Commit graph

7643 commits

Author SHA1 Message Date
Adam J. Stewart
d7fb3fd88e
r requires cairo+pdf (#10350) 2019-01-15 09:58:53 -06:00
Owen Solberg
2585c04b50 explicitly depend_on cairo with X **and** pdf variants (#10351) 2019-01-15 09:58:39 -06:00
Elizabeth Fischer
0628ebefd8 Add useful comment explaining why this is not needed for Python3. (#10326) 2019-01-15 07:31:20 -08:00
Axel Huebl
89a493522c openPMD-api: Dependency Update (#10314)
openPMD-api now only supports Python 3, needs a newer CMake and
ADIOS1 and also learned to read & write JSON :-)
2019-01-15 09:28:13 -06:00
Neil Flood
49dedb2443 vigra: new package (#10337)
* vigra: new package

* Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks.

* Take care of lines too long

* Explicit WITH_HDF5=ON
2019-01-14 20:39:34 -06:00
Andrew Gaspar
04d4b07636 Add span-lite version (#10347) 2019-01-14 18:22:29 -06:00
sknigh
a1994d883c Added latest rust releases and develop branch (#10341)
* Added latest rust releases and develop branch

* Fixed spacing
2019-01-14 17:22:38 -06:00
Levi Baber
d1b7e560bd namd: fixing to reflect renamed charmpp per #9216 (#10342) 2019-01-14 17:22:03 -06:00
sknigh
43e6114db7 Added latest version of libfabric (#10343) 2019-01-14 17:21:33 -06:00
Geoffrey Oxberry
baf595351e feature: py-invoke: new python package (#10225) 2019-01-14 17:13:17 -06:00
George Hartzell
7abc2fb26d bugfix/gdk-pixbuf (#10312)
* docbook processing works correctly for gdk-pixbuf

1. The various bits of documentation in gdk-pixbuf include hardcoded
   references to dtd's and stuff at their canonical, Internet,
   locations.  BUT, gdk-pixbuf runs xslt-proc with the `--nonet`
   option, which forbids it from using the network.  Sadness ensues.

   Traditionally folks use XML Catalogs to map these to local copies.
   Our docbook-xsl package wasn't setting the appropriate env var in
   its dependents environments to use our catalog.

   Now it does.  Less sadness ensues.

2. If we're going to use these things, we should depend on them.

* Add gdk-pixbuf's bin to build environment

The "post-install.sh" script uses gdk-pixbuf-query-loaders, which was
installed earlier.

If py-psyclone can set its own bin on its PATH, so can we...

* Make gdk-pixbuf use recognizable docbook location

Our docbook-xsl package assumes that the canonical location is
`http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl`, but
the gdk-pixbuf's meson build script uses
`http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl`.

This means that our XML Catalog doesn't fix the reference and sadness
happens.

Just patch the build that we see what we want to see, then we can make
it all go away.

* Add commentary re docbook patch

* Make catalog helper a property

Thanks @adamjstewart!

* Run tests if/when run_tests is true

Thanks @adamjstewart!

* Tune up dependencies

Thanks @adamjstewart!

* Wordsmit commentary
2019-01-13 14:40:20 -06:00
Cyrus Harrison
9350db5665 update alpine ascent and friends (#10320)
This adds a lot of fixes and updates for alpine ascent and its dependencies:

* add support for static (via ~shared) and use vtk-m 1.2
* update vtkh package to output cmake configure file and pinning it to vtkm 1.2
* make conduit respect ~python
* fix ascent python logic
* consistant cmake usage
* conditionally add tbb in ascent if vtkh
* enable openmp
* more robust handling of variants
* update ascent and conduit for static builds
* add optional support for mfem in ascent
* enable mfem conduit support for ascent
* add optional adios dep to conduit
* remove ver req from conduit
* ascent: remove confusing comment
* tweaks to conduit and ascent pkg recipes
* fix typo in conduit package
* pref conduit master
* changing mfem to depend on conduit@master to get updated relay
* restore use of conduit 0.3.1 or greater for mfem
* set master as preferred conduit version
* allow mfem to use conduit master
* adding rover package and editing ascent
* updating vtkm cmake dep
* guard ascent python support on +shared
* removing rover to simply ascent package
* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified
* fix fortran compiler check so it can work on cray systems
* working towards cuda fix for vtkm lagrange filter
* update ascent package with more variants, and patch to avoid nvcc issue
* hdf5 flags fix for BGQ
* add post install test
* add testing to ascent
* add testing of the using-with-make example
* add ctest output on error for run_tests
2019-01-12 17:43:39 -08:00
Jiawei Zhuang
07d9d444ea Added osu-micro-benchmarks@5.5 (#10333) 2019-01-12 17:31:13 -08:00
George Hartzell
6c638600d7 Add libxslt v1.1.33 info (#10328) 2019-01-12 17:36:53 -06:00
Denis Davydov
09033e991e dealii: does not support sundials 4.x (#10324) 2019-01-12 15:28:57 -06:00
Neil Flood
04c1af0ee2 gdal: Add variant for GRIB driver (#10322) 2019-01-12 10:33:18 -06:00
Dan Ibanez
f9967d2f6f Omega_h changed its URL (#10315)
From https://github.com/ibaned/omega_h
To https://github.com/SNLComputation/omega_h
2019-01-11 13:29:56 -06:00
Satish Balay
4cbeec07a0 omega-h: fix CMAKE_BUILD_TYPE: breaks with spack deafult 'RelWithDebInfo' (#10297) 2019-01-11 10:08:28 -08:00
Denis Davydov
f4bda74b30 dealii: fix concretization of xsdk package (#10288)
* dealii: fix concretization of xsdk package

* tests: add concretization tests for deal.II and xSDK, which are often broken due to limitations in the concretizer

* use pytest.mark.parametrize
2019-01-11 10:07:28 -08:00
Brian Van Essen
9102cd5790 Updating LBANN and related packages (#10305)
Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA.  Fixed small bugs within both LBANN and Hydrogen
packages.  Added requirements for breathe and cereal to LBANN.
2019-01-10 17:10:11 -08:00
Mark W. Krentel
08c4b9d47a boost: fix the bjam build for Cray (#10295)
Fixes issues #9613 and #3209.

Remove the spack wrapper directories from PATH for the bootstrap step.
This was breaking the build for Cray (and other cross-compile) because
bjam was built for the BE and died on SIGILL on the FE.

This only affects building bjam.  The boost libraries are still built
the normal spack way with the spack wrappers.
2019-01-10 16:34:05 -08:00
Mark W. Krentel
7e8b17b177 hpctoolkit: variants to build for cray and blue gene (#10223)
Add variants 'cray' and 'bgq' to build for Cray and Blue Gene compute
nodes.  These systems need separate options to find the MPI compiler
for hpcprof-mpi.
2019-01-10 12:50:58 -08:00
Cody Balos
60a44d5155 sundials: add version 4.0.1 and remove 4.0.0-dev series (#10306)
The 4.0.1 release is the culmination of the SUNDIALS 4.0.0 preview releases,
i.e. the 4.0.0-dev versions. As such, the 4.0.0-dev releases are now
being removed.
2019-01-10 14:47:48 -06:00
Eric
b25f27d442 py-checkm-genome: Add version 1.0.13 (#10304)
* py-checkm-genome: Add version 1.0.13

* py-checkm-genome: Add missing py-backports-functools-lru-cache dependency

* py-checkm-genome: Fix missing whitespace
2019-01-10 12:28:07 -06:00
Jon Rood
12cf4eb734 Explicitly listing blas and lapack sections in site.cfg for numpy (#8708)
* Explicitly listing blas and lapack sections in site.cfg for numpy when using netlib-lapack so that scipy can find them as well.

* Reducing code to use a function call instead of copying and pasting.

* Fixing flake8 errors.

* Fixing python 3.6 error when site.cfg lists library_dirs multiple times.

* Formatting.

* Verifying blas and lapack are enabled before writing to site.cfg.

* Fixing flake8 errors.

* Fixing conflicts since this package file has been updated.

* Fixing flake8 stuff.

* Handling blas and lapack variants for netlib-lapack in site.cfg for py-numpy.

* Don't write netlib-lapack site.cfg file if no blas or lapack variants enabled in py-numpy.

* Removing redundant if statement.

* Fixing mistake in py-numpy site.cfg generation.

* Separating blas and lapack further in site.cfg for netlib-lapack in py-numpy.
2019-01-10 11:14:24 -06:00
Owen Solberg
586fe32166 update r-rcpp package with new versions (#10301) 2019-01-10 09:07:09 -06:00
Greg Becker
450b0e3059 Allow combinatorial projections in views (#9679)
Allow customizing views with Spec-formatted directory structure

Allow views to specify projections that are more complicated than
merging every package into a single shared prefix. This will allow
sites to configure a view for the way they want to present packages
to their users; for example this can be used to create a prefix for
each package but omit the DAG hash from the path.

This includes a new YAML format file for specifying the simplified
prefix for a spec in a view. This configuration allows the use of
different prefix formats for different specs (i.e. specs depending
on MPI can include the MPI implementation in the prefix).
Documentation on usage of the view projection configuration is
included.

Depending on the projection configuration, paths are not guaranteed
to be unique and it may not be possible to add multiple installs of
a package to a view.
2019-01-09 17:39:35 -08:00
Satish Balay
8ca674a574 petsc: fix petsc+debug to not reset COPTFLAGS - i.e use configure defaults '-g' (#10296) 2019-01-09 17:36:28 -06:00
Daryl W. Grunau
d1bb9caba4 eospac version bump to 6.4.0beta.4 (#10294) 2019-01-09 15:57:05 -06:00
Mark W. Krentel
1b991f9385 elfutils: option to install elf.h header file (#10185)
* elfutils: option to install elf.h header file

Add variant 'elfh' (default False) to install the elf.h header file to
the include directory.  This provides access to a newer version of
elf.h and allows an elf application to build with the same elf.h that
libelf.so was built with.

Add version 0.175.

* Drop the variant 'elfh' and always install elf.h instead.
2019-01-09 14:40:15 -06:00
Eric
b4dc73bed4 py-pyyaml: Add version 3.13 (#10293) 2019-01-09 13:39:34 -06:00
Simon Flood
0b2314bbc4 R: add version 3.5.2 (#10292) 2019-01-09 12:19:58 -06:00
Andreas Baumbach
730c629b09 New package: git-fat-git (#10266)
* new package: git-fat

* backport of rsync -> older versions no longer available

Change-Id: I3a41f17df0f88ca11e08ea6fd2f2d381435e0f09

* fix legal stuff and use new git attribute

Change-Id: Ice156dfe8ad4137a861f7b2938ee92f4024142be

* use date as version number rather than hash

Change-Id: Ib537659e368f69124895306d6a6ac0c5e36061a7

* only use the date once

Change-Id: I2592fa28aaa53fed949ddc82959d712ff3f6f752
2019-01-09 09:07:12 -06:00
marvinbernhardt
7571787a3a gromacs: added simd and rdtscp variants + version 2019 (#9931) 2019-01-09 10:39:05 +01:00
Axel Huebl
efe3e905a3 OpenMPI: Add Development Version (#10257)
Add the development version of OpenMPI from the git repo
in `master`.
2019-01-08 20:48:55 -06:00
sknigh
e3a2c94d60 Updated fish to 3.0.0 (#10286) 2019-01-08 20:47:52 -06:00
Srinath Vadlamani
4fdd3b6794 Armcompiler (#9840)
* Initial compiler support

* added arm.py

* Changed licence to Arm suggested header

* Changed licence to the same as clang.py
Main author of file is Nick Forrington <Nick.Forrington@arm.com>
Minor changes by Srinath Vadlamani <srinath.vadlamani@arm.com>

* compilers: add arm compiler detection to Spack

- added arm.py with support for detecting `armclang` and `armflang`

Co-authored-by: Srinath Vadlamani <srinath.vadlamani@arm.com>

* Changed to using get get_compiler_version

* linking to general cc for arm compiler

* For arm compiler add CFLAGS to use compiler-rt rtlib.

* Escape for special characters in rexep

* Cleaned up for Flake8 to pass.

* libcompiler-rt should be part of the LDFLAGS not CFLAGS

* fixed m4 when using clang to used LDFLAGS.  Fixed comments for arm.py to display compiler --version output with # NOAQ for flakes pass.

* added arm compilers

* proper linked names
2019-01-08 16:31:25 -08:00
Owen Solberg
ee64db4764 r-ape: new versions (#10258)
* updated versions for r-ape

* added type=('build', 'run') to r dependency
2019-01-08 18:15:03 -06:00
Owen Solberg
aa20724519 r-cowplot: new versions, more specific dependencies (#10259)
* updated versions for r-cowplot

* depends_on: added type=('build', 'run') to r, and added r-scales
2019-01-08 18:14:50 -06:00
Owen Solberg
7a816b9a66 r-data-table: new versions (#10260)
* updated versions for r-data-table

* added type=('build', 'run') to r dependency
2019-01-08 18:14:34 -06:00
Owen Solberg
2bd054adff r-dbplyr: new versions (#10262)
* added new versions, and tightened up depends_on() specs

* added type=('build', 'run') to r dependency
2019-01-08 18:14:19 -06:00
thelfer
d3caad4cd7 New package: MGIS (#10273)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)

* Add support for the MFrontGenericInterfaceSupport project (MGIS)

* Style fixes

* Package documentation update

* Package documentation update

* Fix a typo thanks to Andreas Baumbach review

* Follow Adam J. Stewart advices

* Fix type
2019-01-08 15:07:47 -06:00
Eric
45882e1b6f usearch: Make installed binary executable (#10269)
* usearch: Make binary executable

* usearch: remove join_path
2019-01-08 14:20:13 -06:00
sknigh
d9c8d2f27b Added bash 5.0 (#10282) 2019-01-08 13:20:30 -06:00
Owen Solberg
0e50ff7339 r-dt: new versions (#10261)
* updated release and checksums, also tightened depends_on()

* remove blank line at end of file

* removing new version 0.5
2019-01-08 13:06:36 -06:00
Owen Solberg
76dd4ca9ae updated versions (#10263) 2019-01-08 13:00:12 -06:00
Owen Solberg
5c4156cd39 updated versions and depends_on() (#10264) 2019-01-08 12:54:55 -06:00
dorier
0a60cae516 added openpa package (#10265) 2019-01-08 12:53:37 -06:00
Eric
6ce6c79beb libzip: Add zlib dependency (#10270)
* libzip: Add zlib dependency

* libzip: Add version limit
2019-01-08 12:49:03 -06:00
Andreas Baumbach
a33d167c72 new version 1.0.1 for py-html5lib (#10278)
Change-Id: I2837dc098fce142b152d2969687d1873e182bbc8
2019-01-08 12:43:33 -06:00
Ross Miller
2934eda311 Check for ARM compiler in addition to clang (#10280)
Add "-rtlib=compiler-rt" to CFLAGS when building with either Clang or
the ARM compiler.

Refs #10279
2019-01-08 12:41:05 -06:00
Michael Kuhn
48db757be1 go: add 1.11.4 (#10272) 2019-01-08 13:57:25 +01:00
Andreas Baumbach
12b52baf7b new package: py-webencodings (#10277)
Change-Id: Icf20035367a34fa88acfef2d3fa3742c3f3901ac
2019-01-08 13:55:41 +01:00
George Hartzell
b984adb386 bowtie: new versions and %gcc@8.0.0: fix (#10232)
* bowtie: new versions and %gcc@8.0.0: fix

Bowtie development shifted from Sourceforge to GitHub.

This commit adds several versions from GitHub, using the archive
tarballs.  Note that the URL for 1.2.2 tarball is actually an '_p1'
tag....

It leaves the old 1.2 release download info in place.

Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and
1.2.0 are equivalent).

Include a fix that enables %gcc@8.0.0: from:

  https://github.com/BenLangmead/bowtie/issues/87

But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for
%gcc@6.0.0:.

Feel free to tighten this.  I know that:

- 1.2 -> 1.2.2 work with %gcc@5.5.0;
- 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and
- 1.2.2 fails with %gcc@8.2.0

* Tighten to `conflicts('%gcc@8:', when='@1.2.2')`

* Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
2019-01-07 11:30:59 -06:00
Chad Wood
3b59f70751 doxygen: URL and version hashes updated to project's GitHub home (#10250)
* Update package.py

Doxygen has migrated from a private SVN to GitHub. This PR updates the URLs and adds versioned commit hashes from GitHub. It also includes version 1.8.15 as the latest option.

* Update package.py
2019-01-07 10:38:32 +01:00
Massimiliano Culpo
c4521535e7 Multi-valued variants: better support for combinations (#9481)
This enforces conventions that allow for correct handling of
multi-valued variants where specifying no value is an option,
and adds convenience functionality for specifying multi-valued
variants with conflicting sets of values. This also adds a notion
of "feature values" for variants, which are those that are understood
by the build system (e.g. those that would appear as configure
options). In more detail:

* Add documentation on variants to the packaging guide
* Forbid usage of '' or None as a possible variant value, in
  particular as a default. To indicate choosing no value, the user
  must explicitly define an option like 'none'. Without this,
  multi-valued variants with default set to None were not parsable
  from the command line (Fixes #6314)
* Add "disjoint_sets" function to support the declaration of
  multi-valued variants with conflicting sets of options. For example
  a variant "foo" with possible values "a", "b", and "c" where "c"
  is exclusive of the other values ("foo=a,b" and "foo=c" are
  valid but "foo=a,c" is not).
* Add "any_combination_of" function to support the declaration of
  multi-valued variants where it is valid to choose none of the
  values. This automatically defines "none" as an option (exclusive
  with all other choices); this value does not appear when iterating
  over the variant's values, for example in "with_or_without" (which
  constructs autotools option strings from variant values).
* The "disjoint_sets" and "any_combination_of" methods return an
  object which tracks the possible values. It is also possible to
  indicate that some of these values do not correspond to options
  understood by the package's build system, such that methods like
  "with_or_without" will not define options for those values (this
  occurs automatically for "none")
* Add documentation for usage of new functions for specifying
  multi-valued variants
2019-01-04 19:02:34 -08:00
Michael Kuhn
051057caa3 mvapich2: add missing zlib dependency (#10254) 2019-01-04 20:52:00 -06:00
Elizabeth Fischer
f7b78412b1 Added package osmctools (#10249)
* Added package osmctools

* Simplified

Removed functions that did the same as existing defaults

* flake8
2019-01-04 20:51:44 -06:00
Jimmy Tang
5450303c97 Fix download path, the existing one has been removed from nvidia's site (#10253) 2019-01-04 18:13:11 -06:00
Neil Flood
3477d33751 openssl: add location of system certificates for SUSE Linux (#10242) 2019-01-03 10:02:25 -06:00
Axel Huebl
63e75c3972 Catch2: v2.5.0 (#10237)
Add the 2.5.0 release of catch2.
2019-01-02 08:59:36 -06:00
Ben Zwick
0c8fd8734d petsc4py: new versions (up to 3.10.0) and update website (#10238) 2019-01-02 08:59:14 -06:00
Ben Zwick
2577a5e686 slepc4py: new versions (up to 3.10.1) and update website (#10239) 2019-01-02 08:58:45 -06:00
Greg Sjaardema
9f40813004 PARALLEL-NETCDF: Update new version and location (#10172)
* PARALLEL-NETCDF: Update new version and location

PnetCDF-1.11.0 is released.

Also, the canonical download area has been changed and they are now using git, so can also provide a develop and master checkout.
One issue is that they changed the name of the tar files, so 1.11.0 needs special handling (and future versions will also).

All checksums at new location match the checksums from the old location.

* Address concerns in review

Added a `url_for_version` function to handle the name change in the tar files at version 1.11.0 and later.  Updated description to match current shown on website.  Updated `homepage` setting since it has recently moved.

* Address issues in second review
2019-01-01 19:55:29 -06:00
Ben Zwick
aca195367e FEniCS: workaround concretization issue with PETSc (#10235) 2019-01-01 10:39:07 -06:00
George Hartzell
60968a3fbf Add list_url for r-readr, finding old versions (#10231)
r-tidyverse needs r-readr@1.1.1, r-reardr needs a list_url so that it
can find it.
2019-01-01 08:05:53 -06:00
Todd Gamblin
5425a3dad4 flake8: fix flake8 issues with invalid escapes
- in many files, regular strings were used in places where raw strings
  should've been used.

- convert these to raw strings and get rid of new flake8 errors
2019-01-01 00:44:28 -08:00
Todd Gamblin
6f50cd52ed copyright: update license headers for 2013-2019 copyright. 2019-01-01 00:44:28 -08:00
George Hartzell
e6b2f0c179 express: new version, use tags and fix gcc@6.0.0: (#10230)
* express: new version, use tags and fix gcc@6.0.0:

Express fails to build with gcc@6.0.0:.

The debian project [has a
fix](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859) but
they don't seem to have pushed it upstream.

I've opened an issue and a PR in eXpress repo, but eXpress isn't
actively developed, so I'm fixing it here too.

Since the Spack package was created, the eXpress team tagged their
releases.  I've updated the package to use the tags.

Version 1.5.1 used to be known as 2015-11-29 (same commit).  1.5.2 is
new(er).

* Make flake8 happ{y,ier}
2018-12-31 20:28:15 -06:00
George Hartzell
fb52eb2a18 aspell builds with newer gcc's (#10227)
Apply fix from aspell issue (519) for a pointer dereference bug that
newer versions of gcc won't let slip past.

There hasn't been a release that includes the fix, this applies the
change to the latest release.
2018-12-31 16:13:03 -06:00
George Hartzell
51fbd315e9 fastx-toolkit builds with newer gcc's (#10228)
There's a missing break in a switch statement that newer gcc's
dislike.

Our #4696 simply disallowed newer gcc's.

This fixes the problem instead.

It's been [PR'ed upstream](https://github.com/agordon/fastx_toolkit/pull/22).

Tested with gcc@5.5.0 and gcc@8.2.0 on CentOS.
2018-12-31 16:12:51 -06:00
George Hartzell
7aeff18b6f bamutil builds with newer gcc's (#10229)
The most recent release of bamutil that we support uses an embedded
copy of libStatGen that has several issues that keep it from building
with newer releases of gcc.

They've all been fixed upstream and the latest release of bamutil
would pick them up if/when we support it.  The build process has
changed though, plus my team needs *this* version.

This commit backports those fixes.
2018-12-31 16:12:14 -06:00
Justin Stanley
7f528a5ed2 ds: new package at 9.8.0 (#9852)
* ds: new package at 9.8.0rc6

* ds: move patches to patch func

* ds: use built-in configure phase, remove autoreconf skip

* ds: revert to stable 9.8.0

* ds: remove unnecessary dep types

* ds: make url consistent with versions
2018-12-31 16:11:20 -06:00
Gary Klimowicz
a1d651e80f flang, llvm, pgmath: Add release for 2018-09-21 (#10224) 2018-12-31 11:50:04 -06:00
Geoffrey Oxberry
88417492f7 py-sphinxautomodapi: new python package (#10226) 2018-12-31 11:47:48 -06:00
Nichols A. Romero
54f76f7c51 Over specifying Quantum Espresso compiler variables causes problems in some corner cases. (#10216) 2018-12-30 11:29:28 -06:00
Sinan
70c5088a4c xgboost: make sure "libxgboost.so" is provided under prefix/lib (#10208) 2018-12-30 08:15:08 -08:00
Denis Davydov
309f70758b dealii: workaround concretization issue with PETSc (#10217) 2018-12-30 08:43:25 -06:00
Todd Gamblin
527ff860f0 patches: clean up patch.py, directives, and package class properties
- cleanup patch.py:
  - make patch.py constructors more understandable
  - loosen coupling of patch.py with package

- in Package: make package_dir, module, and namespace class properties

  - These were previously instance properties and couldn't be called from
    directives, e.g. in patch.create()

  - make them class properties so that they can be used in class definition

  - also add some instance properties to delegate to class properties so
    that prior usage on Package objects still works
2018-12-30 00:19:08 -08:00
George Hartzell
51cbc278aa Always build glib with iconv (#10219)
* Always build glib with iconv

My early PR, #10165, which added a variant to configure glib to use
libiconv and defaulted to false, seems to be causing more trouble than
the knob is worth.

This changes the glib package to always depend on and use libiconv.

* libiconv depends_on is no longer conditional
2018-12-29 16:01:08 -06:00
Adam J. Stewart
5f957920c4
Add GDAL 2.4.0 (#10215) 2018-12-28 21:20:13 -06:00
Eric
2c76e8feef salmon: Add version 0.12.0 (#10211) 2018-12-28 13:02:36 -06:00
Eric
ada8d5ce5c velvet: Add missing zlib dependency to fix installation errors (#10212) 2018-12-28 13:02:16 -06:00
Eric
722e7058f8 py-testinfra: Add version 1.18.0 (#10210) 2018-12-28 18:24:58 +01:00
Andrew Gaspar
69f1199c55 Add new versions of optional-lite and string-view-lite (#10179) 2018-12-27 17:03:21 +01:00
Justin Stanley
c451733f9a xgboost: new package at 0.81 (#9854) 2018-12-27 07:42:44 +01:00
Lukasz
25129d4a3b fix moab installation for version 5.0.2 removed from ftp (#10201)
* moab install from git repository, fix version 5.0.2 removed from ftp server

* add moab dependencies above verson 5.0.1
2018-12-26 16:18:32 -06:00
StackKorora
39589065b1 Add Stata package (#10189)
* First draft for installing Stata 15

I've tested this works on my systems and gives a successful install of STATA 15.

* Flake8 cleanup

* Another Flake8

* Update license header

* Various improvements

A lot of improvements as suggested by @adamjstewart

* flake8 check
2018-12-26 16:17:42 -06:00
Christoph Junghans
18b128e6c1
pgmath: depend on awk (#10200) 2018-12-26 13:46:52 -07:00
Adam J. Stewart
42de399b18 Fix pkgconf downloads (#10202) 2018-12-26 13:46:30 -07:00
Adam J. Stewart
fc48f65a0f
Fix libxml2+python and libxslt+python import tests (#10196)
* Fix libxml2+python import tests

* Same for libxslt package
2018-12-26 10:36:59 -06:00
Christoph Junghans
58079b13eb mawk: added 1.3.4_p20171017 (#10197) 2018-12-26 08:41:26 -06:00
Satish Balay
0f2f0deee7 slepc: fix homepage URL (#10199) 2018-12-26 08:41:09 -06:00
Denis Davydov
d9da7c98a2 dealii: fix build with some Intel compilers (#10188) 2018-12-24 18:53:53 -06:00
Adam J. Stewart
376ef5f87a
Add latest version of NCCL (#10194) 2018-12-24 17:27:15 -06:00
Adam J. Stewart
9c58dacaec
Add PyTorch 1.0 (#10193) 2018-12-24 17:27:01 -06:00
Eric
791aab8564 manta: Add version 1.5.0 and add missing zlib dependency (#10178) 2018-12-24 21:04:18 +01:00
Satish Balay
908ecf3e74 xsdk-0.4.0: add/update package versions: (#10038)
* xsdk-0.4.0: add/update package versions:
  hypre@2.15.1
  mfem@3.4.0
  superlu-dist@6.1.0
  trilinos@12.14.0-rc1
  petsc@3.10.3
  dealii@9.0.1
  pflotran@xsdk-0.4.0
  alquimia@xsdk-0.4.0
  sundials@3.2.1
  plasma@18.11.1
  magma@2.4.0
  amrex@18.10.1
  slepc@3.10.1
  omega-h@9.19.1
  strumpack@3.1.1
  pumi@2.2.0
  tasmanian@6.0
  phist@1.7.5
  dtk-3.0 [via trilinos features '+dtk+intrepid2+shards']

add option to disable omega-h build [wrt gcc-8 conflict]
  spack install xsdk~omega-h
add option to disable dealii build [wrt cori build error]
  spack install xsdk~dealii

* trilinos: default version should be the prior release
2018-12-23 17:35:03 -08:00
Neil Flood
75b83ef2a7 py-cftime: new package (#10066)
* py-cftime: new package

* Added dependency on py-setuptools, and version range for py-cython, thanks to the ever-vigilant @adamjstewart
2018-12-23 14:56:08 -06:00
Simone Bnà
e7e32cc2d6 openFOAM-paraview-catalyst (#10129)
* paraview: adding variants to use external packages as internal do not compile

* paraview: add latest paraview version

* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5

* catalyst: add latest catalyst version

* catalyst: added ParaView_DIR env variable to catalyst module

* add paraview, catalyst patches

- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436

* - Handle updated library paths for catalyst.

  Versions 5.4 and old places libraries under a paraview subdirectory.
  Eg, "lib/paraview-5.4", they are now placed directly under "lib"

- Minor code style cleanup

* Handle update library and python paths for ParaView-5.5

* catalyst: added ParaView_DIR path to spack_env

* BUG: applied the patch to the extracted catalyst source files

* paraview: added missing self to a member variable

* paraview: added Paraview_DIR to env

* catalyst: added osmesa variant

* of-catalyst: added new package

* add (FOAM,WM)_PROJECT_DIR  also to spack_env environment

* depends on first openfoam release supporting catalyst

* openfoam-com: added missing env variables to module generation

* openfoam: fixed flake8 errors

* of-catalyst: added full variant and openfoam version dependency

* paraview: adding variants to use external packages as internal do not compile

* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5

* catalyst: added ParaView_DIR env variable to catalyst module

* add paraview, catalyst patches

- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436

* - Handle updated library paths for catalyst.

  Versions 5.4 and old places libraries under a paraview subdirectory.
  Eg, "lib/paraview-5.4", they are now placed directly under "lib"

- Minor code style cleanup

* Handle update library and python paths for ParaView-5.5

* catalyst: added ParaView_DIR path to spack_env

* BUG: applied the patch to the extracted catalyst source files

* of-catalyst: added new package

* add (FOAM,WM)_PROJECT_DIR  also to spack_env environment

* depends on first openfoam release supporting catalyst

* paraview: added missing self to a member variable

* openfoam-com: added missing env variables to module generation

* openfoam: fixed flake8 errors

* paraview: added Paraview_DIR to env

* catalyst: added osmesa variant

* of-catalyst: added full variant and openfoam version dependency

* paraview-catalyst: use always external expat and netcdf

* of-catalyst: reformatted package description

* paraview-catalyst: removed duplicated function

* catalyst: fixed flake8 error

* of-catalyst: fixed license header

* of-catalyst: minor changes

* of-catalyst: renamed gitrepo with git

* of-catalyst: removed useless gitrepo parameter
2018-12-23 13:40:25 -06:00
Brian Van Essen
bdc9804078 Feature add breathe and m2r (#10180)
* Added a package for the MDAnalysis toolkit.

* Added python packages for breathe and m2r.  Updated versions and URL
for the sphinx package.

* Fixed flake8 error

* Updated package requirements based on feedback.

* Updated with requirements from the setup.py

* Switched it back to pypi.
2018-12-23 13:39:21 -06:00
Neil Flood
451bfbd1ab py-pynio: new package (#10074)
* py-pynio: new package

* Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers.

* Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions.

* Added descriptions for the new variants, and moved them to above the dependencies
2018-12-23 09:50:41 -06:00
Jim Galarowicz
93d9139ff6 Add missing module env variable setting causing OSS to fail. (#10182) 2018-12-22 17:24:44 -06:00
Justin Stanley
90dce26db9 r-corhmm: new package at 1.22 (#9859) 2018-12-22 19:09:20 +01:00
Satish Balay
fad4ecc90b
petsc-3.10.3: syncs with superlu-dist-6.1. (#10166) 2018-12-22 10:40:08 -06:00
Levi Baber
ec2c5e5b0d gpgme: new package (#10174) 2018-12-21 12:17:45 -06:00
Jordan Ogas
b1944d4cbf add charliecloud 0.9.6 (#10176) 2018-12-21 12:17:33 -06:00
Matthias Wolf
a3ecdf1f41 py-numba: fix py-llvmlite version (#10175) 2018-12-21 11:34:32 -06:00
George Hartzell
7f095cee48 Add libiconv variant to glib (#10165)
Enable explicitly building glib with or without libiconv.

Heads up: if you build with ~iconv but there is something else in the
spec that includes libiconv then glib will *still* automagically
discover it and the build will fail.
2018-12-21 11:33:28 -06:00
Daryl W. Grunau
36ab7be406 R3D spackage (#10164)
* r3d spackage

* address Adam's review comments

* fix flake8: too many blank lines
2018-12-20 17:23:38 -06:00
Sajid Ali
e57ddda4cc update h5py to 2.9.0 (#10169)
* 	modified:   var/spack/repos/builtin/packages/py-h5py/package.py

* Update package.py

* Update package.py
2018-12-20 17:23:17 -06:00
thelfer
00d84b1978 Update TFEL package (#9995)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)
2018-12-20 15:47:24 -06:00
Mark Olesen
7ded7fdbda OpenFOAM-v1812 - new version (#10167) 2018-12-20 13:18:51 -06:00
jthies
9110c727bb packages/phist: add maintainer (#10162) 2018-12-20 13:23:35 +01:00
Greg Sjaardema
93c491f729 CGNS: Allow use of git branch versions (#10156)
* CGNS: Allow use of git branch versions

Add ability to use git `master` and `develop` branches of the CGNS library.  The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released.

* CGNS: Reorder to put newest version on top

Based on review comments, place newest version (develop) first in list.
2018-12-19 20:02:24 -06:00
Mark W. Krentel
84b33523ec dyninst: patch to build dyninst with older gcc (#10160)
* dyninst: patch to build dyninst with older gcc

Add 'v9.3.2-auto.patch'.  This patch changes some 'auto t: type' usage
to the older but equivalent 'type.begin()'.  This allows building
dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax.
This patch is harmless with newer gcc.

* Fix typo in patch.  (My bad for sloppy cut-and-paste.)

* Restrict the patch to gcc 4.7 and earlier.  gcc 4.8 supports the newer
usage and thus doesn't need the patch.
2018-12-19 17:24:43 -08:00
Michael Kuhn
84c547cf6e sqlite: add 3.26.0 (#10138) 2018-12-19 17:07:03 -06:00
Owen Solberg
6b1b9031ea updated checksum for kallisto (#10158) 2018-12-19 17:06:33 -06:00
Michael Kuhn
67ab73d381 fetch_strategy: improve GitFetchStrategy (#10153)
Currently, only the Git repsository's URL shows up in the `spack info`
output, which makes it hard to distinguish different versions:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git
```

This change adds additional information as shown when cloning a Git
repository:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git on branch master
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit af165c4
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit 58ac811
```
2018-12-19 14:33:58 -08:00
jthies
5f3d9a4076 phist tag 1.7.5 was moved (#10155) 2018-12-19 13:36:49 -06:00
sknigh
5adec7e491 Updated Dakota to 6.9 (#10157)
* Updated Dakota to 6.9

* Change comment wording
2018-12-19 13:03:14 -06:00
Adam J. Stewart
adfbe71b1b
Add python bindings to libxslt (#10149) 2018-12-19 11:39:19 -06:00
Adam J. Stewart
654360d2ad
Add missing libiconv dependency to libxml2 (#10148) 2018-12-19 11:38:14 -06:00
Adam J. Stewart
0fcca9f422
Add list_url to docbook-xml (#10146) 2018-12-19 11:37:54 -06:00
Adam J. Stewart
e19e176e67
Add latest version of docbook-xsl (#10147) 2018-12-19 11:37:35 -06:00
Adam J. Stewart
ed0ca18c3c
Restrict patch to oldest version of libbsd (#10145) 2018-12-19 11:37:11 -06:00
Satish Balay
c1e562f333
PETSc: add version 3.10.3 (#10154) 2018-12-19 10:46:02 -06:00
Neil Flood
a6e2f1a96a mapserver: new package (#10067) 2018-12-19 10:04:25 +01:00
Elsa Gonsiorowski, PhD
b091fcdb8e fix for mpifileutils package (#10142)
* proper include & linking of libarchive

* due to linux headers, mfu can't build on mac

* hard code deps in configure line

rather than relying on pkg-config

* +xattr during config

* must also link the lib

* find mfu.h

* long lines
2018-12-18 21:51:24 -06:00
Dave
b27f81ac00 WarpX: Added dependency on fftw when +psatd (#10144) 2018-12-18 20:11:08 -06:00
Matthias Wolf
22d9938560 flatbuffers: add 1.10.0 (#10137)
Also unpin the version from the arrow package.
2018-12-18 10:53:02 -06:00
Adam J. Stewart
f8c650b9c4 Add pdf variant to cairo (#10135) 2018-12-18 16:39:36 +01:00
Justin Stanley
59d7854b89 clp: add build_directory, remove old hack (#10112)
* clp: add build_directory, remove old hack

* clp: use spack-build for building
2018-12-18 08:36:40 -06:00
Adam J. Stewart
d4b5fc141c
Add latest version of libxkbcommon (#10134) 2018-12-17 19:27:58 -06:00
Alberto Chiusole
a41571a1b6 Add variant to ecflow to choose whether to use static boost libraries. (#9933)
When this variant is set, it requires boost to be built with the +pic variant.
2018-12-17 19:23:53 -06:00
David Hows
c70ea22c6f Add thread count variant to atlas (#9999)
* Add thread count variant

Atlas automatically configures itself and optimizes to run with a fixed number of threads. This can be overridden during compile by setting a flag and atlas will tune itself to use the specified number, rather than all system CPUs. 

Default value is the existing logic, autoconfigure.

* Fix Linting

* Another lint for longline
2018-12-17 19:12:00 -06:00
Jannek Squar
09d2df690a Add spack package for saga-gis (#10018)
* Add spack package for saga-gis

* Adjusted license header

* Adjust saga-gis package, added fixme comments

* Removed version constraint

* Fixed fixme comment
2018-12-17 19:10:50 -06:00
Matthias Diener
776f99a414 git: add version 2.20.1 (#10130) 2018-12-17 17:36:57 -06:00
Omar Awile
d313291c2d Added RocksDB package (#10084)
* Added rocksdb package

* Fixes based on @tristan0x and @pramodk comments

* Cleanup

* A couple minor fixes based on @adamjstewart 's advice

* Fixed flake8 errors
2018-12-17 17:36:45 -06:00
Adam J. Stewart
c2b546fa97
Add missing gettext dependency to at-spi2-core (#10124) 2018-12-17 14:00:53 -06:00
Todd Gamblin
37954a78ff
Revert "mark: Create new package. (#7069)" (#10131)
This reverts commit 90b34c96d6.
2018-12-17 11:15:32 -08:00
Adam J. Stewart
bcd65906c9
Add latest version of gdk-pixbuf (#10126) 2018-12-17 13:04:40 -06:00
Adam J. Stewart
5964d14936
Add latest version of ghostscript (#10123) 2018-12-17 13:04:16 -06:00
Adam J. Stewart
fe73043170
Add missing libbsd dependency to libxdmcp (#10122) 2018-12-17 13:04:00 -06:00
Adam J. Stewart
9913b3b846
Add latest version of libbsd (#10121) 2018-12-17 13:03:43 -06:00
Adam J. Stewart
a8a0aee3f3
Add patch to fix windows.h include in freetype (#10075)
* Add patch to fix windows.h include in freetype

* Fix patch
2018-12-17 13:00:43 -06:00
Mark Olesen
cbedd507cf ENH: fixes and updates for openfoam-com build (#10065)
- previous removal of FOAM_EXT_LIBBIN (ThirdParty) from the environment
  during the build could lead to the system scotch library being found
  instead of the spack installation.

  Avoid this largely cosmetic change to the setting in favour of
  improved build robustness. These modifications will be largely
  superfluous in the 1812 release anyhow.

- Split the patching algorithm into 'regular' and '@:1806' since the
  next versions of openfoam will again need fewer patches.

- Add hook into foamCreateManpage to be used where available
2018-12-17 12:58:09 -06:00
Greg Sjaardema
ccce3b79ab SEACAS: Add preliminary support for seacas package (#9972)
* SEACAS: Add preliminary support for seacas package

* Eliminate leftover from package I copied from.

* And remove another stray line

Sorry, thought I had checked this better...

* SEACAS: Shorten long lines; fixup indentation

* SEACAS: Remove unused os import

* Add PLASMA version 18.11.0 and Lua variant (#9689)

* Add PLASMA 18.11.1 with optional Lua and test for headers

* New versions for a few python modules (#9969)

* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4

* SEACAS: Default to mpi on

* SEACAS: Modify to reduce variants

Instead of using an `allpkgs` or explicitly specifying each individual subset,
changed to minimize variants:
 * By default, the exodus and IOSS libraries are built and a few
   executables directly related to the IOSS library.
 * variant `common` defaults to True and builds the "common" seacas
   applications.  This is based on my definition, so there may be
   could be some discussion on what belongs here.
 * variant `legacy` defaults to True and builds the remainder of the
   seacas applications.  These are still used, but mainly in more
   esoteric areas.  Might be better to default to False, but I wanted
   default to just build everything which is what other SEACAS builds
   always do...

Removed the `kokkos` variants for now as I need to do some more
thinking on how best to support this.  Not often used currently,
so shouldn't be an issue.

Cleaned up other issues raised by Adam and found by me.

* SEACAS: Address flake8 issues

* SEACAS: Clean up variant package logic

Fixed package variant logic.
Consolidated some other variant handling logic
Other minor refactors for hopefully better readability

* SEACAS: Fix flake8 error

Missing whitespace around operator fixed.
2018-12-17 12:57:31 -06:00
Ricardo Silva
f979b974a5 GDL: python integration fixes (#9936)
* GDL: python integration fixes

* renamed python-related variants to follow the convention
* building the Python module requires patches currently targetting 0.9.8 othwerwise asking for the Python module *only* builds the Pyhton module
* building the python module also requires patching the vendored (with the GDL) antlr to be built as a shared library

* Typo

Co-Authored-By: rmsds <ricardo.d.silva@gmail.com>

* Rename embed-python variant to embed_python
2018-12-17 12:47:16 -06:00
TZ
a02cf107b5 zoltan: rely on MPI wrappers instead of guessing MPI libraries (#8986)
* zoltan: only add gussed MPI libs if no MPI wrappers are used

- if MPI-wrappers are used for compilation, we can assume that
  linking works without manually specifying MPI libs
  (guessing may result in wrong libs, cf. #8979)
- thus, only guess the NPI libs and add them explicitly if no
  MPI-wrappers are used
- use llnl.util.filesystem.find_libraries instead of a locally
  defined routine to guess the MPI libs if needed
  (cf. #8979)

* zoltan: rely on MPI-wrappers to know the required MPI libs
2018-12-17 12:45:49 -06:00
lingnanyuan
90b34c96d6 mark: Create new package. (#7069)
* mark: Create new package.

* mark: change description.

* mark: change description.

* mark: Delete set_up environment.

* mark: replace join_path(prefix.bin, mark) with prefix.bin.mark
2018-12-17 12:34:16 -06:00
Adam J. Stewart
ae307f5b0f Add latest version of atk (#10125) 2018-12-17 08:48:31 +01:00
jthies
17c77533ee packages/phist: new version 1.7.5 (#10120) 2018-12-16 13:35:44 -06:00
Justin Stanley
87615d54cc r-multitaper: new package at 1.0-14 (#10110) 2018-12-15 20:08:33 +01:00
Justin Stanley
c973d761e9 r-popgenome: new package at 2.6.1 (#10108) 2018-12-15 08:44:20 -06:00
Justin Stanley
3b59bf9efa r-xnomial: new package at 1.0.4 (#10111)
* r-xnomial: new package at 1.0.4

* r-xnomial: add list_url
2018-12-15 08:43:08 -06:00
Adam J. Stewart
caf94253e0
Add latest version of libsigcpp (#10103) 2018-12-14 21:09:33 -06:00
Adam J. Stewart
a55976747e
Add latest version of bdw-gc (#10100) 2018-12-14 21:09:19 -06:00
Adam J. Stewart
316df3cd37
Add latest version of libatomic-ops (#10099) 2018-12-14 21:09:04 -06:00
Levi Baber
7a0c334d81 pbsuite: pythonpath should be prepended not set (#10113) 2018-12-14 18:12:51 -08:00
Justin Stanley
6469f8953d clp: add explicit datadir (#10109) 2018-12-14 16:20:47 -06:00
Andrew Gaspar
e9281cc436 Updates to Google Test: (#10079)
- Add version 1.8.1
- Change to sha256 checksums
2018-12-14 13:23:08 -06:00
Michael Kuhn
f224f4a57e qt: fix openssl dependency for older versions (#10106) 2018-12-14 11:11:31 -06:00
Adam J. Stewart
34499c9b82
Add latest version of libxslt (#10098) 2018-12-14 10:47:23 -06:00
Adam J. Stewart
d7b4160e67
Add latest version of poppler (#10101) 2018-12-14 10:47:07 -06:00
Adam J. Stewart
bfdbadf2bb
Add latest version of cairo (#10102) 2018-12-14 10:46:52 -06:00
Greg Becker
d2d0ab06b7 Fix spack package inheritance for module variables (#10097)
* we weren't properly setting module variables for the root package in a DAG -- just for transitive dependencies.
2018-12-14 08:37:22 -08:00
Adam J. Stewart
05f9c68c30
Add latest version of meson (#10104) 2018-12-14 09:10:55 -06:00
Elsa Gonsiorowski, PhD
76bfdd65fc make dtcmp an autotools spackage (#10095)
* make dtcmp an autotools spackage

* better code
2018-12-14 09:08:57 -06:00
Adam J. Stewart
3432a71430
Add new packages for ELSD and ELSDc (#10072) 2018-12-13 22:05:24 -06:00
Matthias Diener
289ad8f375 cmake: add version 3.13.2 (#10092) 2018-12-13 17:35:58 -06:00
Miles Perry
b7a2192f91 Feature/spm (#10053)
* extract spm12.ctf to get binaries and libraries

* flake8 edits

* flake8 edits

* spm: updates

* spm: previous version
2018-12-13 12:43:45 -06:00
Eric
7f60226662 trf: add version 4.07b and install fixes (#10093)
* trf: add version 4.07 and install fixes

* suggested fixes
2018-12-13 12:42:26 -06:00
Satish Balay
e87d394038
superlu-dist: update v6.1.0 checksum (#10078) 2018-12-13 09:05:47 -06:00
Jon Rood
5dd9a321a4 Add CUDA_HOME variable to cuda module file. (#10088) 2018-12-13 08:05:13 +01:00
Christoph Junghans
0b42cf4d96 lammps: add new stable version (#10086) 2018-12-12 11:08:59 -06:00
Denis Davydov
7d5058ebe4 boost: add 1.69.0 (#10083)
signals (v1) was removed in 1.69.0
2018-12-12 10:14:47 -06:00
Eric
ce00c13297 LEMON: Create new package (#10077) 2018-12-11 23:08:45 -06:00
Elsa Gonsiorowski, PhD
2b483f24f1 added sha256 for scr v1.2.0-2 (#10082) 2018-12-11 22:56:23 -06:00
Mark W. Krentel
ab8870fd51 gcc: fix sys_ustat.h patch for gcc 4.8 and 4.9 (#10081)
The sys_ustat.h.patch to file sanitizer_platform_limits_posix.cc from
PR #10046 does not apply cleanly to gcc 4.8 or 4.9 (or earlier).

GCC up to 4.8.x either don't have libsanitizer or else don't include
ustat.h in sanitizer_platform_limits_posix.cc.

GCC 4.9.x includes ustat.h, but needs a slightly different patch.

The patch applies to GCC 5.x up to 6.4, and 7.x up to 7.3 and also
8.1.0.

The patch is already included in the tar files for gcc 6.5.0, 7.4.0
and 8.2.0.
2018-12-11 22:54:12 -06:00
Stephen Herbein
92229e46e3 flux-core & flux-sched: fix compilation and dependencies (#10049)
* flux-sched: fix compilation errors

configure was being run twice becuase the staging symlinks were
confusing autotools

mirror flux-core in building in a subdirectory to avoid other common
compilation problems, like the one in PR #3543

* flux-core: update dependencies

munge is no longer a dependency

provide hints for lua version so that `spack install flux-core` works
"out-of-the-box". Currently, when no explicity version is provided, the
concretizer attempts to use lua@5.3, which is invalid. Closes #10000
2018-12-11 22:34:58 -06:00
Brian Van Essen
abd575f273 Update LBANN generator and bug fix (#9906)
* Added a package for the MDAnalysis toolkit.

* Added Ninja as the generator for LBANN, Hydrogen, and Aluminum.  Also
fixed a bug in how the Conduit variant is included in LBANN.  Added
new versions for Hydrogen and LBANN.

* Updated lbann package so that the CMAKE parameters are set when the
variant is on and off.
2018-12-10 15:12:43 -08:00
Lukasz
22446d7303 mofem: add new releases and minor changes (#9138) 2018-12-10 14:33:31 +01:00
Matthias Diener
2670823c1e cloc: URLs are now consistent (#10068)
Fixed in upstream:
https://github.com/AlDanial/cloc/issues/352
2018-12-10 14:28:52 +01:00
Tom Payerle
8f0fc259c8 metis: Fix issues with gcc6 and misleading indentation (#10058)
Added patch to GKlibSystem.cmake to disable warnings (which get
promoted to errors) due to -Wmisleading-indentation being added
to -Wall in gcc 6
2018-12-09 13:08:38 -06:00
Matthias Diener
f0326c0ccf gcc: add versions 7.4, 6.5 (#10061) 2018-12-08 09:22:28 -06:00
Jon Rood
2f80432f62 OpenMPI: adding static libraries with slurm support for latest versions. (#10055) 2018-12-08 13:49:09 +01:00
Abhinav Bhatele
05155cbc59 TraceR: add release tag/version (#10054) 2018-12-08 01:09:48 -06:00
Cameron Smith
130706d1b8 pumi: shared variant (#10057) 2018-12-08 01:08:58 -06:00
Matthias Diener
718379eea1 eztrace: add new package (#10060) 2018-12-08 01:06:28 -06:00
Justin Stanley
3955f7cba5 r-expint: new package at 0.1-5 (#10043) 2018-12-07 18:21:40 -08:00
Axel Huebl
892ae2043f Fix Catch2 Single Header (#10022)
Fix the install of the single header amalgate in catch2.

The public API for catch < 2.3.0 was "#include <catch.hpp>".
For 2.3.0+ it is "#include <catch2/catch.hpp>"
2018-12-07 18:13:40 -08:00
James Clark
1650e9c0b2 gcc: Add patch to build GCC with glibc 2.28 and later (#10046) 2018-12-07 18:06:07 -08:00
Justin Stanley
4471f9ea32 pbsuite: new package at 15.8.24 (#10059) 2018-12-07 18:01:44 -08:00
Justin Stanley
4d5b136270 scallop: new package at 0.10.3 (#10041) 2018-12-07 17:39:07 -08:00
Justin Stanley
76ab54caec r-sseq: new package at 1.20.0 (#10042) 2018-12-07 11:24:55 -06:00
Justin Stanley
d72ba01a71 r-blockmodeling: new package at 0.3.1 (#10044) 2018-12-07 11:24:43 -06:00
Mario Melara
138d74f40c Spades: Add version 3.13.0 (#10033)
* Spades: Add version 3.13.0

In version 3.13.0 the CmakeLists.txt dir is at a different location than
in other versions. Versions up to 3.12.0 are located in "src" whereas
3.13.0 is a level deeper at "assemblers/src".

* Remove git and add new version hash
2018-12-07 11:24:17 -06:00
Justin Stanley
fb5880ab14 clp: new package at 1.16.11 (#10040) 2018-12-06 19:31:33 -08:00
Michael Kuhn
6ec8e4146f cdo: fix URLs (#10025) 2018-12-06 18:04:50 -06:00
Gregory Becker
b072c9b457 multimethod: slight refactoring, documentation for code review 2018-12-06 15:48:23 -08:00
Gregory Becker
2621af41d1 fix MRO for multimethod.__call__ using iterative algorithm.
Add tests MRO for inherited multimethods with multiple inheritance
Add tests for inherited and overridden multimethods
2018-12-06 15:48:23 -08:00
Todd Gamblin
61b859193d multimethod uses Spec() instead of parse_anonymous_spec()
- simplify logic in multimethod
- remove the requirement of multimethod invocations to walk up the stack.
2018-12-06 15:48:23 -08:00
Todd Gamblin
e0d22519cd remove spurious print in zlib patch method 2018-12-06 15:48:23 -08:00
Gregory Becker
7bb7b94666 Added test for multimethod inheritance 2018-12-06 15:48:23 -08:00
Satish Balay
f35a91a88a
superlu-dist: update to version 6.1.0 (#10037) 2018-12-06 09:46:17 -06:00
Jon Rood
bba6df4a1f Adding patch to remove unicode character from pyrope readme file (#9988)
* Adding new versions of py-rope.
2018-12-06 11:11:23 +01:00
Nichols A. Romero
298da8e2c4 Quantum ESPRESSO update - Nov 2018 (#9853)
* Add mising QE releases.

* Update QE dependencies and conflicts.

* QE 6.3 install method requires a patch to work properly.

* include QE git develop branch

* QE HDF5 needs Fortran support. HDF5 versions prior to 1.8.16 leads to QE runtime errors.

* Number of MKL related conflicts for QE.

* Flake8 fixes for QE for hdf5 lines.

* Pass in all compilers properly to QE configure

* Fixed external BLAS/LAPACK linkage in QE.

* Library search was problematic in QE.

* Add section headings to QE package.

* External FFTW compatible libraries properly detected in QE.

* Flake8 fixes for QE

* QE configure defaults to False for ELPA, thus Spack package should as well.

* QE depends on FFTW3 provider instead of FFTW explictly.

* Primary QE repo is gitlab.com, not github.com. Github mirror lags behind gitlab site.

* Support both 6.3-backports branch and develop branch in QE.

* QE patch needed for proper MKL detection. MKL_ROOT is detected and preferred, still falls back to finding first MKL installation in /opt/intel.

* Use FFTW-API provider versioned interface for specify QE FFT dependency.

* QE FFTW conflicts no longer need thanks to FFTW-API provider versioned interface.

* Flake8 3.6.0 fix in support of https://github.com/spack/spack/pull/9853

* Fix QE conflict with ilp64 variant in support of https://github.com/spack/spack/pull/9853

* Remove custom url_for_version for QE package and use builtin url instead. In support of https://github.com/spack/spack/pull/9853

* Use FFTW builtin flags for QE instead of custom Python code. In support of https://github.com/spack/spack/pull/9853

* Fix typo in QE package comments. In support of https://github.com/spack/spack/pull/9853

* Future proof QE package patches in anticipation of QE >= 6.3.1. In support of https://github.com/spack/spack/pull/9853
2018-12-06 10:57:52 +01:00
Eric
dcb27c008a DIAMOND: Add version 0.9.23 (#10030) 2018-12-05 19:16:51 -06:00
Jannek Squar
8951cc5d77 Fix doxygen package (#10021) 2018-12-05 19:02:38 -06:00
Matthias Diener
0009854e33 cloc: add version 1.80 (#10029) 2018-12-05 18:55:27 -06:00
sknigh
060d1944d4 Rewrite Rust package (#9998) 2018-12-05 20:15:45 +01:00
Matthias Diener
5434a25076 openblas: add version 0.3.4 (#10016) 2018-12-05 08:41:58 -06:00
Christoph Junghans
d149ab63a9
pfunit: add mpi-test patch (#9387) 2018-12-05 06:15:16 -07:00
Jon Rood
583617ed67 Hwloc and numactl updates (#9987)
* Adding version 2.0.12 of numactl.

* Adding new versions of hwloc.

* Adding NVML variant to hwloc.

* Adding gl variant to hwloc.

* Updating hwloc numactl dependency and gl dependency.

* Using gl virtual package in hwloc.
2018-12-05 10:26:53 +01:00
Justin Stanley
87bf5296c3 biobloom: new package at 2.2.0 (#10014) 2018-12-04 17:20:24 -06:00
Justin Stanley
68a0305e13 sdsl-lite: new package at 2.1.1 (#10013) 2018-12-04 17:20:10 -06:00
Miles Perry
6020123a0b added bwa runtime dep (#10012) 2018-12-04 17:19:56 -06:00
Matthias Diener
deda7fdd60 ffmpeg: add version 4.1 (#10015) 2018-12-04 17:19:40 -06:00
Denis Davydov
121362383b dealii: do not hardcode prefix.include for BLAS/LAPACK (#10008)
* dealii: do not hardcode prefix.include for BLAS/LAPACK

* dealii: rename lapack_blas -> lapack_blas_libs
2018-12-04 16:55:41 -06:00
HAOCHENG LIU
ce485731bb Remove openmp version guard in vtkm and add precision options (#10005)
Clang 8.0 now supports openmp 4.5 and many commerical compilers also support
openmp >= 4.0. This commit removes the openmp version guard and rely on CMake
to throw errors out when openmp version requirement is not satisified.

It also add options for precision control.
2018-12-04 11:53:17 -08:00
Greg Sjaardema
9f8e445510 CGNS: Add option for 64-bit integers (#9990)
* CGNS: Add option for 64-bit integers

Added the `int64` variant which will build the library using 64-bit integers for certain values.  This gives the capability to have models with more than 2 billion cells and/or nodes.  

Beginning with CGNS-3.1.0, two new typedef variables have been introduced to support 64-bit mode. The `cglong_t` typedef is always a 64-bit integer, and `cgsize_t` will be either a 32-bit or 64-bit integer depending on how the library was built. Many of the C functions in the MLL have been changed to to use `cgsize_t` instead of `int` in the arguments. These functions include any that may exceed the 2Gb limit of an` int`, e.g. zone dimensions, element data, boundary conditions, and connectivity. In Fortran, all integer data is taken to be `integer*4` for 32-bit and `integer*8` for 64-bit builds.
2018-12-04 18:13:49 +01:00
Greg Sjaardema
ec67bbec2f EXODUS: Update version and dependencies (#9971)
* EXODUS: Update version and dependencies

Allow pulling master version from git.  Note that I hope to have better versioning "soon"

Add requirement to use Netcdf-4.6.1 or later as those versions no longer require changing the `maxdims` or `maxvars` defines in the netcdf.h include file.  With these versions, Exodus can use an unmodified NetCDF.  These versions of NetCDF are also better than previous versions (code quality, performance, robustness).

It is still possible to run exodusII with previous NetCDF versions, but I don't know how to specify that the dependency where maxdims/maxvars variants are only needed for versions prior to 4.6.0.  

I also removed the explicit dependency on HDF5 as that dependency should be applied through the NetCDF dependency.

* Remove white-space on blank line
2018-12-04 09:48:15 -06:00
Axel Huebl
427993b951 c-blosc: 1.15.0 (#10009)
Add latest version of c-blosc.
2018-12-04 09:10:08 -06:00
Kelly (KT) Thompson
4d26faac81 Provide a new spackage for py-pint. (#9991)
* Provide a new spackage for py-pint.

Pint is a Python package to define, operate and manipulate physical quantities:
the product of a numerical value and a unit of measurement. It allows arithmetic
operations between them and conversions from and to different
units. https://pint.readthedocs.io/en/latest/

* Switch hash from md5 to sha256.
2018-12-04 08:58:11 -06:00
Greg Sjaardema
b471e2768b MATIO: New versions (#9993)
Add several new versions so that current functionality can be accessed.  Current version is now 1.5.13.

Update `url`, `list_url`, and `list_depth` so spack can find available versions
2018-12-04 08:53:15 -06:00
Oliver Breitwieser
3cf998a5db Add tmux@2.8 (#10010) 2018-12-04 08:37:09 -06:00
Greg Sjaardema
231888f3e9 PNETCDF: Update with current versions (#9982)
* PNETCDF: Update with current versions

Added latest versions. (1.10.0, 1.9.0, 1.8.1)

* PNETCDF: Revert version change in url

Reverted the change in the url variable version since not required.
2018-12-04 08:31:41 -06:00
Greg Sjaardema
6e3b016aa2 NETCDF: Add new versions and update url (#9970)
* NETCDF: Add new versions and update url

Added the 4.6.2 version which was recently released.
Changed the url to point to the official Unidata site and added option to retrieve master version from git.

* NETCDF: checksum and version updates

Reverted back to use of previous URL.  The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0.  Since several installations are still providing 4.4.0, thought it best to go back to previous url.  However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2.  Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
2018-12-04 15:03:25 +01:00
Bert Wesarg
262b3f859e boost: 1.68 also needs boost_1.67.0_pgi.patch (#9980)
Its in upstream with the upcoming 1.69 release though.
2018-12-04 14:49:20 +01:00
George Hartzell
0c3f220fb1 Disallow bcl2fastq2 on OS X (#9966)
* Disallow bcl2fastq2 on OS X

[Illumina's computing requirements][reqs] claim support for RHEL/CentOS and
go on to say:

> May be possible to install and run on other 64-bit Linux distributions or Unix variants.

The sufficient issue is its reliance of malloc.h.  There may be more.

[reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html

* Add an informative msg for the user
2018-12-04 13:44:15 +01:00
Neil Flood
e3d204cb8f Expand dependency on qt to allow qt4 (#9964) 2018-12-04 13:37:37 +01:00
Satish Balay
808c2ea5ce petsc: when petsc is built with fortran [default in spack] its best to use hdf5+fortran (#9986) 2018-12-04 13:32:30 +01:00
Neil Flood
47b7016ea7 r-optparse: new package (#9967) 2018-12-04 13:20:08 +01:00
Nick Forrington
9551b34cb5 pgi: Add checksum for PGI 18.10 (#9985) 2018-12-04 13:12:20 +01:00
Matthias Diener
dfb02fd078 cmake: add version 3.13.1 (#9983) 2018-12-04 13:09:49 +01:00
Levi Baber
27e8fcb945 abyss: new version (#9981) 2018-12-04 13:02:36 +01:00
sknigh
a9695bac50 Added missing libtool dependencies to libvterm and unibilium (#10007) 2018-12-04 13:01:37 +01:00
Robert Maynard
0d033a042c Download CMake sources from the Github releases (#10003)
Now that CMake is providing CMake release artifacts on github,
we should prefer those as they have better download speeds and
uptime.
2018-12-03 12:35:51 -06:00
jthies
3a2045b7c0 Phist 1.7.4 (#9996)
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
2018-12-03 09:40:51 -06:00
HAOCHENG LIU
66a62d82c4 Bump vtkm to version 1.3 and add new features (#9968)
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.

[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
2018-11-30 19:48:22 -08:00
Mark W. Krentel
cc5446f25c hpctoolkit: overhaul to use spack dependencies (#9946)
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.

Remove hpctoolkit-externals since it's no longer needed.
2018-11-30 18:11:12 -08:00
jwallior
930debcf35 New versions for a few python modules (#9969)
* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4
2018-11-28 21:44:15 -06:00
Piotr Luszczek
8375b5b571 Add PLASMA version 18.11.0 and Lua variant (#9689)
* Add PLASMA 18.11.1 with optional Lua and test for headers
2018-11-28 16:59:05 -06:00
Ondřej Čertík
62f1cf3678 Add f18 package (#9183)
* Add f18 package

* Fix flake8 errors

* Install the f18 binary into prefix.bin by hand

* Add spack-build into the path

* Fix the license header
2018-11-28 14:13:30 -06:00
Michael Kuhn
5cea4a75d7 glib: disable SELinux explicitly (#9956) 2018-11-28 10:06:17 +01:00
George Hartzell
e4e980ee97 bcl2fastq2 package: recursively delete after copy (#9959)
Fixes #9944

73c978d replaced a move with a copy, which cased rmdir to fail (as
it expects an empty directory). This switches to use `shutil.rmtree`
instead.
2018-11-27 17:22:14 -08:00
Jon Rood
4c3091b05e Fixing problems with lammps dependencies voropp and latte (#9909)
* Fixing problems with lammps dependencies voropp and latte.

* Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
2018-11-27 16:55:21 -07:00
Matthias Diener
2164181d0a git: add version 2.19.2 (#9961)
Also fixes instructions for new releases
2018-11-27 16:32:22 -06:00
Neil Flood
8a78c9c6bc Rename py-proj to py-pyproj, consistent with Spack's current naming conventions (#9962) 2018-11-27 16:31:30 -06:00
thelfer
2e04f3daab new package: add support for the tfel package (#9930) 2018-11-27 07:16:55 +01:00
Michael Kuhn
16d3e44515 py-pygobject: add missing pkgconfig dependency (#9955) 2018-11-26 21:41:44 -06:00
Axel Huebl
b26c85301d OpenMPI: Prefer Last 3.X (#9945)
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.

Let's wait for some point releases.
2018-11-26 16:46:04 -06:00
Eric
20a6dde10b GATK: Add version 4.0.11.0 (#9953) 2018-11-26 14:54:05 -06:00
Eric
d9046e70c1 minced: Add version 0.1.6 (#9951) 2018-11-26 14:22:17 -06:00
Matthias Diener
bab3d7734a hdf5: add version 1.8.21 (#9952) 2018-11-26 12:56:44 -06:00
Michael Kuhn
7df14134c1 go: add 1.11.2 (#9948) 2018-11-26 11:33:55 -06:00
Eric
5cd8233139 metabat: Add version 2.11.2 (#9950) 2018-11-26 11:32:14 -06:00
Miles Perry
28e93a7a79 Feature/gatk (#9872)
* added 3.8-1 version

* fixed flake8 stuff
2018-11-26 11:30:21 -06:00
Adam J. Stewart
06dcf72f14 Uncomment dependencies previously disallowed by concretizer (#9942) 2018-11-26 09:11:16 +01:00
Sinan
096922c39d Package/py scikit learn (#9843)
* add v0.20 specific dependency versions, also add cython and py-test as dependencies

* make flake8 happy

* make cython a build-only dependency
2018-11-24 19:03:30 -06:00
Neil Flood
4c1733bff4 py-pygresql: new package (#9922)
* py-pygresql: new package

* Added dependency on py-setuptools, as the build will use it if present
2018-11-24 17:45:27 -06:00
Neil Flood
e3e01ab3d7 py-psycopg2: new package (#9926)
* py-psycopg2: new package

* Added dependency on py-setuptools, as the build will use it if present
2018-11-24 17:45:16 -06:00
Denis Davydov
058a772a52 p4est: fix a typo (#9932) 2018-11-24 17:45:04 -06:00
Matthias Diener
9d2ea84112 mc: add version 4.8.21 (#9943) 2018-11-24 17:42:46 -06:00
Matthias Diener
e86a28aff7 intel-parallel-studio: add missing updates to 2019.1 (#9941) 2018-11-24 15:44:57 -06:00
Neil Flood
9945a59c47 py-geopandas: New package. (#9919)
* py-geopandas: New package, including packages for its dependencies

* Trailing whitespace removed, etc

* One more trailing whitespace

* Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them.

* Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used.

* Added explicit dependency on py-matplotlib
2018-11-24 15:44:44 -06:00
Matthias Diener
25b9938ad1 cmake: add version 3.13.0 (#9940) 2018-11-24 14:23:10 -06:00
Neil Flood
a0fc573ff4 r-geor: new package, and a couple of its dependencies (#9920)
* r-geor: new package, and a couple of its dependencies

* Update to new copyright header

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages

* Correct dependency types in r-splancs.
2018-11-24 14:21:54 -06:00
Andreas Baumbach
862d1799fb new version 18.1 for py-pip (#9938)
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
2018-11-23 18:09:20 -06:00
Neil Flood
2e510413c3 r-compositions: new package, including its dependencies (#9921)
* r-compositions: new package, including its dependencies

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages
2018-11-23 18:06:57 -06:00
Neil Flood
3557b6e149 libspatialite: new package (#9923) 2018-11-22 13:54:52 -06:00
Nicholas Labello
13f2e68688 munge: update versions and url format to reflect switch to .xz format… (#9916)
* munge: update versions and url format to reflect switch to .xz format in recent releases

* package:munge remove unneeded version-specific urls
2018-11-22 13:13:40 -06:00
Eric
be92d46962 minced: add version 0.3.2 and fix install paths (#9918) 2018-11-22 13:13:06 -06:00
Neil Flood
c42ceb886c qca: new package (#9924) 2018-11-22 12:45:42 -06:00
Neil Flood
b6e664846a qjson: new package (#9925) 2018-11-22 12:45:17 -06:00
Denis Davydov
0f6f3ece95 p4est: apply patches to 2.0 only (#9928) 2018-11-22 12:40:22 -06:00
Michael Kuhn
f7a445e4b0 multitime: new package (#9929) 2018-11-22 12:39:51 -06:00
Michael Kuhn
ffaf617e74 flecsale: add missing dependencies and fix flecsi runtime model (#9774) 2018-11-22 12:38:59 -06:00
Ken Raffenetti
0eb8cd9a8f Add MPICH version 3.3 (#9915) 2018-11-21 14:42:52 -06:00
Mark W. Krentel
27ad0f1269 dyninst: overhaul package.py to CMakePackage (#9871)
Drop versions 8.1.x.  These were > 5 years old, no other spack package
uses them, and they used autotools.  Packages 'stat' and 'mitos' still
use 8.2.1, so we keep that.

Switch class Dyninst to CMakePackage.

Clean up how the versions depend on various packages.  For example,
Dyninst used libelf up to 9.2, and then elfutils starting with 9.3.
This makes things easier going forward.

Add variant 'openmp' (default True) to enable openmp support for
ParseAPI.  This was added in 10.0.0.

Add variant 'static' (default False) to also build static libraries.
This goes back to 9.1.0.

Disable cotire for the 9.3.x versions.  Cotire has no real use in a
one-time build and can break parallel builds with both static and
shared libs.
2018-11-21 10:47:19 -08:00
Elsa Gonsiorowski, PhD
1c5688fcbc correct sha for axl v1.1 (#9907) 2018-11-20 19:28:47 -06:00
Tom Scogland
ba5a251896 package: add asciidoctor gem (#9905)
* package: add asciidoctor gem

Faster, easier to use, less impossible to install correctly
implementation of asciidoc.

* ritual sacrifice of EOF whitespace to flake8
2018-11-20 14:32:44 -06:00
Tiziano Müller
84bc1d6654 CP2K related fixes and update (#9308)
* openblas: enable parallel builds

* cp2k: enable parallel builds

* cp2k: fix building on multilib/Suse distros

use the actual directory path where files where installed to instead of
the default prefix+'/lib'

* cp2k: ensure we have a non-header-only libxsmm

* openblas: disable max num CPU detection on virtualized build

* cp2k: install data and set compiled-in DATA_DIR

* cp2k: make libxc an optional dependency (enabled by default)

* cp2k: link libint statically

* cp2k: declare statically linked library deps as type=build

* cp2k: add support for PGI compiler

* cp2k: rename smm=none to smm=blas for clarification

* cp2k: blacklist unsupported compilers

* cp2k: mark wannier90 a build-time dep since statically linked

* cp2k: make pexsi and elpa optional

* cp2k: add support for v6.1

* libxc: add version 4.2.3

* cp2k: use pkg-config to link properly to libxsmm

* cp2k: fix OpenMP support by making it explicit

Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes
being spawned even though no explicit OpenMP was requested. Now the
`popt` variant should truly be thread free while the `psmp` variant uses
threads also internally.

* cp2k: source tarballs moved to GitHub
2018-11-20 09:23:01 -08:00
dorier
13b95b8ae6 Package: Mercury (#9903)
* added mercury package

* updating mercury package to satisfy flake8

* improved mercury package
2018-11-20 11:14:30 -06:00
Jon Rood
128af27c21 Add 2019.1 and 2018.4 version of the Intel performance libraries. (#9899)
* Add 2019.1 and 2018.4 version of the Intel performance libraries.

* Fixing typo.
2018-11-20 09:30:53 -06:00
Adam Moody
5127bb590f mpifileutils: add v0.8.1 (#9346) 2018-11-19 20:48:50 -06:00
Michael Kuhn
44d1d928e8 openssl: make 1.1.1 the default version (#9836)
* openssl: add 1.0.2p, 1.1.0i and 1.1.1

* openssl: make 1.1.1 the default version
2018-11-19 20:46:38 -06:00
Justin Stanley
7bb9020227 added several new perl modules (#9760) 2018-11-19 20:44:44 -06:00
Justin Stanley
9dfea8ee17 circos: new package starting at 0.69-6 (#9761)
* circos: new package starting at 0.69-6

* circos: add homepage, simplify paths

* circos: simplified more paths
2018-11-19 20:44:01 -06:00
Sinan
0a0e5642df gdk-pixbuf: explicitly disable building of gtk-docs (#9882) 2018-11-19 20:42:56 -06:00
Levi Baber
535035b223 r-rrpp: new package (#9887) 2018-11-19 20:42:45 -06:00
Jon Rood
1972376865 Adding openmpi version 4.0.0 (#9888) 2018-11-19 20:42:34 -06:00
Eric
177c5f3c6d breseq: Add version 0.33.1 (#9889) 2018-11-19 20:42:21 -06:00
Sinan
47a641f13b package/harfbuzz: disable building of gtk-docs, add new version (#9891) 2018-11-19 20:42:08 -06:00
Levi Baber
561a561d23 r-crosstalk: remove unnecessary constraint (#9892) 2018-11-19 20:41:41 -06:00
Levi Baber
71943703f2 r-geomorph: new version (#9890)
* r-geomorph: new version

* r-geomorph: min r version
2018-11-19 20:41:19 -06:00
Levi Baber
43a26d0850 r-diversitree: new package (#9893)
* r-diversitree: new package

* r-diversitree: system reqs
2018-11-19 20:41:01 -06:00
Levi Baber
7e1f96c0aa r-paleotree: new package (#9895) 2018-11-19 20:39:42 -06:00
Sinan
000bb8ca39 package/pango: disable gtk-docs (#9896) 2018-11-19 20:38:52 -06:00
Sinan
71464a8b0a package/gtkplus: disable gtk-docs (#9897) 2018-11-19 20:38:34 -06:00
Mark C. Miller
a6efd22e60 Explicitly set FC= empty for non-fortran builds (#9898) 2018-11-19 20:38:06 -06:00
Eric
0c1988ffdf Trimmomatic: Add version 0.38 (#9883) 2018-11-19 15:56:49 -06:00
Jon Rood
c8a1a81a87 Adding intel-parallel-studio cluster 2019.1 version (#9884) 2018-11-19 15:56:31 -06:00
Daniel Topa
7402112b1f Add UCX v1.4.0 (#9881)
Verification build
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5
==> Installing libsigsegv
==> Installing m4
==> Installing pkgconf
==> Installing ncurses
==> Installing readline
==> Installing gdbm
==> Installing perl
==> Installing autoconf
==> Installing automake
==> Installing libtool
==> Installing numactl
==> Installing zlib
==> Installing openssl
==> Installing diffutils
==> Installing bzip2
==> Installing xz
==> Installing libxml2
==> Installing tar
==> Installing gettext
==> Installing help2man
==> Installing bison
==> Installing flex
==> Installing libnl
==> Installing rdma-core
==> Installing ucx
==> Successfully installed ucx
  Fetch: 1.17s.  Build: 40.59s.  Total: 41.76s.
[+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64
    ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64
            ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64
            ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64
                            ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64
        ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64
        ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64
    ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64
                ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
        ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64
            ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64
                ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64
                ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64
                        ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64
                            ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64
            ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64

Environment:
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ uname -a
Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-11-19 13:20:22 -06:00
Andrea Negri
494d48f012 new package: mongo-cxx-driver (#9880)
* new package: mongo-cxx-driver

* fixed url
2018-11-19 13:19:19 -06:00
Eric
36b4758a97 samtools: make zlib/bzip2 dependencies unconditional (#9866) 2018-11-19 10:36:48 -08:00
Andrea Negri
9aa9359604 libmongoc: updated versions (#9877) 2018-11-18 20:35:24 -06:00
Alberto Chiusole
c61250e2ef New package: ecFlow, a work flow manager. (#9867)
* New package: ecFlow, a work flow manager.

* Fix pep8 style issues.
2018-11-18 10:13:31 -06:00
Sajid Ali
c45080398c Add +x variant to petsc. (#9830)
* 	modified:   var/spack/repos/builtin/packages/petsc/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2018-11-17 21:35:37 -06:00
simo-tuomisto
93879e575d mixcr: Added a new package for MiXCR. (#9864)
* mixcr: Added a new package for MiXCR.

* mixcr: Fixed spack license string.
2018-11-17 21:19:04 -06:00
Christoph Junghans
26e51ff170 lammps package: added new versions (#9868) 2018-11-16 14:52:26 -08:00
Sinan
22cd6494be py-cython: add new versions (#9846) 2018-11-16 13:20:34 -08:00
Justin Stanley
9dff444570 new package: r-gensa (starting at 1.1.7) (#9858) 2018-11-16 13:13:48 -08:00
Eric
dc2911208f py-ply: fix download url (#9862) 2018-11-16 13:12:05 -08:00
Eric
61adf39fe1 vt package: add zlib dependency (#9870) 2018-11-16 12:52:15 -08:00
Levi Baber
0a57f90d75 r-rgl: update url, add new version (#9796) 2018-11-16 15:26:09 +01:00
Michael Kuhn
c645c8e2a6 py-cffi: add missing pkgconfig dependency (#9784) 2018-11-15 19:38:52 +01:00
Michael Kuhn
d4f8bd5b8d py-cryptography: add 2.3.1 (#9785)
Required for openssl@1.1 compatibility.
2018-11-15 18:27:29 +01:00
Michael Kuhn
480951c231 krb5: add missing bison dependency for yacc (#9778) 2018-11-15 17:54:51 +01:00
Michael Kuhn
4d426e63f0 globus-toolkit: add missing pkgconfig dependency (#9775) 2018-11-15 17:54:22 +01:00
Hadrien G
d7983e2aa4 Fix and update verrou (#9847)
* Fix verrou-python integration

* Add verrou 2.1.0

* Patch level changed in v2.1.0
2018-11-15 10:22:13 -06:00
Denis Davydov
32884dbc03 dbcsr: minor fixes due to upstream changes (#9799) 2018-11-15 17:10:50 +01:00
Leonhard Reichenbach
2b64047e07 Updated protobuf and py-protobuf to version 3.6.1 (#9536)
* Updated protobuf and py-protobuf to version 3.6.1

also updated the download link as the repository has moved

* protobuf: modified conflict
2018-11-15 16:59:04 +01:00
Adam J. Stewart
2723db9f73
Add GMT, CitcomS, and fstrack packages (#9768)
* Add initial packages for citcoms and dependencies

* Ignore Pythia imports

* Add py-merlin package

* Add GMT package

* Fixes to get GMT working

* Get hc package building

* Get CitcomS 3.2.0 working

* Add fstrack package

* Fix hash
2018-11-14 23:30:44 -06:00
Levi Baber
b9c50249cf r-cairo: new package (#9794)
* r-cairo: new package

* Update var/spack/repos/builtin/packages/r-cairo/package.py

Co-Authored-By: baberlevi <baberlevi@gmail.com>
2018-11-14 21:44:55 -06:00
dorier
8a41cbf813 Argobots: added @develop version and +valgrind variant (#9664)
* added develop version in argobots package and added valgrind variant

* made autotools required only for develop version

* corrected style

* Added --disable-valgrind

Added --disable-valgrind to explicitly disable it when +valgrind isn't provided.
2018-11-14 21:39:35 -06:00
Justin Stanley
12177e41f0 r-phytools: new package at 0.6-60 (#9766)
* r-phytools: new package at 0.6-60

* r-phytools: add list_url

* r-phytools: add deps, dep versions
2018-11-14 21:39:05 -06:00
Geoffrey Oxberry
605dc8bf85 openblas: add headers property (#9831)
This commit adds only the public headers from the full list of headers
installed by OpenBLAS; this list of headers is the same as in
netlib-lapack.
2018-11-14 21:35:42 -06:00
Mark W. Krentel
b53eb2026a elfutils: add version 0.174. (#9812)
Pass cflags to configure so that configure gets the values from the
spack install line.

Disable -Werror so that we don't fail the build over a stray warning.
2018-11-14 19:05:08 -06:00
Mark W. Krentel
2554e24d09 libunwind: add version for current snapshot (#9770)
Libunwind releases are few and far between, so we need access to
recent snapshots from the git repository.

Pass cflags to configure so that make will respect the value from the
spack install line.
2018-11-14 18:56:52 -06:00
Sergey Kosukhin
75e86a61fe netcdf-fortran: add LDFLAGS to fix contents of libnetcdff.la. (#9647) 2018-11-14 09:40:16 -06:00
Levi Baber
6a08eb88b1 new package: time (#9842) 2018-11-14 09:38:37 -06:00
Michael Kuhn
9a7a532084 node-js: add 10.13.0 and 11.1.0 (#9781)
Required for openssl@1.1 compatibility.
2018-11-13 11:39:52 -06:00
Michael Kuhn
e20efb3f8f cmake: add 3.12.4 (#9758) 2018-11-13 11:34:09 -06:00
Michael Kuhn
eddba22e1c perl-net-ssleay: fix build (#9783)
- Add 1.85
- OPENSSL_PREFIX has to be set in the environment, otherwise Spack's
  openssl will not be found
2018-11-13 11:30:04 -06:00
Justin Stanley
e1f9ddd574 erne: new package starting at 2.1.1 (#9676)
* erne: new package starting at 2.1.1

* erne: remove unused configure args

* erne: remove unused prefix arg

* erne: add explicit mpi disable
2018-11-13 11:02:39 -06:00
Luigi Calori
4f27bb4f4e Fix #9673 : build fonts on powerpc architecture (#9683)
* use AutotoolsPackage so config.guess get updated by autoreconf step, fix build problem on ppc #9673

* same error, same fix under ppc arch
2018-11-13 11:01:46 -06:00
Douglas Duckworth
ab48a96149 added r-bindr v 0.1.1 (#9717) 2018-11-13 10:58:31 -06:00
Levi Baber
b668e66b81 r-genomeinfodbdata: url fix (#9732) 2018-11-13 10:57:04 -06:00
Matthias Diener
8b1a5a8e6c intel-parallel-studio: add missing updates (#9742)
* intel-parallel-studio: add missing updates

* add 2018.4
2018-11-13 10:56:31 -06:00
Levi Baber
25d71e68f2 Packages/trinotate fix (#9745)
* trinotate: fix perl location

* trinotate: not where that is

* trinotate: glob

* trinotate: needs perl-dbd-sqlite
2018-11-13 10:55:59 -06:00
Alberto Chiusole
7938ff9653 Add pic variant to cflags in boost. (#9750)
* Add pic variant to cflags in boost.

* Improve description in pic variant of boost, see #9750.
2018-11-13 10:55:01 -06:00
Miles Perry
63535542a1 new version (#9752) 2018-11-13 10:53:47 -06:00
Michael Kuhn
05a4d5a0c6 glib: add 2.56.3 (#9754) 2018-11-13 10:52:56 -06:00
Michael Kuhn
55f8dbbba0 sqlite: add 3.25.3 (#9756) 2018-11-13 10:50:54 -06:00
Michael Kuhn
c7f2c819a1 gdbm: add 1.18.1 (#9757) 2018-11-13 10:50:30 -06:00
Michael Kuhn
52e990dfa1 lmdb: add 0.9.22 (#9759) 2018-11-13 10:49:24 -06:00
Daryl W. Grunau
ff30ab462b eospac version bump (#9763) 2018-11-13 10:47:11 -06:00
Justin Stanley
c26a965c3b r-combinat: new package at 0.0-8 (#9764)
* r-combinat: new package at 0.0-8

* r-combinat: add list_url
2018-11-13 10:41:54 -06:00