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6654 commits

Author SHA1 Message Date
Levi Baber
3f9fc0f765 breakdancer: fix several issues (#9251) 
* add perl dependencies
* put bam2cfg in path
* fix perl dir
 2018-09-14 20:11:34 -07:00
Miles Perry
301643bdc4 Feature/py picrust (#9184) 2018-09-14 17:24:17 -07:00
Michael Kuhn
c2f6c98ed9 rdma-core: Fix missing pkg-config dependency (#9195) 
rdma-core requires pkg-config, otherwise libnl can not be found.
 2018-09-14 17:21:05 -07:00
Justin Stanley
b09ece58f6 jdk: added 10.0.2_13 (#9203) 2018-09-14 17:17:32 -07:00
Jon Rood
8f80ee7a40 Updating amrvis to allow building with profiling support. (#9204) 
* Updating amrvis to allow building with profiling support.
* Setting MPI default to true.
 2018-09-14 17:16:35 -07:00
Stephen Hudson
ae1420bffc Update py-libensemble package to v0.3.0 (#9210) 2018-09-14 17:15:31 -07:00
Stephen McDowell
ea3c59ed37 add eigen@3.3.5 (#9212) 2018-09-14 17:14:46 -07:00
Geoffrey Oxberry
affea920cf hypre: patch +shared@2.13.0: on darwin (#9220) 2018-09-14 17:14:30 -07:00
snehring
fa5bf11f16 plumed: updating plumed to latest version (#9227) 2018-09-14 17:13:22 -07:00
Sergey Kosukhin
a9c434d7d7 Build Python 3.7 with external libffi. (#9245) 2018-09-14 17:07:13 -07:00
Stephen McDowell
0b800720b1 add opencv@3.4.3 (#9213) 2018-09-14 17:05:05 -07:00
Stephen McDowell
4c41413550 patch flann // gcc // cmake@3.11+ (#9214) 
See: https://github.com/mariusmuja/flann/issues/369
 2018-09-14 17:01:58 -07:00
Abhinav Bhatele
055b0a442c Charmpp: rename charm to charmpp according to ++ conventions (#9216) 
* Charmpp: rename charm to charmpp according to ++ conventions
* modify packages that depend on charmpp
 2018-09-14 17:01:07 -07:00
Levi Baber
e07aef88f8 py-spectra: new version (#9224) 2018-09-14 16:59:50 -07:00
Mario Melara
5b9cbb518a OpenCoarrays: update v2.2.0 (#9215) 
This commit adds a patch that prevents the package from hanging. The package would hang because CMakeLists would look for a system MPI. This patch changes the behavior.
 2018-09-14 16:59:19 -07:00
Christoph Junghans
9661748900 miniamr: added v1.4.1 (#9225) 2018-09-14 16:56:59 -07:00
Adam J. Stewart
cca6b673db py-h5py: add version 2.8.0 (#9231) 2018-09-14 15:56:44 -07:00
Justin Stanley
8276256875 portcullis: new package starting at 1.1.2 (#9218) 2018-09-14 15:55:58 -07:00
Abhinav Bhatele
3bb12e3804 miniQMC: add newer releases and ecp-proxy-app tag (#9233) 2018-09-14 15:54:21 -07:00
Geoffrey Oxberry
69a9a3291a ipopt: add debug variant (#9223) 2018-09-14 15:53:25 -07:00
Geoffrey Oxberry
a76aa36481 hypre: add debug variant (#9222) 2018-09-14 15:53:06 -07:00
Levi Baber
62208afdb9 py-multiqc: needs newer py-spectra (#9226) 2018-09-14 15:52:29 -07:00
Levi Baber
3c33b5efef py-networkx: new version (#9241) 2018-09-14 15:52:02 -07:00
Levi Baber
617ff8f125 py-decorator: new version (#9240) 2018-09-14 15:51:43 -07:00
Levi Baber
49aed4584b py-markdown: fix url and hashes (#9235) 2018-09-14 15:51:20 -07:00
Levi Baber
f52812e571 perl-gdgraph-histogram: new package (#9250) 2018-09-14 15:50:18 -07:00
Ken Raffenetti
881af613b3 bolt: new package starting at 1.0b1 (#9253) 2018-09-14 15:49:36 -07:00
Justin Stanley
31da752402 metasv: add required dependencies (#9254) 
* add runtime deps
* revert to strict dep versions
 2018-09-14 15:49:11 -07:00
Ken Raffenetti
17d4005a4f argobots: new package starting at 1.0b1 (#9238) 2018-09-14 15:48:40 -07:00
Justin Stanley
dda27fc0d1 rmats: new package starting at 4.0.2 (#9243) 
* new package starting at 4.0.2
 2018-09-14 14:54:26 -07:00
Douglas Duckworth
716ed92e32 motioncor2 - added version 1.1.0 and removed old, unlisted versions (#9229) 2018-09-14 13:57:22 -07:00
Matthias Diener
36f396ad5b gdb: add version 8.2 (#9246) 2018-09-14 13:56:15 -07:00
Justin Stanley
ff6b9b99fa gatk: new version (#9202) 
* gatk: added 4.0.8.1, fixed binary install
* gatk: fix flake8 conflict
* gatk: improve comments and modify install
 2018-09-14 13:55:52 -07:00
Justin Stanley
451328d6e6 mxnet: added 1.3.0 (#9236) 
* add version 1.3.0
* change build parameters, install process
  * mxnet will not compile against spack's nnvm and dmlc so we must use
    the distributions provided by the source package.
* also removed 'bin' installation as mxnet is just a shared library.
* improve BLAS linking
* remove unnecessary args
* added variant for python bindings
 2018-09-14 11:01:30 -07:00
sknigh
24dd24600c Added Kibana package, added Elasticsearch to 6.4.0 (#9239) 
* Added kibana, updated elasticsearch
* Update elastic search to 6.4
 2018-09-14 10:50:20 -07:00
Daniel Topa
056960870b Hwloc add update 2.0.2 (#9244) 
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2018-09-14 10:48:38 -07:00
Levi Baber
0ed58374e7 py-colormath: new version, requires newer networkx (#9237) 
* py-colormath: new version requires newer networkx
 2018-09-14 10:35:45 -07:00
Matthias Diener
466bc20874 cmake: add version 3.12.2 (#9248) 2018-09-14 09:36:39 -07:00
Neil Flood
1122fc3d1e r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden d… (#9176) 
* r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden dependency, masked by the package's configure script.

* r-nloptr: Change spelling of variables to satisfy pyflake8

* r-nloptr: Break a long line to satisfy pyflake8

* r-nloptr: larger indent on continuation, to satisfy pyflake8

* r-nloptr: another attempt at larger indent on continuation, to satisfy pyflake8

* r-nloptr: now a smaller indent on continuation, to satisfy pyflake8

* r-nloptr: Another attempt at right amount of indent.

* r-nloptr: Another attempt at right amount of indent.

* Use the correct attributes for finding the nlopt includes and libs.

* Lines too long, split into pieces
 2018-09-14 08:11:16 -05:00
Christoph Junghans
98d8c4d7ca
py-espresso: apply patch to v4.0.0 only (#9196) 2018-09-13 10:00:21 +00:00
Abhinav Bhatele
1e2b3b0768 AMG: update version (#9228) 2018-09-12 14:11:05 -06:00
Ricardo Silva
62977662e9 petsc: fix compilation with intel (#9198) 
* mpiifort doesn't automatically link all run-time libraries
* scalapack was being picked up accidentaly if intel-mkl was in the spec
 2018-09-12 11:18:41 -07:00
Abhinav Bhatele
ff13f3953e ecp-proxy-apps: update dependencies for release 1.0 and 1.1 (#9217) 2018-09-11 15:10:49 -06:00
Tristan Carel
6d0933b2a0 steps: new package starting at 3.3 (#9173) 2018-09-11 14:43:15 +02:00
Adam J. Stewart
ccbff6e0cd
Improve spec['python'].command support for bwpy (#9157) 2018-09-10 17:14:57 -05:00
Christoph Junghans
3dcbe50eb7 py-espresso: added v4.0.0 (#9192) 
Added v4.0.0 and workaround for cmake bug
 2018-09-10 08:55:32 +02:00
Satish Balay
a537d7b56e
trilinos: disable xlf_tpetra.patch for trilinos@develop (#9193) 
This patch does not apply cleanly anymore and breaks clang/Mac builds

balay@asterix /home/balay/git-repo/github/trilinos (develop=)
$ patch -Np1 < /home/balay/git-repo/github/spack/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
|+++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
--------------------------
File to patch:
 2018-09-08 23:51:16 -05:00
Satish Balay
8afc630e96
assimp: fix compile issues with intel compilers on knl/linux [a depen… (#9191) 
* assimp: fix compile issues with intel compilers on knl/linux [a dependency for dealii]

Fixes issue #9189

* assimp: add variant 'shared' with default value 'True'
 2018-09-08 16:18:37 -05:00
Denis Davydov
ffca064778 xsdk: disable assimp in deal.II (#9190) 2018-09-08 16:07:37 -05:00
Josh Deaton
7295c8aaad libMesh: New variant and updated recent versions. (#9186) 
* libmesh: Added SLEPC eigensolver variant.

* libmesh: Added new versions.

* Corrected flake8 errors.

* Corrected SLEPc variant with proper config & conflicts.
 2018-09-07 21:13:34 -07:00