Commit graph

9309 commits

Author SHA1 Message Date
Adam J. Stewart
cea5d04a1e
Fix GDAL Python bindings and add import tests (#8482) 2018-06-15 10:14:50 -05:00
Pramod Kumbhar
a3a9b2ab2b Add newer likwid versions 4.3.1 and 4.3.2 (#8488) 2018-06-15 10:14:00 -05:00
Matthias Maiterth
a85981b250 Package/geopm: Update to version 0.5.0 (#8487) 2018-06-15 08:17:17 -05:00
Veselin Dobrev
a3c989ef3a [mfem] Add BLAS+LAPACK to the required dependencies of SuperLU_DIST. (#8485) 2018-06-15 11:34:04 +02:00
Todd Gamblin
5f852634cd openssl: add new version 1.0.2o (#8486) 2018-06-15 09:54:52 +02:00
Dan FitzGerald
d182d85dd1 Update the clang compiler definition to use IBM XL Fortran compiler (#8389)
on CORAL systems (linux-rhel7-ppc64le).
2018-06-14 20:51:45 -07:00
Dan FitzGerald
54aab585c4 Patch trilinos for xlf when using clang (#8391)
* Add patching for xlf when %clang.  Changes are effective only when Fortran compiler is 'XL'.
* Use the right version for trilinos when patching for seacas.
2018-06-14 20:48:43 -07:00
Dan FitzGerald
64d20a3955 Use no mangling for all spack compiler definitions that use the XL (#8392)
Fortran compiler.
Clang can build with IBM XL Fortran compiler as well, so the name
mangling shoud be avoided for that case as well.
2018-06-14 20:46:09 -07:00
Dan FitzGerald
a67b2e2942 Use the name of the Fortran compiler to determine what name mangling (#8393)
setting to use, instead of the spack compiler.

%clang can use multiple Fortran compilers with different options, so
we need to know what compiler is used in order to provide the correct
options.
2018-06-14 20:45:21 -07:00
健美猞猁
98d8bdebbe A new package: megahit. (#8471) 2018-06-14 13:45:12 -05:00
Matthias Wolf
75c0007cf8 neovim: add info for v0.3.0 (#8472) 2018-06-14 13:44:40 -05:00
Denis Davydov
53517c60b6 oce: add 0.18.3 (#8477) 2018-06-14 13:44:14 -05:00
Praveen C
34c08ed362 netgen should depend on zlib (#8473) 2018-06-14 13:43:43 -05:00
Denis Davydov
b5fcd62891 openblas: add 0.3.0 (#8478) 2018-06-14 13:43:05 -05:00
Denis Davydov
484e54d78e petsc: add 3.9.1 and 3.9.2 (#8479) 2018-06-14 13:42:12 -05:00
Denis Davydov
df657275e4 slepc: add 3.9.1 (#8480) 2018-06-14 13:41:52 -05:00
Denis Davydov
a878e76f93 superlu-dist: add 5.3.0 and 5.4.0 (#8481) 2018-06-14 13:41:35 -05:00
Serban Maerean
ee4050c58f boost package: patch dirent for pgi and boost 1.67 (#8313) 2018-06-13 15:53:14 -07:00
Satish Balay
eac8cf83bd xsdk: fix 'ChecksumError: md5 checksum failed' (#8440)
[error came up with the  prior url pointing to a 'master' branch. so fixing with a switch to a fixed tarball]
2018-06-13 13:46:38 -07:00
Satish Balay
2829ebd485 xsdk: update xsdk@develop dependency on mfem@develop (#8462) 2018-06-13 13:45:34 -07:00
Veselin Dobrev
a0c2a25a72 [mfem] new version: 3.4 (#8453)
* Add new version (3.4.0) with new variant (pumi).
* Fix an issue: skip the tests in examples/pumi as they require
files that are not included in the mfem distribution/repository.
* Use patches to fix the testing issues with PUMI and PETSc v3.9.
* Use the new bit.ly short link for v3.4.
2018-06-13 13:42:21 -07:00
Jim Galarowicz
674feb45f1 Add the ability to build the dyninst master branch under the develop version name. (#8455)
* Add the ability to build the dyninst master branch under the develop version name.  Fix elfutils and libdwarf to work with the various dyninst versions and vice-versa.

* Add reviewer suggested change to dyninst package file.  Remove colon in spec.satisfies clause.

* Add reviewer suggested change to dyninst package file. Remove duplicate lines.

* Add reviewer suggested change to dyninst package file. Encompass all versions under 10.0 with respect to using libdwarf in the build.
2018-06-13 13:35:32 -07:00
Timo Heister
758b813c36 new package: ASPECT (#8459)
* add ASPECT package

* add maintainer

* simplify
2018-06-13 14:42:29 -05:00
Axel Huebl
664f03e329 ADIOS: Revert Patch (#8463)
That patch is only a partial solution and does not solve the
issue. Revert is, unnecessary.
2018-06-13 14:42:13 -05:00
Axel Huebl
6d4909d69b Add: MPILander (#8464)
MPILander - There can only be one (MPI process)!

The final MPI implementation.
2018-06-13 14:40:51 -05:00
Michael Kuhn
04dce19155 gplates: new package (#8336)
This also adds an older 1.x version to gdal that is required by gplates.
2018-06-13 08:57:52 -05:00
Simone Bnà
470d4ddd96 openfoam-com: added submodule flag to git fetch (#8446) 2018-06-13 08:56:52 -05:00
Miles Perry
fa00a04e91 blasr-libcpp: new package (#8366)
* blasr-libcpp: new package

* blasr-libcpp: added version #, and moved make into build phase.

* blasr-libcpp: added prefix.include to PBBAM_INC, added version URL

* blasr-libcpp: indented comments, made list of configure_args, and added prefix.include

* blasr-libcpp: added setup_dependent_environment from blasr

* blasr-libcpp: fixed syntax for configure_args

* blasr-libcpp: fixed configure_args syntax

* blasr-libcpp: fixed syntax

* blasr-libcpp: syntaxtest

* blasr-libcpp: fixed def build error

* blasr-libcpp: edited dependent environment to move after install phase

* blasr-libcpp: rearranged build and install

* blasr-libcpp: added configure_args

* blasr-libcpp: fixed syntax error

* blasr-libcpp: removed .spec from INC and LIB alignment, pbdata, hdf

* blasr-libcpp: seperated configure args

* blasr-libcpp: edited configure and setup_dependent steps

* blasr-libcpp: added CPATH arg

* blasr-libcpp: C_INCLUDE_PATH

* blasr-libcpp: fixed install issues resulting from PacBio change
2018-06-13 08:55:31 -05:00
Satish Balay
c12855dce5 trilinos: use 'branch' option to specify branches such as develop/master [they are not tags] (#8448)
Fixes the following problem:

==> Installing trilinos
==> Warning: Suspicious requests to set or unset 'LD_LIBRARY_PATH' found
==> Warning: 	    	env.unset('LD_LIBRARY_PATH') at /home/balay/spack.new/lib/spack/spack/build_environment.py:269
==> Warning: 	--->	env.set('%s' % key, value) at /home/balay/spack.new/lib/spack/spack/build_environment.py:292
==> Trying to clone git repository: https://github.com/trilinos/Trilinos.git at tag develop
Fetching tags only, you probably meant:
  git fetch --tags
error: pathspec 'develop' did not match any file(s) known to git.
==> Fetching from [git] https://github.com/trilinos/Trilinos.git failed.
==> Error: FetchError: All fetchers failed for trilinos-develop-tgkpnctp6nn4imoizxlw4ymqyztcie4n
2018-06-13 08:54:53 -05:00
Timo Heister
b27da52e4b new package: dealii-parameter-gui (#8456) 2018-06-13 08:44:10 -05:00
Satish Balay
1d14ec7436 petsc: 'master' is a branch - not a tag - so fix it accordingly. (#8457) 2018-06-13 08:43:09 -05:00
Veselin Dobrev
683addc26d [GLVis] Add new version: 3.4 (#8454)
* [glvis] Add new version, 3.4; update all checksums to be SHA-256.

* [GLVis] Use the new bit.ly short link for v3.4.
2018-06-13 08:42:45 -05:00
Elizabeth Fischer
3cbae250f0 new package: pdftk (#8166) 2018-06-12 11:25:20 -07:00
Adam J. Stewart
0f1a1ae94e Add trailing slash when spidering URLs for versions (#8429)
By default, if a package does not specify a list_url and does not download from
a common repository, Spack runs dirname on the package URL. Given a URL
like https://root.cern.ch/download/root_v6.09.02.source.tar.gz, this returns
https://root.cern.ch/download. However, https://root.cern.ch/download
gives a 404, while https://root.cern.ch/download/ works just fine.

Note that some servers *don't* work with a trailing slash, so this tries with and
without the slash. This will double the number of URLs searched but the
slowdown should only affect the "spack versions" command.
2018-06-12 10:33:47 -07:00
Axel Huebl
583af6ef4f Package: ISAAC 1.4.0 (#8447) 2018-06-12 11:11:32 -05:00
Satish Balay
8e7d98c5fa superlu_dist: fix 'spack install superlu-dist@develop' (#8442)
Latest superlu_dist sources now use INCLUDEDIR.
This change should not affect older superlu_dist version builds
2018-06-12 08:21:10 -05:00
Massimiliano Culpo
004e9b8948 Fixed compilation of quantum-espresso (#8439)
The patch to select ELPA API needs to be applied to
version 6.2.0 too.

The link line of hdf5 is computed incorrectly from
the configuration part of the build-system. To fix
this the relevant file (make.inc) is patched.
2018-06-11 11:42:13 -05:00
Denis Davydov
d943754e92 boost: fix cxxstd=default (#8438) 2018-06-11 10:31:27 -05:00
Javier Cervantes
4ec3cb1ddb Add new package: unuran (#8397)
* Add new package: unuran

* Remove list_url and prng variant due to compilation problems

* Make shared library option more explicit
2018-06-11 08:41:32 -05:00
Denis Davydov
69ec8deec8 arpack-ng: add 3.6.0 (#8433) 2018-06-10 15:16:42 -05:00
健美猞猁
35a83540f0 A new package: axel. (#8434)
* A new package: axel.

* Remove duplicate pkgconf.
2018-06-10 15:16:16 -05:00
健美猞猁
80c1984e68 Bump miniconda to 4.5.4. (#8435) 2018-06-10 15:15:43 -05:00
toffer93
8a97aa4c51 py-projectq: Added new package and fixed its dependency py-pybind11 (#8378)
* py-pybind11: Additionally install python extensions e.g. run python setup

* py-projectq: Added new package for quantum computing

* py-projectq: corrected typos

* edited flake8 incompatibilities

* additional flake8 faults

* changes according to suggestions

* flake8 errors fixed

* typo and missing environment variable set

* py-pybind11:added setup_environemt

* py-projectq:changed version according to request

* flake8 correction

* py-pybind11:changed to setup_py and removed noop

* py-projectq:removed dependency and changed type of py-pytest dependency

* py-pybind11: flake8 error corrected

* py-projectq: Small error correction
2018-06-09 16:22:25 -05:00
Kelly (KT) Thompson
689e0cb24b Git's gitk needs TK's wish to be found in PATH (#8360)
* Git's gitk needs TK's wish to be found in PATH

* Add a _runtime_ dependency on `tk`
* Add an environment rule to add the path to TK's `wish` program to $PATH for
  the generated `git` modulefile.

* Make TclTk run environment an optional variant for git.

* Cleanup based on PR recommendations.
2018-06-09 16:16:35 -05:00
Chris Green
15c98fa57c compiler flags: add cxx98 standard support (#7601)
The following improvements are made to cxx standard support
(e.g. compiler.cxxNN_flag functions) in compilers:

* Add cxx98_flag property
* Add support for throwing an exception when a flag is not supported (previously
  if a flag was not supported the application was terminated with tty.die)
* The name of the flag associated with e.g. c++14 standard support changes for
  different compiler versions (e.g. c++1y vs c++14). This makes a few corrections
  on what flag to return for which version.
* Added tests to confirm that versions report expected flags for various c++
  standards (or raise an exception for versions that don't provide a given cxx
  standard)

Note that if a given cxx standard is the default, the associated flag property will
return ""; cxx98 is assumed to be the default standard so this is the behavior for
the associated property in the base compiler class.

Package changes:

* Improvements to the boost spec to take advantage of the improved standard
  flag facility.
* Update the clingo spec to catch the new exception rather than look for an
  empty flag to indicate non-support (which is not part of the compiler flag API)
2018-06-08 13:49:31 -07:00
Yifan Zhu
ceb2790f30 r-mice: new package (#8423)
* r-mice: new package

* flake8 fixed
2018-06-08 14:48:54 -05:00
Elizabeth Fischer
4a53942ee1 tcl package: Install sources (#8153)
The tcl package references the original sources upon install, and the tk build
requires the tcl sources. This updates the tcl package to install its sources following
the example of #4102, and also updates the tclConfig.sh file to properly reference
the installed sources (rather than the staging directory created by Spack).
2018-06-08 11:10:40 -07:00
Oliver Pola
cd860d7554 new version scotch@6.0.5a (#8254)
* new version scotch@6.0.5a

* patch metis headers on scotch@6.0.4 according to https://gforge.inria.fr/tracker/?func=detail&atid=1082&aid=19521&group_id=248
2018-06-08 08:39:03 -05:00
Ricardo Silva
9b2953939b GDL and missing dependencies (#8283)
* GDL and missing dependencies

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>

* GDL and GraphicsMagick improvements

* GDL: sort variants and dependencies, add descriptions
* GDL: add wx variant
* GDL: make variants explicit (in cmake args)
* GraphicsMagick: sort dependencies
* GraphicsMagick: cleanup boilerplate comments

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>

* Improvements/Fixes for gdl, plplot and graphicsmagick

* gdl:
  * variants:
    * openmp
    * be explicit about enabling/disabling x11
  * dependencies:
    * logic for plplot with/without wx
    * some previously missing (where being picked up from the system)

* graphicsmagick: previously missing dependencies (where being picked up from the system)

* plplot: more versions + variants + dependencies

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>

* GDL: hdf4/5 variants

* also sorted explicit enabling/disabling of cmake flags for readability

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>

* plplot: fix variant descriptions

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>

* Add tcl variant, use find_libraries for portability

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>

* plplot: flake8

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
2018-06-08 08:35:28 -05:00
Michael Kuhn
7488ed4ff5 go: Update to 1.10.3 (#8426) 2018-06-08 07:35:43 -05:00