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2016-10-19Update mail map. So many email aliases.Todd Gamblin1-20/+56
2016-10-19Fix cdd package definition, dotted is a property (#2054)George Hartzell1-1/+1
Things that accessed the cdd package, such as `spack info cdd run tripped over a buglet in the *cdd* package, causing them to exit with something like this: ``` Caused by: TypeError: 'str' object is not callable File "/rss/spack/lib/spack/spack/repository.py", line 584, in get self._instances[key] = package_class(copy) File "/rss/spack/lib/spack/spack/package.py", line 398, in __init__ f = fs.for_package_version(self, self.version) File "/rss/spack/lib/spack/spack/fetch_strategy.py", line 852, in for_package_version attrs['url'] = pkg.url_for_version(version) File "/rss/spack/var/spack/repos/builtin/packages/cdd/package.py", line 40, in url_for_version str(version.dotted()).replace('.', '')) ``` @tgamblin pointed out that `dotted` is a property, not a functin call and that the parentheses are therefor inappropriate. This deletes the parentheses. `spack info cdd` now works for me.
2016-10-19Add package for htop (#2051)George Hartzell1-0/+41
Add package for htop, an interactive text-mode process viewer for Unix systems. Think top, with pretty colors and dyanmic bar graphs. More info [here](https://github.com/hishamhm/htop).
2016-10-18Don't cache truncated dag hash for spec (#2048)scheibelp1-2/+2
If Spec.dag_hash was called for the first time with a 'length' specified, the cached hash was truncated. This ensures that the full hash is cached.
2016-10-18`Package.do_install` : removed `install_self` from arguments (#1956)Massimiliano Culpo4-32/+43
* Removes the extra argument from Package.do_install while maintaining the changes in behavior pulled in #1603 * install : removed -i and -d shorthands (breaks backward compatibility) * Change ':' to ','
2016-10-18petsc: minor fixes... (#2036)Denis Davydov1-2/+4
* petsc: require boost for :3.5 only * petsc: turn off download for c2html and hwloc
2016-10-18Support for bazel (#2023)Eric5-1/+379
* Add package bazel * Add support for bazel-based builds
2016-10-18superlu-dist: add 5.1.0 and 5.1.1 (#2038)Denis Davydov1-0/+2
2016-10-18mumps: add 5.0.2 (#2041)Denis Davydov1-0/+1
2016-10-18hypre: add 2.11.1 (#2040)Denis Davydov1-0/+1
2016-10-17Update the Krell Institute products to use the latest features of spa… (#1984)Jim Galarowicz6-316/+253
* Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies.
2016-10-17fix download url for paraver (#2033)Pramod Kumbhar1-2/+4
* fix download url for paraver * added note to remove older version
2016-10-16Ignore GPG/PGP signatures/checksums when finding available downloads (#2028)Adam J. Stewart2-2/+11
* Ignore GPG/PGP signatures/checksums when finding available downloads * Remove duplicated basename
2016-10-15Platform-specific config scopes (#2030)Todd Gamblin3-23/+64
* Add platform-specific configuration scopes. * Update `spack config` to use the new scope arguments.
2016-10-15fix sqlite download url (#2031)Pramod Kumbhar1-1/+1
2016-10-15spack purge : updated documentation fixes #1938 (#2025)Massimiliano Culpo1-4/+9
2016-10-15travis : unit tests will run with and without libyaml (#2024)Massimiliano Culpo1-2/+5
* travis : unit tests will run with and without libyaml * travis : fixed package that are installed
2016-10-14Workaround for illegal package merging in py-matplotlib/py-basemap (#1964)Elizabeth Fischer1-1/+75
* Workaround for illegal package merging in py-matplotlib/py-basemap # Conflicts: # var/spack/repos/builtin/packages/py-basemap/package.py * flake8 * flake8 * Be conservative: only apply the namespace package fix for Python >= 3.5.2 * flake8 * Bug fix
2016-10-14Fix list_url for fish shell (#2022)Adam J. Stewart1-2/+1
2016-10-14py-macs2: New package (#2011)John Finigan1-0/+46
* py-macs2: New package * py-macs2: add py-numpy@1.6: dependency
2016-10-14Add missing 'import os'. (#2012)Kelly Thompson1-0/+1
2016-10-14dealii: remove extra test which are now mostly integrated in make test (#2013)Denis Davydov1-113/+0
2016-10-14Major updates to Contribution Guide (#1968)Adam J. Stewart2-137/+405
* Major updates to Contribution Guide * Grammar changes * Fix missing/extra backticks * Rewording, links, and tips added
2016-10-14Package/petsc slepc new versions (#2019)Denis Davydov2-0/+2
* petsc: add 3.7.4 * slepc: add 3.7.3
2016-10-12Use cYAML if it is available in Python. (#2010)Todd Gamblin3-4/+21
2016-10-12py-matplotlib: Add variants for optional dependencies. (#2008)Elizabeth Fischer1-21/+42
2016-10-12Made optional CGAL dependencies optional. (#2006)Elizabeth Fischer1-17/+34
* Made optional CGAL dependencies optional. * cgal: Added note explaining that the CORE library is not the same as core CGAL functionality. * Bug fix and flake8 * flake8
2016-10-12Mock up Xcode devdir to make Qt5 work on Mac OS X (#1832)Ben Boeckel5-7/+104
* build_environment: allow compilers to set up an environment * clang: mock up a toolchain directory for xcode Some projects ignore CC and CXX flags and instead use xcode to find the toolchain. Clang on Apple should set up the environment properly. Arguably, every compiler could do this on Apple, but let's see how this works out just for AppleClang for now. The Documentation directory is ~1.7G and the excluded platforms add up to about 7G. Ignoring swift saves another 500M. The resulting Xcode.app copy is in the 2G range. * compiler: set member variables early This is required so that later methods can query things such as the version of the compiler. * compiler: support finding the real path of the compiler On Apple, the /usr/bin compilers are actually wrapping tools themselves which query xcrun for the currently selected Xcode installation. Pierce this veil and get the real, full path the to underlying compilers instead. * icu4c: install with rpath On macOS, icu installs with a library ID of the library name. Enabling rpath makes its ID its full installed path which lets Qt5 link against it successfully. * qt: no -no-gtkstyle flag on Qt5 on macOS
2016-10-12spack list : updated documentation (#2004)Massimiliano Culpo1-16/+7
* spack list : updated documentation * spack list : removed space before ':'
2016-10-11Documentation for modules configuration options (#1685)Glenn Johnson1-0/+35
This PR add documentation for the `suffixes` and `hash_length` options for modules.yaml. This resolves #1416.
2016-10-11Make `insecure` option work with curl AND git. (#1786)Todd Gamblin5-28/+46
2016-10-11patchelf: Add version (#1540)Elizabeth Fischer1-1/+3
* patchelf: Add version * flake8 * Removed unnecessary url_for_version() function. * Restored old URL
2016-10-11oce: fix for Sierra (#1934)Denis Davydov2-0/+50
2016-10-11environment modifications : permit to pass parameters along with file to be ↵Massimiliano Culpo3-3/+20
sourced (#1626)
2016-10-11Abinit: Added package(s) (#1995)gmatteo5-0/+307
* First version of Abinit package * Ignore *.swp files * Add libxc, etsf_io packages * AtomPaw package * Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io * etsf_io: install Fortran modules in prefix.include * Remove etsf_io from abinit requirements * Add libxc2.2.1 (required by Abinit and atompaw) * Cleanup * Run make check * Cleanup * Use ld_flags instead of hard-coded libs, fix pep8, add copyright * Put scalapack before lapackblas
2016-10-11Update Package : ExodusII (#1504)Joseph Ciurej4-41/+66
* Added support for the 'maxdims' and 'maxvars' flags for 'NetCDF'. * Added the '+mpi' variant and improved dependencies for 'exodusii'. Improved the 'exodusii' package so that it's less reliant on patches. * Added better type checking to variant values in the 'netcdf' package. * Corrected the required CMake version for the 'exodusii' package. * Fixed the dependencies of the '+mpi' variant of the 'exodusii' package.
2016-10-11Package all of Xorg/X11/XCB (#1740)Adam J. Stewart263-108/+12270
* Updates to Mesa and other Xorg packages * Add packages for all Xorg Protocol extensions * Add packages for first half of Xorg libraries * Add packages for remaining Xorg libraries * Add packages for all Xorg utilities * Add packages for Xorg documentation tools * Add build deps to Xorg protocol headers * Add packages for XCB * Add build deps to Xorg libraries * Add build deps to Xorg utilities * Add packages for Xorg fonts and font-related utilities * Change font deptype from build to default I wasn't sure which deptype was appropriate at first since none of the packages are actually linked together. I initially chose the build deptype for this reason. However, the font packages don't install into their own prefix. They install into font-config. If font-config is a build dependency, that means you can uninstall it without uninstalling the font packages, which wouldn't make sense since they install into font-config. So I switched them back to the default deptype. * Minor formatting changes to ncview * Add half-way done xorg-server package * Add packages for Xorg test suites, not yet tested! * Add packages for Xorg data * Add first quarter of Xorg apps * Add more packages for Xorg apps * Add dependencies to mesa * Remove comments from mesa package * Flake8 * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add package for Sublime Text * Add packages for remaining Xorg apps * Revisit testing packages, add missing dependencies * Add dependencies, clean up FIXMEs
2016-10-11Use python platform.system for system ID (#1499)Mario Melara2-8/+3
* Rebase and merging using platform.system Rebasing and merging using platform.system instead of uname -a. * Add missing import platform statement * Remove subprocess import Remove ununsed import subprocess to make changes flak8 compliant
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.
2016-10-11Merge pull request #1562 from LLNL/features/db-lockingTodd Gamblin14-185/+567
Finer-grained locking
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
2016-10-11Fix bug in `spack debug create-db-tarball`Todd Gamblin1-3/+19
- Fix a bug handling '/' characters in branch names. - Make tarballs use a descriptive name for the top-level directory, not just `opt`.
2016-10-11Roll my my own bit_length function for Python 2.6 compatibility.Todd Gamblin3-4/+11
2016-10-11Use a single lock file for stages and a single file for prefixes.Todd Gamblin5-18/+57
- Locks now use fcntl range locks on a single file. How it works for prefixes: - Each lock is a byte range lock on the nth byte of a file. - The lock file is ``spack.installed_db.prefix_lock`` -- the DB tells us what to call it and it lives alongside the install DB. n is the sys.maxsize-bit prefix of the DAG hash. For stages, we take the sha1 of the stage name and use that to select a byte to lock. With 100 concurrent builds, the likelihood of a false lock collision is ~5.36e-16, so this scheme should retain more than sufficient paralellism (with no chance of false negatives), and get us reader-writer lock semantics with a single file, so no need to clean up lots of lock files.
2016-10-11Add tests for locks with byte ranges.Todd Gamblin1-42/+150
2016-10-11Fix bug with lock upgrades.Todd Gamblin1-12/+16
- Closing and re-opening to upgrade to write will lose all existing read locks on this process. - If we didn't allow ranges, sleeping until no reads would work. - With ranges, we may never be able to take some legal write locks without invalidating all reads. e.g., if a write lock has distinct range from all reads, it should just work, but we'd have to close the file, reopen, and re-take reads. - It's easier to just check whether the file is writable in the first place and open for writing from the start. - Lock now only opens files read-only if we *can't* write them.
2016-10-11Add base32_prefix_bits function to get prefix of DAG hash as an int.Todd Gamblin2-4/+61
2016-10-11Add byte-range parameters to llnl.util.lockTodd Gamblin1-19/+40
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