Commit graph

9256 commits

Author SHA1 Message Date
Adam J. Stewart
2264e30d99
Update URL parsing regexes and tests (#13411)
* Update URL parsing regexes and tests

* Get rid of no longer used README

* Merge py-udunits and py-cf-units

* netcdf -> netcdf-c

* setup_environment -> setup_*_environment

* Fix doc tests

* Few last minute fixes

* Simplify prefix removal copypasta
2019-10-28 20:27:54 -05:00
Jim Galarowicz
4367e16740 Update the module files for cbtf-krell and openspeedshop (#13400)
* Update the module files for cbtf-krell and openspeedshop adding man paths and needed papi and libmonitor paths.

* Update module files for new API.

* Use the same python for both develop and release branches.
2019-10-28 17:36:12 -05:00
Sinan
e5b1dbf4b4 new Package/scs (#13454)
* new package: SCS

* make flake8 happy

* add missing patch, improve style

* fix typo

* Update var/spack/repos/builtin/packages/scs/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* move filefilter to edit phase
2019-10-28 17:33:32 -05:00
Cyrus Harrison
1b3f546ba4 update conduit for 0.5.0 release (#13455)
* add support for static (via ~shared) and use vtk-m 1.2

* updating vtkh package to output cmake configure file and pinning it to vtkm 1.2

* trying a different cmake for vtkh

* removing problematic b

* making conduit respect ~python

* fixing ascent python logic

* update ascent package

* consistant cmake usage

* conditionally add tbb in ascent if vtkh

* applying becker fix

* adding vtkh tag

* fixing vtkh tagged version

* updating ascent and conduit for static builds

* enabling openmp

* reverting files that should not have been changed

* ascent updates

* more robust handling of variants

* fixing ascent package typo

* ascent: add optional support for mfem

* 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

* fixing mfem typo for ascent

* reverting files

* adding mirror for bzip

* 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 prefered conduit version

* allow mfem to use conduit master

* adding rover package and editing ascent

* updating vtkm cmake dep

* updates from axom

* 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

* flake8

* extra guards for cuda patch

* conduit and ascent fortran fix

* fix patch for non cuda case

* add test variant to conduit, tweak ascent pkg

* change min ver of cmake used for ascent

* h5z-zfp package: unset FC when ~fortran

* conform to expected upstream solution

* pinning vtkm

* going back to vtkm master

* add back vtk-m variant for shared libs

* update ascent and vtkh packages

* wire up option to run tests during install

* add post install test

* add testing to ascent

* tweak for blueos xl

* add ctest output on error for run_tests

* enable ctest output on error for run_tests

* add testing of the using-with-make example

* update using-with-make examples

* typo in ascent using-with-cmake test

* fix ascent using test exe names

* more fixes, less sleep

* more fixes, less sleep ...

* remove unwired up version

* improvments suggested on review

* adding new cmake

* Update package.py

* Update package.py

* changes post cori os update

* fix cray hack

* Update package.py

Fixing 'fix'. Inconsistent variable names in conduit package

* type in spack recipes

* add zfp support to conduit

* fix indent error in conduit pkg

* move to use build phases, add sphinx rtd as dep, fix ex names in tests

* add conduit 0.5.0 release

* flake8

* remove old cray hack

* incorp feedback from review

* fix to use proper build env sig
2019-10-28 17:32:16 -05:00
Kelly (KT) Thompson
ffb4e02a53 Fix gcc recipe for RHEL7. (#13460)
* Fix gcc recipe for RHEL7.

+ It appears that macOS related changes to the gcc recipe broke gcc on RHEL7.
  This bug manifests as `libstdc++.so: undefined reference to libiconv` when gcc
  is used.
+ Fixes #13452 by moving
  `--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix)` into the darwin
  OS section of the configuration.
+ Change qualification of `depends_on(libiconv)` to limit dependency to macOS.

* Replace deprecated 'setup_environment' with 'setup_run_environment'.

* Fix cut and paste error.

* Rename 'run_env' to just 'env'.
2019-10-28 17:31:23 -05:00
Jon Rood
8786cb468a Paraview package: add version 5.7.0 and update environment setup (#13255)
Replace setup_environment/setup_dependent_environment with
setup__dependent_build_environment and setup_run_environment
according to 9ddc98e
2019-10-28 14:55:08 -07:00
Brian Van Essen
802c3c0c51 Packages: Add cuDNN versions; update LBANN dependencies (#13412)
* Add cuDNN version 7.6.3-10.1 (for x86_64 and ppc64le)
* Add py-pytest and py-protobuf depenencies to LBANN
2019-10-28 13:24:50 -07:00
Paul
f4e6f28e6d Go package: add versions (including 1.13.3) and update environment setup (#13254)
* Add versinos 1.13.3, 1.13.2, 1.12.12, and 1.12.11
* Replace setup_environment/setup_dependent_environment with
  setup_build_environment and setup_dependent_{build, run}_environment
  according to 9ddc98e
2019-10-28 13:19:14 -07:00
Adam J. Stewart
33a34f9619
Fix PyTorch build with Intel MKL (#13464) 2019-10-28 11:47:21 -05:00
Glenn Johnson
283b3e601c Update emacs to version 26.3 (#13469) 2019-10-28 11:46:27 -05:00
Mark Olesen
cacd0fb139 scotch: added version 6.0.8 (#13467) 2019-10-28 15:58:25 +01:00
wenlibin02
ba69ebc5f7 Add dependency and patch for perl-dbfile (#13261)
* Add dependency and patch perl-dbfile

There are two problems for the building of `perl-dbfile`:

1) this package depends on the package `berkeley-db`
2) fix the building using a patch, which locates the position of `berkeley-db` and modify the configuration file for the building

* Update and reformat the script package.py

* Simplify the patch

* Update package.py

* Update package.py
2019-10-27 22:31:10 -05:00
Nichols A. Romero
c11c3f2710 QE Update Oct 2019 (#13406)
* This filter_file was difficult to maintain and is no longer needed.

* Clarify lack of support for HDF5 in serial QE.

* Update QE and HDF5 conflicts based on user feedback.
2019-10-27 22:27:55 -05:00
Axel Huebl
7b86251bef Add Lizard (LZ5) (#13456)
* Add Lizard (LZ5)

Add a new package for Lizard, formerly LZ5, a very fast compressor
and decompressor library.

* c-blosc2: use external lizard

Use an external Lizard (LZ5) dependency and add missing
"when="s for other compressor dependents.
2019-10-27 22:24:27 -05:00
Glenn Johnson
1d760e79a6 Libbeagle fixes (#13463)
* Fixes for libbeagle

This PR fixes a couple of issues with the libbeagle package.

- Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix)
- Disable the default of compiling with -march=native as Spack now
  inserts architecture specific flags
- Set BEAST_LIB in the beast1 package not in libbeagle.

* Use new setup_run_environment method
2019-10-27 22:24:06 -05:00
Andreas Baumbach
c0a2e8651b new package: py-pandocfilters (#13418)
dependency of py-nbconvert
2019-10-27 22:22:25 -05:00
Andreas Baumbach
ea6e279bbc LLVM code-signing on OSX: link to the offical documentation (#13428)
* LLVM code-signing on OSX: link to the offical documentation

* LLVM: update setup_environment method
2019-10-27 21:59:13 -05:00
Michael Kuhn
82428133d6 mariadb: Fix openssl dependencies (#13443) 2019-10-27 21:55:06 -05:00
Michael Kuhn
929ec39a63 mariadb-c-client: Add 3.1.4 (#13447) 2019-10-27 21:54:04 -05:00
Sinan
57f040753d new package: ecos (#13453) 2019-10-27 21:53:38 -05:00
Adam J. Stewart
59a6226f74
Update PyTorch variable name (#13461) 2019-10-27 19:21:06 -05:00
Axel Huebl
c107b7531c
MPICH: Fix Slurm Find Issue (#13263)
Set include and library path to slurm explicitly.
2019-10-26 22:03:39 -04:00
Adam J. Stewart
d68b554cd3
Add latest version of py-fiscalyear (#13451) 2019-10-26 11:06:37 -05:00
Adam J. Stewart
5582de837e
Add py-twine package (#13449) 2019-10-25 21:27:44 -05:00
Adam J. Stewart
85597be4d7
Add py-pkginfo package (#13448) 2019-10-25 21:27:29 -05:00
Adam J. Stewart
d6735aa5cd
Add latest version of py-tqdm (#13446) 2019-10-25 21:27:12 -05:00
Adam J. Stewart
46ae845b6b
Add latest version of py-requests-toolbelt (#13445) 2019-10-25 21:26:48 -05:00
Adam J. Stewart
3dda714477
Add latest version of py-readme-renderer (#13444) 2019-10-25 21:26:29 -05:00
Glenn Johnson
c566a610c9 New package: gpu-burn (#13108) 2019-10-25 17:14:52 -07:00
Andreas Baumbach
24ccc11242 py-nbformat package: add version 4.4.0 (#13421) 2019-10-25 15:42:49 -07:00
Andreas Baumbach
32c0ef5ebd New package: py-defusedxml (#13419) 2019-10-25 15:40:59 -07:00
Sinan
ca917cfccc New package: OSQP (#13432) 2019-10-25 15:36:28 -07:00
Hans Pabst
92e2758837 LIBXSMM package: add version 1.14 (#13436) 2019-10-25 15:34:54 -07:00
Michael Kuhn
d4ce124b65 lmdb package: add version 0.9.24 (#13437) 2019-10-25 15:34:13 -07:00
Michael Kuhn
2f752d4880 sqlite package: add version 3.30.1 (#13438) 2019-10-25 15:33:47 -07:00
Justin S
1b6ba93668 py-gensim: new package at 3.8.0 (#13136)
* py-gensim: new package at 3.8.0

* py-gensim: add 3.8.1
2019-10-25 16:43:54 -05:00
Greg Becker
a6ea0bbbae
Views: fix python in views when python prefix is under a symlink (#12575)
* Fix python in views when python prefix is under a symlink

* Add todo for future generalization
2019-10-24 16:27:21 -05:00
Adam J. Stewart
0f22e528f3 Add latest version of NetCDF libraries (#13416) 2019-10-24 14:21:12 -06:00
Mikael Simberg
83016e96fd Extend HPX package (#13219)
* Add master branch as version to HPX package

* Remove C++98 option from HPX package

* Add option to turn off examples in HPX package

* Add MPI variant to HPX package
2019-10-24 14:19:25 -06:00
Jannek Squar
5004b20f5c New package: py-cdsapi (#13363)
* New package py-cdsapi to access Climate Data Store for downloading climate and weather reanalysis data

* Improvements
2019-10-24 13:30:21 -05:00
Geoffrey Oxberry
2dd83523e2 mfem: add version 4.0 (without cuda) (#11880)
* mfem: add version 4.0.0 (without cuda, raja, etc)

* mfem@4.0.0: add occa variant

* mfem@4.0.0: add raja variant

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2019-10-24 13:08:51 -05:00
Eric Martin
44485c56b6 blast-legacy: fix build issues (#13370) 2019-10-23 23:16:22 -05:00
Eric Martin
944ffe44a7 subread: add version 2.0.0 (#13368) 2019-10-23 23:07:11 -05:00
Cody Balos
177f661bb3 sundials: add version 5.0.0 and new variant (#13375)
* sundials: add version 5.0.0 and new variant

plus some cleanup

* sundiaks: fix formatting

* sundials: fix dependencies
2019-10-23 23:06:20 -05:00
Eric Martin
d0d0456fa7 vt: add version 0.5772 (#13367) 2019-10-23 23:05:27 -05:00
Greg Becker
8c7a3e55dd add spack dev-build command; deprecate spack diy (#13374)
Rename the `spack diy` command to `spack dev-build` to make the use case clearer.

The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing.  Developers do not notice it, partly because of the obscure name.

The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds.

To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well.

The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought.
2019-10-23 17:08:15 -07:00
Michael Kuhn
bd7265ed52 bison: Fix parallel build (#13402) 2019-10-23 16:49:18 -05:00
Michael Kuhn
420346b275 mysql: Use correct python command (#13393)
* mysql: Use correct python command

python~pythoncmd does not provide a python symlink for python3, so make
sure we pick the right command.

* mysql: Adapt to build env changes
2019-10-23 14:15:30 -05:00
Sarah Osborn
b7536eb332 hypre: Add new variants to expose existing features. (#13373)
* hypre: Add new variants to expost existing features.

* hypre: Add new variants to expose existing features.

* hypre: Shorten description line.

* hypre: Add an explicit else clause to disable some features.
2019-10-23 14:13:21 -05:00
Adam J. Stewart
33499681a4
Add latest version of py-pbr (#13380) 2019-10-23 10:14:04 -05:00