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2020-08-16libssh: add gssapi variant and include krb5 as a dependency accordingly (#18070)Tom Payerle1-0/+7
See #18033 libssh seemed to detect and link to system krb5 libraries if found to provide gssapi support, causing issues/system dependencies/etc. We add a boolean variant gssapi If +gssapi, the spack krb5 package is added as a dependency. If ~gssapi, the Cmake flags are adjusted to not use gssapi so that does not link to any krb5 package.
2020-08-16[xrootd] new version and updated dependency (#18079)vvolkl1-1/+3
2020-08-16[dd4hep] align runtime env with lcg release (#18082)vvolkl1-0/+2
2020-08-16Adding osu-micro-benchmarks version 5.6.3 (#18090)Filippo Spiga1-1/+2
Co-authored-by: Filippo Spiga <fspiga@nvidia.com>
2020-08-16xz: add +pic variant (#18092)Mark W. Krentel1-0/+8
xz-utils already builds a shared library. The +pic variant adds the compiler pic flag to the static archive so that it can be linked into another shared library.
2020-08-16Add boost 1.74.0 package (#18088)Auriane R1-0/+1
2020-08-16New packages: madgraph, syscalc, collier, gosam-contrib (#17601)iarspider6-0/+1238
* Add Collier and SysCalc recipes * Remove extra syscalc version * Build collier with -j1 for @:1.2.4 * Add recipe for gosam-contrib * Update gosam-contrib recipe with 'provides' * Madgraph recipe, first version * Finalize madgraph recipe + flake8 * Make py2 version of madgraph default; fix hash for syscalc; fix patch * Handle virtual packages (#3) * Update package.py * Update packages.yaml * Remove virtual packages - pt. 1 * Remove virtual packages - pt. 2 * Changes from review - pt. 1 * Changes from code review - pt. 2 * Update var/spack/repos/builtin/packages/collier/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/madgraph5amc/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add hash for version 2.7.2 (available in our private mirror) * Fixes for 2.7.3 family * Patches for 2.7.3{.py3,}{.atlas,} * Fix hash of syscalc * Hack to fix concretization (2.7.3 matches 2.7.3.py3) * Add conflict statement (reported to devs) * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Delete madgraph5amc-2.7.2.atlas.patch * Delete madgraph5amc-2.7.2.patch * Update package.py * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: iarspider <iarpsider@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-16New packages Mvapich2x and Mvapich2-GDR (#17883)Nithin Senthil Kumar2-0/+424
* Adding new packages Mvapich2x and Mvapich2-GDR which can be installed only via binary mirrors * Added docstring descriptions to both packages * Removed variant wrapper for cuda dependencies * Fixed multiple flake8 errors * Updated APIs to pass unit tests * Updated APIs for MVAPICH2-X package and fixed flake8 warnings for MVAPICH2-GDR * Changed url back to single line * Removed extra parantesis around URL string Co-authored-by: nithintsk <nithintsk@github.com>
2020-08-15[root] add dataframe cmake option (#17962)vvolkl1-1/+2
* [root] add dataframe cmake option @chissg @HadrienG2 @drbenmorgan This has been a separate cmake option starting v6-19 I believe: https://github.com/root-project/root/commit/31292b90826fbb1aaf0694c445f5996cdde3f358 It should default to true -- not sure why, but this recipe sets it to off. I could add a variant too, but since it has become an integral part of root and doesn't introduce extra dependencies, I'd propose to just set it to true like I do here. * Update package.py
2020-08-14spack config update (bugfix): packages.yaml with empty attributes (#18057)Massimiliano Culpo2-1/+30
Before this PR, packages.yaml files that contained an empty "paths" or "modules" attribute were not updated correctly, since the update function was not reporting them as changed after the update. This PR fixes that issue and adds a unit test to avoid regression.
2020-08-14pugixml: add version 1.10, add option for shared libs (#18072)Chuck Atkins1-1/+13
2020-08-14Python: add spack external find support (#16684)Adam J. Stewart1-0/+76
2020-08-14pkgconfig: add spack external find support (#16690)Adam J. Stewart2-0/+28
2020-08-14Autoconf: add spack external find support (#16692)Adam J. Stewart1-1/+12
2020-08-14M4: add spack external find support (#16693)Adam J. Stewart1-1/+13
2020-08-14bmake: fix compilation error and added v20200710 (#17956)darmac1-0/+4
2020-08-14GDAL: add spack external find support (#18004)Adam J. Stewart1-0/+6
2020-08-14gmake: add spack external find support (#18009)Adam J. Stewart1-1/+9
2020-08-14nextflow: added v20.07.1 (#18058)Levi Baber1-0/+1
2020-08-14Bazel: add spack external find support (#18008)Adam J. Stewart1-0/+10
2020-08-14OpenGL: add spack external find support (#18003)Adam J. Stewart1-2/+9
2020-08-14GMT: add spack external find support (#18007)Adam J. Stewart1-0/+6
2020-08-14Adding external package support for tar. (#18002)Robert Blake1-0/+8
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-14External package recognition for git. (#18010)Robert Blake1-0/+20
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-14external packages: redirect stderr too (#18037)Adam J. Stewart5-7/+6
2020-08-14NETCDF-C: added v4.7.4 (#18051)Greg Sjaardema1-0/+1
2020-08-14SEACAS: added v2020-05-12 and v2020-08-13 (#18053)Greg Sjaardema1-0/+2
2020-08-14ceed: fix @3.0.0 dependency on hypre@2.18.2 (#17983)Jed Brown1-0/+3
Co-authored-by: Veselin Dobrev <dobrev1@llnl.gov>
2020-08-14Matplotlib: added v3.3.1 (#18061)Adam J. Stewart1-4/+9
2020-08-14py-certifi: add v2020.6.20 (#18060)Adam J. Stewart1-1/+2
2020-08-14Bash: add v5.0.18, external package detection (#18062)Adam J. Stewart1-2/+12
2020-08-13fix configure.ac/autotools issue that casues problems on RHEL 7.7 (#17465)Kai Germaschewski1-0/+4
2020-08-13Improve output of the external find command (#18017)Massimiliano Culpo2-6/+38
This commit adds output to the "spack external find" command to inform users of the result of the operation. It also fixes a bug introduced in #17804 due to the fact that a function was not updated to conform to the new packages.yaml format (_get_predefined_externals).
2020-08-13Update the change to add gomp compatibity to llvm-openmp. (#17400)Jim Galarowicz1-1/+11
* Update the change to add gomp compatibity to llvm-openmp. * Update the change to add gomp compatibity to llvm-openmp using append instead of extend. * Fix flake8 issue. Co-authored-by: Jim Galarowicz <jgalarowicz@newmexicoconsortium.org>
2020-08-13Add support for pFUnit version 4 (#17683)Alicia Klinvex1-8/+27
* pFUnit: Added support for version 4 pFUnit v4 uses submodules, so we must fetch from the repo rather than grabbing the tarball (see #11642). * pFUnit: Added conflicts pFUnit 4 causes an internal compiler error with gcc 7.2.0, and several pFUnit versions are incompatible with shared libraries. * pFUnit: Added conflicts for version 4 Verson 4 uses Fortran 2008 features and cannot be built with gcc compilers prior to 8.4. * pFUnit: Fixed conflicts/dependencies as suggested * pFUnit: Version 4 no longer fetches from git Checksummable files are fetched instead. * pFUnit: Simplify major version check Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * pFUnit: Removed unnecessary patch for v4 The patch is still applied to v3. * pFUnit: Modified MPI flag for v4 pFUnit v3 and v4 use different CMake flags to enable/disable MPI support. Also added a conflict for v3 with MPI enabled using gfortran 10, since newer gfortran is more finicky about datatypes. * pFUnit: Rearranged mpi logic * pFUnit: changed m4 to a build dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * pFUnit: Added URL back I did not realize it was needed by "spack versions" and "spack checksum". Thanks @adamjstewart! Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-13AMD ROCm Mathlibs (#17699)Ganesh Kumar7-0/+234
* ROCm Mathlibs * fixed the review comments * fixed flake8 issues
2020-08-13gcc: improve detection functions (#17988)Massimiliano Culpo1-10/+40
* Don't detect Apple's clang as gcc@4.2.1 * Avoid inspecting links except for Cray platforms * Always return string paths from compiler properties * Improved name-based filtering (apt-based packages)
2020-08-13IOR package: added 3.3.0rc1 and develop version (#18036)Nikolay Simakov1-1/+3
* IOR package: added 3.3.0rc1 and develop version * IOR package: reordered versions, set 3.2.1 as preferred
2020-08-13Make mpich buildable without fortran (#17964)Harmen Stoppels1-12/+29
When the user explicitly sets ~fortran, mpich builds without fortran support. This will make building C/C++ libraries using clang easier, since clang does not offer a fortran compiler by default (yet). Since the user has to disable Fortran support explicitly, this change is not breaking.
2020-08-13fix buildcache create for environments with uninstalled root specs (#17859)Harmen Stoppels1-13/+21
* Handle uninstalled rootspecs in buildcache - Do not parse specs / find matching specs when in an environment and no package string is provided - Error only when a spec.yaml or spec string are not installed. In an environment it is fine when the root spec does not exist. - When iterating through the matched specs, simply skip uninstalled packages
2020-08-13"spack config update" can handle comments in YAML files (#18045)Massimiliano Culpo2-1/+37
fixes #18031 With this fix "spack config update" can update YAML files that contain comments, while previously it couldn't.
2020-08-13update vtk-h release (#18052)Matt Larsen1-0/+1
2020-08-13Merge tag 'v0.15.4' into developTodd Gamblin4-6/+27
2020-08-13llvm: added external detection capabilities (#17989)Massimiliano Culpo1-2/+107
* llvm: added external detection capabilities * Added comment with reference to external package detection docs * Fix typo in a comment
2020-08-13update CHANGELOG.md for 0.15.4v0.15.4Todd Gamblin1-0/+17
2020-08-13bump version number for 0.15.4Todd Gamblin3-6/+10
2020-08-13Move Python 2.6 unit tests to Github Actions (#17279)Massimiliano Culpo7-105/+55
* Run Python2.6 unit tests on Github Actions * Skip url tests on Python 2.6 to reduce waiting times * Skip foreground background tests on Python 2.6 to reduce waiting times * Removed references to Travis in the documentation * Deleted install_patchelf.sh (can be installed from repo on CentOS 6)
2020-08-13Buildcache: bindist test without invoking spack compiler wrappers. (#15687)Patrick Gartung8-9/+911
* Buildcache: * Try mocking an install of quux, corge and garply using prebuilt binaries * Put patchelf install after ccache restore * Add script to install patchelf from source so it can be used on Ubuntu:Trusty which does not have a patchelf pat package. The script will skip building on macOS * Remove mirror at end of bindist test * Add patchelf to Ubuntu build env * Revert mock patchelf package to allow other tests to run. * Remove depends_on('patchelf', type='build') relying instead on * Test fixture to ensure patchelf is available. * Call g++ command to build libraries directly during test build * Flake8 * Install patchelf in before_install stage using apt unless on Trusty where a build is done. * Add some symbolic links between packages * Flake8 * Flake8: * Update mock packages to write their own source files * Create the stage because spec search does not create it any longer * updates after change of list command arguments * cleanup after merge * flake8
2020-08-13Use "fetch-depth: 0" to retrieve all history from remoteMassimiliano Culpo4-10/+19
2020-08-13Simplified YAML files for Github Actions workflowsMassimiliano Culpo4-18/+7
Updated actions where needed
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