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6329 commits

Author SHA1 Message Date
Cyrus Harrison
290125f893 openmpi: add c++ exceptions cfg option variant (#8743) 
* openmpi: add c++ exceptions cfg option variant

* address review comments
 2018-07-18 14:54:12 -05:00
Matthias Diener
111512ce7b Cmake: add version 3.12.0 (#8731) 2018-07-17 17:56:04 -05:00
Levi Baber
2ce6299c2b py-pyqi: new package (#8726) 
* py-pyqi: new package

* py-pyqi: cleanup
 2018-07-17 16:07:38 -05:00
Jon Rood
956faa50cc Confine the xlf_seacas.patch for trilinos to version 12.12.1 (#8725) 
* The xlf_seacas.patch fails on the latest trilinos develop branch so confine it up to version 12.12.1.

* Fixing likely mistak in seacas patch version range.
 2018-07-17 14:45:39 -05:00
Massimiliano Culpo
373b3d2444 Packages must be added to DB to be considered installed (#8038) 
Fixes #8036

Before this PR Package.installed was returning True if the spec prefix
existed, without checking the DB. This is wrong for external packages,
whose prefix exists before being registered into the DB. Now the property
checks for both the prefix and a DB entry.
 2018-07-17 11:43:30 -07:00
Christoph Junghans
25062d0bd4
lammps: added v20180629 (#8695) 2018-07-17 11:13:04 -06:00
Christoph Junghans
ab60e2258f fftw: version bump (#8723) 
* fftw: version bump

* fftw: add gcc-8 conflict for v3.3.7
 2018-07-17 11:11:19 -05:00
Lukasz
9f0f18dad6 fix link to blas libs (#8721) 2018-07-17 08:24:52 -05:00
James Dickson
0a80d94a46 Add fix for bug causing MACSio build failure when hdf5 or typhonio enabled (#8722) 
* Add fix for bug causing build failure when hdf5 enabled

* Added correct hdf5 dependency to typhonio
 2018-07-17 08:24:16 -05:00
Levi Baber
b12d5aecaa r: add memory profiling variant (#8717) 
* r: add memory profiling variant

* r: change memory_profiling to underscores
 2018-07-16 22:23:09 -05:00
健美猞猁
d006139e3c aspera-cli: a new package. (#8715) 
* aspera-cli: a new package.

* flak8.
 2018-07-16 13:53:23 -05:00
Matthias Diener
dfc1f70aa4 Charm: set default backend to netlrts (#8714) 
This allows building MPI applications on top of charm/AMPI without
to specify another backend.
 2018-07-15 16:41:36 -05:00
Matthias Diener
badf913fc4 Charm: more info about build targets (#8713) 
* Charm: more info about build targets

* fix whitespace
 2018-07-15 16:41:25 -05:00
Matthias Diener
b25187bfa6 Scotch: update package (#8711) 2018-07-15 15:54:28 -05:00
Matthias Diener
067c8466bd yasm: add develop version (#8712) 2018-07-15 15:54:13 -05:00
Matthias Diener
4df673e401 charm: provide MPI (#8647) 
* Charm: provide MPI
* add mpicc wrappers
* clarify MPI comment
 2018-07-15 08:33:57 -07:00
Jon Rood
5192a3d6d6 Fixing error in amrvis package. (#8710) 2018-07-14 18:19:26 -05:00
Matthias Diener
da5663a52a Py-opentuner: new package (#8707) 2018-07-14 13:51:58 -05:00
Jon Rood
e367d1fb3a Unset F90 and F90FLAGS in mvapich2 (#8698) 
* Unset F90 in mvapich2 when using intel compilers.

* Fixing typo.

* Unset F90 and F90FLAGS for mvapich2 at all times.

* Adding comment.
 2018-07-13 20:32:02 -05:00
Matthias Diener
4c5cbfeb29 py-fn: new package (#8705) 2018-07-13 20:31:39 -05:00
Levi Baber
44c999e2e1 mothur: mpi not used (#8706) 2018-07-13 20:31:25 -05:00
Matthias Diener
2cf9c7955c Scotch: fix compilation of 6.0.5a (#8704) 
Prevent this error:

metis_graph_part.c:301:7: error: non-void function 'METIS_PartGraphVKway' should return a value
      [-Wreturn-type]
 2018-07-13 15:51:04 -05:00
Sajid Ali
aec91d1cca update version for numexpr (#8702) 
* 	modified:   package.py

* 	deleted:    var/spack/repos/builtin/packages/py-numexpr/numexpr-2.6.5.tar.gz
 2018-07-13 15:50:21 -05:00
Sajid Ali
4c5e4cb960 Add py-backcall (#8701) 
* 	new file:   var/spack/repos/builtin/packages/py-backcall/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-07-13 10:59:02 -05:00
Christoph Junghans
d569a9c124
flang: add support for llvm-6 (#8073) 
* flang: add support for llvm-6

* flang: review changes

* pgmath: make flake8 happy
 2018-07-12 18:37:50 -06:00
Tim Law
2a27a37597 Add Git development versions for Typhon and BookLeaf_Cpp. (#8694) 2018-07-12 07:37:42 -05:00
Nicolas Richart
d8921ac323 First try on pytorch (#8649) 
* initial version of the package pyTorch (#171)

* adding version 0.4

* flake8 correction

* reordering version, removing run dependecies

* Changing depends_on type to default
 2018-07-12 07:30:59 -05:00
Levi Baber
1846bc5ed6 mitofates: more deps and a patch to make it functional (#8686) 
* mitofates: more deps and a patch to make it functional
 2018-07-12 10:23:22 +02:00
Adam J. Stewart
ecff47538e Remove unnecessary version-specific URL overrides (#8693) 2018-07-12 07:28:11 +02:00
Levi Baber
2561d1d656 transdecoder: needs perl-uri-escape (#8690) 2018-07-11 17:38:58 -05:00
Levi Baber
f29c1d9096 beast1: new version (#8691) 2018-07-11 17:07:20 -05:00
Levi Baber
feb4701ae3 mothur: new version (#8692) 2018-07-11 17:07:02 -05:00
Massimiliano Culpo
10e628a5a0
py-ply: added version 3.11 (#8383) 2018-07-11 22:21:55 +02:00
Massimiliano Culpo
e3a556cd2a Don't propagate version-specific URL overrides to newer versions (#8565) 
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.
 2018-07-11 13:12:19 -07:00
Levi Baber
aa9bb06b89 py-cutadapt: needs py-setuptools at runtime (#8689) 2018-07-11 14:53:35 -05:00
Howard Pritchard
be9dfc2d73 openmpi: add 3.1.1 (#8684) 
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2018-07-11 12:42:00 -05:00
Jannek Squar
6a3f36c4e3 Adjusted sublime-text package (#8685) 2018-07-11 12:41:48 -05:00
Levi Baber
d27133b3cd perl-math-cephes: new package (#8671) 2018-07-11 12:40:39 -05:00
Jimmy Tang
5780eadf64 Update kaldi (#8682) 
* 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
 2018-07-11 12:38:06 -05:00
健美猞猁
a985dc859c New packages: libbeato bwtool. (#8681) 2018-07-11 10:33:44 -05:00
Adam J. Stewart
f036f17f61
Retire the py-dev package (#8679) 2018-07-11 10:26:38 -05:00
Sergey Kosukhin
6479ec6def Patch for 'netlib-lapack'. (#8677) 2018-07-11 08:52:21 -05:00
健美猞猁
391d89a853 Bump gromacs versions. (#8676) 2018-07-11 08:05:39 -05:00
Jon Rood
a1bfa8eca0 Adding psm as a dependency of mvapich2. (#8674) 2018-07-10 19:32:50 -05:00
Kshitij Mehta
3c4ef576d9 Gtkorvo updates (#8663) 
* 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
 2018-07-10 12:50:10 -05:00
Michael Kuhn
00c3331de9 libxshmfence: Update to 1.3 (#8667) 
libxshmfence@1.2 does not compile with recent versions of glibc.
 2018-07-10 07:58:44 -05:00
Matthias Diener
bc5168e4b1 charm: add possibility to run tests (#8665) 2018-07-09 16:16:27 -05:00
Levi Baber
4ed7931200 libnova: new package (#8666) 
* libnova: new package

* libnova: flake8
 2018-07-09 16:16:09 -05:00
Sergey Kosukhin
8770957b7a Make 'netlib-lapack' a CMakePackage. (#8661) 
* Make 'netlib-lapack' a CMakePackage.

* Add a comment.

* Some refactoring.
 2018-07-09 13:21:55 -05:00
Levi Baber
25c9a5216f express: bamtools lib handling (#8552) 
* express: bamtools lib handling

* express: use libs property

* express: remove old comment
 2018-07-09 13:21:38 -05:00