Commit graph

7740 commits

Author SHA1 Message Date
Audrey Thoma
e941f33eaf meraculous: new package (#6292)
* meraculous: new package

* adding gcc version conflict

* Update package.py

* Update package.py
2017-11-16 09:40:46 -07:00
lingnanyuan
bb3d5fd313 r-rhdf5: Create new package. (#6330) 2017-11-16 09:40:15 -07:00
lingnanyuan
e732a554ff r-shortread: Create new package. (#6332) 2017-11-16 09:30:18 -07:00
lingnanyuan
cca06422fa r-sva: Create new package. (#6333) 2017-11-16 09:28:59 -07:00
David Hows
d89b09493c Minor package fixes (#6334)
* Add no-implicit-fallthrough to MsgpackC

* Add 0.2.1 of Neovim

* Lint
2017-11-16 09:28:40 -07:00
Massimiliano Culpo
9bffa96754 Reduce the calls to the python interpreter during initialization (#6312)
* Reduce the calls to the python interpreter during initialization

This should reduce the delay the users experience when sourcing the
setup file to activate shell support. It works by generating at once
all the commands that needs to evaluated (they are stored in
a string and later `eval`ed by the shell).

* setup_env.sh: changed `read` with an equivalent magic

For some reason `read` breaks when sourced from a running script.
Change the incantation we use to construct the unique python command
that will be evaluated.

* setup_env.sh: python command now constructed with `printf` for portability

This recovers the support for `zsh` that was broken in previous commits.
2017-11-15 17:38:40 -07:00
Stephen Hudson
9d1224e5d8 py-petsc4py: Update version to 3.8.0 and add dependencies (#5792)
* py-petsc4py: Update version to 3.8.0 and add dependencies

- Added explicit dependency on python and numpy

* Kept old version - and corrected minimal python version

* Update to 3.8.1
2017-11-15 16:49:36 -07:00
baip
697f3ea71d cp2k: add dependency on smm and libxc & new version 5.1 (#6194)
* cp2k: add libxsmm dependency

* cp2k: add libxc dependency

* cp2k: add smm variant to select from libxsmm or libsmm

* cp2k: add version 5.1
2017-11-15 16:49:08 -07:00
Christoph Junghans
7da8a02cbf
git grep --files-with-matches github.com/llnl/spack | xargs sed -i '/github.com/s@llnl/spack@spack/spack@' (#6329) 2017-11-15 16:46:39 -07:00
Denis Davydov
cb5fd6035a intel: add 2018.1 (#6322) 2017-11-15 13:13:15 -07:00
Axel Huebl
d1a733bc86 xtensor, xtl, xsimd (#6315)
Adds the QuantStack libs (C++, header-only) needed for
xtensor.
2017-11-15 13:12:31 -07:00
Yifan Zhu
cde0570c56 r-janitor: created new package (#6313) 2017-11-15 13:09:24 -07:00
Yifan Zhu
0d9ab84ebb r-dbplyr: created new package (#6311) 2017-11-15 13:09:11 -07:00
Howard Pritchard
af1b93b3db Open MPI: add 2.0.4 release to package file (#6310)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-11-15 13:03:07 -07:00
健美猫
71f12597a7 Update pgi to 17.10 . (#6306) 2017-11-15 13:02:54 -07:00
Sergey Kosukhin
e77b11674f Update for 'magics' and 'libemos'. (#6275) 2017-11-15 13:01:23 -07:00
scheibelp
b9be9519e8
Fix truncated error messages in directives (#6320)
Fixes #6299

Error messages in 'directives' were split across multiple lines and not
properly concatenated, which led to truncated messages.
2017-11-15 10:33:59 -08:00
Benedikt Riedel
2eb7fabe62 Allow openblas to build on a VM (#6258)
This adds a "virtual_machine" boolean variant which adds build
options that enable building openblas on a VM.
2017-11-15 10:32:02 -08:00
Eric
9acf207023 picard: add versions and fix url format (#6309) 2017-11-14 16:41:27 -07:00
Michael Kuhn
ec5d366bcd likwid: Fix hash for 4.3.0 (#6307)
Prefer 4.2.1 for now because 4.3.0's hash changes regularly.
2017-11-14 16:41:05 -07:00
健美猫
d9a4e7a038 Update miniconda to 4.3.30. (#6233) 2017-11-14 12:11:53 -08:00
Adam J. Stewart
138e9d08c6 Add the latest version of Lmod (#6297) 2017-11-14 10:32:41 -08:00
koebbe
50957bd44f py-h5py: make sure to depend on the hl variant of hdf5 (#6304) 2017-11-14 09:26:58 -07:00
vishalkenchan
0692029273 update trilinos checksums (#6301) 2017-11-14 09:22:34 -07:00
Michael Kuhn
aa27432a1d ncl: Check for ncl binary after installation (#6298)
ncl's build system will happily continue in case of errors, which might
result in the ncl binary not being built.
2017-11-14 09:22:04 -07:00
Michael Kuhn
e31b997162 icu4c: Update to 60.1 (#6295)
Previous versions try to include xlocale.h, which fails on glibc >= 2.26.
2017-11-14 09:21:35 -07:00
Yifan Zhu
a8f9182ef3 r-forcats: created new package (#6291) 2017-11-14 09:21:21 -07:00
Michael Kuhn
93bca2f3a2 libbson, libmongoc: Update to 1.8.1 (#6290) 2017-11-14 09:21:05 -07:00
Eric
137a9e64ac trimgalore: add version 0.4.5 (#6288) 2017-11-14 09:20:20 -07:00
Yifan Zhu
392e25b7e6 r-mnormt: created new package (#6287) 2017-11-14 09:20:06 -07:00
Yifan Zhu
05eb287ed9 r-bindr: created new package (#6285) 2017-11-14 09:19:49 -07:00
Yifan Zhu
c042644b53 r-glue: created new package (#6283) 2017-11-13 16:25:52 -07:00
Douglas Duckworth
c7d2b4dbd6 relion 2.1 - update variant defaults (#6201)
Default precision should be double for CPU. Generally users also want
to use GPUs so the +cuda variant is now also enabled by default.
2017-11-13 12:29:43 -08:00
Massimiliano Culpo
2d6cccdc53 Added an issue template for Github (#6205)
The MD file has been added in the root folder, as CONTRIBUTING.md
2017-11-13 10:51:53 -07:00
Christoph Junghans
bde727e187
mpibash: move to autotools (#6253) 2017-11-13 10:48:31 -07:00
Christoph Junghans
02335fa849
ucx: initial commit (#6265) 2017-11-13 10:47:58 -07:00
Eric
306aca812d ont-albacore: add version 2.1.2 (#6278) 2017-11-13 10:47:40 -07:00
Todd Gamblin
9c93c4a42b
Update tutorial slide links. (#6276) 2017-11-13 07:52:43 -07:00
Todd Gamblin
fffcd77662
Allow types and 'any' in variant definitions. (#4524)
- Previously variant values had to be a tuple or a callable predicate.

- This allows 'any' as shorthand for `lambda x: True` and type objects
  as shorthand for "any value of this type".

- Makes variant definitions more readable, keeps lambdas out of
  packages for common cases.
2017-11-13 00:22:59 -07:00
becker33
9b80f2fd38 basics tutorial: output updated (#6267)
* basics tutorial: output updated through gcc

* finished update for basics tutorial

* missed two lines

* doc error fix
2017-11-13 00:12:23 -07:00
Todd Gamblin
24d636eb30
Updates to build systems tutorial (#6273)
* Get rid of period in command

* formatting

* fix header

* Change GNU Make to Make

* Add variants
2017-11-13 00:11:55 -07:00
Mario Melara
2f1cbb5caa Add build systems tutorial for SC17 (#6125)
* First draft for SC17 build systems portion

Added tutorial_buildsystems.rst file as well as example files under
the tutorial/ directory.

* Remove floating `

* Add requested changes, and examples of subclasses

Added in the requested changes to the documentation. Also added in
information about the subclasses and the defaults that they provide.
Also fixed some phrasing issues, formatting and punctuation.

* Flake8 fixes and new files for classes

Made flake8 fixes to pass tests and also added files to demonstrate code
in the classes.

* Minor edits

Edits in formatting and made some sentence changes

* Flake8 fixes

More flake8 fixes

* Flake8 fix

* Change section order on tutorial and minor edits

Placed the section at the appropriate section for the tutorial and then
added some minor edits that were requested.

* Add requested changes and more details

Added more details to Cmake, Makefile and Python Packages.

* Fixed formatting and minor edits

* Fix doc build error
2017-11-12 23:24:18 -07:00
Adam J. Stewart
9db7eaade8 Last minute edits to the Configuration Tutorial (#6271) 2017-11-12 23:14:44 -07:00
becker33
b77acd0896 Add configuration tutorial for SC17 (#6141) 2017-11-12 20:12:57 -07:00
Matthew LeGendre
265c30b943 Update packaging tutorial (#6270)
* Allow types and 'any' in variant definitions.

- Previously variant values had to be a tuple or a callable predicate.

- This allows 'any' as shorthand for `lambda x: True` and type objects
  as shorthand for "any value of this type".

- Makes variant definitions more readable, keeps lambdas out of
  packages for common cases.

* Update packaging tutorial

* Fix bad file reference in packaging tutorial
2017-11-12 20:09:12 -07:00
becker33
b09341d861 binary packages: do post install hooks (#6269) 2017-11-12 17:57:10 -07:00
Massimiliano Culpo
1ab703448d SC17: advanced packaging tutorial (#6148)
* First draft of the advanced packaging tutorial

* advanced packaging tutorial: improved phrasing

Thanks Denis and Hartzell!

* Fixed typos + reworded a couple of sentences
2017-11-12 00:27:57 -08:00
Massimiliano Culpo
fe889124eb SC17: reworked module file tutorial section (#5657)
* Reworked module file tutorial section

First draft for the SC17 update. This includes:

 - adding an introduction on module files + Spack's module
   generation blueprints
 - adding a set-up section and provide a docker image for easy set-up
 - updating all the relevant snippets
 - extending a bit some of the concepts that were already touched

* Added reference to #5582 + committed Dockerfiles

Also fixed a couple of typos spotted by Denis.

* module file tutorial: added section on template customization

* module file tutorial: fixed minor typos + rephrased a sentence

* module file tutorial: made explicit that Docker image comes with software

* module file tutorial: improved phrasing and layout.

Thanks Hartzell!

* module file tutorial: added vim and nano to editors

* module file tutorial: fixed typo

* Fixed typos

Thanks Adam!

* module file tutorial: updated Dockerfile + minor changes in introduction
2017-11-12 00:27:20 -08:00
becker33
1008975bc0 Don't include build-only dependencies in build cache hash (#6262) 2017-11-11 20:54:17 -08:00
Satish Balay
6fd92e4257 petsc: update to version 3.8.2 (#6244)
Includes pkgconfig fix [for mfem static build failure]
2017-11-11 07:16:03 -07:00