Commit graph

6411 commits

Author SHA1 Message Date
Tom Merrick
51aa604ed2 Fix openmpi to work with slurm/pmi and mxm (#8427)
* Add binutils+libiberty for mxm fabric
* Help find the pmi library when using the slurm scheduler
2018-08-02 14:06:39 -04:00
Levi Baber
c94109c34c Package py-biom-format fixes (#8727)
* py-biom-format: needs py-setuptools at runtime
* py-biom-format: needs py-pyqi
2018-08-02 13:51:51 -04:00
Yifan Zhu
6f2a739053 New package: GRNBoost (#8763) 2018-08-02 13:46:36 -04:00
Michael Kuhn
12fb1cdbe5 Replace pkg-config dependencies with virtual (#8783)
Several packages specified pkg-config as a dependency, which is
a specific implementation of the pkgconfig virtual. Most packages
do not request a specific implementation. The current concretizer
may choose a different implentation of pkgconfig for the nonspecific
dependents, which conflicts with the request for pkg-config. This
replaces all requests for a specific implementation of pkgconfig
with the virtual package as a temporary solution to the issue.
2018-08-02 13:29:04 -04:00
Matthias Wolf
b1c35e1e13 package neovim: add info for version 0.3.1 (#8866) 2018-08-02 13:04:59 -04:00
Adam J. Stewart
d07e9e13ab Update homepage for laghos (#8864) 2018-08-02 13:03:52 -04:00
Matthias Wolf
1aa01873c7 Adding lazy property python module (#47) (#8867) 2018-08-02 11:44:16 -05:00
Michael Kuhn
ec3ffd9d28 sz: fix checksum for 2.0.2.0 (#8868) 2018-08-02 11:43:59 -05:00
Kelly (KT) Thompson
d68338cc8c Trilinos: Update rules for superlu-dist version compatibility. (#8851) 2018-08-02 11:25:30 -05:00
Takayuki Kobayashi
3a919c6abb Update and Bugfix for pexsi/package.py (#8822)
* Update and Bugfix for pexsi/package.py

1. pexsi@0.10.2 is not compatible with superlu-dist@5.4.0 due to [Change LargeDiag to LargeDiag_MC64; Add LargeDiag_AWPM](d7dce5a348).
2. In the 'edit' phase, '@MPICXX_LIB' must be substituted before '@MPICXX' is substituted.

* change dict to list of tuples

Use a list of tuples to remember the order of `substitutions`.

* Update package.py

* Update package.py
2018-08-02 11:24:57 -05:00
Douglas Duckworth
da959ba220 added py-setuptools as dependency (#8843)
* added py-setuptools as dependency

* more changes
2018-08-02 11:24:26 -05:00
Sergey Kosukhin
ec174dae69 CMake: patch for NAG. (#8869) 2018-08-02 11:17:15 -05:00
Michael Kuhn
4a6a19be85 adios2: add 2.2.0 (#8871)
This also enables the bzip2 and zfp variants. The sz variant is
currently broken.
2018-08-02 11:16:17 -05:00
Sergey Kosukhin
03dc78a894 netcdf-fortran: enforce autoreconf when building with NAG. (#8844)
* netcdf-fortran: enforce autoreconf when building with NAG.

* netcdf-fortran: patch the configure script instead of running autoreconf to get rid of additional dependencies.

* netcdf-fortran: add comment for the patch.
2018-08-02 08:32:20 -05:00
Geoffrey Oxberry
c79cd5fe51 suite-sparse: add version 5.3.0 (#8837) 2018-08-02 07:25:57 +02:00
Geoffrey Oxberry
e793f29173 openblas: add version 0.3.2 (#8833) 2018-08-01 19:14:48 -05:00
Kelly (KT) Thompson
432a5ecd36 Dia needs access to gettext and pkg-config. (#8840)
When using spack on a ubuntu baseline system, I was unable to build dia with
adding these build dependencies on gettext and pkg-config.
2018-08-01 19:12:17 -05:00
Sergey Kosukhin
abfb16af78 Small patch for netlib-lapack. (#8854) 2018-08-01 18:55:07 -05:00
Sergey Kosukhin
23b6850849 Conflict for cmake 3.11.x and Intel. (#8855) 2018-08-01 18:53:53 -05:00
Stephen Herbein
de60e9d582 lmod: fix use of custom separator in prepend_path etc. (#8737)
fixes #8736
2018-08-01 12:58:54 +02:00
Geoffrey Oxberry
db79c86ed6 lmod: add version 7.8 (#8838) 2018-07-31 23:19:41 -07:00
Geoffrey Oxberry
f7761d1081 slepc: add blopex variant (#8820) 2018-07-30 18:18:36 -05:00
Jon Rood
15d96f0166 Add extra_rpaths to OpenMPI wrappers (#8687)
If the OpenMPI build finds the infiniband drivers in /usr/lib64, it adds
-Wl,-rpath -Wl,/usr/lib64 to the OpenMPI wrappers. If the wrappers are using
a compiler outside of /usr, and the OpenMPI wrappers are used to build software
outside of Spack, they will rpath /usr/lib64 into the executable which then has
GLIBC, GLIBCXX runtime errors due to it picking up GCC libraries in /usr/lib64.

This adds the directories specified in "extra_rpaths" to the OpenMPI wrappers,
which allows them to use the correct compiler when invoked outside of Spack
builds.
2018-07-30 15:02:09 -04:00
Kelly (KT) Thompson
13cf6d55e4 GSL: 2.5 is a new version. (#8827) 2018-07-30 08:38:37 +02:00
Geoffrey Oxberry
dba7f715cf libunwind: document platform=darwin conflict (#8824) 2018-07-29 08:44:17 -07:00
Miroslav Stoyanov
71f85cff2c added Tasmanian versions 5.1 and development, enabled the Tasmanian options through +~ flags (#8804) 2018-07-27 10:10:32 -05:00
健美猞猁
440a5fbfcb Skip update check. (#8683)
* Skip update check.

* mkefile -> makefile.

* Fix emboss.
2018-07-27 09:57:05 -05:00
Michael Kuhn
d02c4bbd9a gcc: Add 8.2.0 (#8813) 2018-07-27 08:14:49 -05:00
Oliver Breitwieser
90f7fca194 py-numpy: Add CPATH in modulefile (#8466)
Also fix setup_dependent_package to include the ".egg-less"-include
path.

Change-Id: I06e66a505ece25cba8896f47e69a5be374bac6d2
2018-07-26 17:50:00 -05:00
Neil Flood
3494c6e403 Updated llvm to version 6.0.1. The previous 6.0.0 had an incorrectly … (#8801)
* Updated llvm to version 6.0.1. The previous 6.0.0 had an incorrectly declared symbol, discussed at https://reviews.llvm.org/D44140, which, amongst other things, broke py-numba. This version works fine with py-numba.

* Flag the conflict between py-numba and llvm@6.0.0

* Removed a single trailing space to satisfy checks
2018-07-26 17:47:18 -05:00
Sheng Di
bf2c232756 sz: new version 2.0.2.0 (#8786) 2018-07-26 17:46:48 -05:00
Michael Kuhn
3d86c7fef5 hdf5: Fix build with %gcc@8 (#8788) 2018-07-26 15:58:00 -05:00
lingnanyuan
d25866a8f8 halc: Create new package. (#8795)
* halc: Create new package.

* fix flake8 error.

* Modification
2018-07-26 15:55:43 -05:00
Hadrien G
c03dcdedb1 FTGL package workarounds (#8812)
* FTGL package workarounds

* Remove blank line

* Only require doxygen at build time
2018-07-26 15:54:46 -05:00
mic84
61aa1831e3 AMReX: update package.py (#8697) 2018-07-26 13:29:03 -05:00
Hadrien G
8b718e7cd6 Templight package (#8782)
* First draft of a templight recipe

* Let's be explicit for now, we can be clever later on

* The clang6 version does not work, drop it

* Reorder FIXMEs more logically

* Add patch for current templight develop branch

* Create an artificial stable release of templight

* Take some additional inspiration from llvm package

* Added the templight supporting tools

* Remove old notes from the no-url branch

* Avoid unnecessary join_path
2018-07-26 11:19:14 -05:00
Simon Flood
80741bc427 hmmer: added version 3.2.1 & updated URL (#8787)
Add HMMER 3.2.1 and updated URL then removed url_for_version function as no longer required - all HMMER downloads available from updated URL.
2018-07-26 10:07:55 -05:00
Michael Kuhn
643a4fbb59 papi: Update to 5.6.0 and fix build with %gcc@8 (#8796) 2018-07-26 10:02:07 -05:00
Mario Melara
cb410b3003 Add package DMTCP (#8808) 2018-07-26 09:47:55 -05:00
Satish Balay
d5957f147b mfem: mfem-3.3-3.4-petsc-3.9.patch is not needed for latest develop version (#8809) 2018-07-26 09:47:28 -05:00
Mark W. Krentel
af60f962cd intel-tbb: Add tm variant to disable transactional memory. (#8799)
* intel-tbb: Add variant `tm` to disable transactional memory.

Some AMD or very old Intel systems don't support transactional memory. This commit adds a variant `tm` that defaults to `True`, but can be switched off to allow running on those systems.
2018-07-25 23:14:17 -07:00
Adam J. Stewart
7902f3eb49 Add docs on new top-level VCS attributes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
5d07042f23 Unit test fixes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
68c2bdfaf6 Further improvements to version parsing 2018-07-25 23:10:10 -07:00
Adam J. Stewart
e948a54d8e All git URLs end in .git 2018-07-25 23:10:10 -07:00
Adam J. Stewart
31417bf66c Replace git=git with explicit branch names 2018-07-25 23:10:10 -07:00
Adam J. Stewart
3f18c04865 Add top-level attributes for git R-Z packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
a1572bb999 Add top-level attributes for git R (Bioconductor) packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
908d2dcd4d Add top-level attributes for git M-P packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
4c6aca533a Add top-level attributes for hg, svn, and git A-L packages 2018-07-25 23:10:10 -07:00