Commit graph

3123 commits

Author SHA1 Message Date
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