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2022-05-09Windows permissions: uninstalling and cleaning stages (#29714)John W. Parent3-20/+74
When running on Windows, Spack may generate files in the stage/install prefixes that do not have write permissions, which prevents the removal of those directories (e.g. when cleaning stages or uninstalling). There should be a refactoring to avoid this in the first place, but that is assumed to be longer term, so the temporary fix is to make such files writable if they are not. This PR: * Automatically handles these permissions errors when uninstalling packages from the Spack root (makes then writable) * Updates similar already-existing logic when removing Spack-managed stage directories (the error-handling was assuming all errors were permissions errors and was therefore handling other errors inappropriately) Note: these permissions issues only appear on Windows so this logic is only applied there (permissions are not modified for this purpose on Linux etc.). This also adds special handling for a case where calling `isdir` on an `os.DirEntry` object would fail for improperly-created symlinks (e.g. on Windows, using `os.symlink` without `target_is_directory=True`). Note this specific issue only came up when enabling link_tree tests (specifically `source_merge_visitor_cant_be_cyclical`).
2022-05-09hipsycl: add v0.9.2 (#30566)Will Saunders1-0/+4
2022-05-09Updated ACfL package to 22.0.1, removing 21 package, as no licence required ↵Oliver Perks1-17/+12
is now false. (#30562)
2022-05-09mpitrampoline: Correct build environment (#30549)Erik Schnetter1-10/+10
2022-05-09simulationio: add v9.0.2 (#30550)Erik Schnetter1-0/+1
2022-05-09py-radiant-mlhub: add new versions (#30555)Adam J. Stewart2-5/+23
2022-05-09py-cartopy: add new versions (#30554)Adam J. Stewart2-34/+87
2022-05-09py-geocube: add v0.3.1 (#30558)Adam J. Stewart2-2/+30
2022-05-09tcl: add v8.6.12 (#30560)Massimiliano Culpo1-0/+1
2022-05-09CI: fix bootstrapping on Fedora (#30559)Massimiliano Culpo1-0/+6
Fedora updated git, so we need to apply, again, the workaround for CVE-2022-24765
2022-05-09mpitrampoline: New version 4.0.2 (#30548)Erik Schnetter1-0/+1
2022-05-08openssl: Update to 1.1.1o (#30551)Erik Schnetter1-1/+2
2022-05-08Cray manifest file: accept "nvidia" as "nvhpc" (#30428)Peter Scheibel2-13/+132
* create function for translating compiler names on specs/compiler entries in manifest * add tests for translating compiler names on spec/compiler entries * use higher-level function in test and add comment to prefer testing via higher-level function * opensuse clingo check should not fail on account of this pr, but I cannot get it to pass by restarting via CI UI
2022-05-09curl: New version 7.83.0 (#30552)Erik Schnetter1-0/+1
2022-05-07Add latest Lmod 8.6, 8.7 (#30542)Derek Ryan Strong1-0/+2
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-05-07gcc: version 12.1.0 (#30537)Harmen Stoppels1-0/+2
2022-05-07Add mochi-margo 0.9.9 (#30539)Phil Carns1-0/+1
- necessary for compatibility with upcoming Mercury 2.2.0 release
2022-05-07Addition of 1.1.9dev version for py-maestrowf (#30523)Francesco Di Natale1-13/+18
* Addition of 1.1.9dev version. * Small style fix -- extra blank line. * Update var/spack/repos/builtin/packages/py-maestrowf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-maestrowf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-maestrowf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-maestrowf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Additional dependencies and version constraints. * Revert to py-poetry. * Remove run from cryptography (build only). Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-05-07Put make() inside a self.run_test call (#30536)Erik1-2/+2
2022-05-07vim: add +gtk variant to pair with +gui (#30520)Ryan Marcellino1-1/+7
* vim: add +gtk3 variant to pair with +gui * address review comments
2022-05-07Force GCC to always provide a C++14 flag (#29781)Robert Pavel2-4/+2
* Force GCC to always provide a C++14 flag Updated gnu logic so that the c++14 flag for g++ is always propagated. This fixes issues with build systems that error out if passed an empty string for a flag. Engaging in the best kind of software engineering by updating the unit test to pass with the value it is now passed. This should better match the expected flag for g++ compiling with the C++14 standard
2022-05-07nmap: fix build issue (#30429)WYF1-0/+3
2022-05-06Eigen: turn on BUILD_TESTING for build to complete (#30528)JDBetteridge1-0/+8
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-05-06Add sphinx-tabs package (#27698)Sebastian Schmitt2-0/+25
* Add py-docutils@0.16 * Add sphinx-tabs package * Update var/spack/repos/builtin/packages/py-sphinx-tabs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-tabs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-tabs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-05-06openspeedshop: fix missing import statement (#30506)Jim Galarowicz2-0/+4
2022-05-06Fix improper type for InvalidDependencyError argument (#30504)Greg Becker2-3/+5
2022-05-06arborx: inherit from CudaPackage, ROCmPackage (#30490)eugeneswalker1-3/+10
2022-05-06boost: add support for alternate boost-context backends (#30496)Thomas Dickerson1-0/+20
The fcontext backend is the default high-performance backend. The ucontext backend is needed when using Boost context in conjunction with ASAN. The WinFibers backend...also exists. https://www.boost.org/doc/libs/1_79_0/libs/context/doc/html/context/cc/implementations__fcontext_t__ucontext_t_and_winfiber.html
2022-05-06level-zero: add new package (#30253)Ken Raffenetti3-2/+43
Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: Robert Cohn <robert.s.cohn@intel.com> Co-authored-by: John Mellor-Crummey <johnmc@rice.edu>
2022-05-06gdb: fix run issue with v9.2 (#30491)WYF1-0/+3
2022-05-06ci: Enable the ParaView GUI in the DAVSDK pipeline (#30473)Chuck Atkins3-5/+30
* ci: Enable the ParaView GUI in the DAVSDK pipeline * qt: Patch for long paths in ci
2022-05-06py-qrcode: new package (#30529)Seth R. Johnson1-0/+24
2022-05-06slurm: add new versions to address CVEs 2022-29500, 2022-29501 and ↵Todd Gamblin1-7/+12
2022-29502 (#30525) Due to CVE 2022-29500, CVE 2022-29501, and CVE 2022-29502, SLURM versions prior to 21.08.8 and 20.11.9 are deprecated. See: * https://www.schedmd.com/news.php?id=260#OPT_260 * https://cve.report/CVE-2022-29500 * https://cve.report/CVE-2022-29501 * https://cve.report/CVE-2022-29502 - [x] Deprecate versions prior to 21.08.8 and 20.11.9 - [x] Add 21-08-8-1, 21-08-8-2, and 20-11-9-1
2022-05-06docs: jobserver & generated makefiles (#30526)Harmen Stoppels1-6/+8
2022-05-06Added a version for a tag that sets a stable version of master to pull (#30511)Brian Van Essen1-0/+1
2022-05-06build(deps): bump docker/build-push-action from 2.10.0 to 3 (#30515)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2.10.0 to 3. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/ac9327eae2b366085ac7f6a2d02df8aa8ead720a...e551b19e49efd4e98792db7592c17c09b89db8d8) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-05-06build(deps): bump docker/setup-qemu-action from 1.2.0 to 2 (#30518)dependabot[bot]1-1/+1
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 1.2.0 to 2. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/27d0a4f181a40b142cce983c5393082c365d1480...8b122486cedac8393e77aa9734c3528886e4a1a8) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-05-06build(deps): bump docker/setup-buildx-action from 1.7.0 to 2 (#30517)dependabot[bot]1-1/+1
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 1.7.0 to 2. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/f211e3e9ded2d9377c8cadc4489a4e38014bc4c9...dc7b9719a96d48369863986a06765841d7ea23f6) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-05-06build(deps): bump docker/login-action from 1.14.1 to 2 (#30516)dependabot[bot]1-2/+2
Bumps [docker/login-action](https://github.com/docker/login-action) from 1.14.1 to 2. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/dd4fa0671be5250ee6f50aedf4cb05514abda2c7...49ed152c8eca782a232dede0303416e8f356c37b) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-05-06Preserve jobserver file descriptors into build environment (#30302)Tom Scogland3-14/+33
This ensures that multiple spack instances called from `make` will respect the maximum number of jobs in the POSIX jobserver across packages. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-05-05Add two critical fixes and update for version 1.0.4 (#30507)Jim Galarowicz1-5/+11
2022-05-06flux-sched: add patch for signedness compare issue on gcc@9.40 (#30514)Mark Grondona2-0/+14
Problem: GCC 9.4.0 catches a bad integer comparison in resource/hlapi/bindings/c++/reapi_cli_impl.hpp in flux-sched@0.22.0 and current master. Add a patch to work around the problem until an upstream fix is available.
2022-05-05mpich: Add ROCm variant (#30502)Ken Raffenetti1-1/+10
* mpich: Add ROCm variant * fixup
2022-05-05updated stat build dep requirements (#30505)Gregory Lee1-2/+2
2022-05-05neko: Add version 0.3.2 (#30497)Niclas Jansson1-1/+3
* neko: Add version 0.3.2 * Switch to sha256 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Fix url pattern Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-05-05harden unit tests, enable basic parallelism (#29593)Tom Scogland7-23/+39
* use the init.defaultBranch name, not master * make tcl and modules/common independent Both used to use not just the same directory, but the same *file* for their outputs. In parallel this can cause problems, but it can also accidentally allow expected failures to pass if the file is left around by mistake. * use a non-global misc_cache in tests * make pkg tests resilient to gitignore * make source cache and module directories non-global
2022-05-05Makefile generator for parallel spack install of environments (#30254)Harmen Stoppels5-5/+322
`make` solves a lot of headaches that would otherwise have to be implemented in Spack: 1. Parallelism over packages through multiple `spack install` processes 2. Orderly output of parallel package installs thanks to `make --sync-output=recurse` or `make -Orecurse` (works well in GNU Make 4.3; macOS is unfortunately on a 16 years old 3.x version, but it's one `spack install gmake` away...) 3. Shared jobserver across packages, which means a single `-j` to rule them all, instead of manually finding a balance between `#spack install processes` & `#jobs per package` (See #30302). This pr adds the `spack env depfile` command that generates a Makefile with dag hashes as targets, and dag hashes of dependencies as prerequisites, and a command along the lines of `spack install --only=packages /hash` to just install a single package. It exposes two convenient phony targets: `all`, `fetch-all`. The former installs the environment, the latter just fetches all sources. So one can either use `make all -j16` directly or run `make fetch-all -j16` on a login node and `make all -j16` on a compute node. Example: ```yaml spack: specs: [perl] view: false ``` running ``` $ spack -e . env depfile --make-target-prefix env | tee Makefile ``` generates ```Makefile SPACK ?= spack .PHONY: env/all env/fetch-all env/clean env/all: env/env env/fetch-all: env/fetch env/env: env/.install/cdqldivylyxocqymwnfzmzc5sx2zwvww @touch $@ env/fetch: env/.fetch/cdqldivylyxocqymwnfzmzc5sx2zwvww env/.fetch/gv5kin2xnn33uxyfte6k4a3bynhmtxze env/.fetch/cuymc7e5gupwyu7vza5d4vrbuslk277p env/.fetch/7vangk4jvsdgw6u6oe6ob63pyjl5cbgk env/.fetch/hyb7ehxxyqqp2hiw56bzm5ampkw6cxws env/.fetch/yfz2agazed7ohevqvnrmm7jfkmsgwjao env/.fetch/73t7ndb5w72hrat5hsax4caox2sgumzu env/.fetch/trvdyncxzfozxofpm3cwgq4vecpxixzs env/.fetch/sbzszb7v557ohyd6c2ekirx2t3ctxfxp env/.fetch/c4go4gxlcznh5p5nklpjm644epuh3pzc @touch $@ env/dirs: @mkdir -p env/.fetch env/.install env/.fetch/%: | env/dirs $(info Fetching $(SPEC)) $(SPACK) -e '/tmp/tmp.7PHPSIRACv' fetch $(SPACK_FETCH_FLAGS) /$(notdir $@) && touch $@ env/.install/%: env/.fetch/% $(info Installing $(SPEC)) +$(SPACK) -e '/tmp/tmp.7PHPSIRACv' install $(SPACK_INSTALL_FLAGS) --only-concrete --only=package --no-add /$(notdir $@) && touch $@ # Set the human-readable spec for each target env/%/cdqldivylyxocqymwnfzmzc5sx2zwvww: SPEC = perl@5.34.1%gcc@10.3.0+cpanm+shared+threads arch=linux-ubuntu20.04-zen2 env/%/gv5kin2xnn33uxyfte6k4a3bynhmtxze: SPEC = berkeley-db@18.1.40%gcc@10.3.0+cxx~docs+stl patches=b231fcc arch=linux-ubuntu20.04-zen2 env/%/cuymc7e5gupwyu7vza5d4vrbuslk277p: SPEC = bzip2@1.0.8%gcc@10.3.0~debug~pic+shared arch=linux-ubuntu20.04-zen2 env/%/7vangk4jvsdgw6u6oe6ob63pyjl5cbgk: SPEC = diffutils@3.8%gcc@10.3.0 arch=linux-ubuntu20.04-zen2 env/%/hyb7ehxxyqqp2hiw56bzm5ampkw6cxws: SPEC = libiconv@1.16%gcc@10.3.0 libs=shared,static arch=linux-ubuntu20.04-zen2 env/%/yfz2agazed7ohevqvnrmm7jfkmsgwjao: SPEC = gdbm@1.19%gcc@10.3.0 arch=linux-ubuntu20.04-zen2 env/%/73t7ndb5w72hrat5hsax4caox2sgumzu: SPEC = readline@8.1%gcc@10.3.0 arch=linux-ubuntu20.04-zen2 env/%/trvdyncxzfozxofpm3cwgq4vecpxixzs: SPEC = ncurses@6.2%gcc@10.3.0~symlinks+termlib abi=none arch=linux-ubuntu20.04-zen2 env/%/sbzszb7v557ohyd6c2ekirx2t3ctxfxp: SPEC = pkgconf@1.8.0%gcc@10.3.0 arch=linux-ubuntu20.04-zen2 env/%/c4go4gxlcznh5p5nklpjm644epuh3pzc: SPEC = zlib@1.2.12%gcc@10.3.0+optimize+pic+shared patches=0d38234 arch=linux-ubuntu20.04-zen2 # Install dependencies env/.install/cdqldivylyxocqymwnfzmzc5sx2zwvww: env/.install/gv5kin2xnn33uxyfte6k4a3bynhmtxze env/.install/cuymc7e5gupwyu7vza5d4vrbuslk277p env/.install/yfz2agazed7ohevqvnrmm7jfkmsgwjao env/.install/c4go4gxlcznh5p5nklpjm644epuh3pzc env/.install/cuymc7e5gupwyu7vza5d4vrbuslk277p: env/.install/7vangk4jvsdgw6u6oe6ob63pyjl5cbgk env/.install/7vangk4jvsdgw6u6oe6ob63pyjl5cbgk: env/.install/hyb7ehxxyqqp2hiw56bzm5ampkw6cxws env/.install/yfz2agazed7ohevqvnrmm7jfkmsgwjao: env/.install/73t7ndb5w72hrat5hsax4caox2sgumzu env/.install/73t7ndb5w72hrat5hsax4caox2sgumzu: env/.install/trvdyncxzfozxofpm3cwgq4vecpxixzs env/.install/trvdyncxzfozxofpm3cwgq4vecpxixzs: env/.install/sbzszb7v557ohyd6c2ekirx2t3ctxfxp env/clean: rm -f -- env/env env/fetch env/.fetch/cdqldivylyxocqymwnfzmzc5sx2zwvww env/.fetch/gv5kin2xnn33uxyfte6k4a3bynhmtxze env/.fetch/cuymc7e5gupwyu7vza5d4vrbuslk277p env/.fetch/7vangk4jvsdgw6u6oe6ob63pyjl5cbgk env/.fetch/hyb7ehxxyqqp2hiw56bzm5ampkw6cxws env/.fetch/yfz2agazed7ohevqvnrmm7jfkmsgwjao env/.fetch/73t7ndb5w72hrat5hsax4caox2sgumzu env/.fetch/trvdyncxzfozxofpm3cwgq4vecpxixzs env/.fetch/sbzszb7v557ohyd6c2ekirx2t3ctxfxp env/.fetch/c4go4gxlcznh5p5nklpjm644epuh3pzc env/.install/cdqldivylyxocqymwnfzmzc5sx2zwvww env/.install/gv5kin2xnn33uxyfte6k4a3bynhmtxze env/.install/cuymc7e5gupwyu7vza5d4vrbuslk277p env/.install/7vangk4jvsdgw6u6oe6ob63pyjl5cbgk env/.install/hyb7ehxxyqqp2hiw56bzm5ampkw6cxws env/.install/yfz2agazed7ohevqvnrmm7jfkmsgwjao env/.install/73t7ndb5w72hrat5hsax4caox2sgumzu env/.install/trvdyncxzfozxofpm3cwgq4vecpxixzs env/.install/sbzszb7v557ohyd6c2ekirx2t3ctxfxp env/.install/c4go4gxlcznh5p5nklpjm644epuh3pzc ``` Then with `make -O` you get very nice orderly output when packages are built in parallel: ```console $ make -Orecurse -j16 spack -e . install --only-concrete --only=package /c4go4gxlcznh5p5nklpjm644epuh3pzc && touch c4go4gxlcznh5p5nklpjm644epuh3pzc ==> Installing zlib-1.2.12-c4go4gxlcznh5p5nklpjm644epuh3pzc ... Fetch: 0.00s. Build: 0.88s. Total: 0.88s. [+] /tmp/tmp.b1eTyAOe85/store/linux-ubuntu20.04-zen2/gcc-10.3.0/zlib-1.2.12-c4go4gxlcznh5p5nklpjm644epuh3pzc spack -e . install --only-concrete --only=package /sbzszb7v557ohyd6c2ekirx2t3ctxfxp && touch sbzszb7v557ohyd6c2ekirx2t3ctxfxp ==> Installing pkgconf-1.8.0-sbzszb7v557ohyd6c2ekirx2t3ctxfxp ... Fetch: 0.00s. Build: 3.96s. Total: 3.96s. [+] /tmp/tmp.b1eTyAOe85/store/linux-ubuntu20.04-zen2/gcc-10.3.0/pkgconf-1.8.0-sbzszb7v557ohyd6c2ekirx2t3ctxfxp ``` For Perl, at least for me, using `make -j16` versus `spack -e . install -j16` speeds up the builds from 3m32.623s to 2m22.775s, as some configure scripts run in parallel. Another nice feature is you can do Makefile "metaprogramming" and depend on packages built by Spack. This example fetches all sources (in parallel) first, print a message, and only then build packages (in parallel). ```Makefile SPACK ?= spack .PHONY: env all: env spack.lock: spack.yaml $(SPACK) -e . concretize -f env.mk: spack.lock $(SPACK) -e . env depfile -o $@ --make-target-prefix spack fetch: spack/fetch @echo Fetched all packages && touch $@ env: fetch spack/env @echo This executes after the environment has been installed clean: rm -rf spack/ env.mk spack.lock ifeq (,$(filter clean,$(MAKECMDGOALS))) include env.mk endif ```
2022-05-05Enable PyTorch 1.10.x to build on Power systems (#30494)Brian Van Essen1-0/+18
* Use patches from IBM's Open CE project to enable PyTorch to build on Power systems. Cherry-pick a patch to allow earlier versions of PyTorch to build with CUDA 11.4. * Update var/spack/repos/builtin/packages/py-torch/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-05-05package audit: ensure stand-alone test method not include in build-phase ↵Tamara Dahlgren3-2/+22
testing (#30352)
2022-05-05clingo: add v5.5.2 (#30495)Massimiliano Culpo1-12/+14
* clingo add v5.5.2 * Unify dependencies for @spack and @master
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-09 20:14:11 +0000