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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
2016-10-04Fix some documentation build warnings. (#1902)Todd Gamblin3-15/+13
- Fix issue with package_list.py regeneration confusing Sphinx. - Add -E option to avoid caching and make Sphinx happy.
2016-10-04Update documentation URL after switch to readthedocs (#1901)Adam J. Stewart8-15/+15
2016-10-04Rework build environment and cc to use smaller RPATHs. (#1894)Todd Gamblin3-13/+108
- Fixed up dependency management so that: - build deps go in PATH and -I - link deps go in -L args - only *immediate* link deps are RPATH'd The latter reduces the number of libraries that need to be added to DT_NEEDED / LC_RPATH. This removes redundant RPATHs to transitive dependencies.
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.
2016-10-04Fixes #1893: missing importTodd Gamblin1-0/+1
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
2016-10-02Run make clean to prevent warning messages (#1742)Adam J. Stewart1-4/+2
* Run make clean to prevent warning messages * Don't delete temporary files after completion
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
2016-10-02Update tmux to 2.3.0 (#1879)Erik Schnetter1-2/+3
2016-10-02New package: libquo (#1880)Kelly Thompson1-0/+68
* New package: libquo libquo is a high-level, easy to use programming interface tailored specifically for MPI/MPI+X codes that may benefit from evolving process binding policies during their execution. QUO allows for arbitrary process binding policies to be enacted and reverted during the execution of an MPI/MPI+X application as different computational phases are entered and exited, respectively. https://github.com/losalamos/libquo * Remove use of 'which' and fix style non-conformance.
2016-10-02Add boost 1.62.0 (#1882)Bruno Turcksin1-0/+1
2016-10-02Added bash-completion package (#951)Jean-Paul Pelteret1-0/+64
2016-09-30pdt url change to download full installer tarball (#1881)Pramod Kumbhar1-6/+7
2016-09-30Fix read locks on read-only file systems (#1857)Michael Kuhn1-1/+2
2016-09-29Add cube variant for building GUI component with qt, parallel built ↵Pramod Kumbhar1-4/+9
supported (#1525)
2016-09-29updated to latest available package and fixed installation issue (old ↵Pramod Kumbhar1-2/+8
packages are no longer available for download) (#1523)
2016-09-29added libxstream (#1454)Mitchell Devlin1-0/+50
2016-09-29Add libint package (#1264)Adam J. Stewart3-5/+127
* Add libint package * Add Intel optimization flags recommended by CP2K * Add new version and Intel compiler optimization flags for libxc * Add older version of libint * Libint depends on GMP C++ library
2016-09-28Library for manipulating grib1 and grib2 files (#1736)Robert D. French1-0/+50
Pro tips from @adamjstewart: * line too long in package description * name it grib-api instead of grib_api * depend on netcdf without reference to unnecessary constraints
2016-09-28py-pil: Protect against building with Python3. (#1868)Elizabeth Fischer2-0/+4
* py-pil: Does not build with Python3. * Set py-pillow to be the default pil provider * Update package.py * Change to comments requested by adamjstewart * Remove version constraint from extends(), avoid a Spack bug.
2016-09-28Update Qthreads to 1.11 (#1863)Erik Schnetter1-2/+3
2016-09-28Fixes #1860. Subversion builds sequentially due to race.Todd Gamblin2-1/+4
2016-09-28vim8 is out! (#1753)Robert D. French1-0/+3
* depends on ncurses for 8.0 or higher
2016-09-28Fixes #1720: spack reindex fails with invalid ref count. (#1867)Todd Gamblin3-49/+80
* Fixes #1720: spack reindex fails with invalid ref count. - Database graph wasn't being built properly; dependencies were set up incorrectly in the nodes that ended up in the graph on reindex. - Reworked _add to increment ref count properly and to always build bottom-up to make the logic simpler to understand. * Add checks to ensure DB is a valid merkle tree.
2016-09-28Tell Mercurial where to find CA certs (#1873)Adam J. Stewart1-5/+30
2016-09-28Prohibit Python3 in Python version check. (#1872)Elizabeth Fischer1-2/+2
2016-09-28Add single letter arg flags for spack graph (#1871)Adam J. Stewart1-3/+3
2016-09-28Merge pull request #1862 from LLNL/features/graph-improvementsTodd Gamblin9-164/+259
spack graph improvements
2016-09-27Make graph_ascii support deptypes.Todd Gamblin6-27/+37
- fix deptype support - by default, graph command omits build depedencies - update docs to use deptype args
2016-09-27Fixes #1098: spack graph crashes for large graphs.Todd Gamblin1-6/+15
- Fixed logic for collapsing backward edges - Last collapse now depends on whether prior step in left collapse sequence alrady did the collapse.
2016-09-27Improvements to the Spack graph command.Todd Gamblin3-29/+103
- Distinguish between static (package) and dynamic (spec) graphs. - static graphs ignore conditions and multiple instances (hashes) and plot raw dependencies among packages. - dynamic graphs include information from particular specs (instances of packages) and can have multiple instances with hashes. - Allow graphing all packages in the install DB. - useful for debugging.
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