Commit graph

13175 commits

Author SHA1 Message Date
Todd Gamblin
963eb98979 tests: require Python 2.6 tests to pass 2019-05-11 16:20:36 -07:00
Todd Gamblin
dda90a5666 bugfix: Do not run spack spec in the test environment for Python 2.6
- Trying to get our Python 2.6 tests working again.
- This seems to crash travis in the 2.6 environment, for whatever reason.
2019-05-10 13:13:44 -07:00
Todd Gamblin
54920d100a enable coverage for python 2.6 unit tests 2019-05-10 13:13:44 -07:00
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
Todd Gamblin
3903658bfc coverage: only run coverage for subset of unit tests
- Codecov cannot handle as many coverage reports as we are generating

- as a result, our PR coverage pages have been broken for a while, and
  it's hard to tell people where to enhance their testing in PR reviews.

- Scale back to only running coverage for 3.7 and 2.7 unit tests

- This is *probably* better.  We run the build tests for good measure,
  but we do not need to evaluate them for coverage.  The coverage reports
  are about unit tests.
2019-05-11 02:23:22 +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
Greg Becker
f67a59fabc permissions: preserve suid and sgid bits (#10727)
* Don't overwrite suid/sgid bits when setting permissions
* add tests for permission setting
2019-05-10 00:38:13 -07:00
Glenn Johnson
c752af098d Intel packages: multiple installs and optional scalapack libs (#11384)
Add fixes to support multiple installs and dependents using a subset
of IntelPackage functionality.

* Update IntelPackage to only return scalapack libraries if the root
  spec depends on MPI: scalapack requires MPI to be mentioned as a
  dependency in the DAG. Package builds using intel-mkl for its
  blas/lapack implementations but not for scalapack were failing to
  build.

  Ideally it would be possible to ask if any of the packages in the
  DAG are actually requesting the scalapack functionality provided by
  the IntelPackage and only return scalapack libs in that case, but
  that is not easily done at this time.

  Fixes #11314
  Fixes #11289

* set HOME when the intel silent installer is run. This prevents the
  installer from using the ~/intel directory (which can cause
  conflicts for multiple installs of the same IntelPackage)

  Fixes #9713
2019-05-10 10:54:05 +09:00
Greg Becker
3d3cea1c87 modules: use new module function instead of get_module_cmd (#8570)
Use new `module` function instead of `get_module_cmd`

Previously, Spack relied on either examining the bash `module()` function or using the `which` command to find the underlying executable for modules. More complicated module systems do not allow for the sort of simple analysis we were doing (see #6451).

Spack now uses the `module` function directly and copies environment changes from the resulting subprocess back into Spack. This should provide a future-proof implementation for changes to the logic underlying the module system on various HPC systems.
2019-05-09 15:04:24 -07:00
Peter Josef Scheibel
53ec16c9e5 make license check more-strict
The license text is now expected to match almost exactly (not
accounting for formatting in different file types (e.g. rst vs.
bash script vs. python)
2019-05-10 04:37:56 +09:00
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
Todd Gamblin
d95bef06e5
Make CODE_OF_CONDUCT.md more Spack-specific (#11403) 2019-05-08 17:49:03 -07:00
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
Seth R Johnson
6cdbc33c90 Hide some variables in spack-build.env file
Don't arbitrarily reset PWD and OLDPWD when sourcing, as well as other
session-specific IDs
2019-05-08 06:36:52 +09:00
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
Chris Green
01eaca607f Environment path sanitization and sourcing (#8476)
Add two functions to the EnvironmentModifications object to help
users sanitize environment variables in their package definitions:

* deprioritize_system_paths: this keeps system paths in the
  environment variable but moves them to the end.
* prune_duplicate_paths: remove any duplicate paths from the
  variable

This includes testing for the new functions as well as for
(previously-untested) old convenience functions for environment
variable manipulation.

This also adds special handling for bash functions so they
will be defined when the exported environment file is sourced.
2019-05-07 11:29:18 +09:00
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