Commit graph

3356 commits

Author SHA1 Message Date
healther
191bf1e132 add package py-elephant (#3302)
* add package py-elephant

* add variants for docs and pandas
2017-03-03 08:39:06 -06:00
healther
ba21940409 add resource manpages to package git (#3299)
* add resource manpages to package git

* Update package.py

* added manpages per version

* added explaining comment

* fixed synatx error
2017-03-03 08:07:50 -06:00
healther
def42f156d add flex variant to cscope (#3252)
* add flex variant to cscope

* fixed dependency

* fixed typo
2017-03-03 08:06:25 -06:00
健美猫
9df2649d02 Add package mdtest. (#3303) 2017-03-03 08:05:16 -06:00
健美猫
f443490f34 Add package sctk. (#3325) 2017-03-03 08:04:01 -06:00
健美猫
e4a0d8a78e Add packag gradle. (#3326) 2017-03-03 08:02:32 -06:00
healther
bb997d2de5 add package py-spyder (#3312)
* add package py-spyder

* fixed dependencies

* py-flake8 -> py-pycodestyle

* fixed packagename

* Update package.py

* Update package.py
2017-03-03 08:01:20 -06:00
healther
818118c589 add package py-qtawesome (#3308)
* add package py-qtawesome

requires py-qtpy

* fixed url

* remove unnecessary comment
2017-03-03 08:00:21 -06:00
healther
2d395d7d75 add package py-qtpy (#3307)
* add package py-qtpy

* (re)added qt dependence

* changed url
2017-03-03 08:00:01 -06:00
healther
ac0fa0ca6e add package py-numpydoc (#3311)
* add package py-numpydoc

* removed unnecessary dependency

* added dependency
2017-03-03 07:59:28 -06:00
健美猫
7511c9cd1a Add a new version for bamtools 2.4.1. (#3328) 2017-03-03 07:58:41 -06:00
healther
15c311fbeb add package notmuch and dependencies (#3329)
* add package notmuch and dependencies

depends on
* gmime

* flake8 again
2017-03-03 07:57:47 -06:00
healther
4494233c93 add package gmime (#3327)
* add package gmime

* flake8 fix..
2017-03-03 07:57:15 -06:00
Adam J. Stewart
7fcd414050 Fixes to allow Boost to build with Python 3 (#3293)
* Fixes to allow Boost to build with Python 3

* Restrict patch to Python 3 only
2017-03-02 18:36:10 -06:00
Adam J. Stewart
bde0a67415 Add new package for PaGMO/PyGMO (#3210)
* Add new package for PaGMO/PyGMO

* Rename py-pygmo to pagmo

* Fix concretization bug

* Correct Python detection, use correct flags

* Install PyGMO to the pagmo prefix, not the Python prefix
2017-03-02 18:35:19 -06:00
Federico Padua
ecca9abc72 Ior package: fix build issues (#3276)
This commits address build issues reported in issue #3268.
In particular, makes cleaner the dependency on parallel-netcdf
when +ncmpi variant is requested and adds CFLAGS=-D H5_USE_16_API
to handle the fact that Ior uses old 1.6 style APIs when +hdf5 is
requested.
These changes make Ior build fine and create modules for HDF5 versions
1.8.x and 1.10.0.
Even though build is successfull the modules haven't been tested in a
run.
2017-03-02 18:33:36 -06:00
Adam J. Stewart
a7be0d4e5d Convert icu4c to AutotoolsPackage (#3316) 2017-03-02 18:32:04 -06:00
Patrick Gartung
4afb7a729c Make libgcc_s relocatable on Macos by adding @rpath to installname (#1671)
* Make libgcc_s relocatable

* spack specifies full path to lib64

* don't need trailing /

* setting rpath is different on macos

* add -headerpad_max_install_names linker options

* formatting fixes

* Add Adam's recommendation
2017-03-02 16:39:05 -06:00
healther
7baefa83b9 add package py-jedi (#3313) 2017-03-02 16:29:01 -06:00
healther
c67b8173e3 add package py-rope (#3314) 2017-03-02 16:28:42 -06:00
healther
a562d684b7 add various variants to vim (#3255)
* add various variants to vim

* default to --enable-fail-if-missing

* vim package: -{python,ruby,lua,perl} sets build option to `no`

* vim's interpreter build options are `--enable-XXXXinterp={yes,no,dynamic}`
* dynamic seems to work only on windows builds
* `=no` is the default => use it in spack if the variant is disabled
2017-03-02 14:26:52 -06:00
healther
d0835289e8 add package py-chardet (#3310) 2017-03-02 13:50:21 -06:00
healther
73836fccd2 add package py-boltons (#3279)
* add package py-boltons

* added description

* fixed non-utf8 characters
2017-03-02 12:51:00 -06:00
Michael Kuhn
6d0fbe7d96 Update adios to 1.11.1 (#3221)
Add a zfp variant and a patch that resets the interpreter for gpp.py.
2017-03-02 12:44:43 -06:00
healther
acb72c7037 add package py-brian (#3280)
* add package py-brian

* fixed typo

* removed unnecessary dependency

* fixed typo2
2017-03-02 12:44:09 -06:00
healther
c610c197ba Feature/py doxypy (#3283)
* add package py-doxypy

* fixed template and url
2017-03-02 12:44:01 -06:00
healther
9607c55eac add package py-doxypypy (#3284) 2017-03-02 12:43:43 -06:00
healther
98baff0167 add package py-fasteners (#3285)
* add package py-fasteners

* fixed dependencies
2017-03-02 12:43:34 -06:00
healther
a8c57d65c1 add package py-flexx (#3288) 2017-03-02 12:43:24 -06:00
healther
2f0c3d81aa add version 2.0.0 for py-matplotlib (#3289) 2017-03-02 12:43:13 -06:00
healther
0c014bf36c add package py-lazyarray (#3290)
* add package py-lazyarray

* added numpy dependency

* flake8 fixes
2017-03-02 12:43:02 -06:00
healther
7bcc12a3c1 add package py-lazy (#3291) 2017-03-02 12:42:33 -06:00
健美猫
0c1ccd5180 Add simul. (#3300) 2017-03-02 12:42:15 -06:00
Brian Van Essen
5bb22c3024 Added a recipe for the Caffe deep learning toolkit. (#3232)
* Added a recipe for the Caffe deep learning toolkit.

* Added code to extend python and fixed flake8 error.

* Fixed Flake8 error
2017-03-02 12:30:00 -06:00
Massimiliano Culpo
ed582cef68 New interface for passing build information among specs (#1875)
- Added a new interface for Specs to pass build information
  - Calls forwarded from Spec to Package are now explicit
  - Added descriptor within Spec to manage forwarding
  - Added state in Spec to maintain query information
  - Modified a few packages (the one involved in spack install pexsi) to showcase changes

- This uses an object wrapper to `spec` to implement the `libs` sub-calls.
  - wrapper is returned from `__getitem__` only if spec is concrete
  - allows packagers to access build information easily
2017-03-02 10:01:29 -08:00
Denis Davydov
88f97c07de fix build of 64bit PETSc and Trilinos in the same deal.II DAG (#3223)
Declare that (i) Trilinos can be only built against 32bit Hypre
(ii) SLEPc can not be built with Arpack when 64bit indices are used
(iii) reflect those constraints in deal.II's depends_on
While there, add extra release flags for best performance.
2017-03-02 08:16:58 -06:00
Jon Rood
8f915de610 Updating SAMRAI package with new urls and new versions (#3188)
* Updating SAMRAI package file with new urls and new versions. Also using Spack's MPI compilers.

* Using default optimization for Samrai and setting type to build for m4 dependency.

* Adding debug variant to Samrai.

* Converting Samrai to AutotoolsPackage.
2017-03-02 06:52:53 -06:00
healther
ffce6e1c4e add variant shared to yaml-cpp (#3254) 2017-03-01 16:36:46 -06:00
healther
20360f6727 add package py-current (#3282) 2017-03-01 15:34:04 -06:00
eklee15
8b52a87285 Add xl and spectrum mpi support for mumps (#3231)
* Add xl and spectrum mpi support for mumps

* Incorporated Denis's comments. fPIC and if-else
2017-03-01 15:33:41 -06:00
eklee15
4e601bb6d3 Exclude a few packages to build with xl (#3270) 2017-03-01 14:46:58 -06:00
healther
fa294a25db add version 2.2.0 to package bear (#3278) 2017-03-01 13:37:47 -06:00
healther
1ee470c37e Add package: git-review (#3088)
* Add git-review

* Fix flake8 errors

* use PythonPackage for git-review

* added dependencies for git-review

* fix flake8

* moved url's to pypi.io based urls

* fixed flake8... again

* mostly url fixes, not tested, will do tomorrow

* flake8 fix

* changed URL for py-pysocks

* Fixed URL for pysocks

* fixed url
2017-03-01 12:29:22 -06:00
healther
5fe96dec27 add packages vcsh (#3256)
* add packages vcsh

* added git dependency

* added comment regarding makefile
2017-03-01 07:51:36 -06:00
healther
6a1a2d5ec1 add package units (#3257)
* add package units

* removed unnecessary dependency

* readded python dependency
2017-03-01 07:51:17 -06:00
healther
2fb179f55b add package py-xmlrunner and fix unittest2 dependency (#3260)
* add package py-xmlrunner and fix unittest2 dependency

* add setuptools dependency
2017-03-01 07:51:05 -06:00
healther
d5884bdb78 add package py-symfit (#3264)
* add package py-symfit

* added missing dependency

* fixed ordering of versions
2017-03-01 07:50:54 -06:00
healther
4e433f8a03 add package py-statsmodels and py-patsy (#3265)
* add package py-statsmodels and py-patsy

* fixed typo

* fixed urls

* removed rc version
2017-03-01 07:50:28 -06:00
Adam J. Stewart
186d990791 pip requires setuptools during runtime (#3272) 2017-03-01 07:49:57 -06:00
Gregory Lee
ecc8f578af added urls for Intel Parallel Studio (#3220) 2017-02-28 14:57:10 -06:00
healther
37c36cf04e add package py-tqdm (#3262)
* add package py-tqdm

* added py-setuptools dependency
2017-02-28 13:36:32 -06:00
eklee15
bce2accb69 xl support for suite-sparse (#3226)
* xl support for suite-sparse

* make_args.extend([
    'CFLAGS={0}'.format(self.compiler.pic_flag),
    'FFLAGS={0}'.format(self.compiler.pic_flag)
])
2017-02-28 11:26:49 -08:00
eklee15
9be0c06b98 Patch hypre to support ppc64le (#3238)
- Patch applies through v2.11.1
2017-02-28 11:24:43 -08:00
healther
c32a9416ec add package py-tabulate (#3263)
* add package py-tabulate
* added py-setuptools dependency
2017-02-28 11:20:46 -08:00
Jean-Paul Pelteret
86276cd734 Update Adol-C to AutotoolsPackage; Change develop repository (#3246)
The new repository for the development version points to the most
up-to-date official source for Adol-C. The previous SVN repository was
only occasionally sync'd with this repository.
2017-02-28 13:18:40 -06:00
Thierry
315dfe0970 nfft distclean before configure patch (#3241) 2017-02-28 13:05:01 -06:00
healther
d1040b7111 add package py-sh (#3266)
* add package py-sh

* removed constraint on py-setuptools
2017-02-28 12:59:43 -06:00
Adam J. Stewart
c1382f9d02 Fix infinite recursion in swig build (#3249) 2017-02-28 12:58:08 -06:00
Bryce Allen
b2784f3664 add sz package (#3251) 2017-02-28 12:57:16 -06:00
healther
dee2259f3a add package py-saga-python and dependencies (#3267)
* add package py-saga-python and dependencies

* fixed url and dependencies
2017-02-28 12:56:36 -06:00
healther
70d0cdcd0a add package py-attrs (#3253) 2017-02-28 10:51:31 -06:00
healther
be0033ac91 add py-ranger package (#3258) 2017-02-28 10:21:06 -06:00
healther
25f10cca48 add package py-xarray (#3259) 2017-02-28 10:17:43 -06:00
healther
a43f2a49cb add version 0.29.0 to py-wheel (#3261) 2017-02-28 10:12:51 -06:00
Denis Davydov
b5b1e58843 numdiff: add 5.9.0 (#3243) 2017-02-26 08:17:17 -06:00
Eric Müller
ef55b01906 Add py-mock version 2.0.0 (#3234) 2017-02-24 08:05:49 -06:00
Eric Müller
06f366c53f Add bazel version 0.4.4 (#3233) 2017-02-24 08:05:21 -06:00
Javier
9650afd97e Fixing graphviz issue when calling spec (#3225) 2017-02-23 07:56:39 -06:00
Denis Davydov
60b7e13e1a fix py-setuptools (#3217) 2017-02-22 15:15:23 -08:00
Pramod Kumbhar
c9f705ffc2 Add SCOREC Core package for unstructured mesh simulations. (#3202)
* Add SCOREC Core package for unstructured mesh simulations.
2017-02-22 14:03:11 -08:00
Pramod Kumbhar
f86dcd8b4c Fix scotch build on bg-q (#3196)
* Fix build issue #3190 on bg-q :
 - disable parallel build as it produces weired linker errors
   in cross compiling environment
 - update ldflags for bg-q as per Makefile provided Makefile.inc.ppca2_ibm_bgq
* Added note about -lpthread vs -pthread
2017-02-22 11:04:14 -08:00
Kim Serradell
871a94ee41 Updating homepages and sources from two BSC packages (#3216)
* Corrected extrae package homepage and url
* Corrected paraver package homepage and url
* To fix 'undefined reference to libintl_dgettext' appearing in extrae package when using binutils+libiberty
* Adding support to previous paraver version and reverting binutils changes to open another PR
2017-02-22 11:03:25 -08:00
Todd Gamblin
539a454900 Convert Jaspert to AutotoolsPackage (#3212) 2017-02-22 09:29:34 -08:00
eklee15
52fab8fff3 Boost modification for IBM xl compiler (#3205)
Tested with:
spack install boost@1.62.0+iostreams%xl_r^zlib%gcc^bzip2%gcc
2017-02-21 16:40:09 -08:00
healther
177c54ecbf Add packages: mosh (#3098)
* Add packages: mosh

Perl is a run dependency. See https://github.com/mobile-shell/mosh/wiki/Build-Instructions
2017-02-21 09:50:06 -08:00
Javier
3195264546 Fix malformed py-appdirs patch (#3203) 2017-02-21 07:51:19 -06:00
healther
7827a0ff67 Default to OpenSSL 1.0 (#3100)
* Added version 1.1 to openssl
* restore note explaining preferred=True for 1.0.2k
2017-02-20 18:21:27 -08:00
Carlos Bederián
6681fc1a47 parallel-netcdf: use spack_cc for sequential code instead of system gcc (#3143) 2017-02-20 18:19:45 -08:00
Adam J. Stewart
d2a52d6dd6 Fix setuptools bootstrapping now that dependencies are no longer vendored (#3198)
* Fix setuptools bootstrapping now that dependencies are no longer vendored
* Reorder patch and comments
* Use exact same patch as https://github.com/ActiveState/appdirs/pull/84
* Use exact same patch as https://sourceforge.net/p/pyparsing/patches/10/
2017-02-20 18:09:03 -08:00
Javier
fbbcf456e9 Updating package: geant4 (#3197) 2017-02-20 17:33:32 -08:00
Adam J. Stewart
5b6d2754d9 Add MATLAB package (#2614)
* Add MATLAB package
* Remove auto-accept license feature
2017-02-20 16:10:06 -08:00
Barry Smith
ab2d6285c4 Add installer for petsc4py and slepc4py (#3187)
* Add installer for petsc4py and slepc4py
* @adamjstewart requested changes on this pull request; make these type=('build', 'run')
* @citibeth suggestion  Remove unneeded indirect dependencies
2017-02-20 15:43:33 -08:00
Adam J. Stewart
0203545eb8 Update CUDA docstring, no longer need to download manually (#3191)
* Update CUDA docstring, no longer need to download manually
2017-02-20 15:41:31 -08:00
Denis Davydov
031cde6e25 openblas: add develop version to make it work with Kabylake CPUs (#3192)
* openblas: add develop version to make it work with Kabylake CPUs
* dealii: fix develop branch
2017-02-20 15:40:46 -08:00
Pramod Kumbhar
8c2f5baa19 Fix zoltan installation issue on bg-q #3193 (#3194)
Zoltan expects mpi libraries with option --with-mpi-libs.
If this option is not provided then it uses '-lmpi' which
may not be correct. To avoid this, we have to explicitly
pass empty string.

This adds notes to the source explaining the change.
2017-02-20 15:39:51 -08:00
Adam J. Stewart
4de85ab4b7 Add new versions of several Python packages (#3195) 2017-02-20 15:38:30 -08:00
healther
8ebd49c962 add symlink variant (needed for AFS) (#3147)
* add symlink variant (needed for AFS)

* fix flake8

* added missing return statement
2017-02-20 17:14:44 -06:00
healther
c8cfe317c2 Added version 1.49.2 to gobject-introspection (#3090) 2017-02-20 07:53:33 -06:00
Carlos Bederián
4b9a37a357 silo: adding patch to support newer versions of hdf5 (#3162) 2017-02-19 17:45:19 -08:00
Barry Smith
7edea4361f Add installer for SAWs (#3186) 2017-02-19 17:44:16 -08:00
健美猫
a211795a0c Add Intel Parallel Studio XE 2016u4 and 2015u6. (#3182) 2017-02-18 19:12:05 -08:00
Adam J. Stewart
49d7f9db3d Add patches to allow PGI to build Tar properly (#3177) 2017-02-18 19:09:50 -08:00
Adam J. Stewart
4397ce8118 Replace GCC-specific warning flags with valid PGI flags (#3137) 2017-02-18 16:42:45 -06:00
Adam J. Stewart
341b78a96d Add patch to allow M4 make check to pass for PGI (#3108) 2017-02-18 16:42:13 -06:00
Denis Davydov
7f89bc1e1d octave: fix missing --without statements (#3178) 2017-02-18 16:13:00 -06:00
healther
1a5b3e184f Add package: log4cxx (#3097)
* Add log4cxx package

* add missing patch files to log4cxx

* remove unnecessary dependencies

* this fails at 'make check'

* this is the AutotoolsPackage version

* fixed install bug
2017-02-18 16:10:15 -06:00
healther
63a0ca729d Added 2017 Intel libraries (#3084) 2017-02-18 16:02:33 -06:00
healther
5712b524cc Add binutils variant +plugins (#3083)
* Add binutils variant +plugins

* added description to plugins variant
2017-02-18 16:02:01 -06:00
Jim Galarowicz
4da66d71b0 Fix for qt3 specific qt build (#3063)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
2017-02-18 15:56:40 -06:00
sknigh
69b01c617e Added shmem variant to Score-p build (#3024)
* Disable by default to fix builds on Centos 7
2017-02-18 15:54:57 -06:00
Pramod Kumbhar
18334edf1a Bug fix: PDT configure uses -prefix, not --prefix (#2976)
* This bug was introduced in #2845.
2017-02-18 15:45:47 -06:00
serbanmaerean
0d22b3eea9 netlib-lapack: Update package file for netlib-lapack to work with IBM (#3040)
Update package file for netlib-lapack to work with IBM XL compiler

The flag -qzerosize is redundant, as the IBM XL compiler should set this flag
by default.  However, at this time the default flag appears to be ignore.
Hence, I am setting it in the package file as well, as it has no negative
effect if set twice.
2017-02-17 15:51:10 -08:00
healther
5c37c17173 Add package: py-apache-libcloud (#3101)
* Add py-apache-libcloud package
2017-02-17 15:30:49 -08:00
Elizabeth Fischer
7180613218 graphviz: Tame Language Bindings (#1089)
graphviz: 
  * Download from Fedora projet, as main graphviz site not working.
  * Disable java because Spack does not yet support Java, and the system might not have it installed.
  * Added all language binding variants; disabled enough in the default configuration to avoid dependencies.
  * Removed alternate download location (turned into comments).
  * Turn off all language bindings by default.
  * Raise an exception on bindings that have not been verified to work.
  * Added text indicating what works and doesn't work when user runs `spack info`.
2017-02-17 12:07:54 -08:00
健美猫
1de2c53935 Patch openblas Makefile only when version >= 0.2.16. (#3170) 2017-02-17 12:03:43 -08:00
Elizabeth Fischer
682d5cf164 py-git2: New Package (#1971) 2017-02-17 11:55:22 -08:00
Elizabeth Fischer
8cb7f3d262 Keep Curl Bootstrap Working With http:// (#3113)
* Add comments documenting problems in recent versions of NetCDF.
* Add comments to packages required to install curl.
2017-02-17 11:52:08 -08:00
George Hartzell
ea1c582145 go: add support for v1.8 (#3165) 2017-02-17 11:48:45 -08:00
Denis Davydov
3c5024232c abinit: fix compilation on macOS, disable internal netcdf (#3157)
* abinit: fix compilation on macOS
* disable internal netcdf
2017-02-17 11:46:58 -08:00
Carlos Bederián
0f51daff24 hdf5: configure uses FCFLAGS instead of FFLAGS (#3155)
When building `hdf5+pic`, `-fPIC` wasn't being passed to the fortran compiler because `configure` takes `FCFLAGS` instead of `FFLAGS`.
2017-02-17 11:44:16 -08:00
Kelly (KT) Thompson
78962c8978 Provide Random123 header-only package. (#3141)
Add DESRES Random123 package:
- http://www.deshawresearch.com/resources_random123.html
2017-02-17 11:40:14 -08:00
Adam J. Stewart
c719802c83 Add new version of zlib, deprecate 1.2.10 (#3136) 2017-02-17 11:39:21 -08:00
Adam J. Stewart
4f60011121 Add patch to allow ncurses to be built with PGI (#3135) 2017-02-17 11:39:05 -08:00
Justin M Wozniak
163bdfde93 Swift/T: all packages (#3130)
* New package.py for ExM C-Utils: An initial package dependency for Swift/T
* New package.py for ADLB/X: A 2nd package dependency for Swift/T
* New package.py for Turbine
* New package.py for STC
2017-02-17 11:35:45 -08:00
Adam J. Stewart
c2fa7b1254 Add latest version of OpenSSL (#3171) 2017-02-17 07:11:54 -08:00
Ce Qin
f7a0a6fbc4 Add tag master for version develop of dealii. (#3048) 2017-02-16 18:37:20 -08:00
serbanmaerean
7bebfd29c2 spectrum-mpi: Add url info to spectrum-mpi package file (#3042)
Spack wants URL info even for external packages.  Without it, I get
the following error:

NoURLError: Package SpectrumMpi has no version with a URL.
  File "/home_local/serbanspack/spack/lib/spack/spack/repository.py", line 580, in get
    self._instances[key] = package_class(copy)
  File "/home_local/serbanspack/spack/lib/spack/spack/package.py", line 562, in __init__
    f = fs.for_package_version(self, self.version)
  File "/home_local/serbanspack/spack/lib/spack/spack/fetch_strategy.py", line 878, in for_package_version
    url = pkg.url_for_version(version)
  File "/home_local/serbanspack/spack/lib/spack/spack/package.py", line 682, in url_for_version
    raise NoURLError(cls)
2017-02-14 11:28:35 -08:00
Gregory Lee
4a20d170f4 fixes for pygtk and some dependencies (#3077) 2017-02-14 10:52:05 -08:00
Brian Van Essen
56952aaf1f LBANN (#3049)
* Creating a spack package for LLNL's LBANN (Livermore Big
Artificial Neural Network) training toolkit.

* Recipe for building LBANN toolkit.  Contains limited feature set and
is optimized for building with GNU gcc and OpenBLAS.

* Removed unnecessary dependencies based on reviewers feedback.

* Added support for the int64 data type in the Elemental library.  This
is required for supporting indices for large matrices.

* Added a variant to force a sequential weight matrix initialization.
This is slow, but provides an initialization that is independent of
model parallelism.

* Added a guard to prevent building Elemental with the Intel compiler
for versions that have known bugs.
2017-02-13 11:57:46 -08:00
Adam J. Stewart
4dd0b349f9 Add Jmol package (#3041) 2017-02-10 16:18:56 -08:00
Adam J. Stewart
6e2903534a Add patch to allow PGI to build Bison (#3044) 2017-02-10 16:17:55 -08:00
Massimiliano Culpo
e24fdb49ea fix: don't call setup_environment when not needed (#3060)
* Don't call setup_environment when not needed. fixes #3059

* setup_environment and modules: added unit tests
2017-02-10 16:09:43 -08:00
Denis Davydov
cbbf5791ba numdiff: update dependencies and fix (#3061)
compile with -O0 as per upstream known issue with optimization and GMP,
according to Ubuntu folks.
2017-02-10 16:05:07 -08:00
Justin M Wozniak
2305f6434e New package.py for ExM C-Utils and Turbine (#3076)
* New package.py for ExM C-Utils: An initial package dependency for Swift/T
* New package turbine

* Fix package.py as requested by @adamjstewart

* New package.py for ADLB/X: A 2nd package dependency for Swift/T

* Add latest version of GNU Parallel (#3106)

* Address formatting guidelines from @adamjstewart

* WIP on new Turbine package.py

* Formatting fixes

* Complete Turbine package.py
2017-02-10 16:03:40 -08:00
healther
c98249c129 Add version 2017.0.098 to ipp (#3093) 2017-02-10 16:00:52 -08:00
Erik Schnetter
4362caa51a es: Declare readline dependency (#3071) 2017-02-10 16:00:20 -08:00
Adam J. Stewart
57855cab5d Explicitly tell MPC where to find its deps (#3073) 2017-02-10 15:59:46 -08:00
healther
563b6ab73a Add version 2017.0.098 to intel-mkl (#3092) 2017-02-10 15:55:02 -08:00
healther
2aec15a6f9 Add version 2.49.7 to glib (#3089) 2017-02-10 15:52:39 -08:00
Adam J. Stewart
f1ca79ba6c Add latest version of PGI (#3107) 2017-02-09 13:58:17 -08:00
Denis Davydov
b07835904a valgrind: add develop; fix build on macOS with clang (#3066)
- add develop version to valgrind; fix build on macOS with clang
- switch valgrind to AutotoolsPackage
2017-02-09 13:57:50 -08:00
Adam J. Stewart
8d7bcbbbbb Add latest version of GNU Parallel (#3106) 2017-02-09 10:38:08 -08:00
Adam J. Stewart
2a3228e004 Add latest version of NCO (#3080) 2017-02-09 08:33:01 -08:00
Elizabeth Fischer
892955cc46 Add comments documenting problems in recent versions of NetCDF. (#3058) 2017-02-07 18:23:33 -08:00
Denis Davydov
4264051954 fix usage of self.build_directory in espressopp and astyle (#3053) 2017-02-07 18:22:52 -08:00
George Hartzell
b1f5b5f75b Add comment explaining why patch is still needed (#3054)
[The fix](https://github.com/golang/go/issues/17986) for the small buglet addressed by `misc-cgo-testcshared.patch` has been merged into the tree a while back.  I was surprised to see that it wasn't in 1.7.5 and did a bit of digging.  It is *has not* been merged into the 1.7 branch but it *has* been merged into 1.8 (and therefor the patch will no longer be necessary).

Figured I'd document my digging for the next person to come along.
2017-02-07 18:22:30 -08:00
Denis Davydov
7bf7016383 mpfr: add 3.1.5 (#3050) 2017-02-07 18:22:13 -08:00
Matthew Scott Krafczyk
f71df7bda3 move rpath from ALL to other sections of site.cfg (#3028)
* move rpath from ALL to other sections of site.cfg.  Solves #3007
* Add back mac condition to py-numpy
* Refactor py-numpy a bit.
2017-02-07 13:15:02 -08:00
Brian Van Essen
88e9bb586e Added a new version of the Google protobuf to the spack package. (#3046) 2017-02-07 10:05:02 -08:00
serbanmaerean
d78a35bb54 spectrum-mpi: Add new package file for external package (#3005)
* spectrum-mpi: Add new package file for external package

IBM Spectrum MPI is a commercial implementation of MPI based on
OpenMPI.  It is usually install in /opt/ibm/spectrum_mpi.

Users need to add the Spectrum MPI package in their packages.yaml
file as follows:

packages:
    spectrum-mpi:
        version: ['10.1.0.2']
        paths:
            spectrum-mpi@10.1.0.2: /opt/ibm/spectrum_mpi/
        buildable: False

    all:
        providers:
            mpi: [spectrum-mpi@10.1.0.2]

* spectrum-mpi: Added license files and removed the versions

No need for versions as the package is external.

* spectrum-mpi: Remove extraneous defines

Keep only the defines that other MPI implementation define in their
package file:
    self.spec.mpicc
    self.spec.mpicxx
    self.spec.mpif77
    self.spec.mpifc
2017-02-06 10:53:53 -08:00
Brian Van Essen
ffd582b2f6 Elemental (#2991)
* Add a package for the Elemental distributed linear algebra library.
2017-02-06 00:04:41 -08:00
Gregory Lee
158a1b9c36 fix OMPT support in Archer (#3035) 2017-02-05 23:34:38 -08:00
Nicolas Richart
7c09ad5305 Boostrapping the lammps package (#3032)
* First commit for the lammps package
* reviewed by adamjstewart and davydden
2017-02-05 19:34:53 -08:00
sknigh
dfff1f5cf4 Changed spark URL, Added version 2.0.2, 2.1.0 (#3027) 2017-02-05 15:56:34 -08:00
George Hartzell
d1c7f9c8bd Add a package for hunspell (#3029)
Add a package for the hunspell spelling checker.

This was created by `spack create`, trimmed down, and tested on CentOS 7.
2017-02-05 15:55:55 -08:00
健美猫
47f9096073 Use the official Maven site. (#3034) 2017-02-05 15:49:05 -08:00
Gregory Lee
ccb07dc25e added archer OpenMP race detector and its deps (#3030) 2017-02-04 15:42:22 -08:00
Carlos Bederián
5aefaa6ffe Add FFTW 2.1.5 (#2987) 2017-02-03 18:26:27 -08:00
Carlos Bederián
384698157a MKL: Provide scalapack (#2974) 2017-02-03 18:18:31 -08:00
Erik Schnetter
4c1c284e56 New package “es” (extensible shell) (#3009) 2017-02-03 18:09:25 -08:00
George Hartzell
5e2827433c Update go to v1.7.5 (#3023)
Update the go package to v1.7.5.

- This release no longer needs the time-test patch (it's been merged upstream).
- This release still seems to need the cgo-testcshared patch.
- Also add a comment about environment set up that I need to build it successfully on a very large server.

Tested on CentOS 7.
2017-02-03 18:09:01 -08:00
健美猫
864670c0ab Retrive CUDA installers from Internet. (#3012) 2017-02-03 18:07:54 -08:00
sknigh
24553c12bb Flex and Glib builds are dependent on m4 (#3022) 2017-02-03 17:19:23 -08:00
George Hartzell
b28d8345ec Force particular repo to increase predictability (#2746)
The repository used by the texlive installer defaults to a redirector
that sends one off to various URLs depending on <fill in the blank>.

This is problematic because all of the mirrors do not update in
synchrony and bad tarballs often hang around for a while.

This leads to problems that are particularly hard to diagnose because
you're likely to end up using a different repo the next time around.

This commit constraints the package to a particular, mainstream,
repository.  It's not fast, but it's consistent and usually correct.

It also updates the installer digest, because no day is complete
without updating it at least (sigh) once.
2017-02-03 15:44:26 -08:00
George Hartzell
acb9281dbf Different versions of cmake need diff vers of openssl (#2993)
* Different versions of cmake need diff vers of openssl.  See Issue https://github.com/LLNL/spack/issues/2990 for background.

Versions of cmake through 3.6.9 seem to need OpenSSL up to 1.0.99.  Later
versions can use the current release (thanks to @citibeth for
[digging up details](https://cmake.org/pipermail/cmake/2016-November/064631.html)).

@davydden suggested this change.

Without it I *am not* able to build `cmake@3.6.1` on CentOS 7 and I *am*
able to build `cmake@3.7.2`.

Tested with `cmake@3.7.2` and `cmake@3.6.1` on CentOS 7.
With this change I am able to build both `cmake@3.6.1` and `cmake@3.7.2`
on CentOS 7.
2017-02-03 14:35:16 -08:00
George Hartzell
6c1b19f394 Ocaml fails as an AutotoolsPackage (#2995)
Switch the ocaml install bit back to being a Package with its own little install method.

This fix allows me to build Unison on CentOS 7.
2017-02-03 14:22:50 -08:00
George Hartzell
10d36ee343 Fetch tarballs from ant archive dir. (#2997)
There was a new release of Ant (1.9.8) which led to the v1.9.7
tarball disappearing.

This changes the URL to Ant's archive dir, which seems to contain
*everything* including the two current releases (1.9.8 and 1.10.0)

It adds a digest for 1.9.8.

It adds and comments out a digest for 1.10.0 (which requires Java 8),
as I have not tested it.
2017-02-03 14:21:14 -08:00
Mayeul d'Avezac
d7c816386a Add new versions of catch (#3016) 2017-02-03 14:20:41 -08:00
George Hartzell
0929b23d53 Update git package to include 2.11.1 (#3020)
Add git v2.11.1 digest.

Built and lightly tested on CentOS 7.
2017-02-03 14:17:33 -08:00
Carlos Bederián
3d67bf46ba Update Tcl/Tk to 8.6.6 (#3002) 2017-02-03 14:15:15 -08:00
Howard Pritchard
0cdbd74b82 openmpi (#2988)
We just released 2.0.2 yesterday, so add in that release for
spack.  Don't need the PMI patch for this release.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-02-03 14:10:44 -08:00
Adam J. Stewart
dbb18df3f2 Add latest stable Perl release (#2969) 2017-02-03 14:10:08 -08:00
Tom Scogland
95c04f3ab1 llvm: add 3.9.1, only download necessary resources (#3015)
* llvm: add 3.9.1, only download necessary resources

* sacrifice some spaces on the altar of flake8 the vengeful and merciless
2017-02-03 14:04:36 -08:00
健美猫
a08ccbedee Patch OpenMPI 2.0.x to fix pmi_opcaddy_t_class issue. (#2962) 2017-01-31 14:52:38 -05:00
Henrik Bengtsson
4f297f4336 R: Using official cloud URL for CRAN (#2956)
cran.r-project.org runs on a single old-school server in Austria
and could potentially be overloaded if "everyone" used it.

cloud.r-project.org is a cloud-based repository that "automatic redirection to servers worldwide [...]", cf. https://cran.r-project.org/mirrors.html.

I assume, that cloud.* can be scale up as needed. Out of the official CRAN mirror, this should be the safest one to pick if a static CRAN mirror is needed.
2017-01-31 14:47:20 -05:00
Gregory Lee
7d279e06a0 Merge pull request #2964 from Zzzoom/fftw_add_sse2
FFTW: Add SSE2 support to x86_64 target
2017-01-31 09:48:47 -08:00
Adam J. Stewart
2ac0bcfcb0 Add latest version of Xorg util-macros (#2965) 2017-01-31 08:30:08 -08:00
Denis Davydov
2e81fe4fb3 openssl: add extra url to download old versions (#2935) 2017-01-31 10:51:26 -05:00
健美猫
d46a1eadcd Replace FTP retrieval URLs with HTTP/HTTPS serving packages with identical checksum. (#2958) 2017-01-31 09:56:35 -05:00
Adam J. Stewart
0c0a1fdedc Add several new R packages (#2952)
* Add several new R packages

* Add a few more R packages

* Update more versions

* Convert Package to RPackage

* Add a few more packages

* Add missing dependencies
2017-01-31 09:54:34 -05:00
Massimiliano Culpo
19cf7a2833 libmng: fix trying to run configure on an already configured directory fixes #2959 (#2961) 2017-01-31 09:49:29 -05:00
Carlos Bederián
617786707f FFTW: Add SSE2 support to x86_64 target 2017-01-30 18:17:36 -03:00
Adam J. Stewart
75763bb8e3 Make OpenSSL tests optional (#2939)
* Make OpenSSL tests optional

* Add version constraint to Perl dependency in OpenSSL
2017-01-27 11:38:21 -08:00
Denis Davydov
aa7c5d1115 mumps: fix compilation with MKL (#2936) 2017-01-27 11:32:25 -08:00
Adam J. Stewart
c7a1328326 Add missing dependencies to VizGlow package (#2581)
* Add missing dependencies to VizGlow package

* Use a version-specific URL for xterm
2017-01-26 02:30:18 -08:00
Massimiliano Culpo
81a5146b1d AutotoolsPackage: minor improvements (#2859)
* AutotoolsPackage: added configure_directory to permit build out of source. The configure script executable is now invoked with an absolute path. Modified a few packages accordingly.

* build_systems: functions returning directories are now properties

* build_systems: fixed issues with tcl and tk

* AutotoolsPackage: reworked recipe for autoreconf
2017-01-26 02:27:15 -08:00
Jean-Paul Pelteret
f59011f314 Adol-C: Enable trig/erf functions; advanced branching (#2747) 2017-01-26 01:33:20 -08:00
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
Jon Rood
6e8058ad41 Specify Python location in VisIt in a more uniform fashion. (#2803) 2017-01-16 03:21:52 -08:00
Todd Gamblin
de7be6694f Fix issue with Mac OS version detection in m4 package. (#2835) 2017-01-16 03:03:52 -08:00
Denis Davydov
8365dbd959 petsc: add 64bit variant (#2655)
* petsc: add 64bit variant

* hypre: add int64 variant

* superlu-dist: add int64 variant

* petsc: add int64 variant

* metis: rename idx64 to int64 to make it consistent with other packages

* mumps: rename idx64 to int64 to make it consistent with other packages

* dealii: rename 64bit to int64 to make it consistent with other packages
2017-01-16 02:23:07 -08:00
Axel Huebl
e2697e4a37 isl: add latest version (#2834)
added latest version of isl. Needed to get llvm/clang in the latest
trunk to build via spack, but there are more versions available.
what is the policy regarding those? Add what we need for now?
2017-01-16 01:17:35 -08:00
Jon Rood
b2f29b855b Updating BoxLib with the ability to build again. (#2813)
* Updating BoxLib with the ability to build again.

* Using Spack MPI compilers directly.

* Fixing typo.

* Using tarball from github archive for boxlib.
2017-01-15 17:07:44 -08:00
Adam J. Stewart
e3a631c90e Add Astra package (#2800) 2017-01-15 16:23:52 -08:00
Adam J. Stewart
f480e3449e Added customization for make targets in 'build' and 'install' phases for CMakePackage (#2742)
* Added customization for make targets in 'build' and 'install' phases for CMakePackage

* Use rst in build system docs so that Sphinx generates nice API docs

* Allow AutotoolsPackages to be built in a different directory

* Flake8

* Fix missing import

* Allow configure to be located in different directory

* Update espressopp to use build targets

* Flake8

* Sphinx fix, lists must be a new paragraph

* Back out change that allowed a configure script in a different directory than build_directory

* Add missing deps, build in parallel

* Missing space for rst list
2017-01-15 16:23:16 -08:00
Jean-Paul Pelteret
4b7b595e3c New package: CppAD (#2832) 2017-01-15 16:20:26 -08:00
Adam J. Stewart
f2d4c15395 Remove cmake build dep from CMakePackages (#2684) 2017-01-15 03:18:52 -08:00
Adam J. Stewart
7fce4c5083 Add list_url to cmake (#2714) 2017-01-15 03:16:41 -08:00
Axel Huebl
3f7b4ab7aa Clang & Boost: No PCH (#2827)
Although it hurts a little, officially pre-compiled headers in
boost are only supported for gcc & msvc and the latest clang
releases still fail to build boost with it.

Therefore, I disabled building those to get boost build with
clang 3.9.0 on an Ubuntu 14.04 (x86).

Links to documentation and boost bug reports are inline, so
people can later on check if they still apply. Seems just to
be a bug in `Boost.Build` that tries to set `-o` with multiple
output files.
2017-01-15 02:38:14 -08:00
Axel Huebl
5c4d2627ff Packages: Add CUDA8 (#2823)
Adds the latest CUDA release, 8.0.44.
2017-01-15 02:35:53 -08:00
Adam J. Stewart
367f46eee2 Add old version of PGI (#2784) 2017-01-15 02:35:27 -08:00
Adam J. Stewart
12edc4e369 Add latest version of PETSc (#2783) 2017-01-15 02:34:48 -08:00
Massimiliano Culpo
436f6a4ab6 get_std_cmake_args delegates to CMakePackage._std_args fixes #2665 (#2805) 2017-01-15 02:34:15 -08:00
danielsjensen1
957cb968c6 Features/octopus 6.0 (#2819)
* Added support for Octopus 6.0 and the optional libraries: metis, parmetis, netcdf, arpack-ng, and scalapack.

* Fix PEP 8 line too long error.

* Changed format syntax {} to {0} to support Python 2.6.
2017-01-15 02:30:47 -08:00
Gregory Lee
c6c6773c03 added psutil python package (#2812) 2017-01-15 02:30:12 -08:00
Stephen McDowell
1f4ca71e21 Adding the py-ipdb package for more stable debugging with iPython. (#2824)
* Adding the py-ipdb package for more stable debugging with iPython.

* Removing deprecated python support, adding missing dependencies.

* Adding version checks for (i)python
2017-01-15 02:29:29 -08:00
Matthew Scott Krafczyk
28ea72d5b2 Add the package py-sphinx-bootstrap-theme (#2825) 2017-01-15 02:27:17 -08:00
Andrey Prokopenko
1128922b44 boost: fixing boost-1.55.0 for gcc-5 (#2822)
boost-1.55.0 requires patching when compiling with gcc-5. See these
threads:

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197594
https://svn.boost.org/trac/boost/ticket/10125

Fixes #2821.
2017-01-13 08:43:50 -08:00
Jim Galarowicz
481bc91854 Update the boost versions used by openspeedshop. Boost-1.60 to current latest causes compile errors when building openspeedshop. (#2300)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
2017-01-10 12:28:05 -08:00
Massimiliano Culpo
a7a77b5b41 openjpeg: fixes url (#2790) 2017-01-10 09:14:16 -08:00
Adam J. Stewart
1ece25bdc2 Temporary workaround for R concretization bug (#2756) 2017-01-09 19:07:49 -08:00
sknigh
c7ca96b327 Added list_url to r-dt package (#1533) 2017-01-09 14:37:06 -08:00
Elizabeth Fischer
402dfe30f9 Get Rid of nobuild, nolink, and alldeps (#2765)
* Removing the nobuild, nolink, and alldeps dependency types in favor of being explicit.
* This will help with maintenance going forward, as adding more dependency types won't affect existing declared dependencies in weird ways.
* default deptype is still `('build', 'link')`
2017-01-07 19:59:02 -08:00
Adam J. Stewart
68baac0549 Various updates to the NCO package and dependencies (#2639)
* Remove +mpi variant from NCO

* Update NCO deps to AutotoolsPackage

* Update the other NetCDF packages to AutotoolsPackage

* ANTLR has a nolink deptype on java, don't worry about csharp

* Remove restrictions from NCO package, fix homepage

* Add version 4.6.3 of NCO

* Missed AutotoolsPackage for NetCDF-CXX4

* NetCDF tests fail when run in parallel

* Remove commented out dependency

* Add documentation dependency
2017-01-07 18:06:59 -08:00
Adam J. Stewart
a0195371e8 Unset PETSC_DIR during installation (#2768)
* Set PETSC_DIR during installation

* Move env var unsets to setup_environment

* Fix unset var name and number of args
2017-01-07 17:38:53 -08:00
James Wynne III
b7fdc03bd5 Added needed deps for bbcp (#2773) 2017-01-07 16:30:54 -08:00
Adam J. Stewart
daff3c0908 Preliminary RPackage class (#2761) 2017-01-07 16:28:52 -08:00
Todd Gamblin
f379697985 Fix issues linking hDF5 1.8.14 and below on Ubuntu. (#2772) 2017-01-07 09:03:50 -08:00
Cyrus Harrison
e39ba88e9c add conduit 0.2.1 release (#2766) 2017-01-06 12:33:51 -08:00
Bruno Turcksin
2f173bda9c Add boost 1.63.0 (#2743) 2017-01-06 11:44:41 -08:00
Gregory Lee
a016fd01ec Merge pull request #2740 from jrood-nrel/jonrood
Renaming mkl to intel-mkl
2017-01-06 11:01:16 -08:00
Gregory Lee
7b337de93e various python package version and dependency updates (#2751)
* various python package version and dependency updates

* various python package version and dependency updates
2017-01-06 08:50:06 -08:00
Christoph Junghans
8dc056130c espressopp: package for the ESPResSo++ software (#2602)
* espressopp: package for the ESPResSo++ software

This commit adds a package for the ESPResSo++
simulation software.

* Move Espressopp package to CMakePackage

This commit moves Espressopp package to CMakePackage.
Addresses some comments in the PR.

* Remove run_tests and changed type of dependencies

Addressed some comments from @adamjstewart.
Removed global run_tests setting and removed type from many
dependencies. Set type for py-mpi4py to 'nolink'.

* Updated to last version and fix mpi4py dependency

Added latest espressopp version and changed mpi4py (version) dependency for
different espressopp versions.

* Changed mpi4py version requirements for espressopp

Changed py-mpi4py version requirements for espressopp@1.9.4 according
to the package build requirements for that version.
2017-01-05 21:20:55 -08:00
Matthew Krafczyk
8c650303ff Add dependencies and finish the py-tornado package.
This adds the following packages:

 py-backports-shutil-get-terminal-size  py-nbformat
 py-backports-ssl-match-hostname        py-pathlib2
 py-entrypoints                         py-pickleshare
 py-futures                             py-pip
 py-ipykernel                           py-prompt-toolkit
 py-ipython-genutils                    py-ptyprocess
 py-ipywidgets                          py-simplegeneric
 py-jupyter-client                      py-singledispatch
 py-jupyter-console                     py-terminado
 py-jupyter-core                        py-traitlets
 py-jupyter-notebook                    py-wcwidth
 py-monotonic                           py-widgetsnbextension
 py-nbconvert
2017-01-05 16:10:30 -08:00
Jean-Paul Pelteret
6a5185a2a7 Added npm, node.js, and Jupyter dependencies
Adds the following packages:
  node-js  py-backports-abc  py-functools32  py-pycurl   py-vcversione
  npm      py-certifi        py-jsonschema   py-tornado  py-zmq

- Added python packages that are dependencies for the Jupyter suite
- Update new python packaages to use extension package install function.
- Added npm and node-js packages
2017-01-05 16:10:30 -08:00
Elizabeth Fischer
3dd4a01a5e Standardize package names: lower-case, not Mixed_CASE (#2475)
* Rename packages

* Upcasing depends_on() in packages.

* Downcased extends('r')

* Fixed erroneously changed URL that had slipped through.

* Fixed typo

* Fixed link from documentation into package source code.

* Fixed another doc problem.

* Changed underscores to dashes in package names.

* Added test to enforce lowercase, no-underscore naming convention.

* Fix r-xgboost

* Downcase more instances of 'R' in package auto-creation.

* Fix test.

* Converted unit test packages to use dashes not underscores

* Downcase `r` in the docs.

* Update module_file_support.rst

Fix r->R for class R.
2017-01-04 18:24:07 -08:00
Jon Rood
01406251c9 Intel-mkl provides mkl 2017-01-04 14:02:23 -07:00
Jon Rood
c8405b4b5f Renaming mkl to intel-mkl 2017-01-04 13:55:08 -07:00
George Hartzell
4e653254c5 Use zlib's "fossil" site for old tarballs (#2735)
* Use zlib's "fossil" site for old tarballs

Following citibeth's suggestion in #2732, use zlib's "fossil"
site (not to be confused with the sqlite team's VCS...) for retrieving
old tarballs.

Digests for 1.2.{8,10} match and both install for me on CentOS 7.

* Use zlib's "fossil" URL as the one true URL

Everything seems to be available at zlib's "fossil" URL, so just use
it as the one and only url.

(and fix a flake8 complaint about a comment)
2017-01-04 11:43:10 -08:00
Cyrus Harrison
eaa24b08fd add package for conduit (#2670)
* add package for conduit

* try to fix main conduit docstring

* use join_path instead of pjoin

* address a few requests in pr #2670

change name of 'github-master' to 'master'

change 'docs' variant to 'doc', set default to False

remove explicit +shared variant spec for silo and hdf5 deps
(in the conduit +shared case) cases since they default to True

add reference to static rpath issue
(https://github.com/LLNL/spack/issues/2658)

* address pr #2670 requests

add todos and more info on why variants for deps where selected
use python module install python to enable spack activate
use .format instead of %s
2017-01-04 10:20:08 -08:00
Jeffrey Salmond
e57fc3d950 opencoarrays: new version (#2734)
* add version 1.8.0

* remove depends_on('cmake') as it is now unecessary

* remove 'coarrays' as a virtual package
2017-01-04 08:40:55 -08:00
Jean-Paul Pelteret
4ff33d41a7 New package: ccache (#2721) 2017-01-04 08:39:58 -08:00
Elizabeth Fischer
03471469e7 libpng: Upgrade versions to fix vulnerability. (#2723) 2017-01-04 08:32:10 -08:00
George Hartzell
2e24a3a2be zlib@1.2.10 and R do not get along, work around it (#2727)
* zlib@1.2.10 and R do not get along, work around it

R's configure script has trouble with version numbers > 1.2.9.

This works around it by constraining R to 1.2.8.

I'm working with some R folk on getting it fixed going forward.

* Add adamjstewart's change.
2017-01-04 07:51:16 -08:00
Barry Smith
2322deda65 Update to latest zlib version, server no longer provides older version (#2720)
* Update to latest zlib version, server no longer provides older version

Funded-by: IDEAS
Project: IDEAS/xSDK

* Add alternative URL for previous release of zlib
2017-01-03 13:52:14 -08:00
Todd Gamblin
d32d5e45fb Fix issues when a package provides the same vdep twice. (#2710)
* Fix issues when a package provides the same vdep twice.

- provides() now adds to a set of provided vdeps instead of a single one.

* flake8
2017-01-02 18:40:57 -08:00
Adam J. Stewart
040f8a7176 Add latest version of gmp (#2695) 2016-12-30 22:53:54 -08:00
Todd Gamblin
972a277956 Fix Python issue with build failures; Add test case for build failures. (#2687) 2016-12-30 11:37:50 -08:00
Todd Gamblin
5fbab1f4b5 Concretize preserves deptypes (#2681)
Concretization preserves deptypes
2016-12-29 14:43:59 -08:00
Massimiliano Culpo
17b13b161b Directive inheritance: laziness for the win (#2623)
* inheritance of directives: using meta-classes to inject attributes coming from directives into packages + lazy directives

* _dep_types -> dependency_types
* using a meta-class to inject directives into packages
* directives are lazy

fixes #2466

* directives.py: allows for multiple inheritance. Added blank lines as suggested by @tgamblin

* directives.py: added a test for simple inheritance of directives

* Minor improvement requested by @tgamblin

CMakePackage: importing names from spack.directives
directives: wrap __new__ to respect pep8

* Refactoring requested by @tgamblin

directives: removed global variables in favor of class variables. Simplified the interface for directives (they return a callable on a package or a list of them).
2016-12-28 12:37:02 -08:00
Thierry
857dac88c8 init yorick package (#2635)
* init yorick package

* attempt at picking up SPACK's compiler choice, todo ~X variant.

* sphinx docstring error ?

* version# tarball, ~X default, docstring fix

* sphinx docstring fix(?)
2016-12-28 10:08:02 -08:00
George Hartzell
18c10f2bad Cleanup post luafilesystem version de-underscoring (#2683)
The upstream luafilesystem tarball/version had a wayward/inconsistent
underscore in their more recent version tag.  The played badly with
our package fetching machinery (due to recent changes?).

Upstream cleaned up their bit which required some touchups here.

- updated the url
- updated the version (digest)
- updated the format statement for the path to the rockspec.
2016-12-27 11:49:53 -08:00
Mayeul d'Avezac
81c1404b9c Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark (#2627)
* Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark

Tinyxml comes in two flavors, 1 and 2. Each comes in several
versions... So they cannot be easily united into a single package.

* Use CMakePackage and friends, add copyright

Also eleminate debug/release variants, since it no longuer fits in the
CMakePackage format.

* Remove unnecessary url

* spdlog now has tagged releases

* Remove unnecessary url argument

* Fewer quotes in cmake args, because magic

* Incorrect base class for tinyxml
2016-12-27 00:32:29 -08:00
Michael Kuhn
baaa613e44 Update wx to 3.1.0 (#2641) 2016-12-27 00:18:26 -08:00
Adam J. Stewart
29bac34c1d Ensure that every file in Spack has a license (#2659)
* Ensure that every package has a license

Also fixes URLs with http://http:// doubled.

This is a continuation of #2656.

* Add license to every file in Spack

* Make sure Todd is the author of all packages

* Fix flake8 tests

* Don't license external Sphinx docs

* Don't display licenses in tutorial example packages

Also fixes typos and converts command-line examples
from tcsh to bash, which is more common
2016-12-27 00:17:12 -08:00
Matthew Scott Krafczyk
3e92ffde7d Update py-cython with new pypi.io url and new version (#2650) 2016-12-25 19:48:11 -08:00
Bruno Turcksin
e16908b16b Add 64 bit variant to dealii. (#2654) 2016-12-25 18:55:14 -08:00
Adam J. Stewart
b240fdb2b9 Add latest version of Python 2 (#2668) 2016-12-25 18:53:16 -08:00
Michael Kuhn
33592d0142 Update gcc to 6.3.0 (#2669) 2016-12-25 18:52:58 -08:00
George Hartzell
041f96b349 Update the texlive distro digest. (#2679)
sigh.
2016-12-25 12:37:03 -08:00
Massimiliano Culpo
8fe5fb7988 go: fixed GOROOT_BOOTSTRAP without workarounds (#2671) 2016-12-25 12:33:57 -08:00
Michael Kuhn
e340f275b8 Update cairo to 1.14.8, gtkplus to 2.24.31 and pango to 1.40.3 (#2642) 2016-12-21 15:03:28 -08:00
Kim Serradell
70a4c4e105 Bug fontconfig (#2652)
* Added uuid: OSSP uuid is a ISO-C:1999 application programming interface

* Fixed install error in cmor package

* Added uuid: OSSP uuid is a ISO-C:1999 application programming interface

* Fixed install error in cmor package

* Modifiying fontconfig file to allow install in OpenSuse 13.2

* Adding pkg-config dependency to freetype and libxml2

* Removed first possible solution. With @adamjstewart selecting the one adding pkg-config to dependencies
2016-12-21 14:27:15 -08:00
Federico Padua
60dc751225 Fix homepage for the package libspatialindex (#2656)
Small fix for the homepage of the package libspatialindex.
2016-12-21 14:23:32 -08:00
Michael Kuhn
3ce3165ae6 Update gdal to 2.1.2 (#2643) 2016-12-19 17:06:57 -08:00
Adam J. Stewart
b3ba45afa9 Various improvements to H5hut (#2636) 2016-12-19 17:06:14 -08:00
Andrey Prokopenko
d306893d83 moab: changed trilinos dependency to zoltan, and added fortran variant (#2582)
Trilinos dependency is very heavy, the zoltan one is light. I'm not sure
if there is a situation where one needs the former.
2016-12-19 14:41:09 -08:00
Adam J. Stewart
d24186ea84 Update PnetCDF to AutotoolsPackage (#2637) 2016-12-19 14:26:47 -08:00
George Hartzell
d8efeabf77 Update digest for vim@8.0 tarball. (#2600)
* Update digest for vim@8.0 tarball.

The digest appears to have changed.

The new digest value matches the value in their
[MD5SUMS](ftp://ftp.vim.org/pub/vim/unix/MD5SUMS)
file.

* Change ftp.vim.org -> github.com/vim/vim/archive

Vim seems to do weekly releases, but the name of the tarball on
ftp.vim.org doesn't change so we have to regularly play 'update the
digest' (aka Internet whack-a-mole).

This commit changes the url so that we are now downloading particular
versions from the Vim project's github archive.

I didn't walk back through of time to get all of the versions that
used to be explicit.  I grabbed the final `7.4` and the current `8.0`
releases.  If people need more we can add them.
2016-12-19 14:26:16 -08:00
Adam J. Stewart
46436a0909 GSL: Add latest version, update to AutotoolsPackage (#2630) 2016-12-19 09:21:38 -08:00
Adam J. Stewart
08d323b1f8 NCO: Add latest version, update to AutotoolsPackage (#2629) 2016-12-19 08:49:37 -08:00