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2019-06-08Add ADIOS2 option to Trilinos (#11609)Francois Budin1-1/+7
ADIOS2 is the latest implementation of the ADaptable Input Output System, ADIOS. This brand new architecture was designed to continue supporting the performance legacy of ADIOS, and extend its current capabilities to address current and future input/output (IO) challenges in the scientific data lifecycle through effective research and development (R&D) activities. ADIOS2 was recently added as a Third Party Library of Trilinos when it was integrated to IOSS, a library inside the SEACAS package.
2019-06-07spack list: latest version (JSON) (#11652)Axel Huebl4-1/+81
List the latest version of each package in JSON encoding. Preparation for consumption for a "spack badge" service.
2019-06-07Compiler search uses a pool of workers (#10190)Massimiliano Culpo17-302/+503
- spack.compilers.find_compilers now uses a multiprocess.pool.ThreadPool to execute system commands for the detection of compiler versions. - A few memoized functions have been introduced to avoid poking the filesystem multiple times for the same results. - Performance is much improved, and Spack no longer fork-bombs the system when doing a `compiler find`
2019-06-07add openmp variant to lammps (#11643)Jeffrey Salmond1-1/+5
* add openmp variant to lammps * add conflict for %gcc@9: and +openmp
2019-06-06commands: remove unused `spack list --format=rst` (#11651)Todd Gamblin2-79/+0
- We use `spack list --foramt=html` now, as it is much faster and doesn't make the docs build take forever. - Remove `spack list --format=rst` as it is no longer used.
2019-06-06added tix package and python variant for tix (#11599)Gregory Lee4-2/+58
* added tix package and python variant for tix * addressing tix review requests * python +tix requires +tkinter
2019-06-06bugfix: StageComposite must include the `expanded` property` (#11647)Todd Gamblin1-0/+4
2019-06-06bugfix: lua-luafilesystem package should use stage.source_path (#11648)Todd Gamblin1-2/+1
2019-06-06tests: package_sanity now checks packages in 3rd-party repos (#11637)Jennifer Herting1-2/+1
2019-06-05travis: disable `spack spec` for python 2.7 as well as 2.6Todd Gamblin1-1/+1
- keep this disabled until the `compiler find` fork bomb is fixed.
2019-06-05tests: add extra coverage for fetch strategy testsTamara Dahlgren4-8/+142
2019-06-05stage: make `source_path` available before stage is builtTamara Dahlgren6-207/+535
- `stage.source_path` was previously overloaded; it returned `None` if it didn't exist and this was used by client code - we want to be able to know the `source_path` before it's created - make stage.source_path available before it exists. - use a well-known stage source path name, `$stage_path/src` that is available when `Stage` is instantiated but does not exist until it's "expanded" - client code can now use the variable before the stage is created. - client code can test whether the tarball is expanded by using the new `stage.expanded` property instead of testing whether `source_path` is `None` - add tests for the new source_path semantics
2019-06-05refactor: remove unused spack.stage._get_mirrors() functionTamara Dahlgren1-37/+24
2019-06-05tty: make tty.* print exception typesTamara Dahlgren15-26/+55
- make tty.msg, tty.info, etc. print the exception type and stringified message if the message argument is an exception. - simplify parts of the code that call tty.debug(str(e)) - add extra tty.debug statements in places where exceptions were previously ignored
2019-06-05nettle: fix broken build (#11611)Justin S1-0/+3
* nettle: force C99 build * nettle: update to use c99_flag from @alalazo Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2019-06-05lammps: added v20190605 (#11638)Christoph Junghans1-0/+1
2019-06-05clang: fix error messages in c11_flag, cxx17_flag (#11632)Justin S1-2/+2
2019-06-05libxpm: revert change made in unrelated PR (#11634)Patrick Gartung1-3/+3
2019-06-05set GUILE env var when building gnutls, fixes issue #11601 (#11607)Gregory Lee1-0/+7
2019-06-05graph: refactor static graphsTodd Gamblin4-100/+73
- `spack graph --static` (and `spack.graph.dot_graph`) now do the "right thing" and print the possible dependency graph of provided packages. - `spack graph --static` no longer concretizes specs, as it only relies on class level metadata - Previously the behavior was not consistent -- `spack graph --static` would graph possible dependencies of concrete specs, but would only include some of them. The new code properly pursues all possible dependencies, and allows traversing by different dependency types.
2019-06-05spack dependencies: support --deptype argumentTodd Gamblin4-10/+47
- `spack dependencies` can now take a --deptype argument to only traverse particular deptypes - add a new "common" argument for deptype in spack.cmd.common.arguments - Database.installed_relatives() can now also take a deptype argument - this is used by `spack dependencies --installed`
2019-06-05package: make possible_dependencies consider deptypesTodd Gamblin3-16/+93
- `PackageBase.possible_dependencies` now: - accepts a deptype param that controls dependency types traversed - returns a dict mapping possible depnames to their immediate possible dependencies (this lets you build a graph easily) - Add tests for PackageBaes
2019-06-05refactor: remove vestigial ALLOWED_URL_SCHEMES from package.pyTodd Gamblin1-4/+0
2019-06-05refactor: make Package.name consistent with other class attributesTodd Gamblin2-11/+18
- The 'name' attribute for packages was being set in DirectiveMeta, which wasn't consistent with other class properties (like fullname, etc.) - Move it to be a class property of `PackageMeta`, and add the corresponding property method wrapper on `PackageBase`
2019-06-05refactor: make PackageBase.possible_dependencies() a class method.Todd Gamblin1-4/+5
2019-06-05add C standard flags to compiler classes (#11618)Justin S7-0/+90
* add c99_flag, c11_flag to compiler class * implement c99_flag, c11_flag for gcc * implement c99_flag, c11_flag for arm * implement c99_flag for cce * implement c99_flag, c11_flag for clang * implement c99_flag, c11_flag for intel * implement c99_flag, c11_flag for xl
2019-06-04Add Google Benchmark version 1.5.0 (#11626)Andrew Gaspar1-1/+3
2019-06-04Revert "Git: patch to make git relocatable with buildcache. (#11596)" (#11625)Patrick Gartung2-58/+0
This reverts commit 30ec13f37584ad2934ecdf5a4e86d93d35b3a76c.
2019-06-04modules: set permissions based on package configuration (#11337)Greg Becker5-52/+99
Previously, module files were not set with the same permissions as the package installation. For world-readable packages, this would not cause a problem. For group readable packages, it does: ``` packages: mypackage: permissions: group: mygroup read: group write: group ``` In this case, the modulefile is unreadable by members of the group other than the one who installed it. Add logic to the modulefile writers to set the permissions based on the configuration in `packages.yaml`
2019-06-04Buildcache relocate.py error fix (#11616)Patrick Gartung3-5/+5
* Add a trailing / if file --mime does not return a mimetype with a / in it * Flake8
2019-06-04hotspot: new package at 6.0 (#11610)Justin S1-0/+21
2019-06-03mesa: Revert updated meson build and restore autotools build (#11595)Chuck Atkins4-130/+68
Due to the large number of issues this migration has caused, this rolls back to the older autotools build. However, it still keeps the updates wrt variants and virtual packages.
2019-05-31Git: patch to make git relocatable with buildcache. (#11596)Patrick Gartung2-0/+58
* Apply patch to git to make it search for config files from its current location instead of the locations hard coded at install. * Add provenance info for patch * Pass needed flags to make * Environment variables need because of relocation
2019-05-31Build cache: relocate path to spack/bin/sbang in text files. (#11592)Patrick Gartung3-13/+35
* Build cache: relocate path to spack/bin/sbang in text files. * Found in testing. * update packaging test * Make sbang replacement including #!/bin/bash. Add an additional spack prefix replacement to fix stage directory references. * flake8 * Use buildinfo.get() so old buildcaches without buildinfo['spackprefix'] can be read.
2019-05-31Package/tau/tau 2.28.1 update (#11591)sameershende2-2/+14
* Updating the TAU package with 2.28 and public repo * Cleaning up TAU package and fixing binutils to install extras The extras variant will install the extra ELF headers needed by the TAU package. The TAU package has been cleaned up and extended. * Adding some comments to the changes in binutils * Adding correct python support, finding include and lib paths. * Added PDT 3.25.1. * Added TAU v2.28.1 with libdwarf and libelf. * When +libdwarf is activated, +libelf is not automatically activated. It checks separately for libelf.
2019-05-30alan: new package at 2.1.1 (#11593)Justin S1-0/+19
2019-05-30Adds the aml memory management library. (#11590)Valentin Reis1-0/+21
AML is a collection of building blocks for explicit memory management on complex architectures. https://xgitlab.cels.anl.gov/argo/aml https://argo-aml.readthedocs.io/en/latest/
2019-05-30r-randomglm: new package at 1.02-1 (#11589)Justin S1-0/+21
2019-05-30Revbayes update (#11559)Nick Booher1-3/+6
* revbayes: new version * revbayes: pep8
2019-05-30mathematica: new package at 12.0.0 (#11509)Justin S1-0/+39
* mathematica: new package at 12.0.0 * mathematica: add missing os import * mathematica: fix url format
2019-05-29precice: add version 1.5.0 (#11577)Frédéric Simonis1-0/+1
2019-05-29Xrootd: set PYTHON_EXECUTABLE with +python variant (#11581)Patrick Gartung1-0/+5
* Xrootd: set PYTHON_EXECUTABLE with +python variant When building with python3 PYTHON_EXECUTABLE needs to be set for deprecated FindPythonInterp to work as expected. * Add comment * Flake8 * More flake8 * Update package.py * typo
2019-05-29ROOT: set PYTHON_EXECUTABLE (#11583)Patrick Gartung1-2/+2
Per @adamjstewart use spec['python'].command.path
2019-05-29py-flye: new package at 2.4.2 (#11584)Justin S1-0/+18
* py-flye: new package at 2.4.2 * py-flye: better python version constraint
2019-05-29ROSE: add version 0.9.10.0, update to Autotools, add variants (#9484)Justin Too2-52/+248
* Also add versions 0.9.9.104, 0.9.9.52, 0.9.9.0, and 'develop' * Replace version 0.9.7 with 0.9.7.0 * Update Rose to be an Autotools package * Update boost dependency to 1.60.0 or later (previously 1.47.0) * Add EDG binary identifiers for ROSE versions installing from archives (rather than git) * Add variants for mvapich2 backend, c++11, debug symbols, optimization, and ROSE-based projects (codethorn, autopar, and polyopt) * Remove patch add_spack_compiler_recognition
2019-05-29New versions and bugfixes for the ACTS package (#11578)Hadrien G1-3/+11
* Improve C++ standard computation in ACTS package * Use a more clever strategy for aligning ACTS cxxstd with ROOT cxxstd * Add new ACTS releases * ACTS is not compatible with the new Boost CMake build system yet * Explain why Boost 1.70 does not work currently
2019-05-29Add LSF dependency for OpenMPI (#11532)Dustin Wheeler2-0/+26
* Add LSF package, which cannot be installed by Spack and must be system-installed. The package install will fail if no external LSF is registered in packages.yaml (LSF may not be installed in a well-known location and the external entry helps Spack locate it for dependents). * Add LSF dependency to OpenMPI when schedulers=lsf is chosen
2019-05-29Add newer Google Benchmark version (#11580)Patrick Gartung1-0/+1
2019-05-29ROOT: Set PYTHON_EXECUTABLE with +python variant (#11579)Patrick Gartung1-0/+5
* ROOT: Set PYTHON_EXECUTABLE with +python variant After cmake v3.12 FindPythonInterp used by llvm subsystem is deprecated. Setting -DPYTHON_EXECUTABLE=path_to_python fixes this error: 1 error found in build log: 118 -- Doxygen disabled. 119 -- Go bindings disabled. 120 -- LLVM host triple: x86_64-unknown-linux-gnu 121 -- LLVM default target triple: x86_64-unknown-linux-gnu 122 -- Building with -fPIC 123 -- Found PythonInterp: /usr/bin/python2.7 >> 124 CMake Error at interpreter/llvm/src/CMakeLists.txt:613 (if): 125 if given arguments: 126 127 "VERSION_LESS" "2.7" 128 129 Unknown arguments specified 130 * Flake8 * Update var/spack/repos/builtin/packages/root/package.py Co-Authored-By: Javier Cervantes <javiercvilla@gmail.com>
2019-05-29vtkm: fix the directory cmake looks for the source code (#11576)Kenneth Moreland1-2/+1
Previously, the vtkm package was adding a "../" option to the cmake command line. I suppose this was supposed to be pointing to the source code, but did not. Rather, Spack correctly adds the source directory as the first argument to cmake. However, because ../ was added, it used that as the source directory instead. Simply remove this argument to make CMake work correctly.
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