Commit graph

12161 commits

Author SHA1 Message Date
Justin S
cab2af9a71
py-mixedhtseq: new package at 0.1.0 (#17702)
* py-mixedhtseq: new package at 0.1.0

* py-mixedhtseq: flake8 fixes
2020-07-31 11:58:53 -05:00
Justin S
da5bbe3cef
py-gpy: add 0.8.8 (#17548)
* py-gpy: add 0.8.8

* py-gpy: remove unneeded dep

* py-gpy: make cython build-only
2020-07-31 11:55:49 -05:00
Edoardo Aprà
154870da0b
NWChem 7.0.0 (#17779)
* NWChem 7.0.0

* add python2 for 6.8.1. removed 6.8 https://github.com/spack/spack/pull/17779#discussion_r462700413

* nwchem 6.8.1 breaks with gcc 10 and later

* restored extra python bits for version 6.8.1. add env. definition of basis libraries

* changes for flake8

* url fixed

* prevent 6.8.1 being compiled with gcc 10
2020-07-31 10:45:27 -05:00
Andrew W Elble
edba70557d
new package(s): py-torch-geometric (#17768)
* new package(s): py-torch-geometric
(with related dependencies: py-rdflib, py-googledrivedownloader)

* fixes
2020-07-31 10:41:24 -05:00
Claire Guilbaud
fd15fc9c70
sphinx copybutton: new package at v0.2.12 (#17632) 2020-07-31 11:41:56 +02:00
Claire Guilbaud
41f743b45d
recommonmark: new package at v0.6.0 (#17629) 2020-07-31 11:39:53 +02:00
Rémi Lacroix
ccb316964d
Improve Ferret package (#17620)
* Ferret: Add missing dependency with curl.

* Ferret: Don't force using the static version of libgfortran.

* Ferret: Ensure Spack's compiler wrappers are used.

This allows properly setting the rpaths.

* Ferret: Add support for versions 7.3 to 7.6.

* Ferret: Add a variant to install Ferret standard datasets.

* Ferret: Define some useful runtime environnement variables.

* Ferret: Fix flake8.

Also add myself as a maintainer as suggested by @alalazo.
2020-07-30 22:23:49 -05:00
Tom Payerle
58911d8248
kahip: Fix issue #17638 (make SConstruct files python3 friendly) (#17642)
As discussed in issue #17638, wherein kahip fails to build when
scons is dependent on python@3.

This converts the print statements in various SConstruct files
into python3 friendly print functions.

I found most of the affected SConstruct files in both @2.00 and
the later versions I found on web, but some files were only in @2.00.
I split the patches into two files for that reason, but have not
tried the later versions.
2020-07-30 22:22:40 -05:00
vvolkl
f09656e3f8
New Versions: dd4hep, podio (#17659)
* [dd4hep] add new patch version

* [podio] add new version and update env vars

* [dd4hep] add hepmc3 variant
2020-07-30 22:21:02 -05:00
Rémi Lacroix
d609a6dde7
Update LAMMPS package (#17715)
* LAMMPS: Use LATTE 1.2.2 starting with version 20200602.

Version 20200602 and upper requires Latte 1.2.2. This caused the internal Latte distribution to be used instead of the Latte install provided by Spack.

* LAMMPS: Add new versions 20200630 and 20200721.
2020-07-30 22:19:59 -05:00
ketsubouchi
45a67fa0f3
dcmtk: fixed type error (#17758)
* dcmtk: fixed type error

* Update var/spack/repos/builtin/packages/dcmtk/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-30 22:18:55 -05:00
Francine Lapid
32b070a76b
New package: IDL (#17451)
* New package: IDL

* Update var/spack/repos/builtin/packages/idl/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/idl/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* added license header and changed url_for_version to just url

* removed unused imports, addressed comments

* removed trailing whitespace on line 14

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-30 22:17:35 -05:00
darmac
9c7c4a739f
mozjs@1.8.5: fix compile issue (#17594)
* mozjs@1.8.5: fix compile issue

* mozjs: refine method
2020-07-30 22:15:53 -05:00
Tomoki, Karatsu
50f96e15de
vtk: Support for new option to enable MPI. (#17727) 2020-07-30 22:05:20 -05:00
Daryl W. Grunau
7dd5793b75
backport Mesa MR#6053 to prevent multiply-defined symbols (#17720)
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2020-07-30 22:04:24 -05:00
G-Ragghianti
b86e620743
Fixing problems caused by a comfused spack concretizer (#17797) 2020-07-30 22:01:48 -05:00
Harmen Stoppels
6fb8946dd5
Add variants to squashfs for different compression algorithms (#17755) 2020-07-30 22:01:13 -05:00
Lucas Frérot
cfbcf719db
New package: py-uvw (#17719)
* py-uvw: added package for versions 0.0.7 and 0.3.1

* py-uvw: added py-setuptools as dependency
2020-07-30 21:52:17 -05:00
Dr Owain Kenway
8b515f3ba0
flang: make sure to find libstdc++ if needed (#17480) 2020-07-30 14:55:16 +02:00
Adam J. Stewart
d512537417
Python: added v3.8.4, v3.8.5, v3.7.7, v3.7.8, v3.6.11 (#17775)
Also added older version in the 3.6 and 3.5 series
2020-07-30 14:49:01 +02:00
G-Ragghianti
2f5e4e1664
MAGMA isn't compatible with CUDA 11 (#17753)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-30 11:24:21 +02:00
G-Ragghianti
7b051df83f
slate package: resolve issues with cuda version and fortran compiler name (#17759)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-30 11:21:49 +02:00
darmac
b96448269a
couchdb: new package at v3.1.0 (#17595) 2020-07-30 11:17:19 +02:00
Wouter Deconinck
b24a9a383a
lhapdf5: new package at v5.9.1 (#17746)
During configure lhapdf5 searches for python. On one system
I tested on (ubuntu 19.10) it finds a system installed python3
and fails to create the python extension.

Variant named to make explicit that this is only a python2 extension.
2020-07-30 11:11:17 +02:00
Rémi Lacroix
cd1647af66
latte: added v1.2.2 and master (#17714)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-30 10:19:59 +02:00
darmac
d5fc3f267c
zipkin: new package at v2.21.5 (#17780) 2020-07-30 10:03:52 +02:00
Glenn Johnson
f0ce129c43
New package: r-hh (#17667)
* New package: r-hh

* Add short description

Add the project one liner for a short description that will be used for
`module whatis`.
2020-07-29 22:25:01 -05:00
ilbiondo
d61f362211
Updated iq-tree package (#17690) 2020-07-29 22:20:44 -05:00
Robert Mijakovic
8ea597c79a
Intel packages: new versions (#17692)
* update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote.

* Fixes a typo with one of the sha256 checksum..

* Adds version entries for new versions of Intel packages.

* Adds hashes for new versions of Intel packages.

* Adds missing hash of Intel compiler.

* Adds the newest version of Intel MPI 2019.8.

* Fixes hash for intel-parallel-studio and intel-tbb.

* Fixes version number of Intel MPI.

Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
2020-07-29 22:18:32 -05:00
Rémi Lacroix
e7fbd6c53e
CMake: Fix compilation with Intel compilers on some systems. (#17693)
Systems with older GNU compilers were not affected.

This commit fixes #15901 and fixes #17605.
2020-07-29 22:17:32 -05:00
Tiziano Müller
8e49cac433
pgi: update to 20.4 (#17696) 2020-07-29 22:16:30 -05:00
Shayna Kapadia
867e64cb4f
libmodbus: new package (#17778)
* libmodbus:adding new package

* fixing testing failures

* fixing flake 8 errors

* fixing flake 8 errors

Co-authored-by: Kapadia <kapadia2@llnl.gov>
2020-07-29 22:13:58 -05:00
Rao Garimella
3a8815ea7a
update version to 1.1.5 (#17701)
Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2020-07-29 22:12:10 -05:00
Toyohisa Kameyama
d14baf4532
use libquadmath only x86_4 and ppcle. (#17728) 2020-07-29 21:47:18 -05:00
Mark Olesen
badd11e71c
openfoam package updates, scotch version update (#17731)
* openfoam: use MPI 'headers' property (fixes #17730)

* openfoam: +spdp variant, usable for OpenFOAM 1906 and later

in contrast to +float32, which uses single-precision throughout, +spdp
uses the following:

- single-precision for most internals
- double-precision for linear solver

* openfoam: add m4 as build dependency

* scotch: update to 6.0.9 released Oct 2019

Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-07-29 21:45:40 -05:00
Valentin Clement (バレンタイン クレメン)
42dec9eb12
CLAW: Add version 2.0.2 (#17733) 2020-07-29 21:43:14 -05:00
Wouter Deconinck
6b3f9c5d60
New package: vgm (#17741)
* [vgm] new package Virtual Geometry Model (VGM)

* [vgm] Updated description
2020-07-29 21:04:37 -05:00
Wouter Deconinck
ba5aa67303
New package: geant4-vmc (#17745)
* [geant4-vmc] New package

* [geant4-vmc] aligned spacing
2020-07-29 20:44:16 -05:00
David Böhme
21ca7abf8d
Add Caliper v2.4.0 (#17750)
* Add Caliper v2.4.0

* Use built-in gotcha
2020-07-29 20:41:41 -05:00
Julien Loiseau
efb456cb0a
Adding pic support for Kokkos (#17751)
* Adding pic support for Kokkos

* Update pic for kokkos
2020-07-29 20:40:12 -05:00
h-denpo
4e12dc3303
elang add depends_on('ncurses', type='link') (#17761) 2020-07-29 20:30:04 -05:00
Mark W. Krentel
896e83e3e6
libunwind: add +pic variant (#17762)
Libunwind already builds a shared library.  The +pic variant adds the
compiler pic flag to the static archive so that it can be linked into
another shared library.
2020-07-29 20:29:24 -05:00
ketsubouchi
8435016a43
eagle: fix CC=gcc and delete march=native (#17763) 2020-07-29 20:28:31 -05:00
Justin S
416a929f7f
spades: add 3.14.1 (#17776) 2020-07-29 20:03:58 -05:00
Robert Pavel
af778aac0a
Tweak to EOSPAC for gcc@10 Support (#17777)
Eospac's build breaks on gcc@10: due to dependence on -fcommon behavior
and gnu changing to -fno-common. Added conditional argument to support
bleeding edge compilers
2020-07-29 20:03:12 -05:00
tilne
5a5f2c00a8
update URL and sha256 for aws-parallelcluster 2.8.0 (#17685)
Signed-off-by: Tim Lane <tilne@amazon.com>
2020-07-29 19:35:43 -05:00
Jen Herting
5243f97c3b
[bowtie2] added version 2.4.1 (#17748) 2020-07-29 15:15:33 -07:00
Rémi Lacroix
5a42883528
Boost: Update conflicts for version 1.73.0. (#17774)
Variant "+mpi+python cxxstd=98" is fixed in 1.73.0.
2020-07-29 12:08:20 -07:00
ketsubouchi
1827db2859
express: add cast for %fj (#17764) 2020-07-29 11:53:39 -07:00
Toyohisa Kameyama
5b12c0f4a0
clamcv: Add curl dependency. (#17765) 2020-07-29 11:48:07 -07:00
darmac
a0e6145884
Add new package: solr (#17597)
* Add new package: solr

* refine version order
2020-07-29 11:38:44 -07:00
Massimiliano Culpo
e47e972cf2 zlib: style changes to check if set of changed files is computed correctly 2020-07-29 11:23:34 -07:00
Matthias Wolf
90648bb477
qt: fix build with ~ssl. (#17767)
OpenSSL was pulled from the spec too early, leading to failures when
attempting to build with ~ssl.
2020-07-29 10:53:01 -07:00
Andrew W Elble
d1494fe8da
perl: add missing berkeley-db dependency (#17771) 2020-07-29 10:46:24 -07:00
Massimiliano Culpo
cad21d6eb1
lmod: change variant defaults to match Lmod's defaults (#17770) 2020-07-29 10:35:46 -07:00
mic84
a212bb0577
Amrvis: update branch name (#17718) 2020-07-28 09:12:00 -07:00
Patrick Gartung
7c61d6d45f
Update darshan package with mpi variant (#17717)
* Update darshan package with nompi variant.

* Change variant to mpi and default to True
2020-07-27 16:30:29 -05:00
Glenn Johnson
ff529e6dc1
r-adespatial: added new package (#17700)
This PR adds the r-adesaptial package and several other new packages as
dependencies.

- r-adegraphics
- r-adephylo
- r-phylobase
- r-rncl
- r-rnexml
2020-07-27 22:08:48 +02:00
Glenn Johnson
1c0abaa6eb
r-dss: added new package at v2.36.0 with dependencies (#17661)
This PR adds the r-dss package and the r-bsseq package, also new, as a
dependency. This includes the latest versions, which required updates to
the following dependencies:

- r-biocgenerics
- r-iranges
- r-s4vectors
- r-summarizedexperiment

Older versions of r-dss and r-bsseq are included as well to ensure
compatibility with older versions of the above dependencies.
2020-07-27 20:51:27 +02:00
Seth R. Johnson
6c2749536e
qt: fixed build with apple-clang (#17706) 2020-07-27 18:32:29 +02:00
Adam J. Stewart
4e4b8d8249
SciPy: added v1.5.2 (#17708) 2020-07-27 18:26:30 +02:00
ketsubouchi
032a52e006
scons: added support to Fujitsu compilers (#17710) 2020-07-27 18:23:53 +02:00
Hadrien G
e3cc7fc38c
acts: added v0.29 (#17712) 2020-07-27 18:13:56 +02:00
Amjad Kotobi
f2e66730d0
openmpi: added lustre variant to openmpi (#17478) 2020-07-27 18:11:57 +02:00
Claire Guilbaud
0ebdfb3c37
sphinxcontrib-mermaid: new package at v0.4.0 (#17630) 2020-07-27 17:30:22 +02:00
Claire Guilbaud
fdb21e3e91
json logger: new package at v0.1.11 (#17628) 2020-07-27 16:32:56 +02:00
Claire Guilbaud
d66d430ab5
pygments pytest: new package at v1.2.0 (#17626) 2020-07-27 15:44:26 +02:00
Claire Guilbaud
bbfc9fd448
commonmark: new package at v0.9.0 (#17624) 2020-07-27 15:02:56 +02:00
Claire Guilbaud
e960e016af
hieroglyph: new package at v1.0.0 (#17625) 2020-07-27 14:34:40 +02:00
Claire Guilbaud
074c0d622f
python docs theme: new package at v2020.1 (#17627) 2020-07-27 12:53:04 +02:00
Claire Guilbaud
458a9f22da
yolk3k: new package at v0.9 (#17635) 2020-07-27 12:48:58 +02:00
Claire Guilbaud
38730c6e68
sphinxcontrib trio: new package at v1.1.2 (#17631) 2020-07-27 12:14:12 +02:00
Claire Guilbaud
21a4edb1f3
sphinx gallery: new package at v0.7.0 (#17633) 2020-07-27 11:21:48 +02:00
Hadrien G
907f9e8411
[root] Add version 6.22 (#17459)
* Add ROOT v6.22

* Hello xext my old friend...
2020-07-26 10:08:53 -05:00
Patrick Gartung
66d59a90ed
Rename sas static-analysis-package (#17695) 2020-07-24 17:07:01 -07:00
Nicholas Sly
5795f1d7da
Add Totalview package (#17643)
* Add initial totalview package.

* Add maintainer and helpful comments/information.

Co-authored-by: sly <sly@lanl.gov>
2020-07-24 16:01:32 -07:00
t-nojiri
de6dfe3707
brltty (package): Add dependency on alsa-lib (#17616) 2020-07-24 15:56:34 -07:00
Jen Herting
148acfefcc
py-gensim (package): add version 3.8.3; update dependency constraints (#17641) 2020-07-24 15:47:19 -07:00
Matthieu Dorier
b04f9e6774
MPICH (package): add optional support for argobots (#17678) 2020-07-24 15:42:00 -07:00
Christian Tacke
0e090064c4 singularity: Add version 3.6.1 2020-07-24 15:35:40 -07:00
vvolkl
be06803804
WHIZARD (package): add LCIO dependency, Openloops support (#17658)
* WHIZARD: add versions 2.8.4 and 2.8.3
* New package: LCIO
* WHIZARD: add optional dependency on LCIO
* WHIZARD: add optional dependency on Openloops
* WHIZARD: allow building with either hepmc or hepmc3 dependencies
* Openloops: set process_lib_dir in configure
* Openloops: fix reference to variant
2020-07-24 15:25:57 -07:00
Andrew W Elble
99c46e8186
py-astropy: force re-cythonization of distributed .pyx files (#17567)
astropy 3.2.1 fails to build with python 3.8.3 with
errors similar to this:

astropy/stats/_stats.c:318:11: error: too many arguments to function 'PyCode_New'
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)

These are files that are generated by cython, but are included in the
tarball. Since there's apparently been an API change to PyCode_New, they will
need to be re-cythonized to compile correctly.
2020-07-24 17:46:56 +02:00
Andrew W Elble
30d0347825
py-astropy-healpix: new package (#17568) 2020-07-24 17:39:45 +02:00
jdomke
ea50e4036e
scorep: add libunwind dependency (#17580) 2020-07-24 17:30:50 +02:00
Harmen Stoppels
54bce00d4d
Ensure that the stubs directory does not end up in the rpath (#17619) 2020-07-24 17:02:58 +02:00
Jon Rood
d3e4b14997
imagemagick: added dependency on libsm (#17577) 2020-07-24 17:00:25 +02:00
rempke
6bad79fca0
netlib-scalapack: fixed compilation with gcc 10 (#17647) 2020-07-24 16:53:32 +02:00
t-nojiri
13b3578d2f
camx: change compile option for aarch64 (#17653) 2020-07-24 16:39:40 +02:00
Adam J. Stewart
08b5b56566
Qhull: add v2019.1 and v2020.1 (#17648)
* Qhull: add v2019.1 and v2020.1
* Fix compilation with Apple Clang
2020-07-24 16:16:53 +02:00
Adam J. Stewart
c1a2d66804
py-matplotlib: fix freetype and qhull dependencies (#17649) 2020-07-24 16:15:50 +02:00
Mark Olesen
c95c183bc4
openfoam: install META-INFO directory (#17673)
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-07-24 15:32:18 +02:00
Michael Kuhn
ed4b770e1a
gcc: added v10.2.0 (#17681) 2020-07-24 15:24:12 +02:00
Federico Ficarelli
b8c3e3e16f
hipsycl: switch to renamed default branch (#17689) 2020-07-24 15:19:59 +02:00
Rémi Lacroix
d9c1b62d38
CMake: added v3.18.0. (#17688) 2020-07-24 15:02:08 +02:00
ilbiondo
1aa1ddcd78
Updated elmer-fem recipe (#17687) 2020-07-24 09:47:09 +02:00
Adam J. Stewart
5fed42eae8 NumPy: add v1.19.1 2020-07-23 17:56:48 -07:00
ketsubouchi
1bbf8c0635
libgd (package): update configure to find jpeg dependency (#17655) 2020-07-23 17:55:34 -07:00
ketsubouchi
1fe07891e3
cctools (package): remove fstack-protector-all for Fujitsu compiler (#17656)
The Fujitsu C compiler does not support the "fstack-protector-all" option.
2020-07-23 17:49:37 -07:00
Tamara Dahlgren
a88675ffa9
XBraid (package): Switch to Github URL (#17670) 2020-07-23 17:27:25 -07:00
Chuck Atkins
547c71ad78
Revert "Add libglvnd packages/Add EGL support (#14572)" (#17682)
This reverts commit 573489db71.
2020-07-23 17:41:48 -04:00
ilbiondo
f42394daf5
csa-c: added new package at master (#17676)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23 17:07:48 +02:00
ilbiondo
10dacc2588
nn-c: added new package at v1.86.2 (#17675)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23 17:06:35 +02:00
ilbiondo
5067b956f4
Shapeit4: added new package at v4.1.3 (#17674) 2020-07-23 13:22:58 +02:00
Nick Robison
39cfa9630c
[M4] Add missing compiler flag on Cray Compiler (#17604)
* [M4] Add missing compiler flag on Cray Compiler

The new version of the Cray Compiler are based on Clang, which means we
need to add the same LDFLAG as other clang environments.
2020-07-22 23:55:03 -07:00
Adam J. Stewart
4b33558707
Cython: add v0.29.21 (#17650) 2020-07-22 18:36:55 -07:00
Jen Herting
48e8072b26
New Package: py-boto (#17639)
Added py-boto package
2020-07-22 17:52:36 -07:00
Frédéric Simonis
37fa6fe343
precice: Add version 2.1.0 (#17644) 2020-07-22 16:49:36 -07:00
Mark W. Krentel
4c7e52adaa
hpctoolkit: add version 2020.07.21 (#17645) 2020-07-22 13:53:41 -07:00
Ben Bergen
4ca6d1f0f7
Added variant to enable Legion SPY logging. (#17637) 2020-07-22 11:41:20 -06:00
Hadrien G
b8135bd205
[acts] Add version 0.28.0 (#17622)
Add acts v0.28.0
2020-07-22 09:14:51 -07:00
Justin S
dedadcd2ea
hisat2 (package): add version 2.2.0, update homepage (#17600) 2020-07-21 19:29:18 -07:00
Adam J. Stewart
983aeea850
New packages: py-azure-cli and dependencies (#17585) 2020-07-21 19:21:29 -07:00
Hadrien G
b81339cf80
[acts] Add 0.27.x series (#17621)
Add acts v0.27 and v0.27.1
2020-07-21 10:56:18 -07:00
Tiziano Müller
ec1237479e
cp2k: make libint optional (#17618) 2020-07-21 09:13:59 -07:00
t-nojiri
40e2a41477
aegean (package): remove -m64 on aarch64 (#17615) 2020-07-20 23:57:09 -07:00
Hadrien G
f168d63586
acts: added v0.26 (#17602) 2020-07-21 08:37:21 +02:00
Nick Robison
78a84efb4b
flatbuffers: added v0.12.0 (#17603) 2020-07-21 08:30:44 +02:00
Seth R. Johnson
c6891376f4
qt4: add missing libSM dependency (#17611)
See https://github.com/spack/spack/issues/15082 and
https://github.com/spack/spack/pull/16226
2020-07-21 08:12:36 +02:00
Mark W. Krentel
83b281f36b
hpcviewer, ibm-java: new versions (#17612)
Add hpcviewer version 2020.07 and ibm-java 8.0.6.11.
2020-07-21 08:09:53 +02:00
Tamara Dahlgren
86ec698a33
Bugfix: Do not raise InstallError for ascent_ver (#17578) 2020-07-20 18:32:56 -07:00
Justin S
3949a85f9a
py-dp-gp-cluster: new package at 2019-09-22 (#17549)
* py-dp-gp-cluster: new package

* py-dp-gp-cluster: remove master, add 2019-09-22

* py-dp-gp-cluster: require python2, older gpy, sklearn

* py-dp-gp-cluster: remove cython runtime dep
2020-07-20 10:48:17 -05:00
Cyrus Harrison
bab1852340
update ascent package with recent ver dep logic, and dray support (#17502)
* update ascent package with recent ver dep logic, and dray support

* update pmt name, make babelflow logic dep on mpi
2020-07-18 08:53:48 -05:00
Jon Rood
ef814b7a32
Add texlive 2020 version (#17559)
* Add new versions of texlive and poppler.

* Add new versions of harfbuzz which also relocated source location to github.

* Update var/spack/repos/builtin/packages/harfbuzz/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Restore deleted url line in harfbuzz.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-18 08:49:32 -05:00
Amjad Kotobi
e4ba1c1daf
r-devtools: add version 2.3.0; update dependencies (#17408) 2020-07-17 12:11:29 -07:00
Fabien Bruneval
bbbf0466dc
libint (package): add tuning options for MOLGW (#17329) 2020-07-17 12:10:05 -07:00
Cyrus Harrison
dc18b3e3d4
New package: parallelmergetree (#17501) 2020-07-17 12:03:11 -07:00
Adam J. Stewart
a5aa150a98 py-matplotlib: add v3.3.0 2020-07-17 11:05:41 -07:00
Amjad Kotobi
c729c6b93c
subversion: added v1.14.0 amd v1.13.0, added new url (#17519) 2020-07-17 16:33:46 +02:00
Cyrus Harrison
324c383d8e
add devil ray package (#17495)
* add dray with mid-review changes

* remove env import since its impliclity included
2020-07-16 19:51:41 -07:00
Francesco Di Natale
35b7a69456
Updates to maestrowf package (#17470)
* Addition of Chainmap to satisfy Maestro dependency.

* Additional versions and dependencies for Maestro.

* Updated URL to point to pypi.

* Updates to chainmap hashes.

* Updates to pull version from PyPi.

* Corrections to flake8 errors.

* Stricter restrictions on Python versioning.

Maestro actually supports Python 3.5 and later.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Only install chainmap for Python2 versions.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Removal of setuptools python cond.

* Removal of version constaints on setuptools.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16 19:38:45 -05:00
Kelly (KT) Thompson
d69c32d7ef
Version 1.13.2 still needs the XL patch. (#17561) 2020-07-16 19:35:33 -05:00
Scott Wittenburg
27aaff3dc2
adept-utils: 1.0.1 does not build w/ boost 1.73.0 or newer (#17560) 2020-07-16 19:34:47 -05:00
Seth R. Johnson
fc8847cf4e
Mark old icu4c as conflicting (#17562)
GCC 4.8.5 on rhel6:
```
utext.cpp:572:5: error: 'max_align_t' in namespace 'std' does not name a
type
     std::max_align_t    extension;
     ^
utext.cpp: In function 'UText* utext_setup_67(UText*, int32_t,
UErrorCode*)':
utext.cpp:587:73: error: 'max_align_t' is not a member of 'std'
             spaceRequired = sizeof(ExtendedUText) + extraSpace -
sizeof(std::max_align_t);
                                                                         ^
utext.cpp:587:73: note: suggested alternative:
In file included from
/projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/include/c++/4.8.5/cstddef:42:0,
                 from utext.cpp:19:
/projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stddef.h:
425:3: note:   'max_align_t'
 } max_align_t;
   ^
utext.cpp:598:57: error: 'struct ExtendedUText' has no member named
'extension'
                 ut->pExtra    = &((ExtendedUText *)ut)->extension;
                                                         ^
   g++   ...  loadednormalizer2impl.cpp
   g++   ...  chariter.cpp
```
2020-07-16 19:34:02 -05:00
Jon Rood
697c2183d3
Add new dependencies required in latest rsync. (#17558) 2020-07-16 19:25:22 -05:00
Nichols A. Romero
b320be70cb
PySCF new package (#17474)
* Initial version of PySCF.

* Add master branch to xcfun library

* PySCF only compatible with specific commit of xcfun library

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Revert "PySCF only compatible with specific commit of xcfun library"

This reverts commit 8296005400fbe76d0c8339b7ca06e71a801f0a22.

* Revert "Add master branch to xcfun library"

This reverts commit f2b69989316a6bece6530d5d63f1d120ab4c14a8.

* Issues conflict for xcfun library version rather than relying on a random commit.

* Add version xcfun 2.0.0a2 which is needed by PySCF.

* Remove xcfun conflict and express dependency more explictly. Add comment as to why this is necessary.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16 15:58:52 -05:00
downloadico
3f24188d19
Abinit+wannier90 fix (#17417)
* wannier90: add versions 3.0.0 and 3.1.0 and 'shared variant'

Added versions 3.0.0 and 3.1.0

Added shared variant

Added url_for_version function as versions less than 3 are from the
wannier.org site and versions 3 and up are from github.com

Added the MPI libraries to the list of libs substituted into the make.sys file
in place of @LIBS

Made it possible to build a shared object version of the library for versions
< 3 by filtering the src/Makefile.2 file (based off of the patch from a src rpm
from RHEL for version 2.0.1)

Create a modules directory in the install prefix root directory and copy the
Fortran .mod files there.

Set the MPIFC variable to the Spack Fortran MPI compiler wrapper.

* abinit: added 'wannier90' variant  which enables building abinit with wannier90

Added wannier90 variant

Made abinit depend on the shared object ('shared') variant of
wannier90 if the wannier90 variant is selected

Add configure args for wannier90 libs, includes, and binaries and to
set MPIFC

set the dft-flavor to wannier90 when wannier90 is enabled and only
set the dft flavor to 'atompaw+libxc' if wannier90 is not selected

* Update var/spack/repos/builtin/packages/abinit/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

* Update var/spack/repos/builtin/packages/wannier90/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

* Update var/spack/repos/builtin/packages/wannier90/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

* incorporated bbecker's suggestion for making the strings less ugly!

* incorporated bbecker's suggestion to fix the logic for picking which
"DFT flavor" configure argument.
If the wannier variant is enabled, it passes --with-dft-flavor=wannier90
to configure, otherwise it passes --with-dft-flavor=atompaw+libxc to configure

* Changed to using plain strings

* Fixed version tests

* incorporated @adamjstewart's fix for testing if the major version is > 2

* incorporated @adamjstewart's fix to check if mpi is enabled and
only set the MPIFC variable if it is.

* Update var/spack/repos/builtin/packages/wannier90/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Only set MPIFC if '+mpi' is set

* incorporated fixes from @adamjstewart including:
	- using the string=True argument to filter_file (and removed the unneeded
 	  escapes)
	- changing the url to the github location
	- fixing the version checks
	- building a libwannier.dylib on darwin

* incorporated fixes suggested by @adamjstewart including:
	- using the string=True argument to filter_file and cleaned up the escapes
	- only pass the MPIFC argument to configure when '+mpi' is set
	- chaned the url to the github site for Wannier090
	- fixed the version checks
	- build a 'libwannier.dylib' file when building the shared variant on darwin

* Update var/spack/repos/builtin/packages/wannier90/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

* moved a configure argument from it's own '+mpi' check to under the lower one

* Update var/spack/repos/builtin/packages/wannier90/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Cleaned up syntax as suggested by @adamjstewart
It looks *so much better* now!  Thanks!

* removed unneeded import of 'find' from 'llnl.util.filesystem' package
as suggested by @adamjstewart

* Update var/spack/repos/builtin/packages/wannier90/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* incorporated changes from @adamjstewart
changed check to "if '@:2 +shared' in spec:" instead of a nested check of '@:2' and
'+shared'
removed unneeded joins used in filter_file and spliced the list of objs directly into
the filter_file call
used the dso_suffix instead of testing for darwin to determine the name of the
shared library

* removed whitespace from blank line

* fixed bug with '../../wannier90.x: .*' not being treated as a regexp.  Thanks Adam!

* fixed missing whitespace when modifying Makefile.2

Co-authored-by: Greg Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16 15:57:42 -05:00
Themos Tsikas
8e9f4d0078
Update for Build 7020 of nagfor compiler (#17555) 2020-07-16 10:39:06 -05:00
darmac
d7794540b2
Add new package: hibench (#17552) 2020-07-16 08:47:33 -05:00
iarspider
ae44b1d7b9
New package: openloops (#17520)
* New package: OpenLoops

* install() for openloops

* Working OpenLoops recipe

* Flake-8

* Only copy collection file if required; add clarification to num_jobs

* Add __future__ import just in case

* Fix missing space

* Remove __future__ import

* Changes from review, pt. 1

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Replace print() with write()

* Flake-8

Co-authored-by: iarspider <iarpsider@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16 08:33:23 -05:00
Tom Payerle
df12b2bd15
kallisto: remove mpich dependency (#17551)
kallisto does not depend on mpich or MPI, except possibly indirectly
through hdf5 (but that should be handled by hdf5).
2020-07-16 08:28:50 +02:00
darmac
148a6a8860
Add new package: prometheus (#17541) 2020-07-15 21:56:14 -05:00
darmac
efba3731e5
storm: update url, version & runtime depends (#17523)
* storm: update url, version & runtime depends

* fix list_url error
2020-07-15 21:39:03 -05:00
fcannini
6eb332a984
vasp: New package. (#15187)
* vasp: New package.

* Remove unneeded `#noqa`

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Removed a completely needless tty.debug()

* Add compiler conflicts() and minute fixes

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-15 21:33:53 -05:00
Cyrus Harrison
d0a83f318b
add apcomp package (#17494)
* add apcomp package

* add maintainers

* fake8

* Update var/spack/repos/builtin/packages/apcomp/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* review suggestions

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-15 21:31:58 -05:00
Rémi Lacroix
0f67b97065
Update icu4c package (#17461)
* icu4c: Add new versions for older releases.

The old URLs for versions 60.1, 58.2 and 57.1 do not work anymore so add the versions available on Github.

The old versions are kept for reference (cf. #15896).

* icu4c: Add versions 66.1 and 67.1.

* icu4c: Fix compilation of versions 58 and 59 with recent glibc.
2020-07-15 18:57:19 -05:00
kolamsrinivas
d2c2e000a7
changes to py-torch recipe to enable rocm build (#17410)
* changes to recipe to enable rocm build

* fixing flake8 issue

* addressed the review comment
2020-07-15 18:45:22 -05:00
Julius-Plehn
4ac1a532f3
Adds new R package: GSODR (#17529)
* R GSODR package

* use cloud mirror
2020-07-15 12:05:39 -05:00
vvolkl
f42dc4fa4d
[root] fix cmake args for r variant (#17487)
* [root] fix cmake args for r variant

* [root] add readline dependency to +r
2020-07-15 12:04:05 -05:00
Paul
48a9ad3652
Go: added v1.14.5 and v1.13.13. (#17539) 2020-07-15 09:31:49 +02:00
Cyrus Harrison
d55541919d
visit package update, add glu as a linux dep (#17537)
* visit: add glu as a dep for linux

* add note to suggested install command about mesa
2020-07-15 00:01:05 -07:00
Dr. Christian Tacke
0d4740d1b1
curl: add dependency on libidn2 (#17526)
If the system has libidn2 installed, then curl will use it.
spack has a libidn2 package, so let's use that!

Related: #16514
2020-07-15 08:43:38 +02:00
yellowhat
d56711f799
namd: added v2.14b2 (#17395)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-15 08:04:39 +02:00
ketsubouchi
99a47e407e
cantera: better specify dependency on sundials (#17540) 2020-07-15 07:53:36 +02:00
Julius-Plehn
7efb0e541e
New Package: GrADS (#17476)
* grads minimal package

* udpt template

* grads minima

* grads & shapelib package

* hdf4

* cleanup

* hdf5, netcdf variants

* updates environment function

* updating paths and pkgconfig

* cleanup
2020-07-14 22:30:39 -05:00
Hadrien G
7340be98f6
[acts] Add 0.25.x series (#17485)
* Add Acts v0.25 support

* Add Acts v0.25.1

* Add acts v0.25.2
2020-07-14 22:23:07 -05:00
vvolkl
c281eaf69f
[acts] remove false dependency (#17511) 2020-07-14 22:07:39 -05:00
Amjad Kotobi
2110b98829
r-glue: new version (#17517) 2020-07-14 21:56:05 -05:00
darmac
88537d02e4
gpdb: fix runtime issue (#17521) 2020-07-14 21:47:29 -05:00
Jon Rood
a2729fcd7f
zsh (package): add versions; switch to .xz archives (#17489)
* Add new versions including 5.8
* Download .xz archives for existing versions (this requires updating
  the associated checksums)
2020-07-14 19:47:03 -07:00
darmac
bcd41cec71
Add new package: minio (#17522) 2020-07-14 21:45:47 -05:00
Cyrus Harrison
6f6e896795
New package: babelflow (#17500) 2020-07-14 19:42:38 -07:00
darmac
28a25080ca
py-lockfile: depends on py-pbr by setup.py (#17524) 2020-07-14 21:34:59 -05:00
ketsubouchi
14f3f230c1
scons: support Fujitsu Fortran moddir option (#17538) 2020-07-14 21:24:18 -05:00
Jon Rood
d32bbae431
rsync (package): add version 3.2.2 (#17504) 2020-07-14 16:41:11 -07:00
Frank Willmore
710ff8d7ce
libyogrt (package): add variant to enable static builds (#17535) 2020-07-14 16:36:18 -07:00
Jon Rood
683881f912
py-protobuf (package): add version 3.12.2 (#17532)
This matches the current latest version of protobuf in Spack.
Generally the version of py-protobuf and protobuf should match,
but this constraint is not currently recorded in py-protobuf.
2020-07-14 16:31:15 -07:00
vvolkl
11d8aed6cd
dd4hep (package): add version 1.13.0 (#17528) 2020-07-14 16:24:33 -07:00
Andrey Prokopenko
ab68410c4c
Trilinos (package): remove maintainer (#17534) 2020-07-14 16:23:19 -07:00
darmac
fa614404e6
smartdenovo: added patch to fix compile error (debian) (#17435) 2020-07-14 13:02:31 +02:00
Axel Huebl
a6abd530bd
CUDA 11.0.2 (#17423)
- [x] wait for general release candidate
- [x] compute capability support
- [x] compiler conflicts
  - [x] ppc64le
- [x] new download links
2020-07-13 18:32:28 -05:00
Cyrus Harrison
3e13137f6e
add share libs variant to raja (#17496) 2020-07-13 14:57:25 -07:00
Cyrus Harrison
6aa6e19d34
add shared libs variant to umpire (#17497) 2020-07-13 14:57:04 -07:00
Cyrus Harrison
c2d8d8acbd
update vtk-m with pinned version for ascent and related packages (#17498)
* add ascent_ver to vtk-m pkg

* vtk-m:: add patches used by ascent
2020-07-13 14:56:45 -07:00
Cyrus Harrison
299dcdd3eb
update vtk-h package with new version and options (#17499) 2020-07-13 14:55:38 -07:00
Jon Rood
e0f13b298d
tmux (package): add version 3.1b (#17486) 2020-07-13 13:56:33 -07:00
Jon Rood
d2ac26f844
gdb (package): add version 9.2 (#17490) 2020-07-13 13:46:27 -07:00
Jon Rood
fae57d1422
cppcheck (package): add version 2.1 (#17491) 2020-07-13 13:45:37 -07:00
Jon Rood
c84a05b809
bison (package): add versions including 3.6.4 and 3.5.3 (#17492) 2020-07-13 13:44:37 -07:00
Jon Rood
05e8918076
curl (package): add version 7.71.0 (#17493) 2020-07-13 13:42:42 -07:00
Jon Rood
929cb9e62e
vim (package): add version 8.2.1201 (#17503) 2020-07-13 13:31:37 -07:00
Jon Rood
7d1f2abd56
screen (package): add version 4.8.0 (#17505) 2020-07-13 13:28:58 -07:00
Jon Rood
ab5f28aceb
stow (package): add version 2.3.1 (#17506) 2020-07-13 13:28:18 -07:00
Jon Rood
4450377794
gnutls: add version 3.6.14 (#17507) 2020-07-13 13:27:28 -07:00
Jon Rood
45eaa442c3
Global (package): add version 6.6.4 (#17508) 2020-07-13 13:26:39 -07:00
darmac
4fa519134f
bwa: support for aarch64 (#17473)
* bwa: support for aarch64

* bwa: fix build error for non-aarch64 machine
2020-07-13 10:52:23 -05:00
Rémi Lacroix
815f62ce0c
Update gdk-pixbuf package. (#17458)
* gdk-pixbuf: Add new stable versions.

* gdk-pixbuf: Add a missing dependency with libx11.

Also add a variant disabled by default to make it optional since it is considered deprecated
(cf. 3362e94c25).
2020-07-13 10:49:17 -05:00
Mark Olesen
b3b5ea4064
updated sha256 for openfoam-1806 patch (#17483)
- perhaps related to gitlab migration and/or upgrade (Dec 2019)

Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-07-13 10:47:06 -05:00
Omar Padron
573489db71
Add libglvnd packages/Add EGL support (#14572)
* add new package: "libglvnd-frontend"

* add +glvnd variant to opengl package

* add +glvnd variant to mesa package

* add +egl variant to paraview package

* add libglvnd-frontend entries to default packages config

* fix style

* add default providers for glvnd virtuals

add default providers for glvnd-gl, glvnd-glx, and glvnd-egl

* WIP: rough start to external OpenGL documentation

* rename libglvnd-frontend package and backend virtual dependencies

* update documentation

* fix ligvnd-be-* typos

* fix libglvnd-fe package class name

* fix doc parse error
2020-07-13 11:32:36 -04:00
darmac
9c42f246ed
Add new package: atf (#17472) 2020-07-12 21:32:02 -05:00
Jannek Squar
dbdd2cb92f
Magics fix and update (#17477)
* Added new versions to magics and began to set not-so-optional netcdf dependency

* Added enforced netcdf dependency

* Fix also works for version 4.1.0
2020-07-12 21:20:12 -05:00
darmac
73f02b10de
lmbench: fix scripts path for aarch64 (#17456) 2020-07-11 12:53:53 -05:00
Dr Owain Kenway
9629f571bc
llvm-flang: Only build offload code if cuda enabled (#17466)
* llvm-flang Only build offload code if cuda enabled

The current version executes `cmake(*args)` always as part of the post install.  If device offload is not part of the build, this results in referencing `args` without it being set and the error:

```
==> Error: UnboundLocalError: local variable 'args' referenced before assignment

```

Looking at prevoous version of `llvm-package.py` this whole routine appears to be only required for offload, some indent `cmake/make/install` to be under the `if`.

* Update package.py

Add comment
2020-07-11 09:02:53 -05:00
Jen Herting
59bfc22d40
[glew] depends on libsm and libice (#17428)
* [glew] depends on libsm

* [glew] depends on libice
2020-07-10 19:32:26 -05:00
Justin S
1a8a147fe5
energyplus: add 9.3.0 (#17452)
* energyplus: add 9.3.0

* energyplus: fix version order

* energyplus: more concise links

* energyplus: avoid join_path
2020-07-10 19:23:04 -05:00
figroc
0612a9e8e9
tensorflow-serving-client: add new version 2.2.0 (#17462) 2020-07-10 19:10:04 -05:00
Rémi Lacroix
ea546425e8
Update the bbcp package (#17436)
* bbcp: Update the URLs to use HTTPS.

The HTTP URLs do not work anymore.

* bbcp: Add missing libnsl dependency.

* bbcp: Rename the git-based version to match the branch name.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-10 08:27:07 -05:00
ketsubouchi
7269a5bf51
py-pysam: add LDFLAGS to curl (#17434)
* py-pysam: add LDFLAGS to curl

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-10 08:26:21 -05:00
figroc
00d7e817c6
grpc: add versions 1.28/1.29/1.30 (#17433) 2020-07-10 08:25:47 -05:00
iarspider
ed7d485b58
New packages: thepeg, herwig++ (2.x) (#17443)
* New packages: Rivet, Herwig++ 2

* Add patches for thepeg

* Flake-8

* Update package.py

* Delete thepeg-2.1.6.patch

* Delete thepeg-2.1.5.patch

* Delete thepeg-2.1.3.patch

* Delete thepeg-2.2.0.patch
2020-07-10 08:25:21 -05:00
iarspider
38d387c9a5
New packages: looptools + vbfnlo (#17446)
* New package: vbfnlo

* Add new package: vbfnlo

* Add recipe for looptools

* Add patch for looptools

* LoopTools: patch not needed (fixed by developers without changing version)

* Remove patch file as well

* Update package.py

* Update package.py

* Fix vbfnlo recipe for old version

Co-authored-by: iarspider <iarpsider@gmail.com>
2020-07-10 08:24:14 -05:00
Julius-Plehn
02dd90ebf9
New Package: ChaNGa (#17442)
* WIP: changa package

* changa cleanup

* flake8 format

* adds master branch to ChaNGa

* positional arguments

* use install instead of copy
2020-07-10 08:22:20 -05:00
Rémi Lacroix
d9923a05e0
ltrace: Disable "-Werror". (#17444)
Some functions used by ltrace have been deprecated in recent versions of glibc.
2020-07-09 22:27:30 -05:00
Rémi Lacroix
8c6fa66b2a
openslide: Add missing dependencies. (#17445) 2020-07-09 22:26:37 -05:00
Sinan
e02d955aed
new package: ligra (#17425)
* new package: ligra

* setup run environment

* tidy up

* Update var/spack/repos/builtin/packages/ligra/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/ligra/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/ligra/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* flake8

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-08 16:30:53 -05:00
Frank Willmore
b3fff20d1f
enable flatcc to be built with gcc@9.X.X (#17430)
`gcc` 9 and above have more warnings that break the `flatcc` build by default, because `-Werror` is enabled.  This loosens the build up so that we can build with more compilers in Spack.

- [x] Add `-DFLATCC_ALLOW_WERROR=OFF` to `flatcc` CMake arguments

Co-authored-by: Frank Willmore <willmore@anl.gov>
2020-07-08 13:57:09 -07:00
Patrick Gartung
8c41173678
Buildcache: bindist test without invoking spack compiler wrappers. (#15687)
* Buildcache:
   * Try mocking an install of quux, corge and garply using prebuilt binaries
   * Put patchelf install after ccache restore
   * Add script to install patchelf from source so it can be used on Ubuntu:Trusty which does not have a patchelf pat package. The script will skip building on macOS
   * Remove mirror at end of bindist test
   * Add patchelf to Ubuntu build env
   * Revert mock patchelf package to allow other tests to run.
   * Remove depends_on('patchelf', type='build') relying instead on
   * Test fixture to ensure patchelf is available.

* Call g++ command to build libraries directly during test build

* Flake8

* Install patchelf in before_install stage using apt unless on Trusty where a build is done.

* Add some symbolic links between packages

* Flake8

* Flake8:

* Update mock packages to write their own source files

* Create the stage because spec search does not create it any longer

* updates after change of list command arguments

* cleanup after merge

* flake8
2020-07-08 15:05:58 -05:00
iarspider
0bed621d0c
Add missing file (#17426)
Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-07-08 10:50:47 -05:00
Amjad Kotobi
1d2754c3f6
r-usethis: new version and dependencies (#17411)
* r-usethis: new version and dependencies

* r-usethis: fix in dependency
2020-07-08 08:44:47 -05:00
tcojean
ae2a867a7f
Ginkgo: new versions (#17413)
* Add new Ginkgo versions with HIP support.

* Drop HIP support until more ROCm packages are integrated.
2020-07-08 08:42:56 -05:00
ketsubouchi
f0391db096
typhon: fix build with Fujitsu compilers (#17424) 2020-07-08 09:28:41 +02:00
TZ
084994db9c
ncl: fix compilation errors with Intel compilers (#17391)
The Intel compilers are more strict and require special command
line options (like -std=c99) to properly compile NCL.
2020-07-08 08:42:49 +02:00
iarspider
f1f31e3dfe
Fix YODA and Rivet recipes (#17412)
* Fix Rivet recipe; restrict Yoda versions for a give Rivet version

* Fix YODA recipe

* More tweaks to YODA version requirements

* Flake-8
2020-07-07 22:24:48 -05:00
Adam J. Stewart
a63761f875
oneDNN: add v1.5.1 (#17419) 2020-07-07 16:38:47 -05:00
Adam J. Stewart
3ce16c89b7
GDAL: add v3.1.2 (#17416) 2020-07-07 15:45:25 -05:00
Christoph Junghans
90285c7d61
votca-tools: fix build with mkl (#17414) 2020-07-07 13:27:10 -05:00
Frank Willmore
6c300ab717
snappy: added v1.1.8 (#17397) 2020-07-07 17:25:26 +02:00
g-mathias
05d8ba170b
jube: added v2.4.0 (#17404)
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-07-07 16:11:53 +02:00
figroc
51f65152a5
abseil-cpp: added v20200225.2 (#17383) 2020-07-07 14:02:21 +02:00
Harmen Stoppels
1113357e35
libtree: fixed checksums (#17393)
The hash was wrongly computed for the `tar.gz` 
that Github provides, not the custom tarball which 
includes submodules as well.
2020-07-07 12:56:57 +02:00
ketsubouchi
d65a076c0d
bliss: add spaces to __DATE__ (#17385)
C++11 requires a space between literal and string macro.
2020-07-07 11:28:55 +02:00
Glenn Johnson
845139740f
mumax: new package at v3.10beta (#17398)
This PR creates a new spack package for

mumax: GPU accelerated micromagnetic simulator.

This uses the current beta version because
- it is somewhat dated, ~2018
- it is the only one that supports recent GPU kernels
2020-07-07 11:01:59 +02:00
TZ
1f87b07689
nco: added v4.8.[0,1] and v4.9.[0-3] (#17389) 2020-07-07 10:18:27 +02:00
TZ
cbaa1bca1c
ncview: added v2.1.8 (#17388) 2020-07-07 10:09:27 +02:00
Sinan
5fb6a06c37
gunrock: improved package recipe (added variants for applications and others) (#17340)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-07-07 10:02:37 +02:00
Adam Moody
6e38fc56f6 mpifileutils: add v0.10.1 2020-07-06 18:19:29 -07:00
cedricchevalier19
f0275d7e1b
Fix gcc + binutils compilation. (#9024)
* fix binutils deptype for gcc

binutils needs to be a run dependency of gcc

* Fix gcc+binutils build on RHEL7+

static-libstdc++ is not available with system gcc.
Anyway, as it is for bootstraping, we do not really care depending on
a shared libstdc++.

Co-authored-by: Michael Kuhn <michael@ikkoku.de>
2020-07-06 13:02:35 -05:00
iarspider
e62ddcb582
Add Rivet and YODA (#17372)
* Add Rivet and YODA

* Add patches

* Flake-8

* Set level for Rivet patches

* Syntax fix

* Fix dependencies of Rivet

* Update var/spack/repos/builtin/packages/rivet/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-06 10:51:36 -05:00
TZ
b3bc538df6
esmf: set ESMF_COMM=intelmpi also for ^intel-mpi (#17387)
Not only intel-parallel-studio+mpi provides Intel MPI but also
intel-mpi.
2020-07-06 11:40:11 +02:00
fcannini
29fc94e29e
psi4: fix "filter_compilers" signature (#17375) 2020-07-06 09:07:26 +02:00
Adam J. Stewart
466f7fd996
GMT: add v6.1.0 (#17384) 2020-07-05 21:06:05 -05:00
darmac
58cfe4e078
acl: fix depends error (#17341) 2020-07-05 15:28:29 -05:00
darmac
00f7577273
brpc: fix depends issue (#17347) 2020-07-05 15:27:49 -05:00
Wouter Deconinck
4e6d189a94
[opencascade] depends_on freetype, tcl, tk, gl (#17357)
* [opencascade] depends_on freetype, tcl, tk, gl

* [opencascade] new version 7.4.0p1 and url_for_version
2020-07-05 15:25:38 -05:00
iarspider
9abadd4985
New version of LHAPDF: 6.3.0 (#17367) 2020-07-05 15:23:03 -05:00
figroc
66d4bc3f3c
protobuf: add versions (#17381) 2020-07-05 15:22:31 -05:00
yellowhat
52cafe6c96
amdblis bump to 2.2. (#17369) 2020-07-05 15:22:11 -05:00
g-mathias
8d5aa46765
package Amber: amber tools 20 (#17374)
* package amber: added amber_tools 20 hash; added minor version for amber_tools

* fix flake8 issues

Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-07-05 15:17:38 -05:00
Gilles Gouaillardet
e5ec89ad5b
openblas: fix fj compiler support in 0.3.10 (#17376)
The latest 0.3.10 version openblas changed how Fortran libraries
are detected, and this broke Fujitsu compiler support.

This (new) openblas patch addresses that issue.
2020-07-05 15:14:36 -05:00
Timo Heister
7bba9cd2a5
update aspect to 2.2.0 (#17379) 2020-07-05 15:13:22 -05:00
Adam J. Stewart
cce629e791
SciPy: add v1.5.1 (#17380) 2020-07-05 14:58:26 -05:00
TZ
bb15addad5
inel-mpi: fix for wrong structure name instroduced in ea8a0be4 (#17382)
it's    mpi_compiler_wrappers
and not mpi_compiler._wrappers

fixes 2nd part of #17371
2020-07-05 11:10:28 -05:00
Adam J. Stewart
e9e3e88f63
Fix Intel MPI super invocation, again (#17378) 2020-07-05 11:09:24 -05:00
fcannini
c797a0611c
dtfbplus: New package. (#15191)
* dtfbplus: New package.

* dftbplus: Addresses @adamjstewart's comments on PR #15191

* dftbplus: Fixes format() calls that slipped in previous commit.

* dftbplus: Appease flake8.

* dftbplus: Change 'url' and misc. fixes.

* Add a resource to do the job of './utils/get_opt_externals'
2020-07-04 08:27:32 -05:00
Amjad Kotobi
f3eba3c482
py-python-swiftclient: added v3.10.0 (#17352) 2020-07-03 12:25:54 +02:00
g-mathias
02fa7b680f
elpa: added v2019.11.001 and v2020.05.001 (#17368)
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-07-03 11:52:02 +02:00
Paul R. C. Kent
8fcd917e51
libelf: added extra url (#17358) 2020-07-03 11:49:58 +02:00
g-mathias
9c85d87b90
jube: added v2.3.0 (#17366)
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-07-03 10:13:37 +02:00
yellowhat
b45fc97564
Package request: HPCG (#17350)
* use patch from upstream

Co-authored-by: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
2020-07-03 10:05:24 +02:00
ketsubouchi
986f68f7ed
blktrace: use Spack compiler wrappers (#17365) 2020-07-02 23:39:04 -07:00
ketsubouchi
2cd9e1eb62
blat: use SPACK_CC (#17364) 2020-07-02 23:38:23 -07:00