Commit graph

11498 commits

Author SHA1 Message Date
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
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
Patrick Gartung
9a85a7a5aa Binary caches on MacOS - allow expanded RPATHs (#11345)
Fixes #11335

Update the Spack compiler wrappers to add the headerpad_max_install_names
linker flag on MacOS. This allows the install_name_tool to rewrite
the RPATH entry of the binary to be longer if needed. This is
primarily useful for creating and distributing binary caches of
packages (i.e. using the "spack buildcache" command); binary caches
created on MacOS before this commit may not successfully relocate
(if the target root path is larger).
2019-05-04 06:41:57 +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
Massimiliano Culpo
5ffb270714 Added a function that concretizes specs together (#11158)
* Added a function that concretizes specs together

* Specs concretized together are copied instead of being referenced

This makes the specs different objects and removes any reference to the
fake root package that is needed currently for concretization.

* Factored creating a repository for concretization into its own function

* Added a test on overlapping dependencies
2019-05-04 03:04:38 +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
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