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2019-02-17Update CUDA support in QMCPACK (#10587)Nichols A. Romero1-3/+6
* Support in QMCPACK for CUDA_ARCH flag. * No need to have explicit CUDA variant anymore. * Internal QMCPACK CMake assumes a minimum GPU architecture if none is provided.
2019-02-16Fix plural typo in ROOT package (#10614)Hadrien G1-1/+1
2019-02-16[Docker] more base images (#10560)Omar Padron13-21/+90
* Revert "work around an issue with docker/dockerhub (#10547)" This reverts commit 0ef139ac4d475fb99e08b0856dd7f27b97082e50. * Add more docker base image configurations. - Renamed configs - "centos" -> "centos-7" - "fedora" -> "fedora-24" - "opensuse" -> "opensuse-tumbleweed" - "scilinux" -> "scilinux-7" - "ubuntu" -> "ubuntu-1804" - Added configs - "centos-6" - "fedora-29" - "opensuse-leap" - "scilinux-6" - "ubuntu-1604" With these changes, our docker hub image collection will consist of the following: - "spack/archlinux" - "latest" - "spack/centos" - "latest", "centos7", "7" - "centos6", "6" - "spack/fedora" - "latest", "29" - "24" - "spack/opensuse" - "latest", "tumbleweed" - "leap" - "spack/scilinux" - "latest", "7" - "6" - "spack/ubuntu" - "latest", "bionic", "18.04" - "xenial", "16.04"
2019-02-15Dependency libs: filter system paths and always add lib dir (#10622)Peter Scheibel1-7/+16
Fixes #10617 Fixes #10624 Closes: #10619 #8136 dependended entirely on spec.libs to retrieve library directories from dependencies. By default this function only retrieves libraries if their name is something like lib<package> (e.g. "libfoo.so" for a package called "Foo"). This unconditionally adds lib/lib64 directories for each dependency as link/rpath directories. This also filters system paths from link/rpaths/include directories and removes duplicated paths that #8136 could add.
2019-02-15Fix bug getting specs from build caches (#9600)Javier Cervantes1-2/+2
2019-02-14CDash: allow installing from spec.yaml (#10565)Scott Wittenburg2-1/+48
If the -f <specyamlfile> argument to install is used (rather than providing package specs on the command line), CDash throws an exception due to missing the installation command (the packages targeted for install). This fixes that behavior so CDash reporting succeeds in either case.
2019-02-14new variant: simmodsuite for pumi (#8775)Cameron Smith1-1/+25
2019-02-14Removed pkg.headers.directories from the include list (#10604)Massimiliano Culpo3-15/+13
fixes #10601 Due to a bug this attribute is wrong for packages that use directories as namespaces. For instance it will add "<boost-prefix>/include/boost" instead of "<boost-prefix>/include" to the include path. As a minor addition a few loops in the compiler wrappers have been simplified.
2019-02-14cp2k is now a MakefilePackage (#10570)Massimiliano Culpo4-251/+269
* cp2k: archive the Makefile after a successful installation * cp2k: all checksums are now sha256 * libint: all checksums are now sha256 + added versions 2.4.X * libxc: all checksums are now sha256 + added version 4.3.2 * cp2k: os.path.join instead of join_path + simplified openmp flags * cp2k: turned into a MakefilePackage * cp2k: refactored edit method so that Makefile writing happens last
2019-02-13pythia6: fix input verification issue and example data checksum. (#10563)Chris Green1-3/+2
* pythia6: fix issue validating integer input. * pythia6: account for apparent update of example data file.
2019-02-13xrootd: allow specification of C++ standard. (#10577)Chris Green1-1/+39
* xrootd: add cxxstd variant. * xrootd: support for recent and upcoming versions.
2019-02-13icu4c: Add cxxstd variant (#10552)Ben Morgan1-0/+15
* icu4c: Add cxxstd variant For versions supported in Spack, ICU4C defaults to the C++11. Provide a variant to default to this, plus options for C++14 and 17 if dependees require for ABI compatibility. * icu4c: cxxstd variant cannot be multi
2019-02-13Add Gaudi and RELAX packages (#9194)Hadrien G3-0/+118
* Add a RELAX package * Add a Gaudi package
2019-02-13Add a DD4hep package (#9208)Hadrien G1-0/+43
2019-02-13Add new ROOT release, move to SHA-256 checksums (#10583)Hadrien G1-13/+15
2019-02-13Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant ↵Patrick Gartung17-50/+509
(#10518) * Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant so that it is applied consistently. * Make standalone geant4 data packages that are used when data is not installed with geant4. This allows installing the data files are externals that can be common to many compiler version. * move geant4 data package dependencies to umbrella package geant4-data
2019-02-13make SPACK_SHELL detection more robust (#9712)Phil Carns1-1/+12
Spack shell detection in setup-env.sh was originally based on examining the executable name of $$ (from "ps"). In some cases this does not actually give the name of the shell used, for example when setup-env.sh was invoked from a script using "#!". To make shell detection more robust, this adds a preliminary check for shell variables which indicate that the shell is bash or zsh; the executable name of $$ is retained as a fallback if those variables are not defined.
2019-02-13Dynamic library/include paths (#8136)Peter Scheibel9-252/+261
Fixes #7855 Closes #8070 Closes #2645 When searching for library directories (e.g. to add "-L" arguments to the compiler wrapper) Spack was only trying the "lib/" and "lib64/" directories for each dependency install prefix; this missed cases where packages would install libraries to subdirectories and also was not customizable. This PR makes use of the ".headers" and ".libs" properties for more-advanced location of header/library directories. Since packages can override the default behavior of ".headers" and ".libs", it also allows package writers to customize. The following environment variables which used to be set by Spack for a package build have been removed: * Remove SPACK_PREFIX and SPACK_DEPENDENCIES environment variables as they are no-longer used * Remove SPACK_INSTALL environment variable: it was not used before this PR
2019-02-13add latest version of pixman (#10580)Peter Doak1-2/+3
2019-02-13Eigen package: deactivate some dependencies (#10572)Hadrien G1-7/+10
Set defaults in eigen package to omit typically-unused dependencies
2019-02-13Update lbann sw stack dependencies (#10579)Brian Van Essen3-8/+5
* Added a package for the MDAnalysis toolkit. * Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI even when using CUDA. Fixed small bugs within both LBANN and Hydrogen packages. Added requirements for breathe and cereal to LBANN. * Update use case for doc dependencies. * Cleaning up some of the LBANN software stack dependencies.
2019-02-13Bug Fix in permission setter (#10584)abernede1-2/+3
* fix permission setter Fix a typo in islink test when applied to files. * os.walk explicitly set not to follow links The algorithm strongly rely on not following links.
2019-02-13Allow tty output to be timestamped (#10554)sknigh5-6/+103
* Spack debug output now includes microsecond-granularity timestamps. * Timestamps can also be enabled with the `--timestamp` command line argument.
2019-02-13Cnvnator: a new package. (#8959)健美猞猁1-0/+50
2019-02-13enh: allow time like HH:MM in date strings. (#10034)Matthias Wolf2-1/+8
2019-02-12Enhancement to module autoload documentation (#10310)George Hartzell1-1/+15
* Note that `none` is the default for lmod autoload Save a bit of confusion by *explicitly* pointing out that `none` is the default value for autoload in the lmod module file generator. * Add a tip re building software externally Add a tip about using `autoload: all` when building packages outside of the tree that use artifacts (e.g. libraries, includes) within the tree.
2019-02-12Allow secondary generators when building with CMake. (#9324)Chris Green2-4/+50
CMake supports the notion of secondary generators which provide extra information to (e.g.) IDEs over and above that normally provided by the primary generator. Spack only supports the 'Unix Makefiles' and 'Ninja' primary generators but was not parsing out the primary generator when a secondary generator was also included (e.g. for a generator attribute like 'Codeblocks - Ninja'). This adds a regex for extracting the primary generator for validation. Since the secondary generator is irrelevant to a Spack build, it is passed on to CMake without further validation.
2019-02-12casacore: new package (#7471)健美猞猁1-0/+71
2019-02-12xerces-c: Add cxxstd variant (#10561)Ben Morgan1-0/+15
Add variant to support compiling against main C++ standards if needed for ABI compatibility. Use 'default' value as Xerces-C autoconf system does not enforce a minimum, or set a default, C++ standard.
2019-02-12lbann: updated versions (#10568)Brian Van Essen3-0/+7
2019-02-12remove remaining lzma dependencies (#10553)Matthias Diener2-2/+1
2019-02-12openssl: add version 1.1.1a (#10562)Matthias Diener1-0/+1
2019-02-08work around an issue with docker/dockerhub (#10547)Omar Padron1-0/+14
* try to workaround an issue with docker/dockerhub * apply workaround only when running in travis
2019-02-08root package major update (#8428)Javier Cervantes1-51/+416
* Extend current recipe for root package * Add removed old version * Add dependency type for Python and R packages * Add compiler variants * Adding new root version: 6.14.00 * Add back the minimum cmake version required * LZ4 and xxhash support for old (using builtin options) and new versions (external packages) * Set PYTHONPATH in setup_environment * Address typos and issues pointed by HadrienG2 * Add newer ROOT versions * Solve support for asimage * Define incompatible variants * Organize old dependencies * Add support for minuit * Add support for pythia6 * Remove unneeded list_url * Update license header * Remove block of commented old dependencies * Contrain Qt version * Comment pythia8 variant/dependency, not supported by spack * Force not to build pythia8
2019-02-08libarchive: remove lzma dependency (#10517)Matthias Diener1-1/+0
lzma was last updated in 2008 and has compilation issues on some platforms. The format has been superceded by xz (see e.g. https://tukaani.org/xz/).
2019-02-08CudaPackage: fix wrong version range (#10551)Denis Davydov1-1/+1
2019-02-08Adding a package for cardioid. (#10448)Robert Blake1-0/+72
* Adding a package for cardioid. * Changing package to pass flake8 * Removing template leftovers per @ax3l 's advice * Adding a homepage so tests pass. * Removing whitespace for flake8 * Changing the name of master branch to match spack standards.
2019-02-08meson: add 0.49.1 and disable rpath stripping (#10463)Michael Kuhn2-0/+17
rpath stripping breaks (at least) the gtkplus build because at-spi2-atk's dependencies can not be found.
2019-02-07bug report template: suggest --stacktrace instead of -s (#10548)Peter Scheibel1-4/+4
1137b18 removed the -s option from spack such that to see a stack trace you must pass the --stacktrace option. The bug report templates were not updated accordingly.
2019-02-07netlib-scalapack package: add CMake test patch (#10452)Piotr Luszczek2-0/+46
Add patch to fix Fortran mangling in CMake test This is a fix for builds with GCC 6/7/8 and CMake 2/3. It includes a link to the issue where this is reported. For now, the Spack package applies the patch to all releases >= 2.0.2
2019-02-07repeatmasker package: add variant for cross_match engine (#10534)Justin Stanley1-1/+13
2019-02-07New package: py-jupyterhub (#10461)wspear1-0/+31
This package depends on both python 3.5+ and node-js which depends on python 2.7/2.8 to build. Currently it can only be installed if the node-js package's python dependency is manually removed, so node-js will build with python found on the system rather than provided by spack. Upcoming commits may allow spack to reconcile this automatically.
2019-02-07mirdeep2 package: make sure bins are executable (#10515)Justin Stanley1-0/+2
2019-02-07Trilinos package: update superlu-dist dependency (#10511)mathsen1-1/+1
Trilinos master branch gets the latest superlu-dist (currently 6.1.0)
2019-02-07log-parse: fix error message when no error lines are found (#10543)Massimiliano Culpo1-1/+1
2019-02-07petsc: petscvariables is used from user makefiles - so it should not have ↵Satish Balay1-0/+4
spack compilers listed (#10365)
2019-02-07petsc4py and libensemble: add @develop dependencies (#10539)Satish Balay2-0/+4
* py-petsc4py: add @develop * py-libensemble: add @develop dependency on py-petsc4py@develop
2019-02-07petsc@xsdk-0.2.0: fix sowing dependency (#10535)Satish Balay1-0/+1
2019-02-07xsdk@develop fixes (#10521)Satish Balay2-4/+9
* xsdk@develop: switch trilinos from @master to @develop * xsdk@develop: dtk - fix trilinos dependency on dtk. - dkt-3.0 should be used with trilinos-12.4* - dtk/master should be used with trilinos@develop
2019-02-07orthofiller: new package at 1.1.4 (#10373)Justin Stanley1-0/+38
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