spec["python"].command to str in the filter_file
call in _fix_dtrace_shebang to avoid the error
==> Error: TypeError: expected str, bytes or os.PathLike object, not Executable
Not sure why the error is appearing (is it only for specific python versions, etc?),
but the fix should be quite safe.
* e4s: new packages: glvis, laghos
* gl: require: osmesa
* be explicit: glvis ^llvm so that llvm-amdgpu not chosen
* glvis fails on oneapi stack due to issue 42839
Spack merges ranges and concrete versions if they have non-empty
intersection. That is not enough for adjacent version ranges.
This commit ensures that disjoint ranges in version lists are simplified
if their union is not disjoint:
```python
"@1.0:2.0,2.1,2.2:3,4:6" # simplifies to "@1.0:6"
```
Libraries for openexr are named libOpenEXR*.so, etc., so the default libs
handler in spec does not find them.
Add a custom libs property to address this.
Partial fix for #42273
Co-authored-by: payerle <payerle@users.noreply.github.com>
for various reasons had to advance dependency of 5.0.2 to at least
pmix 4.2.4. 5.0.1 and 5.0.0 can also build with 4.2.4 pmix or newer.
related to #42651
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Refactoring `SpackSolverSetup` is a bit easier with type annotations, so I started
adding some. This adds annotations for the (many) instance variables on
`SpackSolverSetup` as well as a few other places.
This also refactors `condition()` to reduce redundancy and to allow
`_get_condition_id()` to be called independently of the larger condition
function.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* py-ipyvuetify: new package
* Limit py-jupyter-packing version to 0.7.x
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix py-jupyterlab version and type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix py-ipyvue version range to exclude 2
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* rm py-wheel, already considered for PythonPackage
* fix: pynpm only required for build, reorder dependencies as in the pyproject.toml
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* snakemake: add Snakemake 8 with dependencies
* snakemake: add missing description
* Whitespace
* Whitespace
* Whitespace
* Whitespace
* py-conda-inject: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-azure-batch: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-cluster-generic: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake: add upper bound for Python
* py-snakemake-executor-plugin-drmaa: specify dependency type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-googlebatch: correct dependency version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-tes: correct dependency version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-storage-plugin-s3: reorder
* snakemake: remove newly added variants
* snakemake: remove newly added variants
* snakemake: remove newly added variant
* snakemake: update version
* snakemake: update version
* snakemake: whitespace
* py-snakemake-storage-plugin-s3: update version
* snakemake: use newer version
* snakemake: whitespace
* snakemake: update interfaces
* py-snakemake-storage-plugin-gcs: link issue
* snakemake: update versions
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* package/libspatialite: add conflict, new version
* depends on new version of freexl
* fix bug
* remove manual download stuff
* improve style
* first depracate
* [@spackbot] updating style on behalf of Sinan81
* get rid of conflict, reorder deps
* remove manual download
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
* Allow awscli-v2 to be installed without examples/ dir
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* Update var/spack/repos/builtin/packages/awscli-v2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The CMake-based build is anticipated to work in all cases where the
Autotools-based build did, and to address all prior issues with less
maintenance of the package. In detail:
* Fixes#42735 (CMake's find_package helps with linking to proper
netcdf-c)
* Replaces older Autotools-based build
* All preexisting variants are handled
* Record hdf5 as an explicit dependency (was missing before)
* Add +tests option
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
* proj: apply stdint.h patch in version 8
* Update var/spack/repos/builtin/packages/proj/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Some builds on Windows break when encountering paths with spaces. This
reencodes some paths in Windows 8.3 filename format (when on Windows):
this serves as an equivalent identifier for the file, but in a form that
does not have spaces.
8.3 filenames are also truncated in length, which could be helpful, but
that is not the primary intended purpose of using this format.
Overall
* nmake/msbuild packages do this generally for the install prefix
* curl/perl require additional modifications (as written now, each package
may require calls to `windows_sfn` to work when the Spack
root/install/staging prefixes contain spaces)
Some items for follow-up:
* Spack itself does not create paths with spaces "on top" of whatever
the user configures or where it is placed (e.g. the Spack root, the
staging directory, etc.), so it might be possible to edit some of these
paths once and avoid a proliferation of individual `windows_sfn`
calls in individual packages.
* This approach may result in the insertion of 8.3-style paths into
build artifacts (on Windows), handling this may require additional
bookkeeping (e.g. when relocating).
* Move spec_list into its own file, instead of __init__.py
* Remove spack.schema.spack
This module was introduced in #33960 It's almost an exact duplicate of
spack.schema.env, and is not used anywhere.
* Fix typo
* adds the spack recipe for py-jwcrypto
* split long line to fix E501
* Specify versions for py-cryptography and py-typing-extensions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* adds the spack recipe for reacton python package
* Fix versions for ipywidgets and typing-extensions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-find-libpython: new package
* Update var/spack/repos/builtin/packages/py-find-libpython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add spack recipe for ipyvue
* Specify version for ipywidgets
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
fix bug.
* Update var/spack/repos/builtin/packages/pdal/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ansible: add v2.16.3
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add specific python version requirements from setup.cfg
* Add additional ranges for py-setuptools
* Update var/spack/repos/builtin/packages/py-ansible/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Compiling version 2.2.4 fails (on a Debian system with only a minimum set of packages installed) with an error because `INT_MAX` is undeclared:
```
263 gd_gd2.c: In function '_gd2GetHeader':
>> 264 gd_gd2.c:212:54: error: 'INT_MAX' undeclared (first use in this function)
265 212 | if (*ncx <= 0 || *ncy <= 0 || *ncx > INT_MAX / *ncy) {
266 | ^~~~~~~
267 gd_gd2.c:87:1: note: 'INT_MAX' is defined in header '<limits.h>'; did you forget to '#include <limits.h>'?
```
* pythia6: deal with dead pythiasix.hepforge.org
* pythia6: rm main81.f from CMakeLists.txt
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Any package `X` used as `depends_on("x", type="build")` will have
`X.setup_run_environment(env)` called, because it has to be able to
"run" in the build environment.
So there is no point in calling `setup_run_environment` from
`setup_dependent_build_environment`.
Also it's redundant to call `setup_run_environment` in
`setup_dependent_run_environment`, cause (a) the latter is called _for
every parent edge_ instead of once per node, and (b) it's only called
after `setup_run_environment` is called anyways. Better to call
`setup_run_environment` once and only once.
fftw object was originally created with spec["fftw:openmp"], but
referencing spec["fftw"] overwrites the 'last_query' in the spec object,
so later use of fftw.libs was not returing FFTW OpenMP libs.
Also allow the post-install fixup to support amdfftw as well as fftw.
Co-authored-by: Branden Moore <branden.moore@amd.com>
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
* new builtin package: py-biobb-model
* Update var/spack/repos/builtin/packages/py-biobb-model/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add package py-jacobi
* fix: add description
* fix: add description
* fix: add description
* [@spackbot] updating style on behalf of jonas-eschle
* Update package.py
* Update package.py
* Update var/spack/repos/builtin/packages/py-jacobi/package.py
I don't think that numpy is used in "build"? But not important
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: jonas-eschle <jonas-eschle@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-google-cloud-storage: add new versions
* py-google-api-core: add new versions
* py-proto-plus: add new package
* py-google-api-core: add grpc variant
* py-google-api-core: add grpc variant
* py-google-api-core: add missing prefix
* py-google-cloud-batch: add new package
* py-google-cloud-logging: add new package
* py-google-cloud-appengine-logging: add new package
* py-google-cloud-audit-log: add new package
* py-grpc-google-iam-v1: add new package
* py-proto-plus: remove obvious dependency
* Whitespace
* Whitespace
* py-google-cloud-audit-log: correct conflict
* py-proto-plus: correct dependency type
* Whitespace
* py-google-auth: add new version
* py-google-resumable-media: add new version
* py-google-cloud-storage: constrain version of dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-grpcio-status: use newer version
* py-google-resumable-media: add upper bound of dependency
* Add types of dependencies.
* py-grpcio: add new version
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-smote-variants: Added package py-smote-variants
Also added py-minisom and py-metric-learn as dependencies
* py-metric-learn: Added build dependency on setuptools
* py-smote-variants: Added a dependency on py-pytest-runner
As well as a comment about why statistics isn't included
* [@spackbot] updating style on behalf of alex391
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* py-charm4py: needs Cython<3.0
* Update var/spack/repos/builtin/packages/py-charm4py/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Kokkos Ecosystem: update for release 4.2.01
Will rebase this on top of develop once Kokkos Core PR merges.
* Kokkos Ecosystem: update license statement to reflect current license
* helics: Add version 3.5.0
* helics: define CMAKE_CXX_STANDARD=20 when GCC>=13 is used to compile
---------
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Ryan Mast <mast9@llnl.gov>
* Add support for clang in oneapi packages with OpenMP
* Add fallback search for libomp in OneApi package with OpenMP threading
* Add requires for the compiler when using threads=openmp in intel-oneapi-mkl
* Cosmetic changes to messages in oneapi.py
* Update error message in oneapi.py
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Update another error message in oneapi.py
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Inline helper error function in oneapi.py
* Update one more error message in oneapi.py
* Wrap long line in oneapi.py
---------
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* allow packages to request no submodules be updated when self.submodules is a
callable function
* Extend the test added in Allow more fine-grained control over what submodules are
updated: part 2 #27293 to include this case
* Update the type signature for the submodules arg of version() in directives.py
---------
Co-authored-by: tjfulle <tjfulle@users.noreply.github.com>
* cmake: Enable CMAKE_EXPORT_COMPILE_COMMANDS
Enabling this option causes CMake to generate a compile_commands.json file
containing a compilation database that can be used to drive third-party tools.
CMAKE_EXPORT_COMPILE_COMMANDS only exists for CMake >= 3.5
Exporting compilation databases is only supported for Makefile and Ninja
generators, so check these conditions as well.
CMAKE_EXPORT_COMPILE_COMMANDS is only enabled in supported configurations
* khmer: new package @2.1.1
* rationalising patch
* adding dep, modifying patch
* Update var/spack/repos/builtin/packages/khmer/package.py
Indeed!
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* possvm: new package @1.2
* black!
* appeasing flake8
* Updating commit ID
* Adding graphing dep
* Update var/spack/repos/builtin/packages/py-markov-clustering/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pysftp: add new package
* py-pysftp: correct version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adds the spack recipe for building the pynpm python package
* fix license header
* Update var/spack/repos/builtin/packages/py-pynpm/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-fastremap: new package @1.14.1
* py-pyqtgraph: new package @0.13.3
* py-roifile: new package @2024.1.10
* py-superqt: new package @0.6.1
* cellpose: new package @2.2.3
* Appeasing black ...
* Dropping the cuda variant
* Update var/spack/repos/builtin/packages/py-fastremap/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding python version dependency
* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-roifile/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-superqt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding missing dep & conflict
* Appeasing black
* Adding missing py- prefix for dep
* Switching over to py-pyqt6
* Switching over to py-pyqt6
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-structure-checking
* Update var/spack/repos/builtin/packages/py-biobb-structure-checking/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* dependencies are also build dependencies
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-io
* Update var/spack/repos/builtin/packages/py-biobb-io/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-gromacs
* Update var/spack/repos/builtin/packages/py-biobb-gromacs/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added setuptools dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Bump up the version for rocm-6.0.2 release
* extend the patches that were created for apps for rocm-6.0.0 and rocm-6.0.2 releases
(but apply hipfft patch for only 6.0.0)
* gitlab: remove requests for unreferenced packages
The packages removed in this commit are not built by any of
our current GitLab CI stacks.
* gitlab: update memory requests for "huge" packages
* gitlab: reduce memory requests for overprovisioned packages
* gitlab: more memory for py-torch (again)
* gitlab: update memory but keep CPU the same
This fixes bugs, performance issues, and removes no longer necessary code.
Short version:
1. Creating views from Python extensions would error if the Spack `opt` dir itself was in some symlinked directory. Use of `realpath` would expand those, and keying into `merge_map` would fail.
2. Creating views from Python extensions (and Python itself, potentially) could fail if the `bin/` dir contains symlinks pointing outside the package prefix -- Spack keyed into `merge_map[target_of_symlink]` incorrectly.
3. In the `python` package the `remove_files_from_view` function was broken after a breaking API change two years ago (#24355). However, the entire function body was redundant anyways, so solved it by removing it.
4. Notions of "global view" (i.e. python extensions being linked into Python's own prefix instead of into a view) are completely outdated, and removed. It used to be supported but was removed years ago.
5. Views for Python extension would _always_ copy non-symlinks in `./bin/*`, which is a big mistake, since all we care about is rewriting shebangs of scripts; we don't want to copy binaries. Now we first check if the file is executable, and then read two bytes to check if it has a shebang, and only if so, copy the entire file and patch up shebangs.
The bug fixes for (1) and (2) basically consist of getting rid of `realpath` entirely, and instead simply keep track of file identifiers of files that are copied/modified in the view. Only after patching up regular files do we iterate over symlinks and check if they target one of those. If so, retarget it to the modified file in the view.
--with-ch4-max-vcis=default is no longer accepted by MPICH configure
since the 4.1 release. Just omit the option from the +vci variant, since
configure will select the default value in its absence.
Problem: Older versions of the flux-core package require czmq and
jsonschema, but these dependencies have been dropped in recent
versions.
Add `when=` arguments to drop these requirements for the appropriate
versions of flux-core.
* fix wrong versioning
use doc version and not the one extrapolated from the path (i.e. 0.2.0.1)
* nvpl-lapack requires nvpl-blas
propagate matching variants to nvpl-blas dependency
Co-authored-by: albestro <albestro@users.noreply.github.com>
* rct: update packages (RE, RG, RP, RS, RU) with new versions
* rct: updated style
* rct: 1.46 release
* rct: RP 1.46.1 (hotfix applied)
* rct: deprecated old versions
* Update var/spack/repos/builtin/packages/py-radical-entk/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-radical-pilot/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-radical-saga/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* rct: brought back dependencies for deprecated versions
* rct: RP hotfix release 1.46.2
* rct: new stack release 1.47.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ucsf-pyem: updating to commit e92cd4d
* py-pyfftw: updating to @0.13:1
* py-ucsf-pyem: correcting install of scripts
* Upper limits
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Upper limits
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* updates from github review
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add new package libsixel
* reorder to group variants and dependencies together
* Switch to using source from fork
The original developer of libsixel, Hayaki Saito (@saitoha), disappeared
in early 2020 and has not updated the repository or been seen since.
However, a fork of the project has been created at libsixel/libsixel,
and that fork has been getting much more regular updates. In this commit
I switch the package to using the better-maintained, now apparently
canonical fork of the project.
That project switched the build system from autotools to Meson, so much
of the build arguments code needed to be rewritten. The newest official
release also contained an error in meson.build which would break on
newer versions of Meson. That error only applied to the libjpeg and
libpng variants, though, so I switched the default to use libgd which
has broader format support anyway.
* blacken
* broke description into multiple lines
* allow libjpeg, etc to be loaded automatically
* apply patch to all compilers as per spack/issues/42007
* [@spackbot] updating style on behalf of Chrismarsh
* Resolve flake8 style issue from spackbot
* fix flake8 trailing whitespace
---------
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
These 7 hooks were not used.
- Six of them related to install phases were unused after `spack`
`monitor` was removed, and the code seems to have bit rotten as there
were reports they were not (always?) triggered when they should.
- The post environment one was made redundant after spack install for
environment started following the common code path for generating
module files in #42147.
It should not be a breaking change to remove, since users cannot define
hooks in extensions, they would have to fork Spack.
If we ever _were_ to make those hooks extendable outside of core Spack,
it would also be better to start with fewer rather than more, cause
everything you expose gets relied upon...
Removing those also allows us to rethink what hooks we really need, and
in particular it seems like we need a hook that runs post install also when
the spec is inserted into the database.
The lack of a rule to avoid enforcing requirements on multi-valued variants, when the condition activating the environment was not met, resulted in multiple optimal solutions. The fix is to prevent imposing a requirement if the when= rule activating it is not met.
The section was highly outdated as it referred to old defaults, and
failed to mention `hide_implicits: true`.
This commit restructures it, moves some deeply nested sections a level
up, and promotes `hide_implicits: true` + `autoload: direct` before
talking about `exclude`.
It is useful to enable/disable stacks in order to handle turning
specific stacks on/off based on runner availability, stack stability,
testing requirements, etc.
The disabled stack list takes precedence over the enable stack list. The
assumption is that stacks that are disabled are so due to some
functionality missing or broken for that stack.
The enable stack list implicitly disables all stacks not listed in the
enable list.
* Registry queries can fail due to simultaneous access from other
processes. Wrap some of these accesses and retry when this may
be the cause (the generated exceptions don't allow pinpointing
this as the reason, but we add logic to identify cases which
are definitely unrecoverable, and retry if it is not one of
these).
* Add make recursion optioal for most registry search functions;
disable recursive search in case where it was originally always
recursive.
* py-pythran: apply patch to fix compilation with GCC 13
* Update var/spack/repos/builtin/packages/py-pythran/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix ipyrad numpy depedencies
ipyrad versions through 0.9.90 use np.int, which is deprecated in numpy 1.20.
* fix whitespace
* Correct numpy dependency restrictions
Fix two separate problems:
1. We want to always visit parents before children while creating views
(when it comes to ignoring conflicts, the first instance generated in
the view is chosen, and we want the parent instance to have precedence).
Our preorder traversal does not guarantee that, but our topological-
order traversal does.
2. For copy style views with packages x depending on y, where
<x-prefix>/foo is a symlink to <y-prefix>/foo, we want to guarantee
that:
* A conflict is not registered
* <y-prefix>/foo is chosen (otherwise, the "foo" symlink would become
self-referential if relocated relative to the view root)
Note that
* This is an exception to [1] (in this case the dependency instance
overrides the dependent)
* Prior to this change, if "foo" was ignored as a conflict, it was
possible to create this self-referential symlink
Add tests for each of these cases
* Sqlite requires the user to provide a command line arg (DYNAMIC_SHELL)
to export shared symbols to import lib from .def
* Add other options recommended by Sqlite docs:
https://github.com/sqlite/sqlite/blob/master/doc/compile-for-windows.md
* Some of these options mean we can restore variants that were
disabled for Windows (fts, functions, rtree).
* Updated with generic test functions
* Added level_zero test
As the compiler is not installed by TAU, it should be loaded first and run with --dirty. Will check if there is a way to make it work without --dirty.
* Update var/spack/repos/builtin/packages/tau/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
The main script body is over-written for power. Putting thet timing
aggregation in the after script allows it to be called on all of the
current pipelines.
* Update package.py
Add support for OpenSubdiv 3.5.x
* Fixed Dependencies
I was getting errors about cmake not being able to find `xf86vm`, and adding a dependency on `libxxf86vm` fixes it.
Sometimes the logs are too long and the copy & paste command is not
shown. In that case I'd like to just copy the failing GitLab job URL in
my browser to `spack reproduce-build <url>`.
Currently, the `SpackSolverSetup` and the `PyclingoDriver` are more coupled than necessary:
1. The driver object needs a setup object to be injected during a solve,
2. And the setup object will get a reference back to the driver
This design is necessary because we use the low-level `clingo.backend` interface to setup our problem. This interface though is meant to bypass the grounder and add symbols directly in the grounded table, which is a feature we don't currently use.
The PR simplifies the encoding by having the setup object returning the problem-specific facts / rules as a list of strings, and the driver ingesting them using the [clingo.Control.add](https://potassco.org/clingo/python-api/5.6/clingo/control.html#clingo.control.Control.add) method. This removes any use of the low level interface.
Using this encoding makes it easy to hash the output of the setup phase, since it is returned as a string.
* py-nbconvert: avoid install-time downloads
* install css files as resources for py-nbconvert
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* py-nbconvert: update dependencies for 7.14.1
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update resources & remove style.min.css file
* Update package.py
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This "breaks" the deprecated schema by allowing unknown attributes
to the attributes section of the job types. The breaking change here is
that deprecated stacks will no longer ignore attributes that are unknown
but rather assume the new CI schema behavior of injecting them into the
generated CI configuration. This change is required to secure
authentication in Spack CI.
Improve naming, so it's clear file "extensions" are not taken in the
`PurePath(path).suffix` sense as the original function name suggests,
but rather that the files are opened and their magic bytes are
classified.
Add type hints.
Fix a bug where `stream.read(num_bytes)` was run on the compressed
stream instead of the uncompressed stream, which can potentially break
detection of tar.bz2 files.
Ensure that when peeking into streams for magic bytes, they are reset to
their original position upon return.
Use new API in `spack logs`.
Relocation of `PT_INTERP` in ELF files already happens to work from long to short path, thanks to generic binary relocation (i.e. find and replace). This PR improves it:
1. Adds logic to grow `PT_INTERP` strings through patchelf (which is only useful if the interpreter and rpath paths are the _only_ paths in the binary that need to be relocated)
2. Makes shrinking `PT_INTERP` cleaner. Before this PR when you would use Spack-built glibc as link dep, and relocate
executables using its dynamic linker, you'd end up with
```
$ file exe
exe: ELF 64-bit LSD pie executable, ..., interpreter /////////////////////////////////////////////////path/to/glibc/lib/ld-linux.so
```
With this PR you get something sensible:
```
$ file exe
exe: ELF 64-bit LSD pie executable, ..., interpreter /path/to/glibc/lib/ld-linux.so
```
When Spack cannot modify the interpreter or rpath strings in-place, it errors out without modifying the file, and leaves both tasks to patchelf instead.
Also add type hints to `elf.py`.
Certain versions of ifx (the majority of those available) have an issue
where they are not compatible with TMP directories with dot chars
This precludes their use with CMake.
Remap TMP to point to the stage directory rather than whatever the TMP
default is
* Add fenics development version and ufl-legacy
* Make sure python and setuptools are added to ufl-legacy and add version 2022.3.0 as well
* Run black and add maintainer to fenics package
* Fix typo
* Use Fiat version 2019.1.0
* Run black
* Add back master branch of fiat
* Remove master from the list of dolfin versions and add one extra line of each deps instead
* Run black
* Do not specify python version in ufl-legacy
* Remove python dependency from ufl-legacy
* Remove python dependency from ffc
* Add special case for master in ffc
* Run black
* Remove master from loop in ffc
* Run black again
* geopm: Mark all as deprecated
- This recipe will be removed in a future release.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-sphinx-emoji
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-dasbus
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-pygobject: Add v3.46.0
- Previous versions error during build phase.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-sphinx-tabs: Add new versions
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add geopm-service
- Previous geopm package is now 2 packages:
geopm-service and geopm-runtime.
- The GEOPM service is designed as a systemd/dbus
service providing a userspace interface to
privileged hardware telemetry and configurations.
- Installing via spack will enable some userspace
testing, but generally most users will want to
install the GEOPM service via the system package
manager as root to get full functionality.
- This recipe will enable the creation of the fully
userspace geopm-runtime recipe which will replace
the old geopm recipe.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
---------
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-textual: New package py-textual
* py-textual: Depend on py-mdit-py-plugins
* py-textual: Added dependency on python@3.8:3
* py-textual: Added a comment about why there is a dependency on
py-mdit-py-plugins
* py-textual: Ran black
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* add pytest-aiohttp
* black
* py-setuptools -> py-setuptools-scm
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
VTK struggles to consume some Spack-derived packages on Windows:
Patch VTK to allow a smoother integration
Also add install for examples as they are not part of the install
interface.
gl2ps tries to build static and shared libs simultaneously with
the same target name on the generator side. This causes a name
clash issue for Ninja on Windows (where the extension is .lib
in both cases).
Add a variant on Windows to force building only one of shared
or static, and patch the CMake build to enable use of this
variant.
* gitlab: remove commented-out duplicate entries
* gitlab: reclassify some packages from "huge" to "large"
Our observed max memory usage for these packages is as follows:
hipblas: 7.7G
qt: 6.6G
visit: 9.7G
All of these should fit within a "large" request (currently 12G).
* gitlab: remove pango from list of huge packages
This package is not currently built by any of our CI stacks.
* gitlab: update requests for high memory packages
Refine resource requests for memory-intensive packages based on
max memory usage data.
- Adds perl-sql-translator and its missing deps:
- Adds perl-import-into
- Adds perl-package-variant
- Adds perl-strictures
Built with build-time tests and comes with a simple run-time test.
Add the empty deptype `spack.deptypes.NONE`.
Test the case `traverse_nodes(deptype=spack.deptypes.NONE)` to not
traverse dependencies, only de-duplicate.
Use the construct in environment views that otherwise would branch on
whether deps are enabled or not.
* ensure umpire~cuda~rocm when ~cuda~rocm
* MDAnalysis: add v2.7.0
* Apply suggestions from code review
* license
* review changes
* add gsd and py-cmake versions
* Update package.py
* py-cmake
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix and reorder
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add py-vl-convert-python
* code format
* Update package.py
add homepage
* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove old versions, add todo
* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove blank line
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package: py-metrics
* [py-metrics] cleaned up extra comment
* Updated copyright and ran black
* py-pathspec: Added version 0.5.5
---------
Co-authored-by: vehrc <vehrc@rit.edu>
Co-authored-by: Jen Herting <jen@herting.cc>
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* py-frozendict: patch up for Python 3.11
See also Marco-Sulla/python-frozendict#68, rely on a pure Python
implementation when 3.11+ is used.
* mention related Github issue
* new builtin package: biobb-common
* removed whitespace for the style test
* replaced ' by " for the style test
* changed import line for the style test
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed test
* using pypi instead of git
I hope this is declared the right way.
I tried to test it locally but I am having problems with a dependency (openblas) thus I can not even try if this works.
* upgraded version
* Added py prefix
* removed biopython version restriction
* directory with new py-prefixed name
* Delete old non-prefixed package
* Update var/spack/repos/builtin/packages/py-biobb-common/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update tarball urls, add new versions and update maintainers
* remove unnecessary variant like cross-compile
* use self.define and self.define_from_variant
* improve regex / bug that matches with -DMPICH_SKIP_MPICXX=1
Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Previously, for abstract specs like:
```
foo ^[virtuals=a] bar ^[virtuals=b] bar
```
the second requirement was silently discarded on concretization. Now they're merged, and the abstract spec is equivalent to:
```
foo ^[virtuals=a,b] bar
```
* Added countdown repo
* Added fixed version of COUNTDOWN
* Style fixes
* Changed mantainer syntax
* Variants listed in alphabetical order by name
* Added conflicts and some reordering
* Fixed conflicts syntax
* Style fixes
* [@spackbot] updating style on behalf of danielecesarini
---------
Co-authored-by: danielecesarini <danielecesarini@users.noreply.github.com>
CMake may write and read from `~/.cmake` through `export(...)` and read `find_package(...)` respectively. We don't want this as it may influence the build in a non-deterministic way, so disable it for all versions of `cmake`.
* Trilinos: Add AMD to SuiteSparse TPL list
When Trilinos is built with SuiteSparse support, it should enable AMD as
one of the TPLs. It was previously enabling only UMFPACK. The Xyce
package uses AMD (but not UMFPACK).
* Xyce: Add 7.8 release and various improvements
In addition to adding the latest Xyce release (7.8), all the earlier
releases were deprecated, with the exception of 7.7.
The Trilinos specification was updated to remove unneeded packages,
explicitly enable all needed packages, and specify additional
do-not-build packages.
The serial build is now the default, with MPI still being an option.
I also epanded the explanation for one of the patches; and, finally, I
took the opportunity to update the Xyce description to better match the
current Xyce README description.
Fixes a bug where Spack did not generate module files of non-roots during
spack install with an active environment.
The reason being that Environment.new_installs only contained roots.
This PR:
Drops special casing of automatic module generation in post-install hooks
When `use_view`, compute environment variable modifications like always, and
applies a view projection to them afterwards, like we do for spack env activate.
This ensures we don't have to delay module generation until after the view is
created.
Fixes another bug in use_view where prefixes of dependencies would not be
projected -- previously Spack would only temporarily set the current spec's prefix.
Removes the one and only use of the post_env_write hook (but doesn't drop it to
make this backportable w/o changes)
Previously `std_args` was called on non-roots in a build context, which is redundant, and also leads to issues when `std_args` expects build deps of the `pkg` to be installed.
HPCToolkit `develop` now can optionally be built via Meson. This PR adds the `build_system=(autotools|meson)` variant and splits the build-system-dependent pieces into `AutotoolsBuilder` and `MesonBuilder`. The default is to build with `autotools`.
As of writing, the Meson is simply a wrapper around the original Autotools build, hence the build requires a native file listing install prefixes of all dependencies (which are internally mapped to `--with-{pkg}={prefix}` arguments for `./configure`). This is an unconventional but temporary state of affairs until the build system is fully ported to Meson and conventional dependency acquisition techniques like `pkg-config` and `cmake` are practically available.
* Environments: fix environment config
* Don't change the lockfile manifest path
* Update activate's comments to tie the manifest to the configuration
* Add spec_list override method
* Remove type checking from 'activate' since already have built-in check
* Refactor global methods tied to the manifest to be in its class
* Restore Environment's 'env_subdir_path' and pass its config_stage_dir to EnvironmentManifestFile
* Restore global env_subdir_path for use by Environment and EnvironmentManifestFile
The CUDA target should be specified at build time, otherwise
by default `autodock-gpu` will be built for compute capabilities
52, 60, 61, 70, which may cause errors on unsopported cards.
Currently requirements allow to express "strong preferences" and "conflicts" from
configuration using a convoluted syntax:
```yaml
packages:
zlib-ng:
require:
# conflict on %clang
- one_of: ["%clang", "@:"]
# Strong preference for +shared
- any_of: ["+shared", "@:"]
```
This PR adds syntactic sugar so that the same can be written as:
```yaml
packages:
zlib-ng:
conflict:
- "%clang"
prefer:
- "+shared"
```
Preferences written in this way are "stronger" that the ones documented at:
- https://spack.readthedocs.io/en/latest/packages_yaml.html#package-preferences
`spack install` early exit behavior was sometimes convenient, except
that it had and has bugs:
1. prior bug: we didn't mark env roots of already installed specs as
explicit in the db
2. current bug: `spack install --overwrite` is ignored
So this PR simplifies by letting the installer do its thing even if
everything is supposedly installed.
* Bump up the version for ROCm-6.0.0
* Adding patch files
* Style check failure fix
* Style check fixes
* Style check error fixes
* Patch to remove hipblas client file installation in 6.0
* Patch need to be applied on all 5.7 relases
* 6.0 update for math libs and other packages, new github url etc
* Correct package-audit failures
* Correcting shasum for rocfft patch and limiting patch in rocblas
* Reverting updates in rocprofiler-dev due to ci-gitlab failure
* Fixes for ci-gitlab failure due to disabling hip backward compatibilit
* Adding patch file to Change HIP_PLATFORM from HCC to AMD and NVCC to NVIDIA
* Use the gcnArchName inplace of gcnArch as gcnArch is deprecated from rocm-6.0.0
* Patches to fix magma and blaspp build error with rocm 6.0.0
* Patch for mfem and arborx for rocm 6.0
* Style check error fix
* Correcting style check errors
* Uodating dependent version
* Update for petsc to build with rocm 6.0
Need reverting-operator-mixup-fix-for-slate.patch for rocm 6.0
* Reverting the change in url for 2.7.4-rocm-enhanced
* hip-tensor 6.0.0 update
This commit ensures that CMake packages that also have Python as a build/link dep get a couple defines for the Python path so that CMake's builtin `FindPython3`, `FindPython`, `FindPythonInterp` modules can locate Python correctly.
The main problem with those CMake modules is that they first search for Python versions known at the time of release, meaning that old CMake maybe find older system Python 3.8 even though Python 3.11 comes first in `CMAKE_PREFIX_PATH` and `PATH`.
Package maintainers can opt out of this by overriding the `find_python_hints = False` attribute in the package class.
* Add nglview package
* Use slightly older version
* py-nglview: Correct py-versioneer version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-nglview: Correct version of py-jupyter-packaging dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-versioneer-518 package
* py-versioneer-518: Correct version
* py-nglview: Numpy is needed during build for the tests
* py-nglview: dependency needed for tests
* py-nglview: Correct dependency types
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* e4s ci: use latest intel/hpckit 2024 based image
* use latest container image: ecpe4s/ubuntu22.04-runner-amd64-oneapi-2024.0.0:2023.12.01
* comment out failing specs
* update to use patched container
* remove generalized package preference for intel-oneapi-mkl@2023
* change packages commented out
* VecGeom: new version 1.2.7 and fix URLs
* vecgeom: remove deprecated ancient RC version with incorrect hash
* geant4: remove support for @10.3+vecgeom
The piece of code that is removed in this PR predates environment views.
Spack would symlink build logs in `<env>/.spack-env/logs/*`, but this is
redundant because:
1. Views already add `<prefix>/.spack` (and there's logic there to avoid
clashes)
2. The code was broken anyways: it would only symlink the logs of
environment roots, not their deps, even if they were just built.
If users disable views, I'm pretty sure they're not waiting for
`.spack-env/logs` either. So, imo we can delete this code, and it was
probably overlooked in the past.
For a requirement like
```
packages:
foo:
require:
- "+debug"
```
(not `one_of:`, `any_of:`, or `spec:`)
`spack config change` would ignore the string. This was particularly evident if toggling a variant for a previously unmentioned package:
```
$ spack config change packages:foo:require:+debug
$ spack config change packages:foo:require:~debug
```
This fixes that and adds a test for it.
```
$ curl 'https://thepeg.hepforge.org/downloads/?f=ThePEG-2.3.0.tar.bz2' | sha256sum
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1904k 0 1904k 0 0 1075k 0 --:--:-- 0:00:01 --:--:-- 1074k
ac35979ae89c29608ca92c156a49ff68aace7a5a12a0c92f0a01a833d2d34572 -
```
* Reduce the size on disk for logs
This PR does two things:
1. Store a compressed `spack-build-out.txt.gz`
2. Get rid of phase logs, as they are duplicates of
`spack-build-out.txt`
The logs are not compressed in the stage dir, so on build failure the
workflow for users is no different.
It's just that on install the logs are rarely used, and if needed, users
can easily `gzip -d` or `zgrep` them.
In the case of GCC installs, the compressed logs are <5% of the original
size, which is typically dozens of MBs.
* get rid of "backwards compat" of file names in stage dirs
Sbangs don't exist on Native Windows, and the hook is causing errors
due to the file comparison + behavior of os.rename on Windows. Skip
the hook on Windows.
New patch 7.5.3p5, new bugfix 7.7.2, new minor 7.8.0.
Only possible impact on spack is the potential addition of a variant to select the memory manager in 7.8.0, see [diff](https://github.com/Open-Cascade-SAS/OCCT/compare/V7_7_2...V7_8_0). Not adding a variant at this time.
Like `spack change` for specs in environments, this can e.g. replace `examplespec+debug` with `examplespec~debug` in a `require:` section.
Example behavior for a config like:
```
packages:
foo:
require:
- spec: +debug
```
* `spack config change packages:foo:require:~debug` replaces `+debug` with `~debug`
* `spack config change packages:foo:require:@1.1` adds a requirement to the list
* `spack config change packages:bar:require:~debug` adds a requirement
As observed in #40944, when using `spack config add <path>`, the `path` might
contain keys that are enclosed in quotes.
This was broken in https://github.com/spack/spack/pull/39831, which assumed that
only the value (if present, the final element of the path) would use quotes.
This preserves the primary intended behavior of #39931 (allowing ":" in values when
using `spack config add`) while also allowing quotes on keys.
This has complicated the function `process_config_path`, but:
* It is not used outside of `config.py`
* The docstring has been updated to account for this
* Created an object to formalize the DSL, added a test for that, and
refactored parsing to make use of regular expressions as well.
* Updated the parsing and also updated the `config_path_dsl` test with an explicit check.
At a higher level, split the parsing to check if something is either a key or not:
* in the first case, it is covered by a regex
* in the second, it may be a YAML value, but in that case it would have to be the last
entry of x:y:z, so in that case I attempt to use the YAML handling logic to parse it as such
- Use MakefilePackage and simplified package.py
- Deprecate old versions - they did not build for me with OCaml 4.13.1
that is currently in Spack. Also, the changes from the previous
versions seem to be quite significant.
Spack packages may not have a public download option, and can implement
`download_instr` to inform users how to obtain the artifacts needed to
build. `spack checksum` however did not account for this and would print
out a confusing error message when invoked on such packages ("Could not
find any remote versions").
This PR updates the error message to output the manual download instructions
if `spack checksum` is invoked on a package with `manual_download = True`.
Currently when you repeatedly create a bootstrap mirror that includes
`clingo-bootstrap@spack` you get different tarballs every time.
This is a general problem with mirroring checkouts from version control
as tarballs. I think it's best to create tarballs ourselves, since that way we
have more control over its contents.
This PR ensures normalized tarballs like we do for build caches:
- normalize file permissions (in fact that was already inspired by git, so
should be good)
- normalized file creation/modification time (timestamp 0)
- uid / guid = 0, no usernames
- normalized gzip header
- dir entries are ordered by `(is_dir, name)` where strings are not locale aware ;)
- POSIX says st_mode of symlinks is unspecified, so work around it and
force mode to `0o755`
R embeds an absolute path to the `which` executable in the sources for
`Sys.which`. This gets ultimately stored as serialized byte code in some
custom database format, which uses compression for entries.
As a result, Spack cannot relocate `<prefix which>/bin/which` when
installing from a build cache.
The patch works around this by making R create a symlink to `which` in
its own prefix, have the R sources call that, so that relocation works
again.
See https://github.com/r-devel/r-svn/pull/151
Explicitly requested namespaces are annotated during
the setup phase, and used to retrieve the correct package
class.
An attribute for the namespace has been added for each node.
Currently, a single namespace per package is allowed
during concretization.
* add new versions of py-altair
* fix year
* Update var/spack/repos/builtin/packages/py-altair/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-altair/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* reorder dependencies
* remove rc
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-nanoplot and py-nanostat
* Add myself as spack package maintainer
* Remove python version requirement
* Remove python dependency
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py: remove python dependency
* Set dependency types
* Update py-nanomath package.py
* Update py-nanoplot package.py
* Update py-nanostat package.py
* Add missing py-python-deprecated dependency
* Make kaleido a source package
* Fix py-nanoget deps
* Kaleido lint
* Nanoget lint
* Nanomath lint
* Nanoplot lint
* Nanostat lint
* Another kaleido lint I missed
* py-nanoplot missed lint
* py-nanostat missed lint
* py-kaleido even more missed lint
* The linter really can't make up its mind
* The linter REALLY can't make up its mind
* Add py-python-deprecated package
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* perl-class-accessor-lvalue: New package
Adds Class::Accessor::Lvalue
* perl-date-utils and deps: New packages
This adds:
- perl-date-utils and its dependencies:
- perl-date-exception
- perl-term-ansicolor-markup
The current `mkdir {{ paths.environment }}` will generate an error if:
* `{{ paths.environment }}` already exists, or
* `{{ paths.environment }}` is nested in non-existing dirs.
Adding `-p` to the command will make this robust to both possibilities.
Set noclobber bash option when writing manifest.
* Add GASNet-EX release 2023.9.0
Add level_zero variant
Deprecate old versions that are no longer supported
Add version enforcement to accelerator variants
* Add UPC++ release 2023.9.0
Deprecate old versions that are no longer supported
Add version enforcement to accelerator variants
* perl-rose-datetime: New package plus updates
- perl-rose-datetime: New package
- perl-datetime: New version, updated dependencies to enable build
time tests and added a runtime test
* Remove copyright line
* New year
* bigdft: convert the use of format strings to fstrings everywhere
* Fix formatting
* reformat with black
* Update compiler flags in bigdft-core
* Revert "Update compiler flags in bigdft-core"
This reverts commit f7524ed784.
* Bump the build cache layout version from 1 to 2
* Version to lists parent directories of the prefix in the tarball too, which is required from some container runtimes
* Move in vs. satisfies to a note and mention special cases of in
* Address feedback: oveoverlap -> intersect
* Re-word the satisfies versus in note.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This fixes an issue where pkg.stage throws because a patch cannot be found,
but the patch is redundant because the spec is reused from a build cache and
will be installed from existing binaries.
Part 4 of reworking all package metadata to key by `when` conditions.
Changes conflict dictionary structure from this:
{ provided_spec: {when_spec, ...} }
to this:
{ when_spec: {provided_spec, ...} }
`make_when_spec()` was being used in the solver, but it has semantics that are specific
to parsing when specs from `package.py`. In particular, it returns `None` when the
`when` spec is `False`, and directives are responsible for ignoring that case and not
adding requirements, deps, etc. when there's an actual `False` passed in from
`package.py`.
In `asp.py`, we know that there won't ever be a raw boolean when spec or constraint, so
we know we can parse them without any of the special boolean handling. However, we
should report where in the file the error happened on error, so this adds some parsing
logic to extract the `mark` from YAML and alert the user where the bad parse is.
- [x] refactor `config.py` so that basic `spack_yaml` mark info is in its own method
- [x] refactor `asp.py` so that it uses the smarter YAML parsing routine
- [x] refactor `asp.py` so that YAML input validation for requirements is done up front
Part 3 of reworking all package metadata to key by `when` conditions.
Changes conflict dictionary structure from this:
{ (requirement_spec, ...): [(when_spec, policy, msg)] }
to this:
{ when_spec: [((requirement_spec, ...), policy, msg), ...] }
Part 2 of reworking all package metadata to key by `when` conditions.
Changes conflict dictionary structure from this:
{ conflict_spec: [(when_spec, msg), ...] }
to this:
{ when_spec: [(conflict_spec, msg), ...] }
Also attempts to consistently name the variables used to iterate over conflict
dictionaries.
Part 1 of making all package metadata indexed by `when` condition. This
will allow us to handle all the dictionaries on `PackageBase` consistently.
Convert the current dependency dictionary structure from this:
{ name: { when_spec: [Dependency ...] } }
to this:
{ when_spec: { name: [Dependency ...] } }
On an M1 mac, this actually shaves 5% off the time it takes to load all
packages, I think because we're able to trade off lookups by spec key
for more lookups by name.
* Boost: add version 1.84.0
* Conflict with 98/03
* Set C++11 as default
Starting with 1.84.0, the minimum required is c++11. It has been a very
long time since 98/03 has been required. It's time to bump the minimum.
* Add OpenMPI 5.0.0/5.0.1 release
* Fix a problem with dlopen syms with 5.0.0
* Crank up lex buffer to 1MB so that Open MPI's compiler wrapper can parse the enormously long lines present in, for example, mpicc-wrapper-data.txt when the spack install is utilizing Spack's path padding feature.
* Disable romio by default for 5.0.0 and beyond owing to problems compiling the romio package when using the Intel OneAPI compiler.
* Patch for addiing cuda lib location in case of non-standard location of libcuda.so
* build accel components as DSOs. It appears from looking at some of the spack CI that it implicitly assumes that Open MPI is built with components as DSOs. The default behavior for Open MPI was changed between the 4.1.x release stream and the 5.0.x release stream changed and this premise is now incorrect.
Turns out that starting with Open MPI 5.0.0 building static
does not work when using a now very important variant, namely cuda.
In older versions of Open MPI the libcuda.so was dlopened at
run time when needed, but now libcuda is linked in to the cuda
components of openmpi directly. This works when using Open MPI's
dynamically loadable component option, but doesn't work now for
a lot of the Spack CI pipelines because they don't include libcuda.so
in LD_LIBRARY_PATH of packages that dont think they are using
cuda themselves.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Co-authored-by: Jack Morrison <jack.morrison@cornelisnetworks.com>
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Needed for #40326, which can changes the iteration order over package dependencies during concretization.
While clingo doesn't have this problem, the original concretizer (which we still use for bootstrapping) can be sensitive to iteration order when evaluating dependency constraints in `when` conditions. This can cause it to ignore conditional dependencies unless the dependencies in the condition are listed first in the package.
The issue was in the way the original concretizer would disconnect specs *every* time `normalize()` ran. When specs were disconnected, `^dependency` constraints wouldn't see the dependency in the dependency condition loop.
We now only only disconnect *all* dependencies at the start of `concretize()` and `normalize()`, and we disconnect any leftover dependents from replaced externals at the *end* of `normalize()`. This trims stale connections while keeping the ones that are needed to trigger dependency conditions.
- [x] refactor `flat_dependencies()` to not disconnect the spec by default.
- [x] `flat_dependencies()` is never called with `copy=True` -- remove the `copy` kwarg.
- [x] disconnect only once at the beginning of `normalize()` or `concretize()`.
- [x] add a test that perturbs dependency iteration order to ensure this doesn't regress.
- [x] disconnect unused dependents at end of `normalize()`
* setup-env: Fix back and forth between two instances
* setup-env.csh: Fix SPACK_ROOT when switch to a different instance
i.e. Always look for the current SPACK_ROOT
* setup-env: Update comments
This adds options to `spack list` that allow you to list only packages from specific
repositories/namespaces, e.g.:
```console
spack list -r builtin
```
only lists packages from the `builtin` repo, while:
```console
spack list -r myrepo -r myrepo2
```
would list packages from `myrepo` and `myrepo2`, but not from `builtin`. Note that you
can use the same argument multiple times.
You can use either `-r` / `--repo` or `-N` / `--namespace`. `-N` is there to match the
corresponding option on `spack find`.
- [x] add `-r` / `--repo` / `-N` / `--namespace` argument
- [x] add test
* Add rust-analyzer as variant to rust build
* Expose cargo module only when +cargo
* rust: add v1.74.0 and v1.75.0 and remove variants in favor of +dev
* [@spackbot] updating style on behalf of alecbcs
* Fix variant typo
---------
Co-authored-by: alecbcs <alecbcs@users.noreply.github.com>
This method is vestigial; the only arg we ever used was `ignore=`, and that was
eliminated in #29317 and #35588.
The `kwargs` field of the extensions dictionary is actually completely unused now. Add a
note for future removal.
Literal compiler config in `test_requires_directive` specifically lists `target:
x86_64`, but it doesn't need to, and the unnecessary target makes the test fail on
non-`x86_64` machines.
- [x] Remove target from config yaml in `test_requires_directive`
* py-torch: set env OpenBLAS_HOME
Because [`FindOpenBLAS.cmake`](https://github.com/pytorch/pytorch/blob/main/cmake/Modules/FindOpenBLAS.cmake) uses a hardcoded list of search paths for includes and libraries, we have to pass the `OpenBLAS_HOME` environment variable.
* py-torch: patch for ${OpenBLAS_HOME}/include/openblas
The context of this patch is unchanged since v0.4.0.
* py-torch: move patch before def patch
* py-torch: also set Atlas_ROOT_DIR and BLIS_HOME
* py-torch: fix openblas patch range to @:2.1
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Xorg pkgs: updated version to current latest
This updates the versions of multiple Xorg packages to their current
latest version. Verified the requirements and version dependencies, and
updated where needed. Modified one homepage (xkbcomp) in the interest of
conformity with the other packages.
Summary of dependency changes:
- libsm:
- depends_on("libice@1.1.0:", when="@1.2.4:")
- libx11:
- depends_on("libxcb@1.11.1:", when="@1.6.4:")
- libxcomposite:
- depends_on("xproto@7.0.22:", when="@0.4.6")
- libxfixes:
- depends_on("fixesproto@5.0:", when="@5")
- depends_on("fixesproto@6.0:", when="@6")
- libxi:
- depends_on("inputproto@2.2.99.1:", when="@1.7:")
- depends_on("inputproto@2.3.99.1:", when="@1.8:")
* xcb-proto, libxcb: new version 1.15
* xorg libs: additional new versions
New minor version upgrades:
- libXcursor (no changed needed)
- libXres
- depends_on("resourceproto@1.0:", when="@1.0")
- depends_on("resourceproto@1.2:", when="@1.2")
* libxpm: ... depends_on ncompress only when 3.5.15
* Xorg libs: add maintainer
* xtrans: new version 1.5.0
* xcb-proto: new version 1.16.0
* libxt: new version 1.3.0
* libxrandr: new version 1.5.4
* libxpm: new versions 3.5.16, 3.5.17
* libxi: new version 1.8.1
* libxft: new version 2.3.8
* libxfixes: new version 6.0.1
* libxcb: new version 1.16
* libx11: new version 1.8.5, 1.8.6, 1.8.7
* libxfixes: comment out problematic fixesproto versions
* libxi: comment out problematic inputproto versions
* libxfixes, libxi: add reference to issue that blocks updates
* patch on variant fftw3; fix for #41577
* a line of doubtful blas/fftw +openmp. Are they needed with nwchem+openmp?
* Update var/spack/repos/builtin/packages/nwchem/package.py
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
---------
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
* gaudi: add a patch for catch2
* Fix indentation
* Add a diff at the end of the path
* gaudi: canonicalize patch url
* gaudi: canonicalize patch url for gitlab diff
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
PAPI CI checks a `spack install` of `papi@master`, and the open range here breaks their
CI with the fix because the patch is no longer needed (see #26784, #27625 for why it's
difficult to avoid this).
The patch issue is going to be fixed in PAPI upstream with whatever release is after
`7.1.0`, so we can restrict the patch to `7.1.0` and avoid this issue.
* shell: fix zsh color formatting for PS1 in environments
The `colorize` function in `llnl.util.tty.color` only applies proper formatting for Bash
ANSI and for console output, but this is not what zsh expects for environment variables.
In particular, when using `zsh`, `spack env activate -p` produces a `PS1` prompt that
looks like this:
```
\[\033[0;92m\][ENVIRONMENT]\[\033[0m\]
```
For zsh the formatting should be:
```
\e[0;92m[ENVIRONMENT]\e0;m
```
- [x] Add a `zsh` option to `colorize()` to enable zsh color formatting
- [x] Add conditional to choose the right `PS1` for `zsh`, `bash`, and `sh`
- [x] Don't use color escapes for `sh`, as they don't print properly
* convert lots of += lines to triple quotes
No online release notes or repository, but the new tarball has the following in `NEWS`:
* ThePEG-2.3.0 release: 2023-12-11
** gcc-12/c++17/c++20 compatibility added
** hepmc3 compatibility added
** rivet interface improved
** inforstructure for dark interaction added
PAPI 7.1.0 unconditionally adds `FFLAGS = -ffree-form` in the sysdetect tests,
regardless of the compiler.
This was added in https://github.com/icl-utk-edu/papi/pull/108 to make a build with
`armflang` work, but it breaks CCE (and our `develop` pipeline).
- [x] Add a patch that fixes both problems
- [x] Patch PAPI when at 7.1.0 or higher
Add a "checked_by" field to the `license()` directive so that we can track who verified
the license for a project. also check the license of 18 or so projects and mark them
checked.
This patch adds license information for about 5,300 packages from automated sources.
The license information was obtained from Alpine Linux and PyPI and processed
using tooling available in https://github.com/boomanaiden154/spack-license-utils.
The license field was added in after all other directives in an automated fashion.
Note that while this license information is probably fairly accurate, it is not
guaranteed to be accurate. In addition some of the license strings from Alpine Linux
might not be valid SPDX license strings. Invalid SPDX identifiers can be picked up
and fixed once we have validation/parsing infrastructure in place for the solver,
and issues can be fixed as they come up.
This adds a few options to `spack gc`.
One to give you a little more control over dependencies:
* `-b` / `--keep-build-dependencies`: By default, `spack gc` considers build dependencies to be "no longer needed" once their dependents are installed. With this option, we'll keep build dependencies of needed installations as well.
And two more to make working with environments easier:
* `-E` / `--except-any-environment`: Garbage collect anything NOT needed by an environment. `spack gc -E` and `spack gc -bE` are now easy ways to get rid of everytihng not used by some environment.
* `-e` / `--except-environment` `ENV`: Instead of considering all environments, garbage collect everything not needed by a *specific* environment. Note that you can use this with `-E` to add directory environments to the list of considered envs, e.g.:
spack gc -E -e /path/to/direnv1 -e /path/to/direnv2 #...
- [x] rework `unused_specs()` method on DB to add options for roots and deptypes
- [x] add `all_hashes()` method on DB
- [x] rework `spack gc` command to add 3 more options
- [x] tests
* Add all versions back to 0.20, add more depends_on (flex, bison, libffi and ccache), add the ability to enable or disable both abc and ccache, abc is enabled by default, ccache is disabled by default
* Fixed style with black
* Removed unused f-string setups
* Fixed style with black (again)
* Add enum34, numdifftools, and updated pyomo packages
* Syntax error
* Apply black style
* Trying to get around Python spec issue
* All SHAs were somehow wrong
* Change enum version
* Change optional dependencies to be on run, not build
* Add Pyomo 6.7.0
* Update SHA and version mismatch
* Remove py-enum34
* Add three new packages to address comments
* Fix linting errors; move casadi to py-casadi
* Update license; add in dependency
* Update setuptools version
* Update class name to python class
* Remove other boielerplate stuff
* Update homepage addresses; update py-casadi
* Add PAPI 7.0.1
* Add comment about skipping PAPI 7.0.0
* Add patch to avoid adding Intel ifort/ifx flag on Cray ftn
* Modify patch to include Cray-specific flags
* Adjust recipe to always apply patch for 7.0.1
* Expand Cray compiler checks in patch
* Forgot to update recipe
* Adjust recipe so it looks for hipcc in the correct path
* Revert "Adjust recipe so it looks for hipcc in the correct path"
This reverts commit 0db3df4fe2.
* Patch HIP_PATH to work with Spack-built HIP
* Patch LDFLAGS with llvm-amdgpu path
* Forgot the depends_on line
* libomptarget only builds with clang
* Try a self-consistent build of llvm-amdgpu
* Try making llvm-amdgpu depend on llvm for llvmoffloadarch library
* Update prereq to use rocm-openmp-extras instead
* Refactor llvm-amdgpu to use a version dict
* Fix typo
* Hack to exclude older versions without matching rocm-openmp-extras
* Add PAPI 7.1.0
* Revert changes to llvm-amdgpu
* Fix PAPI 7.1.0 checksum
For now, this only includes packages that I personally maintain.
Notable removals:
* Anaconda 2
* Catalyst
* Ancient numpy/scipy
* Ancient PyTorch
* Ancient Bazel/TF
To work properly, Spack requires a few directories from its repository to be added to
`sys.path`. Previously these were buried in `spack_installable.main.main()`, but it's
sometimes useful to get the paths separately, e.g., if you want to set up your own
functioning spack environment.
With this change, adding the paths is much simpler:
```python
import spack_installable
sys.path[:0] = get_spack_sys_paths(spack_prefix)
```
- [x] Add `get_spack_sys_paths()` method with extra paths in order.
- [x] Refactor `spack_installable.main.main()` to use it.
With an improper/incomplete/broken installation of Clingo, it can be
importable but not have any of the expected attributes
Improve error reporting in this case
* Restore PackageBase class, and modify only ASP
This prevents a noticeable slowdown in concretization
due to the number of directives involved.
* Fix issue with 'clang' being preferred to 'gcc',
due to runtime version weights
* Constraints on runtimes are declared by compilers
The declaration of available runtime versions, and of
their compatibility constraints are in the associated
compiler class.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
The gcc-runtime package adds a separate node for gcc's dynamic runtime
libraries.
This should help with:
1. binary caches where rpaths for compiler support libs cannot be
relocated because the compiler is missing on the target system
2. creating "minimal" container images
The package is versioned like `gcc` (in principle it could be
unversioned, but Spack doesn't always guarantee not mixing compilers)
If you are calling Spack from the python API, you might have written something like this
before #41529:
```
find = SpackCommand("find")
find('--format={name}', 'saxpy@1.0.0', '+rocm', 'amdgpu_target="gfx90a"')
```
But with the breaking change in #41529, you should write:
```
find = SpackCommand("find")
find('--format={name}', 'gromacs', '+rocm', 'amdgpu_target=gfx90a')
```
Note that we don't need quotes in Python strings, and that this is what would come in
via argv if you typed a quoted variant on the CLI.
The error messages for strings like this are not great -- you get something like this:
```
==> No package matches the query: gromacs+rocm amdgpu_target="gfx90a"
```
Which doesn't indicate that the issue might be your quoting. This is because we were
simply outputting the argv we got, instead of using spec.format() to output the error
message. This PR fixes such errors to use `spec.format()` and to look like this:
```
==> No package matches the query: gromacs+rocm amdgpu_target='"gfx90a"'
```
So users should have an easier time understanding that Spack considers the variant value
to contain quotes here.
- [x] update ConstraintAction to store parsed Specs
- [x] refactor commands to display formatted parsed Specs instead of raw input
Users expect that changes to the externals sections in packages.yaml config apply immediately, but reuse concretization caused this not to be the case. With this commit, the concretizer is only allowed to reuse externals previously imported from config if identical config exists.
This PR adds a flag `--tag/-t` to `buildcache push`, which you can use like
```
$ spack mirror add my-oci-registry oci://example.com/hello/world
$ spack -e my_env buildcache push --base-image ubuntu:22.04 --tag my_custom_tag my-oci-registry
```
and lets users ship a full, installed environment as a minimal container image where each image layer is one Spack package, on top of a base image of choice. The image can then be used as
```
$ docker run -it --rm example.com/hello/world:my_custom_tag
```
Apart from environments, users can also pick arbitrary installed spec from their database, for instance:
```
$ spack buildcache push --base-image ubuntu:22.04 --tag some_specs my-oci-registry gcc@12 cmake
$ docker run -it --rm example.com/hello/world:some_specs
```
It has many advantages over `spack containerize`:
1. No external tools required (`docker`, `buildah`, ...)
2. Creates images from locally installed Spack packages (No need to rebuild inside `docker build`, where troubleshooting build failures is notoriously hard)
3. No need for multistage builds (Spack just tarballs existing installations of runtime deps)
4. Reduced storage size / composability: when pushing multiple environments with common specs, container image layers are shared.
5. Automatic build cache: later `spack install` of the env elsewhere speeds up since the containerized environment is a build cache
These packages were written before the "requires" directive,
and so they are conflicting with all compilers but Fujitsu
to express they _require_ `%fj`
* Ensure a spack libproj is used instead of a system libproj when libproj < 8.
spack/spack/issues/41299
* Fix style as per ci-bot
* Fix style as per ci-bot
* Ensure 3.5:3.8.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add trim function to `Spec` and `--ignore` option to 'spack diff'
Allows user to compare two specs while ignoring the sub-DAG of a particular dependency, e.g.
spack diff --ignore=mpi --ignore=zlib trilinos/abcdef trilinos/fedcba
to focus on differences closer to the root of the software stack
Sometimes env variables computed in `setup_run_environment` depend on tests
w.r.t. files in `spec.prefix`, but Spack temporarily projects `spec.prefix` to
the view.
This is problematic for two reasons:
1. Some packages iterate over `<prefix>/bin`: they expect only the current
package's executables, but find all linked in the view, leading to false
positives.
2. Some packages test for `os.path.islink(...)`, which is always true in a view
`gcc` is an example that does both.
This PR lets Spack compute the environment modifications using the original
prefix, and projects to the view afterwards
Currently, a virtual spec is composed of just a name and a version. When a virtual spec contains other components, such as variants, Spack won't emit warnings or errors but will silently drop them - which is unexpected by users.
This adds three new versions in the 31.* series. Release notes of 31.0.0 at https://github.com/acts-project/acts/releases/tag/v31.0.0. No changes to the CMakeLists.txt files that need addressing in the package recipe.
The only new feature I'm a bit concerned about is https://github.com/acts-project/acts/pull/2626, which replaces testing for C++20 concepts support by the feature-testing macro `__cpp_concepts`, which is also a C++20 feature. So technically we now should require `cxxstd=20` even though Acts itself still allows (and defaults to) 17. Judging by https://en.cppreference.com/w/cpp/compiler_support/20, the support for feature-testing macros was added very early by most compilers.
This PR changes the default behavior of `spack config get` and `spack config blame`
to print a flattened version of the entire spack configuration, including any active
environment, if the commands are invoked with no section arguments.
The new behavior is used in Gitlab CI to help debug CI configuration, but it can also
be useful when asking for more information in issues, or when simply debugging Spack.
Convert the 'develop' section of an environment to a dedicated configuration section.
This means for example that instead of having to define `develop` specs in the
`spack.yaml`, the environment can `include:` another `develop.yaml` configuration
which specifies which specs should be developed in the environment.
This change is not expected to be disruptive given that existing environment `spack.yaml`
files will conform to the new schema.
(Update 11/28/2023) I have implemented the `develop`/`undevelop` commands in terms
of more-generic modification functions added to the `config` module: `change_or_add`
and `update_all`. It is assumed that the semantics added here (described in 11/18 update)
would be desirable to extend to other config update actions (e.g. adding compilers,
changing package requirements, adding mirrors).
(Update 11/18/2023) I have updated this such that `spack develop`, and
`spack undevelop` to potentially modify all writable scopes, like
https://github.com/spack/spack/pull/41147. https://github.com/spack/spack/pull/35307
will be useful for modifying included scopes, but generally speaking specifying a
`--scope` will not be required for `spack develop`: `spack develop` will add new
develop specs to whatever scope already has develop specs defined, or to the
highest-priority writable scope (which should be the env scope).
TODOs:
- [x] If you `spack undevelop` a package which is mentioned at multiple layers of
configuration, then currently this would only modify one of them. That's not
technically a new issue (has always existed for configuration modification), but
may be confusing to users when presented via an interface other than `spack config set`
- [x] Need to add (or confirm) the ability to modify individual config files by providing
a path (rather than using a scope identifier as a key to retrieve associated config).
- [x] `spack develop` adds new develop specs to the scope that defines them
(potentially skipping higher priority scopes to e.g. augment included scope files)
---------
Co-authored-by: scheibelp <scheibelp@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* py-plum-dispatch: add new package
* Update var/spack/repos/builtin/packages/py-plum-dispatch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-htgettoken: use os.environ, avoid AttributeError
This avoids the following error:
```
Warning: could not load runtime environment due to AttributeError: 'EnvironmentModifications' object has no attribute 'get'
```
* py-htgettoken: allow for undefined variables
* py-htgettoken: use dict get()
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* mpifileutils: add DAOS variant
* mpifileutils: Add daos dep when +daos
Add dependency on DAOS when +daos
Pass DAOS prefix to ensure correct DAOS is found by during configuration
* Change in to satisfies for boolean variants
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
* perl-datetime-format-strptime: New package
Adds package:
- perl-datetime-format-strptime
And adds these because they are test dependencies:
- perl-test-file-sharedir
- perl-test2-plugin-nowarnings
- perl-test2-suite
And modifies these to enable build time tests:
- perl-b-hooks-endofscope
- perl-class-singleton
- perl-datetime-locale
- perl-datetime-timezone
- perl-file-sharedir
- perl-namespace-autoclean
- perl-namespace-clean
- perl-params-validationcompiler
- perl-specio
* Add myself as maintainer
* add new cpp compiler version
* empty ftn for 2023.2.3
* OLD ftn in 2023.2.3 version
* tolerate missing fortran compiler
---------
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
* geant4: new version 11.2.0
* geant4: depends_on geant4-data@11.2:
* geant4-data: new version 11.2.0
* g4abla: new version 3.3
* g4emlow: new version 8.4
* g4incl: new version 1.1
* geant4: depends_on vecgeom@1.2.6:
* geant4: depends_on qt@5.9: when @11.2: +qt
* vecgeom: new version 1.2.6
This PR does several things:
- [x] Allow any character to appear in the quoted values of variants and flags.
- [x] Allow easier passing of quoted flags on the command line, e.g. `cflags="-O2 -g"`.
- [x] Handle quoting better in spec output, using single quotes around double
quotes and vice versa.
- [x] Disallow spaces around `=` and `==` when parsing variants and flags.
## Motivation
This PR is motivated by the issues above and by ORNL's
[tips for launching at scale on Frontier](https://docs.olcf.ornl.gov/systems/frontier_user_guide.html#tips-for-launching-at-scale).
ORNL recommends using `sbcast --send-libs` to broadcast executables and their
libraries to compute nodes when running large jobs (e.g., 80k ranks). For an
executable named `exe`, `sbcast --send-libs` stores the needed libraries in a
directory alongside the executable called `exe_libs`. ORNL recommends pointing
`LD_LIBRARY_PATH` at that directory so that `exe` will find the local libraries and
not overwhelm the filesystem.
There are other ways to mitigate this problem:
* You could build with `RUNPATH` using `spack config add config:shared_linking:type:runpath`,
which would make `LD_LIBRARY_PATH` take precedence over Spack's `RUNPATHs`.
I don't recommend this one because `RUNPATH` can cause many other things to go wrong.
* You could use `spack config add config:shared_linking:bind:true`, added in #31948, which
will greatly reduce the filesystem load for large jobs by pointing `DT_NEEDED` entries in
ELF *directly* at the needed `.so` files instead of relying on `RPATH` search via soname.
I have not experimented with this at 80,000 ranks, but it should help quite a bit.
* You could use [Spindle](https://github.com/hpc/Spindle) (as LLNL does on its machines)
which should transparently fix this without any changes to your executable and without
any need to use `sbcast` or other tools.
But we want to support the `sbcast` use case as well.
## `sbcast` and Spack
Spack's `RPATHs` break the `sbcast` fix because they're considered with higher precedence
than `LD_LIBRARY_PATH`. So Spack applications will still end up hitting the shared filesystem
when searching for libraries. We can avoid this by injecting some `ldflags` in to the build, e.g.,
if were were going to launch, say, `LAMMPS` at scale, we could add another `RPATH`
specifically for use with `sbcast`:
spack install lammps ldflags='-Wl,-rpath=$ORIGIN/lmp_libs'
This will put the `lmp_libs` directory alongside `LAMMPS`'s `lmp` executable first in the
`RPATH`, so it will be searched before any directories on the shared filesystem.
## Issues with quoting
Before this PR, the command above would've errored out for two reasons:
1. `$` wasn't an allowed character in our spec parser.
2. You would've had to double quote the flags to get them to pass through correctly:
spack install lammps ldflags='"-Wl,-rpath=$ORIGIN/lmp_libs"'
This is ugly and I don't think many users will easily figure it out. The behavior was added in
#29282, and it improved parsing of specs passed as a single string, e.g.:
spack install 'lammps ldflags="-Wl,-rpath=$ORIGIN/lmp_libs"'
but a lot of users are naturally going to try to quote arguments *directly* on the command
line, without quoting their entire spec. #29282 used a heuristic to detect unquoted flags
and warn the user, but the warning could be confusing. In particular, if you wrote
`cflags="-O2 -g"` on the command line, it would break the flags up, warn, and tell you
that you could fix the issue by writing `cflags="-O2 -g"` even though you just wrote
that. It's telling you to *quote* that value, but the user has to know to double quote.
## New heuristic for quoted arguments from the CLI
There are only two places where we allow arbitrary quoted strings in specs: flags and
variant values, so this PR adds a simpler heuristic to the CLI parser: if an argument in
`sys.argv` starts with `name=...`, then we assume the whole argument is quoted.
This means you can write:
spack install bzip2 cflags="-O2 -g"
directly on the command line, without multiple levels of quoting. This also works:
spack install 'bzip2 cflags="-O2 -g"'
The only place where this heuristic runs into ambiguity is if you attempt to pass
anonymous specs that start with `name=...` as one large string. e.g., this will be
interpreted as one large flag value:
spack find 'cflags="-O2 -g" ~bar +baz'
This sets `cflags` to `"-O2 -g" ~bar +baz`, which is likely not what you wanted. You
can fix this easily by either removing the quotes:
spack find cflags="-O2 -g" ~bar +baz
Or by adding a space at the start, which has the same effect:
spack find ' cflags="-O2 -g" ~bar +baz'
You may wonder why we don't just look for quotes inside of flag arguments, and the
reason is that you *might* want them there. If you are passing arguments like:
spack install zlib cppflags="-D DEBUG_MSG1='quick fox' -D DEBUG_MSG2='lazy dog'"
You *need* the quotes there. So we've opted for one potentially confusing, but easily
fixed outcome vs. limiting what you can put in your quoted strings.
## Quotes in formatted spec output
In addition to being more lenient about characters accepted in quoted strings, this PR fixes
up spec formatting a bit. We now format quoted strings in specs with single quotes, unless
the string has a single quote in it, in which case we JSON-escape the string (i.e., we add
`\` before `"` and `\`).
zlib cflags='-D FOO="bar"'
zlib cflags="-D FOO='bar'"
zlib cflags="-D FOO='bar' BAR=\"baz\""
* adding necessary headers, to fix https://github.com/spack/spack/issues/41398
* deleting something imported by accident
* [@spackbot] updating style on behalf of yizeyi18
* undo commit 7688fed according to suggestion from @msimberg
* patching camp@:2022.10.1 for compatibility with gcc-13
* adding the patch
* fixing paths in the patch
* [@spackbot] updating style on behalf of yizeyi18
* Update camp patch using LLNL/camp@05e1c35
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* changing patch name
---------
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
`setup_dependent_package` is not a build phase, it should just set
globals for a package.
It's called during setup of runtime environment of packages, and there
have been reports of it actually failing due to a read only file system
(not sure under what exact conditions that is possible).
This license annotation is currently invalid as it specifies a URL
rather than an SPDX expression. Remove it for now until we have a
consensus on how to represent this case.
* New package Model Coupling Toolkit (MCT)
* Remove ~mpi variant from mct, build is not working correctly
* Remove boilerplate stuff from var/spack/repos/builtin/packages/mct/package.py
MySQL was performing a core API call to `Spec.flat_dependencies`
when setting up the build environment. This function is an
implementation detail of the old concretizer, where multiple nodes
from the same package are not allowed.
This PR uses a more idiomatic way to check if "python" is
in the DAG.
For reference, see #11356 to check why the call was introduced.
* [protobuf] New versions, explicit cxxstd variant
* New versions 3.15.8, 3.25.0, 3.25.1.
* New explicit variant `cxxstd` with support for older Protobuf
versions.
* Support testing.
* Use Protobuf's `protobuf_BUILD_SHARED_LIBS` instead of
`BUILD_SHARED_LIBS`.
* Support building with LLVM/Clang's `libc++`.
* Address audit issue
* Variant default does not honor `when` clause
* Use `self.spec.satisfies()` instead of `with when()`
* Fix silliness; improve consistency
* Today was apparently a go-back-to-bed day
* initial commit for rocm-5.7.0 and 5.7.1 releases
* bump up ther version for 5.7.0 and 5.7.1 releases
* update recipes to support 5.7.0 and 5.7.1 releases
* bump up the version for ROCm 5.7.0 and ROCm-5.7.1 releases
* bump up the version for composable-kernel amd miopen-hip
* fix style errors
* fix style errors in hip etc
* renaming composable-kernel recipe
* changes for composable_kernel
* Revert "renaming composable-kernel recipe"
This reverts commit 0cf6c6debf.
* Revert "changes for composable_kernel"
This reverts commit 05272a10a7.
* bump up the version for hiprand
* using the checksum for hiprand-5.7.1
* bump up the version for 5.7.0 and 5.7.1 releases
* fix style errors
* fix merge conflicts with the develop.
* temp workaround for the error seen with rocm-5.7.0 when trying
to generate the dependency file for runtime/legion/legion_redop.cu
* fix build issue(work around) with legion
* add patch for migraphx package to turn off ck
* update to hip recipe
* fix hip-path detection inside llvm clang driver
* update llvm-amdgpu and rocm-validation-suite recipes
* fix style errors
* bump up the version for amdsmi for rocm-5.7.0 release
* add support for gfx941,gfx942 for rocm-5.7.0 release onwards
* revert changes to rocm.py file
* added gfx941 and gfx942 to rocm.py and add the gfx942 to kokkos and new checksum
the new version seem to support gfx942
* bump up the version for rccl for 5.7.1
* update the patch for rocm-openmp-extras for 5.7.0
* update mivisionx recipe for 5.7.0 release
* add new dependencies for rocfft tests
* port the fix for avx build, the start address of values_ buffer in KernelParameters is not
correct as it is computed based on 16-byte alignment
* set HIP_PATH=ROCM_PATH for 5.7.0 onwards
* address review comments
* revert adding xnack- and xnack+ to gfx940,gfx941,gfx942 as the prechecks were failing
* Add `signed` property to mirror config
* make unsigned a tri-state: true/false overrides mirror config, none takes mirror config
* test commands
* Document this
* add a test
The new feq-parse version includes fixes for ifort and ifx compilers
Additionally, evaluation of parser objects with multidimension arrays is
now supported.
* samtools/htslib add latest version
* Given I work at the same institute as the authors I think it fair I am willing to review changes, if it's complex I can ask them over tea.
---------
Co-authored-by: James Beal <jb23@sanger.ac.uk>
* New variants:
- `tmvz-cpu`
- `tmvz-gpu`
- `tmvz-pymva`
- `tmvz-sofie`
* Improve X-related dependencies.
* Improve TMVA-related dependencies with more specificity.
* Patch possible missing standard header include in Eve7.
* Patch Protobuf handling to support new Protobuf-provided CMake config
files required to handle transitive `abseil-cpp` dependence.
* Add missing terminal newline to `webgui` patch to remove patch
warning.
* Handle deprecated/removed build options.
* geant4/geant4-data: add builtin_clhep variant and v10.0.4.
* geant4: revert addition of builtin_clhep variant.
* geant4: fix vecgeom variant only being available for v10.3 and above.
Fix filer_compiler_wrapper for cases where the compiler returned in None, this happens on some installed gcc systems that do not have fortran built into them as standard, e.g. gcc@11.4.0 on ubuntu 22.04
Before (hard to read, doesn't fit on small terminals):
:
```console
-I, --install-status show install status of packages
packages can be: installed [+], missing and needed by an installed package [-], installed in an upstream instance [^], or not installed (no annotation)
```
After (fits in 80 columns):
```console
-I, --install-status show install status of packages
[+] installed [^] installed in an upstream
- not installed [-] missing dep of installed package
```
* Fix cdash reporter time stamps (#38818).
The cdash reporter is created before packages are installed so save the
starttime then instead of the endtime.
* Use endtime instead of starttime for the endtime of update
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Participation in the venerable Spack google group has dwindled, though we still have
540+ subscribers there. I've made the mailing list announcement-only, and I've given
a few maintainers posting privileges.
This PR adds some notes to the README indicating that the mailing list is only for
announcements.
* Ensure that additional environment variables are set when a module
file is generated.
* Fixed the detection of the opal_prefix / MPI_ROOT field to use ompi_info.
---------
Co-authored-by: Greg Becker <becker33@llnl.gov>
* depend_on python
There is an ill-named variant "python" that enables the pytrilinos1
variant. This made it through our testing but broke on our actual
CI test machines.
* adjust "python" variant based on Trilinos version
For Trilinos <= 14, enable PyTrilinos(1). For later versions
of Trilinos, enable PyTrilinos2.
We still support directly enabling PyTrilinos2 via the "pytrilinos2"
variant.
* remove pytrilinos2 variant
* correct depends_on constraints
- we don't have a fallback if make is not installed
- we assume file system locking works
- we don't verify that make is gnu make (bootstrapping fails on FreeBSD as a result)
- there are some weird race conditions in writing spack.yaml on concurrent spack install
- the view is updated after every package install instead of post environment install.
Forbid nested dependencies in depends_on declarations, by running an audit in CI.
Fix the packages not passing the new audit:
- amd-aocl
- exago
- palace
- shapemapper
- xsdk-examples
ginkgo: add a commit sha to v1.5.0.glu_experimental
* New variants:
- `tmvz-cpu`
- `tmvz-gpu`
- `tmvz-pymva`
- `tmvz-sofie`
* Improve X-related dependencies.
* Improve TMVA-related dependencies with more specificity.
* Patch possible missing standard header include in Eve7.
* Patch Protobuf handling to support new Protobuf-provided CMake config
files required to handle transitive `abseil-cpp` dependence.
* Add missing terminal newline to `webgui` patch to remove patch
warning.
* Handle deprecated/removed build options.
* Handle unwanted system paths in various `PATH`-like environment
variables.
The condition on swig can be interpreted as "true if true,
false if false" and gives clingo the option to add swig
or not.
If not other optimization criteria break the tie, then
the concretization is non-deterministic.
* added external libxc/elpa choice
* fixed formatting issues and 1 unused variant found by reviewer
* try to fix a string formatting issue
* try to fix some other string formatting issues
* fixed 1 flake8 style issue
* use explicit fftw-api@3
* Add `url_list` to facilitate finding new versions.
* `cxxstd` is not meaningful when `@:2.99.99` as it was a header-only
package before v3.
* Support C++20/23, remove C++14 support.
* Add @greenc-FNAL to maintainers.
* Add CMake arguments to support testing, build of extras and examples.
* Only build tests for proj package if required
Even if tests are not explictly required to be built, proj build them
anyway and tries to download Google Test.
* proj: fix name of test activation flag
* proj: Always set test activation flag
* proj: Patch test activation logic for versions 5.x
* py-python-pptx: new package
* py-python-pptx: use pil instead of pillow, remove version constraint on python
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
* py-tldextract: new package
* py-tldextract: add version 5.1.1
* py-tldextract: fix version constraint on py-setuptools-scm
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
* Add a new version of ruff
* Add a comment about where the dependency can be found
---------
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
* Update py-werkzeug version dependency for py-graphene-tornado@2.6.1
* Add note on diverging version requirements for py-werkzeug in py-graphene-tornado
* legion: correct cuda dependency for cr version
* Update var/spack/repos/builtin/packages/legion/package.py
---------
Co-authored-by: Davis Herring <herring@lanl.gov>
* py-gidgethub: add new package
* Add main branch version and scope flit/flit-core dependency
* Update var/spack/repos/builtin/packages/py-gidgethub/package.py
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* Add optional dependencies as variants of package
* Add git url for main version
* Fix variant and dependency ordering
---------
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* gidgetlab: add new package
* Convert both cachetools and aiohttp to optional deps with variants
* Fix forgotten variant conditional on cachetools dependency
* Add git url and main version for dev workflows
* Fix variant and dependency ordering
* Remove cachetools variant and merge dependency with aiohttp variant
* grep WM_PROJECT_VERSION from etc/bashrc
This fixes the problem when building from a manually checked out repo
which might have a different version wrt the one defined in the spack
package (e.g. anything later than 5.0 is known as 5.x by the build
system)
* patch applies to just 5.0, in newer versions it is already addressed
In `5.20171030` there's a commit
c66fba323c
very similar (almost identical) to what the patch `50-etc.patch` does.
So the patch should not be applied to other than `5.0` otherwise it errors.
References:
- https://github.com/OpenFOAM/OpenFOAM-5.x/commits/20171030/etc/bashrc
- 197d9d3bf2/etc/bashrc (L45-L47)
This was missed while backporting the new `spack info` command from #40326.
Variants should be sorted by name when invoking `spack info --variants-by-name`.
Intel made an incompatible change in XED in 2023.08.21 that breaks
hpctoolkit (at run time). Hpctoolkit develop can adapt (soon will),
but older versions must use xed :2023.07.09.
* Updating the LBANN, Hydrogen, and DiHydrogen recipes for both new
variants and to make sure that RPATHs are properly setup.
Co-authored-by: bvanessen <bvanessen@users.noreply.github.com>
Deprecating intel package, which contains intel classic compilers. This package has not been updated in 3 years. Please use intel-oneapi-compilers instead.
* gipaw.x installed by cmake if version >= 5c4a4ce.
gipaw.x will only be installed with cmake if the qe-gipaw version
is >= 5c4a4ce. Currently, QE source uses the older f5823521 one.
Here a patch to the submodule_commit_hash_records to use a newer
qe-gipaw version.
* Update package.py
* Delete var/spack/repos/builtin/packages/quantum-espresso/gipaw-eccee44.patch
* Update package.py
* Restoring gipaw-eccee44 patch
* Update package.py
* Add fox variant in quantum-espresso
* Fix an issue introduced in #36484. Patches are 7.1 only.
* Change plugin handling.
* formatting.
* Typo correction
* Refine conflict
---------
Co-authored-by: S. Alexis Paz <alexis.paz@gmail.com>
* Add EGL support to ParaView and Glew
add a package for egl that provides GL but also adds
EGL libs and headers for projects that need them
Fix a header problem with the opengl package
Format files using black
* better description for egl variant description
Co-authored-by: Vicente Bolea <vicente.bolea@gmail.com>
* better check/setup of non egl variant dependencies
Co-authored-by: Vicente Bolea <vicente.bolea@gmail.com>
* Add biddisco as maintainer
* Fix unused var style warning
* Add egl conflicts for other gl providers
---------
Co-authored-by: Vicente Bolea <vicente.bolea@gmail.com>
* py-pyglet: version bump
* py-pyglet: use zip instead of whl, update dependencies
* py-pyglet: 2.0.9 and 2.0.10 zips should be downloaded from github
* py-pyglet: style
* py-pyglet: use virtual packages in dependencies
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* py-pyglet: doesn't depend on py-future any more
* py-pyglet: remove glx dependency
* py-pyglet: back to the pypi zipfiles with patch instead
---------
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* Add initial version of verible to spack
* Update to use explict url path for each release, as the release tagh includes extra data, also added the bottom most point of gcc, gcc9
* py-pycma: new package
* rename py-pycma in py-cma; py-cma: use pypi instead of github sources
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
* lammps: add new stable version 20230802.1
* lammps: add missing potential download for +mesont
* lammps: fix python package install
* Update var/spack/repos/builtin/packages/lammps/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* lammps: py-numpy and py-mpi4py should be build and run deps
* lammps: add new 20231121 release
- MPIIO package has been removed -> disable mpiio variant
- LAMMPS_EXCEPTIONS is now always on -> disable exceptions variant
- CMake 3.16+ is now required
- Kokkos 4.1.0 is now supported
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add missing runtime dependency on py-colorama to py-ansimarkup
* Add py-metomi-isodatetime@3.1.0
* New package py-graphql-relay
* Update py-cylc-flowi, add version 8.2.3
* Fix merge conflict
* Revert mistake in var/spack/repos/builtin/packages/py-cylc-flow/package.py
* Update py-metomi-isodatetime dependencies for py-cylc-flow
* Add 'climbfuji' to list of maintainers for py-cylc-flow
* py-beartype: new package with version 0.15.0
* Update var/spack/repos/builtin/packages/py-beartype/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-beartype: depend on python 3.8 or higher
* py-beartype: add new version 0.16.2
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-mpi4py: fix build with Apple Clang
* [@spackbot] updating style on behalf of adamjstewart
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
* mochi-thallium: added a few newer versions
* mochi-thallium: added constraint on the version of margo required
* removed thallium 0.12 which needs updating
* mochi-thallium: fixed hash for version 0.12.0
* removed thallium 0.12 which needs updating (again)
When using `spack external find acfl`, we get the full version string
with 4 components in `packages.yaml`. This PR truncates the version
nubmer when finding the `armpl` component to be able to run without
intervention.
* developer tools stack try 2
This version is actually in use locally and has largely stabilized, at
least on x86. Some packages are still a challenge on ppc64le, but maybe
worth keeping this working as a set.
* add packages, try to get container with newer gcc
* remove reuse: true
* try to get cmake to build on medium, 25 minutes is too long
* add lsd package and add to dev tools stack
* clean up fzf dependency and sorting
* Update share/spack/gitlab/cloud_pipelines/stacks/developer_tools/spack.yaml
* cuda: add 12.3.0 (#40827)
* Switch to dashes
* yet more underscores
---------
Co-authored-by: Paul R. C. Kent <kentpr@ornl.gov>
This looks to me like the best compromise regarding externals in a
build cache. I wouldn't want `spack install` on my machine to install
specs that were marked external on another. At the same time there are
centers that control the target systems on which spack is used, and
would want to use external in buildcaches.
As a solution, reuse concretization will now consider those externals
used in buildcaches that match a locally configured external in
packages.yaml.
So for example person A installs and pushes specs with this config:
```yaml
packages:
ncurses:
externals:
- spec: ncurses@6.0.12345 +feature
prefix: /usr
```
and person B concretizes and installs using that buildcache with the
following config:
```yaml
packages:
ncurses:
externals:
- spec: ncurses@6
prefix: /usr
```
the spec will be reused (or rather, will be considered for reuse...)
* gipaw.x installed by cmake if version >= 5c4a4ce.
gipaw.x will only be installed with cmake if the qe-gipaw version
is >= 5c4a4ce. Currently, QE source uses the older f5823521 one.
Here a patch to the submodule_commit_hash_records to use a newer
qe-gipaw version.
* initial commit to update hipblas rocalution, rocsolver, rocsparse to new syntax
* add rocblas test changes and fixes for hipblas and rocsolver tests
* fix styling
* remove updates for rocblas
* solver: use a unique counter for condition, triggers and effects
* Do not reset counters when re-running setup
What we need is just a unique ID, it doesn't need
to start from zero every time.
* Update SST packages to 13.1.0
* Allow mismatch between sst-core dependency and current macro version
* SST does not work with Python 3.12 yet
* Sanity check install binaries for sst-core
* Elements compiles with OTF2 but not OTF
* Version bounds in specs are inclusive
* Remove not-strictly-necessary file check
* oneapi 2024.0.0 release
* oneapi v2 directory support and some cleanups
* sycl abi change requires 2024 compilers for packages that use sycl
---------
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
* update spack recipe
* [@spackbot] updating style on behalf of toxa81
* change from @develop to @7.5.0
* return dependency on boost_filesystem
* return dependency on boost_filesystem
* remove boost filesystem as agreed by @RMeli and @simonpintarelli
---------
Co-authored-by: toxa81 <toxa81@users.noreply.github.com>
* Update to latest version
* Add dependency
* revert
* address PR comments
* Correct dependencies for 0.7 to 0.8 transition
* Fix cmake line.
* Update nanobind dep
---------
Co-authored-by: Matt Archer <ma595@cam.ac.uk>
Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>
Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>
* add 0.12.0
* remove whitespace
* update deps
* Update var/spack/repos/builtin/packages/py-neo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add dep for python 3.8+
* add dep for python 3.8+ with 0.12.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
PR #40929 reverted the argument parsing to make `spack --verbose
install` work again. It looks like `--verbose` is the only instance
where this kind of argument inheritance is used since all other commands
override arguments with the same name instead. For instance, `spack
--bootstrap clean` does not invoke `spack clean --bootstrap`.
Therefore, fix multi-line aliases again by parsing the resolved
arguments and instead explicitly pass down `args.verbose` to commands.
This commit discards type mismatches or failures to validate a package preference during concretization. The values discarded are logged as debug level messages. It also adds a config audit to help users spot misconfigurations in packages.yaml preferences.
This roughly restores the order of operation from Spack 0.20,
where where `AutotoolsPackage.setup_build_environment` would
override the env variable set in `setup_platform_environment` on
macOS.
When improving the error message, we started #showing in the
answer set a lot more symbols - but we forgot to suppress the
debug messages warning about UNKNOWN SYMBOLs
* onnxruntime: fix the call to as_string() operator
* Update var/spack/repos/builtin/packages/py-onnxruntime/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-onnxruntime/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-onnxruntime/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-onnxruntime: rm now-unused stringpiece_1_10.patch
---------
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* packages/hub: add new version, update to module
Hub now uses a go module to build, needs different env vars, and we're
on a very, very old version before that. Deprecate the old ones so we
can clean out that old build once we pass a spack version.
* cleanup suggested by @adamjstewart
* Update to latest version
* Fix linebreak
* Make suggested changes
* bumped to 0.6.1
* Update var/spack/repos/builtin/packages/py-scikit-build-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Chris Richardson <cnr12@cam.ac.uk>
Co-authored-by: Matt Archer <ma595@cam.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
In practice, one can only compiler for the Intel Data Center Max GPU
via a SYCL build and the oneAPI compiler. This is unlikely to change,
so we can be explicit about that.
* elbencho add new version and git master branch
* Update var/spack/repos/builtin/packages/elbencho/package.py
Co-authored-by: Alec Scott <alec@bcs.sh>
* formatting fix requested by @alecbcs
* remove whitespace added in blank line by github auto resolve
---------
Co-authored-by: Ethan W <mail@ethanwilliams.xyz>
Co-authored-by: Alec Scott <alec@bcs.sh>
* gromacs: Add new variants and clarify existing ones
Add new variants that reflect existing capabilities and defaults in
the upstream build system. Add other existing constraints that were
not yet specified.
* conform to style
* Fix missing hyphens
* Correct cmake variable names
* add elephant version v0.12.0 and 0.13.0
* update copyright
* reformat according to black format errors
* restore maintainers directive
* Update var/spack/repos/builtin/packages/py-elephant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add dependency python 3.8+
* sorted dependencies
* sort dependencies from newest to oldest
* add deps for @master
* removed dependency for master, since it is included in 0.12.0:
* removed dependency for python 3.7+ , since 3.7+ is the lowest supported version anyway
* removed specific deps for master, since master is always newer than all stable releases
* updated numpy dependency for Elephant 0.12.0:
* Update var/spack/repos/builtin/packages/py-elephant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-elephant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed upper bounds for py-quantities, omitting v0.14.0
* add elephant v0.14.0
* update required quantities version
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cleo: add versions 2.0.0 2.0.1; add maintainers
* py-cleo: add forgotten dependence
* py-cleo: update from review: remove preferred version, remove a dependence, fix py-rapidfuzz version
* py-cleo: deprecated version 1.0.0a5; add version 1.0.0; update dependences
* py-cleo: add version 2.1.0; update version range of dependences
* py-crashtest: add version 0.4.1, dependence of py-cleo
* py-cleo: update dependence
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cleo: update dependence py-clikit
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cleo: update dependence py-rapidfuzz
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-rapidfuzz: add version 2.2.0 dependence of py-cleo@2
* py-cleo: fix version range of py-crashtest
* py-rapidfuzz: fix dependences; add py-rapidfuzz-capi and py-jarowinkler
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Using Python 3.12 in a freshly cloned Spack repository results in
warnings such as this:
```
==> Warning: invalid escape sequence '\$'
==> Warning: invalid escape sequence '\('
==> Warning: invalid escape sequence '\.'
==> Warning: invalid escape sequence '\.'
```
These will turn into errors in 3.13, so fix them. All of them actually
do not need to be regexes, so convert them into normal strings.
* add version 0.14.1
* formatting
* style checks
* fix style errors
* remove old versions
* fix typo
* style
* update maintainers directive
* sort dependencies from newest to oldest
* Update var/spack/repos/builtin/packages/py-quantities/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-quantities/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* sort dependencies from newest to oldest
* removed upper bounds for python version
* Update var/spack/repos/builtin/packages/py-quantities/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove dependency on Python 3.7 +, since 3.7 is the lowest supported version anyway
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added recent versions to ecflow/package.py, as well as added a cxxstd variant that is
needed to set BOOST_NO_CXX98_FUNCTION_BASE appropriately when building with C++17 standard.
* Fixed pep8 style error in the ecflow package.py script.
* Remov
* Removed cxxstd variant since the ecflow cmake configuration was already specifying
to use the c++17 standard for newer versions. The use of the BOOST_NO_CXX98_FUNCTION_BASE
define is now triggered by the ecflow version.
* Permit packages that depend on Intel oneAPI packages to access sdk
* Implement and use IntelOneapiLibraryPackageWithSdk
* Restore libs property to IntelOneapiLibraryPackage
* Conform to style
* Provide new class to infrastructure
* Treat sdk/include as the main include
* root: new version 6.30.00
There is a new release of ROOT, v6.30.00, with release notes at https://root.cern/doc/v630/release-notes.html.
In addition to some deprecations of build options, this updates the C++ standard to 17 or higher (well, 20), and increases the vc minimum version.
* vc: new version 1.4.4
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Improves the warning for deprecated preferences, and adds a configuration
audit to get files:lines details of the issues.
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* package/lemon: improve
* fix bug
* final improvements
* use f strings for boolean options, add soplex as TODO
* leave +coin as TODO
* depends on bzip2 when +coin
* tidy
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
* initial commit to enable rocAL and add MIVisionX tests
* fix styling
* updated checksum for libjpeg patches
* update for 5.6
* use satisfies for checking spec version
xsdk: add +sycl variant - with amrex, arborx, ginkgo, petsc, sundials
xsdk: add +pflotran variant
xsdk: enable hypre+rocm
xsdk: enable superlu-dist for GPU - but use trilinos~superlu-dist [as that breaks builds]
xsdk: dealii: disable oce as it can cause intel-tbb-2017.6 to be picked up for some builds (for ex: gcc=13) and result in subsequent build failures
Some environments may have `dd4hep` as a concretized package without having it installed (yet). For those environments, `dd4hep` has property `libs` that is an empty list. Nevertheless, it can be added to a run environment (for example in case `dd4hep` is part of an environment). This results in an IndexError:
```
==> Warning: couldn't load runtime environment due to IndexError: list index out of range
```
To avoid the IndexError, only prepend the `dd4hep` libs if there are actually libs found.
Tests didn't cover the new `--variants-by-name` parameter in #40998.
Add some parameterization to hit that.
This changeset makes me think that the main section-printing loop in `spack info` isn't
factored so well. It makes it difficult to pass different arguments to different helper
functions. I could break it out into if statements if folks think that would be cleaner.
* dealii: 9.5.0
* kokkos+cuda_lambda
* dealii ^kokkos@3.7: require +cuda +cuda_lambda +wrapper
* Added 9.5.1, try ~cgal when +cuda
* Forward Cuda architecture request
* Remove workaround
* Try not enforcing the Kokkos compiler
* Enforce using nvcc_wrapper with Trilinos+Cuda
* Don't define CMAKE_*_COMPILER to point to MPI wrappers
* Use the same compiler as Trilinos/Kokkos
* Only check for Trilinos compiler
* Disable Trilinos+Cuda
* Disable Cuda support
* Try CUDA build without ninja
* Combined examples and examples_compile
* Use f-string for cuda_arch
* p -> _package
* Indentation
* Fix up f-string
---------
Co-authored-by: Luca Heltai <luca.heltai@sissa.it>
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
We have two ways to concretize now:
* `spack concretize` concretizes only the root specs that are not concrete in the environment.
* `spack concretize -f` eliminates all cached concretization data and reconcretizes the *entire* environment.
This PR adds `spack deconcretize`, which eliminates cached concretization data for a spec. This allows
users greater control over what is preserved from their `spack.lock` file and what is reused when not
using `spack concretize -f`. If you want to update a spec installed in your environment, you can call
`spack deconcretize` on it, and that spec and any relevant dependents will be removed from the lock file.
`spack concretize` has two options:
* `--root`: limits deconcretized specs to *specific* roots in the environment. You can use this to
deconcretize exactly one root in a `unify: false` environment. i.e., if `foo` root is a dependent
of `bar`, both roots, `spack deconcretize bar` will *not* deconcretize `foo`.
* `--all`: deconcretize *all* specs that match the input spec. By default `spack deconcretize`
will complain about multiple matches, like `spack uninstall`.
The ^mkl pattern was used to refer to three packages
even though none of software using it was depending
on "mkl".
This pattern, which follows Hyrum's law, is now being
removed in favor of a more explicit one.
In this PR gromacs, abinit, lammps, and quantum-espresso
are modified.
Intel packages are also modified to provide "lapack"
and "blas" together.
And improve the error message (load vs unload).
Of course you could have some uninstalled dependency too, but as long as
it doesn't implement `setup_run_environment` etc, I don't think it hurts
to attempt to load the root anyways, given that failure to do so is a
warning, not a fatal error.
This changes variant display to use a much more legible format, and to use screen space
much better (particularly on narrow terminals). It also adds color the variant display
to match other parts of `spack info`.
Descriptions and variant value lists that were frequently squished into a tiny column
before now have closer to the full terminal width.
This change also preserves any whitespace formatting present in `package.py`, so package
maintainers can make easer-to-read descriptions of variant values if they want. For
example, `gasnet` has had a nice description of the `conduits` variant for a while, but
it was wrapped and made illegible by `spack info`. That is now fixed and the original
newlines are kept.
Conditional variants are grouped by their when clauses by default, but if you do not
like the grouping, you can display all the variants in order with `--variants-by-name`.
I'm not sure when people will prefer this, but it makes it easier to tell that a
particular variant is/isn't there. I do think grouping by `when` is the better default.
* [lcov] Add build and runtime deps necessary for lcov@2.0.0:
+ Many additional Perl package dependecies are required for the new version of lcov.
+ Some of the new dependencies were not known to spack until now.
* Style fix
This commit improves forward compatibility of Spack with newer build cache metadata formats.
Before this commit, invalid or unrecognized metadata would be fatal errors, now they just cause
a mirror to be skipped.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Libgit2 requires python as build dependency. I was getting an error because it was falling back to system Python which is compiled with Intel compilers and thus, `libgit2` was failing because it couldn't find `libimf.so` (which doesn't make sense).
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
The libevent release tarballs ship with a `configure` script generated by an old `libtool`. The `libtool` generated by `configure` is not compatible with `MACOSX_DEPLOYMENT_VERSION` > 10. Regeneration of the `configure` scripts fixes build on macOS.
Original configure contains:
```
case $host_os in
rhapsody* | darwin1.[012])
_lt_dar_allow_undefined='$wl-undefined ${wl}suppress' ;;
darwin1.*)
_lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
darwin*) # darwin 5.x on
# if running on 10.5 or later, the deployment target defaults
# to the OS version, if on x86, and 10.4, the deployment
# target defaults to 10.4. Don't you love it?
case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
10.0,*86*-darwin8*|10.0,*-darwin[91]*)
_lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
10.[012][,.]*)
_lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
10.*)
_lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
esac
```
After re-running `autogen.sh`:
```
case $host_os in
rhapsody* | darwin1.[012])
_lt_dar_allow_undefined='$wl-undefined ${wl}suppress' ;;
darwin1.*)
_lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
darwin*)
case $MACOSX_DEPLOYMENT_TARGET,$host in
10.[012],*|,*powerpc*-darwin[5-8]*)
_lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
*)
_lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
esac
```
* lcov: add version2, perl dep at build and runtime
* lcov: add runtime deps
* namespace-autoclean: new perl package
* datetime: dep on autoclean
* formatting
* abinit: add v9.10.3
Changed configure arguments for specfying how to use Wannier90 for versions
after 9.8.
When the mpi variant is requested, set the F90 environment variable to point
to the MPI Fortran wrapper when building versions after 9.8 instead of FC.
---------
Co-authored-by: Alec Scott <hi@alecbcs.com>
* exago: fix v1.5.1 tag; only allow python up to 3.10 for for @:1.5 (#40676)
* exago: fix v1.5.1 tag; only allow python up to 3.10 for for @:1.5 due to pybind error with py 3.11
* hiop@:1.0 +cuda: constrain to cuda@:11.9
* fixes syntax of maintainers
---------
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
* intel-xed: fix git hash for mbuild, add version 2023.10.11
Fixes#40912
* Fix the git commit hash for mbuild 2022.04.17. This was broken in
commit eef9939c21 by mixing up the hashes for xed versus mbuild.
* Add versions 2023.08.21 and 2023.10.11.
* fix style
Before this PR, variant were not propagated to leaf nodes that could accept
the propagated value, if some intermediate node couldn't accept it.
This PR fixes that issue by marking nodes as "candidate" for propagation
and by setting the variant only if it can be accepted by the node.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Problem: the current configure arguments are added lists to a list,
and this needs to be adding strings to the same list.
Solution: ensure we add each item (string) separately.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* Use `major.minor.patch`, `major.minor`, `major` in tags
* Ensure `latest` is the semver largest version, and not "latest in time"
* Remove Ubuntu 18.04 from the list of images
Modify the packages.yaml schema so that soft-preferences on targets,
compilers and providers can only be specified under the "all" attribute.
This makes them effectively global preferences.
Version preferences instead can only be specified under a package
specific section.
If a preference attribute is found in a section where it should
not be, it will be ignored and a warning is printed to screen.
Most queries will end up calling `spec.satisfies(query)` on everything in the DB, which
will cause Spack to ask whether the query spec is virtual if its name doesn't match the
target spec's. This can be expensive, because it can cause Spack to check if any new
virtuals showed up in *all* the packages it knows about. That can currently trigger
thousands of `stat()` calls.
We can avoid the virtual check for most successful queries if we consider that if there
*is* a match by name, the query spec *can't* be virtual. This PR adds an optimization to
the query loop to save any comparisons that would trigger a virtual check for last.
- [x] Add a `deferred` list to the `query()` loop.
- [x] First run through the `query()` loop *only* checks for name matches.
- [x] Query loop now returns early if there's a name match, skipping most `satisfies()` calls.
- [x] Second run through the `deferred()` list only runs if query spec is virtual.
- [x] Fix up handling of concrete specs.
- [x] Add test for querying virtuals in DB.
- [x] Avoid allocating deferred if not necessary.
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Currently there's some hacky logic in the AppleClang compiler that makes
it also accept `gfortran` as a fortran compiler if `flang` is not found.
This is guarded by `if sys.platform` checks s.t. it only applies to
Darwin.
But on Linux the feature of detecting mixed toolchains is highly
requested too, cause it's rather annoying to run into a failed build of
`openblas` after dozens of minutes of compiling its dependencies, just
because clang doesn't have a fortran compiler.
In particular in CI where the system compilers may change during system
updates, it's typically impossible to fix compilers in a hand-written
compilers.yaml config file: the config will almost certainly be outdated
sooner or later, and maintaining one config file per target machine and
writing logic to select the correct config is rather undesirable too.
---
This PR introduces a flag `spack compiler find --mixed-toolchain` that
fills out missing `fc` and `f77` entries in `clang` / `apple-clang` by
picking the best matching `gcc`.
It is enabled by default on macOS, but not on Linux, matching current
behavior of `spack compiler find`.
The "best matching gcc" logic and compiler path updates are identical to
how compiler path dictionaries are currently flattened "horizontally"
(per compiler id). This just adds logic to do the same "vertically"
(across different compiler ids).
So, with this change on Ubuntu 22.04:
```
$ spack compiler find --mixed-toolchain
==> Added 6 new compilers to /home/harmen/.spack/linux/compilers.yaml
gcc@13.1.0 gcc@12.3.0 gcc@11.4.0 gcc@10.5.0 clang@16.0.0 clang@15.0.7
==> Compilers are defined in the following files:
/home/harmen/.spack/linux/compilers.yaml
```
you finally get:
```
compilers:
- compiler:
spec: clang@=15.0.7
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
flags: {}
operating_system: ubuntu23.04
target: x86_64
modules: []
environment: {}
extra_rpaths: []
- compiler:
spec: clang@=16.0.0
paths:
cc: /usr/bin/clang-16
cxx: /usr/bin/clang++-16
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
flags: {}
operating_system: ubuntu23.04
target: x86_64
modules: []
environment: {}
extra_rpaths: []
```
The "best gcc" is automatically default system gcc, since it has no
suffixes / prefixes.
Add a new config section: `config:aliases`, which is a dictionary mapping aliases
to commands.
For instance:
```yaml
config:
aliases:
sp: spec -I
```
will define a new command `sp` that will execute `spec` with the `-I`
argument.
Aliases cannot override existing commands, and this is ensured with a test.
We cannot currently alias subcommands. Spack will warn about any aliases
containing a space, but will not error, which leaves room for subcommand
aliases in the future.
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Test that setup_run_environment changes to CC/CXX/FC/F77 are dropped in build env
* compilers set in run env shouldn't impact build
Adds `drop` to EnvironmentModifications courtesy of @haampie, and uses
it to clear modifications of CC, CXX, F77 and FC made by
`setup_{,dependent_}run_environment` routines when producing an
environment in BUILD context.
* comment / style
* comment
---------
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
This adds a rather trivial context manager that lets you deduplicate repeated
arguments in directives, e.g.
```python
depends_on("py-x@1", when="@1", type=("build", "run"))
depends_on("py-x@2", when="@2", type=("build", "run"))
depends_on("py-x@3", when="@3", type=("build", "run"))
depends_on("py-x@4", when="@4", type=("build", "run"))
```
can be condensed to
```python
with default_args(type=("build", "run")):
depends_on("py-x@1", when="@1")
depends_on("py-x@2", when="@2")
depends_on("py-x@3", when="@3")
depends_on("py-x@4", when="@4")
```
The advantage is it's clear for humans, the downside it's less clear for type checkers due to type erasure.
Create chains of causation for error messages.
The current implementation is only completed for some of the many errors presented by the concretizer. The rest will need to be filled out over time, but this demonstrates the capability.
The basic idea is to associate conditions in the solver with one another in causal relationships, and to associate errors with the proximate causes of their facts in the condition graph. Then we can construct causal trees to explain errors, which will hopefully present users with useful information to avoid the error or report issues.
Technically, this is implemented as a secondary solve. The concretizer computes the optimal model, and if the optimal model contains an error, then a secondary solve computes causation information about the error(s) in the concretizer output.
Examples:
$ spack solve hdf5 ^cmake@3.0.1
==> Error: concretization failed for the following reasons:
1. Cannot satisfy 'cmake@3.0.1'
2. Cannot satisfy 'cmake@3.0.1'
required because hdf5 ^cmake@3.0.1 requested from CLI
3. Cannot satisfy 'cmake@3.18:' and 'cmake@3.0.1
required because hdf5 ^cmake@3.0.1 requested from CLI
required because hdf5 depends on cmake@3.18: when @1.13:
required because hdf5 ^cmake@3.0.1 requested from CLI
4. Cannot satisfy 'cmake@3.12:' and 'cmake@3.0.1
required because hdf5 depends on cmake@3.12:
required because hdf5 ^cmake@3.0.1 requested from CLI
required because hdf5 ^cmake@3.0.1 requested from CLI
$ spack spec cmake ^curl~ldap # <-- with curl configured non-buildable and an external with `+ldap`
==> Error: concretization failed for the following reasons:
1. Attempted to use external for 'curl' which does not satisfy any configured external spec
2. Attempted to build package curl which is not buildable and does not have a satisfying external
attr('variant_value', 'curl', 'ldap', 'True') is an external constraint for curl which was not satisfied
3. Attempted to build package curl which is not buildable and does not have a satisfying external
attr('variant_value', 'curl', 'gssapi', 'True') is an external constraint for curl which was not satisfied
4. Attempted to build package curl which is not buildable and does not have a satisfying external
'curl+ldap' is an external constraint for curl which was not satisfied
'curl~ldap' required
required because cmake ^curl~ldap requested from CLI
$ spack solve yambo+mpi ^hdf5~mpi
==> Error: concretization failed for the following reasons:
1. 'hdf5' required multiple values for single-valued variant 'mpi'
2. 'hdf5' required multiple values for single-valued variant 'mpi'
Requested '~mpi' and '+mpi'
required because yambo depends on hdf5+mpi when +mpi
required because yambo+mpi ^hdf5~mpi requested from CLI
required because yambo+mpi ^hdf5~mpi requested from CLI
3. 'hdf5' required multiple values for single-valued variant 'mpi'
Requested '~mpi' and '+mpi'
required because netcdf-c depends on hdf5+mpi when +mpi
required because netcdf-fortran depends on netcdf-c
required because yambo depends on netcdf-fortran
required because yambo+mpi ^hdf5~mpi requested from CLI
required because netcdf-fortran depends on netcdf-c@4.7.4: when @4.5.3:
required because yambo depends on netcdf-fortran
required because yambo+mpi ^hdf5~mpi requested from CLI
required because yambo depends on netcdf-c
required because yambo+mpi ^hdf5~mpi requested from CLI
required because yambo depends on netcdf-c+mpi when +mpi
required because yambo+mpi ^hdf5~mpi requested from CLI
required because yambo+mpi ^hdf5~mpi requested from CLI
Future work:
In addition to fleshing out the causes of other errors, I would like to find a way to associate different components of the error messages with different causes. In this example it's pretty easy to infer which part is which, but I'm not confident that will always be the case.
See the previous PR #34500 for discussion of how the condition chains are incomplete. In the future, we may need custom logic for individual attributes to associate some important choice rules with conditions such that clingo choices or other derivations can be part of the explanation.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This PR implements the concept of "default environment", which doesn't have to be
created explicitly. The aim is to lower the barrier for adopting environments.
To (create and) activate the default environment, run
```
$ spack env activate
```
This mimics the behavior of
```
$ cd
```
which brings you to your home directory.
This is not a breaking change, since `spack env activate` without arguments
currently errors. It is similar to the already existing `spack env activate --temp`
command which always creates an env in a temporary directory, the difference
is that the default environment is a managed / named environment named `default`.
The name `default` is not a reserved name, it's just that `spack env activate`
creates it for you if you don't have it already.
With this change, you can get started with environments faster:
```
$ spack env activate [--prompt]
$ spack install --add x y z
```
instead of
```
$ spack env create default
==> Created environment 'default in /Users/harmenstoppels/spack/var/spack/environments/default
==> You can activate this environment with:
==> spack env activate default
$ spack env activate [--prompt] default
$ spack install --add x y z
```
Notice that Spack supports switching (but not stacking) environments, so the
parallel with `cd` is pretty clear:
```
$ spack env activate named_env
$ spack env status
==> In environment named_env
$ spack env activate
$ spack env status
==> In environment default
```
* Add command suggestions
This adds suggestions of similar commands in case users mistype a
command. Before:
```
$ spack spack
==> Error: spack is not a recognized Spack command or extension command; check with `spack commands`.
```
After:
```
$ spack spack
==> Error: spack is not a recognized Spack command or extension command; check with `spack commands`.
Did you mean one of the following commands?
spec
patch
```
* Add package name suggestions
* Remove suggestion to run spack clean -m
This completes to `spack concretize`:
```
spack conc<tab>
```
but this still gets hung up on the difference between `concretize` and `concretise`:
```
spack -e . conc<tab>
```
We were checking `"$COMP_CWORD" = 1`, which tracks the word on the command line
including any flags and their args, but we should track `"$COMP_CWORD_NO_FLAGS" = 1` to
figure out if the arg we're completing is the first real command.
This PR adds support for including separate definitions from `spack.yaml`.
Supporting the inclusion of files with definitions enables user to make
curated/standardized collections of packages that can re-used by others.
Currently module globals aren't set before running
`setup_[dependent_]run_environment` to compute environment modifications
for module files. This commit fixes that.
Looking at the memory profiles of concurrent solves
for environment with unify:false, it seems memory
is only ramping up.
This exchange in the potassco mailing list:
https://sourceforge.net/p/potassco/mailman/potassco-users/thread/b55b5b8c2e8945409abb3fa3c935c27e%40lohn.at/#msg36517698
Seems to suggest that clingo doesn't release memory
until end of the application.
Since when unify:false we distribute work to processes,
here we give a maxtaskperchild=1, so we clean memory
after each solve.
Some providers must provide virtuals "together", i.e.
if they provide one virtual of a set, they must be the
providers also of the others.
There was a bug though, where we were not checking if
the other virtuals in the set were needed at all in
the DAG.
This commit fixes the bug.
* libtheora: regenerate Makefile.in during autoreconf
The patch to inhibit running of configure would exit autogen.sh so early
that it did not yet run autoconf/automake/...
Instead of patching autogen.sh, just pass -V as argument, as this is
passed on to configure and lets it just print its version instead of
configuring the build tree.
Also drop arguments from autogen.sh, as they are unused when configure
does not run.
* libtheora: fix build on macos
Apply upstream patches in order to avoid unresolved symbols during building of libtheoraenc.
These patches require re-running automake/autoconf/...
Error messages:
libtool: link: /Users/ma/git/spack/lib/spack/env/clang/clang -dynamiclib -o .libs/libtheoraenc.1.dylib .libs/apiwrapper.o .libs/fragment.o .libs/idct.o .libs/internal.o .libs/state.o .libs/quant.o .l
ibs/analyze.o .libs/fdct.o .libs/encfrag.o .libs/encapiwrapper.o .libs/encinfo.o .libs/encode.o .libs/enquant.o .libs/huffenc.o .libs/mathops.o .libs/mcenc.o .libs/rate.o .libs/tokenize.o -L/opt/spac
k/darwin-sonoma-m1/apple-clang-15.0.0/libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/lib -logg -lm -Wl,-exported_symbols_list -Wl,/var/folders/zv/qr55pmd9065glf0mcltpx5bm000102/T/ma/spack-stage/spac
k-stage-libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/spack-src/lib/theoraenc.exp -install_name /opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/lib
/libtheoraenc.1.dylib -compatibility_version 3 -current_version 3.2
ld: warning: search path '/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/lib' not found
ld: Undefined symbols:
_th_comment_add, referenced from:
_theora_comment_add in apiwrapper.o
_th_comment_add_tag, referenced from:
_theora_comment_add_tag in apiwrapper.o
_th_comment_clear, referenced from:
_theora_comment_clear in apiwrapper.o
_th_comment_init, referenced from:
_theora_comment_init in apiwrapper.o
_th_comment_query, referenced from:
_theora_comment_query in apiwrapper.o
_th_comment_query_count, referenced from:
_theora_comment_query_count in apiwrapper.o
* libtheora: add git versions
stable as version name for theora-1.1 branch was chosen so that it sorts between 1.1.x and master
* libtheora: remove unused patch
thanks to @michaelkuhn for noticing
* Add 2023.09-0 for x86_64, aarch64, and ppc64le
extend the anaconda3 package.py to support aarch64 and ppc64le.
add the latest version of anaconda3 to each new platform, including the existing x86_64
* formatting
* Fix py-pyside2 to build with newer llvm and to use spack libglx and libxcb headers where system headers are missing
pyside2 needs LLVM_INSTALL_DIR to be set when using llvm 11: and expects system headers for libglx and libxcb and won't build otherwise.
* Fix styling
* remove raw string type
* Update var/spack/repos/builtin/packages/py-pyside2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR makes it possible to select only a subset of virtual dependencies from a spec that _may_ provide more. To select providers, a syntax to specify edge attributes is introduced:
```
hdf5 ^[virtuals=mpi] mpich
```
With that syntax we can concretize specs like:
```console
$ spack spec strumpack ^[virtuals=mpi] intel-parallel-studio+mkl ^[virtuals=lapack] openblas
```
On `develop` this would currently fail with:
```console
$ spack spec strumpack ^intel-parallel-studio+mkl ^openblas
==> Error: Spec cannot include multiple providers for virtual 'blas'
Requested 'intel-parallel-studio' and 'openblas'
```
In package recipes, virtual specs that are declared in the same `provides` directive need to be provided _together_. This means that e.g. `openblas`, which has:
```python
provides("blas", "lapack")
```
needs to provide both `lapack` and `blas` when requested to provide at least one of them.
## Additional notes
This capability is needed to model compilers. Assuming that languages are treated like virtual dependencies, we might want e.g. to use LLVM to compile C/C++ and Gnu GCC to compile Fortran. This can be accomplished by the following[^1]:
```
hdf5 ^[virtuals=c,cxx] llvm ^[virtuals=fortran] gcc
```
[^1]: We plan to add some syntactic sugar around this syntax, and reuse the `%` sigil to avoid having a lot of boilerplate around compilers.
Modifications:
- [x] Add syntax to interact with edge attributes from spec literals
- [x] Add concretization logic to be able to cherry-pick virtual dependencies
- [x] Extend semantic of the `provides` directive to express when virtuals need to be provided together
- [x] Add unit-tests and documentation
* vcftools: adding new version 0.1.16
* Update var/spack/repos/builtin/packages/vcftools/package.py
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
* Make sure sio is in dependent build env for podio
* podio: Fix likely(?) typo in root dependency
* podio: Add latest tag and new variants + dependencies
* podio: Add v00-16-07 tag
* podio: Fix dependencies flagged by package audit
* podio: Simplify root dependency
* podio: Add 0.17.1 tag
Allowing white space around `:` in version ranges introduces an ambiguity:
```
a@1: b
```
parses as `a@1:b` but should really be parsed as two separate specs `a@1:` and `b`.
With white space disallowed around `:` in ranges, the ambiguity is resolved.
Call setup_dependent_run_environment on both link and run edges,
instead of only run edges, which restores old behavior.
Move setup_build_environment into get_env_modifications
Also call setup_run_environment on direct build deps, since their run
environment has to be set up.
* update SPERR package
* remove blank line
* update SPERR to be version 0.7.1
* a little clean up
* bound versions that require zstd
* add USE_ZSTD
* add libpressio-sperr version upbound
* update libpressio-sperr
* address review comments
* improve format
---------
Co-authored-by: Samuel Li <Sam@Navada>
Co-authored-by: Samuel Li <sam@cisl-m121a>
* Add tests to ensure variant propagation syntax can round-trip to/from string
* Add a regression test for the bug in 35298
* Reconstruct the spec constraints in the worker process
Specs do not preserve any information on propagation of variants
when round-tripping to/from JSON (which we use to pickle), but
preserve it when round-tripping to/from strings.
Therefore, we pass a spec literal to the worker and reconstruct
the Spec objects there.
* Added NVML support to the slurm package
* dbus package is required for cgroup support
* Fixing formatting
* Style fix
* Added PAM support
* Added ROCm SMI support
- [x] Add links to information people are going to want to know when adding license
information to their packages (namely OSI licenses and SPDX identifiers).
- [x] Update the packaging docs for `license()` with Spack as an example for `when=`.
After all, it's a dual-licensed package that changed once in the past.
- [x] Add link to https://spdx.org/licenses/ in the `spack create` boilerplate as well.
* Load the script file during enviroment setup so that all the enviroment variables are set properly
* Patch csh/tcsh so that it uses spacks via env
* Update SHA for latest version
* Extend shebang to perl and fix up the regex
* Add liggght patched for newer compiler
Add C++ 17 support
Add Clang and Oneapi support
* Add maintainers
* Fix format in liggghts
* Fix maintainers before versions
Co-authored-by: Alec Scott <alec@bcs.sh>
* Fix style and user to usr
* Update package.py
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-10-29 09:56:27 -07:00
10159 changed files with 219310 additions and 106172 deletions
if [ "${{ needs.prechecks.result }}" == "failure" ] || [ "${{ needs.prechecks.result }}" == "canceled" ]; then
echo "Unit tests failed."
exit 1
else
exit 0
fi
coverage:
needs:[unit-tests, prechecks ]
uses:./.github/workflows/coverage.yml
secrets:inherit
all:
needs:[unit-tests, coverage, bootstrap ]
if:${{ always() }}
runs-on:ubuntu-latest
# See https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/accessing-contextual-information-about-workflow-runs#needs-context
steps:
- name:Status summary
run:|
if [ "${{ needs.unit-tests.result }}" == "failure" ] || [ "${{ needs.unit-tests.result }}" == "canceled" ]; then
message: "If you are referencing Spack in a publication, please cite the paper below."
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
abstract: >-
Large HPC centers spend considerable time supporting software for thousands of users, but the complexity of HPC software is quickly outpacing the capabilities of existing software management tools.
Scientific applications require specific versions of compilers, MPI, and other dependency libraries, so using a single, standard software stack is infeasible.
However, managing many configurations is difficult because the configuration space is combinatorial in size.
We introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages and dependencies.
It allows any number of builds to coexist on the same system, and it ensures that installed packages can find their dependencies, regardless of the environment.
We show through real-world use cases that Spack supports diverse and demanding applications, bringing order to HPC software chaos.
Large HPC centers spend considerable time supporting software for thousands of users, but the
complexity of HPC software is quickly outpacing the capabilities of existing software management
tools. Scientific applications require specific versions of compilers, MPI, and other dependency
libraries, so using a single, standard software stack is infeasible. However, managing many
configurations is difficult because the configuration space is combinatorial in size. We
introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages
and dependencies. It allows any number of builds to coexist on the same system, and it ensures
that installed packages can find their dependencies, regardless of the environment. We show
through real-world use cases that Spack supports diverse and demanding applications, bringing
order to HPC software chaos.
preferred-citation:
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
type: conference-paper
@@ -71,7 +75,7 @@ preferred-citation:
type: doi
value: 10.1145/2807591.2807623
- description: "The DOE Document Release Number of the work"
.. Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
.. Copyright Spack Project Developers. See COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -865,7 +864,7 @@ There are several different ways to use Spack packages once you have
installed them. As you've seen, spack packages are installed into long
paths with hashes, and you need a way to get them into your path. The
easiest way is to use :ref:`spack load <cmd-spack-load>`, which is
described in the next section.
described in this section.
Some more advanced ways to use Spack packages include:
@@ -959,7 +958,86 @@ use ``spack find --loaded``.
You can also use ``spack load --list`` to get the same output, but it
does not have the full set of query options that ``spack find`` offers.
We'll learn more about Spack's spec syntax in the next section.
We'll learn more about Spack's spec syntax in :ref:`a later section <sec-specs>`.
.._extensions:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Python packages and virtual environments
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack can install a large number of Python packages. Their names are
typically prefixed with ``py-``. Installing and using them is no
different from any other package:
..code-block::console
$ spack install py-numpy
$ spack load py-numpy
$ python3
>>> import numpy
The ``spack load`` command sets the ``PATH`` variable so that the right Python
executable is used, and makes sure that ``numpy`` and its dependencies can be
located in the ``PYTHONPATH``.
Spack is different from other Python package managers in that it installs
every package into its *own* prefix. This is in contrast to ``pip``, which
installs all packages into the same prefix, be it in a virtual environment
or not.
For many users, **virtual environments** are more convenient than repeated
``spack load`` commands, particularly when working with multiple Python
packages. Fortunately Spack supports environments itself, which together
with a view are no different from Python virtual environments.
The recommended way of working with Python extensions such as ``py-numpy``
is through :ref:`Environments <environments>`. The following example creates
a Spack environment with ``numpy`` in the current working directory. It also
puts a filesystem view in ``./view``, which is a more traditional combined
prefix for all packages in the environment.
..code-block::console
$ spack env create --with-view view --dir .
$ spack -e . add py-numpy
$ spack -e . concretize
$ spack -e . install
Now you can activate the environment and start using the packages:
..code-block::console
$ spack env activate .
$ python3
>>> import numpy
The environment view is also a virtual environment, which is useful if you are
sharing the environment with others who are unfamiliar with Spack. They can
either use the Python executable directly:
..code-block::console
$ ./view/bin/python3
>>> import numpy
or use the activation script:
..code-block::console
$ source ./view/bin/activate
$ python3
>>> import numpy
In general, there should not be much difference between ``spack env activate``
and using the virtual environment. The main advantage of ``spack env activate``
is that it knows about more packages than just Python packages, and it may set
additional runtime variables that are not covered by the virtual environment
activation script.
See :ref:`environments` for a more in-depth description of Spack
environments and customizations to views.
.._sec-specs:
@@ -1096,6 +1174,17 @@ unspecified version, but packages can depend on other packages with
could depend on ``mpich@1.2:`` if it can only build with version
``1.2`` or higher of ``mpich``.
..note:: Windows Spec Syntax Caveats
Windows has a few idiosyncrasies when it comes to the Spack spec syntax and the use of certain shells
Spack's spec dependency syntax uses the carat (``^``) character, however this is an escape string in CMD
so it must be escaped with an additional carat (i.e. ``^^``).
CMD also will attempt to interpret strings with ``=`` characters in them. Any spec including this symbol
must double quote the string.
Note: All of these issues are unique to CMD, they can be avoided by using Powershell.
For more context on these caveats see the related issues: `carat <https://github.com/spack/spack/issues/42833>`_ and `equals <https://github.com/spack/spack/issues/43348>`_
Below are more details about the specifiers that you can add to specs.
.._version-specifier:
@@ -1119,6 +1208,9 @@ and ``3.4.2``. Similarly, ``@4.2:`` means any version above and including
``4.2``. As a short-hand, ``@3`` is equivalent to the range ``@3:3`` and
includes any version with major version ``3``.
Versions are ordered lexicograpically by its components. For more details
on the order, see :ref:`the packaging guide <version-comparison>`.
Notice that you can distinguish between the specific version ``@=3.2`` and
the range ``@3.2``. This is useful for packages that follow a versioning
scheme that omits the zero patch version number: ``3.2``, ``3.2.1``,
@@ -1130,6 +1222,10 @@ A version specifier can also be a list of ranges and specific versions,
separated by commas. For example, ``@1.0:1.5,=1.7.1`` matches any version
in the range ``1.0:1.5`` and the specific version ``1.7.1``.
^^^^^^^^^^^^
Git versions
^^^^^^^^^^^^
For packages with a ``git`` attribute, ``git`` references
may be specified instead of a numerical version i.e. branches, tags
and commits. Spack will stage and build based off the ``git``
@@ -1262,6 +1358,10 @@ For example, for the ``stackstart`` variant:
mpileaks stackstart==4# variant will be propagated to dependencies
mpileaks stackstart=4# only mpileaks will have this variant value
Spack also allows variants to be propagated from a package that does
not have that variant.
^^^^^^^^^^^^^^
Compiler Flags
^^^^^^^^^^^^^^
@@ -1347,22 +1447,12 @@ the reserved keywords ``platform``, ``os`` and ``target``:
$ spack install libelf os=ubuntu18.04
$ spack install libelf target=broadwell
or together by using the reserved keyword ``arch``:
..code-block::console
$ spack install libelf arch=cray-CNL10-haswell
Normally users don't have to bother specifying the architecture if they
are installing software for their current host, as in that case the
values will be detected automatically. If you need fine-grained control
over which packages use which targets (or over *all* packages' default
target), see :ref:`package-preferences`.
..admonition:: Cray machines
The situation is a little bit different for Cray machines and a detailed
explanation on how the architecture can be set on them can be found at :ref:`cray-support`
.._support-for-microarchitectures:
@@ -1526,6 +1616,30 @@ any MPI implementation will do. If another package depends on
error. Likewise, if you try to plug in some package that doesn't
provide MPI, Spack will raise an error.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Explicit binding of virtual dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are packages that provide more than just one virtual dependency. When interacting with them, users
might want to utilize just a subset of what they could provide, and use other providers for virtuals they
need.
It is possible to be more explicit and tell Spack which dependency should provide which virtual, using a
$ spack mirror set --signed <name> # enable signing and verification for an existing mirror
$ spack mirror set --unsigned <name> # disable signing and verification for an existing mirror
Or you can directly edit the ``mirrors.yaml`` configuration file:
..code-block::yaml
mirrors:
<name>:
url:<url>
signed:false# disable signing and verification
See also :ref:`mirrors`.
----------
Relocation
----------
When using buildcaches across different machines, it is likely that the install
root will be different from the one used to build the binaries.
To address this issue, Spack automatically relocates all paths encoded in binaries
and scripts to their new location upon install.
Note that there are some cases where this is not possible: if binaries are built in
a relatively short path, and then installed to a longer path, there may not be enough
space in the binary to encode the new path. In this case, Spack will fail to install
the package from the build cache, and a source build is required.
To reduce the likelihood of this happening, it is highly recommended to add padding to
the install root during the build, as specified in the :ref:`config <config-yaml>`
section of the configuration:
..code-block::yaml
config:
install_tree:
root:/opt/spack
padded_length:128
.._binary_caches_oci:
---------------------------------
Automatic push to a build cache
---------------------------------
Sometimes it is convenient to push packages to a build cache as soon as they are installed. Spack can do this by setting autopush flag when adding a mirror:
..code-block::console
$ spack mirror add --autopush <name> <url or path>
Or the autopush flag can be set for an existing mirror:
..code-block::console
$ spack mirror set --autopush <name> # enable automatic push for an existing mirror
$ spack mirror set --no-autopush <name> # disable automatic push for an existing mirror
Then after installing a package it is automatically pushed to all mirrors with ``autopush: true``. The command
..code-block::console
$ spack install <package>
will have the same effect as
..code-block::console
$ spack install <package>
$ spack buildcache push <cache> <package> # for all caches with autopush: true
..note::
Packages are automatically pushed to a build cache only if they are built from source.
-----------------------------------------
OCI / Docker V2 registries as build cache
@@ -167,25 +264,30 @@ infrastructure, or to cache Spack built binaries in Github Actions and
GitLab CI.
To get started, configure an OCI mirror using ``oci://`` as the scheme,
and optionally specify a username and password (or personal access token):
and optionally specify variables that hold the username and password (or
.. Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
.. Copyright Spack Project Developers. See COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -17,7 +16,7 @@ case you want to skip directly to specific docs:
*:ref:`config.yaml <config-yaml>`
*:ref:`mirrors.yaml <mirrors>`
*:ref:`modules.yaml <modules>`
*:ref:`packages.yaml <build-settings>`
*:ref:`packages.yaml <packages-config>`
*:ref:`repos.yaml <repositories>`
You can also add any of these as inline configuration in the YAML
@@ -73,9 +72,12 @@ are six configuration scopes. From lowest to highest:
Spack instance per project) or for site-wide settings on a multi-user
machine (e.g., for a common Spack instance).
#.**plugin**: Read from a Python project's entry points. Settings here affect
all instances of Spack running with the same Python installation. This scope takes higher precedence than site, system, and default scopes.
#.**user**: Stored in the home directory: ``~/.spack/``. These settings
affect all instances of Spack and take higher precedence than site,
system, or defaults scopes.
system, plugin, or defaults scopes.
#.**custom**: Stored in a custom directory specified by ``--config-scope``.
If multiple scopes are listed on the command line, they are ordered
@@ -196,6 +198,45 @@ with MPICH. You can create different configuration scopes for use with
mpi: [mpich]
.._plugin-scopes:
^^^^^^^^^^^^^
Plugin scopes
^^^^^^^^^^^^^
..note::
Python version >= 3.8 is required to enable plugin configuration.
Spack can be made aware of configuration scopes that are installed as part of a python package. To do so, register a function that returns the scope's path to the ``"spack.config"`` entry point. Consider the Python package ``my_package`` that includes Spack configurations:
..code-block::console
my-package/
├── src
│ ├── my_package
│ │ ├── __init__.py
│ │ └── spack/
│ │ │ └── config.yaml
└── pyproject.toml
adding the following to ``my_package``'s ``pyproject.toml`` will make ``my_package``'s ``spack/`` configurations visible to Spack when ``my_package`` is installed:
..code-block::toml
[project.entry_points."spack.config"]
my_package="my_package:get_config_path"
The function ``my_package.get_extension_path`` in ``my_package/__init__.py`` might look like
The first step to contribute new runners is to open an issue in the `spack infrastructure <https://github.com/spack/spack-infrastructure/issues/new?assignees=&labels=runner-registration&projects=&template=runner_registration.yml>`_
project. This will be reported to the spack infrastructure team who will guide users through the process
of registering new runners for Spack CI.
The information needed to register a runner is the motivation for the new resources, a semi-detailed description of
the runner, and finallly the point of contact for maintaining the software on the runner.
The point of contact will then work with the infrastruture team to obtain runner registration token(s) for interacting with
with Spack's GitLab instance. Once the runner is active, this point of contact will also be responsible for updating the
GitLab runner software to keep pace with Spack's Gitlab.
Tagging
~~~~~~~
In the initial stages of runner registration it is important to **exclude** the special tag ``spack``. This will prevent
the new runner(s) from being picked up for production CI jobs while it is configured and evaluated. Once it is determined
that the runner is ready for production use the ``spack`` tag will be added.
Because gitlab has no concept of tag exclustion, runners that provide specialized resource also require specialized tags.
For example, a basic CPU only x86_64 runner may have a tag ``x86_64`` associated with it. However, a runner containing an
CUDA capable GPU may have the tag ``x86_64-cuda`` to denote that it should only be used for packages that will benefit from
a CUDA capable resource.
OIDC
~~~~
Spack runners use OIDC authentication for connecting to the appropriate AWS bucket
which is used for coordinating the communication of binaries between build jobs. In
order to configure OIDC authentication, Spack CI runners use a python script with minimal
dependencies. This script can be configured for runners as seen here using the ``pre_build_script``.
.. Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
.. Copyright Spack Project Developers. See COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
.._environments:
=========================
Environments (spack.yaml)
=========================
=====================================
Environments (spack.yaml, spack.lock)
=====================================
An environment is used to group together a set of specs for the
purpose of building, rebuilding and deploying in a coherent fashion.
Environments provide a number of advantages over the *à la carte*
approach of building and loading individual Spack modules:
An environment is used to group a set of specs intended for some purpose
to be built, rebuilt, and deployed in a coherent fashion. Environments
define aspects of the installation of the software, such as:
#.Environments separate the steps of (a) choosing what to
install, (b) concretizing, and (c) installing. This allows
Environments to remain stable and repeatable, even if Spack packages
are upgraded: specs are only re-concretized when the user
explicitly asks for it. It is even possible to reliably
transport environments between different computers running
different versions of Spack!
#. Environments allow several specs to be built at once; a more robust
solution than ad-hoc scripts making multiple calls to ``spack
install``.
#. An Environment that is built as a whole can be loaded as a whole
into the user environment. An Environment can be built to maintain
a filesystem view of its packages, and the environment can load
that view into the user environment at activation time. Spack can
also generate a script to load all modules related to an
environment.
#.*which* specs to install;
#.*how* those specs are configured; and
#.*where* the concretized software will be installed.
Aggregating this information into an environment for processing has advantages
over the *à la carte* approach of building and loading individual Spack modules.
With environments, you concretize, install, or load (activate) all of the
specs with a single command. Concretization fully configures the specs
and dependencies of the environment in preparation for installing the
software. This is a more robust solution than ad-hoc installation scripts.
And you can share an environment or even re-use it on a different computer.
Environment definitions, especially *how* specs are configured, allow the
software to remain stable and repeatable even when Spack packages are upgraded. Changes are only picked up when the environment is explicitly re-concretized.
Defining *where* specs are installed supports a filesystem view of the
environment. Yet Spack maintains a single installation of the software that
can be re-used across multiple environments.
Activating an environment determines *when* all of the associated (and
installed) specs are loaded so limits the software loaded to those specs
actually needed by the environment. Spack can even generate a script to
load all modules related to an environment.
Other packaging systems also provide environments that are similar in
some ways to Spack environments; for example, `Conda environments
<https://conda.io/docs/user-guide/tasks/manage-environments.html>`_ or
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---------------------------------------
Registering Extensions via Entry Points
---------------------------------------
..note::
Python version >= 3.8 is required to register extensions via entry points.
Spack can be made aware of extensions that are installed as part of a python package. To do so, register a function that returns the extension path, or paths, to the ``"spack.extensions"`` entry point. Consider the Python package ``my_package`` that includes a Spack extension:
..code-block::console
my-package/
├── src
│ ├── my_package
│ │ └── __init__.py
│ └── spack-scripting/ # the spack extensions
└── pyproject.toml
adding the following to ``my_package``'s ``pyproject.toml`` will make the ``spack-scripting`` extension visible to Spack when ``my_package`` is installed:
..code-block::toml
[project.entry_points."spack.extenions"]
my_package="my_package:get_extension_path"
The function ``my_package.get_extension_path`` in ``my_package/__init__.py`` might look like
Attributes set this way will be accessible to any method executed
in the package.py file (e.g. the ``install()`` method). Values for these
attributes may be any value parseable by yaml.
These can only be applied to specific packages, not "all" or
virtual packages.
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