Commit graph

8078 commits

Author SHA1 Message Date
Nick Booher
786b59633d Revbayes update (#11559)
* revbayes: new version

* revbayes: pep8
2019-05-30 13:23:32 -04:00
Justin S
9b88f1b851 mathematica: new package at 12.0.0 (#11509)
* mathematica: new package at 12.0.0

* mathematica: add missing os import

* mathematica: fix url format
2019-05-30 13:21:16 -04:00
Frédéric Simonis
8b81f82156 precice: add version 1.5.0 (#11577) 2019-05-29 15:41:48 -05:00
Patrick Gartung
deab45e7c8 Xrootd: set PYTHON_EXECUTABLE with +python variant (#11581)
* Xrootd: set PYTHON_EXECUTABLE with +python variant

When building with python3 PYTHON_EXECUTABLE needs to be set for deprecated FindPythonInterp to work as expected.

* Add comment

* Flake8

* More flake8

* Update package.py

* typo
2019-05-29 15:41:30 -05:00
Patrick Gartung
7438bb7f45 ROOT: set PYTHON_EXECUTABLE (#11583)
Per @adamjstewart  use spec['python'].command.path
2019-05-29 15:41:13 -05:00
Justin S
ca05c2cbd8 py-flye: new package at 2.4.2 (#11584)
* py-flye: new package at 2.4.2

* py-flye: better python version constraint
2019-05-29 15:37:52 -05:00
Justin Too
a49ce3fc32 ROSE: add version 0.9.10.0, update to Autotools, add variants (#9484)
* Also add versions 0.9.9.104, 0.9.9.52, 0.9.9.0, and 'develop'
* Replace version 0.9.7 with 0.9.7.0
* Update Rose to be an Autotools package
* Update boost dependency to 1.60.0 or later (previously 1.47.0)
* Add EDG binary identifiers for ROSE versions installing from
  archives (rather than git)
* Add variants for mvapich2 backend, c++11, debug symbols,
  optimization, and ROSE-based projects (codethorn, autopar, and
  polyopt)
* Remove patch add_spack_compiler_recognition
2019-05-29 12:00:50 -07:00
Hadrien G
ca71f8b044 New versions and bugfixes for the ACTS package (#11578)
* Improve C++ standard computation in ACTS package

* Use a more clever strategy for aligning ACTS cxxstd with ROOT cxxstd

* Add new ACTS releases

* ACTS is not compatible with the new Boost CMake build system yet

* Explain why Boost 1.70 does not work currently
2019-05-29 13:45:09 -05:00
Dustin Wheeler
8804fbd891 Add LSF dependency for OpenMPI (#11532)
* Add LSF package, which cannot be installed by Spack and must be
  system-installed. The package install will fail if no external
  LSF is registered in packages.yaml (LSF may not be installed in a
  well-known location and the external entry helps Spack locate it
  for dependents).
* Add LSF dependency to OpenMPI when schedulers=lsf is chosen
2019-05-29 10:38:55 -07:00
Patrick Gartung
58a4959b1a
Add newer Google Benchmark version (#11580) 2019-05-29 12:02:41 -05:00
Patrick Gartung
3a20a93bfa
ROOT: Set PYTHON_EXECUTABLE with +python variant (#11579)
* ROOT: Set PYTHON_EXECUTABLE with +python variant

After cmake v3.12 FindPythonInterp used by llvm subsystem is deprecated. Setting -DPYTHON_EXECUTABLE=path_to_python fixes this error:

1 error found in build log:
     118    -- Doxygen disabled.
     119    -- Go bindings disabled.
     120    -- LLVM host triple: x86_64-unknown-linux-gnu
     121    -- LLVM default target triple: x86_64-unknown-linux-gnu
     122    -- Building with -fPIC
     123    -- Found PythonInterp: /usr/bin/python2.7
  >> 124    CMake Error at interpreter/llvm/src/CMakeLists.txt:613 (if):
     125      if given arguments:
     126    
     127        "VERSION_LESS" "2.7"
     128    
     129      Unknown arguments specified
     130

* Flake8

* Update var/spack/repos/builtin/packages/root/package.py

Co-Authored-By: Javier Cervantes <javiercvilla@gmail.com>
2019-05-29 12:02:21 -05:00
Kenneth Moreland
a7ffccfc97 vtkm: fix the directory cmake looks for the source code (#11576)
Previously, the vtkm package was adding a "../" option to the
cmake command line. I suppose this was supposed to be pointing
to the source code, but did not. Rather, Spack correctly adds
the source directory as the first argument to cmake. However,
because ../ was added, it used that as the source directory
instead.

Simply remove this argument to make CMake work correctly.
2019-05-29 11:10:12 -04:00
Axel Huebl
643e7806e0 Catch: 2.8.0 (#11570)
Add the latest Catch2 release.
2019-05-28 15:24:18 -05:00
mathsen
9c9a39538e GnuTLS by default depends on Guile, added a guile variant. Updated GnuTLS to 3.6.8 (#11571) 2019-05-28 15:23:59 -05:00
Satish Balay
0b57c3b8e5 petsc: add version 3.11.2 (#11572) 2019-05-28 15:23:00 -05:00
Denis Davydov
e094e19224 dealii: add 9.1.1 (#11573) 2019-05-28 15:22:39 -05:00
Daryl W. Grunau
6698d1dddb Add support for new unittest-cpp package (#11575)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* Add support for new package: unittest-cpp
2019-05-28 15:21:24 -05:00
Levi Baber
36fda22ed9 r-geomorph: new version (#11556) 2019-05-26 23:34:17 -05:00
健美猞猁
47538a21ec Add a new version for gnutls. (#11546)
* Update URL and add a new version.

* Fix flake8 issues.

* Remove newly-added duplicate url_for_version.
2019-05-26 20:45:16 -05:00
Levi Baber
1efaaad344 py-markdown: new version (#11548) 2019-05-26 20:45:01 -05:00
健美猞猁
7433f9d2cc Add new versions for intel-mkl-dnn. (#11549)
* Add new versions for intel-mkl-dnn.

* Remove the last trailing line.

* Update url and set 0.19 as preferred.
2019-05-26 20:44:34 -05:00
Levi Baber
829bbd7884 r-emmli: new package (#11557) 2019-05-26 20:43:22 -05:00
Olaf Mersmann
af2de9eb2a Update GnuPG and associated packages (#11564)
* libassuan: Update to v2.5.3

* gnupg: Update to v2.2.15

* libgpg-error: Update to v1.36

* libgcrypt: Update to v1.8.4
2019-05-26 20:41:37 -05:00
Axel Huebl
86b2156921 New Package: sl (#11565)
Add the sl program.
2019-05-26 20:40:55 -05:00
Satish Balay
727089c4ef
xsdk@0.4.0: update dealii defaults wrt changes in a973ab475 (#11562)
wrt xsdk@develop - ginkgo requires openmp - so disable until we can add openmp dependencies consistantly
2019-05-26 10:43:06 -05:00
Mark W. Krentel
7c32a4c399 mbedtls: add pic variant (#11558)
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.
2019-05-24 21:50:13 -05:00
Stephen Hudson
bb09bdedc6 Update libensemble to v0.5.0 (#11544) 2019-05-24 15:11:56 -05:00
健美猞猁
137cad2915 Add nettle@3.4.1 (#11547) 2019-05-24 15:08:02 -05:00
Massimiliano Culpo
c291866b9a build env: simplify handling of parallel jobs (#11524)
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`)
2019-05-24 11:45:22 -07:00
Massimiliano Culpo
1bd4521f72 Updated lmod (to version 8.1.5) and associated dependencies (#11552)
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.
2019-05-24 12:45:52 -05:00
Adam J. Stewart
6212e0d9b2
Add latest version of py-cython (#11494)
* Add latest version of py-cython

* Fix cython unit tests
2019-05-23 20:01:45 -05:00
Hans Pabst
d6cf3b6718 LIBXSMM 1.12.1 (#11538) 2019-05-23 10:16:32 -05:00
Jon Rood
4c465d2602 Add cppcheck version 1.87. (#11536) 2019-05-22 18:52:48 -05:00
Jon Rood
e57edebb50 Add CMake 3.14.3 and 3.14.4. (#11534) 2019-05-22 15:46:52 -05:00
Omar Padron
a37efefd3d
package vtk - improve gl handling (#11530)
* package vtk - improve gl handling

* package vtk - minor cleanup
2019-05-22 12:04:29 -04:00
Dustin Wheeler
c2e087c411 Fix typo in openmpi@2.1.6 libmpi.so comment. (#11529) 2019-05-22 10:37:33 -05:00
Denis Davydov
a973ab4751 dealii: add 9.1.0 (#11527) 2019-05-21 16:23:03 -05:00
Levi Baber
b13665d065 py-htseq: new version (#11525) 2019-05-21 12:08:31 -05:00
Elizabeth Fischer
a45c4ef33d Add version (#10594) 2019-05-21 10:03:50 -04:00
Michael Kuhn
1f828ce5b8 Update scorep and friends (#11523) 2019-05-21 12:28:12 +02:00
Denis Davydov
5d6461b895 dealii: fix symengine constraints (#11517)
disable symengine constraints due to limitations of Spack
2019-05-21 07:38:58 +02:00
Chuck Atkins
a34142ed30
mesa: Patch missing gl symbols in OSMesa (#11518) 2019-05-20 22:41:41 -04:00
Glenn Johnson
d1ea5ba2cd OpenMPI: update behavior for fabrics/schedulers=auto (#11431)
* 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.
2019-05-20 17:52:17 -07:00
Andrew Gaspar
2168c08ac5 Update optional-lite and span-lite to use CMakePackage (#11407)
* 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
2019-05-20 13:04:06 -05:00
Adam J. Stewart
7fe0230492
Add py-kmodes package (#11497) 2019-05-19 14:17:30 -05:00
Adam J. Stewart
5b6445e519
Add latest version of joblib (#11495) 2019-05-19 14:17:03 -05:00
Adam J. Stewart
ac358a1b4d
Add latest version of setuptools (#11493) 2019-05-19 14:16:37 -05:00
David Beckingsale
866b9b5d13 Update Umpire package with new versions (#11441)
* Update Umpire package with new versions

* Fix version ordering
2019-05-18 23:04:12 -05:00
Denis Davydov
a66cc59bb0 trilinos: add variant to disable chaco from seacas (#11482)
* 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
2019-05-18 23:01:44 -05:00
Mark W. Krentel
e1bb6821aa dyninst: rework the cmake args for version 10.1 and later (#11484)
* 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.
2019-05-18 23:00:48 -05:00