Commit graph

8278 commits

Author SHA1 Message Date
Mark C. Miller
27e6e8715e Adding initial AMReX package (#4467)
* adding initial amrex package

* adding missing fortran variant predicate

* adjusting description text

* adjusting as per @tgamlin guidance
2017-06-15 12:27:52 +02:00
Stas Sergienko
336e3e6a89 Added py-pywavelets package (#4496)
* Added py-pywt  package

* passes flake8 test

* renamed py-pywt to py-pywavelets
2017-06-15 11:51:52 +02:00
Todd Gamblin
8c2447272e Fix dashes in variant parsing (#4498)
- Skip spack flake8 test when flake8 is not installed.
- Fix parsing of dashes in specs broken by new help parser.
    - use argparse.REMAINDER instead of narg='?'
    - don't interpret parts of specs like -mpi as arguments.
2017-06-15 11:32:55 +02:00
Jon Rood
6762714302 Nalu requires Trilinos with Exodus support (#4505)
* Disabling Exodus in Trilinos by default.

* Returning default of Exodus to true in Trilinos.
2017-06-15 11:31:03 +02:00
Adam J. Stewart
e627447417 Prefer vim to vi for default editor (#4230)
* vim > vi
* Allow which to accept multiple args
* Update __init__ to use which with multiple args
* Fix doc tests
2017-06-15 11:27:18 +02:00
Adam J. Stewart
ce11e78530 Add h5utils package (#4506) 2017-06-14 15:41:42 -05:00
Alicia Klinvex
f732598f51 Fix tpetra-related xsdk errors (#4501)
* Fix tpetra-related xsdk errors

Recent changes to the trilinos package broke the xsdk build.
xSDK explicitly disables tpetra, but packages depending on it
(such as ifpack2 and amesos2) are explicitly enabled by default
in the trilinos package.  This commit explicitly disables them
within the xsdk package.py.

* Disabled exodus in the xsdk build

See issue #4502 for details
2017-06-14 13:56:24 -05:00
Luigi Calori
daa5cf7e73 fix intltool_sbang issue #4191 (#4192)
* fix intltool_sbang issue #4191

* add per dep even if already depending on perl-xml-parser

* adding more comment, properly spaced
2017-06-14 13:24:01 -05:00
Michael Kuhn
1ec3c14d23 Improve qt (#4309)
- Introduce an opengl variant that is enabled by default. Disabling it
  allows building qt for X forwarding etc.
- Depend on fontconfig and freetype to make use of system fonts.
  Otherwise qt can not find any fonts.
- libx11 is required when libxcb is used.
- Set MAKEFLAGS to parallelize qmake compilation.
2017-06-14 13:13:39 -05:00
Nicolas Richart
f06c23ef42 Adding package namd (#4321)
* Initial version of the namd package

* Modified charm to consider compile against intel/intel-mpi

* Correction of namd to compile with intel-mkl and intel compiler

* Adding inclue64 in the prefix

* adding property for the build directory

* removing useless function build
2017-06-14 13:11:30 -05:00
Josh Asplund
bc2c4a14c2 Updates rose definition (#4411)
* Adds z3 package

* Adds binwalk package

* Updates spot package definition

* Updates rose package definition

* Modifications for code review

* Fixes string formatting

* Remove python version requirement
2017-06-14 12:43:50 -05:00
Adam J. Stewart
f4f2f25838 Added new package for py-rsa (#4494) 2017-06-14 10:35:10 -05:00
serbanmaerean
0e5fb26dc1 superlu-dist: don't use '_' symbols from BLAS for IBM XL compiler (#4486) 2017-06-14 00:10:51 -07:00
Geoffrey Oxberry
3025f9d303 ipopt 3.12.7 (#4490)
* ipopt: update version to 3.12.7
* ipopt: add +coinhsl option
* ipopt: add +metis option
2017-06-13 18:09:12 -07:00
Geoffrey Oxberry
6af44e63ad coinhsl 2014.01.17: new package (#4482) 2017-06-13 18:03:49 -07:00
Geoffrey Oxberry
56f7c85c93 metis: bugfix: make shared library build portable (#4489)
Fixes #4488. When compiling metis as a shared library, the package
used the syntax `-rpath=`, followed by a path. This syntax is
non-portable, so replace it using Spack's compiler rpath argument
property.
2017-06-13 17:59:25 -07:00
John Roberts
b802524517 visit: Added VisIt version 2.12.2 (#4495) 2017-06-13 18:17:51 -05:00
scheibelp
1e69d9d1a9 Override partial installs by default - part three (#4331)
* During install, remove prior unfinished installs

If a user performs an installation which fails, in some cases the
install prefix is still present, and the stage path may also be
present. With this commit, unless the user specifies
'--keep-prefix', installs are guaranteed to begin with a clean
slate. The database is used to decide whether an install finished,
since a database record is not added until the end of the install
process.

* test updates

* repair_partial uses keep_prefix and keep_stage

* use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not)

* add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
2017-06-13 09:15:51 -07:00
Massimiliano Culpo
9defe2c1c2 espresso: fixed compilation for 6.1 (elpa) and added support for hdf5 (#4483)
* espresso: fixed compilation for 6.1 (elpa) and added support for hdf5

* espresso: addressed items in @davydden review

* espresso: fixed behavior for espresso@:5.4.0
2017-06-13 10:22:12 -05:00
serbanmaerean
df6d8d913b Fix/mumps (#4453)
* Added magma package

* Incorporated Serban's change

* mumps: Fix compiler error with IBM XL

Split the patching between v 5.0.2 and 5.1.1
2017-06-13 08:09:59 -05:00
Michael Kuhn
181fd95057 Fix building shared libraries for gmp (#4464)
If specific compiler flags are set, gmp will not build a shared library,
causing failures further down the line.
2017-06-13 08:06:44 -05:00
Diana Bite
d450e4a93b czmq: Fix invocation when building with clang. (#4479)
Also bump to latest stable version.
2017-06-13 07:43:54 -05:00
Adam J. Stewart
14aa3b63e3 Add list_url for packages from http://ab-initio.mit.edu/ (#4471) 2017-06-12 09:48:20 -05:00
Adam J. Stewart
0de653ff01 Add an installcheck phase to MakefilePackage (#4476)
* Add an installcheck phase to MakefilePackage

* Minor changes to ESMF
2017-06-12 09:47:46 -05:00
Axel Huebl
ab9155eb37 ISAAC Server: Less Strict Deps (#4481)
The dependencies of the server packages were overly strict and pulled in too many dependencies.
This fixes it.
2017-06-12 16:01:17 +02:00
Robert Pavel
f127c4ed27 New Package: bml (#4213)
* New Package: lanl-bml

Added LANL's BML library as Spack Package as dependency for future
packages

* Adjusted lanl-bml versions

Specified current master as develop and added v1.1.0 tagged version

* Renamed lanlbml package to bml
2017-06-11 17:21:51 -05:00
Adam J. Stewart
4db107353e Convert elk to MakefilePackage (#4477) 2017-06-11 18:47:40 +02:00
Milton Woods
a5c6f0412b gcc: use isl@0.14 for gcc@5 (#4474) 2017-06-10 08:16:10 -05:00
Todd Gamblin
c67f647785 Move description to top of spack info (#4475) 2017-06-09 21:02:16 -07:00
Adam J. Stewart
36b8ea2f92 Add default list_url for GitLab, BitBucket, and CRAN (#4439)
* Add default list_url for GitLab, BitBucket, and CRAN

* Fix flake and doc tests
2017-06-09 12:28:39 -05:00
Adam J. Stewart
218992862c Move gpg section of docs to Getting Started (#4446) 2017-06-09 12:27:29 -05:00
Massimiliano Culpo
a3b12a60d1 scala + spark: added legacy versions (#82) (#4461) 2017-06-09 07:15:54 -05:00
Michael Kuhn
23a95de2bd Fix autotools issues (#4463)
Add ACLOCAL_PATH to libtool and pkg-config. Without this, aclocal can
not find the .m4 files.
2017-06-09 07:12:27 -05:00
Denis Davydov
5c5fd4a7e3 add teuchos to Trilinos, update dealii to explicitly require certain packages (#4460) 2017-06-09 07:10:54 -05:00
Adam J. Stewart
85fd8f0b31 Fix url parse offset for SourceForge downloads (#4458) 2017-06-09 08:53:40 +02:00
George Hartzell
a6bbbd4458 Package for mono (#4435)
* First draft package for mono

Mono's vendor'ed boringssl interacts badly with openssl, so
you need to use `cmake~openssl`.

Left to its own devices, it wants to refer to things in
`/usr/share/.mono`.  This doesn't work for installs that don't run as
root, etc...  This package includes a variant to redirect those paths
to `prefix.share`.

* Whitespace/Flake8
2017-06-08 17:55:45 -05:00
Jon Rood
3508909f06 Adding Nalu package. (#4428)
* Adding Nalu package.

* Fixing flake8 stuff.

* Fixing flake8 stuff.

* Reorganizing trilinos package file a little to make it less verbose.

* Reorganizing trilinos package file for more general use as well as use as a dependency of the Nalu package. Setting fpic as default for yaml-cpp and superlu.

* Explicitly stating fpic variants in dependent packages.

* Updating nalu and trilinos package files with suggested changes.

* Fixing formatting issues. Making suggested changes.

* Fixing formatting.

* Reducing amount of explicit variants in Nalu. Adding suggested changes to Trilinos package file.

* Making suggested changes to Nalu package.

* Turning off superlu-dist variant.

* Cleaning up yaml-cpp file.

* Fixing pnetcdf requirements in trilinos.
2017-06-08 17:54:26 -05:00
Gregory Lee
816f4f8b04 fix mfem build for ppc with gcc (#4452) 2017-06-08 10:23:30 -05:00
Howard Pritchard
4e92811939 Open MPI: add 2.0.3 (#4450)
Add Open MPI bug fix release 2.0.3

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-06-07 14:42:49 -05:00
Massimiliano Culpo
69bd119d64 folly: added new package. Also modified double-conversion to use 'pic'. (#4449) 2017-06-07 14:42:15 -05:00
Adam J. Stewart
1b9af88572 Supress output from gpg --version during tests (#4441) 2017-06-07 11:52:28 -05:00
Adam J. Stewart
0bbafb1673 Fix tab completion of Spack subcommands (#4442) 2017-06-07 11:52:07 -05:00
George Hartzell
29090a527a Bug/cctools syscall (#4440)
* Handle missing defn of __NR_memfd_create

Generally SYS_foo is defined to __NR_foo (in sys/syscall.h) which is
then defined to a syscall number (in asm/unistd_64.h).  Certain CentOS
systems have SYS_memfd_create defined to __NR_memfd_create but are
missing the second definition.  This is a belt and suspenders solution
to the problem.

See [this post][syscall] for a nice general description of how these
parts fit together.

[syscall]: https://www.uninformativ.de/blog/postings/2017-02-11/0/POSTING-en.html

* Avoid flake8 warning
2017-06-07 11:51:46 -05:00
Stas Sergienko
8018f6cdf6 Fixed duplicated spec: nag@6.1 line in getting started guide (#4445) 2017-06-07 11:50:56 -05:00
Stas Sergienko
af85014978 Added latest version of image-magick 7.0.5-9 (#4447) 2017-06-07 11:49:39 -05:00
Diana Bite
06e7708728 postgresql: Fix build with threadsafe and add variant. (#4403)
* postgresql: Fix build with threadsafe and add variant.

* postgresql: Convert Package to AutotoolsPackage.

Also add explicit enable flag for +threadsafe variant.
2017-06-07 18:20:17 +02:00
Michael Kuhn
f7b8b75c12 Fix intel-mpi installation (#4438) 2017-06-06 11:24:33 -05:00
George Hartzell
aa51e766cd Add add'l output formats for graphviz (#4431)
* Add add'l output formats for graphviz

Add support for additional output formats to graphviz, including gif,
jpg, pdf, and png.

Graphviz calls its pango+cairo option *pangocairo* so I followed suit.

Libgd was missing jpeg/jpg support.  None of the other supported
formats are conditionalized and there is no --with/--without support,
so I followed suit.

* Fix ghostscript plugin

When I installed thusly:

    spack install graphviz+pangocairo+libgd^cairo+X^pango+X

the ghostscript plugin tripped over some variable names that had
changes in `gs@9.18:`.  This fixes them.

* Remove wayward import of tty
2017-06-06 06:06:36 -05:00
Milton Woods
54cc8dd7fd ncl: cairo and math libraries (#4434)
* ncl: depends on cairo+X (cairo~X is built by default)

* ncl: '-lm' is needed when linking fortran with gcc
2017-06-06 06:05:10 -05:00
Michael Kuhn
08a054afd8 Update bazel to 0.4.5 (#4436) 2017-06-06 05:59:25 -05:00