Commit graph

2525 commits

Author SHA1 Message Date
Geoffrey Oxberry
df79ba0dcf gcc: fix darwin dispatch/object.h header issue (#1518)
Fixes #1203. Apple ships headers in Yosemite (and possibly earlier) that
are gcc-incompatible, but compile fine with clang. The fix is to copy
the offending system header from /usr/include/${REST_OF_HEADER_PATH} to
${GCC_PREFIX}/include/${REST_OF_HEADER_PATH} and replace the non-gcc-
compatible features with gcc-compatible equivalents.

See https://github.com/hashdist/hashstack/pull/771/files for
inspiration, and
http://hamelot.io/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/
for a description of the header issue.
2016-10-02 18:54:43 -07:00
Nicolas Richart
16f99bd0b2 Adding latest version of fenics (#1528)
* Adding last version of fenics and making trilinos not ambiguous on hdf5

* forcing fenics to ignore hdf5 cxx

* Adding deptypes and correcting the hdf5 patch

* flake8 corrections

* cleaning some useless code
2016-10-02 18:51:34 -07:00
Kelly Thompson
621a4d637d Provide newer versions of llvm (3.8.1, 3.9.0) (#1765)
* Provide new versions of llvm.

+ Provide file list and md5 hashes for 3.8.1 and 3.9.0.
+ Clean up indentation for the 'releases' data structure to improve
  consistency.

* Adding a block of code to the 'resources' structure for cfe.

* Merge cfe and clang resources into single entity.
2016-10-02 18:50:42 -07:00
Alfredo Adolfo Gimenez
1ea9582218 Added hadoop, spark, and variant spark+hadoop (#1833)
* Added hadoop, spark, and variant spark+hadoop

* Docstrings, dependency types, urls, copyright

* Flake8 fixes, link dependency for hadoop

* Build type for spark, env problem setting JAVA_HOME
2016-10-02 18:49:30 -07:00
Erik Schnetter
b22956bab2 git: Don't link against -lrt on Darwin (#1877)
There is no librt on Darwin, and it's not necessary either.
2016-10-02 18:37:45 -07:00
Erik Schnetter
28b48f3e1a Update PAPI to 5.5.0 (#1878) 2016-10-02 18:37:26 -07:00
Erik Schnetter
b2ff9dbcd4 Update tmux to 2.3.0 (#1879) 2016-10-02 18:37:17 -07:00
Kelly Thompson
051c5dbc27 New package: libquo (#1880)
* New package: libquo

libquo is a high-level, easy to use programming interface tailored specifically
for MPI/MPI+X codes that may benefit from evolving process binding policies
during their execution. QUO allows for arbitrary process binding policies to
be enacted and reverted during the execution of an MPI/MPI+X application as
different computational phases are entered and exited, respectively.

https://github.com/losalamos/libquo

* Remove use of 'which' and fix style non-conformance.
2016-10-02 18:36:48 -07:00
Bruno Turcksin
e854e053e4 Add boost 1.62.0 (#1882) 2016-10-02 18:36:31 -07:00
Jean-Paul Pelteret
c86d4c8920 Added bash-completion package (#951) 2016-10-02 17:50:39 -07:00
Pramod Kumbhar
4b34ba1035 pdt url change to download full installer tarball (#1881) 2016-09-30 14:31:28 -07:00
Pramod Kumbhar
6c627dbac9 Add cube variant for building GUI component with qt, parallel built supported (#1525) 2016-09-29 15:37:35 -04:00
Pramod Kumbhar
6ec46ca802 updated to latest available package and fixed installation issue (old packages are no longer available for download) (#1523) 2016-09-29 15:37:07 -04:00
Mitchell Devlin
86cad961e5 added libxstream (#1454) 2016-09-29 15:36:37 -04:00
Adam J. Stewart
deb1cb4805 Add libint package (#1264)
* Add libint package

* Add Intel optimization flags recommended by CP2K

* Add new version and Intel compiler optimization flags for libxc

* Add older version of libint

* Libint depends on GMP C++ library
2016-09-29 15:35:10 -04:00
Robert D. French
a77b48f491 Library for manipulating grib1 and grib2 files (#1736)
Pro tips from @adamjstewart:
* line too long in package description
* name it grib-api instead of grib_api
* depend on netcdf without reference to unnecessary constraints
2016-09-28 17:02:29 -04:00
Elizabeth Fischer
3352889d73 py-pil: Protect against building with Python3. (#1868)
* py-pil: Does not build with Python3.

* Set py-pillow to be the default pil provider

* Update package.py

* Change to comments requested by adamjstewart

* Remove version constraint from extends(), avoid a Spack bug.
2016-09-28 16:51:41 -04:00
Erik Schnetter
4040792501 Update Qthreads to 1.11 (#1863) 2016-09-28 15:22:02 -04:00
Todd Gamblin
295742e2b5 Fixes #1860. Subversion builds sequentially due to race. 2016-09-28 15:18:52 -04:00
Robert D. French
fea0a74bec vim8 is out! (#1753)
* depends on ncurses for 8.0 or higher
2016-09-28 15:17:15 -04:00
Adam J. Stewart
66c2ac0bc9 Tell Mercurial where to find CA certs (#1873) 2016-09-28 14:58:51 -04:00
Adam J. Stewart
9b575dd976 Various updates to scipy and numpy (#1856) 2016-09-27 10:56:24 -04:00
Michael Kuhn
00b3aa77ae Update cdo to 1.7.2 (#1858) 2016-09-27 10:56:04 -04:00
Erik Schnetter
88af9f783d Make PETSc build on Darwin (#1835)
Don't set cpp when building on Darwin.
2016-09-26 10:38:02 -07:00
Erik Schnetter
3282eaea8d Update OpenSSL (#1853) 2016-09-26 10:37:40 -07:00
Denis Davydov
1e10309ff7 some fixes to blas/lapack usage in packages (#1852)
* atlas: fix unit test

* openblas: remove symlinks; use lapack_libs.ld_flags in the test

* mkl: fix openmp variant of blas/lapack libs

* intel-parallel-studio: fix openmp variant of blas/lapack libs

* netlib-scalapack: fix blas/lapack for multilib case (e.g. mkl)

* arpack-ng: fix blas/lapack for multilib case (e.g. mkl)

* petsc: explicitly specify blas/lapack

* minor

* cantera: fix blas/lapack usage

* ipopt: fix blas/lapack usage

* netlib-lapack: fix external blas usage

* mfem: fix lapack/blas usage

* superlu-mt: fix blas usage

* flake8 fixes
2016-09-26 10:37:23 -07:00
Todd Gamblin
cb36aadaf6 Fix doc bugs, widen columns in the package list 2016-09-23 18:07:33 -07:00
Patrick Gartung
ec91152a36 a few package used in HEP including ROOT6 2016-09-23 18:07:22 -07:00
Adam J. Stewart
64194a823a Remove duplicate ICU package (#1837)
* Remove duplicate ICU package

* Ignore deleted files during flake8 tests

* Rename Boost ICU variant
2016-09-23 14:16:59 -07:00
Denis Davydov
6ef6428331 m4: fix compilation on Sierra with GCC (#1844)
* m4: fix compilation on Sierra with GCC

* m4: check macOS version
2016-09-23 13:38:29 -07:00
Bruno Turcksin
98d54182d3 Add Trilinos 12.8.1 (#1843) 2016-09-23 13:36:21 -07:00
Erik Schnetter
73ec2a27d0 Don't require git for Julia @0.5: (#1834) 2016-09-23 13:35:12 -07:00
Erik Schnetter
8147a09489 Update jemalloc to 4.2.1 (#1839) 2016-09-23 13:32:57 -07:00
Robert D. French
3d282b9239 Add libmesh, needed for some FEM applications (#1846) 2016-09-23 13:26:27 -07:00
Denis Davydov
df5e151049 hypre: fix a bug with blas/lapack names (#1841) 2016-09-23 10:06:18 -07:00
Erik Schnetter
c0ebbc97c9 Update OpenSSL (#1836)
This is a security update with priority "HIGH".
2016-09-23 08:21:15 -07:00
Denis Davydov
462a4a1353 boost: fix a bug which broke it on macOS with clang+gfortran (#1816)
* dealii: add missing python dependency

* boost: fix a bug which  broke it on macOS with clang+gfortran

Boost was using gcc compiler instead of clang++, which lead to
cryptic Undefined symbols linking errors for boost::python::objects::function_object()
when building other packages against boost+python.

* boost: add exceptions for intel

* boost: use spack_cxx
2016-09-22 13:47:22 -07:00
Adam J. Stewart
a638b62ab1 Updates to CGAL and ICU4C packages (#1828) 2016-09-22 11:50:50 -07:00
Elizabeth Fischer
64c3b11478 suitesparse: Added +fpic (for linking with shared libraries) (#1542) 2016-09-22 11:03:49 -07:00
Erik Schnetter
7ad6c35627 New package "charm" for the Charm++ parallel programming framework (#1766) 2016-09-22 00:48:00 -07:00
Massimiliano Culpo
d848559f70 Reworking of lapack_shared_libs and similar properties (#1682)
* Turned <provider>_libs into an iterable

Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions

* atlas : added pthread variant

* intel packages : added lapack_libs and blas_libs

* find_library_path : removed unused function

* PR review : fixed last issues

* LibraryList : added test on __add__ return type

* LibraryList : added __radd__ fixed unit tests

fix : failing unit tests due to missing `self`

* cp2k and dependecies : fixed blas-lapack related statements in package.py
2016-09-21 12:27:59 -07:00
Todd Gamblin
6b6f868f2a Flake8 fixes. 2016-09-21 04:35:15 -07:00
Todd Gamblin
786ab114b7 Merge branch 'qt-osx' of git://github.com/mathstuf/spack into mathstuf-qt-osx 2016-09-21 04:32:03 -07:00
George Hartzell
51d869493a Add package for bedtools2 (#1572)
Add package for bedtools2, with support for v2.25.0 and v2.26.0.
2016-09-21 04:23:03 -07:00
George Hartzell
db0baaafe3 Add package for bamtools (#1571)
bamtools provides a C++ API & command-line toolkit for working with BAM
data.
2016-09-21 04:22:55 -07:00
Mayeul d'Avezac
3d1c92e22c Update espresso recipe to track change in spack internals (#1734) 2016-09-21 04:18:35 -07:00
Adam J. Stewart
cf925ddc97 Add missing build dependencies to hdf package (#1812) 2016-09-21 04:16:57 -07:00
Kelly Thompson
3d3614e522 Update to allow netlib-scalapack to build against netlib-lapack. (#1539) 2016-09-21 04:10:30 -07:00
Glenn Johnson
c1284a9046 Stop python from linking with system ncurses (#1672)
Python will look to link with libncursesw in preference to libncurses. Since
ncurses in spack is built without suffixes there is no libncursesw and
python will link to the system libncursesw for _curses.so and
_curses_panel.so, as well as libpanelw for _curses_panel.so.

This PR introduces a patch that simple removes the check for ncursesw in
setup.py and therefore sets `curses_library` to `ncurses`.
2016-09-21 04:02:28 -07:00
Glenn Johnson
851b58248d Build pkg-config files for ncurses (#1673) 2016-09-21 04:02:07 -07:00