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2017-06-16Update intel* packages (#4528)Kyle Fernandes, né Jacobs6-2/+24
* Update intel-* packages * Update intel package
2017-06-16Update Scalasca/Score-P/Cube/OTF2 (#4485)David Böhme3-30/+31
* Update Scalasca/Score-P/OTF2/Cube. Should fix #4349# * cube: Fix flake8 warnings * cube, scalasca: Fix version range syntax for deps * otf2: Fix version URL generation * cube: Remove static URLs
2017-06-16Fix OpenMPI CUDA support (#4323)Adam J. Stewart1-2/+20
* Fix OpenMPI CUDA support * Remove --with-cuda-libdir flag, not a real flag * Fix PGI and CUDA 7 support
2017-06-16py-pillow: ensure that RPATH includes graphics libraries (#4522)Milton Woods1-1/+3
2017-06-16oce changes for cgm (#4514)iulian7872-18/+31
* oce changes for cgm cgm can be configured with oce, but oce needs to have X11 enabled, because some libraries (like TKCAF in occ/oce) gets built only of X11 is NOT disabled so introduce a variant +X11 for oce, which is needed when configuring cgm with oce(+X11) * follow up review simplify by removing the patch and different url paths use append instead of extend, when necessary make mpi true by default X11 dependency is still to be addressed; it pulls in some opengl library (on laptop nvidia seem to work, on virtual linux machine mesa was good enough)
2017-06-16bugfix: support EDITOR values with spaces (#4523)Todd Gamblin1-8/+8
- previous code called `which` on $EDITOR, but that doesn't work for EDITORs like `emacs -nw` or `emacsclient -t -nw`. - This patch just trusts EDITOR if it is set (same as previous behavior), and only uses the defaults if it's not.
2017-06-16issue 4492: DependencyMap.concrete checks for unconditional dependencies (#4499)Massimiliano Culpo2-10/+96
* issue 4492: added xfailing test, added owner to DependencyMap * DependencyMap.concrete checks if we have unconditional dependencies This fixes #4492 and #4107 using some heuristics to avoid an infinite recursion among Spec.satisfies, Spec.concrete and DependencyMap.concrete The idea, as suggested by @becker33, is to check just for unconditional dependencies. This is not covering the whole space and a package with just conditional dependencies can still fail in the same way. It should cover though all the **real** packages we have in our repo so far.
2017-06-15Fix tests on cray (#4298)Mario Melara3-5/+4
* Check for CRAYPE_VERSION instead of path Architecture tests would fail on Cray since it would not find the expected path. To make the test correctly work on Cray search for the CRAYPE version instead. * Catch SystemExit error in case flake8 not in path On shared systems having flake8 can involve starting own virtual env. Skip the test if no flake8 is found to avoid failure reporting. * Add compatibility to 1.5 svnadmin create The flag added is needed to correctly create svn repos on NERSC systems. This could be unnecessary for other sites. I'd like to see others test before this change gets merged.
2017-06-15Added package py-oset (#4500)Stas Sergienko1-0/+37
* Added py-oset package * Added package py-oset * changed homepage url
2017-06-15added py-latexcodec package (#4509)Stas Sergienko1-0/+37
* Added py-latexcodec package * removed url line from the file
2017-06-15added py-counter package (#4510)Stas Sergienko1-0/+37
2017-06-15openblas: Fix build on aarch64. (#4487)Diana Bite1-1/+8
- invoke make with the correct TARGET for aarch64 - foforce PILERDRIVER as openblas cannot correctly detect CPU on aarch64 - update url to more recent version
2017-06-15Add latest version of JDK (#4317)Adam J. Stewart2-20/+15
* Add latest version of JDK * Use a more specific URL to get curl to work * Remove failing unit test
2017-06-15Add missing doc variant to fenics package (#4473)Adam J. Stewart1-15/+22
2017-06-15Adding initial AMReX package (#4467)Mark C. Miller1-0/+85
* adding initial amrex package * adding missing fortran variant predicate * adjusting description text * adjusting as per @tgamlin guidance
2017-06-15Added py-pywavelets package (#4496)Stas Sergienko1-0/+42
* Added py-pywt package * passes flake8 test * renamed py-pywt to py-pywavelets
2017-06-15Fix dashes in variant parsing (#4498)Todd Gamblin2-8/+8
- Skip spack flake8 test when flake8 is not installed. - Fix parsing of dashes in specs broken by new help parser. - use argparse.REMAINDER instead of narg='?' - don't interpret parts of specs like -mpi as arguments.
2017-06-15Nalu requires Trilinos with Exodus support (#4505)Jon Rood1-1/+1
* Disabling Exodus in Trilinos by default. * Returning default of Exodus to true in Trilinos.
2017-06-15Prefer vim to vi for default editor (#4230)Adam J. Stewart7-85/+97
* vim > vi * Allow which to accept multiple args * Update __init__ to use which with multiple args * Fix doc tests
2017-06-14Add h5utils package (#4506)Adam J. Stewart2-0/+115
2017-06-14Fix tpetra-related xsdk errors (#4501)Alicia Klinvex1-2/+2
* Fix tpetra-related xsdk errors Recent changes to the trilinos package broke the xsdk build. xSDK explicitly disables tpetra, but packages depending on it (such as ifpack2 and amesos2) are explicitly enabled by default in the trilinos package. This commit explicitly disables them within the xsdk package.py. * Disabled exodus in the xsdk build See issue #4502 for details
2017-06-14fix intltool_sbang issue #4191 (#4192)Luigi Calori2-5/+13
* fix intltool_sbang issue #4191 * add per dep even if already depending on perl-xml-parser * adding more comment, properly spaced
2017-06-14Improve qt (#4309)Michael Kuhn1-2/+10
- Introduce an opengl variant that is enabled by default. Disabling it allows building qt for X forwarding etc. - Depend on fontconfig and freetype to make use of system fonts. Otherwise qt can not find any fonts. - libx11 is required when libxcb is used. - Set MAKEFLAGS to parallelize qmake compilation.
2017-06-14Adding package namd (#4321)Nicolas Richart4-22/+195
* Initial version of the namd package * Modified charm to consider compile against intel/intel-mpi * Correction of namd to compile with intel-mkl and intel compiler * Adding inclue64 in the prefix * adding property for the build directory * removing useless function build
2017-06-14Updates rose definition (#4411)Josh Asplund4-16/+151
* Adds z3 package * Adds binwalk package * Updates spot package definition * Updates rose package definition * Modifications for code review * Fixes string formatting * Remove python version requirement
2017-06-14Added new package for py-rsa (#4494)Adam J. Stewart1-0/+39
2017-06-14superlu-dist: don't use '_' symbols from BLAS for IBM XL compiler (#4486)serbanmaerean1-1/+3
2017-06-13ipopt 3.12.7 (#4490)Geoffrey Oxberry1-0/+20
* ipopt: update version to 3.12.7 * ipopt: add +coinhsl option * ipopt: add +metis option
2017-06-13coinhsl 2014.01.17: new package (#4482)Geoffrey Oxberry1-0/+47
2017-06-13metis: bugfix: make shared library build portable (#4489)Geoffrey Oxberry1-1/+2
Fixes #4488. When compiling metis as a shared library, the package used the syntax `-rpath=`, followed by a path. This syntax is non-portable, so replace it using Spack's compiler rpath argument property.
2017-06-13visit: Added VisIt version 2.12.2 (#4495)John Roberts1-0/+1
2017-06-13Override partial installs by default - part three (#4331)scheibelp5-3/+215
* During install, remove prior unfinished installs If a user performs an installation which fails, in some cases the install prefix is still present, and the stage path may also be present. With this commit, unless the user specifies '--keep-prefix', installs are guaranteed to begin with a clean slate. The database is used to decide whether an install finished, since a database record is not added until the end of the install process. * test updates * repair_partial uses keep_prefix and keep_stage * use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not) * add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
2017-06-13espresso: fixed compilation for 6.1 (elpa) and added support for hdf5 (#4483)Massimiliano Culpo3-43/+113
* espresso: fixed compilation for 6.1 (elpa) and added support for hdf5 * espresso: addressed items in @davydden review * espresso: fixed behavior for espresso@:5.4.0
2017-06-13Fix/mumps (#4453)serbanmaerean3-3/+84
* Added magma package * Incorporated Serban's change * mumps: Fix compiler error with IBM XL Split the patching between v 5.0.2 and 5.1.1
2017-06-13Fix building shared libraries for gmp (#4464)Michael Kuhn1-0/+7
If specific compiler flags are set, gmp will not build a shared library, causing failures further down the line.
2017-06-13czmq: Fix invocation when building with clang. (#4479)Diana Bite1-3/+10
Also bump to latest stable version.
2017-06-12Add list_url for packages from http://ab-initio.mit.edu/ (#4471)Adam J. Stewart3-34/+25
2017-06-12Add an installcheck phase to MakefilePackage (#4476)Adam J. Stewart2-17/+21
* Add an installcheck phase to MakefilePackage * Minor changes to ESMF
2017-06-12ISAAC Server: Less Strict Deps (#4481)Axel Huebl1-2/+4
The dependencies of the server packages were overly strict and pulled in too many dependencies. This fixes it.
2017-06-11New Package: bml (#4213)Robert Pavel1-0/+49
* New Package: lanl-bml Added LANL's BML library as Spack Package as dependency for future packages * Adjusted lanl-bml versions Specified current master as develop and added v1.1.0 tagged version * Renamed lanlbml package to bml
2017-06-11Convert elk to MakefilePackage (#4477)Adam J. Stewart1-12/+5
2017-06-10gcc: use isl@0.14 for gcc@5 (#4474)Milton Woods1-1/+2
2017-06-09Move description to top of `spack info` (#4475)Todd Gamblin1-7/+8
2017-06-09Add default list_url for GitLab, BitBucket, and CRAN (#4439)Adam J. Stewart237-246/+42
* Add default list_url for GitLab, BitBucket, and CRAN * Fix flake and doc tests
2017-06-09Move gpg section of docs to Getting Started (#4446)Adam J. Stewart2-64/+67
2017-06-09scala + spark: added legacy versions (#82) (#4461)Massimiliano Culpo2-3/+7
2017-06-09Fix autotools issues (#4463)Michael Kuhn2-0/+6
Add ACLOCAL_PATH to libtool and pkg-config. Without this, aclocal can not find the .m4 files.
2017-06-09add teuchos to Trilinos, update dealii to explicitly require certain ↵Denis Davydov2-8/+11
packages (#4460)
2017-06-09Fix url parse offset for SourceForge downloads (#4458)Adam J. Stewart2-1/+4
2017-06-08Package for mono (#4435)George Hartzell1-0/+65
* First draft package for mono Mono's vendor'ed boringssl interacts badly with openssl, so you need to use `cmake~openssl`. Left to its own devices, it wants to refer to things in `/usr/share/.mono`. This doesn't work for installs that don't run as root, etc... This package includes a variant to redirect those paths to `prefix.share`. * Whitespace/Flake8