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2023-01-19buildcache create: make "file exists" less verbose (#35019)Harmen Stoppels1-3/+3
Currently we print 3 lines of "file exist" warning per tarball, this is a bit excessive. Instead, it can be a simple single-line tty.warn message.
2023-01-19python: remove `CPATH` from `setup_run_environment` (#34727)Todd Gamblin1-3/+0
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`. We no longer set `CPATH` and other destructive environment variables (like `LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python. Also, the way `python` sets `CPATH` causes issues. Because it does a header search to find directories containing headers, if you bootstrap `mypy` or other style tools on a fresh Ubuntu image with *no* python devel headers installed, you'll get an error like this when trying to load the thing you just installed: ```console [root@980de539843d /]# spack -b load py-mypy ==> Error: Unable to locate python headers in any of these locations: /usr/include/python3.6m /usr/include/3.6 /usr/Headers ``` The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work, so we're failing unnecessarily here. - [x] remove `setup_run_environment()` from `python/package.py`
2023-01-19[py-numpy, py-scipy] Enable MKL & ARMpl (#34979)Stephen Sachs3-10/+15
2023-01-19depfile: --make-target-prefix -> --make-prefix (#35009)Harmen Stoppels4-22/+22
Since SPACK_PACKAGE_IDS is now also "namespaced" with <prefix>, it makes more sense to call the flag `--make-prefix` and alias the old flag `--make-target-prefix` to it.
2023-01-19git: bump. CVE-2022-41903 / CVE-2022-23521 (#35014)Harmen Stoppels1-8/+64
Co-Authored-By: Alec Scott <scott112@llnl.gov> Co-authored-by: Alec Scott <scott112@llnl.gov>
2023-01-18hpctoolkit: update cray support (#34995)Mark W. Krentel1-17/+33
1. add variant cray-static, older crays build hpcprof-mpi static, newer ones build dynamic. 2. move URL patches from github to gitlab. 3. add workaround for a bug where a file is mistakenly overwritten. 4. add conflict for hpcprof-mpi at 2022.10.01. * [@spackbot] updating style on behalf of mwkrentel Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2023-01-18e4s ci: clean up unnecessary constraints (#35006)eugeneswalker1-17/+11
2023-01-18e4s: add sz3 (#35007)eugeneswalker1-0/+1
2023-01-18e4s ci: add veloc (#35003)eugeneswalker1-0/+1
2023-01-18VTK: fix 9.1–9.2 builds (#34589)Adam J. Stewart1-7/+12
* VTK: add missing dependencies * Deal with missing verdict dep * http -> https * Add patch to fix failing cmake * Update netcdf-cxx usage in build recipe * netcdf-cxx4 doesn't work
2023-01-18Bugfix: External Python Extensions (#34202)Greg Becker4-20/+207
Normally when using external packages in concretization, Spack ignores all dependencies of the external. #33777 updated this logic to attach a Python Spec to external Python extensions (most py-* packages), but as implemented there were a couple issues: * this did not account for concretization groups and could generate multiple different python specs for a single DAG * in some cases this created a fake Python spec with insufficient details to be usable (concretization/installation of the extension would fail) This PR addresses both of these issues: * For environment specs that are concretized together, external python extensions in those specs will all be assigned the same Python spec * If Spack needs to "invent" a Python spec, then it will have all the needed details (e.g. compiler/architecture)
2023-01-18license year bump (#34921)Harmen Stoppels7749-7777/+7780
* license bump year * fix black issues of modified files * mypy * fix 2021 -> 2023
2023-01-18hdf5@1.8.21 %oneapi@2023.0.0: -Wno-error=int-conversion (#34983)eugeneswalker1-0/+2
2023-01-18npm: Add latest version, update build (#34947)Todd Gamblin1-17/+75
* npm: Add latest version, update build The `npm` package had gotten a bit long in the tooth and only suported the last version for which running `configure` / `make` / `make install` actually worked. - [x] Update the package to support npm@9, in which `npm install .` works properly and installation is easier. - [x] Update the package so that `npm@6:8` also install successfullly. The incantation that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install` or `npm pack` will fail when run straight from the install directory. So now we just manually copies things over. This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least for me). udpates the `npm` build to support versions 6-9 and fixes the install for all of them on macos. * update for review
2023-01-18e4s: add py-h5py ~mpi variant (#34998)eugeneswalker1-1/+2
2023-01-18lammps: enable linking with armpl-gcc FFT (#34980)Annop Wongwathanarat1-0/+6
2023-01-18depfile: variable with all identifiers (#34678)Harmen Stoppels4-1/+115
With the new variable [prefix/]SPACK_PACKAGE_IDS you can conveniently execute things after each successful install. For example push just-built packages to a buildcache ``` SPACK ?= spack export SPACK_COLOR = always MAKEFLAGS += -Orecurse MY_BUILDCACHE := $(CURDIR)/cache .PHONY: all clean all: push ifeq (,$(filter clean,$(MAKECMDGOALS))) include env.mk endif # the relevant part: push has *all* example/push/<pkg identifier> as prereqs push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS)) $(SPACK) -e . buildcache update-index --directory $(MY_BUILDCACHE) $(info Pushed everything, yay!) # and each example/push/<pkg identifier> has the install target as prereq, # and the body can use target local $(HASH) and $(SPEC) variables to do # things, such as pushing to a build cache example/push/%: example/install/% @mkdir -p $(dir $@) $(SPACK) -e . buildcache create --allow-root --only=package --unsigned --directory $(MY_BUILDCACHE) /$(HASH) # push $(SPEC) @touch $@ spack.lock: spack.yaml $(SPACK) -e . concretize -f env.mk: spack.lock $(SPACK) -e . env depfile -o $@ --make-target-prefix example clean: rm -rf spack.lock env.mk example/ ``
2023-01-18[armpl-gcc] Make pkg-config files available (#34978)Stephen Sachs1-1/+12
* [armpl-gcc] Make pkg-config files available ARMpl pkgconfig files are located in a non-default location and do not have the .pc extension. Changing those both helps pkgconfig pick them up correctly, e.g. in the meson build of `py-scipy`. * Address @annop-w comments * symlink instead of cp. Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-18acfl: update hash for 22.1 on RHEL-7 (#34997)Annop Wongwathanarat1-1/+1
2023-01-18Remove verbose warning message from _try_install_from_binary_cache (#34994)Harmen Stoppels2-38/+18
In the past we checked remote binary mirrors for existence of a spec before attempting to download it. That changed to only checking local copies of index.jsons (if available) to prioritize certain mirrors where we expect to find a tarball. That was faster for CI since fetching index.json and loading it just to order mirrors takes more time than just attempting to fetch tarballs -- and also if we have a direct hit there's no point to look at other mirrors. Long story short: the info message only makes sense in the old version of Spack, so it's better to remove it.
2023-01-18Bug fix for duplicate rpath errors on macOS when creating build caches (#34375)Dom Heinzeller1-3/+11
2023-01-18py-pytorch-lightning: add v1.9.0 (#34996)Adam J. Stewart2-3/+11
2023-01-18Add tiny profile cmake support (#34993)Nate deVelder1-0/+2
2023-01-18spack mirror create takes local paths only (#34992)Harmen Stoppels2-43/+14
spack mirror create cannot work with urls, so it shouldn't promote local paths to file urls.
2023-01-17Subclass PythonExtension instead of custom test method (#34985)Adam J. Stewart3-82/+3
2023-01-17py-itk: add version 5.3.0 (#34968)Glenn Johnson1-3/+71
* py-itk: add version 5.3.0 * Remove wheels for unsupported python versions * Fill out the version specs * Drop th 'm' from the cp37 version strings
2023-01-17py-h5py %oneapi@2023.0.0: ↵eugeneswalker1-0/+7
-Wno-error=incompatible-function-pointer-types,pointer-types-discards-qualifiers (#34984)
2023-01-17py-sphinx-immaterial: new package (#34948)Todd Gamblin1-0/+29
* py-sphinx-immaterial: new package This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear and readable. We *might* consider switching to it for Spack's docs. * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * add note about node.js requirements Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-17rempi: patch rempi_message_manager.h: include string (#34982)eugeneswalker2-3/+15
2023-01-17CDashReporter: remove unused argument (#34869)Massimiliano Culpo4-82/+7
* CDashReporter: remove unused argument * Removed extract_ctest_test_data
2023-01-17Forward lookup of "test_log_file" and "test_failures" (#34882)Massimiliano Culpo5-24/+73
* Forward lookup of "test_log_file" and "test_failures" refers #34531 closes #34487 fixes #34440 * Add unit test * py-libensemble: fix tests * Support stand-alone tests with cached files as install-time tests Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-01-17cp2k: enable linking with armpl-gcc for BLAS and FFT (#34981)Annop Wongwathanarat1-0/+4
2023-01-17python: 3.11.1, use -flto=thin when clang (#34951)Harmen Stoppels1-1/+6
2023-01-17Bump gnupg & libksba, (CVE) (#34976)Harmen Stoppels2-6/+34
* gnupg: 2.4.0 * libksba: 1.6.3 (CVE-2022-47629)
2023-01-17Reduce verbosity in mirrors.yaml (#34210)roottreej4-24/+42
Ensure `spack mirror add <name> <url/path>` without further arguments translates to `<name>: <url>` key value pairs in mirrors.yaml. If --s3-* flags are provided, only store the provided ones. Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-01-17faiss: fixed error when importing faiss python package (#34672)Loïc Pottier1-1/+7
This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs. Signed-off-by: Loïc Pottier <pottier1@llnl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-01-17bubblewrap: 0.7.0 (#34975)Harmen Stoppels1-0/+1
2023-01-17perl-file-temp: add 0.2311 (#34866)Christopher Christofi1-0/+15
2023-01-17libcroco: Get the `doc` variant working (#34735)Glenn Johnson1-7/+29
2023-01-17mvapich: add new package in preparation for v3.0 (#34276)MatthewLieber1-0/+293
* Add new file for MVAPICH 3.0a release Creating this as a new package since it requires some new configuration options and because we are moving to the name "MVAPICH" and droping the 2 (following a similar move by MPICH). Co-authored-by: Nat Shineman <shineman.5@osu.edu> Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-01-17flexiblas: add versions up to v3.3.0 (#34874)Ashwin Kumar1-0/+4
2023-01-17New version for openCARP packages, v12.0 (#34710)Marie Houillon3-2/+12
Co-authored-by: openCARP consortium <info@opencarp.org>
2023-01-17Doc: config.yaml mention $env (#34905)Axel Huebl1-0/+5
Add one more note on the $env variable in `config.yaml`.
2023-01-17build(deps): bump actions/checkout from 3.2.0 to 3.3.0 (#34829)dependabot[bot]7-25/+25
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.2.0 to 3.3.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/755da8c3cf115ac066823e79a1e1788f8940201b...ac593985615ec2ede58e132d2e21d2b1cbd6127c) --- updated-dependencies: - dependency-name: actions/checkout 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>
2023-01-17mfem: support pumi w/zoltan and parmetis (#34864)Cameron Smith1-1/+14
2023-01-17crtm: overhaul package, add crtm-fix (#34715)Dom Heinzeller2-2/+125
Update crtm from JCSDA-EMC spack fork, add crtm-fix
2023-01-17build(deps): bump docker/build-push-action from 3.2.0 to 3.3.0 (#34972)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3.2.0 to 3.3.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/c56af957549030174b10d6867f20e78cfd7debc5...37abcedcc1da61a57767b7588cb9d03eb57e28b3) --- 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>
2023-01-17ncview: bypass compiler check against netcdf-c compiler (#34580)Dom Heinzeller1-9/+10
2023-01-17OpenCV: checksum for 4.5.5, make contrib optional (#34313)iarspider1-5/+11
* OpenCV: checksum for 4.5.5, make contrib optional * [@spackbot] updating style on behalf of iarspider * Add conflicts for contrib modules * Fix typo * Implement changes from review * Update var/spack/repos/builtin/packages/opencv/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: iarspider <iarspider@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-17gcc: add patch for noexcept declarations (#34964)Glenn Johnson1-0/+7
There are some declarations that need to be declared noexcept for valarray. This affects gcc 9.5:11.2.
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