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Fixes an issue on the RHEL8 UBI container where this test would fail because `gr_mem`
was empty for every entry in the `grp` DB.
You have to check *both* the `pwd` database (which has primary groups) and `grp` (which
has other gorups) to do this correctly.
- [x] update `llnl.util.filesystem.group_ids()` to do this
- [x] use it in the `sbang` test
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This PR introduces breadth-first traversal, and moves depth-first traversal
logic out of Spec's member functions, into `traverse.py`.
It introduces a high-level API with three main methods:
```python
spack.traverse.traverse_edges(specs, kwargs...)
spack.traverse.traverse_nodes(specs, kwags...)
spack.traverse.traverse_tree(specs, kwargs...)
```
with the usual `root`, `order`, `cover`, `direction`, `deptype`, `depth`, `key`,
`visited` kwargs for the first two.
What's new is that `order="breadth"` is added for breadth-first traversal.
The lower level API is not exported, but is certainly useful for advanced use
cases. The lower level API includes visitor classes for direction reversal and
edge pruning, which can be used to create more advanced traversal methods,
especially useful when the `deptype` is not constant but depends on the node
or depth.
---
There's a couple nice use-cases for breadth-first traversal:
- Sometimes roots have to be handled differently (e.g. follow build edges of
roots but not of deps). BFS ensures that root nodes are always discovered at
depth 0, instead of at any depth > 1 as a dep of another root.
- When printing a tree, it would be nice to reduce indent levels so it fits in the
terminal, and ensure that e.g. `zlib` is not printed at indent level 10 as a
dependency of a build dep of a build dep -- rather if it's a direct dep of my
package, I wanna see it at depth 1. This basically requires one breadth-first
traversal to construct a tree, which can then be printed with depth-first traversal.
- In environments in general, it's sometimes inconvenient to have a double
loop: first over the roots then over each root's deps, and maintain your own
`visited` set outside. With BFS, you can simply init the queue with the
environment root specs and it Just Works. [Example here](https://github.com/spack/spack/blob/3ec73046995d9504d6e135f564f1370cfe31ba34/lib/spack/spack/environment/environment.py#L1815-L1816)
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Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
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Currently, many tests hardcode to older versions of gcc for comparisons of
concretization among compiler versions. Those versions are too old to concretize for
`aarch64`-family targets, which leads to failing tests on `aarch64`.
This PR fixes those tests by updating the compiler versions used for testing.
Currently, many tests hardcode the expected architecture result in concretization to the
`x86_64` family of architectures.
This PR generalizes the tests that can be generalized, to cover multiple architecture
families. For those that test specific relationships among `x86_64`-family targets, it
ensures that concretization uses the `x86_64`-family targets in those cases.
Currently, many tests rely on the fact that `AutotoolsPackage` imposes no dependencies
on the inheriting package. That is not true on `aarch64`-family architectures.
This PR ensures that the fact `AutotoolsPackage` on `aarch64` pulls in a dependency on
`gnuconfig` is ignored when testing for the appropriate relationships among dependencies
Additionally, 5 tests currently prompt the user for input when `gpg` is available in the
user's path. This PR fixes that issue. And 7 tests fail currently when the user has a
yubikey available. This PR fixes the incorrect gpg argument causing those issues.
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The `spack info <package>` command does not show the `Virtual Packages:` output unless the `--virtuals` command option is passed. Before this changes, the information that the command is supposed to be illustrating is not shown in the example and is confusing.
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This PR solves the issue reported in #32471 specifically for targets and operating systems,
by avoiding to add a default platform to anonymous specs.
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Introduces `spack.util.elf.parse_elf(file_handle)`
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* sundials: add v6.4.1, new ginkgo and kokkos variants, plus some fixes
* add missing kokkos/kokkos-kernels variant
* add v6.4.0
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`coverage` sometimes failed to combine, even if there were multiple reports.
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* superlu-dist: fix rocm variant for the master branch
* simplify superlu-dist
* add mpi include to HIP_HIPCC_FLAGS
Co-authored-by: liuyangzhuan <liuyangzhuan@users.noreply.github.com>
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* Add tracy 0.9
* Add conflict for pika and tracy@0.9:
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* py-ilmbase: add dependency to py-numpy
* fix style
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Co-authored-by: sbulut <sbulut@3vgeomatics.com>
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Previously symlinks were not relocated when they pointed across packages
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Drop the link dependency type for the rocm packages. We don't
actually link, and that adds rpaths that conflict with the app.
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When building ParaView with a newer HDf5 than 1.10, it needs to select the 1.10 API using flags.
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* added polypolish package, comfirmed builds
* added bwa dep
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* julia: don't look for the openlibm libraries when unneeded
Cause spack to *not* check for the existence of the openlibm libraries (by adding it to the pkgs list) when ~openlibm is specified.
* [@spackbot] updating style on behalf of downloadico
Co-authored-by: downloadico <downloadico@users.noreply.github.com>
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Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
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This reverts commit b1559cc831620ee2b2cf8e57fdecc5bb3bf8edfd.
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Packages should depend on the virtual provider, pkgconfig, not on its implementations pkg-config or pkgconf.
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- the updated OpenFOAM wmake rules now allow multiple locations for
compiler flags:
* wmake/General/common/c++Opt [central]
* wmake/linux64Gcc/c++Opt [traditional]
- match both '=' and ':=' make rule lines
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
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Changes to improve locating shared libraries on Windows, which in
turn enables the use of Clingo. This PR attempts to establish a
proper distinction between linking on Windows vs. Linux/Mac: on
Windows, linking is always done with .lib files (never .dll files).
This somewhat complicates the model since the Spec.lib method could
return libraries that were used for both linking and loading, but
since these are not always the same on Windows, it was decided to
treat Spec.libs as being for link-time libraries. Additional functions
are added to help dependents locate run-time libraries.
* Clingo is now the default concretizer on Windows
* Clingo is now the concretizer used for unit tests on Windows
* Fix a permissions issue that can occur while moving Git files during
fetching/staging
* Packages can now implement "win_add_library_dependent" to register
files/directories that include libraries that would need to link
to dependency dlls
* Packages can now implement "win_add_rpath" to register the locations
of dlls that dependents would want to load
* "Spec.libs" on Windows is updated to return link-time libraries
(i.e. .lib files, rather than .dll files)
* PackageBase.rpath on Windows is now updated to return the most-likely
locations where .dlls will be found (which is generally in the bin/
directory)
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* Enable Cuda for AMReX smoke test.
* style fix
* more style fixes
* change /... to join_path
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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* Nalu-Wind: Allow for standard versions of trilinos
This will allow us to utilize custom numeric versions for trilinos in `spack-manager` while we continue to develop `nalu-wind`.
Pinging @eugeneswalker @jrood-nrel @tasmith4
* Update var/spack/repos/builtin/packages/nalu-wind/package.py
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* exago: query and use MPI compilers from spack
* exago: requires explicit location of mpi.h for nvcc
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Currently there's a slow sequential step in binary relocation where all
strings of a binary are collected, with rpaths removed, and then
filtered for the old install root.
This is completely unnecessary, and also incorrect, since we replace
more than just the old install root in the prefix to prefix mapping. And
in fact the prefix to prefix mapping is parallel, and a single pass. So
even as an optimization, this filter makes no sense anymore.
Therefor we remove it
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- single pass over the binary data matching all prefixes
- collect offsets and replacement strings
- do in-place updates with `fseek` / `fwrite`, since typically our
replacement touch O(few bytes) while the file is O(many megabytes)
- be nice: leave the file untouched if some string can't be
replaced
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* New MFEM version: 4.5
Add new MFEM variants: ginkgo, hiop
* mfem: small tweaks
* mfem: tweak testing script
* mfem: try to resolve issue #30483
* mfem: fix style
* mfem: tweak for Spack-built hipsparse
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
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* Deprecate spack bootstrap trust/untrust
* Update CI
* Update tests
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Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
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(#33587)
* phist: add/update conflicts with cray-libsci and/or python@3.11: for versions <1.11.2
* phist: style fix
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(#33586)
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