Commit graph

6433 commits

Author SHA1 Message Date
Mark Olesen
2126c03a28 update for new version: qt-5.9.0 (#4590) 2017-06-23 11:41:44 -05:00
Massimiliano Culpo
087b3885f9 cp2k: added missing macros to the makefile (#88) (#4589) 2017-06-23 11:14:01 -05:00
Jimmy Tang
7fb9c3903f Minor fixes to CNTK package (#4429)
* Remove unneeded patch lines which fail for the most recent CNTK version on the head of the git repo

* Really check for NVML/GDK

* Fix some violations
2017-06-23 09:18:50 -05:00
Milton Woods
a4de317737 Gtkplus icons (#4511)
* gtkplus: set XDG_DATA_DIRS

* shared-mime-info: database of common MIME types

* gtkplus: needs shared-mime-info for correct handling of stock icons

* shared-mime-info: builds with newer intltool than provided by some platforms

* atk: set XDG_DATA_DIRS at run-time

* gdk-pixbuf: set XDG_DATA_DIRS at run-time

* gtkplus: set XDG_DATA_DIRS at run-time

* pango: set XDG_DATA_DIRS at run-time

* shared-mime-info: set XDG_DATA_DIRS at run-time
2017-06-23 09:01:09 -05:00
David Böhme
e27ccac4a5 caliper: Update caliper package (#4532)
* caliper: Update caliper package

* caliper: Explicitly enable/disable cmake options for all variants

* caliper: Fix flake8 warnings

* caliper: Modify defaults for Mac

* caliper: Fix some more flake8 warnings
2017-06-23 08:59:59 -05:00
iulian787
75b8d728bd Moab 5.0 and meshkit 1.5 (#4557)
* enable some of the tools

do not make zoltan default

* modify moab package

add shared, debug options to cgm, too
build some tools by default (mbsize, mbconvert)
add hdf5, netcdf dependency
add pnetcdf variant (dependency), metis, parmetis, zoltan
add shared, debug, fortran options to moab

* few kinks for moab

zoltan should be built without fortran api, otherwise moab
complains (need to fix)
also, notice that when built with cgm, shared can't find
cgm libraries for the new tools/geometry execs

install in serial for the time being (because of example makefile
duplicate?)

for example, these builds are successful:
spack install moab+mpi+hdf5+zoltan ^mpich@3.2
spack install moab+mpi+hdf5+shared ^mpich@3.2

* force hdf5+mpi if both are specified

also, something like this works:
spack install  moab+mpi+hdf5+cgm ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2

use mpich32, and cgm built with oce 0.17.2

* forgot about irel, fbigeom, mbcoupler

* add meshkit package

simple build so far, moab and cgm deps only

also, an example of complex build for cgm
spack install  moab+mpi+hdf5+cgm+irel+fbigeom ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2

* for meshkit, moab needs to have irel, fbigeom

* forgot to self.spec

after building moab with cgm with oce 0.17.2, we can build
meshkit with something like this
spack install meshkit ^moab/tsb75zk

cgm depencency is found out from moab

moab has to be built with irel and fbigeom

* add netgen package and review

do not support yet older versions of meshkit
(which depend on lasso, etc)
add netgen package; tested with meshkit (netgen has to be built without
occ, for meshkit)
We are not enforcing that yet, we may have to test

* use conflicts where needed, suggested by review

remove release candidates

* flake8 alignment errors

* flake8

* reviews

flake8 alignment
explicit options, even for default variants
variant for netgen should be "gui", with the default ~gui (False)
FIXME: with-occ does not work right for netgen ; maybe it should be disabled?
       also, with +gui, it should depend on a lot more, like tk, tcl?

* flake8 issues

whitespaces and a comment in netgen

* add more explicit options

--without-mpi needs fixing for cgm, moab and meshkit
add variable url for netgen (although we don''t know if other
versions will appear)

* flake8, trailing whitespace
2017-06-23 08:53:43 -05:00
Andrey Prokopenko
811ea4f465 ninja-fortran: a Fortran-capable fork of ninja build tool (#4539)
* ninja-fortran: a Fortran-capable fork of ninja build tool

* Use url_for_version for clarity

* Clean ninja-fortran

* Cleanup in the original ninja package
2017-06-23 08:52:57 -05:00
Adam J. Stewart
3e087f2e25 Remove test dependencies from Python packages (#4572)
* Remove test dependencies from Python packages

* Make test deptype more clear for a couple more packages
2017-06-23 08:51:45 -05:00
Geoffrey Oxberry
1d741a2110 suite-sparse: add openmp variant (#4563)
Fixes #4549.
2017-06-23 08:50:49 -05:00
Mark Olesen
b741809bb2 BUG: flex+lex fails with lib64/ installation (issue #4583) (#4584)
- new version 2.6.4 as well
2017-06-23 08:45:17 -05:00
Audrey Thoma
8125780b86 New package augustus (#4586)
* augustus: adding augustus

* augustus: fixing flake8 things

* augustus: simplifying verbose
2017-06-22 16:00:43 -05:00
Adam J. Stewart
a803a5e986 Add latest version of libtiff (#4574) 2017-06-22 12:52:23 -05:00
Adam J. Stewart
6d9494f0d2 Add latest version of libmng (#4575) 2017-06-22 12:52:02 -05:00
Stas Sergienko
6aa3d51939 created py-tomopy package and fixed its dependencies (#4576)
* added py-tomopy package

* fixed dependencies and added import_modules

* edited deps for tomopy with import_modules and added py-olefile pkg

* changed module name

* changed dependency to python because it will not build with setuptools

* fixed dependency list for py-tomopy and py-dxchange

* added py-nose dependency

* fixed tests

* commented out dependency py-counter

* fixed dependency py-pybtex-docutils

* removed nose as a dependency

* fixed flake8 errors

* fixed import_modules

* fixed import_modules indent

* fixed various issues in tomopy and deps files
2017-06-22 12:51:51 -05:00
Audrey Thoma
3c8e65f3d8 New package albert (#4568)
* albert: adding new package albert

* albert: fixing dependency type and build process
2017-06-22 11:12:37 -05:00
Audrey Thoma
2fa918f32c gmap-gsnap: adding gmap-gsnap package (#4570) 2017-06-22 11:12:19 -05:00
Mark Olesen
ff26cb9723 Update for paraview 5.4.0 (#4582)
- paraview 5.2.1 -> 5.4.0 supports both Qt4 and Qt5, but the assumed
  default version changes between versions. So explicitly define
  which QT major version is being used.
2017-06-22 09:29:19 -05:00
becker33
689c1d2f0c fix issue #4577 (#4579) 2017-06-21 18:33:11 -05:00
becker33
a113101126 Module cmd fix (#3250)
* Parse modules in a way that works for both lmod and tcl

* added test and made method more robust

* refactoring for pythonic clarity

* Improved detection of 'module' shell function + refactored module utilities into spack.util.module_cmd

* Improved regex to reject nested parentheses we are not prepared to handle

* make tests backwards compatible with python 2.6

* Improved regex to account for sh being aliased to bash and used in bash module definition on some systems

* Improve test compatibility with lmod

* Added error for None module_cmd

* Add test for get_module_cmd_from_which()

Add test for get_module_cmd_from_which().
Add -c argument to Popen call to typeset -f module in get_module_cmd_from_bash().

* Increased detection options

Included BASH_FUNC_module() variable outside of typeset as a detection option
This should work on bash even in restricted_shell mode
Kept the typeset detection as an option in case the module function is not exported in bash

Also added try statements to tests, with environment recreation in finally blocks.

* More tests added; some hackiness

* increased test coverage for util/module_cmd
2017-06-21 09:58:41 -07:00
Massimiliano Culpo
59b66b0d27 mumps: fixed compilation issues due to scotch not found at link time (#4567) 2017-06-21 11:36:18 -05:00
Mark Olesen
1f2e56e1f3 refactor openfoam packages (#3669)
* Several improvements for the openfoam packages

--

Refactor openfoam packages by adding an OpenfoamArch class

Use separate configure, build, install phases.

Provide FOAM_PROJECT_DIR dependent env for openfoam packages
- easier way to locate

Eliminate intermediate installation directories
- unneeded clutter.
- makes it less than easy to find the etc/bashrc file

Add versioning for all openfoam patches
- no certainty which parts (if any) will be needed in future versions,
  especially if we strive to ensure that the upstream version builds
  well with spack to begin with.

Support build of develop branches
- helps track build regressions for future openfoam releases

STYLE: use common/ and assets/ to provide additional (build) resources ...

* - adjust OpenFOAM provider

Move openfoam-com up front since this is the one being used as a base
for the others
2017-06-21 11:35:31 -05:00
Audrey Thoma
b1fceb75d0 Andi and libdivsufsort (#4559)
* andi: adding andi and libdivsufsort

* andi: adding andi and dependency libdivsufsort

* andi: adding andi and dependency libdivsufsort

* andi: fixing autotool dependency types

* andi: fixed whitespace to make flake8 compliant
2017-06-21 10:51:05 -05:00
Jonathan Wong
cb87edf230 Modified ipopt package to support build on ppc64le (#4561)
Added line in package.py to patch using ipopt_ppc_build.patch. The patch simply adds support in config.guess and Ipopt/config.guess to build ipopt on ppc64le.
2017-06-21 06:47:06 -05:00
Mark C. Miller
2525363c11 adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size (#4466)
* adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size

* fixing homepage url

* removed fortran error message...just build fortran if can, otherwise ignore
2017-06-21 06:46:14 -05:00
Jim Eliot
7c0a759a26 Fix for SAMRAI build debug spec bug (#4564) (#4565) 2017-06-21 06:38:27 -05:00
serbanmaerean
0fe9cb5d1c FFTW: remove search for IBM XL threaded compiler when compiler is not gcc (#4187)
* Added magma package

* Incorporated Serban's change

* fftw: patch configuration file to remove search for xlc_r compiler
when compiler not gcc

FFTW assumes there are only 2 compilers: gcc and IBM XL.  When
building threaded fftw, the configuration file is looking for
the threaded IBM XL's xlc_r compiler when the compiler is not gcc.
The PGI compiler is not gcc.
2017-06-20 16:47:24 -05:00
Audrey Thoma
bcb8615fb0 Add abyss package (#4555)
* abyss

* abyss: deleting attemped test from script

* abyss: adding new package abyss

* abyss: partially fixing mpi dependency issue

* abyss: added mpi provider conflicts
2017-06-20 16:34:42 -05:00
Christoph Junghans
12113c41e4 Features/votca (#4556)
* votca-csg: needs non-mpi version of gromacs

* votca-csg: fixed deps

* votca-moo: new package

* votca-ctp: new package

* votca-ctp: make flake8 happy
2017-06-20 15:34:17 -05:00
George Hartzell
e5560dfbde fontconfig should depend on gperf (#4551)
* Include depends_on for gperf

Sometime around 2.12.2 fontconfig acquired a build-time
dependency on `gperf` (this commit, I think:
59fd9960bbb58fd6257adb13ec0f918882149332).

This adds the dependency.

`gperf` is called in the `src/Makefile`, see line 907 of
`src/Makefile.in`.

* Only depend_on gperf if @2.12.2:

The gperf dependency *seems* to only be required when @2.12.2:.

Earlier releases do not check the arg type of the gperf lookup
function (which requires gperf) and are able to use pre-generated
files so gperf is not required at build time.
2017-06-20 12:46:49 -05:00
Mark C. Miller
ca9e6576db Fix veclibfort for gcc (#4548)
* fixes #967

* Version bump to 0.9.1

- Bugfixes for spack find
- 0.9.1 can read specs from current develop.

* Don't assume spack is in the path when building docs.

* fixing Makefile override of PREFIX and install w/gcc-6
2017-06-20 09:59:40 -05:00
Stas Sergienko
229886aa8f added py-dxchange and its dependencies dxfile,edffile,spefile,tifffile (#4534)
* added py-dxchange and its dependencies dxfile,edffile,spefile,tifffile

* fixed https in homepage of py-dxfile
2017-06-19 16:26:37 -05:00
Adam J. Stewart
9b89272ae0 Various updates to wget and dependencies (#4116)
* Various updates to wget and dependencies

* Add newer version of gnutls
2017-06-19 15:13:18 -05:00
Adam J. Stewart
cf2178f416 Overhaul CONVERGE installation and concretization (#4397) 2017-06-19 10:18:48 -05:00
Diana Bite
b12c0e0f87 fontconfig: Update to latest stable release (#4543) 2017-06-19 10:02:30 -05:00
Todd Gamblin
04af95c69a Add Slack info to READMEmd (#4542)
- Added a badge to show who's online.
- Added a section under "Get involved!"
2017-06-19 01:00:40 -07:00
Todd Gamblin
d1f176541d Update README.md and add analytics. (#4537) 2017-06-17 19:37:33 +02:00
Andrey Prokopenko
cbdee5faf7 votca-csg: fixing develop url (#4536)
Fix #4525.
2017-06-17 09:32:14 -05:00
becker33
541496dfe1 System config (#4518)
* Code changes to enable system config scope in /etc

Files will go in either /etc/spack or /etc/spack/<platform>
Required minor changes to conftest.

* Updated documentation to match new config scope
2017-06-16 12:31:56 -07:00
Stas Sergienko
5c01fadc59 Added py-pybtex package (#4507)
* Added py-pybtex package

* added more dependencies to py-pybtex

* added run to py-latexcodec dependency
2017-06-16 12:45:30 -05:00
John Roberts
4bd05d0c52 Py ase (#4517)
* py-ase: Adding python package py-ase.

* py-ase: Adding Python package py-ase.

* py-ase: Shortened package description.

* py-ase: Splitting package description to multiple lines to avoid char count max.

* py-ase: Removing trailing whitespace. Local flake8 tests passed now that flake8 is working for me.
2017-06-16 12:44:12 -05:00
Stas Sergienko
09ff2afb78 added py-sphinxcontrib-bibtex and py-pybtex-docutils packages (#4520)
* added py-sphinxcontrib-bibtex and py-pybtex-docutils packages

* added dpendency py-ordereddict
2017-06-16 12:42:36 -05:00
Kyle Fernandes, né Jacobs
a8919b07ca Update intel* packages (#4528)
* Update intel-*  packages

* Update intel package
2017-06-16 12:18:25 -05:00
David Böhme
04c2a1caf4 Update Scalasca/Score-P/Cube/OTF2 (#4485)
* Update Scalasca/Score-P/OTF2/Cube. Should fix #4349#

* cube: Fix flake8 warnings

* cube, scalasca: Fix version range syntax for deps

* otf2: Fix version URL generation

* cube: Remove static URLs
2017-06-16 11:45:06 -05:00
Adam J. Stewart
60db73a3f5 Fix OpenMPI CUDA support (#4323)
* Fix OpenMPI CUDA support

* Remove --with-cuda-libdir flag, not a real flag

* Fix PGI and CUDA 7 support
2017-06-16 10:00:19 -05:00
Milton Woods
f6e3ad4d90 py-pillow: ensure that RPATH includes graphics libraries (#4522) 2017-06-16 08:43:18 -05:00
iulian787
fe7bf77afe oce changes for cgm (#4514)
* oce changes for cgm

cgm can be configured with oce, but oce needs
to have X11 enabled, because some libraries
(like TKCAF in occ/oce) gets built only of X11 is NOT disabled
so introduce a variant +X11 for oce, which is needed when
configuring cgm with oce(+X11)

* follow up review

simplify by removing the patch and different url paths
use append instead of extend, when necessary
make mpi true by default

X11 dependency is still to be addressed; it pulls in some opengl
library (on laptop nvidia seem to work, on virtual linux machine
mesa was good enough)
2017-06-16 08:29:59 -05:00
Todd Gamblin
790b06e0c3 bugfix: support EDITOR values with spaces (#4523)
- previous code called `which` on $EDITOR, but that doesn't work for
  EDITORs like `emacs -nw` or `emacsclient -t -nw`.

- This patch just trusts EDITOR if it is set (same as previous
  behavior), and only uses the defaults if it's not.
2017-06-16 14:03:21 +02:00
Massimiliano Culpo
8b5e94976d issue 4492: DependencyMap.concrete checks for unconditional dependencies (#4499)
* issue 4492: added xfailing test, added owner to DependencyMap

* DependencyMap.concrete checks if we have unconditional dependencies

This fixes #4492 and #4107 using some heuristics to avoid an infinite
recursion among Spec.satisfies, Spec.concrete and DependencyMap.concrete

The idea, as suggested by @becker33, is to check just for unconditional
dependencies. This is not covering the whole space and a package with
just conditional dependencies can still fail in the same way. It should
cover though all the **real** packages we have in our repo so far.
2017-06-16 12:41:15 +02:00
Mario Melara
da67ee9790 Fix tests on cray (#4298)
* Check for CRAYPE_VERSION instead of path

Architecture tests would fail on Cray since it would not find
the expected path. To make the test correctly work on Cray search
for the CRAYPE version instead.

* Catch SystemExit error in case flake8 not in path

On shared systems having flake8 can involve starting own virtual env.
Skip the test if no flake8 is found to avoid failure reporting.

* Add compatibility to 1.5 svnadmin create

The flag added is needed to correctly create svn repos on NERSC systems.
This could be unnecessary for other sites. I'd like to see others
test before this change gets merged.
2017-06-15 15:16:14 -07:00
Stas Sergienko
c102be2144 Added package py-oset (#4500)
* Added py-oset package

* Added package py-oset

* changed homepage url
2017-06-15 13:50:48 -05:00