Commit graph

4726 commits

Author SHA1 Message Date
Pramod Kumbhar
9daafc32f1 Packages for Darshan I/O performance characterization tool from ANL (#1900) 2016-10-04 14:40:35 -07:00
Todd Gamblin
544fa3eddb Fix some documentation build warnings. (#1902)
- Fix issue with package_list.py regeneration confusing Sphinx.
- Add -E option to avoid caching and make Sphinx happy.
2016-10-04 12:37:57 -07:00
Adam J. Stewart
7806fded3e Update documentation URL after switch to readthedocs (#1901) 2016-10-04 11:47:25 -07:00
Todd Gamblin
e9d4780bbc Rework build environment and cc to use smaller RPATHs. (#1894)
- Fixed up dependency management so that:
  - build deps go in PATH and -I
  - link deps go in -L args
  - only *immediate* link deps are RPATH'd

The latter reduces the number of libraries that need to be added to
DT_NEEDED / LC_RPATH.  This removes redundant RPATHs to transitive
dependencies.
2016-10-04 09:40:28 -07:00
Sergey Kosukhin
1d981ebd50 A set of tools used in climate modeling and numerical weather prediction. (#1317)
* Update grib-api: switched to cmake building system.

* Update harfbuzz: added pkg-config dependency.

* Update pango: added pkg-config dependency.

* Add libemos package.

* Add Magics (from ECMWF) package.

* Revert "Variant for building cdo without mpi (#1638)":
CDO does not use MPI.

This reverts commit 079d063c6d.

* Update CDO package: full featured implementation.

* Update magics: added python as build dependency.

* Update cdo: added disabling configuration options.
2016-10-04 09:29:22 -07:00
Todd Gamblin
36c79e9df6 Fixes #1893: missing import 2016-10-04 01:49:07 -07:00
Ivo Jimenez
d36028cff4 Adds mpip package (#1886) 2016-10-04 01:30:52 -07:00
Ivo Jimenez
2c701d372e Adds lulesh package (#1887) 2016-10-04 01:28:23 -07:00
Pramod Kumbhar
e546d6246f Spack package for HPCToolkit (#1892)
* Spack package for HPCToolkit (performance analysis tool)

* Correction for PR comments, make flake8 happy

* update note / comments
2016-10-04 01:02:50 -07:00
Massimiliano Culpo
50fcade81b cp2k : added support for libint, fixed compilation issues on elpa (#1889) 2016-10-03 08:25:36 -07:00
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
Adam J. Stewart
2ce1b388c9 Run make clean to prevent warning messages (#1742)
* Run make clean to prevent warning messages

* Don't delete temporary files after completion
2016-10-02 18:51:09 -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
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