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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.
2016-10-04Read-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.
2016-10-04Fix 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.
2016-10-04Rework 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.
2016-10-04Fixes #1893: missing importTodd Gamblin1-0/+1
2016-09-30Fix read locks on read-only file systems (#1857)Michael Kuhn1-1/+2
2016-09-28Fixes #1860. Subversion builds sequentially due to race.Todd Gamblin1-1/+1
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.
2016-09-28Add single letter arg flags for spack graph (#1871)Adam J. Stewart1-3/+3
2016-09-27Make graph_ascii support deptypes.Todd Gamblin5-27/+36
- 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.
2016-09-27Factor out canonical_deptype function, cleanup spec.pyTodd Gamblin2-41/+100
2016-09-27Clean up Exceptions in `spec.py`Todd Gamblin2-63/+6
2016-09-23Fix doc bugs, widen columns in the package listTodd Gamblin1-1/+1
2016-09-22package: fix variable name usage (#1829)Ben Boeckel1-1/+1
2016-09-22Fix spack checksum output indentation (#1826)Adam J. Stewart1-1/+1
2016-09-22Fix sbang for perl (#1802)Eric1-5/+7
* Perform shebang fix for all files * Fix sbang for perl scripts Otherwise perl would look at the #! line and call sbang again, resulting in an infinite loop.
2016-09-22Remove SPACK_DIRTY env var (#1818)Elizabeth Fischer3-10/+6
* Removed SPACK_DIRTY env var support. * Finished removing SPACK_DIRTY support. * Minor changes.
2016-09-22fix : stops infinite recursion for python 2.6 (#1823)Massimiliano Culpo1-2/+3
2016-09-21Reworking of `lapack_shared_libs` and similar properties (#1682)Massimiliano Culpo6-38/+303
* Turned <provider>_libs into an iterable Modifications : - added class LibraryList + unit tests - added convenience functions `find_libraries` and `dedupe` - modifed non Intel blas/lapack providers - modified packages using blas_shared_libs and similar functions * atlas : added pthread variant * intel packages : added lapack_libs and blas_libs * find_library_path : removed unused function * PR review : fixed last issues * LibraryList : added test on __add__ return type * LibraryList : added __radd__ fixed unit tests fix : failing unit tests due to missing `self` * cp2k and dependecies : fixed blas-lapack related statements in package.py
2016-09-21Fixed bug propagating --dirty flag to sub-installs. (#1625)Elizabeth Fischer4-5/+18
* Fixed bug propagating --dirty flag to sub-installs. * Fix syntax error * Allow --dirty flag to be set with SPACK_DIRTY env var. * Added dirty flag to `spack diy` and `spack setup`, as is currently in `spack install` * flake8
2016-09-21Adds all available CrayPE CPU targets to platform by default. (#1745)Matt Belhorn1-42/+67
2016-09-21Set JAVA_HOME on module load and on dependent installs. (#1716)Alfredo Adolfo Gimenez1-0/+1
* Set JAVA_HOME on module load and on dependent installs. * Include environment setup from dependencies in dependee module (#1714)
2016-09-20fix MacOs class for Sierra (#1811)Denis Davydov1-1/+1
2016-09-20fix : failing unit tests due to missing `self` (#1806)Massimiliano Culpo1-2/+2
2016-09-20Fix format string (in class RemoveFailedError) (#1803)Eric1-1/+1
2016-09-20lmod : added support for the creation of hierarchical lua module files (#1723)Massimiliano Culpo8-147/+554
Includes : - treatment of a generic hierarchy (i.e. lapack + mpi + compiler) - possibility to specify which compilers are to be considered Core - correct treatment of the 'family' directive - unit tests for most new features
2016-09-20Allow multi-user installations (#1804)Eric1-1/+1
When re-using previously downloaded tarballs, spack copies from `var/spack/stage/PACKAGE-VERSION-HASH/downloaded_file` to `var/spack/cache/PACKAGE/downloaded_file`. This fails if the source is owned by a different user (`shutil.copy` tries to retain all meta data including file ownership). Change to a non-meta-data copy function (`shutil.copyfile`).
2016-09-15Fix location -p and -P (#1776)Michael Kuhn1-3/+2
2016-09-15Make libstdc++-detection work on Darwin (#1778)Erik Schnetter1-2/+2
2016-09-08Don't overwrite PYTHONPATH in docs Makefile (#1693)Adam J. Stewart1-1/+1
2016-09-07Fix fetching non-expanded resources from mirrors (#1310)scheibelp3-22/+25
This closes #1308, where fetching a non-expanded resource from a mirror will cause an error. This also ensures that when a URL resource is fetched from a mirror, that it will be named as though it were retrieved from the original URL. This is particularly useful for non-expanded resources since it ensures that the resource name is consistent for the installation (this is less important for expanded resources because the build takes place inside the expanded resource).
2016-09-06Add debug command for creating tarball of install DB.Todd Gamblin1-0/+84
2016-09-06modules : ('build',) type dependencies are not accounted when autoloadingalalazo2-1/+24
fixes #1681
2016-09-03spack boostrap: fix missing include (#1657)Axel Huebl1-1/+1
fix a missing include in booststrap. found on debian 8 with python 2.7
2016-09-03added package : pexsi (#1550)Massimiliano Culpo2-0/+8
* pexsi : added package * cp2k : added pexsi (works for gcc+openmpi with and without plumed)
2016-09-02Attributes for directives need to be set at class construction time. (#1718)Todd Gamblin1-3/+6
- moved ensure_dicts() call from Package.__init__ to Package.__metaclass__.
2016-09-02Clean up stable hashing so that specs don't contain !!python/object/applyTodd Gamblin4-50/+51
- only output basic lists, dicts, etc. - spec and database now parse and write specs as ordered data.
2016-09-02Merge branch 'UCL-RITS-hash_stability' into bugfix/hash-collisionTodd Gamblin2-15/+51
2016-09-02Fix hash copying in _dup.Todd Gamblin1-7/+17
- Spec._dup() incorrectly copied cached hashes and normal/concrete values even when dependency structure was not preserved. - Now these are only copied when *all* dependencies are copied.
2016-09-02Fix hash handling in directory layoutTodd Gamblin1-0/+7
- Currently, build dependencies are not currently hashed; we are waiting to hash these until we have smarter concretization that can reuse more installed specs. The layout needs to account for this when checking whethert things are installed.
2016-09-01Fix `spack reindex` so that it will work if DB is corrupt (duh).Todd Gamblin1-16/+45
- Transaction logic had gotten complicated -- DB would not reindex when corrupt, rather the error would be reported (ugh). - DB will now print the error and force a rebuild when errors are detected reading the old databse.
2016-09-01Update tests to reflect new in-memory hashing vs. coarser dag_hash.Todd Gamblin1-7/+18
- Spack currently not hashing build deps (to allow more reuse of packages and less frequent re-installing) - Fast in-memory hash should still hash *all* deptypes, and installed specs will only reflect link and run deps. - We'll revert this when we can concretize more liberally based on what is already installed.
2016-09-01Add option to copy only certain deptypes to Spec.copy()Todd Gamblin1-16/+24
- can now pass these to Spec.copy() and Spec._dup(): - deps=True - deps=False - deps=(list of deptypes) - Makes it easy to filter out only part of a spec.
2016-09-01Faster database loading.Todd Gamblin1-17/+37
- use a 3-pass algorithm to load the installed package DAG. - avoid redundant hashing/comparing on load.
2016-09-01Specs now cache result of "fast" in-memory hash.Todd Gamblin1-8/+22
- Hash causes major slowdown for reading/setting up large DBs - New version caches hash for concrete specs, which includes all specs in the install DB
2016-09-01Fix dependency bug in database. Fixes #1265, #1320.Todd Gamblin1-1/+1
2016-08-31Make gh-pages redirect to readthedocs.ioTodd Gamblin3-1/+22
2016-08-31Expand/clarify description of dependency typesErik Schnetter1-14/+25
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