Commit graph

14528 commits

Author SHA1 Message Date
Robert Kalescky
4d449790d0
r-openssl requires C99. (#15541) 2020-03-18 12:59:27 -05:00
Adam J. Stewart
8ad366a978
py-numpy: add 1.18.2 (#15546) 2020-03-18 11:50:12 -05:00
Amjad Kotobi
6993b81bfd
Add package anaconda3 (#15404) 2020-03-18 11:49:50 -05:00
Brian Van Essen
57ad02ad43
Added a package for the DiHydrogen distributed linear algebra library. (#15426)
* Added a package for the DiHydrogen distributed linear algebra library.

* Updated recipe to provide cuda architecture constaints.

* Addressed reviewer comments

* Fixed flake 8
2020-03-18 11:46:49 -05:00
Nichols A. Romero
e59b506506
QMCPACK Update March 2020 (#15511)
* Clean-up description of variants.

* Support AFQMC with CUDA.
2020-03-18 11:21:48 -05:00
Axel Huebl
958f26073e
openPMD-api: HDF5 1.12.0 Support (#15530)
Fix API breakage in HDF5 1.12.0 for released versions.
2020-03-18 06:47:01 -07:00
Jim Galarowicz
586609102b
Previous qt package file changes broke the openspeedshop gui build. (#15471)
* Previous qt changes broke the openspeedshop gui build.  This puts back the changes that caused the breakage.

* Update the qt version to be more robust.

Co-authored-by: Galarowicz, James <jgalarowicz@newmexicoconsortium.org>
2020-03-18 14:45:17 +01:00
eugeneswalker
847d5d3459
update checksum for intel-tbb@2020.1 (#15528) 2020-03-17 18:45:56 -07:00
Greg Sjaardema
787f89b7db
SEACAS: Add versions 2020-03-16 and 2020-01-16 (#15525) 2020-03-17 18:02:31 -07:00
Sergey Kosukhin
06bf93b270
MPICH: optional libxml2 support; NAG patches (#15235)
* Add patches when building with NAG
* Make libxml2 support optional. Also include conflict for
  @:3.2~hydra+libxml2 since @:3.2~hydra does not require libxml2
  support
* Add '--disable-silent-rules' to get more verbose output during
  the build
2020-03-17 11:41:47 -07:00
Patrick Gartung
be8841cbc5
Remove PatchelfError and change patchelf error message to a warning. (#15518) 2020-03-17 10:49:24 -05:00
wspear
304f0e9ef1
Corrected compiler filtering for TAU makefiles (#15342)
* Implemented working file filtering to replace spack compiler wrapper with real compiler.

* Using string=True instead of re.escape. Using self.prefix.lib instead of appending /lib.

Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
2020-03-17 08:38:53 -07:00
Tomoki, Karatsu
c2e0ee6383
geant4: Removed unnecessary definition of xerces-c. (#15513) 2020-03-17 10:31:31 +00:00
Seth R. Johnson
05d0c7b477
Update and exetend VecGeom (#14520)
* Add new vecgeom versions, add cuda support, automate target options

* Add ROOT, GDML, and external VecCore support to VecGeom

* Address reviewer comments

* Update vecgeom for CUDA

* Update versions
2020-03-17 10:18:40 +00:00
darmac
402d89afa2
nfs-utils: added package at v2.4.2 (#15491) 2020-03-17 08:49:35 +01:00
Massimiliano Culpo
e3f97b37e6
Module files won't use CPATH by default, but language specific vars (#14749)
fixes #11555

Every path in CPATH is equivalent to a -I path to the compiler,
while every path in *_INCLUDE_PATH is equivalent to -isystem.
The latter avoids the noise due to warnings coming from 3rd party
libraries that a project depends on.

Added INCLUDE env variable (Intel Fortran, .mod files)
2020-03-17 08:36:56 +01:00
eugeneswalker
c92847a30c
cap binutils version @:2.33.1 due to build failures with 2.34 (#15504) 2020-03-16 17:47:24 -07:00
Patrick Gartung
e48d24ee45
Warn only if link target is not relative and outside of the install prefix (#15512) 2020-03-16 18:43:11 -05:00
Seth R. Johnson
c9a715b190
veccore: added package at v0.6.0 (#15472) 2020-03-16 20:55:16 +01:00
Patrick Gartung
3029dde7ec
When replacing path text in ELF binaries do not include null byte padding in search string (#15508) 2020-03-16 14:49:55 -05:00
Seth R. Johnson
a8706cc89b
CMakePackage: convert variants to CMake arguments (#14376)
Add a 'define_from_variant` helper function to CMake-based Spack
packages to convert package variants into CMake arguments. For
example:

  args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF'))

can be replaced with:

  args.append(self.define_from_variant('foo'))

The following conversions are handled automatically:

* Flag variants will be converted to CMake booleans
* Multivalued variants will be converted to semicolon-separated strings
* Other variant values are converted to CMake string arguments

This also adds a 'define' helper method to convert any variable to
a CMake argument. It has the same conversion rules as
'define_from_variant' (but operates directly on values rather than
requiring the user to supply the name of a package variant).
2020-03-16 11:41:19 -07:00
Erik Schnetter
55d5adfecf
silo: depends on hdf5@:1.10.999 (#15495)
Silo does not build with HDF5 1.12.
2020-03-16 19:10:06 +01:00
Patrick Gartung
17e4df1e41
Buildcache: Install into non-default directory layouts (#13797)
* Buildcache: Install into non-default directory layouts

Store a dictionary mapping of original dependency prefixes to dependency hashes

Use the loaded spec to grab the new dependency prefixes in the new directory layout.

Map the original dependency prefixes to the new dependency prefixes using the dependency hashes.

Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order.
For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries.

On Linux, patchelf is used to replace the rpaths of elf binaries.
On macOS, install_name_tool is used to replace the rpaths and  dependency libraries  of mach-o binaries and the id of mach-o libraries.
On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries.

Binary text with padding replacement is attempted for all binaries for the following paths:
spack layout root
spack prefix
sbang script location
dependency prefixes
package prefix
 Text replacement is attempted for all text files using the paths above.

Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings.
2020-03-16 08:42:23 -05:00
Melven Roehrig-Zoellner
0301ec32b4
tixi: added package at v3.0.3 (#15490) 2020-03-16 09:02:10 +01:00
Erik Schnetter
77e845d53c
swig: added v4.0.1 (#15496) 2020-03-16 08:45:25 +01:00
Erik Schnetter
1e547f58ab
ncurses: added v6.2 (#15494) 2020-03-16 08:43:21 +01:00
Erik Schnetter
410ad0b158
cmake: added v3.16.5 (#15492) 2020-03-16 08:42:49 +01:00
Matthieu Dorier
d24c64c936
unqlite: added package at v1.1.9 (#15501) 2020-03-16 08:33:42 +01:00
Erik Schnetter
96a037adf7
gcc: Don't apply macOS 9.2.0 patch for 9.3.0 (#15493)
The patch neither applies nor is necessary.
2020-03-15 15:43:23 -07:00
Tim Haines
471f23e456
Limit binutils to <= 2.33.1 (#15470)
HPCToolKit <= 2020.03.01 does not build with binutils 2.34.
2020-03-14 07:45:00 -05:00
Hans Pabst
38d04e29eb
LIBXSMM 1.15 (#15482)
* LIBXSMM 1.15

* LIBXSMM: renamed development version according to the related branch on GitHub.
2020-03-13 14:44:26 -05:00
Adam J. Stewart
262a69c0a9
py-astpretty: add new package (#15484)
* py-astpretty: add new package

* pkg_resources needed at run-time
2020-03-13 14:40:58 -05:00
Michael Kuhn
14441e00dc
package: Add fetch_options variable (#15317)
PR #15212 added a new connect_timeout option that can be overridden
using fetch_options but had to specified per-version. This adds a new
per-package variable that can be used to override fetch_options for
all versions in the package. This includes connect_timeout as well
as 'cookie' (e.g. for the jdk package).

Packages can combine package-level fetch_options with per-version
fetch_options, in which case the version fetch_options completely
override the package-level fetch_options.

This commit includes tests for the added behavior.
2020-03-13 11:41:19 -07:00
Melven Roehrig-Zoellner
7b00712fff
pgi: add missing paths in setup_run_environment (#15480) 2020-03-13 13:07:35 -05:00
Thomas Kluyver
27bd4a5cdd
Add py-h5glance versions 0.5 & 0.6 (#15461)
* Add py-h5glance versions 0.5 & 0.6

* List versions newest to oldest
2020-03-13 08:05:31 -05:00
Hadrien G
a3c319979b
Add new ACTS version (#15479) 2020-03-13 12:57:32 +00:00
Adam J. Stewart
d1bf433d19
gitignore: pytest cache directory (#15476) 2020-03-13 09:39:34 +01:00
Hector
7ddd84ac14
Add source highlight package (#15473)
* add GNU source-highlight package

* fix flake8

* Allows the package to download from GNU mirrors
2020-03-12 19:26:45 -05:00
Michael Kuhn
9806149145
gcc: Add 9.3.0 (#15469) 2020-03-12 16:10:21 -05:00
noguchi-k
fddca6312c
cpprestsdk: fix common error and, use boost@1.69.0 or lower (#15463) 2020-03-12 16:09:07 -05:00
Tamara Dahlgren
f2a13af43e
testing: increase installer coverage (#15237) 2020-03-12 21:20:20 +01:00
David Böhme
b8064df495
Add Caliper v2.3.0 (#15468) 2020-03-12 13:37:15 -05:00
Amjad Kotobi
ed5b10d11f
Add package jblob-3.0 (#15400) 2020-03-12 13:35:30 -05:00
Joe Koning
d87f09cc5e
Change py-merlinwf to py-merlin (#15453)
* Change py-merlinwf to py-merlin to match PyPi.
Change py-merlin to py-merlin-info.

Move to py-merlin_info.

Add py-merlin-info back in.

* Update dependent packages for the new merlin name.

* Remove non-working pyre and the associated packages, exchanger,
py-pythia and py-mlerin-info from citcoms.

* Remove blank line.
2020-03-12 13:27:02 -05:00
Bryce Allen
6887cb3da4
pfunit: add max_array_rank=(int) variant (#15348)
* pfunit: add max_array_rank=(int) variant

* pfunit: flake8 line length fixes
2020-03-12 10:58:18 -06:00
Zhiyi Wu
d95766756c
Update plumed 2.5.4 and 2.6.0 (#15462)
Co-authored-by: zhiyiwu <zhiyi.wu@gtc.ox.ac.uk>
2020-03-12 10:47:26 -06:00
Thomas Gruber
e916a9424c
likwid: add compiler selection for ARM and POWER architecture (#14183)
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-03-12 14:44:43 +01:00
Jeffrey Salmond
ad1a28ee48
plumed: add cython as dependency (#15460) 2020-03-12 12:01:52 +01:00
Massimiliano Culpo
59b6822a47
Creating versions from urls doesn't modify class attributes (#15452)
fixes #15449

Before this PR a call to pkg.url_for_version was modifying
class attributes determining different results for subsequents
calls and an error when the urls was empty.
2020-03-12 09:21:19 +01:00
Massimiliano Culpo
a22d52a67d
Minor updates to CI configuration (#15458)
* Check on Python versions uses action/checkout@v2
* Update the apt cache before installing system packages
2020-03-12 08:19:42 +01:00