Commit graph

14694 commits

Author SHA1 Message Date
Adam J. Stewart
51f8744ab7
py-horovod: set appropriate build env vars (#15548)
* py-horovod: set appropriate build env vars

* mxnet: add maintainer

* py-horovod: fetch git submodules

* py-torch: fix CUDA conflicts
2020-03-18 17:01:20 -05:00
ktsai7
77b11433b3
modified spackage for flecsi and cinch (#15555) 2020-03-18 15:46:29 -06:00
gauthier12
ff29599578
adol-c:updating sources location (#15532)
* adol-c:updating sources location

* Update var/spack/repos/builtin/packages/adol-c/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-03-18 15:13:57 -05:00
Sinan
3bcb5b3a59
package/QGIS: fix cmake/FindPyqt.py (#15455)
* fix cmake/FindPyqt.py

* apply patch

* generalize patch

* rename patch

* fix typo

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@github>
2020-03-18 13:19:46 -05:00
Sinan
056fc99676
Use python extend_path as pyqt sip fix (#15297)
* try extend path to solve PyQt5.sip not found issue

* disable private sip installation in sippackage class

* undo manual PyQt5 dir creation in py-sip site-packages dir

* fix typo

* fix typo

* also apply fix to PyQt4

* tidy up

* flake8 and tidy up

* tidy and undo hardcoding of python_include_dir

* replace hardcoded python inc dir

* fix minor issues

* rethink include dir variable name

* improve style

* add new versions

* implement new sip setup to qsci installation

* set sip-incdir correctly for the new setup

* setup extend_path thing before qsci python bindings

* take care of conflict

* flake8

* also extend for PyQt4

* improve style

* improve style

* SipPackage build sys should depend on py-sip

* consolidate extend_path fixes into SipPackage

* fix typo

* fix bugs

* flake8

* revert sip doc to pre-resource setup

* import os module

* flake8

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-03-18 13:19:27 -05:00
Nick Booher
156b59c2f1
revbayes: Update pre-build process (#15485) 2020-03-18 13:18:45 -05:00
Benjamin Tovar
8cdd78cd1d
Cctools 7.1.0 (#15506)
* update to 7.1.0

* adds gettext as dependency (needed to link with python)

* disable python2 or python3 as needed
2020-03-18 13:14:45 -05:00
darmac
9372783de6
add new package: acl (#15514) 2020-03-18 13:12:40 -05:00
darmac
b52b082627
add new package: userspace-rcu (#15515) 2020-03-18 13:12:02 -05:00
Greg Sjaardema
73321dd3ea
CGNS: Version update (#15523)
* CGNS: Version update

The CGNS library has several new versions.   There was a format-changing change in 3.4.0 which was removed for 3.4.1.  The change was then added again and released with a change to the major version (4.0.0).  Note that 4.0.0 should be close to the functionality of 3.4.0.

* CGNS: Add shared variant

Added the `shared`variant to make the CMake build correctly pick up the RPATH settings.
2020-03-18 13:09:28 -05:00
darmac
c3434e230a
update util-linux to version: 2.33:2.35.1 (#15529) 2020-03-18 13:04:51 -05:00
Toyohisa Kameyama
530e864671
triangle: add X11 dependency. (#15533) 2020-03-18 13:03:03 -05:00
Toyohisa Kameyama
0fce7df1e9
xsetpointer: fix wrong dependency type. (#15534) 2020-03-18 13:02:35 -05:00
gauthier12
cfc5f3caec
adding the fortran option for hdf5 dependency for comptatibility with petsc requirement (#15536) 2020-03-18 13:01:04 -05:00
Toyohisa Kameyama
209ec03f7e
xts: add some dependencies. (#15537) 2020-03-18 13:00:28 -05:00
Robert Kalescky
6bb8b92bc3
Remove trailing newline. (#15539) 2020-03-18 12:59:52 -05:00
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