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2016-10-11Fixed set operation from undefined += to a union (#1963)James Wynne III1-1/+2
Fixed flake8 issues
2016-10-11spack list : merged package-list into list (#1932)Massimiliano Culpo3-128/+116
* spack list : merged package-list into the command * list : removed option for case sensitivity
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
2016-10-11Make CMake-based builds more verbose by default. (#1988)Kelly Thompson1-1/+2
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
2016-10-11uninstall : permits to uninstall all installed software fixes #1477 (#1973)Massimiliano Culpo1-30/+38
2016-10-11md5 : normalizes input before computing the md5 fixes #1508 (#1977)Massimiliano Culpo1-2/+13
Bottomline : - fetcher change the current working directory - relative paths were resolved differently depending on the prder f evaluation
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.
2016-10-10Update 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.
2016-10-07Add documentation for standard python repositories. (#1970)Jean-Paul Pelteret1-0/+30
Fixes #1939
2016-10-07Added symengine and associated packages (#1885)Jean-Paul Pelteret7-4/+365
Symengine and associated packages
2016-10-07Check for `-r` in ccld mode too (#1972)Isuru Fernando1-2/+2
2016-10-07fixes #858 (#1961)Massimiliano Culpo1-1/+1
Fix spack uninstall -f
2016-10-06Restore default RPATH settings but allow packages to limit to immediate ↵Todd Gamblin3-2/+18
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 Ciurej87-99/+90
(#1435) * Updated all Python extension packages to use 'setup_py' on install. * Fixed a few minor style issues with the updated Python packages.
2016-10-06Fix bugs preventing readthedocs from rebuilding the documentation (#1945)Adam J. Stewart2-14/+12
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
2016-10-06[Bug Fix (and docs too)] : Do not select @develop version by default (#1933)Elizabeth Fischer2-5/+47
* This fixes a bug in concretization. Before the recent change to the algorithm, the intent was that the @develop version, although "greater" than numberic versions, is never preferred BY DEFAULT over numeric versions. To test this... suppose you have a package with no `preferred=True` in it, and nothing in `packages.yaml`, but with a `develop` version. For the sake of this example, I've hacked my `python/package.py` to work this way. Without bugfix (WRONG: user should never get develop by default): ``` python@develop%clang@7.3.0-apple~tk~ucs4 arch=darwin-elcapitan-x86_64 ... ``` With bugfix (RIGHT: largest numeric version selected): ``` python@3.5.2%clang@7.3.0-apple~tk~ucs4 arch=darwin-elcapitan-x86_64 ... ``` * Documented version selection in concretization algo. * Fix typos * flake8
2016-10-06add contribution guide focused on Git and PRs (#1664)Denis Davydov2-0/+248
2016-10-06Fix various documentation bugs (#1678)Adam J. Stewart8-108/+97
* Fix various documentation bugs * Keep long option names, but don't include in Command Index * Use long option name * Explicitly designate sections to be listed in the Command Index * Consistent menu bar titles
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.
2016-10-06Fixes bug closing Executable file io-streams (#1890)Matt Belhorn1-3/+3
Input/output/error streams not directed to None or 'str' were not being closed because `close()` method was being called on the argument value (a string type) instead of the open file descriptor object.
2016-10-06Fix fetch() method. Was being called with "wrong" arguments, raising ↵Elizabeth Fischer1-1/+1
exception. (#1916) DIYFetchBugfix
2016-10-06cgal: build out of source. (#1918)Elizabeth Fischer1-4/+4
* cgal: build out of source. * Simplify cmake out-of-source.
2016-10-06Fix Issues with non-numeric versions, as well as preferred=True (#1561)Elizabeth Fischer3-39/+113
* Fix bug in handling of precedence of preferred=True vs. versions given in packages.yaml (#1556) * Standardized comparison of versions: numeric versions are always greater than non-numeric versions; and non-numeric versions are sorted alphabetically. This is a) simple b) ensures that non-numeric versions (such as 'develop') in package.py are not chosen ahead of numeric versions, when nothing is specified in packages.yaml Fixes Issue #1557 * Removed debugging output * Fix variable shadowing bug * Ensure develop < numeric version. * Bug fix. * Passes all unit tests in versions.py * flake8 fixes * flake8 fixes * Changed type test to be more correct. See http://stackoverflow.com/questions/8203336/difference-between-int-and-numbers-integral-in-python
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
2016-10-05Handle packages with unparseable extensions (#1758)scheibelp6-21/+21
This closes #1757 which provides an example of a url scheme where the version appears after the extension. Instead of extending the parsing logic to handle this case, this commit allows the user to specify their extension type. This helps Spack choose the appropriate decompressor and mirror archive filename.
2016-10-05docs/getting_started: s/Macintosn/Macintosh/; (#1928)Geoffrey Oxberry1-1/+1
2016-10-05Documentation Improvements for SC16 (#1676)Elizabeth Fischer11-867/+2759
* Transferred pending changes from efischer/develop * 1. Rewrite of "Getting Started": everything you need to set up Spack, even on old/ornery systems. This is not a reference manual section; items covered here are covered more systematically elsewhere in the manual. Some sections were moved here from elsewhere. 2. Beginning to write three methods of application developer support. Two methods were moved from elsewhere. * Edits... * Moved sections in preparation for additional text to be added from old efischer/docs branch. * Moved 2 more sections. * Avoid accid * Applied proofreading edits from @adamjstewart * Fixed non-standard section characters. * Moved section on profiling to the developer's guide. * Still working on Spack workflows... * Finished draft of packaging_guide.rst * Renamed sample projects. * Updates to docstrings * Added documentation to resolve #638 (content taken from #846) * Added section on resolving inconsistent run dependencies. Addresses #645 * Showed how to build Python extensions only compatible with certain versions of Python. * Added examples of getting the right behavior from depends_on(). See #1035 * Added section on Intel compilers and their GCC masquerading feature. Addresses #638, #1687. * Fixed formatting * Added fixes to filesystem views. Added a caveats section to ``spack setup``. * Updated section on Intel compiler configuration because compiler flags currently do not work (see #1687) * Defined trusted downloads, and updated text based on them. (See #1696) * Added workflow to deal with buggy upstream software. See #1683 * Added proper separation between Spack Docs vs. Reference Manual * Renamed spack_workflows to workflows. Resolves a conflict with the .gitignore file. * Removed repeated section. * Created new "Vendor Specific Compiler Configuration" section and organized existing Intel section into it. Added new PGI and NAG sections; but they need to be expanded / rewritten based on the existing text plus research through Spack issues on GitHub. * Fixed text on `spack load --dependencies` to conform to reality. See #1662 * Added patching as option for upstream bugfixes. * Added section on using licensed compilers. * Added section on non-downloadable tarballs. * Wrote sections on NAG and PGI. Arranged compilers in alphabetical order. * Fix indent. * Fixed typos. * Clarified dependency types. * Applied edits from Adam J. Stewart. Spellchecked workflows and getting_started. * Removed spurious header * Fixed Sphinx errors * Fixed erroneous symbol in docstring. * Fix many typos and formatting problems. * Spacing changes * Added section on fixing Git problems. See #1779 * Fixed signature of install() method. * Addressed system packages in greater detail. See #1794 #1795 * Fixed typos * Fixed quotes * Duplicate section on Spack profiling removed from configuration.rst. It had earlier been moved to developer_guide.rst, where it fits better. * Minor edits - Tweak supported platform language. - Various small changes to the new getting started guide. * Fixed bug with quotes.
2016-10-05New command flag: spack install --dependencies-only (#1603)Elizabeth Fischer5-23/+40
* 1. Renamed ignore_deps variable to install_deps (use positive logic). UI remains the same. 2. install_self kwarg added to do_install(). Enables installation of a package's dependencies without installing the package itself. 3. Added `spack install --dependencies-only <package>` command. * Flak8 fixes * Indentation problem
2016-10-05Add package for CONVERGE CFD (#1905)Adam J. Stewart2-0/+74
2016-10-05Add latest versions, resolve variant resolution bug (#1909)Adam J. Stewart3-8/+14
2016-10-05Added missing function for CMake builds. (#1250)Elizabeth Fischer1-9/+15
* Added missing function for CMake builds. * Update build_environment.py * std_cmake_args Changed std_cmake_args to use get_std_cmake_args(). * Update build_environment.py Delete additional lines subsumed by get_std_cmake_args() * flake8.
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. Stewart11-30/+394
* 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
2016-10-04Read-only locks should close fd before opening for write. (#1906)Todd Gamblin2-0/+37
- Fixes bad file descriptor error in lock acquire, #1904 - Fix bug introduced in previous PR #1857 - Backported fix from soon-to-be merged fine-grained DB locking branch.
2016-10-04Packages for Darshan I/O performance characterization tool from ANL (#1900)Pramod Kumbhar2-0/+106
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