Commit graph

10429 commits

Author SHA1 Message Date
Stephen Herbein
cdbc545793 docs: update spack view argument synatx (#8839)
The `--dependencies` and `--exclude` flags are now arguments to the `spack view`
comand rather than the `spack view symlink` command.
2018-07-31 10:41:41 -07:00
Geoffrey Oxberry
f7761d1081 slepc: add blopex variant (#8820) 2018-07-30 18:18:36 -05:00
Jon Rood
15d96f0166 Add extra_rpaths to OpenMPI wrappers (#8687)
If the OpenMPI build finds the infiniband drivers in /usr/lib64, it adds
-Wl,-rpath -Wl,/usr/lib64 to the OpenMPI wrappers. If the wrappers are using
a compiler outside of /usr, and the OpenMPI wrappers are used to build software
outside of Spack, they will rpath /usr/lib64 into the executable which then has
GLIBC, GLIBCXX runtime errors due to it picking up GCC libraries in /usr/lib64.

This adds the directories specified in "extra_rpaths" to the OpenMPI wrappers,
which allows them to use the correct compiler when invoked outside of Spack
builds.
2018-07-30 15:02:09 -04:00
Kelly (KT) Thompson
13cf6d55e4 GSL: 2.5 is a new version. (#8827) 2018-07-30 08:38:37 +02:00
Todd Gamblin
2c45c3c5b3
spec: Spec.tree() merges deptypes when only covering nodes (#8821)
- previously, output could be confusing when deptypes were only shown for
  one dependent when a node had *multiple* dependents

- also fix default coverage of `Spec.tree()`: it previously defaulted to
  cover only build and link dependencies, but this is a holdover from
  when those were the only types.
2018-07-29 11:54:20 -07:00
Geoffrey Oxberry
dba7f715cf libunwind: document platform=darwin conflict (#8824) 2018-07-29 08:44:17 -07:00
Miroslav Stoyanov
71f85cff2c added Tasmanian versions 5.1 and development, enabled the Tasmanian options through +~ flags (#8804) 2018-07-27 10:10:32 -05:00
健美猞猁
440a5fbfcb Skip update check. (#8683)
* Skip update check.

* mkefile -> makefile.

* Fix emboss.
2018-07-27 09:57:05 -05:00
Massimiliano Culpo
1fd9574353 Fixed a typo in the docs (the docker image to pull was wrong) (#8814) 2018-07-27 09:56:01 -05:00
Michael Kuhn
d02c4bbd9a gcc: Add 8.2.0 (#8813) 2018-07-27 08:14:49 -05:00
Michael Kuhn
53ddefa0df Fix shift warning on zsh (#8805)
When using zsh, trying to shift when there are no arguments left results
in warnings like this: spack:shift:22: shift count must be <= $#
2018-07-27 08:14:01 -05:00
Oliver Breitwieser
90f7fca194 py-numpy: Add CPATH in modulefile (#8466)
Also fix setup_dependent_package to include the ".egg-less"-include
path.

Change-Id: I06e66a505ece25cba8896f47e69a5be374bac6d2
2018-07-26 17:50:00 -05:00
Neil Flood
3494c6e403 Updated llvm to version 6.0.1. The previous 6.0.0 had an incorrectly … (#8801)
* Updated llvm to version 6.0.1. The previous 6.0.0 had an incorrectly declared symbol, discussed at https://reviews.llvm.org/D44140, which, amongst other things, broke py-numba. This version works fine with py-numba.

* Flag the conflict between py-numba and llvm@6.0.0

* Removed a single trailing space to satisfy checks
2018-07-26 17:47:18 -05:00
Sheng Di
bf2c232756 sz: new version 2.0.2.0 (#8786) 2018-07-26 17:46:48 -05:00
Michael Kuhn
3d86c7fef5 hdf5: Fix build with %gcc@8 (#8788) 2018-07-26 15:58:00 -05:00
lingnanyuan
d25866a8f8 halc: Create new package. (#8795)
* halc: Create new package.

* fix flake8 error.

* Modification
2018-07-26 15:55:43 -05:00
Hadrien G
c03dcdedb1 FTGL package workarounds (#8812)
* FTGL package workarounds

* Remove blank line

* Only require doxygen at build time
2018-07-26 15:54:46 -05:00
mic84
61aa1831e3 AMReX: update package.py (#8697) 2018-07-26 13:29:03 -05:00
Hadrien G
8b718e7cd6 Templight package (#8782)
* First draft of a templight recipe

* Let's be explicit for now, we can be clever later on

* The clang6 version does not work, drop it

* Reorder FIXMEs more logically

* Add patch for current templight develop branch

* Create an artificial stable release of templight

* Take some additional inspiration from llvm package

* Added the templight supporting tools

* Remove old notes from the no-url branch

* Avoid unnecessary join_path
2018-07-26 11:19:14 -05:00
Simon Flood
80741bc427 hmmer: added version 3.2.1 & updated URL (#8787)
Add HMMER 3.2.1 and updated URL then removed url_for_version function as no longer required - all HMMER downloads available from updated URL.
2018-07-26 10:07:55 -05:00
Michael Kuhn
643a4fbb59 papi: Update to 5.6.0 and fix build with %gcc@8 (#8796) 2018-07-26 10:02:07 -05:00
Mario Melara
cb410b3003 Add package DMTCP (#8808) 2018-07-26 09:47:55 -05:00
Satish Balay
d5957f147b mfem: mfem-3.3-3.4-petsc-3.9.patch is not needed for latest develop version (#8809) 2018-07-26 09:47:28 -05:00
Todd Gamblin
ab1cd6577c readme: add our @spackpm Twitter handle (#8810) 2018-07-26 09:45:32 -05:00
Mark W. Krentel
af60f962cd intel-tbb: Add tm variant to disable transactional memory. (#8799)
* intel-tbb: Add variant `tm` to disable transactional memory.

Some AMD or very old Intel systems don't support transactional memory. This commit adds a variant `tm` that defaults to `True`, but can be switched off to allow running on those systems.
2018-07-25 23:14:17 -07:00
Adam J. Stewart
7902f3eb49 Add docs on new top-level VCS attributes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
5d07042f23 Unit test fixes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
68c2bdfaf6 Further improvements to version parsing 2018-07-25 23:10:10 -07:00
Adam J. Stewart
e948a54d8e All git URLs end in .git 2018-07-25 23:10:10 -07:00
Adam J. Stewart
31417bf66c Replace git=git with explicit branch names 2018-07-25 23:10:10 -07:00
Adam J. Stewart
3f18c04865 Add top-level attributes for git R-Z packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
a1572bb999 Add top-level attributes for git R (Bioconductor) packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
908d2dcd4d Add top-level attributes for git M-P packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
4c6aca533a Add top-level attributes for hg, svn, and git A-L packages 2018-07-25 23:10:10 -07:00
Todd Gamblin
5f00056490 tests: convert mirror test to pytest with free functions. 2018-07-25 23:10:10 -07:00
Todd Gamblin
020c34e136 tests: add checks and tests for consistent version() arguments
- Previously, Spack didn't check the arguments you put in version()
  directives.

- So, you could do something like this, where there are arguments for a
  URL fetcher AND for a git fetcher:

  version('1.0', md5='abc123', git='https://foo.bar', commit='feda2343')

- Now, we check the arguments before constructing a fetcher, to ensure
  that each package has *only* arguments for a single type of fetcher.

- Also added `test_package_version_consistency()` to the `package_sanity`
  test, so that all builtin packages are required to have valid
  `version()` directives.
2018-07-25 23:10:10 -07:00
Todd Gamblin
6f7eaecfa0 tests: correct name of check_db to check_repo
- this test is checking the package *repository*, not the database.
2018-07-25 23:10:10 -07:00
Todd Gamblin
773cfe088f core: differentiate package-level fetch URLs by args to version()
- packagers can specify two top-level fetch URLs if one is `url`
  - e.g., `url` and `git` or `url` and `svn`

- allow only one VCS fetcher so we can differentiate between URL and VCS.

- also clean up fetcher logic and class structure
2018-07-25 23:10:10 -07:00
Todd Gamblin
04aec9d6f8 core: add check for conflicting top-level fetch attributes in packages
- ensure that packages can't have more than one of git, hg, svn, or url
2018-07-25 23:10:10 -07:00
Todd Gamblin
6837da2ad7 style: clean up exception definitions in package.py 2018-07-25 23:10:10 -07:00
Todd Gamblin
498d8cf04b core: fixes and tests for handling of fetcher attributes in packages
- Packages can remove the top-level `url` attribute and still work

- These are now legal:
  - Packages with *only* version-specific URLs (even with gaps)

  - Packages with a top-level git/hg/svn attribute and `version`
    directives for that.

- If a package has both a top-level hg/git/svn attribute AND a top-level
  url attribute, the url attribute takes precedence.
2018-07-25 23:10:10 -07:00
Adam J. Stewart
5792a805fc core: quick fix for packages without URLs
Some packages do not have a `url` and are instead downloaded via `git`,
`hg`, or `svn`. Some packages like `spectrum-mpi` cannot be downloaded at
all, and are placeholder packages for system installations. Previously,
`__init__()` in `PackageBase` crashed if a package did not have a `url`
attribute defined.

I hacked this section of code out, but I have no idea what the
repercussions of that are.
2018-07-25 23:10:10 -07:00
Satish Balay
f59666587b hypre: 'master' is branch - not a tag 2018-07-25 22:17:37 -07:00
sknigh
b0499cf45e Added latest version of charliecloud (#8792) 2018-07-26 06:54:09 +02:00
Adam J. Stewart
13c52066a5 Fix order of regexes reported by spack url summary 2018-07-24 21:02:28 -07:00
Todd Gamblin
656e935e50 core: make spack.util.crypto initialization less expensive.
- This hard-codes the hash lengths rather than computing them on import.

- Also cleans up the code in `spack.util.crypto` to make it easier to
  understand.
2018-07-24 18:35:02 -07:00
Todd Gamblin
674eb00e53
bugfix: spack module -m error message (#8794)
Fix this output error:

```
$ spack -m module loads mpileaks
==> Error: `spack module loads -m t -m c -m l ...` has been moved. Try this instead:

    $ spack module t loads mpileaks
    $ spack module c loads mpileaks
    $ spack module l loads mpileaks
```
2018-07-24 16:12:47 -07:00
Massimiliano Culpo
5b8b7a5873 The auto-completion file is now consistent with spack module 2018-07-24 11:27:17 -07:00
Massimiliano Culpo
6bb2256043 Die with a meaningful error if a deprecated command is used
In case a deprecated form of the module command is used, the program
will exit non-zero and print an informative error message suggesting
which command should be used instead.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
35cef16974 Grouped all the module commands under spack module
As requested in the review all the commands meant to manage module
files have been grouped under the `spack module` command.

Unit tests have been refactored to match the new command structure.
2018-07-24 11:27:17 -07:00