Commit graph

9460 commits

Author SHA1 Message Date
Sergey Kosukhin
fd85c1f0c0 Package 'gdbm': do not set CC. (#7912) 2018-04-26 08:44:17 -05:00
Geoffrey Oxberry
d54ceb6ce7 mfem: add valid range of hypre version numbers (#7903)
This commit fixes #7900.

In short: in the absence of constraints to the contrary, spack will
download the preferred version of a package, which is usually the most
recent non-develop version. On a clean spack installation without
hypre installed, `spack install mfem` will download hypre 2.14.0,
which is API-incompatible with mfem 3.3.2 (and earlier versions of
mfem), so spack will throw compiler errors re: the API mismatch.

This commit fixes that error by restricting mfem release versions
3.3.2 and earlier to hypre version 2.10.b to 2.13.999 (only 2.13.0
currently exists, but if it has a non-2.14.x maintenance release,
these versions of hypre should also be permitted).
2018-04-26 08:43:20 -05:00
Denis Davydov
2ec701d1dd adol-c: add boost optional dependency (#7905) 2018-04-26 08:42:03 -05:00
健美猫
3b82124d96 A new package: loki. (#7908)
* A new package: loki.

* Flake8.
2018-04-26 08:37:03 -05:00
Massimiliano Culpo
50122a585a
Added the latest versions of a few packages (#7910)
* automake: added version 1.16.1

* lmod: added version 7.7.29

* git: added version 2.17.0

* tmux: added version 2.7

* scala: added version 2.12.5, fixed typo in version 2.10.6

* Added spark@2.3.0, hadoop@3.1.0, jdk@8u172-b11

* picard: added version 2.18.3

* tar: added version 1.30
2018-04-26 14:46:45 +02:00
健美猫
e2092896b9 A new package: openslide. (#7906) 2018-04-26 07:17:15 +02:00
Bruno Turcksin
de9894a063 Add boost 1.67.0 (#7889)
* Add boost 1.67.0

* Remove boost 1.67.0 release candidate and the associated patch
2018-04-25 21:00:22 -05:00
mcneish1
94afb2430c Additional r packages (#7892)
* Add r-bbmisc

* Add r-dicekriging

* Add r-lhs

* Add r-mco

* Add r-misc3d

* Add r-mlr

* Remove boilerplate from r-mlr package

* Add r-mlrMBO

* Add r-parallelmap

* Add r-paramhelpers

* Add r-plot3d

* Add r-rgenoud

* Add r-smoof

* Add r-rinside 0.2.14

* Fix flake8 issues

* Add specific required versions

* Add more up-to-date versions of r-{mco, mlr, mlrMBO, smoof}
2018-04-25 20:59:46 -05:00
Robert Pavel
28901c8104 Added OpenMP Variant for Kokkos (#7902)
Added OpenMP variant for kokkos that can be disabled to build and test
on platforms where OpenMP is not available or desired. Also updated
version list
2018-04-25 10:50:58 -05:00
Levi Baber
a4e786a415 openmpi: libfabric support, ucx cleanup (#7842)
* openmpi: libfabric support, ucx cleanup

* openmpi: remove unnecessary parentheses
2018-04-25 10:37:48 -05:00
Levi Baber
7120e59c6a Libfabric: updating fabrics & adding deps (#7838)
* libfabric: mxm deprecated, adding mlx aka ucx

* libfabric: adding dependencies that we have in spack
2018-04-25 10:35:36 -05:00
Levi Baber
14e0307f04 ucx: needs numactl and rdma-core (#7836) 2018-04-25 10:34:55 -05:00
Levi Baber
a7ecb0364a psm: new package (#7834)
* psm: new package

* psm: setting latest stable to preferred
2018-04-25 10:34:31 -05:00
Levi Baber
0b284b45db rdma-core: new package (#7835)
* rdma-core: new package

* rdma-core: change to platform conflict
2018-04-25 10:33:30 -05:00
Levi Baber
a21571e737 libnl: new package (#7833)
* libnl: new package

* libnl: change platform constraint to a conflict
2018-04-25 10:33:01 -05:00
Sajid Ali
24f15a5f4b Added checksums for newer versions of numpy (#7853)
*  Committer: sajid <sajid@xrmlite.phys.northwestern.edu>

	modified:   var/spack/repos/builtin/packages/py-numpy/package.py

* Corrected typo

* removing whitespace

* remove whitespace

* remove whitespace, if not will do this in vim
2018-04-25 10:30:25 -05:00
Eric
4fdd24effa py-testinfra: Create new package (#7883)
* py-testinfra: Create new package

* py-testinfra: flake8 fixes

* py-testinfra: fix pytest version dependency

* py-testinfra: fix py-importlib version dependency
2018-04-25 10:29:45 -05:00
Levi Baber
0d5dd96762 fabtests: new package (#7837)
* fabtests: new package

* fabtests: fix hashes for github archive behavior & add libfabric dep

* fabtests: both versions confirmed working

* fabtests: use developer provided archive
2018-04-25 10:29:29 -05:00
健美猫
48a3cc67fc Add a new package: gloo. (#7894)
* Add a new package: gloo.

* Remove dependencies.
2018-04-25 10:05:16 -05:00
健美猫
fca267468e Add a new package: cpuinfo. (#7895) 2018-04-25 10:04:45 -05:00
健美猫
7095d4f414 Add a new package: fp16. (#7896) 2018-04-25 07:30:07 -05:00
Daniel Topa
82ac1571c2 Openmpi update multithread (#7893)
--enable-mpi-thread-multiple option not viable in Open MPI 3.0+

Signed-off-by: Dan Topa <dantopa@lanl.gov>
2018-04-25 07:01:17 +02:00
Eric
5f04b0c538 new package: py-weblogo (#7886) 2018-04-24 19:31:37 -07:00
René Widera
caa0c5c687 environment shell: fix spack load (#7747)
Fix `spack load` with extended packe specifications those includes spaces.
Solved by using perfectly parameter forwarding via temporary array.

example:
```
$ spack install zlib
$ spack install zlib cppflags='-O3 -march=native'
$ spack install zlib cppflags='-O2 -march=native'

$ spack find -d -L -f zlib
==> 3 installed packages.
-- linux-linuxmint18-x86_64 / gcc@5.4.0 -------------------------
k5hg4kkxiutkfl6n53ogz5wnlbdrsdtf    zlib@1.2.11%gcc

mse2fyzdxciszdhiqi4b5kl6fxkps3fh    zlib@1.2.11%gcc cppflags="-O2 -march=native"

vrnvj2fikcbxqxrymctnlpmud7wbuahk    zlib@1.2.11%gcc cppflags="-O3 -march=native"

$ spack load zlib cppflags='-O3 -march=native'
==> Error: Unexpected token
['zlib', 'cppflags=-O3', '-march=native']
```
2018-04-24 13:43:32 -07:00
Denis Davydov
f7da156879 petsc and slepc: add 3.9.0; hypre: add 2.14 (needed by petsc) (#7877) 2018-04-24 07:10:46 -05:00
Eric
8e1a7eaafa ARAGORN: Create new package (#7875) 2018-04-23 16:51:42 -05:00
Eric
e3c708fafe prinseq-lite: Create new package (#7873)
* prinseq-lite: Create new package

* prinseq-lite: set variant description and add dependency type
2018-04-23 16:11:27 -05:00
Ross Miller
b5d9a44e17 7851 pmix aarch64 (#7852)
* Fix build issue with PMIx on aarch64

Work around a bug in PMIx that causes build issues on aarch64.  Bug was
fixed in PMIx 2.1.1, so the spack package checks both the architecture
and the PMIx version.  Workaround is to just not build the PMIx test and
example code.

* Minor code cleanups

Minor corrections to make 'spack flake8' happy.

* Add support for version 2.1.1
2018-04-23 14:09:52 -05:00
Mark Olesen
50fb9352f0 New colm, ragel packages (#7867)
- Ragel is a parser and finite state machine generator that can be
  used as an alternative means for solving parsing problems without
  Flex.
2018-04-23 10:50:58 -05:00
健美猫
b33f01c799 Add a new version 5.4.1.7 for mono. (#7866) 2018-04-23 07:31:29 -05:00
Dan Ibanez
130d0c8b2e omega-h: new package (#7861)
* omega-h: new package

* omega-h: fix multiple package.py issues

* omega-h: use tarball checksum to avoid warning

* omega-h: wrap lines for flake8
2018-04-22 17:26:52 -05:00
Sinan
af82f5529d new package: racon (bioinformatics) (#7726)
* new package: racon (bioinformatics)

* add cmake_arg method
2018-04-22 07:54:48 -05:00
健美猫
708fe9f676 Add a new pacakage: HiC-Pro. (#7858)
* HiC-Pro: a new package.

* Flake8.

* Update.

* Remove nektar.
2018-04-21 13:08:56 -05:00
健美猫
b91b4a6c4d A new pacakge: IMP. (#7859) 2018-04-21 13:08:44 -05:00
lingnanyuan
f939895b1b py-mg-rast-tools: Create new package and its dependencies. (#7816)
* r-matr: Create new package.

* shocklibs: Create new package.

* r-biom-utils: Create new package.

* r-mgraster: Create new package

* py-poster: Create new package.

* py-requests-toolbelt: Create new package.

* perl-libwww-perl: Create new package.

* py-mg-rast-tools: Create new package.

* mg-rast-tools: Fix version constraints for dependencies.

* Change dependency type of py-setuptools.
2018-04-21 10:28:44 -05:00
Levi Baber
3274f16780 py-pymol: new package (#7823)
* py-pymol: new package

* py-pymol: needs python+tk
2018-04-21 10:28:09 -05:00
healther
8cc24fa20b add variant htmlreport to package cppcheck (#7824)
Change-Id: I31766d3ceb4fa8852b9bdc82444e36514e760f4b
2018-04-21 10:26:37 -05:00
Denis Davydov
5794f432a9 gnuplot: add 5.2.2 (#7831) 2018-04-21 10:24:36 -05:00
Denis Davydov
2dfd61080b dealii: disable +slepc with ~petsc (#7832) 2018-04-21 10:22:10 -05:00
Eric
a808553fa1 DIAMOND: Add version 0.9.20 (#7847)
* DIAMOND: Add version 0.9.20

* DIAMOND: add version 0.9.21
2018-04-21 09:57:06 -05:00
Levi Baber
5ae960c476 jellyfish: fixing url for v2 package retrieval (#7849) 2018-04-21 09:56:38 -05:00
健美猫
c8e3c94c6f self has no attribute named satisfies. (#7826) 2018-04-19 12:43:12 -05:00
Axel Huebl
26e9b3b74d openPMD-api (#7765)
* openPMD-api

Add a new package for openPMD-api.

openPMD is a meta-data standard (markup, schema) for hierarchical,
scientific particle and mesh based data.

openPMD-api is a library wrapping the underlying backends (HDF5,
ADIOS, ...) into a single, object-aware API.

* Repository: https://github.com/openPMD/openPMD-api
* Project: https://github.com/openPMD http://www.openPMD.org

* mpi variant forwarding: fix concretization
2018-04-19 09:04:07 -05:00
Levi Baber
d65fbf4c68 libxml2: adding subdir to cpath for deps (#7819)
* libxml2: adding subdir to cpath for deps

* libxml2: no join_path

* libxml2: fix cpath for run_env

* libxml2: typo
2018-04-19 09:01:11 -05:00
Levi Baber
7219f4a2aa freetype: adding subdir to cpath for deps (#7818)
* freetype: adding subdir to cpath for deps

* freetype: no join_path

* freetype: fix cpath for run_env
2018-04-19 09:00:49 -05:00
Kelly (KT) Thompson
4869b7312a Suite-sparse: provide patch to fix builts with clang@6.0.0. (#7811)
+ I am unable to build suite-sparse@5.2.0 with clang@6.0.0.  The build fails
  with the error:

```
     2397    [ 99%] Linking C executable wildtype_demo
     2398    make[4]: Leaving directory
  `/tmp/kellyt/spack-stage/spack-stage-w0XYhK/SuiteSparse/GraphBLAS/build'
  >> 2399    libgraphblas.so.2.0.1: undefined reference to `__fpclassify'
  >> 2400    clang-6.0: error: linker command failed with exit code 1 (use -v to
  see invocation)
  >> 2401    make[4]: *** [wildtype_demo] Error 1
```

+ This error appears because libgraphblas.so requires `-lm`, but that link
  dependency is not explicitly listed in GraphBLAS\CMakeLists.txt.
+ A patch file is provided to add this dependency.  The patch is only applied
  when the compiler is `%clang`.
2018-04-19 08:59:55 -05:00
healther
6d1097f99b add variants and conflicts for curl (#7804)
* add variants and conflicts for curl

* darwinssl - Apple's SSL/TLS implementation
* libssh    - use libssh implementation
* add darwin conflict for libssh{,2}
* add linux conflict for darwinssl

* remove openssl when +darwinssl

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2018-04-19 07:23:16 -05:00
Levi Baber
4ed613d7e1 freeglut: new package (#7820) 2018-04-18 19:49:42 -05:00
Levi Baber
ecdb3065ed glew: adding gl dependency (#7817) 2018-04-18 17:58:45 -05:00
Matthew Scott Krafczyk
1b38631781 Add -d option to diy to specify source path move -j to common args (#5963) 2018-04-18 17:26:14 -05:00