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Author SHA1 Message Date
Justin Stanley
011ad24950 salmon: remove static link to libstdc++ (#9343) 2018-10-04 20:57:33 -05:00
Patrick Gartung
d981f28a80 Davix version update (#9304) 
* Replace old version with new version
* Remove patch only needed by CMS
 2018-10-04 16:12:53 -07:00
Patrick Gartung
5a20217a54 VecGeom: add versions and cxxstd variant (#9303) 2018-10-04 16:11:28 -07:00
Patrick Gartung
9b5f3d77f3 Valgrind: add ubsan and only64bit variants. (#9302) 
* Add conflict for +ubsan when building with clang on MacOS
* only64bit is enabled by default
 2018-10-04 16:06:10 -07:00
Matthias Wolf
2b3e7dbd93 py-py4j: add version 0.10.6 (#9418) 2018-10-04 15:32:54 -05:00
dorier
872e3c76f6 Package mesa: added dependency on zlib (#9424) 2018-10-03 19:48:42 -07:00
Denis Davydov
600acbbe66 python: add details on missing library to error message (#9332) 
When a library cannot be found, the exception now includes the name
of the library that was requested.
 2018-10-03 19:46:14 -07:00
Cody Balos
219846684b SUNDIALS: add new versions (#9401) 
* Add SUNDIALS 3.2.0 and 4.0.0-dev.2 releases.
* Update CMake dependency version constraints
* Update CMake args to find raja dependency
 2018-10-03 19:37:54 -07:00
Daryl W. Grunau
7f4b436ab6 ParaView: add versions (#9428) 2018-10-03 19:34:38 -07:00
Geoffrey Oxberry
98cdd616ca py-flake8: enum34 not required for python 3.4 and up (#9415) 
py-flake8 only requires py-enum34 when using a python version
earlier than 3.4
 2018-10-03 19:33:22 -07:00
Robert Pavel
479e71a832 Specified Maximum Matplotlib for Candle (#9425) 
Specifying that Candle-benchmarks requires matplotlib 2.x due to
matplotlib 3.x requiring python 3.x
 2018-10-03 11:47:17 -06:00
Valentin Clement (バレンタイン クレメン)
a97e9cb282 CLAW Compiler: Add Spack Package (#9405) 2018-10-03 17:17:13 +02:00
Matthias Wolf
fe60b2f6de py-progress: new package. (#9420) 2018-10-03 17:12:30 +02:00
Christoph Junghans
63844a97f8
openmc: version bump (#7974) 
* openmc: version bump

* s/mit-crpg/openmc-dev/
 2018-10-03 09:12:14 -06:00
Satish Balay
297f8537b5
trilinos: superlu_dist patch is now in trilinos develop - so removing it (#9422) 
https://github.com/trilinos/Trilinos/pull/3209
 2018-10-03 09:52:12 -05:00
Satish Balay
846e2c7ca9
PETSc: configure use CFLAGS,FFLAGS,CXXFLAGS from spack (#9383) 2018-10-03 08:19:43 -05:00
alcharal
c46a7a61f0 Abyss: added variant maxk (#9280) 2018-10-02 17:27:25 -07:00
dorier
8f29fbb605 Adding new versions to Catalyst package (#9267) 2018-10-02 17:25:56 -07:00
Mario Melara
eff3ad3346 Spades: add version 3.12 (#9286) 2018-10-02 17:24:39 -07:00
sknigh
d056427a00 Added cudnn 7.3 (#9400) 2018-10-02 17:24:13 -07:00
sknigh
89ccaa2472 Added perl 5.28 (#9379) 2018-10-02 15:48:28 -07:00
Abhinav Bhatele
0352b4808e [WIP] Release 2.0 of the ECP Proxy Apps suite (#9368) 
* Release 2.0 of the ECP Proxy Apps suite

* update laghos version

* make install dir structure consistent across all ecp-proxy-apps

* minor

* update macsio version
 2018-10-02 16:35:41 -06:00
Gregory Lee
676b3b0364 added py-matplotlib version 3.0.0 (#9335) 2018-10-02 15:35:06 -07:00
Abhinav Bhatele
d962e65cf2 PICSAR: new package (#9411) 2018-10-02 16:04:49 -06:00
rvinaybharadwaj
46a9121f00 Spackage for Thornado-mini (#9363) 2018-10-02 16:03:58 -06:00
Abhinav Bhatele
f6fb176d10 PICSARlite: actually builds PICSARlite now instead of PICSAR (#9410) 
also removed variants which shouldn't be there
 2018-10-02 15:46:31 -06:00
Abhinav Bhatele
1ba061f6ec MACSio: update package (#9412) 2018-10-02 15:46:09 -06:00
David Orman
e8af5847a0 Intel parallel studio 2019 cluster edition (#9295) 
* untracking file

* intel-parallel-studio: added 2019 cluster edition and checksum
 2018-10-02 13:04:57 -05:00
Abhinav Bhatele
25be114f75 new package: TraceR (#9298) 2018-10-02 11:04:11 -07:00
Justin Stanley
4e031d25a4 raxml: build all matching variants (#9377) 2018-10-02 09:20:47 -05:00
Prasanna Balaprakash
658e42ae3f ytopt: new package (#9403) 2018-10-01 23:16:32 -07:00
Geoff Womeldorff
922c1a5652 kokkos: bugfix for case wherein kokkos backends enabled in spack but not parsed correctly (#9396) 2018-10-01 17:36:55 -06:00
Matthias Diener
f38bfde6f3 nvptx-tools: add new package (#9378) 
* nvptx-tools: add new package

* Update package.py

* Update package.py
 2018-10-01 16:55:41 -05:00
Ricardo Silva
d031bd7461 patching p4est to select the proper openmp lib (#9381) 
* patching p4est to select the proper openmp lib

* For when compiler.openmp_flag isn't supported

* authored by @nrichart, I only tested it

* Adding openmp variant

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
 2018-10-01 22:43:40 +02:00
Geoff Womeldorff
57236fa2ce kokkos: add serial backend explicitly. add kokkos options and kokkos cuda options. (#9276) 2018-10-01 10:24:43 -06:00
Justin Stanley
691a19226c redundans: add py-numpy dep, snap-berkeley version constraint (#9354) 2018-10-01 05:54:50 -05:00
Abhinav Bhatele
a6ab5edea6 Laghos: add version 1.1 (#9389) 2018-09-30 05:38:52 -06:00
Justin Stanley
bf757bd231 lighttpd: install to bin vs sbin (#9337) 2018-09-28 18:38:51 -07:00
Justin Stanley
ad13a9989f gsnap: add 2018-07-04 (#9356) 2018-09-28 17:07:08 -05:00
Levi Baber
017199b5d6
py-flake8-polyfill: removing unnecessary build_args (#9284) 2018-09-28 14:49:45 -05:00
Levi Baber
6ac167a891
libsigcpp: add a real homepage (#9282) 2018-09-28 14:48:31 -05:00
Aronnax, Miles V. [ISU/LAS]
e9863f56f3 Gapfiller 1.10 f01 (#9163) 
* GapFiller.pl fixes: line endings, env perl, convert to Getopt::Std, requires perl with threads.

* GapFiller.pl fixed source path, install location.

* Fixed missing space.
 2018-09-28 14:45:54 -05:00
Justin Stanley
d6daa8fab5 perl-dbd-sqlite: new package starting at 1.56 (#9338) 2018-09-28 14:08:14 -05:00
Levi Baber
6d0b3f0e71
r-biocparallel: new link dependency added in last version (#9274) 2018-09-28 13:56:46 -05:00
Levi Baber
5d3fb74e24
r-misc3d: add a real homepage (#9283) 2018-09-28 13:54:50 -05:00
Justin Stanley
43ae3bd2c9 perl-cgi: new package starting at 4.37 (#9339) 2018-09-28 13:53:40 -05:00
Justin Stanley
a5d6f79fe0 r-rots: fix package type (#9344) 2018-09-28 13:11:09 -05:00
Serban Maerean
2ac648407e Add PETSc 3.10.1 to PETSc's spackage file (#9382) 
* Add version 3.10.1 to the PETSc spackage file.
* Makefile changes required for building PETSc native tests with the XL compiler.
 2018-09-28 10:46:21 -07:00
snehring
3c713661b8 gmap-gsnap: set default value for simd variant (#9366) 
Also add zlib/bzip2 dependencies.
 2018-09-28 10:41:41 -07:00
Mark W. Krentel
f641a72a8b libpfm4: add version and compiler flags (#9291) 
Set default optimization level (-O2) if not specified in cflags.
 2018-09-28 10:36:27 -07:00
Denis Davydov
2cd7783e9e mpich: fix 3.2 patch (#9330) 
patch does not apply to 3.2.1 (released in late 2017).
Given that it fixes the issue discussed in May 2016, most likely
it shall apply only to 3.2
 2018-09-28 08:18:55 -05:00
Eric Müller
1e75aef0e9 Bazel: update env handling, add versions (#9369) 
Building bazel yielded errors since commit cd9691d. The first commit
fixes the build for older bazel versions, the second commit adds new
versions and ports the patches to these versions.
 2018-09-27 19:37:31 -07:00
sknigh
bd801da1bf Set libs property for tcl and tk (#9372) 2018-09-27 19:34:18 -07:00
sknigh
496bc3cd23 Added legacylaunchers variant to openmpi (#9336) 
Lots of programs still have mpiexec/mpirun baked in.
 2018-09-27 19:29:15 -07:00
sknigh
5047d86732 yaml-cpp: conflict with gcc 4.7 instead of 4.8 (#9371) 
4.8 has c++11 support, and RHEL/Centos 7 still use 4.8.5
 2018-09-27 13:37:36 -07:00
sknigh
7db31c6671 Added slurm 17.11 and 18.08 (#9345) 2018-09-27 13:34:41 -07:00
sknigh
2155163a37 Added Cuda 10 (#9310) 2018-09-27 13:33:53 -07:00
Abhinav Bhatele
37918e0536 ember: put all READMEs into docs and add executables in bin (#9362) 2018-09-27 05:49:15 -06:00
dorier
9e448d4c4f py-pybind11: add version 2.2.4 (#9355) 2018-09-26 19:19:46 -07:00
Denis Davydov
12c59c5b55 arpack-ng: add version 3.6.3 (#9331) 2018-09-26 19:12:41 -07:00
Justin Stanley
e41677b560 new package: r-processx (#9342) 2018-09-26 19:12:06 -07:00
Justin Stanley
bf4ac40ade new package: r-ps (#9341) 2018-09-26 19:08:55 -07:00
Justin Stanley
b35dccf875 paml: remove old version, added 4.9h (#9360) 2018-09-26 19:03:35 -07:00
Daniel Topa
c9d8226bc6 new package versions: ucx, libhio, and hwloc (#9365) 2018-09-26 18:53:54 -07:00
Abhinav Bhatele
d0ed39f51a miniVite: new package (#9348) 2018-09-26 19:48:34 -06:00
Abhinav Bhatele
41b35a783e fix build errors, make mpi variant default and add openmp variant (#9364) 2018-09-26 19:47:51 -06:00
Peer-Timo Bremer
2f28bd7d7f new package: TALASS (#9326) 2018-09-26 18:15:47 -07:00
Abhinav Bhatele
d5cdb1a2a7 update URLs for Laghos and MACSio (#9351) 2018-09-26 17:22:05 -06:00
dorier
4be8ae2b70 VTK package: don't require "+llvm" for mesa dependency (#9256) 2018-09-26 11:20:01 -07:00
lingnanyuan
f88735c1eb gmap-gsnap: Add variant for different cpu support. (#8087) 
* gmap-gsnap: Add variant for different cpu support.

* gmap-gsnap: fix flake8 error.

* gmap-gsnap: remove sys import.

* Change variant type to multi-valued.

* remove if-statement.

* gmap-gsnap: Build in seperate directories.

* gmap-gsnap: remove make distclean.

* gmap-gsnap: rewrite the recipe.
 2018-09-26 11:56:39 -05:00
Justin Stanley
6c0f0dbdfd qt: fix dbus builds (#9315) 2018-09-25 11:33:19 -05:00
Satish Balay
2c4a057fe4
petsc: add new versions 3.9.4 and 3.10.0 (#9319) 
* petsc: add new versions 3.9.4 and 3.10.0

* petsc:update superlu_dist dependency for version 3.10 [might have to change this later for xsdk]

* slepc: add in new releases 3.9.2 and 3.10.0
 2018-09-24 23:57:38 -05:00
Satish Balay
6b1b84267d superlu_dist: (master) has cxx11 sources - so update make.inc to list cxx11 compilers (#9316) 2018-09-24 21:53:14 -05:00
Justin Stanley
43b0948457 lighttpd: new package starting at 1.4.50 (#9325) 2018-09-24 21:33:39 -05:00
Denis Davydov
79eaa16118 intel: add 2019.0 (#9328) 2018-09-24 21:27:43 -05:00
Strahinja Trecakov
8947b6b909 New package: r-animation (#9314) 
* adding r-animation package
 2018-09-24 11:28:05 -07:00
Strahinja Trecakov
82f19f72f7 new versions of r-dplyr,r-plogr,r-rlang (#9313) 2018-09-24 11:22:04 -07:00
rvinaybharadwaj
e227542500 Spack package for PICSARlite (#9288) 2018-09-24 11:12:01 -06:00
rvinaybharadwaj
2656ed63eb Spack package for Ember (#9292) 2018-09-21 13:04:39 -06:00
Andrew Gaspar
72be5c86fa Add newer versions of spdlog (#9290) 2018-09-20 17:53:15 +02:00
sknigh
2bc895083b Added llvm 7.0.0 (#9296) 2018-09-20 17:21:42 +02:00
Axel Huebl
9e2ff95ec5 Catch2: 2.3.0+ (#9300) 
* Catch2: 2.3.0+

Add the latest two releases of Catch2.
In 2.3.0+, the include changed to a future-proof
`<catch2/catch.hpp>` path which dependent projects will break upon.

* openPMD-api: Catch2 2.3.0+

openPMD-api just updated to use the new, future-proof Catch2
headers `<catch2/catch.hpp>`.
 2018-09-20 15:55:18 +02:00
Christoph Junghans
7b2b2fb969
sw4lite: add v1.1 (#9289) 2018-09-19 13:30:28 -06:00
Adam J. Stewart
133dd7a4ac Fix version parsing for cistem package (#9260) 
Adds 'code' to the list of suffixes that are excluded from version
parsing of URLs, such that if a URL contains the string
'cistem-1.0.0-beta-source-code', a version X will substitute in to
produce a URL with cistem-X-source-code ('source' was already excluded).
The 'cistem' package version is updated to make use of this (and fix
a fetching bug with the cistem package). A unit test is added to check
this parsing case.
 2018-09-18 19:29:18 -07:00
sknigh
467d501060 sst-macro package: add versions and variants (#9271) 
Added variants for: mpi support, clang skeletonizer, building as
static and/or shared, and more.
 2018-09-18 19:06:13 -07:00
Geoffrey Lentner
3f04ebf600 hadoop package: fix url and checksum (#9263) 2018-09-18 18:49:52 -07:00
Geoffrey Oxberry
c971f6f1eb apple-libunwind: update path to library (#9265) 2018-09-18 18:48:53 -07:00
Levi Baber
d14971b061 new package: rclone (#9268) 2018-09-18 18:39:07 -07:00
Howard Pritchard
21884d804f libhio: add patch for 1.4.1.2 release (#9270) 
Turns out that there was a configury problem in libhio
which caused issues building the package on non-cray
systems, aka when using mpicc and friends.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
 2018-09-18 17:26:34 -06:00
Christoph Junghans
41de79a1b6
xsbench: added v18 (#9269) 2018-09-18 14:07:37 -06:00
Christoph Junghans
5135f03c03
Packages/candle benchmarks (#9266) 
* candle-benchmarks: added v0.1

* ecp-proxy-apps: v1.0 now depends on candle-benchmarks@0.0
 2018-09-18 13:02:03 -06:00
Douglas Duckworth
842d754338 star - added latest versions with shasum (#9257) 
* star - added latest versions with shasum

* star - added latest versions with shasum
 2018-09-16 15:44:33 -05:00
Geoffrey Oxberry
f9aed03e83 coinhsl: add @2015.06.23, explain versions, SHA256 (#9258) 2018-09-16 15:03:26 -05:00
Pramod Kumbhar
50378c15a9 Update rdma-core : new version and conflict with intel (#9255) 
* Update rdma-core : new version and conflict with intel

* address review comments
 2018-09-15 19:42:45 -05:00
toffer93
b3bdf92f26 changed to new install_tree formalism (#9181) 2018-09-15 09:40:50 -05:00
Matthias Diener
4942237278 gdb: add lzma support by default (#9247) 
This is required at least on RedHat/Fedora.

Many (most?) other people distribute gdb with this support enabled:
http://tomszilagyi.github.io/2018/03/Remote-gdb-with-stl-pp
https://bugzilla.redhat.com/show_bug.cgi?id=1596490
 2018-09-15 09:06:16 -05:00
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
Mike Pozulp
e678266550 Tanim (#9158) 
* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement

* flake8 fixes

* fix formatting in jdk version cmd

* Added type=('build', 'run') to some R package dependencies,
added some missing dependencies to r-ks. Thanks Adam.

* fix flake8 error
 2018-09-07 16:00:52 -05:00
Denis Davydov
18ca196753 xsdk: add dealii (#7529) 2018-09-06 19:22:17 -05:00
Satish Balay
b6b8c7058a
Balay/xsdk trilinos develop (#9182) 
* xsdk: update xsdk@develop dependency on trilinos@develop

* trilinos: enable tpetra, ifpack2, zoltan2, amesos2
 2018-09-06 12:01:53 -05:00
Tristan Carel
733458347a gmodel: new package starting at 2.1.0 (#9170) 2018-09-06 10:48:08 +02:00
Tristan Carel
26b68a2bc5 gmsh: add git master and 4.0.0 versions (#9172) 2018-09-06 10:42:40 +02:00
Axel Huebl
901d76ef53 openPMD-api: ^py-numpy@1.15+ (#9178) 
Due to an internal bug regarding the handling of scalars
(ndim must be 0) in numpy prior to 1.15.0, openPMD-api
will require the latest numpy 1.15+.

Since there is a small regression with datetime pickling in
1.15.0 from the required fix and spack only packages 1.15.1
currently, we depend on 1.15.1 in the recipe.
 2018-09-06 10:41:45 +02:00
Tristan Carel
a779e87442 omega-h: add versions and variants (#9169) 
* add 5 most recent versions and git master branch
* add trilinos, gmodel, throw, examples, optimize, symbols,
  and warnings variants
* disable XSDK so that Trilinos dependencies are found.
 2018-09-05 11:01:45 -07:00
健美猞猁
501669faba Pack dlang's stdlib into dmd. (#9131) 
* Update dmd.

* Build dmd and druntime.

* Build dmd.

* Restore edit.

* Flake8.
 2018-09-04 14:49:28 -05:00
健美猞猁
8b9b89b931 Onedrive: a new package. (#9130) 
* skilion-onedrive: a new package.

* Fix flake8 issues.
 2018-09-04 14:35:49 -05:00
健美猞猁
9fe7000dda Bamdst: a new package. (#9113) 
* Bamdst: a new package.

* Remove duplicate make() in install().
 2018-09-04 14:35:33 -05:00
Levi Baber
5737155dd0 trinity: full dependencies (#9064) 2018-09-04 14:35:06 -05:00
Levi Baber
059daa2012 r-summarizedexperiment: new version (#9054) 
* r-summarizedexperiment: new version

* r-summarizedexperiment: add ending range for r3.4 dep

* r-summarizedexperiment: fix range
 2018-09-04 14:34:45 -05:00
Miles Perry
447db2fe8d Feature/py pycogent New-Version (#9095) 
* added py-pycogent

* flake8 edits

* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py

* changed python min version to 2.6

* fixed cython to py-cython dep

* fixed mpi4py to py-mpi4py

* fixed py-sqlalchemy

* added 1.5.3 version

* fixed version 1.5.3 install

* changed deps names to reflect convention

* added variants

* changed download URL and added SHA256 hash

* fixed deps

* added github url for 1.5.3

* removed unneeded deps

* doesn't require py-setuptools

* fixed url and added py-setuptools specific to version 1.9

* fixed variant names and changed cython to normal dependency instead of variant

* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi

* fixed dependencies and added py-pymysql dep

* added setup-environment step

* changed download url for 1.5.3 to pypi

* fixed flake8 issue

* updated

* added changes
 2018-09-04 14:34:18 -05:00
Francesco Di Natale
e85f737d1f py-maestrowf: Addition of new releases. (#9135) 
* Addition of latest maestrowf releases.

* Addition of filelock to dependencies.

* Addition of when clause to depends_on for filelock and tabulate.

* Correction of the tar url.
 2018-09-04 14:33:55 -05:00
Levi Baber
3c9b0ee2ea r-genomicalignments: new version (#9055) 
* r-genomicalignments: new version

* r-genomicalignments: ending range for r3.4 dep

* r-genomicalignments: fix range
 2018-09-03 21:04:22 -05:00
Levi Baber
35d87bdf09 r-biomart: new version; (#9058) 
* r-biomart: new version;

* r-biomart: ending range for r3.4 dep

* r-biomart: fix version range
 2018-09-03 21:03:47 -05:00
Levi Baber
cb9a95fc37 r-deseq2: new version (#9062) 
* r-deseq2: new version

* r-deseq2: fix r 3.4 dep range
 2018-09-03 21:03:08 -05:00
Hadrien G
930e266a36 New package: AIDA (#9094) 
* Trying to package old AIDA

* Document the incompleteness

* Install the jars too
 2018-09-03 21:02:06 -05:00
Miles Perry
cb9e8eda8f Feature/py picrust New Package (#9096) 
* added py-picrust

* flake8 edits

* fixed boilerplate, added type='build', 'run'

* fixed errors

* added deps

* fixed error

* fixed numpy max version

* fixed future version

* fixed version issues
 2018-09-03 20:58:49 -05:00
Neil Flood
ee14d273e5 nlopt: Only support release>=2.5.0, since earlier release tarballs were actually AutoTools, not CMake. (#9110) 2018-09-03 20:56:48 -05:00
Miles Perry
ad8fbe3c7f aperture-photometry: new package (#9119) 2018-09-03 20:52:11 -05:00
Miles Perry
585c69b94c py-pymysql: new package (#9122) 
* py-pymysql: new package

* added type build and run
 2018-09-03 20:50:39 -05:00
Geoffrey Oxberry
4bdfa19d97 openblas: add @0.3.1, patch CMake export bug in @0.3.1:0.3.2 (#9123) 
* openblas@0.3.1:0.3.2: patch CMake export bug

See https://github.com/xianyi/OpenBLAS/pull/1703.

* openblas@0.3.1: new version
 2018-09-03 20:49:45 -05:00
Abhinav Bhatele
ed657e97fa New package: CODES simulation framework (#9133) 
* New package: CODES simulation framework

* CODES: add comments

* CODES: remove -fi from extra autoreconf flags
 2018-09-03 20:43:50 -05:00
Edoardo Aprà
187e110ab0 NWChem 6.8.1 (#9140) 2018-09-03 20:36:49 -05:00
rice31
6e7af3362e added version for kull support (#9141) 2018-09-03 20:36:15 -05:00
Timo Heister
89c77051fe aspect: new version (#9146) 2018-09-03 20:35:45 -05:00
Jim Galarowicz
ccd96a2fed Update openspeedshop and cbtf version numbers (#9150) 
Update the version numbers and now depend on
the develop version of dyninst because of a
feature in openspeedshop depends on new code
in the dyninst develop tree.  Without dyninst
develop, openspeedshop will not build.
 2018-09-03 20:35:25 -05:00
Levi Baber
e3bae8f936 py-matplotlib: incorporate 8532 w/ version range (#9151) 
* py-matplotlib: Add patch to fix FreeType library detection

Adds patch to add $CPATH to locations searched for FreeType header file

Patch has been upstreamed:
https://github.com/matplotlib/matplotlib/pull/11457

* py-matplotlib: Add patch to fix FreeType library detection

* Make patch only apply to versin 2.2.2 (as already upstreamed)
* Fix flake8 format issue

* py-matplotlib: add range to freetype patch

* py-matplotlib: whitespace
 2018-09-03 20:34:41 -05:00
Adam Moody
801f1a0a7d mpifileutils: add v0.8 (#9152) 2018-09-03 20:34:07 -05:00
Matthias Wolf
4df60caf5b msgpack-c, snappy: explicitly depend on googletest (#9167) 2018-09-03 20:25:17 -05:00
David Wells
734d6306a2 Fix two dependencies with silo. (#9153) 
1. I presently get errors of the sort

==> Error: KeyError: 'No spec with name mpi in silo@4.10.2%gcc@8.1.0+fortran+mpi
[...]
$HOME/spack/var/spack/repos/builtin/packages/silo/package.py:84, in configure_args:
         81                'FCFLAGS={0}'.format(self.compiler.pic_flag)]
         82
         83        if '+mpi' in self.spec:
  >>     84            config_args.append('CC=%s' % self.spec['mpi'].mpicc)
         85            config_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
         86            config_args.append('FC=%s' % self.spec['mpi'].mpifc)

without the extra explicit MPI dependency.

2. Silo uses zlib, so we should explicitly depend on it.
 2018-09-03 16:43:00 +02:00
Adam J. Stewart
4920f1cff1
Vim: add version 8.1.0338 (#9155) 2018-09-01 08:12:14 -05:00
Adam J. Stewart
c5c3b65c60
GDAL: add version 2.3.1 (#9156) 2018-09-01 07:32:24 -05:00
Cody Balos
e7df911026 SUNDIALS: add new versions, update hashes, and apply clang fix (#9115) 
Added SUNDIALS 3.1.2 and 4.0.0-dev.1 versions and relevant dependencies
(3.1.2 requires CMake 2.8.12). Updated all versions to use sha256 hashes.
Addressed issue specific to clang compiler on macOS.
 2018-08-31 12:14:15 -07:00
Francesco Di Natale
3d92b975f3 py-filelock: new package (#9136) 
* Addition of py-filelock and first page of versions.

* Addition of setup.py patch for setuptools.

* flake8 failure fixes.

* Reduced url declaration to a single line.

* Correction to py-filelock to use distutils.
 2018-08-31 11:21:55 -07:00
Geoffrey Oxberry
d54a91fd2b openblas@0.3.3: new version (#9143) 2018-08-31 11:14:37 -07:00
rice31
20a914374e libpng package: add version (#9142) 2018-08-31 10:26:13 -07:00
Levi Baber
535b09d811 singularity: new version 2018-08-31 08:47:24 -07:00
Michael Sternberg
a86f22d755 Intel prefixes (#7469) 
Consolidate prefix calculation logic for intel packages into the
IntelPackage class.

Add documentation on installing Intel packages with Spack an
(alternatively) adding them as external packages in Spack.
 2018-08-29 21:09:34 -07:00
Mark W. Krentel
e860307c31 binutils: add variant 'nls' for native language support (#9124) 
Add variant 'nls' for native language support with default True.
The default inside binutils was always on, but this gives a way of
turning it off, if desired.

Adjust the dependencies.  Flex is never used for a one-time build.
Bison and m4 should not be needed, except that prior to rev 2.30, gold
did not include its generated files, so bison is needed when +gold.

Drop configure option --enable-interwork.  This option does not exist.
 2018-08-29 20:32:41 -07:00
Adam J. Stewart
1383834d15
Add MDB driver support to GDAL (#8614) 2018-08-29 12:35:56 -05:00
Andreas Baumbach
1e0c337fe9 New package: NEST Simulator (#9092) 2018-08-29 13:30:29 -04:00
Abhinav Bhatele
23f89ccc0b ROSS package: fix build error and add v7.0.0 (#9128) 2018-08-29 13:13:50 -04:00
Andrew Gaspar
ebf21d1d87 Adds a package for optional-lite header-only library (#9117) 2018-08-29 18:14:59 +02:00
Christoph Junghans
5de47da740
flecsi: fix build (#9129) 2018-08-29 09:23:02 -06:00
Andrew Gaspar
f540b2ca1b Adds a package for span-lite header-only library (#9118) 2018-08-29 11:01:35 +02:00
Geoffrey Oxberry
eeaa924a6f hdf5@1.10.3: new version (#9121) 2018-08-29 10:58:24 +02:00
Geoffrey Oxberry
c7a8b47e74 ipopt@3.12.10: new version (#9120) 2018-08-29 10:58:05 +02:00
Massimiliano Culpo
cf807f6fd1
New package: channelflow (#9111) 2018-08-29 10:54:34 +02:00
Douglas Duckworth
1a7e9e58d0 added star 2.6.1a (#9103) 2018-08-29 07:34:04 +02:00
Michael Kuhn
3d7457edde go: Update to 1.11 (#9101) 2018-08-29 07:00:40 +02:00
Andrew Gaspar
168c6d9428 Add string-view-lite package for header only library (#9125) 2018-08-29 06:54:20 +02:00
Christoph Junghans
cefc1069e6 gasnet:version bump (#9127) 2018-08-29 06:48:52 +02:00
Jannek Squar
b78ccb74d8 atk package: hotfix #9099 (#9102) 
Adds explicit python3 dependency for meson
 2018-08-28 16:35:30 -04:00
Adam J. Stewart
be42b8df19 Java updates: new versions, classpath, and JAVA_HOME (#8613) 
This PR includes the following changes:

* Added JDK 10
* Changed the JDK version numbers according to the consensus reached
  in #2284
* Added spec['java'].home and spec['java'].libs, similar to #3367
  (JDK and IcedTea)
* Added a check to prevent people from installing JDK on macOS
* Set CLASSPATH for packages depending on Java (JDK and IcedTea)
* Add TODO for extending virtual packages (not currently possible)
* Add TODO for adding Java dependents to views
* Add TODO for packages which extend multiple packages (e.g. Java
  and Python)
 2018-08-28 14:35:13 -04:00
Douglas Duckworth
04c25ac468 perl-star-fusion package: update latest version (#9104) 2018-08-28 13:22:18 -04:00
Sasha Nícolas
2fdfa46735 dyninst: add dependency on libiberty (#8806) 
* Adding dependency of libiberty to Dyninst package configuration.
* Now it depends on libiberty package and not binutils.
 2018-08-27 14:34:05 -07:00
Alan Williams
c56992587e Add line in trilinos/stk configuration to enable stk_ngp package. (#9082) 
The Trilinos/stk configuration is pretty Nalu specific right
now (and is acknowledged as such in a comment in package.py), and
this commit enables a module that Nalu will be needing.
 2018-08-26 19:49:35 -05:00
Levi Baber
bba5967dcc r-goseq: new package (#8939) 
* r-goseq: new package

* r-goseq: git not url

* r-goseq: adding packages needed at runtime

* r-goseq: package type

* r-goseq: dep types

* r-goseq: one more
 2018-08-26 19:45:23 -05:00
lingnanyuan
7c06492d94 braker: add new version 2.1.0 (#8946) 
* braker: add new version 2.1.0

* Set verison in descending order.

* Update URL.

* url

* braker: change url format.
 2018-08-26 19:44:53 -05:00
TZ
2ae1bfd283 patch for OF.com@18.06 to correctly find KAHIP (#8982) 
- OpenFOAM-v1806/wmake/scripts/have_kahip must check
  $KAHIP_ARCH_PATH instead of $METIS_ARCH_PATH to detect the KAHIB
  library
- use a local patch file until the issue is hopefully fixed upstream
 2018-08-26 19:44:06 -05:00
Adam J. Stewart
cc01e89d6b
Update to latest version of pytest and dependencies (#9087) 
* Update to latest version of pytest and dependencies

* Fix bug in installation tests
 2018-08-25 14:12:46 -05:00
Todd Gamblin
3c292de6bd bugfix: 'submodules' attribute should imply git fetch 
- 'submodules' wasn't properly declared as an optional attribute for git
  fetcher

- add it and add a test.
 2018-08-25 10:20:39 -07:00
Hadrien G
a7f3fa01d5 new package: GSL - C++ Guideline Support Library (#9091) 
Since "GSL" is a highly overloaded acronym, the package name is "cppgsl".
 2018-08-24 17:45:18 -04:00
Hadrien G
afff196a06 Update the pocl package (#9090) 
* Update the pocl package

* Use url_for_version

* Clarify hwloc version requirements

* Apply hwloc dependency suggestion
 2018-08-24 12:26:17 -05:00
Hadrien G
b7e4be4d29 Add new CLHEP releases and move to sha256 hashes (#9089) 2018-08-24 09:49:38 -05:00
Hadrien G
4fbcecd0cd range-v3 package (#9093) 
* Add first version of a Range-v3 package

* Add C++ standard variant to range-v3 package
 2018-08-24 09:41:25 -05:00
Matthias Diener
95ca99bbdd htop: add version 2.2.0 (#9086) 2018-08-23 18:50:01 -05:00
Matthias Diener
30cbca2c32 bison: add new version (#9085) 2018-08-23 17:00:26 -05:00
Christoph Junghans
ca2e1e9019 lammps: add v20180822 (#9081) 2018-08-23 12:17:27 -05:00
Brian Spilner
87c2214b02 add cdo releases 1.9.4 and 1.9.5 (#9079) 2018-08-23 10:27:35 -05:00
Michael Kuhn
983957f7c0 mvapich2: Use rdma-core for mrail and nemesis*ib* fabrics (#9072) 2018-08-23 07:32:46 -05:00
Daniel Topa
05c4ff4e92 Open mpi add v3.1.2 (#9078) 
* Add latest release 3.0.2
https://www.open-mpi.org/software/ompi/v3.0/:x

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* 1. Added correct md5 sum for Open MPI v3.1.1 (https://www.open-mpi.org//software/ompi/v3.1/)
2. Made v3.1.1 the default version
3. Added libmpiso versions for v3.1.1 and 3.0.2

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* Added Open MPI v2.14 to version list; Tested build; Added libmpi.so version

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* Open MPI 3.1.2 built and tested

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2018-08-22 23:17:48 -05:00
Sam Gutiérrez
8c89e67669 libquo: Packaging updates. (#9076) 
* libquo: Packaging updates.

This commit accomplishes a few things:
* Changes distribution fetch source
* Removes a deprecated version (1.2.9)
* Changes dependencies based on version type
* Adds a custom autoreconf stage when using the 'develop' version,
  omitting this step when building from a distribution

* Reintroduce v1.2.9.
 2018-08-22 23:17:15 -05:00
Michael Kuhn
a6826a7a2d glib: Add 2.56.2 (#9071) 
This should finally fix build failures on RHEL6-based distributions.
Also fix the patch to apply to the correct versions and distributions.
 2018-08-22 14:21:54 -05:00
Sam Gutiérrez
66971f6ac8 libfabric: Add develop version option. (#9074) 
Add develop version option to libfabric, conditionally bringing in
additional build dependencies: m4, autoconf, automake, libtool.
 2018-08-22 14:21:30 -05:00
Michael Kuhn
0b2a4aea6d leveldb: Fix header installation (#9069) 
leveldb headers are typically included via <leveldb/c.h>. The migration
to install_tree in 73c978ddd9 caused the
headers to end up in prefix.include, which breaks existing applications.
 2018-08-22 09:46:11 -05:00
Levi Baber
8b092c242f r-genefilter: new version (#9063) 
* r-genefilter: new version

* r-genefilter: fix version in dep
 2018-08-22 09:45:56 -05:00
Levi Baber
0b47741400 r-annotate: new version (#9061) 2018-08-22 09:45:11 -05:00
Levi Baber
51b3edc4f4 r-geneplotter: new version (#9060) 2018-08-22 09:44:48 -05:00
Levi Baber
96913f1876 r-qvalue: new version (#9059) 2018-08-22 09:44:21 -05:00
Levi Baber
b474e0bdc9 r-rtracklayer: new version (#9056) 2018-08-22 09:43:25 -05:00
Levi Baber
bfe58cd4a9 r-genomicfeatures: new version (#9057) 2018-08-22 09:41:38 -05:00
Levi Baber
711c3d7d69 r-delayedarray: new version (#9053) 2018-08-22 09:39:52 -05:00
Levi Baber
9a98f45064 r-genomicranges: new version (#9052) 2018-08-22 09:39:23 -05:00
Levi Baber
c0aabecbb1 r-genomeinfodb: new version (#9051) 2018-08-22 09:38:28 -05:00
Levi Baber
a38e7c783d r-genomeinfodbdata: new version (#9050) 2018-08-22 09:37:56 -05:00
Levi Baber
b1a619fdeb r-rsamtools: new version (#9049) 2018-08-22 09:37:03 -05:00
Matthias Diener
6ca7654df9 intel-parallel-studio: add version 2018.3 (#9047) 
* intel-parallel-studio: add version 2018.3

* update intel package too
 2018-08-22 09:36:33 -05:00
Denis Davydov
3a041b3fea dealii: patch boost 1.68.0 (#9070) 
* dealii: patch boost 1.68.0

* indent for readability
 2018-08-22 09:34:47 -05:00
Levi Baber
2f6a6a45a9 r-biostrings: new version (#9048) 2018-08-22 12:21:43 +02:00
Todd Gamblin
c0855d9bd5 tests: add tests for warnings in build output 
- add tests for build warnings and error messages
- simplify some code in build environment with plural() function
 2018-08-21 21:21:53 -07:00
Levi Baber
db508a8f89 r-iranges: new version (#9041) 
* r-iranges: new version

* r-iranges: typo
 2018-08-21 15:02:52 -05:00
Levi Baber
db09b71be1 r-biobase: new version (#9038) 
* r-biobase: new version

* r-biobase: reordering versions
 2018-08-21 14:15:42 -05:00
Levi Baber
1340abf1bc r-biocgenerics: new version (#9039) 
* r-biocgenerics: new version

* r-biocgenerics: reordering versions
 2018-08-21 14:15:30 -05:00
Levi Baber
2c92d50495 r-annotationdbi : new version (#9040) 
* r-annotationdbi: new version

* r-annotationdbi: dep type

* r-annotationdbi: reordering versions
 2018-08-21 14:15:17 -05:00
Sam Gutiérrez
c9fdb610f2 Add 1.6.1 release. (#9042) 2018-08-21 14:14:17 -05:00
Levi Baber
c62c9257d7 r-s4vectors: new version (#9043) 2018-08-21 14:14:05 -05:00
Levi Baber
efbb2c0733 r-zlibbioc: new version (#9044) 2018-08-21 14:13:52 -05:00
Levi Baber
eb74f49363 r-xvector: new version (#9045) 2018-08-21 14:13:39 -05:00
Levi Baber
af2dc7f3d3 r-biocparallel: new version (#9046) 2018-08-21 14:13:27 -05:00
Denis Davydov
271633ee93 dealii: add constraint on suite-sparse for old gcc (#9026) 2018-08-20 10:43:30 -05:00
Denis Davydov
5aa126d850 dealii: blacklist boost 1.68.0 due to segmentation fault in serialization lib (#9023) 2018-08-20 09:40:10 -05:00