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2022-11-09updates and fixes for libpressio (#33789)Robert Underwood6-2/+77
* updates and fixes for libpressio * differentiate between standalone and build tests * add e4s tags Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-11-09New package: py-darshan (#33430)Jean Luca Bez1-0/+45
* include py-darshan * include requested changes * fix required versions * fix style * fix style * Update package.py * Update var/spack/repos/builtin/packages/py-darshan/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-09always use the cxx compiler as a host compiler (#33771)Chris White1-7/+1
2022-11-09Adding libpfm 4.12.0 (#33779)Filippo Spiga1-1/+2
2022-11-09sentieon-genomics: adding version 202112.06 (#33786)snehring1-0/+1
2022-11-09Update package.py (#33787)James Willenbring1-1/+1
Proposing to add myself as a maintainer of the Trilinos Spack package after a related conversation with @kuberry.
2022-11-09Boost: Change comment to conflict for MPI/Python (#33767)kwryankrattiger1-4/+7
Boost 1.64.0 has build errors when building the python and MPI modules. This was previously just a comment in the package.py which allowed broken specs to concretize. The comments are now expressed in conflicts to prevent this.
2022-11-09postgresql: fix weird spack message (#33770)snehring1-1/+1
2022-11-09Revert "fix racy sbang (#33549)" (#33778)Harmen Stoppels3-65/+43
This reverts commit 4d28a6466188ea9fe3b55a4c3d7690dd66e0dc8f.
2022-11-09ensure external PythonPackages have python deps (#33777)Greg Becker5-0/+54
Currently, external `PythonPackage`s cause install failures because the logic in `PythonPackage` assumes that it can ask for `spec["python"]`. Because we chop off externals' dependencies, an external Python extension may not have a `python` dependency. This PR resolves the issue by guaranteeing that a `python` node is present in one of two ways: 1. If there is already a `python` node in the DAG, we wire the external up to it. 2. If there is no existing `python` node, we wire up a synthetic external `python` node, and we assume that it has the same prefix as the external. The assumption in (2) isn't always valid, but it's better than leaving the user with a non-working `PythonPackage`. The logic here is specific to `python`, but other types of extensions could take advantage of it. Packages need only define `update_external_dependencies(self)`, and this method will be called on externals after concretization. This likely needs to be fleshed out in the future so that any added nodes are included in concretization, but for now we only bolt on dependencies post-concretization. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2022-11-08Account for patchelf binaries when creating local bootstrap mirror (#33776)Massimiliano Culpo1-0/+2
This was overlooked when we added binary patchelf buildcaches
2022-11-08MFEM: more updates for v4.5 (#33603)Veselin Dobrev3-48/+113
* [mfem] updates related to building with cuda * [hypre] tweak to support building with external ROCm/HIP * [mfem] more tweaks related to building with +rocm * [mfem] temporary (?) workaround for issue #33684 * [mfem] fix style * [mfem] fix +shared+miniapps install
2022-11-08Add checksum for py-protobuf 4.21.7, protobuf 21.7; remove protobuf and ↵iarspider4-175/+59
py-protobuf 2.x (#32977) * Add checksum for py-protobuf 4.21.7, protobuf 21.7 * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Delete protoc2.5.0_aarch64.patch * Update package.py * Restore but deprecate py-protobuf 3.0.0a/b; deprecate py-tensorflow 0.x * Fix audit Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-08Patch `fmt` for hipcc/dpcpp (#33733)Mikael Simberg1-0/+8
* Patch fmt for hipcc/dpcpp * Add msimberg as fmt maintainer
2022-11-08environment-modules: add version 5.2.0 (#33762)Xavier Delaruelle1-1/+2
2022-11-08hepmc3: new version 3.2.5 (#33748)Wouter Deconinck1-0/+1
Changelog at https://gitlab.cern.ch/hepmc/HepMC3/-/tags/3.2.5 Maintainer: @vvolkl
2022-11-08fix racy sbang (#33549)Harmen Stoppels3-43/+65
Spack currently creates a temporary sbang that is moved "atomically" in place, but this temporary causes races when multiple processes start installing sbang. Let's just stick to an idempotent approach. Notice that we only re-install sbang if Spack updates it (since we do file compare), and sbang was only touched 18 times in the past 6 years, whereas we hit the sbang tempfile issue frequently with parallel install on a fresh spack instance in CI. Also fixes a bug where permissions weren't updated if config changed but the latest version of the sbang file was already installed.
2022-11-08hypre +rocm: needs explicit rocprim dep (#33745)eugeneswalker1-0/+1
2022-11-08use pwd for usernames on unix (#19980)Greg Becker1-1/+13
2022-11-08python: 3.11.0 (#33507)Harmen Stoppels3-8/+293
2022-11-08Install from source if binary cache checksum validation fails (#31696)Stephen Sachs1-0/+10
* Fix https://github.com/spack/spack/issues/31640 Some packages in the binary cache fail checksum validation. Instead of having to go back and manually install all failed packages with `--no-cache` option, requeue those failed packages for installation from source ```shell $ spack install py-pip ==> Installing py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7 ==> Fetching https://binaries.spack.io/releases/v0.18/build_cache/linux-amzn2-graviton2-gcc-7.3.1-py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7.spec.json.sig gpg: Signature made Wed 20 Jul 2022 12:13:43 PM UTC using RSA key ID 3DB0C723 gpg: Good signature from "Spack Project Official Binaries <maintainers@spack.io>" ==> Fetching https://binaries.spack.io/releases/v0.18/build_cache/linux-amzn2-graviton2/gcc-7.3.1/py-pip-21.3.1/linux-amzn2-graviton2-gcc-7.3.1-py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7.spack ==> Extracting py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7 from binary cache ==> Error: Failed to install py-pip due to NoChecksumException: Requeue for manual installation. ==> Installing py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7 ==> Using cached archive: /shared/spack/var/spack/cache/_source-cache/archive/de/deaf32dcd9ab821e359cd8330786bcd077604b5c5730c0b096eda46f95c24a2d ==> No patches needed for py-pip ==> py-pip: Executing phase: 'install' ==> py-pip: Successfully installed py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7 Fetch: 0.01s. Build: 2.81s. Total: 2.82s. [+] /shared/spack/opt/spack/linux-amzn2-graviton2/gcc-7.3.1/py-pip-21.3.1-s2cx4gqrqkdqhashlinqyzkrvuwkl3x7 ``` * Cleanup style * better wording Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Update lib/spack/spack/installer.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * changes quotes for style checks * Update lib/spack/spack/installer.py Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com> * Addressing @kwryankrattiger comment to use local 'use_cache` Co-authored-by: Stephen Sachs <stesachs@amazon.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
2022-11-08cosma: Add shared option (#33751)Dave Love1-4/+6
2022-11-08gromacs: enable linking with armpl-gcc FFT (#33750)Annop Wongwathanarat1-0/+7
2022-11-08scons: fix Scons builder after multi build-system refactoring (#33753)Massimiliano Culpo1-6/+10
2022-11-08r: fix order of execution for Makeconf filtering (#33752)Massimiliano Culpo1-2/+3
fixes #33747
2022-11-08More jobs in Gitlab CI (#33688)Harmen Stoppels16-0/+31
Use at most 32 jobs when available.
2022-11-08Rework unit test to avoid tripping into concretization slowdown (#33749)Massimiliano Culpo1-23/+9
2022-11-07intel oneapi classic bootstrapping (#31285)Greg Becker8-30/+119
The `intel` compiler at versions > 20 is provided by the `intel-oneapi-compilers-classic` package (a thin wrapper around the `intel-oneapi-compilers` package), and the `oneapi` compiler is provided by the `intel-oneapi-compilers` package. Prior to this work, neither of these compilers could be bootstrapped by Spack as part of an install with `install_missing_compilers: True`. Changes made to make these two packages bootstrappable: 1. The `intel-oneapi-compilers-classic` package includes a bin directory and symlinks to the compiler executables, not just logical pointers in Spack. 2. Spack can look for bootstrapped compilers in directories other than `$prefix/bin`, defined on a per-package basis 3. `intel-oneapi-compilers` specifies a non-default search directory for the compiler executables. 4. The `spack.compilers` module now can make more advanced associations between packages and compilers, not just simple name translations 5. Spack support for lmod hierarchies accounts for differences between package names and the associated compiler names for `intel-oneapi-compilers/oneapi`, `intel-oneapi-compilers-classic/intel@20:`, `llvm+clang/clang`, and `llvm-amdgpu/rocmcc`. - [x] full end-to-end testing - [x] add unit tests
2022-11-07mpich: patch @3.4 to fix checking whether the datatype is contiguous (#33328)Sergey Kosukhin2-1/+144
Co-authored-by: Thomas Jahns <jahns@dkrz.de> Co-authored-by: Thomas Jahns <jahns@dkrz.de>
2022-11-07PyTorch: add v1.13.0 (#33596)Adam J. Stewart7-65/+186
* PyTorch: add v1.13.0 * py-torchaudio: add v0.13.0 * py-torchaudio: add all versions * py-torchvision: jpeg required for all backends * py-torchtext: add v0.14.0 * py-torchtext: fix build * py-torchaudio: fix build * py-torchtext: update version tag * Use Spack-built sox * Explicitly disable sox build * https -> http
2022-11-07Add zstd support for elfutils (#33695)Cédric Chevalier1-0/+4
* Add zstd support for elfutils Not defining `+zstd` implies `--without-zstd` flag to configure. This avoids automatic library detection and thus make the build only depends on Spack installed dependencies. * Use autotools helper "with_or_without" * Revert use of with_or_without Using `with_or_without()` with `variant` keyword does not seem to work.
2022-11-08"spack uninstall": don't modify env (#33711)Peter Scheibel10-109/+395
"spack install foo" no longer adds package "foo" to the environment (i.e. to the list of root specs) by default: you must specify "--add". Likewise "spack uninstall foo" no longer removes package "foo" from the environment: you must specify --remove. Generally this means that install/uninstall commands will no longer modify the users list of root specs (which many users found problematic: they had to deactivate an environment if they wanted to uninstall a spec without changing their spack.yaml description). In more detail: if you have environments e1 and e2, and specs [P, Q, R] such that P depends on R, Q depends on R, [P, R] are in e1, and [Q, R] are in e2: * `spack uninstall --dependents --remove r` in e1: removes R from e1 (but does not uninstall it) and uninstalls (and removes) P * `spack uninstall -f --dependents r` in e1: will uninstall P, Q, and R (i.e. e2 will have dependent specs uninstalled as a side effect) * `spack uninstall -f --dependents --remove r` in e1: this uninstalls P, Q, and R, and removes [P, R] from e1 * `spack uninstall -f --remove r` in e1: uninstalls R (so it is "missing" in both environments) and removes R from e1 (note that e1 would still install R as a dependency of P, but it would no longer be listed as a root spec) * `spack uninstall --dependents r` in e1: will fail because e2 needs R Individual unit tests were created for each of these scenarios.
2022-11-08Fix missing "*.spack*" files in views (#30980)Jordan Galby3-1/+79
All files/dirs containing ".spack" anywhere their name were ignored when generating a spack view. For example, this happened with the 'r' package.
2022-11-072022.3.1 oneAPI release promotion (#33742)akhursev15-0/+95
2022-11-07reorder packages.yaml: requirements first, then preferences (#33741)Harmen Stoppels1-80/+83
* reorder packages.yaml: requirements first, then preferences * expand preferences vs reuse vs requirements
2022-11-07gitlab ci: Add "script_failure" as a reason for retrying service jobs (#33420)Scott Wittenburg1-1/+8
Somehow a network error when cloning the repo for ci gets categorized by gitlab as a script failure. To make sure we retry jobs that failed for that reason or a similar one, include "script_failure" as one of the reasons for retrying service jobs (which include "no specs to rebuild" jobs, update buildcache index jobs, and temp storage cleanup jobs.
2022-11-07encode development requirements in pyproject.toml (#32616)Tom Scogland5-50/+145
Add a `project` block to the toml config along with development and CI dependencies and a minimal `build-system` block, doing basically nothing, so that spack can be bootstrapped to a full development environment with: ```shell $ hatch -e dev shell ``` or for a minimal environment without hatch: ```shell $ python3 -m venv venv $ source venv/bin/activate $ python3 -m pip install --upgrade pip $ python3 -m pip install -e '.[dev]' ``` This means we can re-use the requirements list throughout the workflow yaml files and otherwise maintain this list in *one place* rather than several disparate ones. We may be stuck with a couple more temporarily to continue supporting python2.7, but aside from that it's less places to get out of sync and a couple new bootstrap options. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-07build(deps): bump docker/setup-buildx-action from 2.2.0 to 2.2.1 (#33399)dependabot[bot]1-1/+1
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.2.0 to 2.2.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/c74574e6c82eeedc46366be1b0d287eff9085eb6...8c0edbc76e98fa90f69d9a2c020dcb50019dc325) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-patch ... 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>
2022-11-07build(deps): bump actions/upload-artifact from 3.1.0 to 3.1.1 (#33471)dependabot[bot]2-3/+3
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3.1.0 to 3.1.1. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/3cea5372237819ed00197afe530f5a7ea3e805c8...83fd05a356d7e2593de66fc9913b3002723633cb) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... 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>
2022-11-07binary_distribution: Speed up buildcache update-index (#32796)Scott Wittenburg1-36/+168
This change uses the aws cli, if available, to retrieve spec files from the mirror to a local temp directory, then parallelizes the reading of those files from disk using multiprocessing.ThreadPool. If the aws cli is not available, then a ThreadPool is used to fetch and read the spec files from the mirror. Using aws cli results in ~16 times speed up to recreate the binary mirror index, while just parallelizing the fetching and reading results in ~3 speed up.
2022-11-07eckit: fix underlinking (#33739)Sergey Kosukhin1-0/+8
2022-11-07Remove known issues (#33738)Harmen Stoppels2-41/+0
2022-11-07Bump docker/build-push-action from 3.1.1 to 3.2.0 (#33271)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3.1.1 to 3.2.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/c84f38281176d4c9cdb1626ffafcd6b3911b5d94...c56af957549030174b10d6867f20e78cfd7debc5) --- updated-dependencies: - dependency-name: docker/build-push-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>
2022-11-07Bump dorny/paths-filter from 2.10.2 to 2.11.1 (#33270)dependabot[bot]1-1/+1
Bumps [dorny/paths-filter](https://github.com/dorny/paths-filter) from 2.10.2 to 2.11.1. - [Release notes](https://github.com/dorny/paths-filter/releases) - [Changelog](https://github.com/dorny/paths-filter/blob/master/CHANGELOG.md) - [Commits](https://github.com/dorny/paths-filter/compare/b2feaf19c27470162a626bd6fa8438ae5b263721...4512585405083f25c027a35db413c2b3b9006d50) --- updated-dependencies: - dependency-name: dorny/paths-filter 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>
2022-11-07Bump docker/setup-qemu-action from 2.0.0 to 2.1.0 (#33269)dependabot[bot]1-1/+1
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2.0.0 to 2.1.0. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/8b122486cedac8393e77aa9734c3528886e4a1a8...e81a89b1732b9c48d79cd809d8d81d79c4647a18) --- updated-dependencies: - dependency-name: docker/setup-qemu-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>
2022-11-07Bugfix: Compiler bootstrapping for compilers that are independently present ↵Greg Becker2-1/+47
in env (#32228) The compiler bootstrapping logic currently does not add a task when the compiler package is already in the install task queue. This causes failures when the compiler package is added without the additional metadata telling the task to update the compilers list. Solution: requeue compilers for bootstrapping when needed, to update `task.compiler` metadata.
2022-11-07Apply dev specs for dependencies of roots (#30909)Greg Becker2-17/+45
Currently, develop specs that are not roots and are not explicitly listed dependencies of the roots are not applied. - [x] ensure dev specs are applied. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2022-11-07Rust: don't apply constraints to nightly/beta versions (#33723)Adam J. Stewart2-4/+6
2022-11-07quantum-espresso: improve concretization for intel libraries (#33312)Laura Bellentani1-0/+1
2022-11-07singularity: add new versions (#33462)Yang Zongze2-0/+7
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