Commit graph

21937 commits

Author SHA1 Message Date
Evan Bollig
204e8f4fa4
gromacs: added v2021 (#21473)
Fixed broken gromacs builds. gmxapi requires mpicxx to link properly

Gromacs requires mpicc override on CMAKE_C_COMPILER, not MPI_C_COMPILER
2021-02-05 11:47:22 +01:00
Evan Bollig
52058ad5a7
New versions of libfabric (1.11.1, 1.11.2) (#21496) 2021-02-04 16:36:57 -08:00
Evan Bollig
38e6d411a3
libjwt: Added openssl to resolve broken CICD pipeline (#21443) 2021-02-04 16:35:43 -08:00
Robert Pavel
87512df699
Disabled Non-Existant miniamr~mpi Variant (#21495)
Identified build error for miniamr~mpi. Upon further investigation, the
MPI dependencies are hard coded in that tag
2021-02-04 22:13:15 +00:00
Tom Payerle
935ad53649
lammps: Add support for a number of new LAMMPS add-on packages (#21494)
mliap
user-adios
user-awpmd
user-bocs
user-cgsdk
user-colvars
user-diffraction
user-dpd
user-drude
user-eff
user-fep
user-manifold
user-mesodpd
user-mesont
user-mgpt
user-mofff
user-phonon
user-plumed
user-ptm
user-qtb
user-reaction
user-sdpd
user-smd
user-smtbq
user-sph
user-tally
user-uef
user-yaff
2021-02-04 21:29:49 +00:00
Cody Balos
4ec044817b
sundials: add new version (#21488) 2021-02-04 12:19:12 -08:00
Sergei Shudler
10204826db
superlu: Add e4s testsuite-inspired smoke test (#21230) 2021-02-04 12:10:15 -08:00
Laurent Aphecetche
e0b7ca47d8
config: (darwin only) change prefix of external libuuid (#21480) 2021-02-04 14:01:40 -06:00
Adam J. Stewart
6fdb9309d6
py-xarray: add v0.16.2 (#21489) 2021-02-04 11:15:50 -08:00
Kelly (KT) Thompson
473f075896
[pkg][new version] Provide draco@7.9.1 (#21486)
+ Provide optional variant `pythontools` (default False) that adds a run-time dependency on
  `py-matplotlib`.
+ Latest versions require `cmake@3.18:` to support cuda features.
+ Enable a cmake option that forcibly disables qt support.  Previously, draco would enable qt
  support if it was available in the local build environment (outside of spack).
2021-02-04 10:37:36 -08:00
Kurt Sansom
f506b9c7f8
update: update pfunit releases (#21485) 2021-02-04 10:29:52 -08:00
m-shunji
0910f37f45
parallelio: add necessary resources (#21477)
Co-authored-by: Toyohisa Kameyama <kameyama@riken.jp>
2021-02-04 10:13:30 -08:00
Kelly (KT) Thompson
331a1b59b1
Provide eospac-6.4.2. (#21476) 2021-02-04 10:07:34 -08:00
Adam J. Stewart
ba70f90ee0
Fix usage of PythonPackage.test outside of PythonPackage (#20555) 2021-02-04 11:00:37 -06:00
Tomoki, Karatsu
f0cafd21ce
py-numpy: Fix for new version of numpy with Fujitsu compiler. (#21479)
* Change the version to apply patches.

* Change the name of the Fujitsu compiler to 'fujitsu' in numpy.
2021-02-04 10:58:48 -06:00
Adam J. Stewart
df5992293a
Python: add maintainer(s) (#21125)
* Python: add maintainer(s)

* Fix unit tests
2021-02-04 10:00:21 -06:00
Adam J. Stewart
d14a6dc1f7
py-mypy: add v0.800 (#21386) 2021-02-04 10:00:03 -06:00
Seth R. Johnson
31722ac994
Graphviz: don't build ghostscript when ~ghostscript (#19615)
* graphviz: Remove ghostscript requirement when ~ghostscript

* Add doc variant and patch for 2.44.1

* Patch does not apply

* Update graphviz versions, using archives rather than git hash

* Complete implementation of doc variant

* Fix typo
2021-02-04 09:59:24 -06:00
Harmen Stoppels
39a429b2a3
dbcsr: add opencl as a third backend (#21468) 2021-02-04 13:44:59 +00:00
Massimiliano Culpo
694d633a2c
spack external find: allow to search by tags (#21407)
This commit adds an option to the `external find`
command that allows it to search by tags. In this
way group of executables with common purposes can
be grouped under a single name and a simple command
can be used to detect all of them.

As an example introduce the 'build-tools' tag to
search for common development tools on a system
2021-02-04 13:17:32 +01:00
Andrew-Dunning-NNL
e9ae44fd8c
py-flufl-lock: new recipe (#21334)
* py-flufl-lock: new recipe

* py-flufl-lock: fix typing extension when no longer provisional
2021-02-03 21:15:48 -06:00
Greg Becker
457fc4c095
link gettext properly for git when gettext does not provide libintl (#21472) 2021-02-04 01:45:53 +00:00
Frank Willmore
beb4d968ef
intel-oneapi-compilers/mpi: add module support (#20808)
Facilitate running intel-oneapi-mpi outside of Spack (set PATH,
LD_LIBRARY_PATH, etc. appropriately).

Co-authored-by: Robert Cohn <rscohn2@gmail.com>
2021-02-03 16:21:54 -08:00
Frank Willmore
eb345faa57
intel-oneapi-compilers: add to LD_LIBRARY_PATH so that it finds libimf.so (#20717)
* add  to LD_LIBRARY_PATH so that it finds libimf.so

* amrex: fix handling of CUDA arch (#20786)

* amrex: fix handling of CUDA arch
* amrex: fix style
* amrex: fix bug
* Update var/spack/repos/builtin/packages/amrex/package.py
* Update var/spack/repos/builtin/packages/amrex/package.py

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* ecp-data-vis-sdk: Combine the vis and io SDK packages (#20737)

This better enables the collective set to be deployed togethor satisfying
eachothers dependencies

* r-sf: fix dependency error (#20898)

* improve documentation for Rocm (hip amd builds) (#20812)

* improve documentation

* astyle: Fix makefile for install parameter (#20899)

* llvm-doe: added new package (#20719)

The package contains duplicated code from llvm/package.py,
will supersede solve.

* r-e1071: added v1.7-4 (#20891)

* r-diffusionmap: added v1.2.0 (#20881)

* r-covr: added v3.5.1 (#20868)

* r-class: added v7.3-17 (#20856)

* py-h5py: HDF5_DIR is needed for ~mpi too (#20905)

For the `~mpi` variant, the environment variable `HDF5_DIR` is still required.  I moved this command out of the `+mpi` conditional.

* py-hovorod: fix typo on variant name in conflicts directive (#20906)

* fujitsu-fftw: Add new package (#20824)

* pocl: added v1.6 (#20932)

Made version 1.5 or lower conflicts with a64fx.

* PCL: add new package (#20933)

* r-rle: new package (#20916)

Common 'base' and 'stats' methods for 'rle' objects, aiming to make it
possible to treat them transparently as vectors.

* r-ellipsis: added v0.3.1 (#20913)

* libconfig: add build dependency on texinfo (#20930)

* r-flexmix: add v2.3-17 (#20924)

* r-fitdistrplus: add v1.1-3 (#20923)

* r-fit-models: add v0.64 (#20922)

* r-fields: add v11.6 (#20921)

* r-fftwtools: add v0.9-9 (#20920)

* r-farver: add v2.0.3 (#20919)

* r-expm: add v0.999-6 (#20918)

* cln: add build dependency on texinfo (#20928)

* r-expint: add v0.1-6 (#20917)

* r-envstats: add v2.4.0 (#20915)

* r-energy: add v1.7-7 (#20914)

* r-ellipse: add v0.4.2 (#20912)

* py-fiscalyear: add v0.3.0 (#20911)

* r-ecp: add v3.1.3 (#20910)

* r-plotmo: add v3.6.0 (#20909)

* Improve gcc detection in llvm. (#20189)

Co-authored-by: Tom Scogland <tom.scogland@gmail.com>
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>

* hatchet: updated urls (#20908)

* py-anuga: add new package (#20782)

* libvips: added v8.10.5 (#20902)

* libzmq: add platform conditions to libbsd dependency (#20893)

* r-dtw: add v1.22-3 (#20890)

* r-dt: add v0.17 (#20889)

* r-dosnow: add v1.0.19 (#20888)

* add version 1.0.16 to r-doparallel (#20886)

* add version 1.3.7 to r-domc (#20885)

* add version 0.9-15 to r-diversitree (#20884)

* add version 1.3-3 to r-dismo (#20883)

* add version 0.6.27 to r-digest (#20882)

* add version 1.5 to r-rngtools (#20887)

* add version 1.5.8 to r-dicekriging (#20877)

* add version 1.4.2 to r-httr (#20876)

* add version   1.28 to r-desolve (#20875)

* add version   2.2-5 to r-deoptim (#20874)

* add version   0.2-3 to r-deldir (#20873)

* add version   1.0.0 to r-crul (#20870)

* add version   1.1.0.1 to r-crosstalk (#20869)

* add version   1.0-1 to r-copula (#20867)

* add version 5.0.2 to r-rcppparallel (#20866)

* add version   2.0-1 to r-compositions (#20865)

* add version 0.4.10 to r-rlang (#20796)

* add version 0.3.6 to r-vctrs (#20878)

* amrex: add ROCm support (#20809)

* add version 2.0-0 to r-colorspace (#20864)

* add version 1.3-1 to r-coin (#20863)

* add version   0.19-4 to r-coda (#20862)

* add version 1.3.7 to r-clustergeneration (#20861)

* add version 0.3-58 to r-clue (#20860)

* add version 0.7.1 to r-clipr (#20859)

* add version 2.2.0 to r-cli (#20858)

* add version 0.4-3 to r-classint (#20857)

* add version 0.1.2 to r-globaloptions (#20855)

* add version 2.3-56 to r-chron (#20854)

* add version 0.4.10 to r-checkpoint (#20853)

* add version 2.0.0 to r-checkmate (#20852)

* add version 1.18.1 to r-catools (#20850)

* add version 1.2.2.2 to r-modelmetrics (#20849)

* add version 3.0-4 to r-cardata (#20847)

* add version 1.0.1 to r-caracas (#20846)

* r-lifecycle: new package at v0.2.0 (#20845)

* add version 3.0-10 to r-car (#20844)

* add version 3.4.5 to r-processx (#20843)

* add version 1.5-12.2 to r-cairo (#20842)

* add version 0.2.3 to r-cubist (#20841)

* add version 2.6 to r-rmarkdown (#20838)

* add version 1.2.1 to r-blob (#20819)

* add version 4.0.4 to r-bit (#20818)

* add version 2.4-1 to r-bio3d (#20816)

* add version 0.4.2.3 to r-bibtex (#20815)

* add version 3.1-4 to r-bayesm (#20807)

* add version 1.2.1 to r-backports (#20806)

* add version 2.0.3 to r-argparse (#20805)

* add version 5.4-1 to r-ape (#20804)

* add version 0.8-18 to r-amap (#20803)

* r-pixmap: added new package (#20795)

* zoltan: source code location change (#20787)

* refactor path logic

* added some paths to make compilers and libs discoverable

* add  to LD_LIBRARY_PATH so that it finds libimf.so
and cleanup PEP8

* refactor path logic

* adding paths to LIBRARY_PATH so compiler wrappers will find -lmpi

* added vals for CC=icx, CXX=icpx, FC=ifx to generated module

* back out changes to intel-oneapi-mpi, save for separate PR

* Update var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py

path is joined in _ld_library_path()

Co-authored-by: Robert Cohn <rscohn2@gmail.com>

* set absolute paths to icx,icpx,ifx

* dang close parenthesis

Co-authored-by: Robert Cohn <rscohn2@gmail.com>
Co-authored-by: mic84 <mrosso@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Chuck Atkins <chuck.atkins@kitware.com>
Co-authored-by: darmac <xiaojun2@hisilicon.com>
Co-authored-by: Danny Taller <66029857+dtaller@users.noreply.github.com>
Co-authored-by: Tomoyasu Nojiri <68096132+t-nojiri@users.noreply.github.com>
Co-authored-by: Shintaro Iwasaki <siwasaki@anl.gov>
Co-authored-by: Glenn Johnson <glenn-johnson@uiowa.edu>
Co-authored-by: Kelly (KT) Thompson <KineticTheory@users.noreply.github.com>
Co-authored-by: Henrique Mendonça <henrique@users.noreply.github.com>
Co-authored-by: h-denpo <57649496+h-denpo@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Thomas Green <tomgreen66@hotmail.com>
Co-authored-by: Tom Scogland <tom.scogland@gmail.com>
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>
Co-authored-by: Abhinav Bhatele <bhatele@cs.umd.edu>
Co-authored-by: a-saitoh-fj <63334055+a-saitoh-fj@users.noreply.github.com>
Co-authored-by: QuellynSnead <quellyn@lanl.gov>
2021-02-03 12:04:23 -08:00
Andrew-Dunning-NNL
22ee367794
py-atpublic: new recipe (#21332) 2021-02-03 13:53:54 -06:00
Hadrien G
91d64dd223
acts: Add version 5.0 (#21466) 2021-02-03 11:50:28 -08:00
Brian Van Essen
db402ed2e3
Set the variant to alway be true since it is requires cuda. (#21358) 2021-02-03 20:44:53 +01:00
Massimiliano Culpo
ba42c36f00
concretizer: simplify "fact" method (#21148)
The "fact" method before was dealing with multiple facts
registered per call, which was used when we were emitting
grounded rules from knowledge of the problem instance.

Now that the encoding is changed we can simplify the method
to deal only with a single fact per call.
2021-02-03 10:12:03 -08:00
Frank Willmore
8be833b242
adding environment to OneMKL packages so that examples will build (#21377) 2021-02-03 09:50:37 -08:00
Josh Essman
61641ecff2
sundials: expose monitoring build option (#21429) 2021-02-03 09:39:57 -08:00
Harmen Stoppels
b597e01e33
Add cuda as opencl provider (#21464) 2021-02-03 09:06:49 -08:00
Tomoyasu Nojiri
2b7547c03c
http-load: Fix checksum error (#21459) 2021-02-03 11:03:50 -06:00
Tomoyasu Nojiri
1a6fe52486
http-post: Fix checksum error (#21460) 2021-02-03 11:03:28 -06:00
Tomoyasu Nojiri
4d194dc5e4
http-get: Fix checksum error (#21458) 2021-02-03 11:03:00 -06:00
Tomoyasu Nojiri
6f4b7870f2
http-ping: Fix checksum error (#21457) 2021-02-03 11:02:42 -06:00
Tomoyasu Nojiri
0a0e0b9b67
symlinks: Fix checksum error (#21456) 2021-02-03 11:02:07 -06:00
Tomoyasu Nojiri
54763a16f4
py-dulwich: Fix python depend (#21461) 2021-02-03 11:00:45 -06:00
iarspider
95fcd9ac13
superchic: added new package (#21463)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-02-03 15:29:52 +01:00
sameershende
d5d1cb09ad
Updated TAU v2.30.1. (#21453) 2021-02-02 15:21:30 -08:00
mic84
e2294ea0b0
amrex: new version 21.02 (#21426) 2021-02-02 14:49:51 -08:00
iarspider
4691177bbf
New package: apfel (#21440) 2021-02-02 14:42:07 -08:00
Axel Huebl
d8ba71993c
openPMD-api: 0.13.2 (#21450) 2021-02-02 14:25:18 -08:00
Andrew-Dunning-NNL
09190c0876
py-bash-kernel: new package (#21441)
* py-bash-kernel: new package

* py-bash-kernel: remove git bash kernel dependency
2021-02-02 15:42:08 -06:00
Bryan Herman
182ab78940
add py-python-fsutil recipe (#21449) 2021-02-02 15:41:21 -06:00
Mark W. Krentel
040204c261
intel-xed: add patch to 12.0.1 to fix segfault (#21436)
Fix segfault due to uninitialized data when trying to decode some cases of data that aren't a valid instruction.
2021-02-02 12:40:24 -08:00
Greg Becker
7dcf3f7aed
add intel oneapi to compiler/pkg translations (#21448) 2021-02-02 19:11:51 +00:00
bryanherman
d048048911
py-nbsphinx: new package (#21444)
* added py-nbsphinx package

* added a comment about nbsphinx use
2021-02-02 11:24:28 -06:00
Andrew-Dunning-NNL
959df6bb12
py-grandalf: new recipe (#21348)
* py-grandalf: new recipe

* py-grandalf: add runtime dependency

* py-grandalf: add runtime dependency)
2021-02-02 11:22:36 -06:00
Andrew-Dunning-NNL
59a54905ea
py-dictdiffer: fix offline dependencies (#21345)
* py-dictdiffer: fix offline dependencies

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-02-02 11:21:58 -06:00
Andrew-Dunning-NNL
8b6c468cdf
py-ftfy: new recipe (#21333)
* py-ftfy: new recipe

* py-ftfy: depend on python>3.5
2021-02-02 11:19:02 -06:00