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2022-10-21py-instrain: added required + optional dependency (#33465)Luke Diorio-Toth1-0/+8
* added py-instrain dependencies * fixed style * removed coverm dep until I have a working coverm package * added dep documentation
2022-10-21updated python version requirements (#33466)Luke Diorio-Toth1-4/+7
* updated python version requirements * updated sha256 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-21py-checkm-genome and py-pysam: bumped version and updated deps (#33449)Luke Diorio-Toth2-7/+16
* py-checkm-genome and py-pysam: bumped version and updated deps * updated setuptools dep type Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-21gitlab: Retry protected publish jobs in certain cases (#32496)Scott Wittenburg1-0/+3
When we lose a running pod (possibly loss of spot instance) or encounter some other infrastructure-related failure of this job, we need to retry it. This retries the job the maximum number of times in those cases.
2022-10-21Relocation should take hardlinks into account (#33460)Harmen Stoppels7-62/+190
Currently `relocate_text` and `relocate_text_bin` are unsafe in the sense that they run in parallel, and lead to races when modifying different items pointing to the same inode. This leads to the issue observed in #33453. This PR: 1. Renames those functions to `unsafe_*` so people are aware 2. Adds logic to deal with hardlinks in current binary packages 3. Adds logic to deal with hardlinks when creating new binary tarballs, so the install side doesn't have to de-dupe hardlinks. 4. Adds a test for 3 The assumption is that all our relocation logic preserves inodes. That is, we should never copy a file, modify it, and then move it back. I quickly verified, and its seems like this is true for (binary) text relocation, as well as rpath patching in patchelf (even when the file grows) and mach-o fixes.
2022-10-21axom@0.7.0: require cmake@3.21: (#33450)eugeneswalker1-2/+2
* axom@0.7.0: require cmake@3.21: * Update var/spack/repos/builtin/packages/axom/package.py Co-authored-by: Chris White <white238@llnl.gov> Co-authored-by: Chris White <white238@llnl.gov>
2022-10-21git: new versions and deprecations (#33408)Harmen Stoppels1-3/+35
2022-10-21gitlab: when_possible -> false (#33443)Harmen Stoppels2-2/+2
`reuse` and `when_possible` concretization broke the invariant that `spec[pkg_name]` has unique keys. This invariant is relied on in tons of places, such as when setting up the build environment. When using `when_possible` concretization, one may end up with two or more `perl`s or `python`s among the transitive deps of a spec, because concretization does not consider build-only deps of reusable specs. Until the code base is fixed not to rely on this broken property of `__getitem__`, we should disable reuse in CI.
2022-10-21intel-tbb: add in versions 2021.7.0, 2021.6.0 (#33445)Satish Balay1-6/+3
2021.7.0 fixes build on linux-ubuntu20.04-skylake / oneapi@2022.2.0
2022-10-21Remove "spack buildcache copy" in v0.19.0 (#33437)Massimiliano Culpo2-91/+1
2022-10-20e4s ci: add raja +rocm (#32505)eugeneswalker1-1/+1
2022-10-20replaced package shortbred with py-shortbred (#33404)Luke Diorio-Toth2-1/+30
* fixed version numbers to python 2 and old biopython * changed shortbred pacakge to pypi, removed python 2 version * added package description * re-added shortbred package with depreciated flag * fixed style and removed unnecessary python dep (it can't build with python 2 anyway) * removed whitespace and readded the python2.7.9+ dep * fixed style
2022-10-20Add Boost 1.80.0 (#32879)Mikael Simberg2-2/+10
* Add Boost 1.80.0 * Add conflict for Boost 1.80.0 and dealii * Add conflict for Boost 1.80 and %oneapi
2022-10-20hiop: add v0.7.0 (#33441)eugeneswalker1-0/+1
* hiop: add v0.7.0 * Update var/spack/repos/builtin/packages/hiop/package.py Co-authored-by: Cameron Rutherford <cameron.rutherford@me.com> Co-authored-by: Cameron Rutherford <cameron.rutherford@me.com>
2022-10-20kokkos and kokkos-kernels: add new versions (#33301)Cody Balos2-0/+5
* kokkos: add version 3.7.00 * kokkos-kernels: add versions 3.6.01 and 3.7.00 * add correct kokkos dependence
2022-10-20butterflypack: add version 2.2.2 and openmp variant (#33416)Satish Balay1-0/+6
- add conflcit with gcc < 7 - fails with MacOS sed - so add in (gnu) sed as build dependency
2022-10-20Update OpenFAST package file (#33438)Jon Rood1-17/+24
* Update OpenFAST package file. * Add comment.
2022-10-20ophidia-primitives: new package at v1.7 (#33434)SoniaScard1-0/+41
* ophidia-primitives: new package at v1.7 * ophidia-primitives: Add mantainers * ophidia-primitives: Fix style Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
2022-10-20py-rasterio: add v1.3.3 (#33428)Adam J. Stewart1-0/+1
2022-10-20spdlog: Add version 1.10.0 (#33431)Rémi Lacroix1-0/+1
2022-10-20gitlab: Do not use root_spec['pkg_name'] anymore (#33403)Scott Wittenburg5-147/+27
* gitlab: Do not use root_spec['pkg_name'] anymore For a long time it was fine to index a concrete root spec with the name of a dependency in order to access the concrete dependency spec. Since pipelines started using `--use-buildcache dependencies:only,package:never` though, it has exposed a scheduling issue in how pipelines are generated. If a concrete root spec depends on two different hashes of `openssl` for example, indexing that root with just the package name is ambiguous, so we should no longer depend on that approach when scheduling jobs. * env: make sure exactly one spec in env matches hash
2022-10-20Change scalapack to test-only dependency (#33433)G-Ragghianti1-3/+5
2022-10-20arpack-ng %cce: add -hnopattern to fflags (#33424)eugeneswalker1-0/+5
2022-10-20py-bakta: new package (#33417)Luke Diorio-Toth1-0/+36
2022-10-20FIX CI after git update (#33429)Massimiliano Culpo2-0/+8
Add `protocol.file.allow always` to git configuration in CI
2022-10-19e4s ci: add umpire +rocm (#32504)eugeneswalker1-1/+1
2022-10-19singularity-eos: new version 1.6.2 (#33415)Richard Berger1-0/+1
2022-10-19depfile: buildcache support (#33315)Harmen Stoppels4-47/+219
When installing some/all specs from a buildcache, build edges are pruned from those specs. This can result in a much smaller effective DAG. Until now, `spack env depfile` would always generate a full DAG. Ths PR adds the `spack env depfile --use-buildcache` flag that was introduced for `spack install` before. This way, not only can we drop build edges, but also we can automatically set the right buildcache related flags on the specific specs that are gonna get installed. This way we get parallel installs of binary deps without redundancy, which is useful for Gitlab CI.
2022-10-19Simplify TIOGA package (#33396)Jon Rood1-26/+5
* Update TIOGA package. * Add comment. * Remove cuda variant and MPI_ROOT. * Style.
2022-10-19py-pandas: add v1.5.1 (#33412)Adam J. Stewart1-0/+1
2022-10-19mpich: enable building when @3.4~cuda (#33325)Sergey Kosukhin1-1/+1
2022-10-19patch std::filesystem check as done in llnl/umpire pr#784 (#33250)eugeneswalker2-0/+34
2022-10-19umpire +rocm: use hipcc as CMAKE_CXX_COMPILER (#33377)eugeneswalker1-0/+3
2022-10-19raja +rocm: use hipcc as CMAKE_CXX_COMPILER (#33375)eugeneswalker1-0/+7
2022-10-19pilercr: new package (#33251)Luke Diorio-Toth1-0/+28
* new package * fixed style * actually building now
2022-10-19axom: python only reliably available when +python, +devtools (#33414)eugeneswalker1-1/+1
2022-10-19Add a command to bootstrap Spack right now (#33407)Massimiliano Culpo2-1/+17
2022-10-19Relocate "run" type dependencies too (#33191)Stephen Sachs1-2/+2
When downloading from binary cache not only replace RPATHs to dependencies, but also text references to dependencies. Example: `autoconf@2.69` contains a text reference to the executable of its dependency `perl`: ``` $ grep perl-5 /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/autoconf-2.69-q3lo/bin/autoreconf eval 'case $# in 0) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0";; *) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0" "$@";; esac' ``` These references need to be replace or any package using `autoreconf` will fail as it cannot find the installed `perl`. Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-10-19Update the binary index before attempting direct fetches (#32137)Jonathon Anderson4-19/+48
"spack install" will not update the binary index if given a concrete spec, which causes it to fall back to direct fetches when a simple index update would have helped. For S3 buckets in particular, this significantly and needlessly slows down the install process. This commit alters the logic so that the binary index is updated whenever a by-hash lookup fails. The lookup is attempted again with the updated index before falling back to direct fetches. To avoid updating too frequently (potentially once for each spec being installed), BinaryCacheIndex.update now includes a "cooldown" option, and when this option is enabled it will not update more than once in a cooldown window (set in config.yaml). Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-18spack checksum: warn if version is deprecated (#32438)Tamara Dahlgren5-2/+42
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-18intel-oneapi-compilers: do not pass -Wno-unused-command-line-argument to icc ↵Robert Cohn1-27/+21
+ refactor (#33389)
2022-10-18Docs: Spack info option updates (#33376)Tamara Dahlgren3-10/+27
2022-10-18Reusable --use-buildcache with better validation (#33388)Harmen Stoppels4-31/+76
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-18go,gcc: Support external go compilers for Go bootstrap (#27769)Bernhard Kaindl4-11/+56
For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64)
2022-10-18papi: fix for Intel OneAPI compiler (#33225)Howard Pritchard1-0/+5
Without this patch one hits this error trying to compiler papi with Intel OneAPI: icx: error: Note that use of '-g' without any optimization-level option will turn off most compiler optimizations similar to use of '-O0' [-Werror,-Wdebug-disables-optimization] Signed-off-by: Howard Pritchard <howardp@lanl.gov> Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-10-18vsearch: add v2.22.1 (#33327)snehring1-0/+4
2022-10-18mothur: add v1.48.0 and variants (#33326)snehring1-20/+63
2022-10-18build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (#33384)dependabot[bot]1-1/+1
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/95cb08cb2672c73d4ffd2f422e6d11953d2a9c70...c74574e6c82eeedc46366be1b0d287eff9085eb6) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-10-18intel-oneapi-compilers: fix Python 2.7 compliance (#33383)Massimiliano Culpo1-2/+2
2022-10-17py-fiona: add v1.8.22 (#33372)Adam J. Stewart1-1/+2