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2019-05-01mesa: re-written to new meson build system (#10482)Chuck Atkins16-202/+164
* mesa: re-writen to new meson build system * xorg-server: Remove unneeded mesa dependency * glx: provide the virtual GLX package * Convert most "mesa" dependencies to use virtual gl and glx dependencies * mesa: Switch to always building from the git repo instead of a tarball * Use gl and glx version ranges instead of exact versions * glx: provide a default package * add auto to swr variant * Revert "add auto to swr variant" This reverts commit 2e7cd8a8aca07767c00657d0d09985ddd6306883. * update mesa package to version 19.0 * set +glx by default only when running on linux * fix style issues in geant4 package * remove virtual package "egl"
2019-05-02add PMDK 1.6Phil Carns1-2/+1
- also remove superflous ncurses dependency for PMDK 1.5
2019-05-02trilinos: add variant for ShyLU support (#11294)Kelly (KT) Thompson1-0/+4
2019-05-02ffmpeg package: add aom support (#11210)Sean McGrath2-1/+30
* Add Aom package * Add aom variant to ffmpeg package which controls whether to build with the Aom dependency
2019-05-01Supernova package: add version 2.1.1 (#11285)xfzhao1-3/+6
2019-05-01Add margo package and add rc1 tag for argobots package (#11281)Francois Budin2-0/+51
margo package is a required dependency for unifycr but the package was not available in spack. margo requires a recent version of argobots that has the ABT_SCHED_BASIC_WAIT scheduler (rc1 does while previously available versions of this package in spack did not have it).
2019-05-01veloc package: add version 1.1 and update master dependencies (#11270)Francois Budin1-1/+3
* Add version 1.1 and set it as preferred * Add pdsh as a dependency for `master`
2019-05-01Darshan 3.1.7 and develop versions fpr darshan-runtime and darshan-util (#11269)Francois Budin2-0/+6
* Add version 3.1.7 * Add develop branch (git master)
2019-05-01Lua: Fix unresolved symbols in shared library by linking with libdl.so (#11260)Thomas Gruber1-1/+2
The current lua package.py does not link with libdl.so, so you get unresolved symbols while linking with lua. This PR adds libdl to fix the issue.
2019-05-01openfoam-com package: build without kahip by default (#11259)Greg Becker1-1/+1
Kahip does not build with clang (conflicts('%clang') in kahip package. Because of this, openfoam-com %clang fails concretization. Therefore, this changes the default openfoam-com variant for kahip to False.
2019-05-01CP2K package: add versions and tests, adjust optimization flags (#11263)Tiziano Müller1-3/+20
* Remove -ffast-math optimization flag * Add 'develop' version which points to git repo * Depend on libint for all versions >= 3.0 * Build directory is different for versions >= 7 (including develop) * Add "make test" as post install check
2019-05-01Fix spack flake8 to use Travis's target as base when neededTodd Gamblin2-3/+7
2019-05-01OpenCV: New versions, adjust protobuf dependency (#11243)Jannek Squar1-1/+16
* Add versions 3.4.4 through 4.1.0 and 4.1.0-openvino * Add conflict for gcc version >= 7 when building with +cuda * Later version of protobuf is required for later versions of OpenCV * Explicitly remove protobuf dependency with CMake option when not building with +dnn
2019-04-30Masurca (#11286)xfzhao1-3/+3
* py-pauvr:new package * falcon-unzip: new package * supernova: updating * masurca: updating * rm extra files * modifying available versions and adding url * fixing deleted supernova
2019-04-30git-lfs: add version 2.7.2 (#11311)Matthias Diener1-0/+1
2019-04-30remove myself from maintainers of some packages (#11319)Denis Davydov4-8/+0
2019-04-30vtk: Use the vendored libharu (#11293)Chuck Atkins1-9/+1
VTK requires a patched libharu that is not maintained upstream See https://github.com/libharu/libharu/pull/157
2019-04-27environment-modules: add version 4.2.4 (#11307)Xavier Delaruelle1-1/+2
2019-04-26py-dateutil: add missing dependency on py-setuptools-scm (#11282)Daryl W. Grunau1-0/+1
Confirmed that versions before 2.7.5 do not require this dependency.
2019-04-26QuantumEspresso package: add version 6.4 (#11302)Felix Mayr1-0/+1
2019-04-26precice: add version 1.4.1 (#11276)Frédéric Simonis1-0/+1
2019-04-24root: new versions, variants and patches (#11215)Chris Green5-76/+337
* root: new versions, variants and patches to bring in to line with FNAL's use. * Support MySQL. * Patches: * Bigger stringbuf. * Find MySQL even when it's called mariadb-c-client. * Honor external provision of unuran. * Properly handle the ROOT7 web GUI for 6.16/00. * `memstat` variant is now default-OFF due to version-related constraints. * Add missing dependencies. * Propagate `python` to `libxml2`. * Handle external FTGL dependency with X / OpenGL: depends on PR #### * Force `SPACK_INCLUDE_DIRS` to avoid warning. * New `gminimal` variant default ON per discussion with Javier Cervantes. * Style fixes per flake8. * Remove redundant `PATH_SUFFIX` per https://github.com/root-project/root/pull/1993#discussion_r276840329 * Comment patches per https://github.com/spack/spack/pull/11215#discussion_r276887199. * Reflect the fact that MariaDB support patch is now upstream. * Restore ncurses dependency for libtinfo.
2019-04-24Fix handling of MODULEPATH in setup-env.sh (#11274)Toyohisa Kameyama1-1/+1
Usage of double quotes was preventing word-splitting when parsing module roots in setup-env.sh, which lead to an error when multiple module roots are used (in particular when Spack is pointed to use an upstream module root in addition to its own).
2019-04-24nest: change cmake_options to args. (#11273)Toyohisa Kameyama1-6/+6
2019-04-24py-pandas: Add version 0.20.0 (#11264)Eric Martin1-0/+1
2019-04-24squashfs should depend_on('zlib') (#11265)George Hartzell1-0/+1
Add zlib dependency to squashfs On my CentOS system it was getting linked in (from Spack, no less) fortuitously. On a minimal Ubuntu system it failed until it was added as an explicit dependency.
2019-04-24_valid_tokens list is missing intended comma (#11271)Daryl W. Grunau1-1/+1
* _valid_tokens list is missing a needed comma
2019-04-23ftgl: update to 2.1.3-rc5. (#11214)Chris Green2-15/+161
* ftgl: update to 2.1.3-rc5. This updates to the last release (from 2008) with patches required to work with Spack and Root. * Working 2.1.2 with/without docs, 2.1.3-rc5 without.
2019-04-23py-umi-tools: Add latest versions (#11256)Eric Martin1-0/+3
2019-04-22Install squashfs exe's into prefix.bin, not prefix (#11246)George Hartzell1-1/+1
The squashfs Makefile's `INSTALL_DIR` args is the path to the `bin` directory, not the top of the install tree. Adjust accordingly.
2019-04-23Update tutorial page with RIKEN tutorial slides. (#11254)Todd Gamblin1-13/+28
- Add link to container image, as well as a description of VMs - Update slide link to point to latest RIKEN tutorial
2019-04-22Fix transitions between tutorial sections (#11251)Greg Becker3-11/+21
2019-04-20spack edit: use execv instead of Executable (#11245)Todd Gamblin3-37/+262
- `spack edit` previously used `spack.util.executable` `Executable` objects, and didn't `exec` the editor like you'd expect it to - This meant that Spack was still running while your editor was, and stdout/stdin were being set up in weird ways - e.g. on macOS, if you call `spack edit` with `EDITOR` set to the builtin `emacs` command, then type `Ctrl-g`, the whole thing dies with a `==> Error: Keyboard interrupt` - Fix all this by changing spack.util.editor to use `os.execv` instead of Spack's `Executable` object
2019-04-20OpenBLAS: Allow enabling/disabling AVX2/512 supportJanne Blomqvist1-1/+18
Allow specifying whether AVX2 or AVX512 should be enabled or disabled on x86 targets. As AVX2 hardware and toolchain support is quite ubiquitous by now, AVX2 is enabled by default. Also AVX2 support is not disabled when building the +virtual_machine variant. AVX512 is not supported in older but still supported toolchains, hardware is still expensive, and OpenBLAS AVX512 kernels still have bugs. Thus AVX512 is disabled by default.
2019-04-20Fix detection of LLVM-enabled PGI compilers (#10704)Adam J. Stewart2-2/+12
* Fix detection of LLVM-enabled PGI compilers * Add unit tests for LLVM-enabled PGI compiler version detection
2019-04-20hdf5: add symbols (#10991)Matthias Diener1-0/+1
2019-04-20Mercury package: add version 1.0.1 and update dependencies (#10906)Adam J. Stewart3-32/+136
* Add Mercury version 1.0.1 * Remove cci and bmi dependency requirements: these are not currently defined in Spack. If +bmi is enabled, the effect is that it may use a system install of bmi * Add a note that fabtests is deprecated and has been folded into the libfabric package. Add the fabtests resource to the libfabric package * Add CMake option settings to Mercury based on variant settings * Mercury: Set OFI testing protocol depending on how libfabric was built * Mercury: add version constraints to dependencies
2019-04-20Move NoLibrariesError/NoHeadersError into error.py (#10997)Denis Davydov3-11/+20
Also add constructor to NoLibrariesError which can either take an error message (like other SpackErrors) or a name and prefix (in which case the error message is constructed).
2019-04-20dealii: add patch for build with boost@1.70.0 (#11239)Satish Balay1-0/+5
Ref: https://github.com/dealii/dealii/issues/7934
2019-04-19miniconda 2 and 3 packages: add version 4.6.14 (#11232)Sajid Ali2-2/+4
2019-04-19Fix outdated R packages failing to fetch (#11039)Justin S1-3/+4
PR #10758 made a slight change to find_versions_of_archive() which included archive_url in the search process. While this fixed `spack create` and `spack checksum` missing command-line arguments, it caused `spack install` to prefer those URLs over those it found in the scrape process. As a result, the package url was treated as a list_url causing all R packages to stop fetching once the package was updated on CRAN. This patch is more selective about including the archive_url in the remote versions, explicitly overriding it with matching versions found by the scraper.
2019-04-19mysql: 5.7.X versions link boost (#11237)Chris Green1-4/+4
Fixes #11226 MySQL 5.7.X and Boost 1.59.0 have a closer relationship than MySQL >= 8.0 and their corresponding Boost versions: 5.7.X needs to link against boost libraries which is indicated by marking boost as a link dependency (removing the 'type' reverts to the default, which includes link and build).
2019-04-19jdk package: Fix fetching with curl 7.64.0+ (#11108)Oliver Breitwieser1-2/+2
Starting with version 7.64.0, curl skips cookies specified with "-H" (generic custom header specification) when following redirects, which causes the "accept-license"-cookie for jdk to disappear. The result is that jdk fails to download. This uses the "-b" option (which is used specifically for configuring cookies) instead, which is more permissive.
2019-04-19MUMPS: add version 5.2.0 (#11234)Satish Balay1-0/+1
2019-04-19hypre: add @osborn9 to maintainers (#11233)Satish Balay1-1/+1
2019-04-19Fix backwards compatibility for module naming (#11236)Greg Becker1-0/+4
f242f5f8 changed the format strings but maintained backwards compatibility in all cases except one: The list of valid tokens for the module naming schemes was not updated properly to contain both the new and old styles for compilers and package names. This PR re-adds the old tokens into the list of valid tokens.
2019-04-19added libsodium 1.0.16 and 1.0.17 (#11231)kustowski11-0/+2
2019-04-19petsc: fix suitesparse configure options. (#11188)Satish Balay1-1/+1
spec['dep'].libs.ld_flags can return system paths in some cases. This is a targeted fix for the petsc package when retrieving suite-sparse dependency libraries.
2019-04-19hpx: overhaul of the package recipe (#11194)Massimiliano Culpo1-6/+111
* added latest versions + malloc variant * added a variant to activate different instrumentations * added a variant to activate or not networking * added a variant to activate or not cuda and tools * enforce c++ standard and make it consistent with boost
2019-04-18memsurfer: add new packageHarsh Bhatia1-0/+48