- [x] allow caller of `condition()` to pass lists of transforms
- [x] all transform functions now take trigger *and* effect as parameters
- [x] add some utility functions to simplify `condition()`
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>
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