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2018-07-15Charm: set default backend to netlrts (#8714)Matthias Diener1-1/+1
This allows building MPI applications on top of charm/AMPI without to specify another backend.
2018-07-15Charm: more info about build targets (#8713)Matthias Diener1-0/+1
* Charm: more info about build targets * fix whitespace
2018-07-15Scotch: update package (#8711)Matthias Diener1-0/+1
2018-07-15yasm: add develop version (#8712)Matthias Diener1-0/+6
2018-07-15charm: provide MPI (#8647)Matthias Diener1-0/+19
* Charm: provide MPI * add mpicc wrappers * clarify MPI comment
2018-07-14clean up of spack clean (#8610)Andreas Baumbach2-37/+15
* update help of `clean --all` to include `-p` * remove old orphaned `.pyc` removal * restrict removal or orphaned pyc files to `lib/spack` and `var/spack`
2018-07-14Fixing error in amrvis package. (#8710)Jon Rood1-4/+4
2018-07-14Py-opentuner: new package (#8707)Matthias Diener1-0/+44
2018-07-13Unset F90 and F90FLAGS in mvapich2 (#8698)Jon Rood1-0/+3
* Unset F90 in mvapich2 when using intel compilers. * Fixing typo. * Unset F90 and F90FLAGS for mvapich2 at all times. * Adding comment.
2018-07-13py-fn: new package (#8705)Matthias Diener1-0/+37
2018-07-13mothur: mpi not used (#8706)Levi Baber1-3/+0
2018-07-13Scotch: fix compilation of 6.0.5a (#8704)Matthias Diener2-0/+12
Prevent this error: metis_graph_part.c:301:7: error: non-void function 'METIS_PartGraphVKway' should return a value [-Wreturn-type]
2018-07-13update version for numexpr (#8702)Sajid Ali1-1/+2
* modified: package.py * deleted: var/spack/repos/builtin/packages/py-numexpr/numexpr-2.6.5.tar.gz
2018-07-13Add py-backcall (#8701)Sajid Ali1-0/+34
* new file: var/spack/repos/builtin/packages/py-backcall/package.py * Update package.py * Update package.py * Update package.py * Update package.py
2018-07-12flang: add support for llvm-6 (#8073)Christoph Junghans2-8/+65
* flang: add support for llvm-6 * flang: review changes * pgmath: make flake8 happy
2018-07-12locks: improve errors and permission checkingTodd Gamblin2-52/+145
- Clean up error messages for when a lock can't be created, or when an exclusive (write) lock can't be taken on a file. - Add a number of subclasses of LockError to distinguish timeouts from permission issues. - Add an explicit check to prevent the user from taking a write lock on a read-only file. - We had a check for this for when we try to *upgrade* a lock on an RO file, but not for an initial write lock attempt. - Add more tests for different lock permission scenarios.
2018-07-12locks: llnl.util.lock now only writes host info when in debug modeTodd Gamblin2-13/+98
- write locks previously wrote information about the lock holder (host and pid), and read locks woudl read this in. - This is really only for debugging, so only enable it then - add some tests that target debug info, and improve multiproc lock test output
2018-07-12tests: Separate tests for llnl.util.lock and spack.util.lockTodd Gamblin4-161/+169
- llnl.util.lock tests are now independent of Spack
2018-07-12refactor: move spack.util.multiproc to llnl.util.multiprocTodd Gamblin5-12/+12
- multiproc doesn't depend on Spack - llnl.util.lock test uses it, but shouldn't use parts of Spack.
2018-07-12tests: add lib/spack/spack/test/.cache to gitignore for pytestTodd Gamblin1-1/+1
- this shoudl have been moved when we moved pytest.ini to lib/spack/spack/test
2018-07-12Add Git development versions for Typhon and BookLeaf_Cpp. (#8694)Tim Law2-0/+6
2018-07-12First try on pytorch (#8649)Nicolas Richart1-0/+93
* initial version of the package pyTorch (#171) * adding version 0.4 * flake8 correction * reordering version, removing run dependecies * Changing depends_on type to default
2018-07-12mitofates: more deps and a patch to make it functional (#8686)Levi Baber2-0/+39
* mitofates: more deps and a patch to make it functional
2018-07-12Remove unnecessary version-specific URL overrides (#8693)Adam J. Stewart5-19/+10
2018-07-11transdecoder: needs perl-uri-escape (#8690)Levi Baber1-0/+1
2018-07-11beast1: new version (#8691)Levi Baber1-0/+2
2018-07-11mothur: new version (#8692)Levi Baber1-0/+1
2018-07-11py-ply: added version 3.11 (#8383)Massimiliano Culpo1-2/+3
2018-07-11Don't propagate version-specific URL overrides to newer versions (#8565)Massimiliano Culpo3-18/+52
When a user specifies a URL for a specific version of a package, Spack originally would use that URL for all newer versions of the package. This behavior has proven to be generally more harmful than useful, so this PR removes the feature such that a version-specific URL override affects only that version.
2018-07-11py-cutadapt: needs py-setuptools at runtime (#8689)Levi Baber1-1/+1
2018-07-11openmpi: add 3.1.1 (#8684)Howard Pritchard1-0/+1
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-07-11Adjusted sublime-text package (#8685)Jannek Squar1-2/+3
2018-07-11perl-math-cephes: new package (#8671)Levi Baber1-0/+35
2018-07-11Update kaldi (#8682)Jimmy Tang1-8/+8
* Update kaldi always use the --fst-version otherwise it does the wrong thing with selecting the fst version. also enable speex by default * Give version a more meaningful name * Update older version with a date string instead
2018-07-11New packages: libbeato bwtool. (#8681)健美猞猁2-0/+72
2018-07-11Retire the py-dev package (#8679)Adam J. Stewart2-48/+0
2018-07-11Patch for 'netlib-lapack'. (#8677)Sergey Kosukhin2-0/+31
2018-07-11Bump gromacs versions. (#8676)健美猞猁1-0/+2
2018-07-10Adding psm as a dependency of mvapich2. (#8674)Jon Rood1-1/+5
2018-07-10Gtkorvo updates (#8663)Kshitij Mehta5-9/+57
* gtkorvo-atl: Updated to version 2.2 * gtkorvo-dill: Updated to version 2.4 * gtkorvo-enet: Updated to version 1.3.14 * libevpath: Updated to version 4.4.0 * libffs: Updated to version 1.5 * gtkorvo-atl: Bugfix: Fixed cmake args * gtkorvo-enet: Switched order of versions to have the latest version on the top * gtkorvo-atl: Cleaned up cmake_args. Added conditional self.run_tests * gtkorvo-dill: Cleaned up cmake_args. Added conditional self.run_tests * libffs: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests * libevpath: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests * gtkorvo-atl: Removed unused option from cmake args
2018-07-10fetch: remove 'trying' when cloning repos (#8651)Matthias Diener2-5/+5
* fetch: remove 'trying' when cloning repos This makes it similar to what the URL strategy prints. * change svn/hg names
2018-07-10libxshmfence: Update to 1.3 (#8667)Michael Kuhn1-2/+3
libxshmfence@1.2 does not compile with recent versions of glibc.
2018-07-09charm: add possibility to run tests (#8665)Matthias Diener1-0/+6
2018-07-09libnova: new package (#8666)Levi Baber1-0/+42
* libnova: new package * libnova: flake8
2018-07-09Add ccache support (#3761)Christoph Junghans5-1/+41
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available ccache executable when compiling c/c++ code. This feature is disabled by default (i.e. "ccache: false") and the documentation is updated with how to enable ccache support
2018-07-09Make 'netlib-lapack' a CMakePackage. (#8661)Sergey Kosukhin1-48/+70
* Make 'netlib-lapack' a CMakePackage. * Add a comment. * Some refactoring.
2018-07-09express: bamtools lib handling (#8552)Levi Baber1-5/+2
* express: bamtools lib handling * express: use libs property * express: remove old comment
2018-07-08trilinos: update dtk dependencies (#8660)Andrey Prokopenko1-0/+3
2018-07-08fix typo in help of `spack clone` prefix is singular (#8658)Andreas Baumbach1-1/+1
Change-Id: I3bfe5b4ba497fae57d5382502ea9a1b054688fdb
2018-07-07blasr: new package (#8367)Miles Perry1-0/+96
* blasr: new package * blasr: changed version release, created list with 9 things, seperated make into build phase. * blasr: fixed build phase by adding : * blasr: fixed syntax for configure_args * blasr: flake8 edits * blasr-libcpp: fixed configure_args syntax * blasr: fixed install issues resulting from PacBio changes * blasr: removed accidental blasr-libcpp upload * blasr: removed accidental blasr-libcpp upload * blasr: removed blasr-libcpp * blasr: edited out comment
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