Commit graph

15286 commits

Author SHA1 Message Date
Axel Huebl
7be7d672b7
OpenBLAS: Fix LLVM 9.0.0 ICE on macOS (#16471)
Recently added patch to port the LLVM 9.0.0 ICE with OpenBLAS and
AVX-512 instructions as well to AppleClang (11.0.3).
2020-05-05 13:45:01 -05:00
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
Greg Becker
3ae76d8c1e
bugfix: config:install_hash_length ignored (#15919) 2020-05-04 23:10:25 -07:00
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
Greg Becker
8e2f5ba861
environments: allow sigils to apply to entire reference (#15245)
* environments: allow sigils to apply to entire reference
2020-05-04 15:11:10 -07:00
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
Oliver Breitwieser
1cff717ca8 Fix git-related commands not working in worktrees
If spack is checked out in a git worktree (see [1]), all git-related
commands fail because the `spack_is_git_repo()`-check is not thorough
enough.

When developing in a feature-branch in a seperate worktree, this is
annoying as all unittests regarding git-related spack commands fail,
cluttering the test results with false-positives.

[1]: https://git-scm.com/docs/git-worktree

Change-Id: I94b573a2c0e058e9ccc169e7ee6561626fbb06fd
2020-05-04 14:39:25 -07:00
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
Peter Scheibel
40df44e021
Revert "Testing: fix unintended interactions between tests (#16003)" (#16420)
This was breaking tests on develop.
2020-05-01 13:39:43 -07:00