* 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>
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 ]
@@ -94,8 +101,19 @@ jobs:
secrets:inherit
all:
needs:[coverage, bootstrap ]
needs:[unit-tests, coverage, bootstrap ]
if:${{ always() }}
runs-on:ubuntu-latest
# See https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/accessing-contextual-information-about-workflow-runs#needs-context
steps:
- name:Success
run:"true"
- name:Status summary
run:|
if [ "${{ needs.unit-tests.result }}" == "failure" ] || [ "${{ needs.unit-tests.result }}" == "canceled" ]; then
# Copyright 2013-2024 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)
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