Commit graph

13463 commits

Author SHA1 Message Date
Hadrien G
3497098978 Update templight pseudo-release to remove need for patching (#10290)
* Update templight+LLVM combo

* Bring back old pseudo-release
2019-01-16 10:36:34 -06:00
Massimiliano Culpo
4bc3936004 Openblas: added version 0.3.5 (#10364) 2019-01-16 08:11:07 -06:00
sknigh
b31ecb0342 Added latest version of singularity 2.x (#10354) 2019-01-16 13:14:32 +01:00
George Hartzell
1f9fe02309 Add package for Hugo (static website generator) (#10358) 2019-01-16 13:11:15 +01:00
Tom Payerle
01bd67eb43 py-modred: New package (#10309)
* py-modred: New package

Parallelized python module for finding modal decompositions and
reduced order models.

* fix license
I think?

* Add dependency on py-numpy

and remove commented out code
2019-01-15 16:42:20 -06:00
sknigh
eaa340eba7 Added hpl 2.3 (#10345)
* Added hpl 2.3

* Added requested build fixes, added step to copy HPL.dat in 2.3+
2019-01-15 16:41:33 -06:00
Adam J. Stewart
d7fb3fd88e
r requires cairo+pdf (#10350) 2019-01-15 09:58:53 -06:00
Owen Solberg
2585c04b50 explicitly depend_on cairo with X **and** pdf variants (#10351) 2019-01-15 09:58:39 -06:00
Elizabeth Fischer
0628ebefd8 Add useful comment explaining why this is not needed for Python3. (#10326) 2019-01-15 07:31:20 -08:00
Axel Huebl
89a493522c openPMD-api: Dependency Update (#10314)
openPMD-api now only supports Python 3, needs a newer CMake and
ADIOS1 and also learned to read & write JSON :-)
2019-01-15 09:28:13 -06:00
Neil Flood
49dedb2443 vigra: new package (#10337)
* vigra: new package

* Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks.

* Take care of lines too long

* Explicit WITH_HDF5=ON
2019-01-14 20:39:34 -06:00
Andrew Gaspar
04d4b07636 Add span-lite version (#10347) 2019-01-14 18:22:29 -06:00
sknigh
a1994d883c Added latest rust releases and develop branch (#10341)
* Added latest rust releases and develop branch

* Fixed spacing
2019-01-14 17:22:38 -06:00
Levi Baber
d1b7e560bd namd: fixing to reflect renamed charmpp per #9216 (#10342) 2019-01-14 17:22:03 -06:00
sknigh
43e6114db7 Added latest version of libfabric (#10343) 2019-01-14 17:21:33 -06:00
Geoffrey Oxberry
baf595351e feature: py-invoke: new python package (#10225) 2019-01-14 17:13:17 -06:00
Todd Gamblin
618741fce2 tutorial: update tutorial materials for ECP19 2019-01-14 01:03:38 -06:00
Gregory Becker
dc005f3ff1 version bump: v0.12.1 2019-01-13 14:26:39 -08:00
George Hartzell
7abc2fb26d bugfix/gdk-pixbuf (#10312)
* docbook processing works correctly for gdk-pixbuf

1. The various bits of documentation in gdk-pixbuf include hardcoded
   references to dtd's and stuff at their canonical, Internet,
   locations.  BUT, gdk-pixbuf runs xslt-proc with the `--nonet`
   option, which forbids it from using the network.  Sadness ensues.

   Traditionally folks use XML Catalogs to map these to local copies.
   Our docbook-xsl package wasn't setting the appropriate env var in
   its dependents environments to use our catalog.

   Now it does.  Less sadness ensues.

2. If we're going to use these things, we should depend on them.

* Add gdk-pixbuf's bin to build environment

The "post-install.sh" script uses gdk-pixbuf-query-loaders, which was
installed earlier.

If py-psyclone can set its own bin on its PATH, so can we...

* Make gdk-pixbuf use recognizable docbook location

Our docbook-xsl package assumes that the canonical location is
`http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl`, but
the gdk-pixbuf's meson build script uses
`http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl`.

This means that our XML Catalog doesn't fix the reference and sadness
happens.

Just patch the build that we see what we want to see, then we can make
it all go away.

* Add commentary re docbook patch

* Make catalog helper a property

Thanks @adamjstewart!

* Run tests if/when run_tests is true

Thanks @adamjstewart!

* Tune up dependencies

Thanks @adamjstewart!

* Wordsmit commentary
2019-01-13 14:40:20 -06:00
Cyrus Harrison
9350db5665 update alpine ascent and friends (#10320)
This adds a lot of fixes and updates for alpine ascent and its dependencies:

* add support for static (via ~shared) and use vtk-m 1.2
* update vtkh package to output cmake configure file and pinning it to vtkm 1.2
* make conduit respect ~python
* fix ascent python logic
* consistant cmake usage
* conditionally add tbb in ascent if vtkh
* enable openmp
* more robust handling of variants
* update ascent and conduit for static builds
* add optional support for mfem in ascent
* enable mfem conduit support for ascent
* add optional adios dep to conduit
* remove ver req from conduit
* ascent: remove confusing comment
* tweaks to conduit and ascent pkg recipes
* fix typo in conduit package
* pref conduit master
* changing mfem to depend on conduit@master to get updated relay
* restore use of conduit 0.3.1 or greater for mfem
* set master as preferred conduit version
* allow mfem to use conduit master
* adding rover package and editing ascent
* updating vtkm cmake dep
* guard ascent python support on +shared
* removing rover to simply ascent package
* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified
* fix fortran compiler check so it can work on cray systems
* working towards cuda fix for vtkm lagrange filter
* update ascent package with more variants, and patch to avoid nvcc issue
* hdf5 flags fix for BGQ
* add post install test
* add testing to ascent
* add testing of the using-with-make example
* add ctest output on error for run_tests
2019-01-12 17:43:39 -08:00
Adam J. Stewart
dc6dca3c36 cc: clean up cray compilers, fix issues with case-insensitive filesystems (#10323)
* Remove Cray CC compilers causing problems on case-insensitive filesystems
* cray -> cce
* Ensure that compiler-specific directory comes first in build-env
* Point to compiler-specific symlinks
2019-01-12 17:37:20 -08:00
Jiawei Zhuang
07d9d444ea Added osu-micro-benchmarks@5.5 (#10333) 2019-01-12 17:31:13 -08:00
Omar Padron
8e71ba8aa0 fix typo in docker test script (#10334) 2019-01-12 17:30:35 -08:00
George Hartzell
6c638600d7 Add libxslt v1.1.33 info (#10328) 2019-01-12 17:36:53 -06:00
Denis Davydov
09033e991e dealii: does not support sundials 4.x (#10324) 2019-01-12 15:28:57 -06:00
Neil Flood
04c1af0ee2 gdal: Add variant for GRIB driver (#10322) 2019-01-12 10:33:18 -06:00
Omar Padron
c2529358f2 fix archlinux docker build (#10289) 2019-01-12 00:52:50 -08:00
Greg Becker
c63c4a048c Binary caching bugfix: symlink relocation (#10073)
Binary caches of packages with absolute symlinks had broken symlinks.
As a stopgap measure, #9747 addressed this by replacing symlinks with
copies of files when creating binary cached packages.

This reverts #9747 and instead, either relative-izes the symlink or
rewrites the target. If the binary cache is created using '--rel' (as
in "spack buildcache create --rel...") then absolute symlinks will be
replaced with relative symlinks (in addition to making RPATHs relative
as before); otherwise they are rewritten (when the binary cache is
unpacked and installed).
2019-01-11 14:52:01 -08:00
Matthias Wolf
3c6d484150 enh: buildcache list should behave similar to find (#10052)
The current output of buildcache list is very verbose and I feel like
some details are getting lost. By making the output similar to find, I
think users will be able to get a better overview of what is stored in
the cache.
2019-01-11 13:57:10 -08:00
Dan Ibanez
f9967d2f6f Omega_h changed its URL (#10315)
From https://github.com/ibaned/omega_h
To https://github.com/SNLComputation/omega_h
2019-01-11 13:29:56 -06:00
Satish Balay
4cbeec07a0 omega-h: fix CMAKE_BUILD_TYPE: breaks with spack deafult 'RelWithDebInfo' (#10297) 2019-01-11 10:08:28 -08:00
Denis Davydov
f4bda74b30 dealii: fix concretization of xsdk package (#10288)
* dealii: fix concretization of xsdk package

* tests: add concretization tests for deal.II and xSDK, which are often broken due to limitations in the concretizer

* use pytest.mark.parametrize
2019-01-11 10:07:28 -08:00
Brian Van Essen
9102cd5790 Updating LBANN and related packages (#10305)
Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA.  Fixed small bugs within both LBANN and Hydrogen
packages.  Added requirements for breathe and cereal to LBANN.
2019-01-10 17:10:11 -08:00
Mark W. Krentel
08c4b9d47a boost: fix the bjam build for Cray (#10295)
Fixes issues #9613 and #3209.

Remove the spack wrapper directories from PATH for the bootstrap step.
This was breaking the build for Cray (and other cross-compile) because
bjam was built for the BE and died on SIGILL on the FE.

This only affects building bjam.  The boost libraries are still built
the normal spack way with the spack wrappers.
2019-01-10 16:34:05 -08:00
Mark W. Krentel
7e8b17b177 hpctoolkit: variants to build for cray and blue gene (#10223)
Add variants 'cray' and 'bgq' to build for Cray and Blue Gene compute
nodes.  These systems need separate options to find the MPI compiler
for hpcprof-mpi.
2019-01-10 12:50:58 -08:00
Cody Balos
60a44d5155 sundials: add version 4.0.1 and remove 4.0.0-dev series (#10306)
The 4.0.1 release is the culmination of the SUNDIALS 4.0.0 preview releases,
i.e. the 4.0.0-dev versions. As such, the 4.0.0-dev releases are now
being removed.
2019-01-10 14:47:48 -06:00
Eric
b25f27d442 py-checkm-genome: Add version 1.0.13 (#10304)
* py-checkm-genome: Add version 1.0.13

* py-checkm-genome: Add missing py-backports-functools-lru-cache dependency

* py-checkm-genome: Fix missing whitespace
2019-01-10 12:28:07 -06:00
Jon Rood
12cf4eb734 Explicitly listing blas and lapack sections in site.cfg for numpy (#8708)
* Explicitly listing blas and lapack sections in site.cfg for numpy when using netlib-lapack so that scipy can find them as well.

* Reducing code to use a function call instead of copying and pasting.

* Fixing flake8 errors.

* Fixing python 3.6 error when site.cfg lists library_dirs multiple times.

* Formatting.

* Verifying blas and lapack are enabled before writing to site.cfg.

* Fixing flake8 errors.

* Fixing conflicts since this package file has been updated.

* Fixing flake8 stuff.

* Handling blas and lapack variants for netlib-lapack in site.cfg for py-numpy.

* Don't write netlib-lapack site.cfg file if no blas or lapack variants enabled in py-numpy.

* Removing redundant if statement.

* Fixing mistake in py-numpy site.cfg generation.

* Separating blas and lapack further in site.cfg for netlib-lapack in py-numpy.
2019-01-10 11:14:24 -06:00
Owen Solberg
586fe32166 update r-rcpp package with new versions (#10301) 2019-01-10 09:07:09 -06:00
Adam J. Stewart
72a41a4918 spack versions: only list safe versions (#10004)
* spack versions: only list safe versions
* Add unit tests for spack versions -s
2019-01-10 00:32:47 -08:00
Greg Becker
450b0e3059 Allow combinatorial projections in views (#9679)
Allow customizing views with Spec-formatted directory structure

Allow views to specify projections that are more complicated than
merging every package into a single shared prefix. This will allow
sites to configure a view for the way they want to present packages
to their users; for example this can be used to create a prefix for
each package but omit the DAG hash from the path.

This includes a new YAML format file for specifying the simplified
prefix for a spec in a view. This configuration allows the use of
different prefix formats for different specs (i.e. specs depending
on MPI can include the MPI implementation in the prefix).
Documentation on usage of the view projection configuration is
included.

Depending on the projection configuration, paths are not guaranteed
to be unique and it may not be possible to add multiple installs of
a package to a view.
2019-01-09 17:39:35 -08:00
Greg Becker
f5bb93c75b tutorial basics section: fix gcc install version (#10298) 2019-01-09 17:37:37 -06:00
Satish Balay
8ca674a574 petsc: fix petsc+debug to not reset COPTFLAGS - i.e use configure defaults '-g' (#10296) 2019-01-09 17:36:28 -06:00
Daryl W. Grunau
d1bb9caba4 eospac version bump to 6.4.0beta.4 (#10294) 2019-01-09 15:57:05 -06:00
Mark W. Krentel
1b991f9385 elfutils: option to install elf.h header file (#10185)
* elfutils: option to install elf.h header file

Add variant 'elfh' (default False) to install the elf.h header file to
the include directory.  This provides access to a newer version of
elf.h and allows an elf application to build with the same elf.h that
libelf.so was built with.

Add version 0.175.

* Drop the variant 'elfh' and always install elf.h instead.
2019-01-09 14:40:15 -06:00
Eric
b4dc73bed4 py-pyyaml: Add version 3.13 (#10293) 2019-01-09 13:39:34 -06:00
Simon Flood
0b2314bbc4 R: add version 3.5.2 (#10292) 2019-01-09 12:19:58 -06:00
Andreas Baumbach
730c629b09 New package: git-fat-git (#10266)
* new package: git-fat

* backport of rsync -> older versions no longer available

Change-Id: I3a41f17df0f88ca11e08ea6fd2f2d381435e0f09

* fix legal stuff and use new git attribute

Change-Id: Ice156dfe8ad4137a861f7b2938ee92f4024142be

* use date as version number rather than hash

Change-Id: Ib537659e368f69124895306d6a6ac0c5e36061a7

* only use the date once

Change-Id: I2592fa28aaa53fed949ddc82959d712ff3f6f752
2019-01-09 09:07:12 -06:00
marvinbernhardt
7571787a3a gromacs: added simd and rdtscp variants + version 2019 (#9931) 2019-01-09 10:39:05 +01:00
Axel Huebl
efe3e905a3 OpenMPI: Add Development Version (#10257)
Add the development version of OpenMPI from the git repo
in `master`.
2019-01-08 20:48:55 -06:00