merge upstream changes #9
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Support spackbot rebuilding all specs from source when asked (with "rebuild everything") - Allow overriding --prune-dag cli opt with env var - Use job variable to optionally prevent rebuild jobs early exit behavior - ci rebuild: Use new install argument to insist deps are always installed from binary, but package is only installed from source. - gitlab: fix bug w/ untouched pruning - ci rebuild: install from hash rather than json file - When doing a "rebuild everything" pipeline, make sure that each install job only consumes binary dependencies from the mirror being populated by the current pipeline. This avoids using, e.g. binaries from develop, when rebuilding everything on a PR. - When running a pipeline to rebuild everything, do not die because we generated a hash on the broken specs list. Instead only warn in that case. - bugfix: Replace broken no-args tty.die() with sys.exit(1)
Currently `traverse_dependencies` fixes deptypes to traverse once and for all in the recursion, but this is incorrect, since deptypes depend on the node (e.g. if it's a dependency and cache-only, don't follow build type edges, even if the parent is build from sources and needs build deps.)
* py-horovod: add v0.26 * py-petastorm: add v0.12.0
When installing an individual spec `spack --only=package --cache-only /xyz` from a buildcache, Spack currently issues tons of warnings about missing build deps (and their deps) in the database. This PR disables these warnings, since it's fine to have a spec without its build deps in the db (they are just "missing").
* Classic Intel compilers do not support gcc-toolchain This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel compilers. AFAIK this option is only supported for Clang based compilers. This lead to an issue when installing cmake. Reproducer: ``` spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt build_type=Release arch=linux-amzn2-skylake_avx512 ``` Tagging maintainer @rscohn2 * Add `-gcc-name` for icc .. and `-gxx-name` for icpc. AFAIK this is used for modern C++ support, so we can ignore `ifort`. Co-authored-by: Stephen Sachs <stesachs@amazon.com>
* version bump to 1.6.0 * added py-isal, updated URL
* Add libpressio and dependencies; some of these packages are maintained as forks of the original repositories and in those cases the docstring mentions this. * Add optional dependency in adios2 on libpressio * cub package: set CUB_DIR environment variable for dependent installations * Clear R_HOME/R_ENVIRON before Spack installation (avoid sources outside of Spack from affecting the installation in Spack) * Rename dlib to dorian3d-dlib and update dependents; add new dlib implementation. Pending an official policy on how to handle packages with short names, reviewer unilaterally decided that the rename was acceptable given that the new Spack dlib package is referenced more widely (by orders of magnitude) than the original Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
* libbigwig: adding new package libbigwig * methyldackel: adding new package methyldackel * libbigwig: tighten up curl variant
This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`.
* Fixed two bugs in the HIP package recipe. The first is that the HIP_PATH was being set to the actual spec, and not the spec prefix. The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and /opt/rocm-x.y.z/lib. This means that the external detection logic may find it in either and it turns out that some modules only expose one of those two locations. Logic is added to ensure that the internal HIP_PATH and associated ROCM_PATH are correctly set in both cases. * Added support for Aluminum to use the libfabric plugin with either RCCL or NCCL.
) 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](docker/setup-buildx-action@95cb08c...c74574e) --- 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>
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>
For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
… to icc + refactor (#33389)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
"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>
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>
* new package * fixed style * actually building now
luke-dt
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1. support version 3.1.3, which now depends on sundials@6 2. support version 3.1.2:, which broke the two patch files and therefore the two patch files have been replaced by more flexible filter_file() commands inside a patch() function. 3. rename the variant for python extension from using the package name "+pyuqtk" to the more standard "+python" 4. add maintainers @omsai and the upstream developer @bjdebus who offered to help with the spack packaging. 5. swig should only be a build-time dependency. swig is only necessary until @:3.1.0 6. confirmed python dependencies are correct by inspecting imports, subset python dependencies type to build, run, and confirmed all 31 build-time tests pass including the 9 python tests: ```console $ spack env create uqtk-dev $ spack add uqtk@3.1.3 $ spack install --test root && cat $(spack location -i uqtk)/.spack/install-time-test-log.txt ==> Testing package uqtk-3.1.3-nok6fut ==> [2023-04-19-14:56:25.005361] Running build-time tests ==> [2023-04-19-14:56:25.005536] RUN-TESTS: build-time tests [check] ==> [2023-04-19-14:56:25.009543] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'test' ==> [2023-04-19-14:56:25.014903] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' 'test' Running tests... /home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/cmake-3.26.3-zjmsfz23j5l4ytniz26uzvxonlu5qebr/bin/ctest --force-new-ctest-process Test project /tmp/omsai/spack-stage/spack-stage-uqtk-3.1.3-nok6fut47h42cnaau7wkoohgqy5f2qqa/spack-build-nok6fut Start 1: ArrayReadAndWrite Start 2: ArrayDelColumn Start 3: Array1DMiscTest Start 4: Array2DMiscTest 1/31 Test #1: ArrayReadAndWrite ................ Passed 0.01 sec Start 5: ArraySortTest 2/31 Test #2: ArrayDelColumn ................... Passed 0.01 sec Start 6: MultiIndexTest 3/31 Test #3: Array1DMiscTest .................. Passed 0.01 sec Start 7: CorrTest 4/31 Test #4: Array2DMiscTest .................. Passed 0.01 sec Start 8: QuadLUTest 5/31 Test #5: ArraySortTest .................... Passed 0.02 sec Start 9: MCMC2dTest 6/31 Test #6: MultiIndexTest ................... Passed 0.01 sec Start 10: MCMCRandomTest 7/31 Test #8: QuadLUTest ....................... Passed 0.02 sec Start 11: MCMCNestedTest 8/31 Test #10: MCMCRandomTest ................... Passed 0.02 sec Start 12: Deriv1dTest 9/31 Test #12: Deriv1dTest ...................... Passed 0.01 sec Start 13: SecondDeriv1dTest 10/31 Test #13: SecondDeriv1dTest ................ Passed 0.01 sec Start 14: GradHessianTest 11/31 Test #11: MCMCNestedTest ................... Passed 0.03 sec Start 15: GradientPCETest 12/31 Test spack#14: GradHessianTest .................. Passed 0.01 sec Start 16: PCE1dTest 13/31 Test spack#15: GradientPCETest .................. Passed 0.01 sec Start 17: PCEImplTest 14/31 Test spack#16: PCE1dTest ........................ Passed 0.01 sec Start 18: PCELogTest 15/31 Test spack#18: PCELogTest ....................... Passed 0.01 sec Start 19: Hessian2dTest 16/31 Test spack#19: Hessian2dTest .................... Passed 0.01 sec Start 20: BCS1dTest 17/31 Test spack#20: BCS1dTest ........................ Passed 0.01 sec Start 21: BCS2dTest 18/31 Test spack#21: BCS2dTest ........................ Passed 0.01 sec Start 22: LowRankRegrTest 19/31 Test spack#22: LowRankRegrTest .................. Passed 0.01 sec Start 23: PyModTest 20/31 Test spack#17: PCEImplTest ...................... Passed 0.07 sec Start 24: PyArrayTest 21/31 Test spack#23: PyModTest ........................ Passed 0.08 sec Start 25: PyArrayTest2 22/31 Test spack#25: PyArrayTest2 ..................... Passed 0.30 sec Start 26: PyQuadTest 23/31 Test spack#24: PyArrayTest ...................... Passed 1.44 sec Start 27: PyBCSTest1D 24/31 Test spack#26: PyQuadTest ....................... Passed 1.68 sec Start 28: PyBCSTest2D 25/31 Test spack#27: PyBCSTest1D ...................... Passed 1.66 sec Start 29: PyBADPTest 26/31 Test #7: CorrTest ......................... Passed 3.43 sec Start 30: PyRegressionTest 27/31 Test spack#28: PyBCSTest2D ...................... Passed 1.50 sec Start 31: PyGalerkinTest 28/31 Test #9: MCMC2dTest ....................... Passed 3.90 sec 29/31 Test spack#29: PyBADPTest ....................... Passed 1.66 sec 30/31 Test spack#30: PyRegressionTest ................. Passed 1.72 sec 31/31 Test spack#31: PyGalerkinTest ................... Passed 1.63 sec 100% tests passed, 0 tests failed out of 31 Total Test time (real) = 5.35 sec ==> [2023-04-19-14:56:30.382797] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'check' ==> [2023-04-19-14:56:30.385983] Target 'check' not found in Makefile ```
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