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2020-05-09Add maintainers and variants for building with default earlier api versions. ↵Larry Knox1-0/+12
(#16534) * Add maintainers. Add variants for building with default earlier api versions. * Update var/spack/repos/builtin/packages/hdf5/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09New package: py-addict (#16535)Jen Herting1-0/+19
* [py-addict] created template * [py-addict] added homepage and description * [py-addict] cleaned up fixmes * [py-addict] depends on py-setuptools
2020-05-09QMCPACK Update May 2020 (#16542)Nichols A. Romero1-23/+2
* Add naromero77 as a maintainer for QMCPACK Spack package. * Add QMCPACK 3.9.2 * Remove QE-to-QMCPACK wave function converter from QMCPACK Spack package. Already been moved to QE Spack package.
2020-05-09Fix dependency of geant4 (amends #16497) (#16504)iarspider3-10/+14
* Fix dependency of geant4 (amends #16497) * Update geant4-data dependencies * Reviewer comments (part 1/2) * Reviewer comments (part 2/2) * Update var/spack/repos/builtin/packages/geant4-data/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09update visit package with 3.1.1 release and add comments (#16498)Cyrus Harrison3-7/+154
2020-05-08spaCy: add new package for en_core_web_sm model (#16539)Adam J. Stewart1-0/+17
2020-05-08Metall: add version 0.2 (#16502)Keita Iwabuchi1-0/+2
2020-05-08Add new package:py-pytest-check-links (#16503)takanori-ihara1-0/+19
2020-05-08py-netcdf4: a couple of improvements (#16505)Sergey Kosukhin2-0/+30
* py-netcdf4: avoid recompilation and make the older versions to work with HDF5@1.10: * py-netcdf4: add a new version and introduce a maintainer list.
2020-05-08precice: Fix conflict with boost 1.73.0 (#16507)Frédéric Simonis1-0/+1
2020-05-08graphviz: fix cairo backend (#16511)Christoph Junghans1-1/+1
2020-05-08Gaudi: separate variant for building documentation (#16515)iarspider1-2/+4
* Gaudi: separate variant for building documentation * Update package.py
2020-05-08New package (#16519)h-denpo1-0/+26
Large Scale Assembly, Structural Correspondence, Multi Dynamics Simulator.In this program, a part of functions of ADVENTURE_Solid ver.1.1 module
2020-05-08Gaudi: syntax fix (#16523)iarspider1-3/+3
2020-05-08new version xrootd-4.12.0 (#16528)Amjad Kotobi1-0/+1
2020-05-08new version r-git2r-0.27.1 (#16529)Amjad Kotobi1-0/+1
2020-05-07Revert changes to `qt` (#16516)Elizabeth Fischer1-3/+0
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-07GDAL: add 3.1.0 (#16509)Adam J. Stewart1-0/+1
2020-05-07NAG Compiler 7.0 (Build 7017) download checksum (#16510)Themos Tsikas1-1/+1
2020-05-07Add Rust 1.43.1 (#16512)Andrew Gaspar1-0/+7
2020-05-07ADD New package revocap-refiner (#16499)h-denpo1-0/+57
* ADD New package revocap-refiner """The University of Tokyo, CISS Project: Geometric processing, mesh processing, mesh generation""" * Modify homepage = "https://github.com/FrontISTR/REVOCAP_Refiner" Modify version('master', branch='master') Modify depends_on('swig', type='build') Modify install_tree('Refiner', prefix.include.refine) Delete mkdirp(prefix.include)
2020-05-07Add new package: ganglia (#16382)darmac1-0/+35
* Add new package: ganglia * ganglia: fix the libexpat depends
2020-05-07Adapt to the latest Acts developments (#16385)Hadrien G1-16/+56
* Adapt to the latest Acts developments A long time ago, the Acts project (whose name was then capitalized ACTS) used to maintain multiple software repositories: - The heart of the tracking toolkit was located in the `acts-core` repository - Fast simulation extensions were located in the `acts-fatras` repository - Advanced usage examples were located in the `acts-framework` repository This multi-repository organization, however, has been a source of constant pain, which is why the various projects were gradually merged into a single mono-repo, called `acts`. Today, with the integration of `acts-framework`, this merging process is reaching completion. The present pull request adapts the Acts package to this evolution by... - Renaming the package to `acts`, reflecting the new repository name - Renaming the `test` variant to `unit_tests`, reflecting current CMake naming - Adding the new build variants that were inherited from `acts-framework` - Acknowledging the change of semantics of the `examples` variant, and only supporting the new ones (as the former variant was almost unused) - Liberally using alphabetical order to make the package code more readable - Recording a large number of conflicts, some of which are introduced by the merging of `acts-framework` and some of which already existed before - Using the new capitalization of "Acts" * Add acts v0.23 * Update dd4hep version requirement * Add acts v0.22.1 bugfix
2020-05-07Add PGI version 19.7 and export OMPI variables (#16484)asmaahassan901-0/+11
* add PGI version 19.7 * use openmpi in pgi exporting openmpi enviroment variables when installed with pgi * fix lint
2020-05-07neovim: added v0.4.3 (#16410)Eisuke Kawashima1-16/+37
Use neovim's vendored dependencies for 0.4 and later
2020-05-06openfoam: correspond to build with Fujitsu compiler. (#15941)Tomoki, Karatsu1-4/+32
* openfoam: correspond to build with Fujitsu compiler. * openfoam: add rules for Fujitsu compiler (on linuxARM64) - the Fujitsu compiler is a clang derivative, so use a modified version of the clang rules if upstream does not supply anything
2020-05-06Add new package:py-json5 (#16273)takanori-ihara1-0/+19
* Add new package:py-json5 * Remove unnecessary line
2020-05-06New version of pylint + fix dependencies (#16443)iarspider1-3/+10
* New version of pylint + fix dependencies * Update package.py * Update package.py
2020-05-06Install RMPISNOW wrapper in prefix.bin for r-snow (#16479)Glenn Johnson1-0/+5
If using mpirun, the R sessions can be started with a wrapper script that helps set up the R session cluster. Put this wrapper in the PATH so it is easily accessible.
2020-05-06py-shapely: fix unit tests (#16500)Adam J. Stewart1-4/+13
2020-05-06py-netcdf4: make sure we don't use system hdf5. (#16492)Sergey Kosukhin2-0/+13
2020-05-06Bazel: add new versions (#16493)Adam J. Stewart2-2/+29
2020-05-06TensorFlow: add new version (#16494)Adam J. Stewart1-8/+15
2020-05-06OpenMPI - Update to 3.1.6 (#16496)Kevin Manalo1-1/+2
2020-05-06Add new version of Geant4 (#16497)iarspider1-0/+1
2020-05-06PyTorch/Torchvision: fix deptype (#16495)Adam J. Stewart2-4/+4
2020-05-06blis: FIX threads option, HPL: enable opemp variant for 2.3 (#16476)yellowhat2-4/+12
* blis: FIX threads option * HPL: openmp variant is ignored for 2.3 * blis: FIX flake8 * blis: FIX spacing * Update var/spack/repos/builtin/packages/hpl/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * hpl: FIX spec --> self.spec, FIX blas with amdblis * HPL: fix flake8 * HPL: FIX flake8 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-06qscintilla (#16182)Elizabeth Fischer1-0/+3
* qscintilla * Revert "qscintilla" This reverts commit 00bd00ea3c5af4f29de5dd6961acf03fb51e2ea0. * Move logic to qt package. * flake8 Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-06margo: update dependency on argobots (#16489)Scott Wittenburg1-1/+1
2020-05-05Automatically find externals (#15158)Peter Scheibel3-0/+76
Add a `spack external find` command that tries to populate `packages.yaml` with external packages from the user's `$PATH`. This focuses on finding build dependencies. Currently, support has only been added for `cmake`. For a package to be discoverable with `spack external find`, it must define: * an `executables` class attribute containing a list of regular expressions that match executable names. * a `determine_spec_details(prefix, specs_in_prefix)` method Spack will call `determine_spec_details()` once for each prefix where executables are found, passing in the path to the prefix and the path to all found executables. The package is responsible for invoking the executables and figuring out what type of installation(s) are in the prefix, and returning one or more specs (each with version, variants or whatever else the user decides to include in the spec). The found specs and prefixes will be added to the user's `packages.yaml` file. Providing the `--not-buildable` option will mark all generated entries in `packages.yaml` as `buildable: False`
2020-05-05PyTorch: add patches to fix build (#16477)Adam J. Stewart2-3/+58
2020-05-05kokkos: add v3.1.01 (#16470)Christoph Junghans2-10/+7
* kokkos: add v3.1.01 * kokkos: fix up versions * kokkos-kernels: follow upstream versioning
2020-05-05cray platform: support cray Cluster and XC type machines (#12989)Greg Becker2-14/+66
Cray has two machine types. "XC" machines are the larger machines more common in HPC, but "Cluster" machines are also cropping up at some HPC sites. Cluster machines run a slightly different form of the CrayPE programming environment, and often come without default modules loaded. Cluster machines also run different versions of some software, and run a linux distro on the backend nodes instead of running Compute Node Linux (CNL). Below are the changes made to support "Cluster" machines in Spack. Some of these changes are semi-related general upkeep of the cray platform. * cray platform: detect properly after module purge * cray platform: support machines running OSs other than CNL Make Cray backend OS delegate to LinuxDistro when no cle_release file favor backend over frontend OS when name clashes * cray platform: target detection uses multiple strategies This commit improves the robustness of target detection on Cray by trying multiple strategies. The first one that produces results wins. If nothing is found only the generic family of the frontend host is used as a target. * cray-libsci: add package from NERSC * build_env: unload cray-libsci module when not explicitly needed cray-libsci is a package in Spack. The cray PrgEnv modules load it implicitly when we set up the compiler. We now unload it after setting up the compiler and only reload it when requested via external package. * util/module_cmd: more robust module parsing Cray modules have documentation inside the module that is visible to the `module show` command. Spack module parsing is now robust to documentation inside modules. * cce compiler: uses clang flags for versions >= 9.0 * build_env: push CRAY_LD_LIBRARY_PATH into everything Some Cray modules add paths to CRAY_LD_LIBRARY_PATH instead of LD_LIBRARY_PATH. This has performance benefits at load time, but leads to Spack builds not finding their dependencies from external modules. Spack now prepends CRAY_LD_LIBRARY_PATH to LD_LIBRARY_PATH before beginning the build. * mvapich2: setup cray compilers when on cray previously, mpich was the only mpi implementation to support cray systems (because it is the MPI on Cray XC systems). Cray cluster systems use mvapich2, which now supports cray compiler wrappers. * build_env: clean pkgconf from environment Cray modules silently add pkgconf to the user environment This can break builds that do not user pkgconf. Now we remove it frmo the environment and add it again if it is in the spec. * cray platform: cheat modules for rome/zen2 module on naples/zen node Cray modules for naples/zen architecture currently specify rome/zen2. For now, we detect this and return zen for modules named `craype-x86-rome`. * compiler: compiler default versions When detecting compiler default versions for target/compiler compatibility checks, Spack previously ran the compiler without setting up its environment. Now we setup a temporary environment to run the compiler with its modules to detect its version. * compilers/cce: improve logic to determine C/C++ std flags * tests: fix existing tests to play nicely with new cray support * tests: test new functionality Some new functionality can only be tested on a cray system. Add tests for what can be tested on a linux system. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-05-05OpenBLAS: Fix LLVM 9.0.0 ICE on macOS (#16471)Axel Huebl2-0/+40
Recently added patch to port the LLVM 9.0.0 ICE with OpenBLAS and AVX-512 instructions as well to AppleClang (11.0.3).
2020-05-05minor (#16467)Sajid Ali1-1/+2
2020-05-05Make usage example consistent with current MV variants (#16468)Massimiliano Culpo2-2/+2
Since #9481 Python's None is not permitted as a value for MV variants. The string 'none' is used instead. Add the same fix for the amgx and lammps packages
2020-05-05CMake: Cray XC40 system errors bootstrapping CMake (#16459)Jennifer Green2-0/+16
* CMake: fix https://github.com/spack/spack/issues/16453 with a patch addressing both libhugetlbfs and icpc warnings on Cray XC40 systems * Including CMake v3.17.2 in the patched versions
2020-05-05cabana: add v0.3.0 & shared variant (#16466)Christoph Junghans1-1/+5
2020-05-05Add Axom spack package (#15432)Chris White5-37/+613
* Add OpenMP variant to Umpire * Initial implementation of Axom package * Add Axom spack package and fix required dependencies * Fix overzealous tag replacement * Attempt to fix version error * Fix python version attempt #2 * Update raja and umpire * remove sys_type check * Address comments in axom package * Address Greg's comments * Fix flake8 * more flake8 * Simplify MPIEXEC and MPIEXEC_NUMPROC_FLAG * Fix typo * Revert back to slurm check, fix cuda_arch checks * Fix cuda_arch variant forwarding * Add cub variant * Add py-shroud * Address comments * Fix shroud path in axom * Fix merge conflict * Fix backwards if * Fix flake8 and add copyright * format for consistency
2020-05-05exonerate-gff3: new package at 2.3.0 (#11830)Justin S1-0/+22
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