Commit graph

11952 commits

Author SHA1 Message Date
Greg Becker
4ff2773704
ncurses: remove TERMINFO from build env (#12086) 2019-07-23 10:13:41 -05:00
Marco Comparato
7ea4e50587 font-util: add missing autoconf automake dependencies (#12053) 2019-07-23 09:41:04 -05:00
Todd Gamblin
3cb40e1c02 commands: add tests for all subcommands of spack pkg 2019-07-22 23:01:45 -07:00
Todd Gamblin
0b17bccdce commands: add spack pkg changed subcommand, better test support
- Add `spack pkg changed` to show changed and added packages for a
  commit.

- Make `spack pkg` support tests better.
2019-07-22 23:01:45 -07:00
Daniel Topa
07f3921838 Add UCX 1.6.0 (#12089)
https://github.com/openucx/ucx/releases/tag/v1.6.0
Released 2019-07-17

Verification builds on LANL Darwin x86_64 and Power9:

dantopa@cn2037:pr-update-ucx.spack $ date
Mon Jul 22 17:04:14 MDT 2019

dantopa@cn2037:pr-update-ucx.spack $ pwd
/scratch/users/dantopa/repos/spack/pr-update-ucx.spack

dantopa@cn2037:pr-update-ucx.spack $ spack find -ldf ucx

==> 2 installed packages
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
w7fp4n6    ucx@1.6.0%gcc
tt2hkol        ^numactl@2.0.12%gcc
srhy7ry        ^rdma-core@20%gcc
kvgvhpv            ^libnl@3.3.0%gcc

-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
cji3ce7    ucx@1.6.0%gcc
pmgndwh        ^numactl@2.0.12%gcc
qymrwx6        ^rdma-core@20%gcc
2263pm5            ^libnl@3.3.0%gcc

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-07-22 21:43:35 -05:00
Matthias Diener
19968a0035 scons: add version 3.1.0 (#12084) 2019-07-22 17:35:40 -05:00
Chuck Atkins
69c302f455 cmake: Move cxx11 flags for fujitsu into the flag_handler method (#12056)
* cmake: Move cxx11 flags for fujitsu into the flag_handler method

* cmake: sanitization and error checking in flag_handler

* cmake: Fix fujitsu flag check from 'fc' to 'fj'
2019-07-22 17:33:40 -05:00
Denis Davydov
8cef81363c gcc: support without command line tools (#11040) 2019-07-22 16:53:50 -05:00
Adam J. Stewart
2d144316a8 Fix version scraping for CRAN packages (#12021)
* Fix version scraping for CRAN packages
* Remove set literals
2019-07-22 13:05:55 -07:00
Todd Gamblin
cc4094bb9b bugfix: env.write() should stringify Spec lists.
- Setting specs from lockfiles was not correctly stringifying concretized
  user specs.

- Fix `_set_user_specs_from_lockfile`

- Add some validation code to `SpecList` constructor
2019-07-22 13:45:34 -05:00
Peter Josef Scheibel
7ec1d320a8 hashes: consolidate and make hashing logic more consistent
Spack has evolved to have three types of hash functions, and it's
becoming hard to tell when each one is called. Whlie we aren't yet ready
to get rid of them, we can refactor them so that the code is clearer and
easier to track.

- Add a `hash_types` module with concise descriptors for hashes.

- Consolidate hashing logic in a private `Spec._spec_hash()` function.

- `dag_hash()`, `build_hash()`, and `full_hash()` all call `_spec_hash()`

- `to_node_dict()`, `to_dict()`, `to_yaml()` and `to_json()` now take a
  `hash` parameter consistent with the one that `_spec_hash()` requires.

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2019-07-22 13:45:34 -05:00
Peter Josef Scheibel
0715b512a1 env: environments index specs by full DAG w/build deps
- ensure that Spec._build_hash attr is defined
- add logic to compute _build_hash when it is not already computed (e.g. for specs prior to this PR)
- add test to ensure that different instance of a build dep are preserved
- test conversion of old env lockfile format to new format
- tests: avoid view creation, DAG display in tests using MockPackage
- add regression test for more-general bug also fixed by this PR
- update lockfile version since the way we are maintaining hashes has changed
- write out backup for version-1 lockfiles and test that
2019-07-22 13:45:34 -05:00
zschulte
db7127c56d openjdk (#10446)
* openjdk

* Removing preferred from latest and adding a few lines for readability.

* Remove bad whitesapce

* removing formatting changes

* stable url for openjdk 1.8

* remove extra blank line

* actual binary
2019-07-22 13:11:45 -05:00
Toyohisa Kameyama
58c84423b1 tealeaf: Don't add -march=native on ARM and gcc 5.x or before. (#12080) 2019-07-22 13:03:43 -05:00
Hironori-Yamaji
8e92409263 jdk: Add JDK 12.0.2_10 (#12081) 2019-07-22 12:40:11 -05:00
Mark W. Krentel
6111758b48 hpctoolkit: add version gpu and variant cuda (#12068)
Add version for 'gpu' and variant for 'cuda'.  These are currently available from the 'master-gpu' branch.

* hpctoolkit: add version gpu and variant cuda
* The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
2019-07-21 22:29:08 -07:00
Toyohisa Kameyama
8ca90e26d9 libsharp: Don't add -march=native on ARM (#12064)
* libsharp: Don't add -march=native on ARM

* Add preferred=True to version 1.0.0.
2019-07-21 21:56:14 -05:00
Omar Padron
1d5ab13be8 docker: fix builds, remove extra distros, add ci builds (#11621)
* fix docker builds/remove extra builds/add ci builds
* preinstall vim in CI builder images
* simplify & streamline docker resources
* restore os-container-mapping.yaml file
2019-07-20 14:46:06 -07:00
Adam J. Stewart
7d954720ff Add OpenMP flag for Apple Clang (#12049) 2019-07-20 13:40:36 -07:00
Massimiliano Culpo
a2cb26f520 tests: speed up tests that rely on the database fixture (#12031)
The database and mutable_database fixtures were installing and uninstalling the same specs multiple times to ensure the database for tests has the correct state.

This commit optimizes the procedure by caching the state in an external directory, and copying it in instead of going through the installation or uninstallation again.

The database fixture is meant not to be modified by tests. This commit enforces this invariant by making the database read-only before starting the test.

* Added missing db markers to tests
* Added test for uninstall_by_spec
* `database` fixture now returns a read-only database
* Tests that modify the DB now use `mutable_database` fixture
2019-07-20 10:18:50 -07:00
Mark W. Krentel
930011c124 hpcviewer: add version 2019.07 (#12067)
ibm-java: fix the URL to only use a machine type that ibm-java
supports so that 'spack info' doesn't report a non-existent URL on
platforms that it doesn't support.
2019-07-20 10:07:15 -07:00
Greg Becker
67cd524e93 environment views: refactor stripping build deps (#12069) 2019-07-20 09:45:20 -07:00
Greg Becker
8ec098716b compilers: don't raise errors for duplicate compiler definitions (#11910)
Summary:
- Allow multiple definitions of compiler in compilers.yaml (use first instance)
- Still print debug messages when there are duplicates, to assist users in finding this issue.

Merging configs from different scopes can result in multiple compiler being present in the same configuration list.  Instead of raising when there are duplicates, take the one with highest precedence.

Print a debug message instead of raising, so that we can still diagnose this.  We don't have a good way of warning the user about inconsistent configuration *in the same file* -- we'd need to dig into YAML file/line info for that.
2019-07-20 00:42:12 -07:00
Todd Gamblin
993ee7f199 environments: add activate/deactivate tests, work wtih set -u
- [x] Add shell tests to ensure that `spack env activate`, `spack env
  deactivate`, and `despacktivate` continue to work.

- [x] Also ensure that activate and deactivate both work with `set -u`
2019-07-20 00:36:56 -07:00
Greg Becker
4f9131fdc2 Package inheritance: Find patch files defined in parent classes using MRO (#12051)
Fixes #8908, 11844

Use Python MRO to find patch files from parent classes.
2019-07-19 18:08:05 -07:00
Peter Scheibel
4b6de78062
font-util package: add autoconf/automake build deps (#12071)
Fixes #12026

These are required on some systems
2019-07-19 17:45:22 -07:00
albestro
3a026f1412 Fix #11240 (#11995)
* extends mkdirs with permissions for intermediate folders

Does not use os.makedirs mode parameter because its behavior is changed
with Python 3.7 (it ignores it for intermediate dirs), and moreover it
was not possible to set different modes for newly-created folders
and leaf folder.

reference:
- https://bugs.python.org/issue19930
- https://docs.python.org/3.7/library/os.html#os.makedirs

* comment mkdirp step easing code understanding

* revert mkdir to default for package metapath

since metapath is nested in package folder, there is no need
to specify permissions for intermediate folders because the prefix
already exists.

* comment create_install_directory package modes
2019-07-19 10:13:29 -05:00
Michael Kuhn
cadff917c7 leveldb: add 1.22 (#12044) 2019-07-19 09:26:09 -05:00
Chris Green
9b763980b6
libxpm: cope with system gettext if configured. (#10881)
* If gettext is installed in the system it won't be in the spec tree.
2019-07-19 08:36:58 -05:00
Gregory Becker
ba0cd4d912 concretization: fix transient hang in python 3.5
Bug relates to the interplay between:
1. random dict orders in python 3.5
2. bugfix in initial implementation of stacks for `_concretize_dependencies`
   when `self._dependencies` is empty
3. bug in coconcretization algorithm computation of split specs

Result was transient hang in coconcretization.
Fixed #3 (bug in coconcretization) to resolve.
2019-07-18 19:28:50 -07:00
Gregory Becker
ec6e5b0fd3 stacks: add option to link only roots or all specs, default to all 2019-07-18 19:28:50 -07:00
Gregory Becker
7ec89aa036 stacks: refactor view descriptors into a separate object 2019-07-18 19:28:50 -07:00
Gregory Becker
6661cb1926 refactor: clean up Environment class
- remove redundant code in Environment.__init__
- use socket.gethostname() instead of which('hostname')
- refactor updating SpecList references
- refactor 'specs' literals to a single variable for default list name
- use six.string_types for python 2/3 compatibility
2019-07-18 19:28:50 -07:00
Gregory Becker
88295d927e bugfix: spec lists can now include multiple references 2019-07-18 19:28:50 -07:00
Gregory Becker
9577ade3ce stacks: use new format string syntax in environments code
- Change old spec expressions to use Spack's new spec formatting sytnax.
2019-07-18 19:28:50 -07:00
Gregory Becker
2f6af64157 docs: Add documentation for views in environments 2019-07-18 19:28:50 -07:00
Gregory Becker
cebf1fd668 stacks: update view management for multiple/combinatorial views
This adds notion of a default view, other views in environments
2019-07-18 19:28:50 -07:00
Gregory Becker
d0bfe0d6a8 stacks: environment add/remove respect multiply-defined lists 2019-07-18 19:28:50 -07:00
Gregory Becker
f9e6de5474 stacks: allow force-removing from a speclist used in a matrix 2019-07-18 19:28:50 -07:00
Gregory Becker
533a8d7c82 stacks: update environment add/remove algorithms 2019-07-18 19:28:50 -07:00
Gregory Becker
6cfbfcc967 concretization: regression test for constrain() with deps
- ensure that `Spec('foo').constrain('foo ^bar')` works
- prior to stacks implementation, this constraint would have done nothing.
2019-07-18 19:28:50 -07:00
Gregory Becker
12c8996294 docs: initial documentation for environments 2019-07-18 19:28:50 -07:00
Gregory Becker
d450a2fce2 stacks: initial implementation of stacks on environments
- stack syntax in env schema
- switch environment specs over to SpecList object
- add stack functionality to environments
- handle definition extensions through stack.yaml and SpecList
- implement conditional definitions
- tests
2019-07-18 19:28:50 -07:00
Matthias Diener
5be1ff83d1 cmake: add version 3.15.0 (#12058) 2019-07-18 18:28:21 -05:00
Adam J. Stewart
032075af74
Add master version to sklearn (#12057) 2019-07-18 15:56:48 -05:00
Matthieu Dorier
6eba9febaa pkg PRRTE: added version 1.0.0 (#12054) 2019-07-18 13:59:39 -05:00
Matthieu Dorier
3120e06359 added version 3.1.3 of PMIx (#12055) 2019-07-18 13:59:02 -05:00
Adam J. Stewart
c96d687c7c
Workaround for #9149 (#12050) 2019-07-18 13:57:37 -05:00
Justin S
620d728aa5 py-mlxtend: new package at 0.16.0 (#12039)
* py-mlxtend: new package at 0.16.0

* py-mlxtend: fix dependencies
2019-07-18 12:25:41 -05:00
Phil Carns
7428fc66f7 update web site and git url for BMI package (#12036) 2019-07-17 21:28:39 -05:00