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2021-09-18updating htslib to 1.13 (#26012)Vanessasaurus1-1/+2
2021-09-18updating nco to 5.0.1 (#26014)Vanessasaurus1-1/+2
2021-09-18updating graphviz to 2.49.0 (#26011)Vanessasaurus1-0/+1
2021-09-18updating veloc to 1.5 and cleaning up spacing (#26025)Vanessasaurus1-7/+7
2021-09-18updating cloc to 1.9.0 (#26009)Vanessasaurus1-1/+2
2021-09-18updating poppler (#26016)Vanessasaurus1-1/+2
2021-09-18updating raxml to 8.2.12 (#26018)Vanessasaurus1-1/+2
2021-09-18updating protobuf (Gooooogle!) to 3.18.0 (#26017)Vanessasaurus1-39/+40
2021-09-18updating samtools to 1.13 (#26019)Vanessasaurus1-1/+2
2021-09-18updating spades to 3.15.3 (#26022)Vanessasaurus1-1/+2
2021-09-18updating gatk to 4.2.2.0 (#26010)Vanessasaurus1-73/+21
2021-09-17Convert RAJA, CHAI and Umpire to CachedCMakePackages (#25788)David Beckingsale3-105/+191
* Switch Umpire to CMakeCachedPackage * Fix missing import * Correct tests option in Umpire * Switch RAJA to CachedCMakePackage * Convert CHAI to CachedCMakePackage * Corrections in RAJA * Patches in Umpire & RAJA for BLT target export * Fixup style * Fixup incorrect use of cmake_cache_string
2021-09-17update tutorial version of hdf5 (#25368)Chris White5-117/+417
2021-09-17Bootstrap should search for compilers after switching config scopes (#26029)Massimiliano Culpo6-47/+80
fixes #25992 Currently the bootstrapping process may need a compiler. When bootstrapping from sources the need is obvious, while when bootstrapping from binaries it's currently needed in case patchelf is not on the system (since it will be then bootstrapped from sources). Before this PR we were searching for compilers as the first operation, in case they were not declared in the configuration. This fails in case we start bootstrapping from within an environment. The fix is to defer the search until we have swapped configuration.
2021-09-17Bump reframe (#25970)Harmen Stoppels1-0/+1
2021-09-17Add ccache v4.4.1. (#25957)Olli Lupton1-0/+1
2021-09-17improve ascent package to use stages and cmake base (#25720)Cyrus Harrison1-73/+70
* improve ascent package to use stages and cmake base * style * more style
2021-09-17fmt: add variant for shared library (#25969)iarspider1-1/+5
2021-09-17variant build: openmp_ref should be openmp (#26006)eugeneswalker1-1/+1
2021-09-17gosam: new version 2.1.1 (#25985)iarspider1-4/+8
2021-09-16GCC: patch for gcc 10.3.0 ICE when using nvcc (#25980)Kurt Sansom1-0/+3
* fix: patch for gcc 10.3.0 ICE when using nvcc * fix: use URL reference instead * fix: add missing sha256sum
2021-09-16added package.py for GPTL (#25993)Edward Hartnett1-0/+47
2021-09-16Filter UserWarning out of test output (#26001)Massimiliano Culpo1-0/+2
2021-09-16workaround a cmake/rocm bug in heffte (#25948)Miroslav Stoyanov1-0/+4
2021-09-16Add v7.0.2 to Admixtools (#25997)Alec Scott1-6/+7
2021-09-16Fix for problem with cmake@3.21 (#25989)G-Ragghianti1-0/+3
2021-09-16New package: ROMS (#25990)AMD Toolchain Support1-0/+141
Co-authored-by: Mohan Babu <mohbabul@amd.com>
2021-09-16cc: Use parameter expansion instead of basename (#24509)Michael Kuhn1-1/+1
While debugging #24508, I noticed that we call `basename` in `cc`. The same can be achieved by using Bash's parameter expansion, saving one external process per call. Parameter expansion cannot replace basename for directories in some cases, but is guaranteed to work for executables.
2021-09-16Recommend Git's manyFiles feature (#25977)Michael Kuhn3-3/+3
Git 2.24 introduced a feature flag for repositories with many files, see: https://github.blog/2019-11-03-highlights-from-git-2-24/#feature-macros Since Spack's Git repository contains roughly 8,500 files, it can be worthwhile to enable this, especially on slow file systems such as NFS: ``` $ hyperfine --warmup 3 'cd spack-default; git status' 'cd spack-manyfiles; git status' Benchmark #1: cd spack-default; git status Time (mean ± σ): 3.388 s ± 0.095 s [User: 256.2 ms, System: 625.8 ms] Range (min … max): 3.168 s … 3.535 s 10 runs Benchmark #2: cd spack-manyfiles; git status Time (mean ± σ): 168.7 ms ± 10.9 ms [User: 98.6 ms, System: 126.1 ms] Range (min … max): 144.8 ms … 188.0 ms 19 runs Summary 'cd spack-manyfiles; git status' ran 20.09 ± 1.42 times faster than 'cd spack-default; git status' ```
2021-09-16Bump sirius 7.2.x (#25939)Harmen Stoppels1-0/+2
2021-09-16Add a deprecation warning when using the old concretizer (#25966)Massimiliano Culpo1-0/+8
2021-09-16Update HPX package (#25775)Mikael Simberg2-40/+82
* Add support for C++20 to HPX package * Enable unity builds in HPX package when available * Add support for HIP/ROCm to HPX package * Rearrange and update required versions for HPX package * Add C++20 option to asio package
2021-09-16Improve bootstrapping docs a hair (#25962)Harmen Stoppels2-50/+51
2021-09-16Fix NameError in foreground/background test (#25967)Harmen Stoppels1-2/+4
2021-09-16Inform the user about bootstrapping (#25964)Harmen Stoppels1-0/+3
2021-09-15bedops: Fix checksum for 2.4.40 (#25958)jacorvar1-1/+1
Fixes #25951
2021-09-15py-pybind11: use PythonPackage install method (#25650)Adam J. Stewart1-6/+5
2021-09-15build(deps): bump codecov/codecov-action from 2.0.3 to 2.1.0 (#25925)dependabot[bot]1-4/+4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.0.3 to 2.1.0. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v2.0.3...v2.1.0) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-09-15Raise exception when 1+ stand-alone tests fail (#25857)Tamara Dahlgren1-0/+14
2021-09-15Added LvArray 0.2.2 (#25950)Ben Corbett1-0/+1
2021-09-14Make clingo the default solver (#25502)Massimiliano Culpo7-18/+41
Modifications: - [x] Change `defaults/config.yaml` - [x] Add a fix for bootstrapping patchelf from sources if `compilers.yaml` is empty - [x] Make `SPACK_TEST_SOLVER=clingo` the default for unit-tests - [x] Fix package failures in the e4s pipeline Caveats: 1. CentOS 6 still uses the original concretizer as it can't connect to the buildcache due to issues with `ssl` (bootstrapping from sources requires a C++14 capable compiler) 1. I had to update the image tag for GitlabCI in e699f14. 1. libtool v2.4.2 has been deprecated and other packages received some update
2021-09-14Add a __reduce__ method to Environment (#25678)Adam J. Stewart2-0/+27
* Add a __reduce__ method to Environment * Add unit test * Convert Path to str
2021-09-14Adding ability to compare git references to spack install (#24639)Vanessasaurus12-43/+638
This will allow a user to (from anywhere a Spec is parsed including both name and version) refer to a git commit in lieu of a package version, and be able to make comparisons with releases in the history based on commits (or with other commits). We do this by way of: - Adding a property, is_commit, to a version, meaning I can always check if a version is a commit and then change some action. - Adding an attribute to the Version object which can lookup commits from a git repo and find the last known version before that commit, and the distance - Construct new Version comparators, which are tuples. For normal versions, they are unchanged. For commits with a previous version x.y.z, d commits away, the comparator is (x, y, z, '', d). For commits with no previous version, the comparator is ('', d) where d is the distance from the first commit in the repo. - Metadata on git commits is cached in the misc_cache, for quick lookup later. - Git repos are cached as bare repos in `~/.spack/git_repos` - In both caches, git repo urls are turned into file paths within the cache If a commit cannot be found in the cached git repo, we fetch from the repo. If a commit is found in the cached metadata, we do not recompare to newly downloaded tags (assuming repo structure does not change). The cached metadata may be thrown out by using the `spack clean -m` option if you know the repo structure has changed in a way that invalidates existing entries. Future work will include automatic updates. # Finding previous versions Spack will search the repo for any tags that match the string of a version given by the `version` directive. Spack will also search for any tags that match `v + string` for any version string. Beyond that, Spack will search for tags that match a SEMVER regex (i.e., tags of the form x.y.z) and interpret those tags as valid versions as well. Future work will increase the breadth of tags understood by Spack For each tag, Spack queries git to determine whether the tag is an ancestor of the commit in question or not. Spack then sorts the tags that are ancestors of the commit by commit-distance in the repo, and takes the nearest ancestor. The version represented by that tag is listed as the previous version for the commit. Not all commits will find a previous version, depending on the package workflow. Future work may enable more tangential relationships between commits and versions to be discovered, but many commits in real world git repos require human knowledge to associate with a most recent previous version. Future work will also allow packages to specify commit/tag/version relationships manually for such situations. # Version comparisons. The empty string is a valid component of a Spack version tuple, and is in fact the lowest-valued component. It cannot be generated as part of any valid version. These two characteristics make it perfect for delineating previous versions from distances. For any version x.y.z, (x, y, z, '', _) will be less than any "real" version beginning x.y.z. This ensures that no distance from a release will cause the commit to be interpreted as "greater than" a version which is not an ancestor of it. Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-09-15gcc: apply backported fixes to v4.9.3 (#25945)David Beckingsale1-1/+1
2021-09-14dealii: add version 9.3.1 (#25915)Satish Balay1-0/+1
2021-09-14Pipelines: (Re)enable E4S on Power stack (#25921)Scott Wittenburg2-21/+21
Pipelines: (Re)enable E4S on Power stack
2021-09-14Add missing mumps TPL commands (#25940)Weston Ortiz1-0/+1
2021-09-14Update spack monitor to support new spec (#25928)Vanessasaurus1-1/+3
This PR coincides with tiny changes to spack to support spack monitor using the new spec the corresponding spack monitor PR is at https://github.com/spack/spack-monitor/pull/31. Since there are no changes to the database we can actually update the current server fairly easily, so either someone can test locally or we can just update and then test from that (and update as needed). Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-14Add py-pot with patch (#25712)Harmen Stoppels2-0/+88
2021-09-14reframe: set PYTHONPATH at runtime (#25842)Harmen Stoppels1-0/+1
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