Commit graph

2929 commits

Author SHA1 Message Date
Denis Davydov
d324d13456 py-numpy: rework blas/lapack (#2365)
* py-numpy: fix blas/lapack section title

* py-numpy: rework BLAS/LAPACK

including a workaround for MKL due to
limited config system of numpy
2017-01-26 00:46:35 -08:00
scheibelp
e4d2d747ce Spec.satisfies accesses Spec.concrete as property (#2928)
* Spec.satisfies accesses Spec.concrete as property

Fixes #2760

When copying a spec, _concrete is always set to False for each
dependency. "Spec.satisfies" was accessing the member "_concrete"
directly instead of using the property "concrete". This means that
if you copy a spec, the dependencies will be considered equal, but
did not necessarily satisfy one another. Spec.satisfies is a
prerequisite for a package to be considered an extension; as a
consequence, an extension with run-time dependencies that were also
extensions did not activate those extensions. This updates
Spec.satisfies to avoid checking the cached member "_concrete"
directly.

* Added test to check for activation of dependency extension

* Added test to check for transitive satisfiability between a spec and its copy
2017-01-25 21:43:12 -07:00
Sam Gutiérrez
596190c83c Update libquo's homepage, url, and description. (#2925)
* Update libquo's homepage, url, and description.

Recently LANL moved to lanl (from losalamos).

* Fix formatting.

Conform to style guidelines.

* More style updates.

Doesn't appear to be necessary, but for good measure.
2017-01-25 21:41:26 -07:00
Adam J. Stewart
b18b6bad6f Remove intel-parallel-studio +all checks (#2905) 2017-01-25 21:41:09 -07:00
Denis Davydov
c24dc9072e oce: fix fetching (#2921)
* oce: fix fetching

apparently the fetcher is confused when there is a mixture of 3-digits
versions and 2-digits versions, i.e. 0.18 and 0.17.2

* flake8
2017-01-25 21:39:40 -07:00
Erik Schnetter
1ddd9c75c6 c-blosc: Add variant to disable AVX2 support (#2931)
Not all compilers support AVX2 instructions, and the package’s test for this is much too simplistic.
2017-01-25 21:39:10 -07:00
Timothy Brown
11454280e7 Updating udunits version. (#2922)
* Updating udunits.

Udunits 2.2.21 is no longer on the unidata ftp site.
The latest is 2.2.23, adding that and it's md5sum.

* Updating udunits2 download URL.

The Unidata ftp site does not keep previous versions of udunits.
However all the tagged versions are in their github.com repository.
Updating the URL to use github.

* Updating udunits2 with a autoreconf def.

The udunits packages on github do not contain a configure script.
One has to run autoreconf to generate it, so adding that to
package file.

Also updated to the latest version and all md5 checksums.
2017-01-25 21:38:44 -07:00
Jean-Paul Pelteret
a4f594a68d Update valgrind to 3.12.0 (#2929) 2017-01-25 17:14:55 -08:00
Massimiliano Culpo
fc866ae0fe build systems: simpler, clearer decorators: run_after, run_before (#2860)
* PackageMeta: `run_before` is an alias of `precondition`, `run_after` an alias of `sanity_check`

* PackageMeta: removed `precondition` and `sanity_check`

* PackageMeta: decorators are now free-standing

* package: modified/added docstrings. Fixed the semantics of `on_package_attributes`.

* package: added unit test assertion as side effects of install

* build_systems: factored build-time test running into base class

* r: updated decorators in package.py

* docs: updated decorator names
2017-01-25 08:57:01 -07:00
George Hartzell
90d47a3ead Add dependency on perl (#2909)
* Add dependency on perl

The build process uses perl and also needs `Test::More`.

Some distros, e.g. CentOS, break the core Perl distribution
into separate packages, so it's possible to "have perl" but
not have all the bits one needs to build OpenSSL.

We'll just install one of ours, which comes with all of its
factory parts included.

* Remove uninformative comment

>  # Also requires make

doesn't really add any value...
2017-01-24 14:07:13 -07:00
Adam J. Stewart
268347ccbf Add latest version of flex (#2914) 2017-01-24 14:06:56 -07:00
Adam J. Stewart
fae36b8489 Add latest version of NetCDF (#2915) 2017-01-24 14:06:42 -07:00
Adam J. Stewart
a04ac74c4c Add latest version of xz (#2916) 2017-01-24 14:01:10 -07:00
Jason Sarich
6e895c4ccc add static options for some libraries (#2876)
* add static options for some libraries

* make requested changes: add comments and use configure_args
2017-01-24 12:48:01 -07:00
Jean-Paul Pelteret
416e52c150 Update SymEngine package (#2919)
Take advantage of new configuration options in the @develop branch
2017-01-24 10:00:27 -07:00
Mayeul d'Avezac
db7a786d1c Simplifying gbenchmark (#2892)
Also, it seems the cmake_args API has changed in spack
2017-01-23 16:12:31 -08:00
Adam J. Stewart
f8c7dab826 Convert xerces-c to AutotoolsPackage (#2907) 2017-01-23 15:50:34 -08:00
Adam J. Stewart
e317f2639c Add latest version of PnetCDF (#2906) 2017-01-23 15:30:01 -08:00
Adam J. Stewart
bcef90fe10 Add --without-x when building r~X (#2864)
* Add --without-x when building r~X

* Add latest version of R

* Run patch for latest version as well
2017-01-23 15:29:48 -08:00
Denis Davydov
c76088906e oce & trilinos: force rpath on Sierra to avoid issues with load commands size (#2855)
* oce: force rpath on Sierra to avoid issues with load commands size

* trilinos: use rpath on Sierra to avoid load commands limit
2017-01-23 13:59:16 -08:00
Michael Kuhn
72f2f845e7 Update lz4 to 1.7.5 (#2878) 2017-01-23 10:26:21 -08:00
Jason Sarich
3686d0ceb3 have trilinos search for static libraries first when not using shared variant (#2896) 2017-01-23 10:24:21 -08:00
George Hartzell
162be154d2 Fix configure's zlib version check (#2901)
* Fix configure's zlib version check

R wants a version of zlib that is 1.2.5 or newer.

The version checking code just does a lexicographic comparison
of the first 5 characters of the string, so it seesthat the latest
zlib version, 1.2.10, as 1.2.1 and fails.

This patch changes the comparison to use zlibs' hex ZLIB_VERNUM
so that it does not suffer from this problem.

A version of this patch is wending it's way through the R comunity
community and will/should be included in a future release.

I tested the patch with the current R, 3.3.1.

* Tighten zlib dependency version (>= 1.2.5)

* Convert patch to level=1 format.
2017-01-23 10:20:54 -08:00
Michael Kuhn
7fd936735c Add zstd package (#2897) 2017-01-23 10:18:51 -08:00
Gregory Lee
6bc7be9217 updated config file name for Python 3.6 (#2881) 2017-01-23 09:34:50 -08:00
Erik Schnetter
19699a7607 libevent: Properly declare OpenSSL dependency version bounds (#2888)
* libevent: Properly declare OpenSSL dependency version bounds

* libevent: Handle ~openssl variant correctly
2017-01-20 13:57:15 -08:00
John Wohlbier
3e8106955b For qt3, append to LD_LIBRARY_PATH, do not nuke it (#2862)
* libmonitor does not exist at
http://libmonitor.googlecode.com/svn/trunk/

Change location to HPCToolkit version at github. Specify the hash corresponding
to the 20130218 version.

* When xcb is version 1.11, patch the configure file so it doesn't trip on
pthread-stubs and xau.

* Add os.getcwd()/lib to LD_LIBRARY_PATH, instead of nuking
existing LD_LIBRARY_PATH.
2017-01-20 10:34:40 -08:00
Erik Schnetter
adac3ebbf9 cfitsio: Allow building as shared libraries (#2887)
* cfitsio: Allow building as shared libraries

- Allow building as shared libraries
- Also add optional bzip2 variant
- Also update to newest version

This requires the recent correction to “fix_darwin_install_name”.

* cfitsio: Simplify code, default to +shared
2017-01-20 10:28:07 -08:00
Erik Schnetter
4e390e6689 m4: Update version (#2872) 2017-01-20 10:23:53 -08:00
Erik Schnetter
56cdb1d1ab swig: Update version (#2871) 2017-01-20 10:23:23 -08:00
Jason Sarich
bc37a1012c let pflotran depend on hdf 1.8.12 and above (#2875) 2017-01-20 10:18:58 -08:00
Michael Kuhn
042307d5f1 Update c-blosc to 1.11.1 (#2877) 2017-01-20 10:17:46 -08:00
Erik Schnetter
a0c4fe247f OpenSSL: Update to version 1.1.0c (#2885) 2017-01-20 10:12:09 -08:00
Denis Davydov
1223e43827 p4est: add 2.0 (#2890) 2017-01-20 10:11:11 -08:00
Denis Davydov
c350bd1216 dealii: fix config without mpi (#2856)
* dealii: fix config without mpi

* dealii: add check of variants
2017-01-19 11:24:09 -08:00
Quinn
f511f7b558 Adding some fixes to packages that use configure_args function without setting spec set or directly referencing it (#2868)
* Adding 'self.' to the spec call for configure_args

* Updating this to set spec to self.spec

* More updates to the configure_args spec calls

* Another spec issue

* Another spec issue.

* And another spec issue

* Switching cmor back to self.spec.
2017-01-19 06:26:39 -08:00
Erik Schnetter
9b7001fda1 OpenMPI: Update auto-detection of Verbs library location (#2124) 2017-01-18 14:54:39 -08:00
Adam J. Stewart
02f92fc7f8 Massive conversion from Package to AutotoolsPackage (#2845)
* Massive conversion from Package to AutotoolsPackage

* Forgot to convert p4est to AutotoolsPackage

* Fix typo

* Fix broken link in docs
2017-01-18 10:34:09 -08:00
Denis Davydov
5812081b80 gmsh: add 2.16 (#2857) 2017-01-18 09:34:05 -08:00
Denis Davydov
ddfbb14ad9 octave: add 4.2.0; fix Blas/Lapack; use AutotoolsPackage (#2858)
* octave: add 4.2.0; fix Blas/Lapack; use AutotoolsPackage

* fix a bug
2017-01-18 09:33:45 -08:00
Adam J. Stewart
026e2d0fe6 Convert 3 more new packages to PythonPackage (#2841) 2017-01-18 08:51:38 -08:00
Erik Schnetter
6242aaef6c papi: Update to 5.5.1 (#2849) 2017-01-18 08:18:38 -08:00
Erik Schnetter
70042f9e7d hwloc: Update to 1.11.5 (#2851) 2017-01-18 08:18:08 -08:00
Erik Schnetter
b452a7619c curl: update to 7.52.1 (#2852) 2017-01-18 08:17:50 -08:00
Erik Schnetter
a23fcd2a93 cmake: Update to 3.7.2 (#2853) 2017-01-18 08:17:31 -08:00
Erik Schnetter
3bd0101fb9 jemalloc: Update to 4.4.0 (#2850) 2017-01-18 08:16:59 -08:00
Denis Davydov
a040c8c743 oce: add 0.18 and fix patching (#2844)
* oce: add 0.18 and fix patching

* oce: simplify the patch
2017-01-17 14:40:07 -08:00
Denis Davydov
190a5b575c p4est: switch to AutotoolsPackage (#2839) 2017-01-17 11:05:34 -08:00
Adam J. Stewart
c0aaa8fcea Add PythonPackage base class
- Add a PythonPackage class with build system support.
  - Support build phases in PythonPackage
  - Add a custom sanity check for PythonPackages
  - Get rid of nolink dependencies in python packages

- Update spack create to use new PythonPackage class

- Port most of Python packages to new PythonPackage class

- Conducted a massive install and activate of Python packages.
  - Fixed bugs introduced by install and activate.

- Update API docs on PythonPackage
2017-01-16 20:00:31 -08:00
Mario Melara
beafcfd3ef Set MPI environment variables to the compiler wrappers on Cray (#2762)
* Set MPI[lang] env var to compiler wrappers on cray

Sets MPICC, MPICXX, MPIFC etc to point to the compiler wrappers on Cray systems.
Some packages look for MPIs via environment variables - e.g adios

* Use spec to check for Cray

* os is no longer used.
2017-01-16 16:15:37 -08:00