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This fixes some errors with setting up test configuration. These
errors do not cause current Spack tests to fail but do create
red herring issues elsewhere (see #15666). Fixing these errors
leads to more errors in tests that depended on the original
misconfigured state, so those are also addressed here.
This is an update to #16003 which accounts for some unit tests with
conflicting config/mutable_config fixtures. These conflicts were
not exposed until the mutable_config fixture was fixed. Details are
included below. The change which builds on #16003 is prefixed with
"(new)".
* For tests that use the real Spack package repository, the config
needs to avoid using MPI providers that are not intended to be
installed by Spack. Without this, it is possible that Spack tests
which concretize the MPI virtual will end up trying to use an
implementation that it shouldn't (e.g. one that is always
provided externally). See #15666 for an example.
* The mutable_config test fixture was not initializing the scope
roots to the right directories (so the resulting config was empty).
* The current_host fixture in the concretize.py tests was using the
config fixture rather than mutable_config, and was polluting the
config cache for other tests.
* One test in concretize.py was clearing a nonexistent cache
(PackagePrefs._packages_config_cache). This reference has been
removed.
* The test 'test_preferred_compilers' was was depending on cross
test config pollution to succeed. The initial spec before
concretization has been updated to updated to be explicit about
the desired result.
* (new) For tests that use install_mockery and mutable_config,
replace install_mockery with a separate install_mockery_mutable_config
fixture that is exactly the same as install_mockery but uses the
mutable_config fixture to avoid conflicts.
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* ADD New package revocap-refiner
"""The University of Tokyo, CISS Project:
Geometric processing, mesh processing, mesh generation"""
* Modify homepage = "https://github.com/FrontISTR/REVOCAP_Refiner"
Modify version('master', branch='master')
Modify depends_on('swig', type='build')
Modify install_tree('Refiner', prefix.include.refine)
Delete mkdirp(prefix.include)
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* Add new package: ganglia
* ganglia: fix the libexpat depends
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* Adapt to the latest Acts developments
A long time ago, the Acts project (whose name was then capitalized ACTS) used
to maintain multiple software repositories:
- The heart of the tracking toolkit was located in the `acts-core` repository
- Fast simulation extensions were located in the `acts-fatras` repository
- Advanced usage examples were located in the `acts-framework` repository
This multi-repository organization, however, has been a source of constant
pain, which is why the various projects were gradually merged into a single
mono-repo, called `acts`. Today, with the integration of `acts-framework`,
this merging process is reaching completion.
The present pull request adapts the Acts package to this evolution by...
- Renaming the package to `acts`, reflecting the new repository name
- Renaming the `test` variant to `unit_tests`, reflecting current CMake naming
- Adding the new build variants that were inherited from `acts-framework`
- Acknowledging the change of semantics of the `examples` variant, and only
supporting the new ones (as the former variant was almost unused)
- Liberally using alphabetical order to make the package code more readable
- Recording a large number of conflicts, some of which are introduced by the
merging of `acts-framework` and some of which already existed before
- Using the new capitalization of "Acts"
* Add acts v0.23
* Update dd4hep version requirement
* Add acts v0.22.1 bugfix
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* add PGI version 19.7
* use openmpi in pgi
exporting openmpi enviroment variables when installed with pgi
* fix lint
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Fixed #15884.
Spack asks every package linked into an environment to tell us how
environment variables should be modified when a spack environment is
activated. As part of this, specs in an environment are symlinked into
the environment's view (see #13249), and the package calculates
environment modifications with *the default view as the prefix*.
All of this works nicely for pointing the user's environment at the view
*if* every package is successfully linked. Unfortunately, right now we
only track what specs "should" be in a view, not which specs actually
are. So we end up calculating environment modifications on things that
aren't linked into thee view, and the exception isn't caught, so lots of
spack commands end up failing.
This fixes the issue by ignoring and warning about specs where
calculating environment modifications fails. So we can still keep using
Spack even if the current environment is incomplete.
We should probably also just avoid computing env modifications *entirely*
for unlinked packages, but right now that is a slow operation (requires a
lot of YAML parsing). We should revisit that when we have some better
state management for views, but the fix adopted here will still be
necessary, as we want spack commands to be resilient to other types of
bugs in `setup_run_environment()` and friends. That code is in packages
and we have to assume it could be buggy when we call it outside of builds
(as it might fail more than just the build).
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Use neovim's vendored dependencies for 0.4 and later
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* openfoam: correspond to build with Fujitsu compiler.
* openfoam: add rules for Fujitsu compiler (on linuxARM64)
- the Fujitsu compiler is a clang derivative, so use a modified
version of the clang rules if upstream does not supply anything
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* Add new package:py-json5
* Remove unnecessary line
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* New version of pylint + fix dependencies
* Update package.py
* Update package.py
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If using mpirun, the R sessions can be started with a wrapper script
that helps set up the R session cluster. Put this wrapper in the PATH so
it is easily accessible.
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* blis: FIX threads option
* HPL: openmp variant is ignored for 2.3
* blis: FIX flake8
* blis: FIX spacing
* Update var/spack/repos/builtin/packages/hpl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* hpl: FIX spec --> self.spec, FIX blas with amdblis
* HPL: fix flake8
* HPL: FIX flake8
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* qscintilla
* Revert "qscintilla"
This reverts commit 00bd00ea3c5af4f29de5dd6961acf03fb51e2ea0.
* Move logic to qt package.
* flake8
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
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Add nightly builds for popular and commonly used packages on
macOS that should improve the onramp user experience if
working well.
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Add a `spack external find` command that tries to populate
`packages.yaml` with external packages from the user's `$PATH`. This
focuses on finding build dependencies. Currently, support has only been
added for `cmake`.
For a package to be discoverable with `spack external find`, it must define:
* an `executables` class attribute containing a list of
regular expressions that match executable names.
* a `determine_spec_details(prefix, specs_in_prefix)` method
Spack will call `determine_spec_details()` once for each prefix where
executables are found, passing in the path to the prefix and the path to
all found executables. The package is responsible for invoking the
executables and figuring out what type of installation(s) are in the
prefix, and returning one or more specs (each with version, variants or
whatever else the user decides to include in the spec).
The found specs and prefixes will be added to the user's `packages.yaml`
file. Providing the `--not-buildable` option will mark all generated
entries in `packages.yaml` as `buildable: False`
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* kokkos: add v3.1.01
* kokkos: fix up versions
* kokkos-kernels: follow upstream versioning
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Cray has two machine types. "XC" machines are the larger
machines more common in HPC, but "Cluster" machines are
also cropping up at some HPC sites. Cluster machines run
a slightly different form of the CrayPE programming environment,
and often come without default modules loaded. Cluster
machines also run different versions of some software, and run
a linux distro on the backend nodes instead of running Compute
Node Linux (CNL).
Below are the changes made to support "Cluster" machines in
Spack. Some of these changes are semi-related general upkeep
of the cray platform.
* cray platform: detect properly after module purge
* cray platform: support machines running OSs other than CNL
Make Cray backend OS delegate to LinuxDistro when no cle_release file
favor backend over frontend OS when name clashes
* cray platform: target detection uses multiple strategies
This commit improves the robustness of target
detection on Cray by trying multiple strategies.
The first one that produces results wins. If
nothing is found only the generic family of the
frontend host is used as a target.
* cray-libsci: add package from NERSC
* build_env: unload cray-libsci module when not explicitly needed
cray-libsci is a package in Spack. The cray PrgEnv
modules load it implicitly when we set up the compiler.
We now unload it after setting up the compiler and
only reload it when requested via external package.
* util/module_cmd: more robust module parsing
Cray modules have documentation inside the module
that is visible to the `module show` command.
Spack module parsing is now robust to documentation
inside modules.
* cce compiler: uses clang flags for versions >= 9.0
* build_env: push CRAY_LD_LIBRARY_PATH into everything
Some Cray modules add paths to CRAY_LD_LIBRARY_PATH
instead of LD_LIBRARY_PATH. This has performance benefits
at load time, but leads to Spack builds not finding their
dependencies from external modules.
Spack now prepends CRAY_LD_LIBRARY_PATH to
LD_LIBRARY_PATH before beginning the build.
* mvapich2: setup cray compilers when on cray
previously, mpich was the only mpi implementation to support
cray systems (because it is the MPI on Cray XC systems).
Cray cluster systems use mvapich2, which now supports cray
compiler wrappers.
* build_env: clean pkgconf from environment
Cray modules silently add pkgconf to the user environment
This can break builds that do not user pkgconf.
Now we remove it frmo the environment and add it again if it
is in the spec.
* cray platform: cheat modules for rome/zen2 module on naples/zen node
Cray modules for naples/zen architecture currently specify
rome/zen2. For now, we detect this and return zen for modules
named `craype-x86-rome`.
* compiler: compiler default versions
When detecting compiler default versions for target/compiler
compatibility checks, Spack previously ran the compiler without
setting up its environment. Now we setup a temporary environment
to run the compiler with its modules to detect its version.
* compilers/cce: improve logic to determine C/C++ std flags
* tests: fix existing tests to play nicely with new cray support
* tests: test new functionality
Some new functionality can only be tested on a cray system.
Add tests for what can be tested on a linux system.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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Recently added patch to port the LLVM 9.0.0 ICE with OpenBLAS and
AVX-512 instructions as well to AppleClang (11.0.3).
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Since #9481 Python's None is not permitted as a value for
MV variants. The string 'none' is used instead.
Add the same fix for the amgx and lammps packages
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* CMake: fix https://github.com/spack/spack/issues/16453 with a patch addressing both libhugetlbfs and icpc warnings on Cray XC40 systems
* Including CMake v3.17.2 in the patched versions
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* Add OpenMP variant to Umpire
* Initial implementation of Axom package
* Add Axom spack package and fix required dependencies
* Fix overzealous tag replacement
* Attempt to fix version error
* Fix python version attempt #2
* Update raja and umpire
* remove sys_type check
* Address comments in axom package
* Address Greg's comments
* Fix flake8
* more flake8
* Simplify MPIEXEC and MPIEXEC_NUMPROC_FLAG
* Fix typo
* Revert back to slurm check, fix cuda_arch checks
* Fix cuda_arch variant forwarding
* Add cub variant
* Add py-shroud
* Address comments
* Fix shroud path in axom
* Fix merge conflict
* Fix backwards if
* Fix flake8 and add copyright
* format for consistency
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* perl-bio-searchio-hmmer: new package at 1.7.3
* perl-bio-searchio-hmmer: add dependencies
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Add additionally required dependencies to WarpX that are needed
for transformations in RZ geometry with spectral (PSATD) solvers.
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* change homepage to readthedocs
* update cctools version to 7.1.5
* change http to https
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* libspatialite
* flake8
* Added proper version constrain
* Update var/spack/repos/builtin/packages/libspatialite/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/libspatialite/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* libsecret
* Update package.py
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
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Otherwise, if I run `xenv` after `spack load py-xenv` it fails with:
```
Traceback (most recent call last):
File "/home/vavolkl/spack/opt/spack/linux-centos7-broadwell/gcc-8.3.0/py-xenv-develop_2018-12-20-lqbxakapsepqo5w3sjhhokj5o7c5jei2/bin/xenv", line 6, in <module>
from pkg_resources import load_entry_point
ModuleNotFoundError: No module named 'pkg_resources'
```
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* [gaudi] fixes and patches
* Update var/spack/repos/builtin/packages/gaudi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/gaudi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [gaudi] add older versions and fold +tests into +optional
* [gaudi] set run environment
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* environments: allow sigils to apply to entire reference
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