Commit graph

12648 commits

Author SHA1 Message Date
Chuck Atkins
b7c31cb561 rhash: Fix broken RPATH info on darwin
The PREFIX variable in the makefiles is directly used to construct the
install name on the library metadata on darwin.  If not passed, the
default /usr/local is used and the resulting librhash.dylib contains
usage informaiton of /usr/local/lib/librhash.0.dylib.  This adds the
PREFIX= variable directly to the make command so the resulting usage
metadata contains the correct valid library path.
2019-01-29 16:31:15 -06:00
Stephen Herbein
67a1e56e4d add flux-core@0.11.0 and flux-sched@0.7.0 (#10447)
* flux-core: add v0.11.0 and updated dependencies

libuuid hasn't been a direct dependency of flux-core since 2015 (well
before any of the versions listed in the package).

The yaml-cpp dependency moved to flux-sched when we moved the jobpsec
library from core to sched.

Some python3 incompatibilities were found in 0.11.0, so bump the python3
support back a version.

* flux-sched: add v0.7.0 and make boost dependency more precise
2019-01-28 21:20:01 -07:00
Chuck Atkins
6535eae5c7 llvm: various updates (#10427)
* llvm: Bump version to 7.0.1

* llvm: Added perl-data-dumper build dependency for openmp

* llvm: Enable exception handling and RTTI

Useful to have turned on in general with RTTI but also necessary
to workaround some lldb stability issues with some versions of
libstdc++.
2019-01-29 00:32:30 +01:00
Ralph Castain
3b1fb7d9ff Update the PMIx package (#10442)
* Update the PMIx package

- Add latest releases to the list.
- Add dependency on hwloc for versions >= 3.0
- Flag preferred versions for libevent and hwloc
- Improve the description
- Point the project URL to the correct site

Signed-off-by: Ralph Castain <rhc@pmix.org>

* Only install the hwloc dependency for versions >= 3.0.0

Thanks to @ax3l for the suggestion

Signed-off-by: Ralph Castain <rhc@pmix.org>

* Add myself as a listed maintainer

Signed-off-by: Ralph Castain <rhc@pmix.org>
2019-01-26 21:25:18 +01:00
Cameron Smith
4e14752dd6 add variant for a debug build (#10409) 2019-01-26 18:42:24 +01:00
Nichols A. Romero
4ab89f4de1 QMCPACK Update - Jan 2019 (#10252)
* Add warnings for existing conflicts. New versions of QMCPACK require a compiler with C++14 support.

* QMCPACK now requires a newer release of CMake.

* Switch QMCPACK to using FFTW-api provider.

* Relax dependencies on QMCPACK +da variant.

* Add QMCPACK 3.6.0 release.

* QMCPACK compiler-CUDA conflicts.

* QMCPACK fix typo in expressing conflict.

* Conditional needed since these variables are only used when FFTW is a dependency to QMCPACK.

* QMCPACK QE variant dependency was underspecified. Must include MPI as a hard dependency on QE.

* Update QMCPACK dependencies for HDF5, CMake and Boost.

* QMCPACK clean-up, more consistent use of spec vs. self.spec.

* Add support for collective I/O variant of QMCPACK.

* Update QMCPACK conflicts for QE and PHDF5 variants.

* Use built-in install method for QMCPACK starting with 3.6.0

* QMCPACK compiler C++14 conflicts were off by one version.

* QMCPACK package needs to setup_environment method.

* In support of PR#10252, get rid of slashes in string.

* Migrate these to the CUDA package and make a seperate PR.

* In support of PR#10252, get rid of join_path for nexus.

* In support of PR#10252, work around concretizer limitation.

* In support of PR#10252, convert to conditionals to if-else clauses for compactness.

* In support of PR#10252, get rid of extra space and new line in warning messages.
2019-01-26 10:13:51 -06:00
Abhinav Bhatele
a307822fd9 laghos: update version (#10420) 2019-01-26 16:29:32 +01:00
Satish Balay
d071c6d341 petsc: configure works with python3 in current petsc@develop - and will work in future releases [3.11+] (#10380) 2019-01-26 16:28:20 +01:00
Matthias Diener
f299507fa9 diffutils: add version 3.7 (#10406) 2019-01-26 16:26:47 +01:00
Matthias Diener
2826d37a45 rust: add version 1.32.0 (#10407) 2019-01-26 16:26:16 +01:00
Ricardo Silva
3fc8203b93 bcftools: do not use bundled htslib (#10445)
* if the path to htslib is not specified the bundled one is built instead
* additionally this fixes the build with the intel compiler
2019-01-26 16:21:04 +01:00
Chuck Atkins
e867319ac3 perl-data-dumper: New package (#10425)
This package is added to satisfy a build time dependency for llvm-openmp
2019-01-26 16:16:03 +01:00
Chuck Atkins
76c757de22 libuv: Bump version to 1.25.0 (#10423) 2019-01-26 16:11:45 +01:00
Chuck Atkins
3266c69352 cmake: Use system libs by default (#10424)
This also fixes the libuv version dependency for 3.11+
2019-01-26 16:11:32 +01:00
wspear
68eb2a1418 Added the py-send2trash package as a pre-req for py-jupyterhub (#10441) 2019-01-26 16:10:02 +01:00
Piotr Luszczek
b94c8c2d53 magma: add version 2.5.0 (#10438) 2019-01-26 16:03:05 +01:00
Levi Baber
248452df4f capstone: new package (#10449) 2019-01-26 15:52:39 +01:00
Peter Scheibel
5abf29c971
Environments: fix bug for install of external packages (#10437)
"spack install" will install all packages added to the current
environment. When this included external packages, the environment
update would fail because it would attempt to copy log files that
were only generated if Spack handled the install itself. This skips
that step for external packages.
2019-01-24 21:29:21 -06:00
Greg Becker
98e0b5b0db
Allow spack install --overwrite for nonexistent or multiple packages (#9201)
* Allow overwrite nonexistent and multiple packages

initial implementation
give one prompt to users instead of a prompt per spec
testing

* flake

* bugfix: install overwrite check each spec against installed

* python3 compliance for filter/map
2019-01-24 12:10:32 -08:00
Omar Padron
7d64994cbd fix issue where docker images were being pushed without login (#10379) 2019-01-24 10:08:38 -08:00
sameershende
7d12ff6e16 Update ecp st tau pdt (#8192)
* Updated MPI and TAU versions in the TAU package
* Updated PDT versions
* Added support for Python (+python), default to `False`
* Cleaned up binutils, python, mpi usage.
* Updated binutils install to add additional header files to the include/extra directory.
* Resolving review problems with TAU and binutils packages.
  The binutils package was updated to include support for installing
  the ELF headers as a +headers variant.  The TAU package was updated
  to use all known Spack dependencies.
2019-01-23 20:40:58 -08:00
Justin Stanley
9252f7f957 trinotate: remove perl-dbd-mysql, move runtime files to HOME (#9850) 2019-01-22 14:26:31 -06:00
Justin Stanley
7baea68278 r-gamlss: new package (and data) at 5.1-2 (#10360)
* r-gamlss-data: new package at 5.1-0

* r-gamlss-dist: new package at 5.1-1

* r-gamlss: new package at 5.1-2

* r-gamlss: add mass, survival, nlme imports
2019-01-22 14:25:57 -06:00
Justin Stanley
bb942e1fc5 entrezdirect: new package (#10374) 2019-01-22 14:25:10 -06:00
Justin Stanley
4b7510ec38 py-whatshap: new package at 0.17 (#10377)
* py-whatshap: new package at 0.17

* py-whatshap: remove unused build_args
2019-01-22 14:24:45 -06:00
Justin Stanley
c1a1415e90 r-rrcov: new package at 1.4-7 (#10387) 2019-01-22 14:22:37 -06:00
Justin Stanley
e8014be017 r-robust: new package at 0.4-18 (#10391) 2019-01-22 14:22:24 -06:00
Justin Stanley
1bcc6e4d9c r-dynamictreecut: new package at 1.63-1 (#10388) 2019-01-22 14:22:09 -06:00
Peter Scheibel
c0972a3260
Exclude system mkl installs from numpy (#10383)
Fixes #10361
Fixes #6634

When mkl isnt in the spec, still write an explicit mkl entry to
prevent numpy from looking in system dirs and using a system install
of mkl. Do the same for openblas and atlas (although mkl was the only
system install reported to interfere with Spack's choice).
2019-01-22 12:18:54 -06:00
Justin Stanley
636d6007ba py-pyvcf: new package at 0.6.0 (#10375) 2019-01-22 17:11:19 +01:00
Adam J. Stewart
39725e0784 Typo fixes in .flake8 comments (#10399) 2019-01-21 12:35:11 +01:00
Justin Stanley
bb1f8b0e3e py-pyfaidx: new package at 0.5.5.2 (#10376) 2019-01-20 14:16:43 +01:00
Matthias Diener
ab00de9e81 cmake: add version 3.13.3 (#10397) 2019-01-20 14:14:37 +01:00
Jon Rood
e896ce7457 Update Nalu-Wind and dependencies (#10204)
* Updating nalu-wind, nalu, openfast, and tioga packages. Includes
  improved handling of +shared variant.
* Add fftw and catalyst support to nalu-wind.
* Restrict ParaView to use matplotlib versions before 3 (which
  require Python 3)
2019-01-18 18:43:59 -06:00
Owen Solberg
7a2315aa38 adding checksum for latest lmod release (#10381) 2019-01-18 08:49:26 +01:00
Hadrien G
3497098978 Update templight pseudo-release to remove need for patching (#10290)
* Update templight+LLVM combo

* Bring back old pseudo-release
2019-01-16 10:36:34 -06:00
Massimiliano Culpo
4bc3936004 Openblas: added version 0.3.5 (#10364) 2019-01-16 08:11:07 -06:00
sknigh
b31ecb0342 Added latest version of singularity 2.x (#10354) 2019-01-16 13:14:32 +01:00
George Hartzell
1f9fe02309 Add package for Hugo (static website generator) (#10358) 2019-01-16 13:11:15 +01:00
Tom Payerle
01bd67eb43 py-modred: New package (#10309)
* py-modred: New package

Parallelized python module for finding modal decompositions and
reduced order models.

* fix license
I think?

* Add dependency on py-numpy

and remove commented out code
2019-01-15 16:42:20 -06:00
sknigh
eaa340eba7 Added hpl 2.3 (#10345)
* Added hpl 2.3

* Added requested build fixes, added step to copy HPL.dat in 2.3+
2019-01-15 16:41:33 -06:00
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