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2016-10-11Merge branch 'develop' of https://github.com/LLNL/spack into ↵alalazo138-259/+1329
features/install_with_phases_rebase Conflicts: lib/spack/spack/build_environment.py lib/spack/spack/cmd/install.py lib/spack/spack/cmd/setup.py lib/spack/spack/package.py var/spack/repos/builtin/packages/gmp/package.py var/spack/repos/builtin/packages/hdf5/package.py
2016-10-11hypre: fix blas/lapack for MKL (#1993)Denis Davydov1-2/+2
2016-10-11Merge pull request #1989 from KineticTheory/cray_compile_wrappersTodd Gamblin1-4/+12
On Cray machines, use the Cray compile wrappers instead of MPI wrappers.
2016-10-11Add variant to MPICH to enable ROMIO support (#1944)Adam J. Stewart1-32/+32
2016-10-11tethex: add a new package (#1991)Denis Davydov1-0/+49
2016-10-11More specific dependency versions, wrap make check (#1962)Adam J. Stewart3-12/+25
2016-10-11Update libjpeg-turbo: added new version and removed redundant dependency. ↵Sergey Kosukhin1-7/+12
(#1897)
2016-10-11pango: add missing dependency (#1958)Denis Davydov1-0/+1
2016-10-11libcerf: fix for modern clang (#1959)Denis Davydov1-1/+7
2016-10-11[WIP] Use boost system layout by default (#1955)scheibelp2-8/+28
Use boost system layout by default
2016-10-11Charm++: Ignore compiler warnings while configuring (#1981)Erik Schnetter2-0/+18
2016-10-11Trilinos: Use more flexible option for locating the BLAS library directory. ↵Kelly Thompson2-9/+2
(#1987) + This change fixes a problem that manifests when trilinos is built against a MKL installation defined as an external package. In this scenario, the MKL libraries are found one directory deeper than for the case where spack provides MKL. The extra directory is a platform name like 'intel64'. + The changes in this PR were recommended by contributor @davydden. I implemented and tested with intel@16.0.3. These changes fix the issue I reported. I did not attempt building trilinos against other BLAS implementations. + fixes #1923
2016-10-11hpx5 version update (#1967)Pramod Kumbhar1-2/+3
2016-10-11Mfem 3.2 (#1202)Geoffrey Oxberry1-15/+55
* mfem: add tarball extension Add tarball extension as a result of a feature added in PR#1926, which fixes earlier issues in this PR (PR#1202). Prior to adding this feature, Spack would not autodetect the extension of the tarball downloaded from the redirected, shorted Google URL, requiring a messy hack. This hack worked for mfem version 3.1, but led to errors when adding mfem version 3.2 because the files downloaded from Google did not contain the package name, version number, or extension. Adding the extension enables Spack to rename the tarball downloaded from Google to a sensible name that is compatible with its filename parsing algorithms so that Spack "does the right thing" (detects that the file is a GZipped tarball, decompresses it, runs GNU Make) in fetching and staging the package. * mfem: add linkage to KLU & BTF Add linkage to the KLU & BTF solvers, which are now enabled in MFEM for versions 3.2 and later. * mfem: Add superlu-dist variant Add linkage to SuperLU_DIST, which is a new linear solver interface for MFEM versions 3.2 and later. * mfem: add netcdf variant for cubit mesh support Add NetCDF variant for MFEM versions 3.2 and later; installing the NetCDF interfaces enables CUBIT mesh support.
2016-10-10On Cray machines, use the Cray compile wrappers instead of MPI wrappers.Kelly (KT) Thompson1-4/+12
+ Cray compile wrappers are MPI wrappers. + Packages that need to be compiled with MPI compile wrappers normally use 'mpicc', 'mpic++' and 'mpif90' provided by the MPI vendor. However, when using cray-mpich as the MPI vendor, the compile wrappers 'CC', 'cc' and 'ftn' must be used. + In this scenario, the mpich package is hijacked by specifying cray-mpich as an external package under the 'mpich:' section of packages.yaml. For example: packages: mpich: modules: mpich@7.4.2%intel@16.0.3 arch=cray-CNL-haswell: cray-mpich/7.4.2 buildable: False all: providers: mpi: [mpich] + This change allows packages like parmetis to be built using the Cray compile wrappers. For example: 'spack install parmetis%intel@16.0.3 ^mpich@7.4.2 os=CNL' + This commit relies on the existence of the environment variable CRAYPE_VERSION to determine if the current machine is running a Cray environment. This check is insufficient, but I'm not sure how to improve this logic. + Fixes #1827
2016-10-10Update package to use MPI compile wrappers as specified in MPI package. (#1985)Kelly Thompson1-6/+4
+ Previouly, these strings were hard coded to 'mpicc', 'mpic++', and 'mpifort'.
2016-10-10fix blas-lapack in scipy and numpy (#1949)Denis Davydov2-19/+14
* fix blas-lapack in scipy and numpy * py-numpy: do not set rpath on macOS * py-scipy: do not set Blas/Lapack. This appears to be picked up from py-numpy * py-numpy: don't write rpath= in Sierra only * py-numpy: add a link to build notes
2016-10-10Correct Charm++ install procedure (#1957)Erik Schnetter1-0/+16
Charm++ only creates symbolic links instead of copying files. Correct this.
2016-10-07Added symengine and associated packages (#1885)Jean-Paul Pelteret7-4/+365
Symengine and associated packages
2016-10-06Restore default RPATH settings but allow packages to limit to immediate ↵Todd Gamblin1-0/+4
deps. (#1954) - Some packages (netcdf) NEED RPATHs for transitive deps. - Others (dealii) will exceed OS limits when the DAG is too large.
2016-10-06atlas: add 3.10.3 (#1952)Denis Davydov1-0/+3
2016-10-06Feature Proposal : Make All Python Extensions User Configuration Independent ↵Joseph Ciurej86-94/+90
(#1435) * Updated all Python extension packages to use 'setup_py' on install. * Fixed a few minor style issues with the updated Python packages.
2016-10-06Update gmp: fixed an issue with intel compiler. (#1898)Sergey Kosukhin1-2/+8
2016-10-06Updated nettle to have m4 as an immediate dependency (#1946)Jay1-0/+1
* Updated nettle to have m4 as an immediate dependency to match new PATH construction logic which only includes immediate dependencies. * Update package.py
2016-10-06Sqlite ppc64le configure build guess fix (#1684)James Wynne III1-1/+10
* Added check for ppc64le because configure cant guess the build type for rhel on ppc64le Expand/clarify description of dependency types Refactored getting the arch so that its less verbose * Fixed flake8 issues
2016-10-06Update pixman: mmx is disabled only for MacOS. (#1896)Sergey Kosukhin1-3/+9
2016-10-06Update libtiff: updated homepage and fetch urls. (#1895)Sergey Kosukhin1-2/+3
* Update libtiff: updated homepage and fetch urls. * Update libtiff: new version 4.0.6.
2016-10-06cgal: build out of source. (#1918)Elizabeth Fischer1-4/+4
* cgal: build out of source. * Simplify cmake out-of-source.
2016-10-06add python options to vtk package (#1931)Jeffrey Salmond1-1/+5
2016-10-05mumps: Add alternate download location (in comments) (#1919)Elizabeth Fischer1-0/+2
2016-10-05Add package for CONVERGE CFD (#1905)Adam J. Stewart1-0/+69
2016-10-05Add latest versions, resolve variant resolution bug (#1909)Adam J. Stewart3-8/+14
2016-10-05everytrace: New package (#1543)Elizabeth Fischer2-0/+98
* everytrace: New package Everytrace ensures that stack trace is obtained every time a program exits, for whatever reason. * everytrace: Change CMake to build dependency * Renamed to everytrace-example, flake8 and copyright issues. * flake8 * Missing type=build
2016-10-05Add missing dependencies for Flake8 (#1883)Adam J. Stewart9-26/+364
* Warn user if flake8 can't find setuptools * Add missing dependencies of flake8 * Updates to py-autopep8, make packages activateable * Check for presence of setuptools for Sphinx too * Fix bug in order of commands
2016-10-05PNGwriter, libSplash: Add `master` version (#1744)Axel Huebl2-0/+8
* PNGwriter, libSplash: Add `master` version * PNGwriter, libSplash: Add `dev` versions Can be used for now, `develop` is currently discouraged.
2016-10-05boost: set 1.61 as preffered until 1.62 is fixed (#1908)Denis Davydov1-2/+2
2016-10-05Merge branch 'develop' of https://github.com/LLNL/spack into ↵alalazo161-714/+3985
features/install_with_phases_rebase Conflicts: lib/spack/spack/cmd/setup.py lib/spack/spack/package.py var/spack/repos/builtin/packages/gmp/package.py
2016-10-04Packages for Darshan I/O performance characterization tool from ANL (#1900)Pramod Kumbhar2-0/+106
2016-10-04Update documentation URL after switch to readthedocs (#1901)Adam J. Stewart8-15/+15
2016-10-04A set of tools used in climate modeling and numerical weather prediction. ↵Sergey Kosukhin8-19/+367
(#1317) * Update grib-api: switched to cmake building system. * Update harfbuzz: added pkg-config dependency. * Update pango: added pkg-config dependency. * Add libemos package. * Add Magics (from ECMWF) package. * Revert "Variant for building cdo without mpi (#1638)": CDO does not use MPI. This reverts commit 079d063c6d94be84974f1ddd6eb880e902c95b4a. * Update CDO package: full featured implementation. * Update magics: added python as build dependency. * Update cdo: added disabling configuration options.
2016-10-04Adds mpip package (#1886)Ivo Jimenez1-0/+44
2016-10-04Adds lulesh package (#1887)Ivo Jimenez2-0/+115
2016-10-04Spack package for HPCToolkit (#1892)Pramod Kumbhar2-0/+94
* Spack package for HPCToolkit (performance analysis tool) * Correction for PR comments, make flake8 happy * update note / comments
2016-10-03cp2k : added support for libint, fixed compilation issues on elpa (#1889)Massimiliano Culpo3-5/+22
2016-10-02gcc: fix darwin dispatch/object.h header issue (#1518)Geoffrey Oxberry1-0/+14
Fixes #1203. Apple ships headers in Yosemite (and possibly earlier) that are gcc-incompatible, but compile fine with clang. The fix is to copy the offending system header from /usr/include/${REST_OF_HEADER_PATH} to ${GCC_PREFIX}/include/${REST_OF_HEADER_PATH} and replace the non-gcc- compatible features with gcc-compatible equivalents. See https://github.com/hashdist/hashstack/pull/771/files for inspiration, and http://hamelot.io/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/ for a description of the header issue.
2016-10-02Adding latest version of fenics (#1528)Nicolas Richart3-11/+44
* Adding last version of fenics and making trilinos not ambiguous on hdf5 * forcing fenics to ignore hdf5 cxx * Adding deptypes and correcting the hdf5 patch * flake8 corrections * cleaning some useless code
2016-10-02Provide newer versions of llvm (3.8.1, 3.9.0) (#1765)Kelly Thompson1-61/+91
* Provide new versions of llvm. + Provide file list and md5 hashes for 3.8.1 and 3.9.0. + Clean up indentation for the 'releases' data structure to improve consistency. * Adding a block of code to the 'resources' structure for cfe. * Merge cfe and clang resources into single entity.
2016-10-02Added hadoop, spark, and variant spark+hadoop (#1833)Alfredo Adolfo Gimenez2-0/+128
* Added hadoop, spark, and variant spark+hadoop * Docstrings, dependency types, urls, copyright * Flake8 fixes, link dependency for hadoop * Build type for spark, env problem setting JAVA_HOME
2016-10-02git: Don't link against -lrt on Darwin (#1877)Erik Schnetter1-0/+4
There is no librt on Darwin, and it's not necessary either.
2016-10-02Update PAPI to 5.5.0 (#1878)Erik Schnetter1-0/+1
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