Commit graph

11556 commits

Author SHA1 Message Date
Phil Carns
2c2228df59 add BMI package (#11310)
- also enable optional dependency in Mercury
2019-05-03 09:11:31 +02:00
Nichols A. Romero
42b01c02b1 QMCPACK: compiler flags and mpi wrapper updates (#11326)
* Set mpi compiler wrappers using CC/etc. variables as recommended
  at https://spack.readthedocs.io/en/latest/packaging_guide.html#compiler-wrappers
  rather than setting CMake variables like -DCMAKE_C_COMPILER
* Use convenience functionality provided by inherited CMakePackage to
  export all compiler flags as CMake options
2019-05-03 11:13:19 +09:00
Christoph Junghans
54c19ce16c py-espresso: added v4.0.2 2019-05-03 10:40:54 +09:00
Patrick Schratz
dd668cb00c grass package: use url_for_version, add versions (#11324) 2019-05-03 10:40:23 +09:00
Vanessasaurus
4aeb0d19bd Singularity package: new version, legacy builds, and root permissions (#11094)
* Remove old Singularity versions, add version 3.1.1
* Recent versions of Singularity build with go rather than autotools:
  update dependencies and build logic
* Move old Singularity versions to new singularity-legacy package
  which uses the autotools build system
* Some binaries built by Singularity need to be run as root: include
  a script that the user can run after the Spack Singularity install
  to change these permissions.
* The Singularity go build expects to work with a custom stage
  directory relative to GOPATH: override the stage phase to create
  this expected path.
* Update Singularity install config to point to Spack-installed
  makesquashfs dependency
2019-05-03 10:27:13 +09:00
Chuck Atkins
f44443ed3a llvm: depend on python only when +python (#11348)
Based on the LLVM documentation [1], Python is used to run the automated
test suite. Therefore is it always a dependency for LLVM. However, if
build without Python (~python), we limit it to a build time dependency.

Note that py-lit is not added as a spack dependency even though it is
available as a spack package. This is because it is already included
in llvm and llvm is difficult to configure using an external py-lit
(several CMake variables to set correctly). Additionally, having
py-lit as a spack dependency adds Python as a runtime dependency
for llvm even though it is not required at runtime.

[1] https://llvm.org/docs/GettingStarted.html#requirements
2019-05-02 16:21:06 -04:00
Denis Davydov
5b82bf47af extend Version class so that 2.0 > 1.develop > 1.1 and develop > master > head > trunk > 9999 (#1983)
* extend Version class so that 2.0 > 1.develop > 1.1

* add concretization tests, with preferences and preferred version.

* add master, head, trunk as develop-like versions, develop > master > head > trunk

* update documentation on version comparison
2019-05-03 03:32:40 +09:00
Omar Padron
0bbd41c7f7
install spack under /opt/spack in docker images (#10969)
* install spack under /opt/spack
2019-05-02 12:05:42 -04:00
Levi Baber
9e72fc48c8
fix error when adding package to env in container (#11321) 2019-05-02 11:04:21 -05:00
Patrick Gartung
309122c329
Don't use buildcache to install patchelf (#11343) 2019-05-02 10:02:25 -05:00
Hans Pabst
0e9513be97 LIBXSMM: add version 1.11, update wrapper settings (#11317)
Remove makefile editing to set compiler wrappers (which was not
working) and instead set them as arguments to 'make'.
2019-05-02 08:45:00 +09:00
Simon Flood
ff2be5e866 R: add version 3.6.0 2019-05-02 08:34:00 +09:00
Daryl W. Grunau
7a3be1bf15 New package: py-pydv (#11313) 2019-05-02 08:28:21 +09:00
tcojean
68c4849f77 Ginkgo package: update to release 1.0.0 (#11312)
* Version 1.0.0 was released and the master branch tracks the
  latest release.
* Multiple issues with MacOS have been fixed. The static patch is
  now unneeded.
* Add support for building Ginkgo with the full Block Jacobi
  performance (compilation takes a long time).
* Do not build anything which is not useful for the installation.
  Namely, documentation, benchmarks, examples and tests.
2019-05-02 08:25:39 +09:00
Phil Carns
396955b9ba New package: libpmemobj-cpp (#11309) 2019-05-02 08:12:01 +09:00
Felix Mayr
c2e280b794 python: add versions 3.7.3, 3.5.7, and 3.4.10 (#11300) 2019-05-02 08:01:30 +09:00
Chuck Atkins
9f848205e4 mesa: re-written to new meson build system (#10482)
* 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"
2019-05-01 17:57:33 -05:00
Phil Carns
a698ac9711 add PMDK 1.6
- also remove superflous ncurses dependency for PMDK 1.5
2019-05-02 03:37:22 +09:00
Kelly (KT) Thompson
2e6eaa2c0a trilinos: add variant for ShyLU support (#11294) 2019-05-02 03:36:00 +09:00
Sean McGrath
a605fc7e06 ffmpeg package: add aom support (#11210)
* Add Aom package
* Add aom variant to ffmpeg package which controls whether to build
  with the Aom dependency
2019-05-02 03:33:03 +09:00
xfzhao
2a1ba0e142 Supernova package: add version 2.1.1 (#11285) 2019-05-01 09:56:53 +09:00
Francois Budin
b56e418dfe Add margo package and add rc1 tag for argobots package (#11281)
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).
2019-05-01 09:47:34 +09:00
Francois Budin
52752efa4d veloc package: add version 1.1 and update master dependencies (#11270)
* Add version 1.1 and set it as preferred
* Add pdsh as a dependency for `master`
2019-05-01 09:44:51 +09:00
Francois Budin
e2825d0ad4 Darshan 3.1.7 and develop versions fpr darshan-runtime and darshan-util (#11269)
* Add version 3.1.7
* Add develop branch (git master)
2019-05-01 09:42:32 +09:00
Thomas Gruber
06ed77bdfa Lua: Fix unresolved symbols in shared library by linking with libdl.so (#11260)
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.
2019-05-01 08:41:08 +09:00
Greg Becker
7b715564d0 openfoam-com package: build without kahip by default (#11259)
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.
2019-05-01 08:26:54 +09:00
Tiziano Müller
d2786ec064 CP2K package: add versions and tests, adjust optimization flags (#11263)
* 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
2019-05-01 04:52:13 +09:00
Todd Gamblin
8e5e36dc0b Fix spack flake8 to use Travis's target as base when needed 2019-05-01 04:44:02 +09:00
Jannek Squar
f41103770d OpenCV: New versions, adjust protobuf dependency (#11243)
* 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
2019-05-01 03:37:47 +09:00
xfzhao
e10dd6f779 Masurca (#11286)
* py-pauvr:new package

* falcon-unzip: new package

* supernova: updating

* masurca: updating

* rm extra files

* modifying available versions and adding url

* fixing deleted supernova
2019-04-30 08:24:12 -05:00
Matthias Diener
c43296e00d git-lfs: add version 2.7.2 (#11311) 2019-04-30 10:20:03 +02:00
Denis Davydov
a11b252a1b remove myself from maintainers of some packages (#11319) 2019-04-30 10:16:53 +02:00
Chuck Atkins
d2a5a10f08 vtk: Use the vendored libharu (#11293)
VTK requires a patched libharu that is not maintained upstream
See https://github.com/libharu/libharu/pull/157
2019-04-30 10:07:29 +02:00
Xavier Delaruelle
1a920ee64f environment-modules: add version 4.2.4 (#11307) 2019-04-27 20:32:57 +02:00
Daryl W. Grunau
c860d743f9 py-dateutil: add missing dependency on py-setuptools-scm (#11282)
Confirmed that versions before 2.7.5 do not require this dependency.
2019-04-26 20:28:35 +09:00
Felix Mayr
a195ffada2 QuantumEspresso package: add version 6.4 (#11302) 2019-04-26 20:25:40 +09:00
Frédéric Simonis
c951d1cb98 precice: add version 1.4.1 (#11276) 2019-04-26 09:49:11 +02:00
Chris Green
1b2817ee0a root: new versions, variants and patches (#11215)
* 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.
2019-04-24 08:48:52 +02:00
Toyohisa Kameyama
ac7f9ef93d Fix handling of MODULEPATH in setup-env.sh (#11274)
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).
2019-04-24 11:53:25 +09:00
Toyohisa Kameyama
3d46dcd6f0 nest: change cmake_options to args. (#11273) 2019-04-24 11:09:49 +09:00
Eric Martin
e6bd4d27ea py-pandas: Add version 0.20.0 (#11264) 2019-04-24 09:01:56 +09:00
George Hartzell
b0080c705c squashfs should depend_on('zlib') (#11265)
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 09:01:36 +09:00
Daryl W. Grunau
edca0cde1c _valid_tokens list is missing intended comma (#11271)
* _valid_tokens list is missing a needed comma
2019-04-24 08:55:20 +09:00
Chris Green
597037c9ff ftgl: update to 2.1.3-rc5. (#11214)
* 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.
2019-04-23 09:42:10 -05:00
Eric Martin
bc080d753c py-umi-tools: Add latest versions (#11256) 2019-04-23 18:23:44 +09:00
George Hartzell
efe62b7d6d Install squashfs exe's into prefix.bin, not prefix (#11246)
The squashfs Makefile's `INSTALL_DIR` args is the path to the `bin` directory, not the top of the install tree.

Adjust accordingly.
2019-04-22 20:16:57 +02:00
Todd Gamblin
552c9c57fd
Update tutorial page with RIKEN tutorial slides. (#11254)
- Add link to container image, as well as a description of VMs
- Update slide link to point to latest RIKEN tutorial
2019-04-23 01:53:47 +09:00
Greg Becker
5aa4edb939 Fix transitions between tutorial sections (#11251) 2019-04-22 17:14:26 +09:00
Todd Gamblin
0aed3bcea6 spack edit: use execv instead of Executable (#11245)
- `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
2019-04-20 20:51:45 -07:00
Janne Blomqvist
5fb6145f6f OpenBLAS: Allow enabling/disabling AVX2/512 support
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.
2019-04-20 16:43:11 -07:00