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2019-05-24mbedtls: add pic variant (#11558)Mark W. Krentel1-1/+15
Add variant 'pic' for including in shared libraries. Add build dependency on perl. Compiling mbedtls runs several perl scripts. Add versions 2.7.10 and 2.16.1, the heads of the two main stable branches.
2019-05-24Update libensemble to v0.5.0 (#11544)Stephen Hudson1-3/+5
2019-05-24Add nettle@3.4.1 (#11547)健美猞猁1-0/+1
2019-05-24build env: simplify handling of parallel jobs (#11524)Massimiliano Culpo11-37/+104
This PR implements several refactors requested in #11373, specifically: - Config scopes are used to handle builtin defaults, command line overrides and package overrides (`parallel=False`) - `Package.make_jobs` attribute has been removed; `make_jobs` remains as a module-scope variable in the build environment. - The use of the argument `-j` has been rationalized across commands - move '-j'/'--jobs' argument into `spack.cmd.common.arguments` - Add unit tests to check that setting parallel jobs works as expected - add new test to ensure that build job setting is isolated to each build - Fix packages that used `Package.make_jobs` (i.e. `bazel`)
2019-05-24Updated lmod (to version 8.1.5) and associated dependencies (#11552)Massimiliano Culpo3-8/+22
Lmod version 8.1.5 Lua version 5.3.5 Lua Filesystem 1.7.0.2 Turned tcl to a link dependency so that Lmod's configure can find it.
2019-05-23Add latest version of py-cython (#11494)Adam J. Stewart1-5/+21
* Add latest version of py-cython * Fix cython unit tests
2019-05-23docs: truncate `spack list` output in basic usageTodd Gamblin1-3/+6
`spack list` output is very long and takes up a lot of space in the docs. Truncate it to just 10 lines and link to the package list page.
2019-05-23LIBXSMM 1.12.1 (#11538)Hans Pabst1-26/+27
2019-05-22Add cppcheck version 1.87. (#11536)Jon Rood1-0/+1
2019-05-22Add CMake 3.14.3 and 3.14.4. (#11534)Jon Rood1-0/+2
2019-05-22package vtk - improve gl handling (#11530)Omar Padron1-21/+20
* package vtk - improve gl handling * package vtk - minor cleanup
2019-05-22Fix typo in openmpi@2.1.6 libmpi.so comment. (#11529)Dustin Wheeler1-1/+1
2019-05-21Add Fujitsu compiler to Spack. (#11287)t-karatsu7-5/+87
* Add Fujitsu compiler to Spack. * Fixes for flake8 * Chenges location of FCC to subdirectory called case-insensitive * Add compiler tests for Fujitsu compiler * Modify the logic of taking compiler version for new version of Fujitsu compiler
2019-05-21dealii: add 9.1.0 (#11527)Denis Davydov1-2/+3
2019-05-21py-htseq: new version (#11525)Levi Baber1-0/+1
2019-05-21Add version (#10594)Elizabeth Fischer1-0/+1
2019-05-21Update scorep and friends (#11523)Michael Kuhn4-1/+5
2019-05-21dealii: fix symengine constraints (#11517)Denis Davydov1-7/+8
disable symengine constraints due to limitations of Spack
2019-05-20mesa: Patch missing gl symbols in OSMesa (#11518)Chuck Atkins2-0/+49
2019-05-20OpenMPI: update behavior for fabrics/schedulers=auto (#11431)Glenn Johnson1-10/+19
* When fabrics=auto or schedulers=auto, the intent is to defer to the OpenMPI configure and let it determine and use what it finds available on the system. The current behavior for 'with_or_without' in the case of 'auto' explicitly disables all possible values. This updates the logic to call 'with_or_without' only when the value of fabrics/schedulers is not 'auto'. * To allow explicitly disabling all fabrics/schedulers, each of these variants has added support for 'none' (which is also the default value). * Add a conflict for the loadleveler scheduler for openmpi-3 and above as it is no longer a valid configure option.
2019-05-20Make flake8 check spack script as well as .py files (#11513)Adam J. Stewart1-1/+1
* Make flake8 check bin/spack
2019-05-20Get Cray OS version from PrgEnv-cray (#10774)Mario Melara1-2/+2
The regex used for finding the Cray OS version from the PrgEnv-cray module was not exact and was at times pulling the version from other PrgEnv modules. This updates the regular expression to be more exact.
2019-05-20Update optional-lite and span-lite to use CMakePackage (#11407)Andrew Gaspar3-3/+70
* Update optional-lite and span-lite to use CMakePackage These packages only have CMake installs on their most recent versions. Therefore, we overload all of the CMake stages to fallback to the old versions (no-op for most, copytree for install), and use CMakePackage on the new versions. * Add new string-view-lite version with CMake install support * Only override phases for old versions of *-lite packages
2019-05-19Add py-kmodes package (#11497)Adam J. Stewart1-0/+25
2019-05-19Add latest version of joblib (#11495)Adam J. Stewart1-4/+7
2019-05-19Add latest version of setuptools (#11493)Adam J. Stewart1-1/+2
2019-05-18Update Umpire package with new versions (#11441)David Beckingsale1-1/+17
* Update Umpire package with new versions * Fix version ordering
2019-05-18trilinos: add variant to disable chaco from seacas (#11482)Denis Davydov2-2/+23
* trilinos: add variant to disable chaco from seacas keep it OFF by default due to the presence of the global symbol "divide" that can lead to symbol clash with other libraries, for example see https://github.com/dealii/dealii/issues/8170#issuecomment-492700787 * dealii: add conflict statement for adol-c and Trilinos SEACAS Chaco
2019-05-18dyninst: rework the cmake args for version 10.1 and later (#11484)Mark W. Krentel1-22/+41
* dyninst: rework the cmake args for version 10.1 and later Add a separate when() case for the cmake args for Dyninst 10.1.0 and later. The prereq args have changed enough that this makes things easier going forward. (My previous commit 26b9369c was inaccurate and temporary.) Dyninst 10.1.0 accepts boost 1.70, but earlier dyninst are restricted to <= 1.69 (not worth back porting every boost change). Change all the dyninst versions to 3 digits for clarity and consistency. * Add version 10.1.0.
2019-05-18QMCPACK Update May 2019 (#11492)Nichols A. Romero1-7/+8
* Add QMCPACK 3.7.0 * SOA is now the default. * Add QMCPACK converter based on QE 6.4
2019-05-18Add conflicts in deal.II package between SymEngine and Trilinos variants ↵Jean-Paul Pelteret1-0/+7
(#11499)
2019-05-18Fix typo in spack executable (#11512)Adam J. Stewart1-1/+1
2019-05-18intel-tbb: fix patch for old compilers (#11371)Owen Solberg2-5/+42
* added patch for intel-tbb@2019.1: with old compilers * sparately specify when @:2018 and @2019 the reason we can't say @:2019 is that would include @2019.1 where the patch doesn't work. * should be possible to list when constraint as @:2019 According to my reading of ["Version ranges" in the Spack docs](https://spack.readthedocs.io/en/latest/packaging_guide.html#version-ranges), this should apply to up to `2019` but not `2019.1:` * @:2019.0 appears to be necessary to specify 2019 but not 2019.1 * specifying 2019.1 2019.2 2019.3 2019.4 separately and explcitly * flake8 fixes for long lines. * add comments to explain why so many different patch directives * remove blank like for flake8 * revert spec %gcc@4.8.0:4.99999 -> %gcc@4.8.0:
2019-05-18Typos: funciton, woudl, hm,... (#11511)George Hartzell1-3/+3
2019-05-18Execute modulecmd in bash shell (#11510)Mario Melara1-2/+4
Adds executable=/bin/bash into Popen. We discovered this bug while working in a csh/tsch environment. By executing with /bin/bash we ensure that the module command works.
2019-05-17r-popvar: new package at 1.2.1 (#11490)Justin S1-0/+22
2019-05-17smof: new package at 2.13.1 (#11502)Justin S1-0/+29
2019-05-17r-bglr: new package at 1.0.8 (#11489)Justin S1-0/+19
2019-05-17r-rrblup: new package at 4.6 (#11488)Justin S1-0/+18
2019-05-17r-qtl: new package at 1.44-9 (#11487)Justin S1-0/+18
2019-05-17py-metasv: new package at 0.5.4 (#11476)Justin S1-0/+21
2019-05-17py-pybedtools: new package at 0.6.9 (#11475)Justin S1-0/+23
* py-pybedtools: new package at 0.6.9 * py-pybedtools: add bedtools2 dep
2019-05-17repeatmodeler: new package at 1.0.11 (#11472)Justin S1-0/+66
2019-05-17added branch multisplice to the parsplice package (#11504)Sriram Swaminarayan1-2/+7
2019-05-17gasnet: 2019.3.0 (#11503)Christoph Junghans1-0/+10
2019-05-17parsplice: needs LAMMPS_EXCEPTIONS (#11500)Christoph Junghans2-0/+5
2019-05-17Add version 2.5.1-alpha1 of MAGMA (#11486)Piotr Luszczek1-2/+3
2019-05-17cmake: default to +ownlibs to improve build times (#11483)Todd Gamblin1-2/+6
- CMake is built *very* frequently, and the number of dependencies it has accumulated can take a very long time on some systems. - Use +ownlibs by default to avoid the build overhead. This won't interfere with other packages by introducing conflicting libraries, as CMake is nearly always a build dependency.
2019-05-16OpenSpeedShop/CBTF package updates and fixes (#11470)Jim Galarowicz8-13/+18
This avoids using Boost 1.70.0, fixes library access in OpenSpeedShop packages, adds new versions, and updates QT dependency constraints in CBTF and OpenSpeedShop packages - Constrain Boost dependency to 1.69.0 or earlier to avoid issues with 1.70.0 for Open|SpeedShop and CBTF packages - Update DYNINSTAPI_RT_LIB environment variable to use single library from "find_libraries" (which returns a list) in OpenSpeedShop packages Fixes #11443 - Add version 1.9.3 for CBTF Argo Navis, CBTF Krell, CBTF LANL, and CBTF packages - Add version 2.4.1 for OpenSpeedShop Utils and OpenSpeedShop packages - Update QT dependency to 5.10.0 or greater for QtGraph and CBTF Argo Navis packages
2019-05-16CDO package: Fix build with gcc@9 (#11464)Michael Kuhn2-0/+212
This makes several changes to make CDO work with gcc@9: - Add version 1.9.7rc2 - Add a patch to make version 1.9.7rc2 build with gcc@9: - Add a conflict with GCC 9 for earlier versions of CDO It also adds a pkgconfig build dependency as configure checks for it.