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11194 Commits

Author SHA1 Message Date
Sajid Ali
eff8e1d20b
minor (#16467) 2020-05-05 13:43:00 -05:00
Massimiliano Culpo
aa9c98b6a2
Make usage example consistent with current MV variants (#16468) 
Since #9481 Python's None is not permitted as a value for
MV variants. The string 'none' is used instead.

Add the same fix for the amgx and lammps packages
 2020-05-05 20:22:32 +02:00
Jennifer Green
de71b2828f
CMake: Cray XC40 system errors bootstrapping CMake (#16459) 
* CMake: fix https://github.com/spack/spack/issues/16453 with a patch addressing both libhugetlbfs and icpc warnings on Cray XC40 systems

* Including CMake v3.17.2 in the patched versions
 2020-05-05 14:02:49 -04:00
Christoph Junghans
ff3769e2e2
cabana: add v0.3.0 & shared variant (#16466) 2020-05-05 11:59:28 -05:00
Chris White
2cb4ae747d
Add Axom spack package (#15432) 
* Add OpenMP variant to Umpire

* Initial implementation of Axom package

* Add Axom spack package and fix required dependencies

* Fix overzealous tag replacement

* Attempt to fix version error

* Fix python version attempt #2

* Update raja and umpire

* remove sys_type check

* Address comments in axom package

* Address Greg's comments

* Fix flake8

* more flake8

* Simplify MPIEXEC and MPIEXEC_NUMPROC_FLAG

* Fix typo

* Revert back to slurm check, fix cuda_arch checks

* Fix cuda_arch variant forwarding

* Add cub variant

* Add py-shroud

* Address comments

* Fix shroud path in axom

* Fix merge conflict

* Fix backwards if

* Fix flake8 and add copyright

* format for consistency
 2020-05-05 08:52:32 -07:00
Justin S
70c9dd37a7
exonerate-gff3: new package at 2.3.0 (#11830) 2020-05-05 10:51:59 -05:00
Justin S
0e60ec7f1c
perl-bio-searchio-hmmer: new package at 1.7.3 (#16281) 
* perl-bio-searchio-hmmer: new package at 1.7.3

* perl-bio-searchio-hmmer: add dependencies
 2020-05-05 10:50:06 -05:00
Axel Huebl
6013060c60
WarpX: RZ + PSATD (#16464) 
Add additionally required dependencies to WarpX that are needed
for transformations in RZ geometry with spectral (PSATD) solvers.
 2020-05-05 10:48:23 -05:00
Tim Haines
33b129b919
Boost: Add version 1.73.0 (#16442) 2020-05-05 08:26:11 -05:00
vvolkl
c2791a4baa
[dd4hep] fix python setup (#16461) 2020-05-05 08:25:26 -05:00
Benjamin Tovar
f1bb0f8aad
cctools to 7.1.5 (#16450) 
* change homepage to readthedocs

* update cctools version to 7.1.5

* change http to https
 2020-05-05 08:24:42 -05:00
Christoph Junghans
04cb1800a6
lammps: added v20200505 (#16463) 2020-05-05 09:54:30 +02:00
Adam J. Stewart
b9ed788589
py-shapely: add master version (#16465) 2020-05-04 23:42:17 -05:00
Elizabeth Fischer
4c323e49bf
libspatialite: Update for proj@6 (#16173) 
* libspatialite

* flake8

* Added proper version constrain

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

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

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-05-04 19:44:54 -05:00
Elizabeth Fischer
76bd143c30
libsecret (#16174) 
* libsecret

* Update package.py

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
 2020-05-04 19:44:23 -05:00
vvolkl
e575ba2773
bugfix: Update run-time dependencies of py-xenv (#16460) 
Otherwise, if I run `xenv` after `spack load py-xenv` it fails with:
```
Traceback (most recent call last):
  File "/home/vavolkl/spack/opt/spack/linux-centos7-broadwell/gcc-8.3.0/py-xenv-develop_2018-12-20-lqbxakapsepqo5w3sjhhokj5o7c5jei2/bin/xenv", line 6, in <module>
    from pkg_resources import load_entry_point
ModuleNotFoundError: No module named 'pkg_resources'
```
 2020-05-04 19:41:19 -05:00
vvolkl
befd472594
[gaudi] fixes and patches (#16433) 
* [gaudi] fixes and patches

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

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

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

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

* Apply suggestions from code review

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

* [gaudi] add older versions and fold +tests into +optional

* [gaudi] set run environment

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-05-04 19:40:13 -05:00
Amjad Kotobi
6c07260d27
ecFlow added UI & GUI flag with new version (#16444) 
* ecFlow added UI & GUI flag with new version

* Fix1
 2020-05-04 16:57:06 -05:00
Elizabeth Fischer
5adf703414
py-palletable: Add new version (#16445) 
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
 2020-05-04 16:55:54 -05:00
Elizabeth Fischer
43d2c7f3b5
py-cf-units: Add new version (#16446) 
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
 2020-05-04 16:53:12 -05:00
René Widera
e808a52176
update isaac and issac-server to v1.5.0 (#16452) 
Update package.py with the latest release [ISAAC v1.5.0].
 2020-05-04 16:47:12 -05:00
Matthias Diener
fe350224b6
pocl: add version 1.5 (#16455) 
* pocl: add version 1.5

* update clang version
 2020-05-04 16:46:30 -05:00
Matthias Diener
0a4e078648
hwloc: add version 2.2.0 (#16456) 2020-05-04 16:45:55 -05:00
Shintaro Iwasaki
0475edfbf2
BOLT: add 1.0 (#16457) 2020-05-04 16:45:28 -05:00
Shintaro Iwasaki
acf0c90283
argobots: mark 1.0 as preferred (#16458) 
By default, Spack chooses 1.0rc2 instead of 1.0 though 1.0 is the stable and
newer release.  We manually mark the version 1.0 as preferred.
 2020-05-04 16:44:50 -05:00
Elizabeth Fischer
dea5d913db
Updates to Python for macOS (#16449) 
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
 2020-05-04 16:30:59 -05:00
Elizabeth Fischer
7b31f5474b
grass: new versions (#16181) 
* grass

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

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

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-05-04 16:25:19 -05:00
Axel Huebl
87f78137a5
LAPACKC++: added "shared" variant (#16419) 
We can control the shared/static build of CMake and the default in
Spack is to build shared libraries. The old, uncontrolled default
of this package is a static build.
 2020-05-04 09:39:20 +02:00
Dr. Christian Tacke
d5adad6953
singularity: added missing dependencies (#16430) 
See:

https://sylabs.io/guides/3.5/user-guide/quick_start.html#install-system-dependencies

for pkg-config and libseccomp
 2020-05-04 09:02:38 +02:00
Nichols A. Romero
860c54335d
QE-to-QMCPACK wave function converter relocation + some bug fixes (#16422) 
* Revise description of patch variant.

* Add qmcpack variant. Apply QE-to-QMCPACK wave function converter patch.

* Clean-up, document, and re-organize.

* ELPA patches did not nead when=`+patch` variant.

* Need to be more precise here with QE version numbers.

* satisfies seems to be necessary here in order to get correct behaviour.

* Buglet with zlib link line.

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

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

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

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

* Fix for QE-to-QMCPACK wave function converter w.r.t. QE 6.3. Also adjust comments to reflect changes in code.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-05-03 14:53:01 -06:00
Adam J. Stewart
caad59e7c7
NumPy: add 1.18.4 (#16441) 2020-05-03 13:29:15 -05:00
vvolkl
ed9e19df06
Add new HEP package: fastjet (#16439) 
* [fastjet] initial commit

* [fastjet] remove beta versions
 2020-05-03 13:27:18 -05:00
vvolkl
3c2f46aabf
Add new HEP package: Delphes (#16440) 
* [delphes] initial commit

* [delphes] formatting fixes
 2020-05-03 11:13:03 -05:00
Adam J. Stewart
1af31d24fd
GEOS: add new version (#16437) 2020-05-02 23:38:46 -05:00
Adam J. Stewart
eb4451dd1e
py-shapely: new version, Python 3.7 fix (#16438) 2020-05-02 23:38:30 -05:00
Adam J. Stewart
2e63e08192
py-cartopy: update package, fix PROJ.6 support (#16436) 2020-05-02 20:13:12 -05:00
Matthias Diener
1bc104e00e
colordiff: add version 1.0.19 (#16431) 2020-05-02 13:26:56 -05:00
Jonathon Anderson
08f88b4be6
Add a gpfs variant to openmpi package (#15793) 
Open MPI will detect and link against GPFS if it is present
on the system. This variant allows this to be disabled, even
if GPFS is present.
 2020-05-02 11:07:50 -05:00
Sajid Ali
adafdf0644
add hydra/pmix conflict (#16428) 2020-05-01 20:51:54 -05:00
Matthias Diener
668dcb78a1
py-opentuner: add version 0.8.2 (#16423) 2020-05-01 20:50:54 -05:00
Jen Herting
acabe2deba
[ncbi-magicblast] added version 1.5.0 (#16424) 2020-05-01 20:50:26 -05:00
Justin S
cf59220edc
stata: add version 16 (#16425) 2020-05-01 20:50:13 -05:00
mic84
c7552c0c72
amrex: New version 20.05 (#16427) 2020-05-01 20:47:18 -05:00
Kelly (KT) Thompson
b5b7ef2ce6
Provide update for py-pyside2 version 5.14.2.1. (#16426) 2020-05-01 17:32:31 -05:00
Justin S
f38820f89c
tbl2asn: new package at 20200301 (#16280) 
* tbl2asn: new package at 20200301

* tbl2asn: remove unused url

* tbl2asn: use spack decompression, fix permissions

* tbl2asn: change version
 2020-05-01 16:40:09 -05:00
Toyohisa Kameyama
40f70c4d4f
mt-metis: New package. (#16380) 
* mt-metis: New package.

* variant to 1 line.

* delete useless lines.
 2020-05-01 10:51:27 -05:00
Matt Larsen
69a0fbd2cb
raja: add awareness of the cuda architecture (#16377) 2020-05-01 10:07:12 +02:00
Jean-Laurent Picard
4f6c4743e3
arborx: fix build with new kokkos-legacy (#16413) 2020-05-01 09:30:27 +02:00
Christoph Junghans
7a56e6fce1
gromacs: add v2020.2 (#16408) 2020-04-30 19:01:07 -06:00
Satish Balay
4c69bc9d16
amrex: repo went through history rewrite - so use updates sha256sums (#16379) 2020-04-30 15:13:45 -05:00
Michael Kuhn
a24a12f229
sqlite: Add 3.31.1 (#16404) 2020-04-30 15:12:51 -05:00
Michael Kuhn
efbd8c1555
readline: Fix homepage (#16403) 2020-04-30 15:12:38 -05:00
Michael Kuhn
9920684600
gettext: Add 0.20.2 (#16402) 2020-04-30 15:12:26 -05:00
Michael Kuhn
f04b0d99a8
glib: Add 2.64.2 (#16401) 2020-04-30 15:12:13 -05:00
Michael Kuhn
d2fc61a019
libffi: Add 3.3 (#16400) 2020-04-30 15:12:00 -05:00
Michael Kuhn
c2704a6037
perl: Add 5.30.2 (#16396) 2020-04-30 15:11:46 -05:00
Michael Kuhn
7adcb23978
libxml2: Add 2.9.10 (#16399) 2020-04-30 14:29:50 -05:00
Michael Kuhn
15c1fbc677
meson: Add 0.54.1 (#16398) 2020-04-30 14:29:36 -05:00
Michael Kuhn
6855e8e10f
pcre: Add 8.44 (#16397) 2020-04-30 14:29:24 -05:00
Ben Bergen
6d7daf0def
Resolves: https://github.com/spack/spack/issues/16394 (#16395) 
Build problem with gcc 10.x
 2020-04-30 11:16:00 -06:00
Adam J. Stewart
b55b7d5707
Fix kokkos-kernels tuple unpacking (#16393) 2020-04-30 11:36:50 -05:00
Christoph Junghans
cfb307b8e7
lammps: fix build with kokkos (#16390) 2020-04-30 10:29:08 -06:00
Adam J. Stewart
6c24142ebd
Fix coreutils configure_args (#16391) 2020-04-30 11:13:23 -05:00
Christoph Junghans
74c9ba551a
cabana: add v0.2 and fix kokkos deps (#16389) 2020-04-30 09:49:02 -06:00
darmac
b0ecaa1093
Add new package: bashtop (#16383) 2020-04-30 10:45:48 -05:00
Satish Balay
b2df39ea3a
petsc: switch hdf5 spec from --with-hdf5-dir to --with-hdf5-lib (#16376) 
This way - we can detect and use hdf5:hl,fortran - if enabled, but not require it as a dependency
 2020-04-30 10:40:25 -05:00
Satish Balay
3a3f871718
xsdk: update to mfem and py-petsc4py changes (#16378) 
mfem variant hypre is now rolled into variant mpi - so update spec accordingly

mfem@4.0.1-xsdk+superlu-dist is broken and unsupported - so disable it

with the addition of py-petsc4py@3.13.0 - conretizer gets confused and is not picking py-petsc4py@3.12.0 as a compatible dependency with petsc@3.12. So manually specify it.
Also depends_on('py-libensemble@0.5.2+petsc4py ^py-petsc4py@3.12.0' causes concretizer to hang forever
 2020-04-30 10:33:02 -05:00
Christoph Junghans
d5d4e16f3d
graphviz: fix cairo dep (#16387) 2020-04-30 10:29:20 -05:00
Christoph Junghans
f005ec016b
kokkos: fix typos (#16388) 2020-04-30 09:09:13 -06:00
Jeremy
598c233f78
Update kokkos for new 3.x build systems (#16358) 
* change old Makefile-based Kokkos to kokkos-legacy

* add Kokkos 3.x packages

Co-authored-by: Jeremiah J Wilke <jjwilke@kokkos-dev-2.sandia.gov>
 2020-04-30 08:13:47 -06:00
Teodor Nikolov
9627cbbe1b
lapackpp and blaspp: added packages (develop branch) (#16373) 2020-04-30 16:05:45 +02:00
Toyohisa Kameyama
54b71b2b69
JHPCN-DF: added package at v1.1.0 (#16384) 2020-04-30 15:03:35 +02:00
Benoit Coste
6c751f931c
py-pyquaternion: added package at v0.9.5 (#16386) 2020-04-30 14:50:28 +02:00
Carson Woods
d12e588c60
charliecloud: add more checksummed versions (#16146) 
* Add more checksummed versions

* Remove all versions not supported by autotools build method

* Add old build system for older versions

* Add suggested changes
 2020-04-29 17:22:22 -05:00
Adam J. Stewart
eef75ddd45
py-mypy: setuptools needed at run-time (#16375) 2020-04-29 13:50:34 -05:00
Dr. Christian Tacke
0385e84775
boost: Patch for boostorg/process/issues/116 (#16371) 
Patch for "Unable to compile code using boost/process.hpp"
See: https://github.com/boostorg/process/issues/116
 2020-04-29 12:53:58 -05:00
darmac
42d7fd30c4
Add new package: brpc (#16309) 
* Add new package: brpc

* change a patch for brpc

* refine brpc version

* refine brpc patch constraint
 2020-04-29 09:58:35 -05:00
darmac
5697894b22
Add new package: graylog2-server (#16370) 2020-04-29 09:58:09 -05:00
darmac
890059c635
Add new package: libconfuse (#16368) 2020-04-29 09:57:38 -05:00
darmac
35b9901fa0
Add new package: fping (#16367) 2020-04-29 09:57:16 -05:00
darmac
0d9b003169
Add new package: trident (#16342) 
* Add new package: trident

* remove unused source code
 2020-04-29 08:20:05 -05:00
Jonathan R. Madsen
39bbe8f9d4
Update timemory to support new dependencies and expose more build options (#16241) 
* Update timemory/package.py to support new dependencies and expose more build options

* Added missing 'use_arch' option handling

* Fixes for python 2.6

* Fix pyflake error F632

* F632 flake fixes

* Update package.py

* Update package.py

* 80 char width + added extra conflicts + fixed kokkos_modules reference

* 79 char width

* Removed submodule builds

- added allinea_map variant
- disabled caliper by default
- added ompt_{standalone,llvm} variants

* flake8 updates

* 79 char width
 2020-04-29 08:19:17 -05:00
Joseph Ciurej
97e67b385c
ffmpeg: add v1.0.10, v2.8.15; add '+avresample'; improve variant handling (#16359) 
* ffmpeg: add older versions (i.e. 2.8.15, 1.0.10), add 'avresample' variant

* ffmpeg: update variant handling to support older versions (i.e. 2.8.15, 1.0.10)
 2020-04-29 09:33:22 +02:00
Joseph Ciurej
c37857f995
openscenegraph: add v3.4.0, v3.4.1; add '+ffmpeg' (#16360) 
* openscenegraph: add v3.4.0/3.4.1, update versioning to use git, improve dependency handling (esp. for ffmpeg, opengl)

* openscenegraph: add '+ffmpeg' variant, add 'jasper' dependency, clean up cmake config variables

* openscenegraph: reverted fetches to use checksums to improve reliability

* openscenegraph: add a few more explicit dependencies (e.g. png, tiff, glib).
 2020-04-29 09:27:27 +02:00
Ryan Mast
6c0d4fb5e5
helics: fixed dependency on boost (#16363) 2020-04-29 09:10:33 +02:00
Dr. Christian Tacke
67ad8ed546
root: added v6.20.04, better variant handling (#16362) 
* Add version 6.20.04
* This version still requires numpy for +python
* ROOT 6.20 renamed the define from python to pyroot:
  Add appropiate handling
 2020-04-29 09:05:17 +02:00
Adam J. Stewart
8b4b7aacbb
py-pandas: add 1.0.X release (#16366) 2020-04-28 23:14:17 -05:00
Ryan Mast
25c17e0ca6
helics: Add version 2.5.0 (#16364) 
Add HELICS package version 2.5.0
 2020-04-28 19:21:22 -05:00
Hadrien G
2d02769bea
[dd4hep] Fix inappropriate patch line break (#16361) 
Sometimes, text editors automate things a little too much...
 2020-04-28 19:17:13 -05:00
Jeffrey Salmond
703111c01b
Add amgx (#16357) 
* add amgx package

* add amgx variants for mkl and magma support

* fix typo in cmake option

* flake8 fix formatting

* Apply suggestions from code review - use mkl virtual provider

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Apply suggestions from code review - fix copypasta

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-04-28 14:36:55 -05:00
Carson Woods
6e63ff1688
netcdf-fortran: add new variants (#16046) 
* Add additional variants to netcdf-fortran

* Fix duplicate variant

* Clean up variants based on review feedback

* Addtional variant changes

* Convert jna variant to single line

* Fix proper version constraints for jna variant
 2020-04-28 11:15:19 -05:00
Stephen McDowell
4ed5cee940
jsoncpp add 1.9.2, patch %clang@10 for implicit conversion (#16153) 
* add 1.9.2, patch %clang@10 for implicit conversion

* flake8: "fix" hanging indent (squash: because is that really more readable?)
 2020-04-28 11:14:36 -05:00
darmac
af9c3b31de
Add new package: figlet (#16355) 2020-04-28 11:12:50 -05:00
Cameron Smith
d3ffb12274
kokkos: add versions 3.0.00 and 3.1.00 (#16354) 2020-04-28 11:11:50 -05:00
darmac
48de131b08
bazel: support for aarch64 platform (#16350) 2020-04-28 11:07:46 -05:00
darmac
a1e03151b2
Add new package: etcd (#16348) 2020-04-28 11:07:02 -05:00
darmac
2f88af4d2c
Add new package: kubernetes (#16347) 2020-04-28 11:06:24 -05:00
Jeffrey Salmond
4aed5daeba
adjust petsc to build cuda only when requested explicitly (#16275) 
* adjust petsc+cuda to build cuda only when requested explicitly

* activate petsc library support only when explicitly requested

* flake8 fixes
 2020-04-28 10:52:39 -05:00
Carson Woods
27b7d4bd21
openmpi: add additional variants (#16044) 
* Add variants to OpenMPI

* Add variant for toggling runpath

* Fix typo

* Remove blank line whitespace
 2020-04-28 10:51:30 -05:00
Tom Payerle
aec3589679
netcdf-c: Patch to support hdf linked against libtirpc (#15994) 
If hdf was built with +libtirpc, we need to add -ltirpc to our link
flags.
 2020-04-28 09:43:53 -05:00