Commit graph

3111 commits

Author SHA1 Message Date
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