Commit graph

4706 commits

Author SHA1 Message Date
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
Michael Kuhn
8d1ec0df3d Fix read locks on read-only file systems (#1857) 2016-09-30 09:45:08 -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
Todd Gamblin
cb229f0842 Fixes #1720: spack reindex fails with invalid ref count. (#1867)
* Fixes #1720: spack reindex fails with invalid ref count.

- Database graph wasn't being built properly; dependencies were set up
  incorrectly in the nodes that ended up in the graph on reindex.

- Reworked _add to increment ref count properly and to always build
  bottom-up to make the logic simpler to understand.

* Add checks to ensure DB is a valid merkle tree.
2016-09-28 15:00:26 -04:00
Adam J. Stewart
66c2ac0bc9 Tell Mercurial where to find CA certs (#1873) 2016-09-28 14:58:51 -04:00
Elizabeth Fischer
9aa77178f3 Prohibit Python3 in Python version check. (#1872) 2016-09-28 12:36:25 -04:00
Adam J. Stewart
6df84a794b Add single letter arg flags for spack graph (#1871) 2016-09-28 12:09:31 -04:00
Todd Gamblin
78f4081bc9 Merge pull request #1862 from LLNL/features/graph-improvements
spack graph improvements
2016-09-28 00:10:14 -04:00
Todd Gamblin
05d52752ff Make graph_ascii support deptypes.
- fix deptype support
- by default, graph command omits build depedencies
- update docs to use deptype args
2016-09-27 23:49:41 -04:00
Todd Gamblin
f082d26ddd Fixes #1098: spack graph crashes for large graphs.
- Fixed logic for collapsing backward edges

- Last collapse now depends on whether prior step in left collapse
  sequence alrady did the collapse.
2016-09-27 23:28:51 -04:00
Todd Gamblin
0d3d74e5c2 Improvements to the Spack graph command.
- Distinguish between static (package) and dynamic (spec) graphs.

  - static graphs ignore conditions and multiple instances (hashes) and
    plot raw dependencies among packages.

  - dynamic graphs include information from particular specs (instances of
    packages) and can have multiple instances with hashes.

- Allow graphing all packages in the install DB.

  - useful for debugging.
2016-09-27 11:00:50 -04:00
Todd Gamblin
43ca805248 Factor out canonical_deptype function, cleanup spec.py 2016-09-27 11:00:50 -04:00
Todd Gamblin
cd960caf8d Clean up Exceptions in spec.py 2016-09-27 11:00:45 -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
Ben Boeckel
c7860322f5 package: fix variable name usage (#1829) 2016-09-22 11:47:25 -07:00
Adam J. Stewart
f1f301ad3b Fix spack checksum output indentation (#1826) 2016-09-22 11:33:29 -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
Eric
025b779a30 Fix sbang for perl (#1802)
* Perform shebang fix for all files

* Fix sbang for perl scripts

Otherwise perl would look at the #! line and call sbang again, resulting
in an infinite loop.
2016-09-22 00:43:47 -07:00
Elizabeth Fischer
98f9dd266f Remove SPACK_DIRTY env var (#1818)
* Removed SPACK_DIRTY env var support.

* Finished removing SPACK_DIRTY support.

* Minor changes.
2016-09-22 00:43:33 -07:00
Massimiliano Culpo
1db2552644 fix : stops infinite recursion for python 2.6 (#1823) 2016-09-22 00:31:28 -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