Commit graph

9520 commits

Author SHA1 Message Date
Christoph Junghans
8bc3f7d726 Add ccache support (#3761)
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available
ccache executable when compiling c/c++ code. This feature is disabled by default
(i.e. "ccache: false") and the documentation is updated with how to enable
ccache support
2018-07-09 14:06:10 -07:00
Sergey Kosukhin
8770957b7a Make 'netlib-lapack' a CMakePackage. (#8661)
* Make 'netlib-lapack' a CMakePackage.

* Add a comment.

* Some refactoring.
2018-07-09 13:21:55 -05:00
Levi Baber
25c9a5216f express: bamtools lib handling (#8552)
* express: bamtools lib handling

* express: use libs property

* express: remove old comment
2018-07-09 13:21:38 -05:00
Andrey Prokopenko
de4b6e6100 trilinos: update dtk dependencies (#8660) 2018-07-08 15:45:21 -05:00
Andreas Baumbach
21a46fb2ce fix typo in help of spack clone prefix is singular (#8658)
Change-Id: I3bfe5b4ba497fae57d5382502ea9a1b054688fdb
2018-07-08 20:28:46 +02:00
Miles Perry
53c0c5701c blasr: new package (#8367)
* blasr: new package

* blasr: changed version release, created list with 9 things, seperated make into build phase.

* blasr: fixed build phase by adding :

* blasr: fixed syntax for configure_args

* blasr: flake8 edits

* blasr-libcpp: fixed configure_args syntax

* blasr: fixed install issues resulting from PacBio changes

* blasr: removed accidental blasr-libcpp upload

* blasr: removed accidental blasr-libcpp upload

* blasr: removed blasr-libcpp

* blasr: edited out comment
2018-07-07 10:05:57 -05:00
Elsa Gonsiorowski, PhD
c907937ff4 ECP VELOC (#8581)
* kvtree package file

* MPI is default on

* proper mpi compiler

* rankstr package

* better rankstr description

* typo

* redset package

* shuffile package

* er package

* axl package

* proper pythor

* mpi is default on

* alpha releases and master versions

* veloc package with boost headers dep

* cmake version

* added C++11 requirement

* flake8

* flake8

* ecp tag

* axl: better async api option handling

* veloc package description

* prettier args list

* C++11 flag handler

* v1.0 of veloc
2018-07-07 09:56:56 -05:00
estebanpauli
891aa6ad7a Added support for uncrustify 0.67. (#8655)
* Added support for uncrustify 0.67.

Since the build system changed for uncrustify at version 0.64,
I had to change the package from an AutotoolsPackage to a plain
Package and use @when annotations to build the packages differently.

* Removed blank line at end of file

* Added support for python2.6 in uncrustify configuration.
2018-07-06 19:59:34 -05:00
George Hartzell
64d5847f05 Fix security issue in singularity + misc cleanups (#8657)
- Versions before 2.5.2 suffer from a serious security problem
  (https://nvd.nist.gov/vuln/detail/CVE-2018-12021).  Deleted all
  versions prior to v2.5.2.
- Update homepage (looks like singularity's going Freemium).
- Use release tarball instead of automagically generated archive
  tarball (digest values are more stable).
- No longer need autotools for released versions, just @devel.
- Install needs to be single-threaded, otherwise when installed as
  root the various 'chmod' operations race against the copies.
2018-07-06 19:59:17 -05:00
George Hartzell
71076bc9c5 Fix digests for git@2.17.0 and git@2.17.1 (#8652)
The entries for git@2.17.1 and git@2.17.0 were swapped.

This fixes them.
2018-07-06 14:57:45 -05:00
George Hartzell
48c0ce2b04 Update nettle package with info for v3.4 (#8653) 2018-07-06 14:57:32 -05:00
George Hartzell
7f814971a5 Clear up a bit of modules/dotkit confusion (#8650)
`use` is an overloaded word between dotkit, modules and spack.  Add additional words to make the distinction clear in the docs.
2018-07-06 12:06:53 -05:00
Adam J. Stewart
cf140b5f4c
Add url_for_version and list_url to Ruby package (#8216) 2018-07-06 07:22:38 -05:00
Mark Olesen
f946a83c8c precice: new package (issue #8643) (#8644)
preCICE (Precise Code Interaction Coupling Environment) is a
  coupling library for partitioned multi-physics simulations.
  Partitioned means that preCICE couples existing programs (solvers)
  capable of simulating a subpart of the complete physics involved in
  a simulation.

of-precice: new package

  preCICE adapter for OpenFOAM
2018-07-06 07:19:30 -05:00
Andreas Baumbach
7098937c03 switch git to kernel.org source and sha256 (#8580)
* switch git to kernel.org source and sha256

Change-Id: I5fe15689adb1163e9ed2b7127b52c95bd0d48564

* fix forgotton md5s

Change-Id: Ib01f21e20678d9aac3344b6ee311134a90b87bdd

* remove old url

Change-Id: I717a084a0357a84b83bc6c8542749aac7e04f68b
2018-07-06 07:16:54 -05:00
Adam J. Stewart
c31ac174c6
Glog: make is a function (#8648) 2018-07-06 07:15:47 -05:00
twang15
4b15391dab cleverleaf: Intel compiler fails compilation without c++11 flag (#8550) (#8598) 2018-07-05 21:54:05 -05:00
Adam J. Stewart
7fa3e7a9aa
Add missing dependencies and variants to wcslib (#8603)
* Add missing dependencies and variants to wcslib

* Add flex version requirement
2018-07-05 21:36:29 -05:00
lingnanyuan
1fa2212543 ncbitoolkit: Create new package. (#8591)
* ncbitoolkit: Create new package.

* Fix Flake8 Error.

* Add version constraints and change format.

* Fix version constraints.
2018-07-05 21:34:38 -05:00
Gregory Lee
f8f3fe5b8f added rpy2 2.9.4 and added py-jinja2 dependency (#8645) 2018-07-05 21:33:32 -05:00
Michael Kuhn
8a1bbc5d84 gcc: Fix build of older versions with recent versions of glibc (#8510) 2018-07-04 07:39:07 -05:00
Matthias Wolf
81668c524b Parquet: new packages (#8601)
* parquet: new package

Includes the following dependencies:

* arrow
* flatbuffers

Changes for compilation:

* snappy
* thrift
* zstd

* parquet: improve recipes (including dependencies)

* arrow: remove unused import in recipe

* parquet: fix line length for flake8/py27

* parquet, arrow: fix py26 format strings

* Address review comments.

* arrow: simplify recipe
2018-07-04 07:24:38 -05:00
becker33
aab5488154 disable openblas intel openmp patch for versions > 0.2.20, fixed upstream (#8638) 2018-07-03 16:25:12 -05:00
健美猞猁
9a60698ef8 Add new versions for log4cplus. (#8621)
* Add new versions for log4cplus.

* Update log4cplus versions.

* Add urls.

* Add url_for_version.

* Remove url_for_version.
2018-07-03 10:08:22 -05:00
健美猞猁
52a997208c Bump sbt to 1.1.6. (#8634) 2018-07-03 10:03:49 -05:00
Adam J. Stewart
6c24f686ce
Fix base class for py-pyserial (#8633) 2018-07-02 22:47:56 -05:00
Matthias Diener
30a6a17507 Pxz: new package (#8631) 2018-07-02 21:33:44 -05:00
Matthias Diener
c987987ca4 screen: update package (#8630) 2018-07-02 16:03:22 -05:00
Satish Balay
b0f8b7130f petsc: add in latest release 3.9.3. (#8627)
xl related fixes are 3.9.3 so remove xlc-test-3.9.0.diff
2018-07-02 15:48:13 -05:00
Matthias Diener
6f7e012cab byobu: update package (#8628) 2018-07-02 15:17:39 -05:00
健美猞猁
2601fd66f6 Bump gradle to 4.8.1. (#8625) 2018-07-02 12:46:46 -05:00
Jon Rood
f98657491d Add Amrvis package (#8590)
* First draft of amrvis package file.

* More additions to amrvis.

* Formatting.

* Forcing compiler environment variables to point to spack mpi compilers when using mpi.

* Disabling intel compiler for amrvis.

* Comments.

* Refining amrvis package file.

* Moving library and include locations variables to be inserted at the first lines of the makefile.

* Globbing amrvis binary instead of constructing its name.

* Making env variable setting consistent and fixing globbing of executable.

* Using iglob instead of glob.

* Turning MPI on by default for Amrvis.
2018-07-02 11:42:09 -05:00
Mark Olesen
a4ca2bb889 ENH: Building OpenFOAM sub-packages (issue #8579) (#8592)
* ENH: Building OpenFOAM sub-packages (issue #8579)

* Some support for packages building with OpenFOAM

- Adjust the wrappers calling the OpenFOAM Allwmake script. Have them
  look for a Allwmake-spack file first, which is assumed to contain
  special adjustments for compiling with spack.

  This file could be delivered as part of a tarball (which is unlikely)
  or generated on the fly by the spack sub-package as part of its
  patch or configure stage.

CONFIG: change the default paraview variant for openfoam to be False

- the different combinations of paraview backends, off-screen etc
  make it difficult to suggest that building with paraview as
  a standard dependency makes much sense.
  Additionally, building paraview with qt can become quite an issue.
  So it makes much more sense to only enable that upon request.

ENH: add a +vtk variant.

- for VTK with off-screen rendering to be used by the runTimePostProcessing
  function object, which is a fairly simple framework for generating images of
  some OpenFOAM derived objects (eg, sampling planes).

SPACK spec problem:

- reflect the flex restriction impose by the scotch dependency within
  the openfoam spec as well, as partial workaround for buggy or annoying
  spec resolution.

OTHER:

- updated the backstop foamEtcFile file to include args handling
  as per the OpenFOAM-v1806 updates.

* new version: OpenFOAM-v1806

- https://www.openfoam.com/releases/openfoam-v1806/
2018-07-02 10:02:48 -05:00
健美猞猁
bd3f981fbb A new package: xhmm. (#8620)
* A new package: xhmm.

* Flake8.

* Support general BLAS.
2018-07-02 07:54:41 -05:00
Adam J. Stewart
a0c13229e8
Add Python 3.7.0 (#8619) 2018-06-29 16:25:39 -05:00
Stephen Hudson
02b8502212 Update py-libensemble package (#8617) 2018-06-29 14:51:30 -05:00
Christoph Junghans
ec46c7c4a6 numactl: fix build with glibc-2.26 (#8615) 2018-06-29 14:41:52 -05:00
Christoph Junghans
b1d7fd886a latte: version bump (#8611) 2018-06-29 09:19:24 -05:00
Paul Chelarescu
719f324423 Removed duplicate word (#8609) 2018-06-29 07:44:23 -05:00
健美猞猁
13ee2c04e1 r-aer: a new package. (#8567)
* r-aer: a new package.

* Flake8.

* Add list_url and dependency versions.
2018-06-28 15:40:00 -05:00
Ian Lee
e792c148bc Added nmap version 7.70 (#8606) 2018-06-28 15:32:43 -05:00
Adam J. Stewart
8b3bcd189d
Add CFITSIO 3.450 (#8602) 2018-06-28 11:28:22 -05:00
Adam J. Stewart
795e701ae3
Add kealib 1.4.9 (#8597) 2018-06-28 10:51:30 -05:00
David Böhme
51bd319fcf Add Caliper 1.7.0 and Gotcha 1.0.2 (#8572)
* Update Gotcha and Caliper versions

* caliper: Use spack-built gotcha

* caliper: Enable sampling support on Linux

* More robust check for Linux
2018-06-27 17:21:23 -05:00
Mark Olesen
e3f208e4cb New version mesa-18.1.2 (#8589)
- compiles with newer LLVM.

  The older mesa-17 versions balk at the changes in the llvm::FastMath
  class, where a member function has been removed.
2018-06-27 14:57:55 -05:00
Andreas Baumbach
8966a4987d Provide new version of sbt (simple build tool) (#8576) 2018-06-27 10:43:24 -07:00
Andreas Baumbach
b495c43783 Add package tcl-itcl (#8578)
* Add package tcl-itcl

Change-Id: I0eeaefe0554d0b62614f56204d635e3d8d216e4a

* fix naming

Change-Id: Id8adc7299f41b217b48999304a74827525533598

* and fix name of file accordingly

Change-Id: I0f32f8b66f2695fd99eee4a326353cd5af4aa334
2018-06-27 10:05:00 -05:00
Cameron Smith
da011bc7fb pumi: add fortran variant (#8584) 2018-06-27 10:03:46 -05:00
Cameron Smith
cdf9823599 zoltan: depends on metis.h and libmetis (#8583)
the parmetis build system does not install metis.h and libmetis
2018-06-26 23:29:22 -07:00
scheibelp
3560f6dbe9 views: packages can customize how they're added to views (#7152)
Functional updates:

- `python` now creates a copy of the `python` binaries when it is added
  to a view

- Python extensions (packages which subclass `PythonPackage`) rewrite
  their shebang lines to refer to python in the view

- Python packages in the same namespace will not generate conflicts if
  both have `...lib/site-packages/namespace-example/__init__.py`

  - These `__init__` files will also remain when removing any package in
    the namespace until the last package in the namespace is removed


Generally (Updated 2/16):

- Any package can define `add_files_to_view` to customize how it is added
  to a view (and at the moment custom definitions are included for
  `python` and `PythonPackage`)

  - Likewise any package can define `remove_files_from_view` to customize
    which files are removed (e.g. you don't always want to remove the
    namespace `__init__`)

- Any package can define `view_file_conflicts` to customize what it
  considers a merge conflict

- Global activations are handled like views (where the view root is the
  spec prefix of the extendee)

  - Benefit: filesystem-management aspects of activating extensions are
    now placed in views (e.g. now one can hardlink a global activation)

  - Benefit: overriding `Package.activate` is more straightforward (see
    `Python.activate`)

  - Complication: extension packages which have special-purpose logic
    *only* when activated outside of the extendee prefix must check for
    this in their `add_files_to_view` method (see `PythonPackage`)

- `LinkTree` is refactored to have separate methods for copying a
  directory structure and for copying files (since it was found that
  generally packages may want to alter how files are copied but still
  wanted to copy directories in the same way)


TODOs (updated 2/20):

- [x] additional testing (there is some unit testing added at this point
  but more would be useful)

- [x] refactor or reorganize `LinkTree` methods: currently there is a
  separate set of methods for replicating just the directory structure
  without the files, and a set for replicating everything

- [x] Right now external views (i.e. those not used for global
  activations) call `view.add_extension`, but global activations do not
  to avoid some extra work that goes into maintaining external views. I'm
  not sure if addressing that needs to be done here but I'd like to
  clarify it in the comments (UPDATE: for now I have added a TODO and in
  my opinion this can be merged now and the refactor handled later)

- [x] Several method descriptions (e.g. for `Package.activate`) are out
  of date and reference a distinction between global activations and
  views, they need to be updated

- [x] Update aspell package activations
2018-06-26 16:14:05 -07:00