add version 0.4.2.3 to r-bibtex #20815

glennpj · 2021-01-12T23:32:55Z

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…f.so (#20717) * add to LD_LIBRARY_PATH so that it finds libimf.so * amrex: fix handling of CUDA arch (#20786) * amrex: fix handling of CUDA arch * amrex: fix style * amrex: fix bug * Update var/spack/repos/builtin/packages/amrex/package.py * Update var/spack/repos/builtin/packages/amrex/package.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * ecp-data-vis-sdk: Combine the vis and io SDK packages (#20737) This better enables the collective set to be deployed togethor satisfying eachothers dependencies * r-sf: fix dependency error (#20898) * improve documentation for Rocm (hip amd builds) (#20812) * improve documentation * astyle: Fix makefile for install parameter (#20899) * llvm-doe: added new package (#20719) The package contains duplicated code from llvm/package.py, will supersede solve. * r-e1071: added v1.7-4 (#20891) * r-diffusionmap: added v1.2.0 (#20881) * r-covr: added v3.5.1 (#20868) * r-class: added v7.3-17 (#20856) * py-h5py: HDF5_DIR is needed for ~mpi too (#20905) For the `~mpi` variant, the environment variable `HDF5_DIR` is still required. I moved this command out of the `+mpi` conditional. * py-hovorod: fix typo on variant name in conflicts directive (#20906) * fujitsu-fftw: Add new package (#20824) * pocl: added v1.6 (#20932) Made version 1.5 or lower conflicts with a64fx. * PCL: add new package (#20933) * r-rle: new package (#20916) Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors. * r-ellipsis: added v0.3.1 (#20913) * libconfig: add build dependency on texinfo (#20930) * r-flexmix: add v2.3-17 (#20924) * r-fitdistrplus: add v1.1-3 (#20923) * r-fit-models: add v0.64 (#20922) * r-fields: add v11.6 (#20921) * r-fftwtools: add v0.9-9 (#20920) * r-farver: add v2.0.3 (#20919) * r-expm: add v0.999-6 (#20918) * cln: add build dependency on texinfo (#20928) * r-expint: add v0.1-6 (#20917) * r-envstats: add v2.4.0 (#20915) * r-energy: add v1.7-7 (#20914) * r-ellipse: add v0.4.2 (#20912) * py-fiscalyear: add v0.3.0 (#20911) * r-ecp: add v3.1.3 (#20910) * r-plotmo: add v3.6.0 (#20909) * Improve gcc detection in llvm. (#20189) Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> * hatchet: updated urls (#20908) * py-anuga: add new package (#20782) * libvips: added v8.10.5 (#20902) * libzmq: add platform conditions to libbsd dependency (#20893) * r-dtw: add v1.22-3 (#20890) * r-dt: add v0.17 (#20889) * r-dosnow: add v1.0.19 (#20888) * add version 1.0.16 to r-doparallel (#20886) * add version 1.3.7 to r-domc (#20885) * add version 0.9-15 to r-diversitree (#20884) * add version 1.3-3 to r-dismo (#20883) * add version 0.6.27 to r-digest (#20882) * add version 1.5 to r-rngtools (#20887) * add version 1.5.8 to r-dicekriging (#20877) * add version 1.4.2 to r-httr (#20876) * add version 1.28 to r-desolve (#20875) * add version 2.2-5 to r-deoptim (#20874) * add version 0.2-3 to r-deldir (#20873) * add version 1.0.0 to r-crul (#20870) * add version 1.1.0.1 to r-crosstalk (#20869) * add version 1.0-1 to r-copula (#20867) * add version 5.0.2 to r-rcppparallel (#20866) * add version 2.0-1 to r-compositions (#20865) * add version 0.4.10 to r-rlang (#20796) * add version 0.3.6 to r-vctrs (#20878) * amrex: add ROCm support (#20809) * add version 2.0-0 to r-colorspace (#20864) * add version 1.3-1 to r-coin (#20863) * add version 0.19-4 to r-coda (#20862) * add version 1.3.7 to r-clustergeneration (#20861) * add version 0.3-58 to r-clue (#20860) * add version 0.7.1 to r-clipr (#20859) * add version 2.2.0 to r-cli (#20858) * add version 0.4-3 to r-classint (#20857) * add version 0.1.2 to r-globaloptions (#20855) * add version 2.3-56 to r-chron (#20854) * add version 0.4.10 to r-checkpoint (#20853) * add version 2.0.0 to r-checkmate (#20852) * add version 1.18.1 to r-catools (#20850) * add version 1.2.2.2 to r-modelmetrics (#20849) * add version 3.0-4 to r-cardata (#20847) * add version 1.0.1 to r-caracas (#20846) * r-lifecycle: new package at v0.2.0 (#20845) * add version 3.0-10 to r-car (#20844) * add version 3.4.5 to r-processx (#20843) * add version 1.5-12.2 to r-cairo (#20842) * add version 0.2.3 to r-cubist (#20841) * add version 2.6 to r-rmarkdown (#20838) * add version 1.2.1 to r-blob (#20819) * add version 4.0.4 to r-bit (#20818) * add version 2.4-1 to r-bio3d (#20816) * add version 0.4.2.3 to r-bibtex (#20815) * add version 3.1-4 to r-bayesm (#20807) * add version 1.2.1 to r-backports (#20806) * add version 2.0.3 to r-argparse (#20805) * add version 5.4-1 to r-ape (#20804) * add version 0.8-18 to r-amap (#20803) * r-pixmap: added new package (#20795) * zoltan: source code location change (#20787) * refactor path logic * added some paths to make compilers and libs discoverable * add to LD_LIBRARY_PATH so that it finds libimf.so and cleanup PEP8 * refactor path logic * adding paths to LIBRARY_PATH so compiler wrappers will find -lmpi * added vals for CC=icx, CXX=icpx, FC=ifx to generated module * back out changes to intel-oneapi-mpi, save for separate PR * Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py path is joined in _ld_library_path() Co-authored-by: Robert Cohn <rscohn2@gmail.com> * set absolute paths to icx,icpx,ifx * dang close parenthesis Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: mic84 <mrosso@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com> Co-authored-by: darmac <xiaojun2@hisilicon.com> Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com> Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com> Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov> Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu> Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com> Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com> Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu> Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com> Co-authored-by: QuellynSnead <quellyn@lanl.gov>

…f.so (spack#20717) * add to LD_LIBRARY_PATH so that it finds libimf.so * amrex: fix handling of CUDA arch (spack#20786) * amrex: fix handling of CUDA arch * amrex: fix style * amrex: fix bug * Update var/spack/repos/builtin/packages/amrex/package.py * Update var/spack/repos/builtin/packages/amrex/package.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * ecp-data-vis-sdk: Combine the vis and io SDK packages (spack#20737) This better enables the collective set to be deployed togethor satisfying eachothers dependencies * r-sf: fix dependency error (spack#20898) * improve documentation for Rocm (hip amd builds) (spack#20812) * improve documentation * astyle: Fix makefile for install parameter (spack#20899) * llvm-doe: added new package (spack#20719) The package contains duplicated code from llvm/package.py, will supersede solve. * r-e1071: added v1.7-4 (spack#20891) * r-diffusionmap: added v1.2.0 (spack#20881) * r-covr: added v3.5.1 (spack#20868) * r-class: added v7.3-17 (spack#20856) * py-h5py: HDF5_DIR is needed for ~mpi too (spack#20905) For the `~mpi` variant, the environment variable `HDF5_DIR` is still required. I moved this command out of the `+mpi` conditional. * py-hovorod: fix typo on variant name in conflicts directive (spack#20906) * fujitsu-fftw: Add new package (spack#20824) * pocl: added v1.6 (spack#20932) Made version 1.5 or lower conflicts with a64fx. * PCL: add new package (spack#20933) * r-rle: new package (spack#20916) Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors. * r-ellipsis: added v0.3.1 (spack#20913) * libconfig: add build dependency on texinfo (spack#20930) * r-flexmix: add v2.3-17 (spack#20924) * r-fitdistrplus: add v1.1-3 (spack#20923) * r-fit-models: add v0.64 (spack#20922) * r-fields: add v11.6 (spack#20921) * r-fftwtools: add v0.9-9 (spack#20920) * r-farver: add v2.0.3 (spack#20919) * r-expm: add v0.999-6 (spack#20918) * cln: add build dependency on texinfo (spack#20928) * r-expint: add v0.1-6 (spack#20917) * r-envstats: add v2.4.0 (spack#20915) * r-energy: add v1.7-7 (spack#20914) * r-ellipse: add v0.4.2 (spack#20912) * py-fiscalyear: add v0.3.0 (spack#20911) * r-ecp: add v3.1.3 (spack#20910) * r-plotmo: add v3.6.0 (spack#20909) * Improve gcc detection in llvm. (spack#20189) Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> * hatchet: updated urls (spack#20908) * py-anuga: add new package (spack#20782) * libvips: added v8.10.5 (spack#20902) * libzmq: add platform conditions to libbsd dependency (spack#20893) * r-dtw: add v1.22-3 (spack#20890) * r-dt: add v0.17 (spack#20889) * r-dosnow: add v1.0.19 (spack#20888) * add version 1.0.16 to r-doparallel (spack#20886) * add version 1.3.7 to r-domc (spack#20885) * add version 0.9-15 to r-diversitree (spack#20884) * add version 1.3-3 to r-dismo (spack#20883) * add version 0.6.27 to r-digest (spack#20882) * add version 1.5 to r-rngtools (spack#20887) * add version 1.5.8 to r-dicekriging (spack#20877) * add version 1.4.2 to r-httr (spack#20876) * add version 1.28 to r-desolve (spack#20875) * add version 2.2-5 to r-deoptim (spack#20874) * add version 0.2-3 to r-deldir (spack#20873) * add version 1.0.0 to r-crul (spack#20870) * add version 1.1.0.1 to r-crosstalk (spack#20869) * add version 1.0-1 to r-copula (spack#20867) * add version 5.0.2 to r-rcppparallel (spack#20866) * add version 2.0-1 to r-compositions (spack#20865) * add version 0.4.10 to r-rlang (spack#20796) * add version 0.3.6 to r-vctrs (spack#20878) * amrex: add ROCm support (spack#20809) * add version 2.0-0 to r-colorspace (spack#20864) * add version 1.3-1 to r-coin (spack#20863) * add version 0.19-4 to r-coda (spack#20862) * add version 1.3.7 to r-clustergeneration (spack#20861) * add version 0.3-58 to r-clue (spack#20860) * add version 0.7.1 to r-clipr (spack#20859) * add version 2.2.0 to r-cli (spack#20858) * add version 0.4-3 to r-classint (spack#20857) * add version 0.1.2 to r-globaloptions (spack#20855) * add version 2.3-56 to r-chron (spack#20854) * add version 0.4.10 to r-checkpoint (spack#20853) * add version 2.0.0 to r-checkmate (spack#20852) * add version 1.18.1 to r-catools (spack#20850) * add version 1.2.2.2 to r-modelmetrics (spack#20849) * add version 3.0-4 to r-cardata (spack#20847) * add version 1.0.1 to r-caracas (spack#20846) * r-lifecycle: new package at v0.2.0 (spack#20845) * add version 3.0-10 to r-car (spack#20844) * add version 3.4.5 to r-processx (spack#20843) * add version 1.5-12.2 to r-cairo (spack#20842) * add version 0.2.3 to r-cubist (spack#20841) * add version 2.6 to r-rmarkdown (spack#20838) * add version 1.2.1 to r-blob (spack#20819) * add version 4.0.4 to r-bit (spack#20818) * add version 2.4-1 to r-bio3d (spack#20816) * add version 0.4.2.3 to r-bibtex (spack#20815) * add version 3.1-4 to r-bayesm (spack#20807) * add version 1.2.1 to r-backports (spack#20806) * add version 2.0.3 to r-argparse (spack#20805) * add version 5.4-1 to r-ape (spack#20804) * add version 0.8-18 to r-amap (spack#20803) * r-pixmap: added new package (spack#20795) * zoltan: source code location change (spack#20787) * refactor path logic * added some paths to make compilers and libs discoverable * add to LD_LIBRARY_PATH so that it finds libimf.so and cleanup PEP8 * refactor path logic * adding paths to LIBRARY_PATH so compiler wrappers will find -lmpi * added vals for CC=icx, CXX=icpx, FC=ifx to generated module * back out changes to intel-oneapi-mpi, save for separate PR * Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py path is joined in _ld_library_path() Co-authored-by: Robert Cohn <rscohn2@gmail.com> * set absolute paths to icx,icpx,ifx * dang close parenthesis Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: mic84 <mrosso@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com> Co-authored-by: darmac <xiaojun2@hisilicon.com> Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com> Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com> Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov> Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu> Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com> Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com> Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu> Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com> Co-authored-by: QuellynSnead <quellyn@lanl.gov>

* py-ipykernel: fix install (#19617) There is a post-install routine in `ipykernel` that needs to be called for proper registration with jupyter. * hip support for umpire, chai, raja, camp (#19715) * create HipPackage base class and do some refactoring * comments and added conflict to raja for openmp with hip * fix error handling for spack test results command (#19987) * py-ipykernel: fix bug in phase method (#19986) * py-ipykernel: fix bug in phase method * Fix bug in executable calling * recognize macOS 11.1 as big sur (#20038) Big Sur versions go 11.0, 11.0.1, 11.1 (vs. prior versions that only used the minor component) Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> * Docs: remove duplication in Command Reference (#20021) * concretizer: treat conditional providers correctly (#20086) refers #20040 This modification emits rules like: provides_virtual("netlib-lapack","blas") :- variant_value("netlib-lapack","external-blas","False"). for packages that provide virtual dependencies conditionally instead of a fact that doesn't account for the condition. * concretizer: allow a bool to be passed as argument for tests dependencies (#20082) refers #20079 Added docstrings to 'concretize' and 'concretized' to document the format for tests. Added tests for the activation of test dependencies. * concretizer: prioritize matching compilers over newer versions (#20020) fixes #20019 Before this modification having a newer version of a node came at higher priority in the optimization than having matching compilers. This could result in unexpected configurations for packages with conflict directives on compilers of the type: conflicts('%gcc@X.Y:', when='@:A.B') where changing the compiler for just that node is preferred to lower the node version to less than 'A.B'. Now the priority has been switched so the solver will try to lower the version of the nodes in question before changing their compiler. * concretizer: treat target ranges in directives correctly (#19988) fixes #19981 This commit adds support for target ranges in directives, for instance: conflicts('+foo', when='target=x86_64:,aarch64:') If any target in a spec body is not a known target the following clause will be emitted: node_target_satisfies(Package, TargetConstraint) when traversing the spec and a definition of the clause will then be printed at the end similarly to what is done for package and compiler versions. * Typos: add missing closing parens (#20174) * concretizer: swap priority of selecting provider and default variant (#20182) refers #20040 Before this PR optimization rules would have selected default providers at a higher priority than default variants. Here we swap this priority and we consider variants that are forced by any means (root spec or spec in depends_on clause) the same as if they were with a default value. This prevents the solver from avoiding expected configurations just because they contain directives like: depends_on('pkg+foo') and `+foo` is not the default variant value for pkg. * concretizer: remove ad-hoc rule for external packages (#20193) fixes #20040 Matching compilers among nodes has been prioritized in #20020. Selection of default variants has been tuned in #20182. With this setup there is no need to have an ad-hoc rule for external packages. On the contrary it should be removed to prefer having default variant values over more external nodes in the DAG. * spec: return early from concretization if a spec is already concrete (#20196) * Fixes compile time errors (#20006) Co-authored-by: michael laufer <michael.laufer@toganetworks.com> * concretizer: don't optimize emitting version_satisfies() (#20128) When all versions were allowed a version_satisfies rule was not emitted, and this caused conditional directives to fail. * boost: disable find_package's config mode for boost prior to v1.70.0 (#20198) * Fix hipcc once more (#20095) * concretizer: try hard to infer the real version of compilers (#20099) fixes #20055 Compiler with custom versions like gcc@foo are not currently matched to the appropriate targets. This is because the version of spec doesn't match the "real" version of the compiler. This PR replicates the strategy used in the original concretizer to deal with that and tries to detect the real version of compilers if the version in the spec returns no results. * concretizer: call inject_patches_variants() on the roots of the specs (#20203) As was done in the old concretizer. Fixes an issue where conditionally patched dependencies did not show up in spec (gdal+jasper) * avoid circular import (#20236) * environment installs: fix reporting. (#20004) PR #15702 changed the invocation of the report context when installing specs, do the same when building environments. * concretizer: restrict maximizing variant values to MV variants (#20194) * concretizer: each external version is allowed by definition (#20247) Registering external versions among the lists of allowed ones generates the correct rules for `version_satisfies` * VTK-m: update to specify correct requirements to kokkos (#20097) * concretizer: refactor handling of special variants dev_build and patches Other parts of the concretizer code build up lists of things we can't know without traversing all specs and packages, and they output these list at the very end. The code for this for variant values from spec literals was intertwined with the code for traversing the input specs. This only covers the input specs and misses variant values that might come from directives in packages. - [x] move ad-hoc value handling code into spec_clauses so we do it in one place for CLI and packages - [x] move handling of `variant_possible_value`, etc. into `concretize.lp`, where we can automatically infer variant existence more concisely. - [x] simplify/clarify some of the code for variants in `spec_clauses()` * bugfix: work around issue handling packages not in any repo * concretizer: try hard to obtain all needed variant_possible_value()'s (#20102) Track all the variant values mentioned when emitting constraints, validate them and emit a fact that allows them as possible values. This modification ensures that open-ended variants (variants accepting any string or any integer) are projected to the finite set of values that are relevant for this concretization. * Tests: enable re-use of post-install tests in smoke tests (#20298) * concretizer: remove clingo command-line driver (#20362) I was keeping the old `clingo` driver code around in case we had to run using the command line tool instad of through the Python interface. So far, the command line is faster than running through Python, but I'm working on fixing that. I found that if I do this: ```python control = clingo.Control() control.load("concretize.lp") control.load("hdf5.lp") # code from spack solve --show asp hdf5 control.load("display.lp") control.ground([("base", [])]) control.solve(...) ``` It's just as fast as the command line tool. So we can always generate the code and load it manually if we need to -- we don't need two drivers for clingo. Given that the python interface is also the only way to get unsat cores, I think we pretty much have to use it. So, I'm removing the old command line driver and other unused code. We can dig it up again from the history if it is needed. * package sanity: ensure all variant defaults are allowed values (#20373) * concretizer: don't use one_of_iff for range constraints (#20383) Currently, version range constraints, compiler version range constraints, and target range constraints are implemented by generating ground rules from `asp.py`, via `one_of_iff()`. The rules look like this: ``` version_satisfies("python", "2.6:") :- 1 { version("python", "2.4"); ... } 1. 1 { version("python", "2.4"); ... } 1. :- version_satisfies("python", "2.6:"). ``` So, `version_satisfies(Package, Constraint)` is true if and only if the package is assigned a version that satisfies the constraint. We precompute the set of known versions that satisfy the constraint, and generate the rule in `SpackSolverSetup`. We shouldn't need to generate already-ground rules for this. Rather, we should leave it to the grounder to do the grounding, and generate facts so that the constraint semantics can be defined in `concretize.lp`. We can replace rules like the ones above with facts like this: ``` version_satisfies("python", "2.6:", "2.4") ``` And ground them in `concretize.lp` with rules like this: ``` 1 { version(Package, Version) : version_satisfies(Package, Constraint, Version) } 1 :- version_satisfies(Package, Constraint). version_satisfies(Package, Constraint) :- version(Package, Version), version_satisfies(Package, Constraint, Version). ``` The top rule is the same as before. It makes conditional dependencies and other places where version constraints are used work properly. Note that we do not need the cardinality constraint for the second rule -- we already have rules saying there can be only one version assigned to a package, so we can just infer from `version/2` `version_satisfies/3`. This form is also safe for grounding -- If we used the original form we'd have unsafe variables like `Constraint` and `Package` -- the original form only really worked when specified as ground to begin with. - [x] use facts instead of generating rules for package version constraints - [x] use facts instead of generating rules for compiler version constraints - [x] use facts instead of generating rules for target range constraints - [x] remove `one_of_iff()` and `iff()` as they're no longer needed * Fix comparisons for abstract specs (#20341) bug only relevant for python3 * unit-tests: ensure that installed packages can be reused (#20307) refers #20292 Added a unit test that ensures we can reuse installed packages even if in the repository variants have been removed or added. * ci: fixes for compiler bootstrapping (#17563) This PR addresses a number of issues related to compiler bootstrapping. Specifically: 1. Collect compilers to be bootstrapped while queueing in installer Compiler tasks currently have an incomplete list in their task.dependents, making those packages fail to install as they think they have not all their dependencies installed. This PR collects the dependents and sets them on compiler tasks. 2. allow boostrapped compilers to back off target Bootstrapped compilers may be built with a compiler that doesn't support the target used by the rest of the spec. Allow them to build with less aggressive target optimization settings. 3. Support for target ranges Backing off the target necessitates computing target ranges, so make Spack handle those properly. Notably, this adds an intersection method for target ranges and fixes the way ranges are satisfied and constrained on Spec objects. This PR also: - adds testing - improves concretizer handling of target ranges Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * asp: memoize the list of all target_specs to speed-up setup phase (#20473) * asp: memoize the list of all target_specs to speed-up setup phase * asp: memoize using a cache per solver object * concretizer: add #defined statements to avoid warnings. `version_satisfies/2` and `node_compiler_version_satisfies/3` are generated but need `#defined` directives to avoid " info: atom does not occur in any rule head:" warnings. * concretizer: pull _develop_specs_from_env out of main setup loop * concretizer: spec_clauses should traverse dependencies There are currently no places where we do not want to traverse dependencies in `spec_clauses()`, so simplify the logic by consolidating `spec_traverse_clauses()` with `spec_clauses()`. * concretizer: move conditional dependency logic into `concretize.lp` Continuing to convert everything in `asp.py` into facts, make the generation of ground rules for conditional dependencies use facts, and move the semantics into `concretize.lp`. This is probably the most complex logic in Spack, as dependencies can be conditional on anything, and we need conditional ASP rules to accumulate and map all the dependency conditions to spec attributes. The logic looks complicated, but essentially it accumulates any constraints associated with particular conditions into a fact associated with the condition by id. Then, if *any* condition id's fact is True, we trigger the dependency. This simplifies the way `declared_dependency()` works -- the dependency is now declared regardless of whether it is conditional, and the conditions are handled by `dependency_condition()` facts. * concretizer: avoid redundant grounding on dependency types * concretizer: emit facts for constraints on imposed dependencies * concretizer: emit facts for integrity constraints * concretizer: fix failing unit tests * concretizer: optimized loop on node platforms We can speed-up the computation by avoiding a double loop in a cardinality constraint and enforcing the rule instead as an integrity constraint. * concretizer: optimize loop on compiler version Similar to the optimization on platform * concretizer: refactor conditional rules to be less repetitious (#20507) We have to repeat all the spec attributes in a number of places in `concretize.lp`, and Spack has a fair number of spec attributes. If we instead add some rules up front that establish equivalencies like this: ``` node(Package) :- attr("node", Package). attr("node", Package) :- node(Package). version(Package, Version) :- attr("version", Package, Version). attr("version", Package, Version) :- version(Package, Version). ``` We can rewrite most of the repetitive conditions with `attr` and repeat only for each arity (there are only 3 arities for spec attributes so far) as opposed to each spec attribute. This makes the logic easier to read and the rules easier to follow. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Add Intel oneAPI packages (#20411) This creates a set of packages which all use the same script to install components of Intel oneAPI. This includes: * An inheritable IntelOneApiPackage which knows how to invoke the installation script based on which components are requested * For components which include headers/libraries, an inheritable IntelOneApiLibraryPackage is provided to locate them * Individual packages for DAL, DNN, TBB, etc. * A package for the Intel oneAPI compilers (icx/ifx). This also includes icc/ifortran but these are not currently detected in this PR * bugfix: do not write empty default dicts/lists in envs (#20526) Environment yaml files should not have default values written to them. To accomplish this, we change the validator to not add the default values to yaml. We rely on the code to set defaults for all values (and use defaulting getters like dict.get(key, default)). Includes regression test. * concretizer: generate facts for externals Generate only facts for external specs. Substitute the use of already grounded rules with non-grounded rules in concretize.lp * bugfix: infinite loop when building a set from incomplete specs (#20649) This code in `SpecBuilder.build_specs()` introduced in #20203, can loop seemingly interminably for very large specs: ```python set([spec.root for spec in self._specs.values()]) ``` It's deceptive, because it seems like there must be an issue with `spec.root`, but that works fine. It's building the set afterwards that takes forever, at least on `r-rminer`. Currently if you try running `spack solve r-rminer`, it loops infinitely and spins up your fan. The issue (I think) is that the spec is not yet complete when this is run, and something is going wrong when constructing and comparing so many values produced by `_cmp_key()`. We can investigate the efficiency of `_cmp_key()` separately, but for now, the fix is: ```python roots = [spec.root for spec in self._specs.values()] roots = dict((id(r), r) for r in roots) ``` We know the specs in `self._specs` are distinct (they just came out of the solver), so we can just use their `id()` to unique them here. This gets rid of the infinite loop. * concretizer: more detailed section headers in concretize.lp * concretizer: make _condtion_id_counter an iterator * concretizer: consolidate handling of virtuals into spec_clauses * concretizer: convert virtuals to facts; move all rules to `concretize.lp` This converts the virtual handling in the new concretizer from already-ground rules to facts. This is the last thing that needs to be refactored, and it converts the entire concretizer to just use facts. The previous way of handling virtuals hinged on rules involving `single_provider_for` facts that were tied to the virtual and a version range. The new method uses the condition pattern we've been using for dependencies, externals, and conflicts. To handle virtuals as conditions, we impose constraints on "fake" virtual specs in the logic program. i.e., `version_satisfies("mpi", "2.0:", "2.0")` is legal whereas before we wouldn't have seen something like this. Currently, constriants are only handled on versions -- we don't handle variants or anything else yet, but they key change here is that we *could*. For a long time, virtual handling in Spack has only dealt with versions, and we'd like to be able to handle variants as well. We could easily add an integrity constraint to handle variants like the one we use for versions. One issue with the implementation here is that virtual packages don't actually declare possible versions like regular packages do. To get around that, we implement an integrity constraint like this: :- virtual_node(Virtual), version_satisfies(Virtual, V1), version_satisfies(Virtual, V2), not version_constraint_satisfies(Virtual, V1, V2). This requires us to compare every version constraint to every other, both in program generation and within the concretizer -- so there's a potentially quadratic evaluation time on virtual constraints because we don't have a real version to "anchor" things to. We just say that all the constraints need to agree for the virtual constraint to hold. We can investigate adding synthetic versions for virtuals in the future, to speed this up. * concretizer: remove rule generation code from concretizer Our program only generates facts now, so remove all unused code related to generating cardinality constraints and rules. * concretizer: simplify handling of virtual version constraints Previously, the concretizer handled version constraints by comparing all pairs of constraints and ensuring they satisfied each other. This led to INCONSISTENT ressults from clingo, due to ambiguous semantics like: version_constraint_satisfies("mpi", ":1", ":3") version_constraint_satisfies("mpi", ":3", ":1") To get around this, we introduce possible (fake) versions for virtuals, based on their constraints. Essentially, we add any Versions, VersionRange endpoints, and all such Versions and endpoints from VersionLists to the constraint. Virtuals will have one of these synthetic versions "picked" by the solver. This also allows us to remove a special case from handling of `version_satisfies/3` -- virtuals now work just like regular packages. * concretizer: use consistent naming for compiler predicates (#20677) Every other predicate in the concretizer uses a `_set` suffix to implement user- or package-supplied settings, but compiler settings use a `_hard` suffix for this. There's no difference in how they're used, so make the names the same. - [x] change `node_compiler_hard` to `node_compiler_set` - [x] change `node_compiler_version_hard` to `node_compiler_version_set` * concretizer: make rules on virtual packages more linear fixes #20679 In this refactor we have a single cardinality rule on the provider, which triggers a rule transforming a dependency on a virtual package into a dependency on the provider of the virtual. * Remove hard-coded standard C++ library selection and add more releases in llvm package (#19933) * Restore OS based Clang default choice of C++ standard library. * Add LLVM 11.0.1 release * fix mpi lib paths, add virtual provides (#20693) * intel-oneapi-compilers package: correct module file (#20686) This properly sets PATH/CPATH/LIBRARY_PATH etc. to make the Spack-generated module file for intel-oneapi-compilers useful (without this, 'icx' would not be found after loading the module file for intel-oneapi-compilers). * intel-oneapi-mpi: virtual provider support (#20732) Set up environment and dependent packages properly when building with intel-oneapi-mpi as a dependency MPI provider (e.g. point to mpicc compiler wrapper). * restore ability of dev-build to skip patches (#20351) At some point in the past, the skip_patch argument was removed from the call to package.do_install() this broke the --skip-patch flag on the dev-build command. * libyogrt: remove conflicts triggered by an invalid value (#20794) fixes #20611 The conflict was triggered by an invalid value of the 'scheduler' variant. This causes Spack to error when libyogrt facts are validated by the ASP-based concretizer. * concretizer: dependency conditions cannot hold if package is external fixes #20736 Before this one line fix we were erroneously deducing that dependency conditions hold even if a package was external. This may result in answer sets that contain imposed conditions on a node without the node being present in the DAG, hence #20736. * concretizer: require at least a dependency type to say the dependency holds fixes #20784 Similarly to the previous bug, here we were deducing conditions to be imposed on nodes that were not part of the DAG. * py-hovorod: fix typo on variant name in conflicts directive (#20906) * [WIP] relocate.py: parallelize test replacement logic (#19690) * sbang pushed back to callers; star moved to util.lang * updated unit test * sbang test moved; local tests pass Co-authored-by: Nathan Hanford <hanford1@llnl.gov> * store sbang_install_path in buildinfo, use for subsequent relocation (#20768) * Print groups properly for spack find -d (#20028) * llvm: "master" branch is now "main" branch (#21411) * add intel oneapi to compiler/pkg translations (#21448) * adding environment to OneMKL packages so that examples will build (#21377) * intel-oneapi-compilers: add to LD_LIBRARY_PATH so that it finds libimf.so (#20717) * add to LD_LIBRARY_PATH so that it finds libimf.so * amrex: fix handling of CUDA arch (#20786) * amrex: fix handling of CUDA arch * amrex: fix style * amrex: fix bug * Update var/spack/repos/builtin/packages/amrex/package.py * Update var/spack/repos/builtin/packages/amrex/package.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * ecp-data-vis-sdk: Combine the vis and io SDK packages (#20737) This better enables the collective set to be deployed togethor satisfying eachothers dependencies * r-sf: fix dependency error (#20898) * improve documentation for Rocm (hip amd builds) (#20812) * improve documentation * astyle: Fix makefile for install parameter (#20899) * llvm-doe: added new package (#20719) The package contains duplicated code from llvm/package.py, will supersede solve. * r-e1071: added v1.7-4 (#20891) * r-diffusionmap: added v1.2.0 (#20881) * r-covr: added v3.5.1 (#20868) * r-class: added v7.3-17 (#20856) * py-h5py: HDF5_DIR is needed for ~mpi too (#20905) For the `~mpi` variant, the environment variable `HDF5_DIR` is still required. I moved this command out of the `+mpi` conditional. * py-hovorod: fix typo on variant name in conflicts directive (#20906) * fujitsu-fftw: Add new package (#20824) * pocl: added v1.6 (#20932) Made version 1.5 or lower conflicts with a64fx. * PCL: add new package (#20933) * r-rle: new package (#20916) Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors. * r-ellipsis: added v0.3.1 (#20913) * libconfig: add build dependency on texinfo (#20930) * r-flexmix: add v2.3-17 (#20924) * r-fitdistrplus: add v1.1-3 (#20923) * r-fit-models: add v0.64 (#20922) * r-fields: add v11.6 (#20921) * r-fftwtools: add v0.9-9 (#20920) * r-farver: add v2.0.3 (#20919) * r-expm: add v0.999-6 (#20918) * cln: add build dependency on texinfo (#20928) * r-expint: add v0.1-6 (#20917) * r-envstats: add v2.4.0 (#20915) * r-energy: add v1.7-7 (#20914) * r-ellipse: add v0.4.2 (#20912) * py-fiscalyear: add v0.3.0 (#20911) * r-ecp: add v3.1.3 (#20910) * r-plotmo: add v3.6.0 (#20909) * Improve gcc detection in llvm. (#20189) Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> * hatchet: updated urls (#20908) * py-anuga: add new package (#20782) * libvips: added v8.10.5 (#20902) * libzmq: add platform conditions to libbsd dependency (#20893) * r-dtw: add v1.22-3 (#20890) * r-dt: add v0.17 (#20889) * r-dosnow: add v1.0.19 (#20888) * add version 1.0.16 to r-doparallel (#20886) * add version 1.3.7 to r-domc (#20885) * add version 0.9-15 to r-diversitree (#20884) * add version 1.3-3 to r-dismo (#20883) * add version 0.6.27 to r-digest (#20882) * add version 1.5 to r-rngtools (#20887) * add version 1.5.8 to r-dicekriging (#20877) * add version 1.4.2 to r-httr (#20876) * add version 1.28 to r-desolve (#20875) * add version 2.2-5 to r-deoptim (#20874) * add version 0.2-3 to r-deldir (#20873) * add version 1.0.0 to r-crul (#20870) * add version 1.1.0.1 to r-crosstalk (#20869) * add version 1.0-1 to r-copula (#20867) * add version 5.0.2 to r-rcppparallel (#20866) * add version 2.0-1 to r-compositions (#20865) * add version 0.4.10 to r-rlang (#20796) * add version 0.3.6 to r-vctrs (#20878) * amrex: add ROCm support (#20809) * add version 2.0-0 to r-colorspace (#20864) * add version 1.3-1 to r-coin (#20863) * add version 0.19-4 to r-coda (#20862) * add version 1.3.7 to r-clustergeneration (#20861) * add version 0.3-58 to r-clue (#20860) * add version 0.7.1 to r-clipr (#20859) * add version 2.2.0 to r-cli (#20858) * add version 0.4-3 to r-classint (#20857) * add version 0.1.2 to r-globaloptions (#20855) * add version 2.3-56 to r-chron (#20854) * add version 0.4.10 to r-checkpoint (#20853) * add version 2.0.0 to r-checkmate (#20852) * add version 1.18.1 to r-catools (#20850) * add version 1.2.2.2 to r-modelmetrics (#20849) * add version 3.0-4 to r-cardata (#20847) * add version 1.0.1 to r-caracas (#20846) * r-lifecycle: new package at v0.2.0 (#20845) * add version 3.0-10 to r-car (#20844) * add version 3.4.5 to r-processx (#20843) * add version 1.5-12.2 to r-cairo (#20842) * add version 0.2.3 to r-cubist (#20841) * add version 2.6 to r-rmarkdown (#20838) * add version 1.2.1 to r-blob (#20819) * add version 4.0.4 to r-bit (#20818) * add version 2.4-1 to r-bio3d (#20816) * add version 0.4.2.3 to r-bibtex (#20815) * add version 3.1-4 to r-bayesm (#20807) * add version 1.2.1 to r-backports (#20806) * add version 2.0.3 to r-argparse (#20805) * add version 5.4-1 to r-ape (#20804) * add version 0.8-18 to r-amap (#20803) * r-pixmap: added new package (#20795) * zoltan: source code location change (#20787) * refactor path logic * added some paths to make compilers and libs discoverable * add to LD_LIBRARY_PATH so that it finds libimf.so and cleanup PEP8 * refactor path logic * adding paths to LIBRARY_PATH so compiler wrappers will find -lmpi * added vals for CC=icx, CXX=icpx, FC=ifx to generated module * back out changes to intel-oneapi-mpi, save for separate PR * Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py path is joined in _ld_library_path() Co-authored-by: Robert Cohn <rscohn2@gmail.com> * set absolute paths to icx,icpx,ifx * dang close parenthesis Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: mic84 <mrosso@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com> Co-authored-by: darmac <xiaojun2@hisilicon.com> Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com> Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com> Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov> Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu> Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com> Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com> Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu> Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com> Co-authored-by: QuellynSnead <quellyn@lanl.gov> * intel-oneapi-compilers/mpi: add module support (#20808) Facilitate running intel-oneapi-mpi outside of Spack (set PATH, LD_LIBRARY_PATH, etc. appropriately). Co-authored-by: Robert Cohn <rscohn2@gmail.com> * apple-clang: add correct path to compiler wrappers (#21662) Follow-up to #17110 ### Before ```bash CC=/Users/Adam/spack/lib/spack/env/clang/clang; export CC SPACK_CC=/usr/bin/clang; export SPACK_CC PATH=...:/Users/Adam/spack/lib/spack/env/apple-clang:/Users/Adam/spack/lib/spack/env/case-insensitive:/Users/Adam/spack/lib/spack/env:...; export PATH ``` ### After ```bash CC=/Users/Adam/spack/lib/spack/env/clang/clang; export CC SPACK_CC=/usr/bin/clang; export SPACK_CC PATH=...:/Users/Adam/spack/lib/spack/env/clang:/Users/Adam/spack/lib/spack/env/case-insensitive:/Users/Adam/spack/lib/spack/env:...; export PATH ``` `CC` and `SPACK_CC` were being set correctly, but `PATH` was using the name of the compiler `apple-clang` instead of `clang`. For most packages, since `CC` was set correctly, nothing broke. But for packages using `Makefiles` that set `CC` based on `which clang`, it was using the system compilers instead of the compiler wrappers. Discovered when working on `py-xgboost@0.90`. An alternative fix would be to copy the symlinks in `env/clang` to `env/apple-clang`. Let me know if you think there's a better way to do this, or to test this. * Resolve (post-cherry-picking) flake8 errors * Update CHANGELOG and release version * updates for new tutorial update s3 bucket update tutorial branch * update tutorial public key * respect -k/verify-ssl-false in _existing_url method (#21864) * use package supplied autogen.sh (#20319) * Python 3.10 support: collections.abc (#20441) (cherry picked from commit 40a40e0265d6704a7836aeb30a776d66da8f7fe6) * concretizer: simplify "fact" method (#21148) The "fact" method before was dealing with multiple facts registered per call, which was used when we were emitting grounded rules from knowledge of the problem instance. Now that the encoding is changed we can simplify the method to deal only with a single fact per call. (cherry picked from commit ba42c36f00fe40c047121a32117018eb93e0c4b1) * Improve error message for inconsistencies in package.py (#21811) * Improve error message for inconsistencies in package.py Sometimes directives refer to variants that do not exist. Make it such that: 1. The name of the variant 2. The name of the package which is supposed to have such variant 3. The name of the package making this assumption are all printed in the error message for easier debugging. * Add unit tests (cherry picked from commit 7226bd64dc3b46a1ed361f1e9d7fb4a2a5b65200) * Updates to support clingo-cffi (#20657) * Support clingo when used with cffi Clingo recently merged in a new Python module option based on cffi. Compatibility with this module requires a few changes to spack - it does not automatically convert strings/ints/etc to Symbol and clingo.Symbol.string throws on failure. manually convert str/int to clingo.Symbol types catch stringify exceptions add job for clingo-cffi to Spack CI switch to potassco-vendored wheel for clingo-cffi CI on_unsat argument when cffi (cherry picked from commit 93ed1a410c4a202eab3a68769fd8c0d4ff8b1c8e) * Run clingo-cffi tests in a container (#21913) There clingo-cffi job has two issues to be solved: 1. It uses the default concretizer 2. It requires a package from https://test.pypi.org/simple/ The former can be fixed by setting the SPACK_TEST_SOLVER environment variable to "clingo". The latter though requires clingo-cffi to be pushed to a more stable package index (since https://test.pypi.org/simple/ is meant as a scratch version of PyPI that can be wiped at any time). For the time being run the tests in a container. Switch back to PyPI whenever a new official version of clingo will be released. * repo: generalize "swap" context manager to also accept paths The method is now called "use_repositories" and makes it clear in the docstring that it accepts as arguments either Repo objects or paths. Since there was some duplication between this contextmanager and "use_repo" in the testing framework, remove the latter and use spack.repo.use_repositories across the entire code base. Make a few adjustment to MockPackageMultiRepo, since it was stating in the docstring that it was supposed to mock spack.repo.Repo and was instead mocking spack.repo.RepoPath. (cherry picked from commit 1a8963b0f4c11c4b7ddd347e6cd95cdc68ddcbe0) * Move context manager to swap the current store into spack.store The context manager can be used to swap the current store temporarily, for any use case that may need it. (cherry picked from commit cb2c233a97073f8c5d89581ee2a2401fef5f878d) * Move context manager to swap the current configuration into spack.config The context manager can be used to swap the current configuration temporarily, for any use case that may need it. (cherry picked from commit 553d37a6d62b05f15986a702394f67486fa44e0e) * bugfix for target adjustments on target ranges (#20537) (cherry picked from commit 61c1b71d38e62a5af81b3b7b8a8d12b954d99f0a) * Added a context manager to swap architectures This solves a few FIXMEs in conftest.py, where we were manipulating globals and seeing side effects prior to registering fixtures. This commit solves the FIXMEs, but introduces a performance regression on tests that may need to be investigated (cherry picked from commit 4558dc06e21e01ab07a43737b8cb99d1d69abb5d) * make `spack fetch` work with environments (#19166) * make `spack fetch` work with environments * previously: `spack fetch` required the explicit statement of the specs to be fetched, even when in an environment * now: if there is no spec(s) provided to `spack fetch` we check if an environment is active and if yes we fetch all uninstalled specs. * clingo: prefer master branch Most people installing `clingo` with Spack are going to be doing it to use the new concretizer, and that requires the `master` branch. - [x] make `master` the default so we don't have to keep telling people to install `clingo@master`. We'll update the preferred version when there's a new release. * Clingo: fix missing import (#21364) * clingo: added a package with option for bootstrapping clingo (#20652) * clingo/clingo-bootstrap: added a package with option for bootstrapping clingo package builds in Release mode uses GCC options to link libstdc++ and libgcc statically * clingo-bootstrap: apple-clang options to bootstrap statically on darwin * clingo: fix the path of the Python interpreter In case multiple Python versions are in the same prefix (e.g. when clingo is built against an external Python), it may happen that the Python used by CMake does not match the corresponding node in the current spec. This is fixed here by defining "Python_EXECUTABLE" properly as a hint to CMake. * clingo: the commit for "spack" version has been updated. * clingo: fix typo (#22444) * clingo-bootstrap: account for cray platform (#22460) (cherry picked from commit 138312efabd534fa42d1a16e172e859f0d2b5842) * Bootstrap clingo from sources (#21446) * Allow the bootstrapping of clingo from sources Allow python builds with system python as external for MacOS * Ensure consistent configuration when bootstrapping clingo This commit uses context managers to ensure we can bootstrap clingo using a consistent configuration regardless of the use case being managed. * Github actions: test clingo with bootstrapping from sources * Add command to inspect and clean the bootstrap store Prevent users to set the install tree root to the bootstrap store * clingo: documented how to bootstrap from sources Co-authored-by: Gregory Becker <becker33@llnl.gov> (cherry picked from commit 10e9e142b75c6ca8bc61f688260c002201cc1b22) * bootstrap: account for platform specific configuration scopes (#22489) This change accounts for platform specific configuration scopes, like ~/.spack/linux, during bootstrapping. These scopes were previously not accounted for and that was causing issues e.g. when searching for compilers. (cherry picked from commit 413c422e53843a9e33d7b77a8c44dcfd4bf701be) * concretizer: unify logic for spec conditionals This builds on #20638 by unifying all the places in the concretizer where things are conditional on specs. Previously, we duplicated a common spec conditional pattern for dependencies, virtual providers, conflicts, and externals. That was introduced in #20423 and refined in #20507, and roughly looked as follows. Given some directives in a package like: ```python depends_on("foo@1.0+bar", when="@2.0+variant") provides("mpi@2:", when="@1.9:") ``` We handled the `@2.0+variant` and `@1.9:` parts by generating generated `dependency_condition()`, `required_dependency_condition()`, and `imposed_dependency_condition()` facts to trigger rules like this: ```prolog dependency_conditions_hold(ID, Parent, Dependency) :- attr(Name, Arg1) : required_dependency_condition(ID, Name, Arg1); attr(Name, Arg1, Arg2) : required_dependency_condition(ID, Name, Arg1, Arg2); attr(Name, Arg1, Arg2, Arg3) : required_dependency_condition(ID, Name, Arg1, Arg2, Arg3); dependency_condition(ID, Parent, Dependency); node(Parent). ``` And we handled `foo@1.0+bar` and `mpi@2:` parts ("imposed constraints") like this: ```prolog attr(Name, Arg1, Arg2) :- dependency_conditions_hold(ID, Package, Dependency), imposed_dependency_condition(ID, Name, Arg1, Arg2). attr(Name, Arg1, Arg2, Arg3) :- dependency_conditions_hold(ID, Package, Dependency), imposed_dependency_condition(ID, Name, Arg1, Arg2, Arg3). ``` These rules were repeated with different input predicates for requirements (e.g., `required_dependency_condition`) and imposed constraints (e.g., `imposed_dependency_condition`) throughout `concretize.lp`. In #20638 it got to be a bit confusing, because we used the same `dependency_condition_holds` predicate to impose constraints on conditional dependencies and virtual providers. So, even though the pattern was repeated, some of the conditional rules were conjoined in a weird way. Instead of repeating this pattern everywhere, we now have *one* set of consolidated rules for conditions: ```prolog condition_holds(ID) :- condition(ID); attr(Name, A1) : condition_requirement(ID, Name, A1); attr(Name, A1, A2) : condition_requirement(ID, Name, A1, A2); attr(Name, A1, A2, A3) : condition_requirement(ID, Name, A1, A2, A3). attr(Name, A1) :- condition_holds(ID), imposed_constraint(ID, Name, A1). attr(Name, A1, A2) :- condition_holds(ID), imposed_constraint(ID, Name, A1, A2). attr(Name, A1, A2, A3) :- condition_holds(ID), imposed_constraint(ID, Name, A1, A2, A3). ``` this allows us to use `condition(ID)` and `condition_holds(ID)` to encapsulate the conditional logic on specs in all the scenarios where we need it. Instead of defining predicates for the requirements and imposed constraints, we generate the condition inputs with generic facts, and define predicates to associate the condition ID with a particular scenario. So, now, the generated facts for a condition look like this: ```prolog condition(121). condition_requirement(121,"node","cairo"). condition_requirement(121,"variant_value","cairo","fc","True"). imposed_constraint(121,"version_satisfies","fontconfig","2.10.91:"). dependency_condition(121,"cairo","fontconfig"). dependency_type(121,"build"). dependency_type(121,"link"). ``` The requirements and imposed constraints are generic, and we associate them with their meaning via the id. Here, `dependency_condition(121, "cairo", "fontconfig")` tells us that condition 121 has to do with the dependency of `cairo` on `fontconfig`, and the conditional dependency rules just become: ```prolog dependency_holds(Package, Dependency, Type) :- dependency_condition(ID, Package, Dependency), dependency_type(ID, Type), condition_holds(ID). ``` Dependencies, virtuals, conflicts, and externals all now use similar patterns, and the logic for generating condition facts is common to all of them on the python side, as well. The more specific routines like `package_dependencies_rules` just call `self.condition(...)` to get an id and generate requirements and imposed constraints, then they generate their extra facts with the returned id, like this: ```python def package_dependencies_rules(self, pkg, tests): """Translate 'depends_on' directives into ASP logic.""" for _, conditions in sorted(pkg.dependencies.items()): for cond, dep in sorted(conditions.items()): condition_id = self.condition(cond, dep.spec, pkg.name) # create a condition and get its id self.gen.fact(fn.dependency_condition( # associate specifics about the dependency w/the id condition_id, pkg.name, dep.spec.name )) # etc. ``` - [x] unify generation and logic for conditions - [x] use unified logic for dependencies - [x] use unified logic for virtuals - [x] use unified logic for conflicts - [x] use unified logic for externals LocalWords: concretizer mpi attr Arg concretize lp cairo fc fontconfig LocalWords: virtuals def pkg cond dep fn refactor github py * bugfix: do not generate dep conditions when no dependency We only consider test dependencies some of the time. Some packages are *only* test dependencies. Spack's algorithm was previously generating dependency conditions that could hold, *even* if there was no potential dependency type. - [x] change asp.py so that this can't happen -- we now only generate dependency types for possible dependencies. * bugfix: allow imposed constraints to be overridden in special cases In most cases, we want condition_holds(ID) to imply any imposed constraints associated with the ID. However, the dependency relationship in Spack is special because it's "extra" conditional -- a dependency *condition* may hold, but we have decided that externals will not have dependencies, so we need a way to avoid having imposed constraints appear for nodes that don't exist. This introduces a new rule that says that constraints are imposed *unless* we define `do_not_impose(ID)`. This allows rules like dependencies, which rely on more than just spec conditions, to cancel imposed constraints. We add one special case for this: dependencies of externals. * spack location: bugfix for out of source build dirs (#22348) * Channelflow: Fix the package. (#22483) A search and replace went wrong in 2264e30d99d8b9fbdec8fa69b594e53d8ced15a1. Thanks to @wadudmiah who reported this issue. * Make SingleFileScope able to repopulate the cache after clearing it (#22559) fixes #22547 SingleFileScope was not able to repopulate its cache before this change. This was affecting the configuration seen by environments using clingo bootstrapped from sources, since the bootstrapping operation involved a few cache invalidation for config files. * ASP-based solver: model disjoint sets for multivalued variants (#22534) * ASP-based solver: avoid adding values to variants when they're set fixes #22533 fixes #21911 Added a rule that prevents any value to slip in a variant when the variant is set explicitly. This is relevant for multi-valued variants, in particular for those that have disjoint sets of values. * Ensure disjoint sets have a clear semantics for external packages * clingo: modify recipe for bootstrapping (#22354) * clingo: modify recipe for bootstrapping Modifications: - clingo builds with shared Python only if ^python+shared - avoid building the clingo app for bootstrapping - don't link to libpython when bootstrapping * Remove option that breaks on linux * Give more hints for the current Python * Disable CLINGO_BUILD_PY_SHARED for bootstrapping * bootstrapping: try to detect the current python from std library This is much faster than calling external executables * Fix compatibility with Python 2.6 * Give hints on which compiler and OS to use when bootstrapping This change hints which compiler to use for bootstrapping clingo (either GCC or Apple Clang on MacOS). On Cray platforms it also hints to build for the frontend system, where software is meant to be installed. * Use spec_for_current_python to constrain module requirement (cherry picked from commit d5fa509b072f0e58f00eaf81c60f32958a9f1e1d) * Externals are preferred even when they have non-default variant values fixes #22596 Variants which are specified in an external spec are not scored negatively if they encode a non-default value. * Enforce uniqueness of the version_weight atom per node fixes #22565 This change enforces the uniqueness of the version_weight atom per node(Package) in the DAG. It does so by applying FTSE and adding an extra layer of indirection with the possible_version_weight/2 atom. Before this change it may have happened that for the same node two different version_weight/2 were in the answer set, each of which referred to a different spec with the same version, and their weights would sum up. This lead to unexpected result like preferring to build a new version of an external if the external version was older. * bugfix for active when pkg is already active error (#22587) * bugfix for active when pkg is already active error Co-authored-by: Greg Becker <becker33@llnl.gov> * Fix clearing cache of InternalConfigScope (#22609) Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Bootstrap: add _builtin config scope (#22610) (cherry picked from commit a37c916dff5a5c6e72f939433931ab69dfd731bd) * Bootstrapping: swap store before configuration (#22631) fixes #22294 A combination of the swapping order for global variables and the fact that most of them are lazily evaluated resulted in custom install tree not being taken into account if clingo had to be bootstrapped. This commit fixes that particular issue, but a broader refactor may be needed to ensure that similar situations won't affect us in the future. * Remove erroneous warnings about quotes for from_source_file (#22767) * "spack build-env" searches env for relevant spec (#21642) If you install packages using spack install in an environment with complex spec constraints, and the install fails, you may want to test out the build using spack build-env; one issue (particularly if you use concretize: together) is that it may be hard to pass the appropriate spec that matches what the environment is attempting to install. This updates the build-env command to default to pulling a matching spec from the environment rather than concretizing what the user provides on the command line independently. This makes a similar change to spack cd. If the user-provided spec matches multiple specs in the environment, then these commands will now report an error and display all matching specs (to help the user specify). Co-authored-by: Gregory Becker <becker33@llnl.gov> * ASP-based solver: assign OS correctly with inheritance from parent (#22896) fixes #22871 When in presence of multiple choices for the operating system we were lacking a rule to derive the node OS if it was inherited. * Externals with merged prefixes (#22653) We remove system paths from search variables like PATH and from -L options because they may contain many packages and could interfere with Spack-built packages. External packages may be installed to prefixes that are not actually system paths but are still "merged" in the sense that many other packages are installed there. To avoid conflicts, this PR places all external packages at the end of search paths. * ASP-based solver: suppress warnings when constructing facts (#23090) fixes #22786 Trying to get optimization flags for a specific target from a compiler may trigger warnings. In the context of constructing facts for the ASP-based solver we don't want to show these warnings to the user, so here we simply ignore them. * Use Python's built-in machinery to import compilers (#23290) * Add "spack [cd|location] --source-dir" (#22321) * spack location: fix usage without args (#22755) * Import hooks using Python's built-in machinery (#23288) The function we coded in Spack to load Python modules with arbitrary names from a file seem to have issues with local imports. For loading hooks though it is unnecessary to use such functions, since we don't care to bind a custom name to a module nor we have to load it from an unknown location. This PR thus modifies spack.hook in the following ways: - Use __import__ instead of spack.util.imp.load_source (this addresses #20005) - Sync module docstring with all the hooks we have - Avoid using memoization in a module function - Marked with a leading underscore all the names that are supposed to stay local * ASP-based solver: no intermediate package for concretizing together (#23307) The ASP-based solver can natively manage cases where more than one root spec is given, and is able to concretize all the roots together (ensuring one spec per package at most). Modifications: - [x] When concretising together an environment the ASP-based solver calls directly its `solve` method rather than constructing a temporary fake root package. * ASP-based solve: minimize compiler mismatches (#23016) fixes #22718 Instead of trying to maximize the number of matches (preferred behavior), try to minimize the number of mismatches (unwanted behavior). * performance: speed up existence checks in packages (#23661) Spack doesn't require users to manually index their repos; it reindexes the indexes automatically when things change. To determine when to do this, it has to `stat()` all package files in each repository to make sure that indexes up to date with packages. We currently index virtual providers, patches by sha256, and tags on packages. When this was originally implemented, we ran the checker all the time, at startup, but that was slow (see #7587). But we didn't go far enough -- it still consults the checker and does all the stat operations just to see if a package exists (`Repo.exists()`). That might've been a wash in 2018, but as the number of packages has grown, it's gotten slower -- checking 5k packages is expensive and users see this for small operations. It's a win now to make `Repo.exists()` check files directly. **Fix:** This PR does a number of things to speed up `spack load`, `spack info`, and other commands: - [x] Make `Repo.exists()` check files directly again with `os.path.exists()` (this is the big one) - [x] Refactor `Spec.satisfies()` so that a checking for virtual packages only happens if needed (avoids some calls to exists()) - [x] Avoid calling `Repo.exists(spec)` in `Repo.get()`. `Repo.get()` will ultimately try to load a `package.py` file anyway; we can let the failure to load it indicate that the package doesn't exist, and avoid another call to exists(). - [x] Fix up some comments in spec parsing - [x] Call `UnknownPackageError` more consistently in `repo.py` * Style fixes for v0.16.2 release * Update CHANGELOG and release version for v0.16.2 * Update command to setup tutorial (#24488) * Flake8, bash completion Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com> Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Martin Aumüller <aumuell@reserv.at> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: George Hartzell <hartzell@alerce.com> Co-authored-by: MichaelLaufer <70094649+MichaelLaufer@users.noreply.github.com> Co-authored-by: michael laufer <michael.laufer@toganetworks.com> Co-authored-by: Andrew W Elble <aweits@rit.edu> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Robert Maynard <robert.maynard@kitware.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@googlemail.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: Ye Luo <xw111luoye@gmail.com> Co-authored-by: Frank Willmore <frankwillmore@gmail.com> Co-authored-by: Robert Underwood <robertu94@users.noreply.github.com> Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com> Co-authored-by: Nathan Hanford <8302958+nhanford@users.noreply.github.com> Co-authored-by: Nathan Hanford <hanford1@llnl.gov> Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Co-authored-by: Yang Zongze <yangzongze@gmail.com> Co-authored-by: mic84 <mrosso@lbl.gov> Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com> Co-authored-by: darmac <xiaojun2@hisilicon.com> Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com> Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov> Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu> Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com> Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu> Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com> Co-authored-by: QuellynSnead <quellyn@lanl.gov> Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov> Co-authored-by: Phil Tooley <32297355+ptooley@users.noreply.github.com> Co-authored-by: Josh Essman <68349992+joshessman-llnl@users.noreply.github.com> Co-authored-by: Andreas Baumbach <healther@users.noreply.github.com> Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com> Co-authored-by: Rémi Lacroix <remi.lacroix@idris.fr> Co-authored-by: Cyrus Harrison <cyrush@llnl.gov> Co-authored-by: Peter Scheibel <scheibel1@llnl.gov> Co-authored-by: Todd Gamblin <gamblin2@llnl.gov>

* py-ipykernel: fix install (#19617) There is a post-install routine in `ipykernel` that needs to be called for proper registration with jupyter. * hip support for umpire, chai, raja, camp (#19715) * create HipPackage base class and do some refactoring * comments and added conflict to raja for openmp with hip * fix error handling for spack test results command (#19987) * py-ipykernel: fix bug in phase method (#19986) * py-ipykernel: fix bug in phase method * Fix bug in executable calling * recognize macOS 11.1 as big sur (#20038) Big Sur versions go 11.0, 11.0.1, 11.1 (vs. prior versions that only used the minor component) Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> * Docs: remove duplication in Command Reference (#20021) * concretizer: treat conditional providers correctly (#20086) refers #20040 This modification emits rules like: provides_virtual("netlib-lapack","blas") :- variant_value("netlib-lapack","external-blas","False"). for packages that provide virtual dependencies conditionally instead of a fact that doesn't account for the condition. * concretizer: allow a bool to be passed as argument for tests dependencies (#20082) refers #20079 Added docstrings to 'concretize' and 'concretized' to document the format for tests. Added tests for the activation of test dependencies. * concretizer: prioritize matching compilers over newer versions (#20020) fixes #20019 Before this modification having a newer version of a node came at higher priority in the optimization than having matching compilers. This could result in unexpected configurations for packages with conflict directives on compilers of the type: conflicts('%gcc@X.Y:', when='@:A.B') where changing the compiler for just that node is preferred to lower the node version to less than 'A.B'. Now the priority has been switched so the solver will try to lower the version of the nodes in question before changing their compiler. * concretizer: treat target ranges in directives correctly (#19988) fixes #19981 This commit adds support for target ranges in directives, for instance: conflicts('+foo', when='target=x86_64:,aarch64:') If any target in a spec body is not a known target the following clause will be emitted: node_target_satisfies(Package, TargetConstraint) when traversing the spec and a definition of the clause will then be printed at the end similarly to what is done for package and compiler versions. * Typos: add missing closing parens (#20174) * concretizer: swap priority of selecting provider and default variant (#20182) refers #20040 Before this PR optimization rules would have selected default providers at a higher priority than default variants. Here we swap this priority and we consider variants that are forced by any means (root spec or spec in depends_on clause) the same as if they were with a default value. This prevents the solver from avoiding expected configurations just because they contain directives like: depends_on('pkg+foo') and `+foo` is not the default variant value for pkg. * concretizer: remove ad-hoc rule for external packages (#20193) fixes #20040 Matching compilers among nodes has been prioritized in #20020. Selection of default variants has been tuned in #20182. With this setup there is no need to have an ad-hoc rule for external packages. On the contrary it should be removed to prefer having default variant values over more external nodes in the DAG. * spec: return early from concretization if a spec is already concrete (#20196) * Fixes compile time errors (#20006) Co-authored-by: michael laufer <michael.laufer@toganetworks.com> * concretizer: don't optimize emitting version_satisfies() (#20128) When all versions were allowed a version_satisfies rule was not emitted, and this caused conditional directives to fail. * boost: disable find_package's config mode for boost prior to v1.70.0 (#20198) * Fix hipcc once more (#20095) * concretizer: try hard to infer the real version of compilers (#20099) fixes #20055 Compiler with custom versions like gcc@foo are not currently matched to the appropriate targets. This is because the version of spec doesn't match the "real" version of the compiler. This PR replicates the strategy used in the original concretizer to deal with that and tries to detect the real version of compilers if the version in the spec returns no results. * concretizer: call inject_patches_variants() on the roots of the specs (#20203) As was done in the old concretizer. Fixes an issue where conditionally patched dependencies did not show up in spec (gdal+jasper) * avoid circular import (#20236) * environment installs: fix reporting. (#20004) PR #15702 changed the invocation of the report context when installing specs, do the same when building environments. * concretizer: restrict maximizing variant values to MV variants (#20194) * concretizer: each external version is allowed by definition (#20247) Registering external versions among the lists of allowed ones generates the correct rules for `version_satisfies` * VTK-m: update to specify correct requirements to kokkos (#20097) * concretizer: refactor handling of special variants dev_build and patches Other parts of the concretizer code build up lists of things we can't know without traversing all specs and packages, and they output these list at the very end. The code for this for variant values from spec literals was intertwined with the code for traversing the input specs. This only covers the input specs and misses variant values that might come from directives in packages. - [x] move ad-hoc value handling code into spec_clauses so we do it in one place for CLI and packages - [x] move handling of `variant_possible_value`, etc. into `concretize.lp`, where we can automatically infer variant existence more concisely. - [x] simplify/clarify some of the code for variants in `spec_clauses()` * bugfix: work around issue handling packages not in any repo * concretizer: try hard to obtain all needed variant_possible_value()'s (#20102) Track all the variant values mentioned when emitting constraints, validate them and emit a fact that allows them as possible values. This modification ensures that open-ended variants (variants accepting any string or any integer) are projected to the finite set of values that are relevant for this concretization. * Tests: enable re-use of post-install tests in smoke tests (#20298) * concretizer: remove clingo command-line driver (#20362) I was keeping the old `clingo` driver code around in case we had to run using the command line tool instad of through the Python interface. So far, the command line is faster than running through Python, but I'm working on fixing that. I found that if I do this: ```python control = clingo.Control() control.load("concretize.lp") control.load("hdf5.lp") # code from spack solve --show asp hdf5 control.load("display.lp") control.ground([("base", [])]) control.solve(...) ``` It's just as fast as the command line tool. So we can always generate the code and load it manually if we need to -- we don't need two drivers for clingo. Given that the python interface is also the only way to get unsat cores, I think we pretty much have to use it. So, I'm removing the old command line driver and other unused code. We can dig it up again from the history if it is needed. * package sanity: ensure all variant defaults are allowed values (#20373) * concretizer: don't use one_of_iff for range constraints (#20383) Currently, version range constraints, compiler version range constraints, and target range constraints are implemented by generating ground rules from `asp.py`, via `one_of_iff()`. The rules look like this: ``` version_satisfies("python", "2.6:") :- 1 { version("python", "2.4"); ... } 1. 1 { version("python", "2.4"); ... } 1. :- version_satisfies("python", "2.6:"). ``` So, `version_satisfies(Package, Constraint)` is true if and only if the package is assigned a version that satisfies the constraint. We precompute the set of known versions that satisfy the constraint, and generate the rule in `SpackSolverSetup`. We shouldn't need to generate already-ground rules for this. Rather, we should leave it to the grounder to do the grounding, and generate facts so that the constraint semantics can be defined in `concretize.lp`. We can replace rules like the ones above with facts like this: ``` version_satisfies("python", "2.6:", "2.4") ``` And ground them in `concretize.lp` with rules like this: ``` 1 { version(Package, Version) : version_satisfies(Package, Constraint, Version) } 1 :- version_satisfies(Package, Constraint). version_satisfies(Package, Constraint) :- version(Package, Version), version_satisfies(Package, Constraint, Version). ``` The top rule is the same as before. It makes conditional dependencies and other places where version constraints are used work properly. Note that we do not need the cardinality constraint for the second rule -- we already have rules saying there can be only one version assigned to a package, so we can just infer from `version/2` `version_satisfies/3`. This form is also safe for grounding -- If we used the original form we'd have unsafe variables like `Constraint` and `Package` -- the original form only really worked when specified as ground to begin with. - [x] use facts instead of generating rules for package version constraints - [x] use facts instead of generating rules for compiler version constraints - [x] use facts instead of generating rules for target range constraints - [x] remove `one_of_iff()` and `iff()` as they're no longer needed * Fix comparisons for abstract specs (#20341) bug only relevant for python3 * unit-tests: ensure that installed packages can be reused (#20307) refers #20292 Added a unit test that ensures we can reuse installed packages even if in the repository variants have been removed or added. * ci: fixes for compiler bootstrapping (#17563) This PR addresses a number of issues related to compiler bootstrapping. Specifically: 1. Collect compilers to be bootstrapped while queueing in installer Compiler tasks currently have an incomplete list in their task.dependents, making those packages fail to install as they think they have not all their dependencies installed. This PR collects the dependents and sets them on compiler tasks. 2. allow boostrapped compilers to back off target Bootstrapped compilers may be built with a compiler that doesn't support the target used by the rest of the spec. Allow them to build with less aggressive target optimization settings. 3. Support for target ranges Backing off the target necessitates computing target ranges, so make Spack handle those properly. Notably, this adds an intersection method for target ranges and fixes the way ranges are satisfied and constrained on Spec objects. This PR also: - adds testing - improves concretizer handling of target ranges Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * asp: memoize the list of all target_specs to speed-up setup phase (#20473) * asp: memoize the list of all target_specs to speed-up setup phase * asp: memoize using a cache per solver object * concretizer: add #defined statements to avoid warnings. `version_satisfies/2` and `node_compiler_version_satisfies/3` are generated but need `#defined` directives to avoid " info: atom does not occur in any rule head:" warnings. * concretizer: pull _develop_specs_from_env out of main setup loop * concretizer: spec_clauses should traverse dependencies There are currently no places where we do not want to traverse dependencies in `spec_clauses()`, so simplify the logic by consolidating `spec_traverse_clauses()` with `spec_clauses()`. * concretizer: move conditional dependency logic into `concretize.lp` Continuing to convert everything in `asp.py` into facts, make the generation of ground rules for conditional dependencies use facts, and move the semantics into `concretize.lp`. This is probably the most complex logic in Spack, as dependencies can be conditional on anything, and we need conditional ASP rules to accumulate and map all the dependency conditions to spec attributes. The logic looks complicated, but essentially it accumulates any constraints associated with particular conditions into a fact associated with the condition by id. Then, if *any* condition id's fact is True, we trigger the dependency. This simplifies the way `declared_dependency()` works -- the dependency is now declared regardless of whether it is conditional, and the conditions are handled by `dependency_condition()` facts. * concretizer: avoid redundant grounding on dependency types * concretizer: emit facts for constraints on imposed dependencies * concretizer: emit facts for integrity constraints * concretizer: fix failing unit tests * concretizer: optimized loop on node platforms We can speed-up the computation by avoiding a double loop in a cardinality constraint and enforcing the rule instead as an integrity constraint. * concretizer: optimize loop on compiler version Similar to the optimization on platform * concretizer: refactor conditional rules to be less repetitious (#20507) We have to repeat all the spec attributes in a number of places in `concretize.lp`, and Spack has a fair number of spec attributes. If we instead add some rules up front that establish equivalencies like this: ``` node(Package) :- attr("node", Package). attr("node", Package) :- node(Package). version(Package, Version) :- attr("version", Package, Version). attr("version", Package, Version) :- version(Package, Version). ``` We can rewrite most of the repetitive conditions with `attr` and repeat only for each arity (there are only 3 arities for spec attributes so far) as opposed to each spec attribute. This makes the logic easier to read and the rules easier to follow. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Add Intel oneAPI packages (#20411) This creates a set of packages which all use the same script to install components of Intel oneAPI. This includes: * An inheritable IntelOneApiPackage which knows how to invoke the installation script based on which components are requested * For components which include headers/libraries, an inheritable IntelOneApiLibraryPackage is provided to locate them * Individual packages for DAL, DNN, TBB, etc. * A package for the Intel oneAPI compilers (icx/ifx). This also includes icc/ifortran but these are not currently detected in this PR * bugfix: do not write empty default dicts/lists in envs (#20526) Environment yaml files should not have default values written to them. To accomplish this, we change the validator to not add the default values to yaml. We rely on the code to set defaults for all values (and use defaulting getters like dict.get(key, default)). Includes regression test. * concretizer: generate facts for externals Generate only facts for external specs. Substitute the use of already grounded rules with non-grounded rules in concretize.lp * bugfix: infinite loop when building a set from incomplete specs (#20649) This code in `SpecBuilder.build_specs()` introduced in #20203, can loop seemingly interminably for very large specs: ```python set([spec.root for spec in self._specs.values()]) ``` It's deceptive, because it seems like there must be an issue with `spec.root`, but that works fine. It's building the set afterwards that takes forever, at least on `r-rminer`. Currently if you try running `spack solve r-rminer`, it loops infinitely and spins up your fan. The issue (I think) is that the spec is not yet complete when this is run, and something is going wrong when constructing and comparing so many values produced by `_cmp_key()`. We can investigate the efficiency of `_cmp_key()` separately, but for now, the fix is: ```python roots = [spec.root for spec in self._specs.values()] roots = dict((id(r), r) for r in roots) ``` We know the specs in `self._specs` are distinct (they just came out of the solver), so we can just use their `id()` to unique them here. This gets rid of the infinite loop. * concretizer: more detailed section headers in concretize.lp * concretizer: make _condtion_id_counter an iterator * concretizer: consolidate handling of virtuals into spec_clauses * concretizer: convert virtuals to facts; move all rules to `concretize.lp` This converts the virtual handling in the new concretizer from already-ground rules to facts. This is the last thing that needs to be refactored, and it converts the entire concretizer to just use facts. The previous way of handling virtuals hinged on rules involving `single_provider_for` facts that were tied to the virtual and a version range. The new method uses the condition pattern we've been using for dependencies, externals, and conflicts. To handle virtuals as conditions, we impose constraints on "fake" virtual specs in the logic program. i.e., `version_satisfies("mpi", "2.0:", "2.0")` is legal whereas before we wouldn't have seen something like this. Currently, constriants are only handled on versions -- we don't handle variants or anything else yet, but they key change here is that we *could*. For a long time, virtual handling in Spack has only dealt with versions, and we'd like to be able to handle variants as well. We could easily add an integrity constraint to handle variants like the one we use for versions. One issue with the implementation here is that virtual packages don't actually declare possible versions like regular packages do. To get around that, we implement an integrity constraint like this: :- virtual_node(Virtual), version_satisfies(Virtual, V1), version_satisfies(Virtual, V2), not version_constraint_satisfies(Virtual, V1, V2). This requires us to compare every version constraint to every other, both in program generation and within the concretizer -- so there's a potentially quadratic evaluation time on virtual constraints because we don't have a real version to "anchor" things to. We just say that all the constraints need to agree for the virtual constraint to hold. We can investigate adding synthetic versions for virtuals in the future, to speed this up. * concretizer: remove rule generation code from concretizer Our program only generates facts now, so remove all unused code related to generating cardinality constraints and rules. * concretizer: simplify handling of virtual version constraints Previously, the concretizer handled version constraints by comparing all pairs of constraints and ensuring they satisfied each other. This led to INCONSISTENT ressults from clingo, due to ambiguous semantics like: version_constraint_satisfies("mpi", ":1", ":3") version_constraint_satisfies("mpi", ":3", ":1") To get around this, we introduce possible (fake) versions for virtuals, based on their constraints. Essentially, we add any Versions, VersionRange endpoints, and all such Versions and endpoints from VersionLists to the constraint. Virtuals will have one of these synthetic versions "picked" by the solver. This also allows us to remove a special case from handling of `version_satisfies/3` -- virtuals now work just like regular packages. * concretizer: use consistent naming for compiler predicates (#20677) Every other predicate in the concretizer uses a `_set` suffix to implement user- or package-supplied settings, but compiler settings use a `_hard` suffix for this. There's no difference in how they're used, so make the names the same. - [x] change `node_compiler_hard` to `node_compiler_set` - [x] change `node_compiler_version_hard` to `node_compiler_version_set` * concretizer: make rules on virtual packages more linear fixes #20679 In this refactor we have a single cardinality rule on the provider, which triggers a rule transforming a dependency on a virtual package into a dependency on the provider of the virtual. * Remove hard-coded standard C++ library selection and add more releases in llvm package (#19933) * Restore OS based Clang default choice of C++ standard library. * Add LLVM 11.0.1 release * fix mpi lib paths, add virtual provides (#20693) * intel-oneapi-compilers package: correct module file (#20686) This properly sets PATH/CPATH/LIBRARY_PATH etc. to make the Spack-generated module file for intel-oneapi-compilers useful (without this, 'icx' would not be found after loading the module file for intel-oneapi-compilers). * intel-oneapi-mpi: virtual provider support (#20732) Set up environment and dependent packages properly when building with intel-oneapi-mpi as a dependency MPI provider (e.g. point to mpicc compiler wrapper). * restore ability of dev-build to skip patches (#20351) At some point in the past, the skip_patch argument was removed from the call to package.do_install() this broke the --skip-patch flag on the dev-build command. * libyogrt: remove conflicts triggered by an invalid value (#20794) fixes #20611 The conflict was triggered by an invalid value of the 'scheduler' variant. This causes Spack to error when libyogrt facts are validated by the ASP-based concretizer. * concretizer: dependency conditions cannot hold if package is external fixes #20736 Before this one line fix we were erroneously deducing that dependency conditions hold even if a package was external. This may result in answer sets that contain imposed conditions on a node without the node being present in the DAG, hence #20736. * concretizer: require at least a dependency type to say the dependency holds fixes #20784 Similarly to the previous bug, here we were deducing conditions to be imposed on nodes that were not part of the DAG. * py-hovorod: fix typo on variant name in conflicts directive (#20906) * [WIP] relocate.py: parallelize test replacement logic (#19690) * sbang pushed back to callers; star moved to util.lang * updated unit test * sbang test moved; local tests pass Co-authored-by: Nathan Hanford <hanford1@llnl.gov> * store sbang_install_path in buildinfo, use for subsequent relocation (#20768) * Print groups properly for spack find -d (#20028) * llvm: "master" branch is now "main" branch (#21411) * add intel oneapi to compiler/pkg translations (#21448) * adding environment to OneMKL packages so that examples will build (#21377) * intel-oneapi-compilers: add to LD_LIBRARY_PATH so that it finds libimf.so (#20717) * add to LD_LIBRARY_PATH so that it finds libimf.so * amrex: fix handling of CUDA arch (#20786) * amrex: fix handling of CUDA arch * amrex: fix style * amrex: fix bug * Update var/spack/repos/builtin/packages/amrex/package.py * Update var/spack/repos/builtin/packages/amrex/package.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * ecp-data-vis-sdk: Combine the vis and io SDK packages (#20737) This better enables the collective set to be deployed togethor satisfying eachothers dependencies * r-sf: fix dependency error (#20898) * improve documentation for Rocm (hip amd builds) (#20812) * improve documentation * astyle: Fix makefile for install parameter (#20899) * llvm-doe: added new package (#20719) The package contains duplicated code from llvm/package.py, will supersede solve. * r-e1071: added v1.7-4 (#20891) * r-diffusionmap: added v1.2.0 (#20881) * r-covr: added v3.5.1 (#20868) * r-class: added v7.3-17 (#20856) * py-h5py: HDF5_DIR is needed for ~mpi too (#20905) For the `~mpi` variant, the environment variable `HDF5_DIR` is still required. I moved this command out of the `+mpi` conditional. * py-hovorod: fix typo on variant name in conflicts directive (#20906) * fujitsu-fftw: Add new package (#20824) * pocl: added v1.6 (#20932) Made version 1.5 or lower conflicts with a64fx. * PCL: add new package (#20933) * r-rle: new package (#20916) Common 'base' and 'stats' methods for 'rle' objects, aiming to make it possible to treat them transparently as vectors. * r-ellipsis: added v0.3.1 (#20913) * libconfig: add build dependency on texinfo (#20930) * r-flexmix: add v2.3-17 (#20924) * r-fitdistrplus: add v1.1-3 (#20923) * r-fit-models: add v0.64 (#20922) * r-fields: add v11.6 (#20921) * r-fftwtools: add v0.9-9 (#20920) * r-farver: add v2.0.3 (#20919) * r-expm: add v0.999-6 (#20918) * cln: add build dependency on texinfo (#20928) * r-expint: add v0.1-6 (#20917) * r-envstats: add v2.4.0 (#20915) * r-energy: add v1.7-7 (#20914) * r-ellipse: add v0.4.2 (#20912) * py-fiscalyear: add v0.3.0 (#20911) * r-ecp: add v3.1.3 (#20910) * r-plotmo: add v3.6.0 (#20909) * Improve gcc detection in llvm. (#20189) Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> * hatchet: updated urls (#20908) * py-anuga: add new package (#20782) * libvips: added v8.10.5 (#20902) * libzmq: add platform conditions to libbsd dependency (#20893) * r-dtw: add v1.22-3 (#20890) * r-dt: add v0.17 (#20889) * r-dosnow: add v1.0.19 (#20888) * add version 1.0.16 to r-doparallel (#20886) * add version 1.3.7 to r-domc (#20885) * add version 0.9-15 to r-diversitree (#20884) * add version 1.3-3 to r-dismo (#20883) * add version 0.6.27 to r-digest (#20882) * add version 1.5 to r-rngtools (#20887) * add version 1.5.8 to r-dicekriging (#20877) * add version 1.4.2 to r-httr (#20876) * add version 1.28 to r-desolve (#20875) * add version 2.2-5 to r-deoptim (#20874) * add version 0.2-3 to r-deldir (#20873) * add version 1.0.0 to r-crul (#20870) * add version 1.1.0.1 to r-crosstalk (#20869) * add version 1.0-1 to r-copula (#20867) * add version 5.0.2 to r-rcppparallel (#20866) * add version 2.0-1 to r-compositions (#20865) * add version 0.4.10 to r-rlang (#20796) * add version 0.3.6 to r-vctrs (#20878) * amrex: add ROCm support (#20809) * add version 2.0-0 to r-colorspace (#20864) * add version 1.3-1 to r-coin (#20863) * add version 0.19-4 to r-coda (#20862) * add version 1.3.7 to r-clustergeneration (#20861) * add version 0.3-58 to r-clue (#20860) * add version 0.7.1 to r-clipr (#20859) * add version 2.2.0 to r-cli (#20858) * add version 0.4-3 to r-classint (#20857) * add version 0.1.2 to r-globaloptions (#20855) * add version 2.3-56 to r-chron (#20854) * add version 0.4.10 to r-checkpoint (#20853) * add version 2.0.0 to r-checkmate (#20852) * add version 1.18.1 to r-catools (#20850) * add version 1.2.2.2 to r-modelmetrics (#20849) * add version 3.0-4 to r-cardata (#20847) * add version 1.0.1 to r-caracas (#20846) * r-lifecycle: new package at v0.2.0 (#20845) * add version 3.0-10 to r-car (#20844) * add version 3.4.5 to r-processx (#20843) * add version 1.5-12.2 to r-cairo (#20842) * add version 0.2.3 to r-cubist (#20841) * add version 2.6 to r-rmarkdown (#20838) * add version 1.2.1 to r-blob (#20819) * add version 4.0.4 to r-bit (#20818) * add version 2.4-1 to r-bio3d (#20816) * add version 0.4.2.3 to r-bibtex (#20815) * add version 3.1-4 to r-bayesm (#20807) * add version 1.2.1 to r-backports (#20806) * add version 2.0.3 to r-argparse (#20805) * add version 5.4-1 to r-ape (#20804) * add version 0.8-18 to r-amap (#20803) * r-pixmap: added new package (#20795) * zoltan: source code location change (#20787) * refactor path logic * added some paths to make compilers and libs discoverable * add to LD_LIBRARY_PATH so that it finds libimf.so and cleanup PEP8 * refactor path logic * adding paths to LIBRARY_PATH so compiler wrappers will find -lmpi * added vals for CC=icx, CXX=icpx, FC=ifx to generated module * back out changes to intel-oneapi-mpi, save for separate PR * Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py path is joined in _ld_library_path() Co-authored-by: Robert Cohn <rscohn2@gmail.com> * set absolute paths to icx,icpx,ifx * dang close parenthesis Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: mic84 <mrosso@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com> Co-authored-by: darmac <xiaojun2@hisilicon.com> Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com> Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com> Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov> Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu> Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com> Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com> Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu> Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com> Co-authored-by: QuellynSnead <quellyn@lanl.gov> * intel-oneapi-compilers/mpi: add module support (#20808) Facilitate running intel-oneapi-mpi outside of Spack (set PATH, LD_LIBRARY_PATH, etc. appropriately). Co-authored-by: Robert Cohn <rscohn2@gmail.com> * apple-clang: add correct path to compiler wrappers (#21662) Follow-up to #17110 ### Before ```bash CC=/Users/Adam/spack/lib/spack/env/clang/clang; export CC SPACK_CC=/usr/bin/clang; export SPACK_CC PATH=...:/Users/Adam/spack/lib/spack/env/apple-clang:/Users/Adam/spack/lib/spack/env/case-insensitive:/Users/Adam/spack/lib/spack/env:...; export PATH ``` ### After ```bash CC=/Users/Adam/spack/lib/spack/env/clang/clang; export CC SPACK_CC=/usr/bin/clang; export SPACK_CC PATH=...:/Users/Adam/spack/lib/spack/env/clang:/Users/Adam/spack/lib/spack/env/case-insensitive:/Users/Adam/spack/lib/spack/env:...; export PATH ``` `CC` and `SPACK_CC` were being set correctly, but `PATH` was using the name of the compiler `apple-clang` instead of `clang`. For most packages, since `CC` was set correctly, nothing broke. But for packages using `Makefiles` that set `CC` based on `which clang`, it was using the system compilers instead of the compiler wrappers. Discovered when working on `py-xgboost@0.90`. An alternative fix would be to copy the symlinks in `env/clang` to `env/apple-clang`. Let me know if you think there's a better way to do this, or to test this. * Resolve (post-cherry-picking) flake8 errors * Update CHANGELOG and release version * updates for new tutorial update s3 bucket update tutorial branch * update tutorial public key * respect -k/verify-ssl-false in _existing_url method (#21864) * use package supplied autogen.sh (#20319) * Python 3.10 support: collections.abc (#20441) (cherry picked from commit 40a40e0265d6704a7836aeb30a776d66da8f7fe6) * concretizer: simplify "fact" method (#21148) The "fact" method before was dealing with multiple facts registered per call, which was used when we were emitting grounded rules from knowledge of the problem instance. Now that the encoding is changed we can simplify the method to deal only with a single fact per call. (cherry picked from commit ba42c36f00fe40c047121a32117018eb93e0c4b1) * Improve error message for inconsistencies in package.py (#21811) * Improve error message for inconsistencies in package.py Sometimes directives refer to variants that do not exist. Make it such that: 1. The name of the variant 2. The name of the package which is supposed to have such variant 3. The name of the package making this assumption are all printed in the error message for easier debugging. * Add unit tests (cherry picked from commit 7226bd64dc3b46a1ed361f1e9d7fb4a2a5b65200) * Updates to support clingo-cffi (#20657) * Support clingo when used with cffi Clingo recently merged in a new Python module option based on cffi. Compatibility with this module requires a few changes to spack - it does not automatically convert strings/ints/etc to Symbol and clingo.Symbol.string throws on failure. manually convert str/int to clingo.Symbol types catch stringify exceptions add job for clingo-cffi to Spack CI switch to potassco-vendored wheel for clingo-cffi CI on_unsat argument when cffi (cherry picked from commit 93ed1a410c4a202eab3a68769fd8c0d4ff8b1c8e) * Run clingo-cffi tests in a container (#21913) There clingo-cffi job has two issues to be solved: 1. It uses the default concretizer 2. It requires a package from https://test.pypi.org/simple/ The former can be fixed by setting the SPACK_TEST_SOLVER environment variable to "clingo". The latter though requires clingo-cffi to be pushed to a more stable package index (since https://test.pypi.org/simple/ is meant as a scratch version of PyPI that can be wiped at any time). For the time being run the tests in a container. Switch back to PyPI whenever a new official version of clingo will be released. * repo: generalize "swap" context manager to also accept paths The method is now called "use_repositories" and makes it clear in the docstring that it accepts as arguments either Repo objects or paths. Since there was some duplication between this contextmanager and "use_repo" in the testing framework, remove the latter and use spack.repo.use_repositories across the entire code base. Make a few adjustment to MockPackageMultiRepo, since it was stating in the docstring that it was supposed to mock spack.repo.Repo and was instead mocking spack.repo.RepoPath. (cherry picked from commit 1a8963b0f4c11c4b7ddd347e6cd95cdc68ddcbe0) * Move context manager to swap the current store into spack.store The context manager can be used to swap the current store temporarily, for any use case that may need it. (cherry picked from commit cb2c233a97073f8c5d89581ee2a2401fef5f878d) * Move context manager to swap the current configuration into spack.config The context manager can be used to swap the current configuration temporarily, for any use case that may need it. (cherry picked from commit 553d37a6d62b05f15986a702394f67486fa44e0e) * bugfix for target adjustments on target ranges (#20537) (cherry picked from commit 61c1b71d38e62a5af81b3b7b8a8d12b954d99f0a) * Added a context manager to swap architectures This solves a few FIXMEs in conftest.py, where we were manipulating globals and seeing side effects prior to registering fixtures. This commit solves the FIXMEs, but introduces a performance regression on tests that may need to be investigated (cherry picked from commit 4558dc06e21e01ab07a43737b8cb99d1d69abb5d) * make `spack fetch` work with environments (#19166) * make `spack fetch` work with environments * previously: `spack fetch` required the explicit statement of the specs to be fetched, even when in an environment * now: if there is no spec(s) provided to `spack fetch` we check if an environment is active and if yes we fetch all uninstalled specs. * clingo: prefer master branch Most people installing `clingo` with Spack are going to be doing it to use the new concretizer, and that requires the `master` branch. - [x] make `master` the default so we don't have to keep telling people to install `clingo@master`. We'll update the preferred version when there's a new release. * Clingo: fix missing import (#21364) * clingo: added a package with option for bootstrapping clingo (#20652) * clingo/clingo-bootstrap: added a package with option for bootstrapping clingo package builds in Release mode uses GCC options to link libstdc++ and libgcc statically * clingo-bootstrap: apple-clang options to bootstrap statically on darwin * clingo: fix the path of the Python interpreter In case multiple Python versions are in the same prefix (e.g. when clingo is built against an external Python), it may happen that the Python used by CMake does not match the corresponding node in the current spec. This is fixed here by defining "Python_EXECUTABLE" properly as a hint to CMake. * clingo: the commit for "spack" version has been updated. * clingo: fix typo (#22444) * clingo-bootstrap: account for cray platform (#22460) (cherry picked from commit 138312efabd534fa42d1a16e172e859f0d2b5842) * Bootstrap clingo from sources (#21446) * Allow the bootstrapping of clingo from sources Allow python builds with system python as external for MacOS * Ensure consistent configuration when bootstrapping clingo This commit uses context managers to ensure we can bootstrap clingo using a consistent configuration regardless of the use case being managed. * Github actions: test clingo with bootstrapping from sources * Add command to inspect and clean the bootstrap store Prevent users to set the install tree root to the bootstrap store * clingo: documented how to bootstrap from sources Co-authored-by: Gregory Becker <becker33@llnl.gov> (cherry picked from commit 10e9e142b75c6ca8bc61f688260c002201cc1b22) * bootstrap: account for platform specific configuration scopes (#22489) This change accounts for platform specific configuration scopes, like ~/.spack/linux, during bootstrapping. These scopes were previously not accounted for and that was causing issues e.g. when searching for compilers. (cherry picked from commit 413c422e53843a9e33d7b77a8c44dcfd4bf701be) * concretizer: unify logic for spec conditionals This builds on #20638 by unifying all the places in the concretizer where things are conditional on specs. Previously, we duplicated a common spec conditional pattern for dependencies, virtual providers, conflicts, and externals. That was introduced in #20423 and refined in #20507, and roughly looked as follows. Given some directives in a package like: ```python depends_on("foo@1.0+bar", when="@2.0+variant") provides("mpi@2:", when="@1.9:") ``` We handled the `@2.0+variant` and `@1.9:` parts by generating generated `dependency_condition()`, `required_dependency_condition()`, and `imposed_dependency_condition()` facts to trigger rules like this: ```prolog dependency_conditions_hold(ID, Parent, Dependency) :- attr(Name, Arg1) : required_dependency_condition(ID, Name, Arg1); attr(Name, Arg1, Arg2) : required_dependency_condition(ID, Name, Arg1, Arg2); attr(Name, Arg1, Arg2, Arg3) : required_dependency_condition(ID, Name, Arg1, Arg2, Arg3); dependency_condition(ID, Parent, Dependency); node(Parent). ``` And we handled `foo@1.0+bar` and `mpi@2:` parts ("imposed constraints") like this: ```prolog attr(Name, Arg1, Arg2) :- dependency_conditions_hold(ID, Package, Dependency), imposed_dependency_condition(ID, Name, Arg1, Arg2). attr(Name, Arg1, Arg2, Arg3) :- dependency_conditions_hold(ID, Package, Dependency), imposed_dependency_condition(ID, Name, Arg1, Arg2, Arg3). ``` These rules were repeated with different input predicates for requirements (e.g., `required_dependency_condition`) and imposed constraints (e.g., `imposed_dependency_condition`) throughout `concretize.lp`. In #20638 it got to be a bit confusing, because we used the same `dependency_condition_holds` predicate to impose constraints on conditional dependencies and virtual providers. So, even though the pattern was repeated, some of the conditional rules were conjoined in a weird way. Instead of repeating this pattern everywhere, we now have *one* set of consolidated rules for conditions: ```prolog condition_holds(ID) :- condition(ID); attr(Name, A1) : condition_requirement(ID, Name, A1); attr(Name, A1, A2) : condition_requirement(ID, Name, A1, A2); attr(Name, A1, A2, A3) : condition_requirement(ID, Name, A1, A2, A3). attr(Name, A1) :- condition_holds(ID), imposed_constraint(ID, Name, A1). attr(Name, A1, A2) :- condition_holds(ID), imposed_constraint(ID, Name, A1, A2). attr(Name, A1, A2, A3) :- condition_holds(ID), imposed_constraint(ID, Name, A1, A2, A3). ``` this allows us to use `condition(ID)` and `condition_holds(ID)` to encapsulate the conditional logic on specs in all the scenarios where we need it. Instead of defining predicates for the requirements and imposed constraints, we generate the condition inputs with generic facts, and define predicates to associate the condition ID with a particular scenario. So, now, the generated facts for a condition look like this: ```prolog condition(121). condition_requirement(121,"node","cairo"). condition_requirement(121,"variant_value","cairo","fc","True"). imposed_constraint(121,"version_satisfies","fontconfig","2.10.91:"). dependency_condition(121,"cairo","fontconfig"). dependency_type(121,"build"). dependency_type(121,"link"). ``` The requirements and imposed constraints are generic, and we associate them with their meaning via the id. Here, `dependency_condition(121, "cairo", "fontconfig")` tells us that condition 121 has to do with the dependency of `cairo` on `fontconfig`, and the conditional dependency rules just become: ```prolog dependency_holds(Package, Dependency, Type) :- dependency_condition(ID, Package, Dependency), dependency_type(ID, Type), condition_holds(ID). ``` Dependencies, virtuals, conflicts, and externals all now use similar patterns, and the logic for generating condition facts is common to all of them on the python side, as well. The more specific routines like `package_dependencies_rules` just call `self.condition(...)` to get an id and generate requirements and imposed constraints, then they generate their extra facts with the returned id, like this: ```python def package_dependencies_rules(self, pkg, tests): """Translate 'depends_on' directives into ASP logic.""" for _, conditions in sorted(pkg.dependencies.items()): for cond, dep in sorted(conditions.items()): condition_id = self.condition(cond, dep.spec, pkg.name) # create a condition and get its id self.gen.fact(fn.dependency_condition( # associate specifics about the dependency w/the id condition_id, pkg.name, dep.spec.name )) # etc. ``` - [x] unify generation and logic for conditions - [x] use unified logic for dependencies - [x] use unified logic for virtuals - [x] use unified logic for conflicts - [x] use unified logic for externals LocalWords: concretizer mpi attr Arg concretize lp cairo fc fontconfig LocalWords: virtuals def pkg cond dep fn refactor github py * bugfix: do not generate dep conditions when no dependency We only consider test dependencies some of the time. Some packages are *only* test dependencies. Spack's algorithm was previously generating dependency conditions that could hold, *even* if there was no potential dependency type. - [x] change asp.py so that this can't happen -- we now only generate dependency types for possible dependencies. * bugfix: allow imposed constraints to be overridden in special cases In most cases, we want condition_holds(ID) to imply any imposed constraints associated with the ID. However, the dependency relationship in Spack is special because it's "extra" conditional -- a dependency *condition* may hold, but we have decided that externals will not have dependencies, so we need a way to avoid having imposed constraints appear for nodes that don't exist. This introduces a new rule that says that constraints are imposed *unless* we define `do_not_impose(ID)`. This allows rules like dependencies, which rely on more than just spec conditions, to cancel imposed constraints. We add one special case for this: dependencies of externals. * spack location: bugfix for out of source build dirs (#22348) * Channelflow: Fix the package. (#22483) A search and replace went wrong in 2264e30d99d8b9fbdec8fa69b594e53d8ced15a1. Thanks to @wadudmiah who reported this issue. * Make SingleFileScope able to repopulate the cache after clearing it (#22559) fixes #22547 SingleFileScope was not able to repopulate its cache before this change. This was affecting the configuration seen by environments using clingo bootstrapped from sources, since the bootstrapping operation involved a few cache invalidation for config files. * ASP-based solver: model disjoint sets for multivalued variants (#22534) * ASP-based solver: avoid adding values to variants when they're set fixes #22533 fixes #21911 Added a rule that prevents any value to slip in a variant when the variant is set explicitly. This is relevant for multi-valued variants, in particular for those that have disjoint sets of values. * Ensure disjoint sets have a clear semantics for external packages * clingo: modify recipe for bootstrapping (#22354) * clingo: modify recipe for bootstrapping Modifications: - clingo builds with shared Python only if ^python+shared - avoid building the clingo app for bootstrapping - don't link to libpython when bootstrapping * Remove option that breaks on linux * Give more hints for the current Python * Disable CLINGO_BUILD_PY_SHARED for bootstrapping * bootstrapping: try to detect the current python from std library This is much faster than calling external executables * Fix compatibility with Python 2.6 * Give hints on which compiler and OS to use when bootstrapping This change hints which compiler to use for bootstrapping clingo (either GCC or Apple Clang on MacOS). On Cray platforms it also hints to build for the frontend system, where software is meant to be installed. * Use spec_for_current_python to constrain module requirement (cherry picked from commit d5fa509b072f0e58f00eaf81c60f32958a9f1e1d) * Externals are preferred even when they have non-default variant values fixes #22596 Variants which are specified in an external spec are not scored negatively if they encode a non-default value. * Enforce uniqueness of the version_weight atom per node fixes #22565 This change enforces the uniqueness of the version_weight atom per node(Package) in the DAG. It does so by applying FTSE and adding an extra layer of indirection with the possible_version_weight/2 atom. Before this change it may have happened that for the same node two different version_weight/2 were in the answer set, each of which referred to a different spec with the same version, and their weights would sum up. This lead to unexpected result like preferring to build a new version of an external if the external version was older. * bugfix for active when pkg is already active error (#22587) * bugfix for active when pkg is already active error Co-authored-by: Greg Becker <becker33@llnl.gov> * Fix clearing cache of InternalConfigScope (#22609) Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Bootstrap: add _builtin config scope (#22610) (cherry picked from commit a37c916dff5a5c6e72f939433931ab69dfd731bd) * Bootstrapping: swap store before configuration (#22631) fixes #22294 A combination of the swapping order for global variables and the fact that most of them are lazily evaluated resulted in custom install tree not being taken into account if clingo had to be bootstrapped. This commit fixes that particular issue, but a broader refactor may be needed to ensure that similar situations won't affect us in the future. * Remove erroneous warnings about quotes for from_source_file (#22767) * "spack build-env" searches env for relevant spec (#21642) If you install packages using spack install in an environment with complex spec constraints, and the install fails, you may want to test out the build using spack build-env; one issue (particularly if you use concretize: together) is that it may be hard to pass the appropriate spec that matches what the environment is attempting to install. This updates the build-env command to default to pulling a matching spec from the environment rather than concretizing what the user provides on the command line independently. This makes a similar change to spack cd. If the user-provided spec matches multiple specs in the environment, then these commands will now report an error and display all matching specs (to help the user specify). Co-authored-by: Gregory Becker <becker33@llnl.gov> * ASP-based solver: assign OS correctly with inheritance from parent (#22896) fixes #22871 When in presence of multiple choices for the operating system we were lacking a rule to derive the node OS if it was inherited. * Externals with merged prefixes (#22653) We remove system paths from search variables like PATH and from -L options because they may contain many packages and could interfere with Spack-built packages. External packages may be installed to prefixes that are not actually system paths but are still "merged" in the sense that many other packages are installed there. To avoid conflicts, this PR places all external packages at the end of search paths. * ASP-based solver: suppress warnings when constructing facts (#23090) fixes #22786 Trying to get optimization flags for a specific target from a compiler may trigger warnings. In the context of constructing facts for the ASP-based solver we don't want to show these warnings to the user, so here we simply ignore them. * Use Python's built-in machinery to import compilers (#23290) * Add "spack [cd|location] --source-dir" (#22321) * spack location: fix usage without args (#22755) * Import hooks using Python's built-in machinery (#23288) The function we coded in Spack to load Python modules with arbitrary names from a file seem to have issues with local imports. For loading hooks though it is unnecessary to use such functions, since we don't care to bind a custom name to a module nor we have to load it from an unknown location. This PR thus modifies spack.hook in the following ways: - Use __import__ instead of spack.util.imp.load_source (this addresses #20005) - Sync module docstring with all the hooks we have - Avoid using memoization in a module function - Marked with a leading underscore all the names that are supposed to stay local * ASP-based solver: no intermediate package for concretizing together (#23307) The ASP-based solver can natively manage cases where more than one root spec is given, and is able to concretize all the roots together (ensuring one spec per package at most). Modifications: - [x] When concretising together an environment the ASP-based solver calls directly its `solve` method rather than constructing a temporary fake root package. * ASP-based solve: minimize compiler mismatches (#23016) fixes #22718 Instead of trying to maximize the number of matches (preferred behavior), try to minimize the number of mismatches (unwanted behavior). * performance: speed up existence checks in packages (#23661) Spack doesn't require users to manually index their repos; it reindexes the indexes automatically when things change. To determine when to do this, it has to `stat()` all package files in each repository to make sure that indexes up to date with packages. We currently index virtual providers, patches by sha256, and tags on packages. When this was originally implemented, we ran the checker all the time, at startup, but that was slow (see #7587). But we didn't go far enough -- it still consults the checker and does all the stat operations just to see if a package exists (`Repo.exists()`). That might've been a wash in 2018, but as the number of packages has grown, it's gotten slower -- checking 5k packages is expensive and users see this for small operations. It's a win now to make `Repo.exists()` check files directly. **Fix:** This PR does a number of things to speed up `spack load`, `spack info`, and other commands: - [x] Make `Repo.exists()` check files directly again with `os.path.exists()` (this is the big one) - [x] Refactor `Spec.satisfies()` so that a checking for virtual packages only happens if needed (avoids some calls to exists()) - [x] Avoid calling `Repo.exists(spec)` in `Repo.get()`. `Repo.get()` will ultimately try to load a `package.py` file anyway; we can let the failure to load it indicate that the package doesn't exist, and avoid another call to exists(). - [x] Fix up some comments in spec parsing - [x] Call `UnknownPackageError` more consistently in `repo.py` * Style fixes for v0.16.2 release * Update CHANGELOG and release version for v0.16.2 * Update command to setup tutorial (#24488) * Fix fetching for Python 3.9.6 (#24686) When using Python 3.9.6, Spack is no longer able to fetch anything. Commands like `spack fetch` and `spack install` all break. Python 3.9.6 includes a [new change](https://github.com/python/cpython/pull/25853/files#diff-b3712475a413ec972134c0260c8f1eb1deefb66184f740ef00c37b4487ef873eR462) that means that `scheme` must be a string, it cannot be None. The solution is to use an empty string like the method default. Fixes #24644. Also see https://github.com/Homebrew/homebrew-core/pull/80175 where this issue was discovered by CI. Thanks @branchvincent for reporting such a serious issue before any actual users encountered it! Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> * clang/llvm: fix version detection (#19978) This PR fixes two problems with clang/llvm's version detection. clang's version output looks like this: ``` clang version 11.0.0 Target: x86_64-unknown-linux-gnu ``` This caused clang's version to be misdetected as: ``` clang@11.0.0 Target: ``` This resulted in errors when trying to actually use it as a compiler. When using `spack external find`, we couldn't determine the compiler version, resulting in errors like this: ``` ==> Warning: "llvm@11.0.0+clang+lld+lldb" has been detected on the system but will not be added to packages.yaml [reason=c compiler not found for llvm@11.0.0+clang+lld+lldb] ``` Changing the regex to only match until the end of the line fixes these problems. Fixes: #19473 * Fix use of quotes in Python build system (#22279) * Cray: fix extracting paths from module files (#23472) Co-authored-by: Tiziano Müller <tm@dev-zero.ch> * Use AWS CloudFront for source mirror (#23978) Spack's source mirror was previously in a plain old S3 bucket. That will still work, but we can do better. This switches to AWS's CloudFront CDN for hosting the mirror. CloudFront is 16x faster (or more) than the old bucket. - [x] change mirror to https://mirror.spack.io * locks: only open lockfiles once instead of for every lock held (#24794) This adds lockfile tracking to Spack's lock mechanism, so that we ensure that there is only one open file descriptor per inode. The `fcntl` locks that Spack uses are associated with an inode and a process. This is convenient, because if a process exits, it releases its locks. Unfortunately, this also means that if you close a file, *all* locks associated with that file's inode are released, regardless of whether the process has any other open file descriptors on it. Because of this, we need to track open lock files so that we only close them when a process no longer needs them. We do this by tracking each lockfile by its inode and process id. This has several nice properties: 1. Tracking by pid ensures that, if we fork, we don't inadvertently track the parent process's lockfiles. `fcntl` locks are not inherited across forks, so we'll just track new lockfiles in the child. 2. Tracking by inode ensures that referencs are counted per inode, and that we don't inadvertently close a file whose inode still has open locks. 3. Tracking by both pid and inode ensures that we only open lockfiles the minimum number of times necessary for the locks we have. Note: as mentioned elsewhere, these locks aren't thread safe -- they're designed to work in Python and assume the GIL. Tasks: - [x] Introduce an `OpenFileTracker` class to track open file descriptors by inode. - [x] Reference-count open file descriptors and only close them if they're no longer needed (this avoids inadvertently releasing locks that should not be released). * Ensure all roots of an installed environment are marked explicit in db (#24277) * docker: Fix CentOS 6 build on Docker Hub (#24804) This change make yum usable again on CentOS 6 * docker: remove boto3 from CentOS 6 since it requires and updated pip (#24813) * Remove centos:6 image references This was EOL November 30th, 2020. I believe the "builds" are failing on develop because of it. * Fix style tests * Bump version and update changelog Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com> Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Martin Aumüller <aumuell@reserv.at> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: George Hartzell <hartzell@alerce.com> Co-authored-by: MichaelLaufer <70094649+MichaelLaufer@users.noreply.github.com> Co-authored-by: michael laufer <michael.laufer@toganetworks.com> Co-authored-by: Andrew W Elble <aweits@rit.edu> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Robert Maynard <robert.maynard@kitware.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@googlemail.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: Ye Luo <xw111luoye@gmail.com> Co-authored-by: Frank Willmore <frankwillmore@gmail.com> Co-authored-by: Robert Underwood <robertu94@users.noreply.github.com> Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com> Co-authored-by: Nathan Hanford <8302958+nhanford@users.noreply.github.com> Co-authored-by: Nathan Hanford <hanford1@llnl.gov> Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Co-authored-by: Yang Zongze <yangzongze@gmail.com> Co-authored-by: mic84 <mrosso@lbl.gov> Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com> Co-authored-by: darmac <xiaojun2@hisilicon.com> Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com> Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov> Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu> Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com> Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: Tom Scogland <tom.scogland@gmail.com> Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk> Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu> Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com> Co-authored-by: QuellynSnead <quellyn@lanl.gov> Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov> Co-authored-by: Phil Tooley <32297355+ptooley@users.noreply.github.com> Co-authored-by: Josh Essman <68349992+joshessman-llnl@users.noreply.github.com> Co-authored-by: Andreas Baumbach <healther@users.noreply.github.com> Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com> Co-authored-by: Rémi Lacroix <remi.lacroix@idris.fr> Co-authored-by: Cyrus Harrison <cyrush@llnl.gov> Co-authored-by: Peter Scheibel <scheibel1@llnl.gov> Co-authored-by: Todd Gamblin <gamblin2@llnl.gov> Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de> Co-authored-by: Tiziano Müller <tm@dev-zero.ch>

add version 0.4.2.3 to r-bibtex

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alalazo approved these changes Jan 15, 2021

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alalazo merged commit 13d0618 into spack:develop Jan 15, 2021

glennpj deleted the r-bibtex branch January 15, 2021 17:13

frankwillmore pushed a commit to frankwillmore/spack that referenced this pull request Jan 15, 2021

add version 0.4.2.3 to r-bibtex (spack#20815)

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loulawrence pushed a commit to loulawrence/spack that referenced this pull request Jan 19, 2021

add version 0.4.2.3 to r-bibtex (spack#20815)

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add version 0.4.2.3 to r-bibtex #20815

add version 0.4.2.3 to r-bibtex #20815

glennpj commented Jan 12, 2021

add version 0.4.2.3 to r-bibtex #20815

add version 0.4.2.3 to r-bibtex #20815

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glennpj commented Jan 12, 2021