Commit graph

8034 commits

Author SHA1 Message Date
Sinan
54d56db1f1 New package: py-pyrosar (#11428) 2019-05-15 10:53:30 +09:00
Sinan
733c2a2554 New package: py-spatialist (#11427) 2019-05-15 10:52:31 +09:00
Sinan
63af41c0c6 New package: py-tblib (#11425) 2019-05-15 10:51:37 +09:00
Sinan
e2ce4386e2 New package: py-scoop (#11423) 2019-05-15 10:50:41 +09:00
Sinan
249845e80b New package: py-progressbar2 (#11421) 2019-05-15 10:49:28 +09:00
Sinan
544cf085b4 New package: py-python-utils (#11422) 2019-05-15 10:47:28 +09:00
Christoph Junghans
6083de3baa
nut: add v0.1.1 (#11444) 2019-05-14 16:36:31 -06:00
Justin S
723eea00f3 r-construct: new package at 1.0.3 (#11452) 2019-05-14 16:24:01 -05:00
Justin S
1ceeac8603 r-rstan: add 2.18.2 (#11447) 2019-05-14 16:23:14 -05:00
Justin S
fc890c80fb r-loo: new package at 2.1.0 (#11448) 2019-05-14 16:22:29 -05:00
Brian Van Essen
92040a475f LBANN: add support for new python front end (#11395)
* LBANN: add python dependency and required python library dependencies
* LBANN: add version 0.99 as alias for develop branch
* LBANN: build Conduit library by default
* LBANN: CUB is included with Hydrogen for later versions
* New package: py-graphviz (dependency for LBANN)
* New package: py-texttable (dependency for LBANN)
* New package: py-onnx (dependency for LBANN)
* New package: py-typing-extensions (dependency for py-onnx)
* Conduit: add version 0.4.0
* NCCL: Add versions 2.4.6-1 and 2.4.2-1
* Protobuf: Add versions 3.7.1 and 3.7.0
* py-protobuf: add version 3.7.1
* py-typing: add version 3.6.4
* cuDNN: add versions. The source differs depending on the
  architecture, so the versions include a suffix to encode this.
  For example this adds 7.5.1-10.1-x86_64 as well as
  7.5.1-10.1-ppc64le
* cuDNN: Newer versions require newer versions of CUDA
* Hydrogen: add configure options for CUB and Aluminum
2019-05-15 06:20:00 +09:00
Justin S
7ff4105ab5 gmap-gsnap: add 2019-05-12 (#11453) 2019-05-14 15:58:48 -05:00
Justin S
f726e14a0a r-rstantools: new package at 1.5.1 (#11451) 2019-05-14 15:57:54 -05:00
Justin S
ea49b64c44 r-caroline: new package at 0.7.6 (#11450) 2019-05-14 15:57:33 -05:00
Justin S
a4ceffa4ff r-stanheaders: add 2.18.1 (#11446) 2019-05-14 15:18:03 -05:00
Justin S
4f1717998a r-withr: add 2.1.2 (#11445) 2019-05-14 15:17:25 -05:00
Justin S
c6d34076dc repeatmasker: add 4.0.9, refactor interactive config (#11385) 2019-05-14 15:16:32 -05:00
Jon Rood
5cd593743e PNetCDF package: enable option required by NetCDF (#11420)
The --enable-relax-coord-bound option was added in 1.8.0. NetCDF
4.6.3 enabled relax coords by default and required it from PNetCDF.
PNetCDF 1.10.0 enabled it by default but for versions between 1.8.0
and 1.10.0 it should be enabled explicitly.
2019-05-15 05:15:38 +09:00
Peter Scheibel
c54f23d405
CUDA package: exclude compat libs (#11449)
CUDA 10.0 provides Compatability libraries for running newer versions
of CUDA with older drivers. These do not work with newer drivers.
2019-05-15 04:59:12 +09:00
Justin S
a5cf50df2e megadock: new package at 4.0.3 (#10537)
* megadock: new package at 4.0.3

* megadock: remove CudaPackage redundancies

* megadock: move env vars to build targets, use cuda_arch variant

* megadock: flake8 fixes, more flexible mathlib
2019-05-14 14:47:19 -05:00
Jon Rood
f7a778af3c Fix py-yt for Python 2 by requesting older py-ipython version (#11416)
* Fix py-yt for Python 2 by requesting older py-ipython version.
* Add conflicts statement to py-ipython because version 7: is not
  compatible with python@2.7
2019-05-15 04:24:52 +09:00
william-dawson
76dd7a92e1 New Package: NTPoly (#11412) 2019-05-15 04:06:10 +09:00
Jon Rood
4a013adc3e Add new versions of metaphysicl and change masa to use branch instead of tag. (#11436) 2019-05-14 08:56:52 +09:00
Justin S
4fcd70cc29 r-bh: add 1.69.0-1 (#11435) 2019-05-14 08:56:14 +09:00
Levi Baber
71d8b8a9b6 rename py-pauvr to py-pauvre (#11437)
* rename py-pauvr to py-pauvre
2019-05-14 08:55:53 +09:00
George Zagaris
a27f2978b9 m4 package: fix OS version check (#11290)
f242f5f removed spec.architecture.platform_os, which was used to test
an option in the 'm4' package. The attribute is now accessed as
'spec.architecture.os'.
2019-05-14 04:53:23 +09:00
Adam J. Stewart
f283487670 Add master branch of leveldb (#11405) 2019-05-13 14:35:15 -04:00
Shane R. Spencer
dcbe798ca7 New package: py-pycares (starting at 3.0.0) (#11340) 2019-05-11 03:48:37 +09:00
Chuck Atkins
418d9f07dc mesa: Add 19.0.4 (#11415) 2019-05-10 13:25:26 -05:00
Hans Pabst
8f0fe5939f LIBXSMM 1.12 (#11414) 2019-05-10 13:11:47 -05:00
Jon Rood
feac68d248 Add new version of PGI compiler. (#11417) 2019-05-10 13:11:23 -05:00
Chris Green
7467a46c2c sqlite: add versions; restore old versions; variant resolves security issues. (#11336)
* Add versions 3.27.{0,1,2} and 3.28.0
* Add url_for_version: the URL format includes the year so this
  function maps version ranges to years
* Restore patches for versions removed in 84c547c: this commit
  removed versions before 3.26.0 due to a security issue with FTS
  support. Add a +fts variant (default true) that enables FTS
  support along with a conflict for +fts with earlier versions.
2019-05-11 02:58:23 +09:00
Chuck Atkins
85fa2dbe36
paraview: Fix OpenGL search to ignore glvnd (#11400) 2019-05-10 09:47:20 -04:00
xfzhao
d0bfe753be py-pauvr:new package (#11292)
* py-pauvr:new package

* py-pauvr: using url and Releases

* py-pauvr: remove extra comments
2019-05-10 08:29:45 -05:00
Peter Josef Scheibel
7e94774214 update aom package license 2019-05-10 04:37:56 +09:00
Peter Josef Scheibel
57a65acedc update license date range for simgrid 2019-05-10 04:37:56 +09:00
Mark W. Krentel
26b9369c57 dyninst: update cmake args and boost dependency (#11378)
* Starting with the upcoming 10.1 release, Dyninst changed the names of
  some cmake args to camel case: LIBELF_* to LibElf_* and LIBDWARF_* to
  LibDwarf_*.  This change is needed now for @develop and will be used
  for 10.1 when it is released.
* New versions of Dyninst now requires cmake version 3.4.0 or later.
* Restrict boost dependency version to < 1.70.0 to avoid build error
2019-05-10 03:58:41 +09:00
David Gardner
ac3cbfd69a update to texlive 2019 (#11365) 2019-05-09 13:47:43 -05:00
Tiziano Müller
92c4567404 elpa: override headers prop for common include-dir localization
... and apply this in SIRIUS, CP2K & QE.

Thanks to @scheibelp for the idea.
2019-05-10 03:43:02 +09:00
Tiziano Müller
f87722b74d packages/cp2k: require libxsmm 1.11+ 2019-05-10 03:43:02 +09:00
Tiziano Müller
4b3e43cc64 packages/cp2k: build with -ggdb with GNU for backtraces 2019-05-10 03:43:02 +09:00
Tiziano Müller
f343d6fc68 packages/cp2k: add support for sirius 2019-05-10 03:43:02 +09:00
Tiziano Müller
844a993605 packages/json-fortran: initial commit, required by CP2K+sirius 2019-05-10 03:43:02 +09:00
Tiziano Müller
a3341bbdf3 packages/sirius: initial commit 2019-05-10 03:43:02 +09:00
Tiziano Müller
3b72d71d9c packages/libvdwxc: initial commit, required for SIRIUS 2019-05-10 03:43:02 +09:00
Jerome Soumagne
a5f88d6ec8 Clean up mercury package and add boostsys, shared variants (#11368)
Use tarballs instead of git tags

Fix openpa dependency on gcc < 4.9

Fix boost dependency

Change sm variant default to true
2019-05-09 12:56:10 -05:00
Michael Kuhn
d284ea39a1 nco: Add 4.7.9 (#11389)
Earlier versions do not compile with gcc@9.
2019-05-09 12:33:36 -05:00
Michael Kuhn
ebc32319f6 netcdf: Fix build if curl is not installed (#11387)
For 4.7.0, configure fails if curl is not installed.
2019-05-09 13:23:49 -04:00
Michael Kuhn
4e0c909d0a qt: Fix build with gcc@9 (#11391) 2019-05-09 11:28:56 -05:00
Michael Kuhn
2b378f27a2 papi: Add 5.7.0 (#11390)
This also fixes the GCC patch to be applied for versions 8 and up.
2019-05-09 11:26:05 -05:00
Michael Kuhn
220cf08f82 gcc: Add 9.1.0 (#11386) 2019-05-09 11:25:29 -05:00
Michael Kuhn
a9febea40f mesa: Add missing dependencies (#11394) 2019-05-09 07:56:37 -04:00
Chuck Atkins
5ac0172b33
qt: sqlite needs to be a run dep because of the qt plugin infrastructure (#11399) 2019-05-08 18:41:25 -04:00
Chuck Atkins
a0dc4dc94d
mesa: Add 19.0.{1,2,3} (#11401) 2019-05-08 18:40:26 -04:00
Christoph Junghans
5445e17089
nut: fix nut build (#11393) 2019-05-08 11:34:48 -06:00
Kelly (KT) Thompson
bcdf9572e5 Provide a patched version of random123 that will work on ARM platforms (#11388)
+ The additional patch enables a non-optimized random123 code path that will
  work on ARM architectures. This solution is provided only for version 1.09 to
  allow the most current version of Random123 to function on ARM architectures.
+ A more complete, long term solution will be the addition of a native ARM
  intrinsics-based implementation of random123.  This solution is being worked
  on but it is several weeks or months away.  Once the full implementation is
  available it will be provided to the author/maintainer of Random123.
2019-05-08 08:38:47 -06:00
Chuck Atkins
e4ce4e5c2c llvm: Adjust default supported targets
The default install for llvm should just be the common typical case, i.e.
support for local host and cpu architectures.  Enablingsupport for the wide
array of auxiliary architectures should be explicit rather than implicit.
2019-05-08 04:36:43 +09:00
Janne Blomqvist
4a83b4710c Add OpenBLAS 0.3.6 (#11375)
Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
2019-05-07 13:36:38 -05:00
Levi Baber
43204049aa py-scikit-learn: needs setuptools (#11379) 2019-05-07 13:35:32 -05:00
Mark W. Krentel
119d04d53f hpcviewer: add version 2019.04 (#11380) 2019-05-07 13:34:05 -05:00
Chuck Atkins
251f3f5058
ninja: drop python as a run dep (#11347)
* ninja: Make python a build-only dependency

* ninja, ninja-fortran: allow the packages to provide eachother
2019-05-07 13:07:24 -04:00
xfzhao
65ff6ed8f6 py-pysam: update (#11377) 2019-05-07 08:29:05 -05:00
Felix Niederwanger
6de3e1c7b6 New package: CCfits (#11262) 2019-05-07 03:58:29 +09:00
George Hartzell
96a95bb5bf Mesa should depend_on('glproto') (#11360)
* Mesa should depend_on('glproto')

The mesa package refers to `GL/glproto.h`.  On systems that don't have
the OS packages installed, this leads to failures during the build
[e.g. this comment in
01482](https://github.com/spack/spack/pull/10482#issuecomment-488786745).

This fixes it.  Tested on a minimally provisioned CentOS 7.

* Constrain glproto prereq to when +glx

* mesa: make glproto a build only dep
2019-05-06 14:37:13 -04:00
G-Ragghianti
b64a286820 SLATE package: fix variant/header errors (#11353)
* The 'mkl' variant implementation was not complete and was
  preventing the package from building, so remove it.
* The slate.hh file has moved in the 'develop' version (which is
  currently the only version of SLATE listed)
2019-05-07 02:52:40 +09:00
Todd Kordenbrock
dd3573b78d FAODEL: Add FAODEL package to spack (#11323)
* FAODEL: Add FAODEL package to spack

FAODEL (Flexible, Asynchronous, Object Data-Exchange Libraries) is a collection
of software libraries that are used to implement different data management
services on high-performance computing (HPC) platforms. This project is part of
the Advanced Technology Development and Mitigation (ATDM) effort for NNSA's ASC
program at Sandia National Laboratories.

(cherry picked from commit 6afe045d25b5c000b612116a5695aebbec56b61a)

* FAODEL: Update FAODEL package

  Dependencies: set minimum versions for boost, cmake and libfabric
  Dependencies: add conflict for boost v1.59.0
  Patch: add a patch for v1.1803.1
  Patch: add a when= for the v1.1811.1 specific patches
  Compiler: check for C++11 support in gcc

(cherry picked from commit fb6ed2b3cf20d7e4fff647cba5a70887a78f627f)

* FAODEL: Update FAODEL package

  * replace previous maintainers with @tkordenbrock and @craigulmer
  * default to shared libs to meet Spack policy
  * increase min boost version to 1.60.0 and remove boost 1.59.0 conflict
  * replace complex version check with conflict for gcc <= 4.8.0 (C++11 support required)
  * set type=build for cmake
  * enable googletest for all versions with type=build
  * enable tests for for all versions except when MPI is disabled

* FAODEL: Update FAODEL package

  * add version v1.1811.2
  * limit comment line length
2019-05-06 13:44:32 -04:00
Justin M Wozniak
4c6fb4cefe Turbine package: add m4 dependency (#10948)
m4 is a build and run dependency for Turbine: it is used at run time
to generate scheduler job files for the workflows.
2019-05-07 02:36:32 +09:00
Cameron Smith
78ade980d4 omega-h package: add version 9.27.0 (#11366) 2019-05-04 06:59:26 +09:00
Bili Dong
74295a1217 py-yt package: add versions 3.5.0, 3.5.1, 4.0 development branch (#11350) 2019-05-04 06:49:11 +09:00
cedricchevalier19
328a3f97fd cURL package: add gssapi option (#11344)
This option allows curl and its dependents (git, ...) to work with
proxy using Kerberos authentification.
2019-05-04 05:43:56 +09:00
Sinan
ddf485ee6d New package: GMTSAR (#11315) 2019-05-04 05:40:14 +09:00
Thilina Rathnayake
c2f9061a3c Nek5000: Fix CFLAGS and FFLAGS handling (#11339) 2019-05-04 03:52:45 +09:00
Justin S
9b0000d04f New package: PASTA (#11338) 2019-05-04 03:50:54 +09:00
Sinan
df15969a7d rJava package: add version 0.9-11 (#11334) 2019-05-04 03:45:35 +09:00
Owen Solberg
c031cff2bc BLAST-Plus package: add versions 2.9.0 and 2.8.1 (#11333) 2019-05-04 03:33:35 +09:00
Greg Sjaardema
74fe12bb4e NETCDF: add version 4.7.0 (#11330) 2019-05-04 03:31:36 +09:00
Greg Sjaardema
5d9d8171bb PARALLEL-NETCDF: add version 1.11.1 (#11329) 2019-05-04 03:30:35 +09:00
Sinan
ba58b2f43a GDAL package: add version 2.4.1 (#11328) 2019-05-04 03:30:10 +09:00
Leonhard Reichenbach
edac053cf5 libunistring: added newer versions and patch older ones (#11255)
* Add versions 0.9.10, 0.9.9, and 0.9.8
* Port a change in 0.9.10 to earlier versions as a patch
2019-05-04 03:21:43 +09:00
Federico Ficarelli
0425670942 arm-forge: add all available versions (#11198)
* arm-forge: add all available versions

* Add TODO for the version hell

* Fix linting

Looks like 'black' formatter isn't Spack friendly

* Fix versions ordering

* Remove obsolete package (allinea-forge → arm-forge)
2019-05-03 08:14:25 -07:00
Chris Green
2d8708e542 range-v3: New versions 0.3.7, 0.4.0, 0.5.0. (#11358) 2019-05-03 09:13:50 +02:00
Chris Green
2155d611df libxml2: New version 2.9.9. (#11357) 2019-05-03 09:13:22 +02:00
Chris Green
fe7e85e6d9 cppunit: New version 1.14.0. (#11359) 2019-05-03 09:12:22 +02:00
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
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