Commit graph

14974 commits

Author SHA1 Message Date
Michael Kuhn
3268cf4b96
libfyaml: new package (#21604) 2021-02-11 16:41:16 +01:00
Michael Kuhn
ef5b15be40
libcyaml: new package (#21598) 2021-02-11 16:40:28 +01:00
Michael Kuhn
da46da1c2a
libyaml: add 0.2.5 (#21597) 2021-02-11 16:40:06 +01:00
Chuck Atkins
a57598defe
doxygen: fix gcc getting stuck in an infinite loop (#21614) 2021-02-11 16:35:51 +01:00
Michael Kuhn
e2084ea6fd
glib: add 2.66.6 (#21605) 2021-02-11 16:27:57 +01:00
M. Eric Irrgang
dea9334189
Apply compiler filters to GROMACS installation. (#21621)
The GROMACS package embeds references to its build tool chain.
Use the Spack utilities to make sure these references are correct
outside of the isolated Spack build environment.
2021-02-11 14:52:32 +00:00
victorusu
fd8eac7052
Add sanity checks to reframe recipe (#21622) 2021-02-11 15:35:57 +01:00
victorusu
2fbc8caf86
pygelf: add v0.4.0 (#21620) 2021-02-11 15:23:55 +01:00
M. Eric Irrgang
944cb5dec6
Update GROMACS package (#21617)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-02-11 15:16:27 +01:00
Michael Kuhn
fc00944900
meson: remove cmake dependency (#21607)
cmake was added as a runtime dependency to meson in #20449. This
introduces an unnecessary implicit cmake dependency, which increases
build time for meson considerably. cmake is only one of many methods for
finding dependencies (pkg-config, qmake etc.), which are also not
runtime dependencies of meson. Add cmake as a build dependency to mesa
instead.
2021-02-10 23:46:52 -05:00
Axel Huebl
48af2ac8f9
adios2: Add 2.7.1 release (#21584)
Add the latest release of ADIOS2.
2021-02-10 23:44:42 -05:00
Jen Herting
5828a2cd31
[py-chalice] py-typing causes issues with python >= 3.5 (#21202)
* [py-chalice] py-typing causes issues with python >= 3.5

* [py-chalice] changed upperbound on typing
2021-02-10 21:31:02 +00:00
eugeneswalker
e15a3438a8
ascent: add version v0.6.0 (#21573) 2021-02-10 10:14:16 -08:00
a-saitoh-fj
24dd5d12a5
py-llvmlite: Changing build options when using the FUJITSU compiler (#21585) 2021-02-10 09:58:10 -06:00
vvolkl
08972014f8
[py-uproot4] add new versions (#21588) 2021-02-10 09:57:10 -06:00
a-saitoh-fj
bd836540f2
New package: py-dask-sphinx-theme (#21582) 2021-02-10 10:22:03 +01:00
a-saitoh-fj
cf9a7bc7f6
pandoc modified:package.py (#21581) 2021-02-10 10:20:47 +01:00
h-denpo
7d48bbfd3a
raxml-ng: Fixed typo: (#21580) 2021-02-10 10:17:28 +01:00
Matt Schramm
175d614bc6
Update package.py (#21577) 2021-02-10 10:16:22 +01:00
Shintaro Iwasaki
ca6ec59a86
sollve: deprecate the sollve package (#21578) 2021-02-10 01:49:20 +00:00
Jen Herting
a938cc512b
New package: py-moviepy (#20751)
* [py-moviepy] created template

* [py-moviepy] added dependencies

* [py-moviepy] removed fixmes, added homepage and description

* [py-moviepy] updated to pypi and updated checksum

* [py-moviepy] added setuptools dependency

* [py-moviepy] more specific version limit

* [py-moviepy] added checksum for version 1.0.1

* [py-moviepy] numpy restriction not nesessary here
2021-02-09 23:18:51 +00:00
kean-smullen-nnl
32056da93b
New Package: py-xgboost (#21470)
* new python package py-xgboost added

* py-xgboost spack style applied

* py-xgboost: Addressing PR #21470 comments. Added variant descriptions and fixed scikit-learn when clause
2021-02-09 23:12:20 +00:00
Satish Balay
42e8a64660
xsdk: update petsc4py, strumpack dependencies (#21569) 2021-02-10 00:10:09 +01:00
Adam J. Stewart
d580ac302d
3DTK: add new package (#20931)
* 3DTK: add new package

* Add missing opencv variants

Co-authored-by: Michael Kuhn <michael@ikkoku.de>

* Fix cmake version req, add eigen dep

* Prefer trunk version

* Tell 3dtk where to find eigen

* Fix installation

* Fix installation

Co-authored-by: Michael Kuhn <michael@ikkoku.de>
2021-02-09 16:45:41 -06:00
Ethan Stam
865d38afa7
ParaView, LLVM: add -shared-intel to solve intel linking failures (#18195) 2021-02-09 23:26:49 +01:00
Desmond Orton
2697c73097
New Package r-reproducible (#21434) 2021-02-09 14:11:14 -08:00
Glenn Johnson
d01edbb48e
Fix groff build with long interpeter line (#21549)
This PR fixes the case where groff fails to build if the spack install
path is really long. There are a couple of perl scripts that get built,
and used, during the build phase that will fail when the perl
interpreter line is too long. Filtering the lines will not work because
the files don not exist after the configure phase and patching after the
build phase is too late.  This PR runs the scripts explicitly with the
spack perl via the $(PERL) variable in the call to the script.
2021-02-09 13:54:51 -08:00
Glenn Johnson
f7a9fbc688
Update the Spack R BioConductor packages to Bioconductor-3.12 (#21575) 2021-02-09 15:35:30 -06:00
takanori-ihara
fe863b68b2
biobambam2: Add test method and test scripts. (#21504)
Co-Authored-By: Tamara Dahlgren <dahlgren1@llnl.gov>
2021-02-09 12:33:55 -08:00
Jordan Ogas
02a4abadfa
add charliecloud 0.22 (#21574) 2021-02-09 12:15:03 -08:00
Dr. Christian Tacke
11711fcbe5
root: 6.22.04 works with xrootd 5 (#21572)
ROOT version 6.22.04 has been ported to support xrootd 5.
So let's support that.

See: https://github.com/root-project/root/commit/a33b156e3bf809343eda08150666154a
2021-02-09 11:33:14 -08:00
Evan Bollig
cc6d055786
Relion 3.1.1 patch for Ubuntu18.04 (#21556) 2021-02-09 11:07:06 -08:00
Cyrus Harrison
533d4bbc3c
add conduit 0.7.0 release (#21558) 2021-02-09 11:02:30 -08:00
Adam J. Stewart
7ccb9992a6
Procedure to deprecate old versions of software (#20767)
* Procedure to deprecate old versions of software

* Add documentation

* Fix bug in logic

* Update tab completion

* Deprecate legacy packages

* Deprecate old mxnet as well

* More explicit docs
2021-02-09 13:51:18 -05:00
Toyohisa Kameyama
b802e75274
penblas: fix link error in dependent packages. (#21561) 2021-02-09 09:53:09 -08:00
Harmen Stoppels
0760c7c704
Add more cmake patch releases (#21562) 2021-02-09 09:48:34 -08:00
Adam J. Stewart
341eec8dfb
py-pandas: add v1.2.2 (#21568) 2021-02-09 09:32:58 -08:00
Shintaro Iwasaki
3c874e22b5
bolt: add new versions (#21550) 2021-02-09 09:43:12 +01:00
Sreenivasa Murthy Kolam
bff4469d8f
replace libelf with elfutils in hip-rocclr (#21421) 2021-02-09 08:21:05 +01:00
Jen Herting
58f3d0986d
New package: py-msgpack-numpy (#21548)
* [py-msgpack-numpy] created template

* [py-msgpack-numpy] added dependencies

* [py-msgpack-numpy] added homepage and description. removed fixmes. fixed copyright date

* [py-msgpack-numpy] url -> pypi
2021-02-08 21:20:07 +00:00
Andrew W Elble
dc1a05d273
py-tensorflow-estimator: update for 2.4.0 (#21546)
* py-tensorflow-estimator: update for 2.4.0

* build/run deptypes, switch to common tmpfile logic
2021-02-08 21:14:20 +00:00
Andrew W Elble
7fd8b775ad
py-tensorboard: add new versions (#21545) 2021-02-08 14:38:09 -06:00
ketsubouchi
0e3b12776c
xforms: new package (#21535) 2021-02-08 12:27:36 -08:00
Jen Herting
843e1993ae
New package: py-imageio-ffmpeg (#20749)
* [py-imageio-ffmpeg] created template

* [py-imageio-ffmpeg] added dependencies

* [py-imageio-ffmpeg] added runtime dependency

* [py-imageio-ffmpeg] removed fixmes, added homepage and description

* [py-imageio-ffmpeg] url -> pypi and updated checksum
2021-02-08 13:30:45 -06:00
AMD Toolchain Support
fc374febf2
amdtoolchain support for openfoam (#21536) 2021-02-08 13:22:59 -06:00
Sergei Shudler
6447ec6ff5
Smoke test for parallel-netcdf package (#21400) 2021-02-08 11:21:52 -08:00
Satish Balay
c01065ee73
petsc: update to version 3.14.4, and petsc4py to 3.14.1 (#21544) 2021-02-08 13:05:52 -06:00
Pieter Ghysels
b37c601a01
Strumpack slate variant (#21542)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-02-08 18:27:41 +00:00
Toyohisa Kameyama
512c8a1f1a
ldak: build only x86_64 linux. (#21414) 2021-02-08 10:22:47 -08:00
Howard Pritchard
45040589c8
paraview: disable VTK_PYTHON_OPTIONAL_LINK for cce (#21357)
when building paraview 5.8 or newer.

See https://gitlab.kitware.com/vtk/vtk/-/merge_requests/7482for background info.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2021-02-08 09:53:06 -08:00
Satish Balay
66dc7d8c53
petsc4py: workaround LDSHARED change in 3cc5b7adc7 (#21541) 2021-02-08 11:43:46 -06:00
victorusu
9d8b8553f1
Add ReFrame 3.4 (#21540) 2021-02-08 17:00:12 +01:00
Andrew-Dunning-NNL
aba9207254
py-dvc: new package (#21516)
* py-dvc: new package

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

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

* py-dvc: add version dependency for py-networkx

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-02-08 09:54:28 -06:00
AMD Toolchain Support
9eb5c8f843
cp2k: added support for AMD toolchain (#21371) 2021-02-08 11:03:56 +01:00
Tomoyasu Nojiri
83f7541420
libqglviewer: add dependency on glu (#21438) 2021-02-08 10:55:56 +01:00
Tomoyasu Nojiri
b760dbc502
pangolin: add dependency on glu (#21439) 2021-02-08 10:46:24 +01:00
lpoirel
aa86523aaa
mumps: don't put absolute path in soname (#21247) 2021-02-08 10:30:27 +01:00
Adam J. Stewart
824f6ad3f4
py-matplotlib: clarify backend variant description (#21520) 2021-02-08 09:36:35 +01:00
Adam J. Stewart
8a2fc484fa
py-fiscalyear: add v0.3.1 (#21523) 2021-02-08 09:30:50 +01:00
Adam J. Stewart
480e4f0b4c
py-numpy: add v1.20.1 (#21525) 2021-02-08 09:27:31 +01:00
darmac
f4f2647134
libproxy: add v0.4.17 (#21526)
Added dependency on Python and zlib
2021-02-08 09:25:10 +01:00
darmac
1bee682d67
pciutils: add a PREFIX parameter to make invocation (#21527) 2021-02-08 09:22:55 +01:00
darmac
ca24b6c740
bird: add build dependencies (#21528) 2021-02-08 09:20:48 +01:00
Desmond Orton
de99535f9a
Package/r require and subpackage dep fix (#21433) 2021-02-07 13:48:14 -06:00
Sreenivasa Murthy Kolam
fef79b7e9b
fix build failure with boost-1.58.0 by using higher revision (#21376) 2021-02-07 13:32:59 +01:00
Mark Abraham
9414b11490
Clarify GROMACS relaxed double option (#21510)
* Clarify relaxed double precision option

This is only intended for use on the Fujitsu PRIMEHPC platform

* Fix typo

* Shorten line to keep linter happy
2021-02-07 05:29:53 -07:00
Richarda Butler
5f75221522
Bugfix: Install font-util (#20179)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
2021-02-07 12:52:07 +01:00
m-shunji
6e29a36d88
mpas-model: add a necessary resource (#21478) 2021-02-07 12:47:54 +01:00
Aurelien Bouteiller
eb3338ed1b
Parsec: new release (#21481) 2021-02-07 12:47:20 +01:00
Hanqi Guo
4f73dff204
adding new package FTK (the feature tracking kit) (#21493) 2021-02-07 12:46:08 +01:00
Robert Pavel
3387cefe1e
Fixed xsbench~mpi Spec (#21498) 2021-02-07 12:45:43 +01:00
Christoph Junghans
d5953d75bf
libecpint: add v1.0.5 (#21502) 2021-02-07 12:44:23 +01:00
Adam J. Stewart
f37ffbe932
py-xarray: fix smoke tests (#21503) 2021-02-07 12:43:40 +01:00
marvinbernhardt
d58ed20239
handle other architectures than Intel (#21509) 2021-02-07 12:37:56 +01:00
Robert Pavel
d630d63755
Added Conflict for macsio@1.1 ~mpi (#21513)
Added conflict for macsio@1.1~mpi after investigating source code. As of
1.1 tag macsio does not properly guard out MPI commands. This is
verified as corrected in @develop
2021-02-07 12:34:00 +01:00
Filippo Spiga
7d371e5b55
Adding NVIDIA HPC SDK 21.1 (#21514) 2021-02-07 12:33:08 +01:00
Robert Pavel
35b5d37f10
Fixed Typo in Examinimd Spackage (#21515) 2021-02-07 12:29:24 +01:00
darmac
adb350c23c
collectd: add test dependency (#21522) 2021-02-07 12:28:49 +01:00
Phil Carns
b54e9b0b31
mercury variant to control checksumming feature (#21467) 2021-02-07 12:26:49 +01:00
Adam Moody
121e55832a
mpifileutils: add v0.11 (#21432) 2021-02-07 12:18:42 +01:00
darmac
7bfb4a2d7d
gobject-introspection: enable gobject option in cairo (#21404) 2021-02-07 12:09:20 +01:00
kkauder
1b9be33f84
Removed boost dependence and other outdated bits (#21394) 2021-02-07 12:06:59 +01:00
darmac
7b38221798
aspcud: update version to fix build error (#21521) 2021-02-07 11:55:37 +01:00
darmac
7020c86874
r-rmariadb: add mariadb library path (#21406) 2021-02-07 02:49:42 +00:00
eugeneswalker
f3f8a72bbd
trilinos: @develop requires cxxstd>=14 (#21519) 2021-02-06 13:24:30 -05:00
Jean-Paul Pelteret
a544030517
Add package: py-fava (#21275)
* Add package: py-beancount-fava

* Rename package; fixes

* Fixes

* Cleanup; simplify regex used to ignore files
2021-02-05 21:12:29 +00:00
Adam J. Stewart
c3206656bc
mxnet: convert to CMakePackage (#21385)
* mxnet: convert to CMakePackage

* Package isn't installed yet, can't find libs

* Fix bug with GCC 8+ and CUDA 10 on PowerPC

* Add space

* Add patch to fix cmake cuda flags

* Space no longer needed

* Add patch to fix OpenBLAS linking

* Add missing CMake flag

* Fix env set, default to Distribution

* Add new version, patch
2021-02-05 12:48:20 -06:00
Bryan Herman
67667c96db
py-python-benedict: new package (#21501)
* added py-python-benedict recipe

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-02-05 10:38:17 -06:00
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
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
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
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
Andrew-Dunning-NNL
71309f75b2
py-dulwich: new recipe (#21330)
* py-dulwich: new recipe

* py-dulwhich: add python dependency

* py-dulwich: fix flake8 whitespace
2021-02-02 11:15:34 -06:00
Andrew-Dunning-NNL
49b3ab684e
py-flatten-dict: new recipe (#21329)
* py-flatten-dict: new recipe

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

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

* py-flatten-dict: fix dependencies

* py-flatten-dict: fix dependency

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-02-02 11:14:12 -06:00
apreifsteck
df0cc9ee02
OSU mvapich2 GDR 2.3.5 package.py update (#21270)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: NOWLAB PACKAGER <mvapich-help@cse.ohio-state.edu>
2021-02-01 18:48:16 -08:00
Sergei Shudler
8f2acc3123
mfem: Add e4s testsuite-inspired smoke test (#21228) 2021-02-01 17:49:20 -08:00
Desmond Orton
71b12e9b27
New R Package Pegas@0.14 (#21359) 2021-02-01 16:42:44 -08:00
Desmond Orton
6cc23e6137
New Feature r-quickplot (#21430) 2021-02-01 18:02:14 -06:00
iarspider
eac95c866a
FastJet: add optional patch to make random generator thread-local (#21395) 2021-02-01 11:18:04 -08:00
Phil Carns
03fce1f0c9
replace margo pkg with updated mochi-margo pkg (#20273) 2021-02-01 12:38:02 -06:00
iarspider
586ff05af1
New package: frontier-client (#21405) 2021-02-01 10:23:56 -08:00
iarspider
5add6c4e03
New package: unigen (#21338) 2021-02-01 10:21:02 -08:00
Ryan Mast
5cb8d1894b
libgcrypt: add versions up to 1.9.1 (#21401) 2021-02-01 10:11:51 -08:00
Jose E. Roman
4523cce791
SLEPc: add v3.14.2 (#21422) 2021-02-01 09:42:13 -08:00
Adam J. Stewart
1d636bed6a
R: add maintainer(s) (#21119)
* R: add maintainer(s)

* Add maintainer to base class
2021-02-01 11:33:33 -06:00
Andrew-Dunning-NNL
f781403615
py-colored-traceback: new package (#21423) 2021-02-01 11:14:00 -06:00
eugeneswalker
0b58499d7a
llvm: "master" branch is now "main" branch (#21411) 2021-02-01 08:32:36 -06:00
iarspider
af988fc32d
sqlite: add v3.32.03 (#21417) 2021-02-01 15:04:19 +01:00
Tomoki, Karatsu
6feb697b62
abinit: fix build with Fujitsu compilers (#21213) 2021-02-01 15:03:03 +01:00
iarspider
260706c186
coin3d: depend on gl/glu (virtual packages), not on opengl/openglu (#21419) 2021-02-01 15:01:05 +01:00
Tomoyasu Nojiri
c279983c10
cgdb: add a few build dependencies (#20927) 2021-02-01 15:00:52 +01:00
Jean-Paul Pelteret
a04e0d2525
Add package: py-beancount (#21274)
* Add package: py-beancount

* Fixes
2021-01-31 12:29:29 -06:00
darmac
f7929aaeb1
chrony: add missing dependency (#21403) 2021-01-31 12:21:23 -05:00
Jean-Paul Pelteret
6ac3d98f4c
Add package: py-flask-babel (#21272) 2021-01-31 10:50:16 -06:00
Jean-Paul Pelteret
6c03c9996a
Add package: py-markdown2 (#21273) 2021-01-31 10:49:49 -06:00
Adam J. Stewart
c950f4a4ff
py-numpy: add v1.20.0 (#21409) 2021-01-31 06:28:21 +01:00
Toyohisa Kameyama
c175c05af9
quantum-expresso: fix for Fujitsu compiler (#21368) 2021-01-29 17:36:58 -08:00
Harmen Stoppels
371247c14a
Fix https://github.com/spack/spack/pull/21391#issuecomment-769961025 (#21397) 2021-01-29 17:21:56 -08:00
Massimiliano Culpo
13ac7198d3
clingo: added a package with option for bootstrapping clingo (#20652)
* clingo/clingo-bootstrap: added a package with option for bootstrapping clingo

package builds in Release mode
uses GCC options to link libstdc++ and libgcc statically

* clingo-bootstrap: apple-clang options to bootstrap statically on darwin

* clingo: fix the path of the Python interpreter

In case multiple Python versions are in the same prefix
(e.g. when clingo is built against an external Python),
it may happen that the Python used by CMake does not
match the corresponding node in the current spec.

This is fixed here by defining "Python_EXECUTABLE"
properly as a hint to CMake.

* clingo: the commit for "spack" version has been updated.
2021-01-29 12:22:57 -08:00
Robert Underwood
0611036abd
doxygen: add support for external detection (#20642) 2021-01-29 21:05:48 +01:00
Peter Lindstrom
0f82fa5151
zfp: several package improvements (#21244)
- add variants for build targets, language bindings, backends
- ensure selected variants are compatible with zfp version
- point to GitHub (not LLNL) tar balls
- add dependencies
- update link to homepage
- add maintainers

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-29 17:51:30 +01:00
albestro
47c85059fb
it seems like there was a bug in the version of APEX that we set by default in 1.5.x (#21391) 2021-01-29 16:51:28 +01:00
a-saitoh-fj
9761c13878
dssp: added smoke tests (#21366) 2021-01-29 10:29:42 +01:00
Tomoyasu Nojiri
e3a0c48599
py-cheetah: restrict valid python interpreter to 2.7.X, add v2.4.4 (#21363) 2021-01-29 09:43:43 +01:00
Tomoyasu Nojiri
7b6c99655c
py-cheetah3: add new package at v3.2.6 (#21387) 2021-01-29 09:41:32 +01:00
Tomoyasu Nojiri
bc639fe60b
wtdbg2: enable build for aarch64 (#21390)
Use sse2neon to maintain the same API calls for aarch64
2021-01-29 09:37:00 +01:00
Tomoyasu Nojiri
b18479a2bd
swarm: add v3.0.0 (#21389) 2021-01-29 09:18:41 +01:00
Adam J. Stewart
519ba5590c
py-graphviz: add v0.8.4 (#21383) 2021-01-28 18:25:07 -08:00
Cyrus Harrison
57c23b964a
add new package: bloaty (#21355) 2021-01-28 16:44:07 -08:00
Dan Lipsa
5a9da90d07
Use utf8 for latex build. (#21360)
Patch provided by @Billae

Avoid the following error:
  File "/home/danlipsa/projects/spack/lib/spack/llnl/util/tty/log.py", line 768, in _writer_daemon
    line = _retry(in_pipe.readline)()
  File "/home/danlipsa/projects/spack/lib/spack/llnl/util/tty/log.py", line 830, in wrapped
    return function(*args, **kwargs)
  File "/usr/lib/python3.8/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x97 in position 220: invalid start byte
2021-01-28 15:58:55 -05:00
Massimiliano Culpo
f523ea8c4e
perl: add v5.32.1 (#21375)
Make it such that BigSur is seen as 10.16 rather than 11.1, since the latter causes troubles with Perl configuration
2021-01-28 21:54:28 +01:00
Desmond Orton
b095dfb44b
New Package r-fpCompare@0.2.3 (#21380) 2021-01-28 14:29:57 -06:00
iarspider
f28026c040
pacparser: new package at v1.3.7 (#21372)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-28 20:42:53 +01:00
Tomoyasu Nojiri
6ae8d5c380
openmx: Fix for aarch64 (#21367) 2021-01-28 10:20:18 -08:00
Ali Ahmed
b6d52fa466
New package: libpulsar (#21369) 2021-01-28 10:12:12 -08:00
Adam J. Stewart
aa15246280
py-matplotlib: add v3.3.4 (#21378) 2021-01-28 10:09:17 -08:00
bryanherman
ff8ef48806
New package: py-pytest-doctestplus (#21335)
* added package py-pytest-doctestplus

* setuptools required for run
2021-01-28 11:00:03 -06:00
bryanherman
ff0a92e6a8
New package: py-pytest-openfiles (#21339)
* added package py-pytest-openfiles

* remove wheel dep
2021-01-28 10:59:35 -06:00
bryanherman
bf33fe4805
openmc: add v0.11.0, v0.12.0 (#21349)
Also added new variants to fine tune the build
2021-01-28 17:04:34 +01:00
iarspider
9baecd0d78
umesimd: add new package (#21370) 2021-01-28 16:22:21 +01:00
Sergey Kosukhin
d577b6fcdf
autoconf: fix v2.70 and patching procedure of bin/autom4te.in (#21255)
This PR adds:

1.  A patch that fixes a bug in version 2.70 
    (will be fixed upstream in the next release: https://savannah.gnu.org/support/?110396).
2. A fix for the way we patch shebang in bin/autom4te.in. 

For 2, we need to keep the original modification timestamp of the file. 
Otherwise, we either get an empty man page for autom4te (versions 2.69 and before)
or a failure at the build time (versions 2.70 and after). 

The difference has to do with the update of the missing script: https://git.savannah.gnu.org/cgit/automake.git/commit/lib/missing?id=a22717dffe37f30ef2ad2c355b68c9b3b5e4b8c7

It will take time until developers of Autotools-based packages adjust their scripts 
to the new version, therefore, 2.69 is marked as preferred.
2021-01-28 11:21:04 +01:00
Adam J. Stewart
5b4d636d73
Clingo: fix missing import (#21364) 2021-01-28 00:38:01 -08:00
Tomoyasu Nojiri
181f921c1a
libpeas: restrict python version range, use pkgconfig virtual dependency (#21313) 2021-01-28 09:31:54 +01:00
Tomoyasu Nojiri
bcb0e80548
fox: add dependency to glu virtual package (#21280) 2021-01-28 09:29:36 +01:00
Jen Herting
0ebefcc92b
New package: py-proglog (#20750)
* [py-proglog] created template

* [py-proglog] added dependencies

* [py-proglog] fixed pypi url

* [py-proglog] removed fixmes, added homepage and description

* [py-proglog] url -> pypi

* [py-proglog] added dependency on setuptools
2021-01-27 20:59:19 -06:00
Rao Garimella
3dc5ffaf65
Update MSTK version (#21356)
* New interface reconstruction package

* forgot to put in CMake option for Jali

* cleanup whitespace

* fix lines with more than 79 chars

* more long line cleanup

* fix typo WONTON_ENABLE_Kokkos ---> TANGRAM_ENABLE_Kokkos

* New interface reconstruction package

* forgot to put in CMake option for Jali

* cleanup whitespace

* fix lines with more than 79 chars

* more long line cleanup

* fix typo WONTON_ENABLE_Kokkos ---> TANGRAM_ENABLE_Kokkos

* fix bugs in CMake section

* more compact cmake block

* update hash for 1.2.10 and add 1.2.11

* update recipe for Portage 3.0.0

* removing old versions - they won't build with the new recipe and the url specification doesn't work for them

* update version to 3.3.6

Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2021-01-27 20:58:02 -06:00
bryanherman
fe05b16922
New package: py-pytest-benchmark (#21324)
* added pytest-benchmark recipe

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

Added Python2 dependence.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:57:24 -06:00
bryanherman
d1ce461a81
New package: py-pytest-cpp (#21328)
* added package py-pytest-cpp

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

package is !=5.4.0 use @:5.3.999

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:57:09 -06:00
bryanherman
4efeb39e95
New package: py-pytest-timeout (#21340)
* added package py-pytest-timeout

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

Added Python2.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:56:52 -06:00
bryanherman
f7a47e4048
New package: py-openmc (#21351)
* added package py-openmc

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

specify branch when using branch names for versions

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

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

use run after fixture to install openmc lib

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

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

Simplify copying openmc library to py-openmc prefix using install

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

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

NumPy should be 1.9+

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

* fix paren missing

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

fixed parens

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

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

use v0.11.0 in URL

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:56:35 -06:00
eugeneswalker
74fbad4742
autoconf: add version 2.70 (#21362) 2021-01-27 17:59:03 -08:00
Stephen Herbein
71375b3446
flux: update to latest releases (#21306) 2021-01-27 17:56:45 -08:00
bryanherman
cc28bcddd1
fix cpio for intel@18 (#21322) 2021-01-27 17:48:26 -08:00
Harmen Stoppels
3172fc3681
Add conflict for mpich 3.4.x for clang <= 7" (#21326) 2021-01-27 17:45:38 -08:00
Michael Kuhn
f9fef22ce8
rdma-core: add 33.1 (#21361) 2021-01-27 17:31:01 -08:00
Greg Becker
0d521d56ec
openmpi find external fixup (#21354) 2021-01-27 15:27:17 -08:00
Desmond Orton
18b3688cd1
Package/spades (#21227)
Co-authored-by: codeandkey <jtst@iastate.edu>
2021-01-27 23:28:37 +01:00
bryanherman
71bac42357
added gawk version 5.1.0 (#21342) 2021-01-27 13:48:53 -08:00
Christoph Junghans
6b63441281
libecpint: initial add (#21353)
* libecpint: initial add

* flake8
2021-01-27 14:19:48 -07:00
Rémi Lacroix
5ef2daaa4a
ELPA: Switch to HTTPS links. (#21352) 2021-01-27 22:06:44 +01:00
Andrew-Dunning-NNL
895c8b33d9
py-dpath: new recipe (#21331) 2021-01-27 14:46:40 -06:00
bryanherman
68a144eaa3
added package py-pytest-flakes (#21337) 2021-01-27 14:38:30 -06:00
Andrew-Dunning-NNL
52c32047ad
py-mailchecker: new recipe (#21346) 2021-01-27 14:33:23 -06:00
Andrew-Dunning-NNL
54f163f7dc
py-jsonpath-ng: new recipe (#21347) 2021-01-27 14:23:20 -06:00
Brian Van Essen
3cbc35dbdd
LBANN: add support for building with OneDNN. (#21305) 2021-01-27 21:11:31 +01:00
Brian Van Essen
aac3699748
OneDNN: add versions up to v2.1-rc (#21304) 2021-01-27 21:10:16 +01:00
Rao Garimella
f2c98a8537
portage: added v3.0.0, deleted old versions (#21293)
old versions won't build with the new recipe and the url 
specification doesn't work for them

Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2021-01-27 20:13:22 +01:00
Ben Morgan
5667759bf5
vecgeom: add v1.1.9 release (#21341) 2021-01-27 19:50:31 +01:00
Sergey Kosukhin
3cc5b7adc7
Python extensions: consistently set LDSHARED to get Spack RPATHs (#21149)
Python extensions use CC and LDSHARED from the sysconfig module to
build. When Spack installs Python, it replaces the Spack compiler
wrappers in these values with the underlying compilers (since these
wrappers are not useful outside of the context of running Spack).
In order to use the Spack compiler wrappers when building Python
extensions with Spack, Spack sets the LDSHARED environment variable
when running `Python.setup_py` (which overrides sysconfig). However,
many Python extensions use an alternative method to build (namely
PythonPackage.setup_py), which meant that LDSHARED was not set (and
RPATHs were not inserted for dependencies).

This commit makes the following changes:

* Sets LDSHARED in the environment: this applies to all commands
  executed during the build, rather than for a single command
  invocation
* Updates the logic to set LDSHARED: this replaces the compiler
  executable in LDSHARED with the Spack compiler wrapper. This
  means that for some externally-built instances of Python,
  Spack will now switch to using the Spack wrappers when building
  extensions. The behavior is expected to be the same for Spack-
  built instances of Python.
* Performs similar modifications for LDCXXSHARED (to ensure RPATHs
  are included for C++ codes)
2021-01-27 10:20:36 -08:00
William Downs
6ba2e3ee5d
gchp: added new package (#21310)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-27 18:02:55 +01:00
Luca Heltai
8a7487773b
dealii: added support for simplices, updated sundials (#20621) 2021-01-27 17:02:15 +01:00
bryanherman
c52e95d681
cxxtest: added new package (#21323) 2021-01-27 16:26:26 +01:00
bryanherman
fbdc8b65b1
mesa: add dependency on zlib (#21325)
When installing mesa in an offline environment, mesa tries to download zlib.
2021-01-27 15:19:03 +01:00
Baptiste Jonglez
0efe54f722
mxnet: Fix python lib installation (#21298) 2021-01-27 07:53:09 -06:00
Ben Morgan
561557d2f5
py-h5py: add build dependency on py-wheel (#21320)
h5py requires wheel at build time from version 3.0.0, based on
the project's pyproject.toml.
2021-01-27 08:43:21 -05:00
Brian Van Essen
b8b432c3aa
lbann: add support for building just the LBANN core library (#21235)
Variants to disable vision libraries and NumPy support.
2021-01-27 13:42:49 +01:00
bryanherman
cbdf87cd28
boost: restrict lower bound of ranges for two patches (#21321) 2021-01-27 13:28:29 +01:00
Mohan
4977dcfe9b
knem: added a patch for v1.1.4 (#21312)
Co-authored-by: amd-toolchain-support <toolchainsupport@amd.com>
2021-01-27 13:27:10 +01:00
Brian Spilner
258bfff1da
cdo: add v1.9.10 (#21315) 2021-01-27 11:32:49 +01:00
takanori-ihara
e83cce313b
fujitsu-ssl2: remove mentions of libfj90rt2.a (#21308) 2021-01-27 11:32:23 +01:00
Glenn Johnson
84234e224c
mafft: add v7.475 and build extensions (#21301) 2021-01-27 10:55:51 +01:00
darmac
88325cada8
r-xvector: add dependency on zlib (#21286) 2021-01-27 10:22:34 +01:00
Tomoyasu Nojiri
503f2f1bbc
xterm: add dependency on termcap (#21314) 2021-01-27 09:50:21 +01:00
Brian Van Essen
46153a8201
NVSHMEM package (#21279) 2021-01-27 09:49:53 +01:00
Baptiste Jonglez
3626ab2697
libsodium: Fix build on ppc64le (#21256)
On ppc64le and aarch64, Spack tries to execute any "config.guess" and
"config.sub" scripts it finds in the source package.

However, in the libsodium tarball, these files are present but not
executable.  This causes the following error when trying to install
libsodium with spack:

    Error: RuntimeError: Failed to find suitable substitutes for config.sub, config.guess

Fix this by chmod-ing the scripts in the patch() function of libsodium.
2021-01-27 09:40:10 +01:00
Michael Kuhn
0366d49c6e
mpich: add 3.4.1 (#21302) 2021-01-26 23:13:14 +01:00
Anton Loukianov
fe35ada685
nextflow: new version (#21276) 2021-01-26 22:59:49 +01:00
Vicente Bolea
104c826e33
ParaView: add ParaView-5.9.0 new release (#21268) 2021-01-26 22:58:48 +01:00
bryanherman
5cd0a9ab8e Update var/spack/repos/builtin/packages/py-shtab/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:24:18 -06:00
bryanherman
86c906e24f Update var/spack/repos/builtin/packages/py-shtab/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:24:18 -06:00
bryanherman
52630d9b96 Update var/spack/repos/builtin/packages/py-shtab/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:24:18 -06:00
Bryan Herman
430b7f3ebd added package py-shtab 2021-01-26 15:24:18 -06:00
bryanherman
4a6676c441 Update var/spack/repos/builtin/packages/py-paramiko/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:23:17 -06:00
Bryan Herman
b527e43615 added invoke variant to py-paramiko 2021-01-26 15:23:17 -06:00
Bryan Herman
3455647011 added package py-sortedcollections 2021-01-26 15:23:02 -06:00
bryanherman
4e465e230e Update var/spack/repos/builtin/packages/py-rich/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:22:48 -06:00
bryanherman
93a7f57299 Update var/spack/repos/builtin/packages/py-rich/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:22:48 -06:00
bryanherman
eb1270d917 Update var/spack/repos/builtin/packages/py-rich/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-26 15:22:48 -06:00
Bryan Herman
53f299d0d5 dont cap future python versions 2021-01-26 15:22:48 -06:00
Bryan Herman
08413844f1 added py-rich package 2021-01-26 15:22:48 -06:00
Paul
c03a2d0697
Added Go versions 1.15.7 and 1.14.14 (#21294) 2021-01-26 22:19:13 +01:00
Harsh Bhatia
04225d3cef new package: callflow 2021-01-26 14:40:28 -06:00
Harsh Bhatia
a4e67c35de added flask-cors 2021-01-26 14:40:28 -06:00
kean-smullen-nnl
889c86bdb1
dakota: fix build dependencies (#20697) 2021-01-26 19:04:39 +01:00
Erik Schnetter
325510da5c
qthreads: New version 1.16 (#21159) 2021-01-26 18:53:46 +01:00
Tomoyasu Nojiri
90009d67a9
py-prompt-toolkit: Add version 2.0.10 for py-spatialist (#21281) 2021-01-26 11:26:26 -06:00
bryanherman
6b16d61a80
Added package py-nanotime (#21287) 2021-01-26 11:22:19 -06:00
bryanherman
a678c1966f
added version 2.4.7 to py-pyparsing (#21290) 2021-01-26 11:18:03 -06:00
bryanherman
fbf13e19ed
added missing dep, py-wheel, to py-pynacl (#21292) 2021-01-26 11:16:26 -06:00
Claire Guilbaud
31cf77aec6
recipe: add version 6.1.1 for pytest (#20831)
* recipe: add version 6.1.1 for pytest

add recipe for new dependency py-iniconfig
recipe: add version 6.1.1 for pytest

add recipe for new dependency py-iniconfig

* fix: 'SyntaxError: invalid syntax' during unittests

* requested changes on the pull request done

* requested changes on dep for py-pytest

* change constaint on python for importlib-metadata

* undo change on py-importlib-metada as requested

* bug fix

* bug fix on py-wcwidth

* fix as requested

* forget @ in when param

* forget a colon

* add new versions py-pytest and py-py

* fix setuptools* version

* add rule for more-itertools
2021-01-26 09:08:36 -06:00
Harmen Stoppels
feaaa8b194
umpire's device allocator exports device functions, which requires static libs (#21264) 2021-01-26 15:57:10 +01:00
Baptiste Jonglez
79afe20bb0
mxnet: Add optional cuda_arch spec support, enable CUDA by default (#21266) 2021-01-26 07:58:41 -06:00
vvolkl
b45a31aefe
[dd4hep] fix assimp variant (#21226) 2021-01-26 08:57:13 +01:00
Jen Herting
eb60c858a0
New package: py-intel-openmp (#20748)
* [py-intel-openmp] created template

* [py-intel-openmp] is wheel

* [py-intel-openmp] fixed version for linux

* [py-intel-openmp] removed fixmes, added homepage and description

* [py-intel-openmp] added macos support

* [py-intel-openmp] style fix
2021-01-25 22:34:10 -06:00
Jen Herting
f536ded328
New package: py-bayesian-optimization (#20746)
* [py-bayesian-optimization] created template

* [py-bayesian-optimization] added dependencies

* [py-bayesian-optimization] removed fixmes, added homepage and description

* [py-bayesian-optimization] added dependency on setuptools

* [py-bayesian-optimization] changed url to pypi and updated checksum

* [py-bayesian-optimization] url -> pypi
2021-01-25 22:32:55 -06:00
Jean-Paul Pelteret
b5c9318160
Py-cheroot: Add dependency (#21271) 2021-01-25 22:31:51 -06:00
Tomoyasu Nojiri
48310e8988
process-in-process: Add systemtap depend (#21164) 2021-01-25 22:28:25 -06:00
Michael Kuhn
26d4d54a42
mpich: add 3.4 (#21007)
This also switches the default device to ch4 and the default netmod to
ofi (tcp does not exist for ch4).
2021-01-25 18:00:30 -06:00
Adam J. Stewart
5447dd6fb8
py-geopandas: add v0.8.2 (#21269) 2021-01-25 16:51:12 -06:00
Evan Bollig
cc006a7847
Updated gromacs for 2021.rc1. Updated GMX_GPU values (#20797) 2021-01-25 22:40:55 +01:00
ketsubouchi
ddf022d308
Itensor: Add new package (#20689) 2021-01-25 22:33:23 +01:00
albestro
3a8e04bfab
add drafts variant (#20643) 2021-01-25 22:32:13 +01:00
Thomas Madlener
4e6b5282c9
Delphes: add 3.4.3pre08 tag as version (#21221) 2021-01-25 22:29:29 +01:00
Chris Richardson
ced55fbfe7
Fenicsx: update for basix (#21220) 2021-01-25 22:29:06 +01:00
Tomoyasu Nojiri
5af2b1a933
gdl: Add libtirpc and libgeotiff depend (#21212) 2021-01-25 22:28:15 +01:00
Peter Scheibel
fd8d14f7c5
Kokkos package: rocm support (#21157) 2021-01-25 22:19:54 +01:00
Baptiste Jonglez
7bed6a7077
mxnet: Fix cuda build (#21267) 2021-01-25 22:09:56 +01:00
Axel Huebl
ef2e1bc3f7
WarpX: Increase openPMD-api Dependency (#21263) 2021-01-25 22:08:53 +01:00
Baptiste Jonglez
7d7315ba93
libsodium: Fix download URLs for older versions (#21257) 2021-01-25 22:07:53 +01:00
Adam J. Stewart
37bbe21692
expect: add v5.45.4 and fix build with Apple Clang (#21232) 2021-01-25 22:04:09 +01:00
darmac
3893ce8f71
es-shell: add missing dependency on YACC (#21234) 2021-01-25 16:32:28 +01:00
Vicente Bolea
bfa480d87d
pugixml: add v1.11.4 (#21224) 2021-01-25 14:16:50 +01:00
iarspider
2378376aa9
py-pythonsollya: new package (#21241) 2021-01-25 13:44:28 +01:00
iarspider
9d1d37c432
sollya: new package at v7.0 (#21240) 2021-01-25 09:33:56 +01:00
Adam J. Stewart
05c4506b62
py-pygeos: add v0.9 (#21243) 2021-01-25 09:25:33 +01:00
lpoirel
dd505e2269
petsc: forward variant +int64 to parmetis (#21245) 2021-01-25 08:41:29 +01:00
ketsubouchi
b2f89f8157
imake: add run dependency to xorg-cf-files (#21251) 2021-01-25 08:18:06 +01:00
Pariksheet Nanda
91db8c5234
picard: add v2.24.0 (#21249) (#21250) 2021-01-25 08:12:58 +01:00
Phil Carns
f269b4d7c1
opa-psm2: add v11.2.185 (#21208)
- also update to reflect Cornelis Networks as source maintainer rather Intel
- also replace explicit install prefix patch with edit step file filter
2021-01-25 07:33:59 +01:00
iarspider
577f6e8ade
New package: mpfi (#21238) 2021-01-24 17:54:52 -06:00
Glenn Johnson
cf35661d3c
Updates of R CRAN packages (#21223) 2021-01-24 17:54:25 -06:00
lpoirel
88cafacd09
petsc: add a +mkl-pardiso variant (#21219)
* petsc: add a +mkl-pardiso variant

mkl_pardiso solver is distributed with intel-mkl

* petsc: depend on mkl instead of intel-mkl

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-24 12:09:35 -06:00
iarspider
8f45b27836
New package: py-bigfloat (#21239)
* New package: py-bigfloat

* Changes from review
2021-01-23 16:27:42 -06:00
iarspider
e791725180
New package: fplll (#21236)
* New package: fplll

* Change from review
2021-01-23 16:26:48 -06:00
bryanherman
5a2fe8add3
Fix git svn modules (#21169)
* added Git run env to support svn variant modules

* perl-alien-svn needs arp-util to be link

* Update var/spack/repos/builtin/packages/git/package.py
2021-01-23 10:33:39 -05:00
Pieter Ghysels
dba6a26920
Add strumpack v5.1.0, add support for ROCm/HIP (#21203) 2021-01-23 09:31:23 +01:00
Nicholas Sly
82ada16668
Add flang variant to llvm package. (#21229)
Co-authored-by: sly <sly@lanl.gov>
2021-01-22 15:39:44 -08:00
Baptiste Jonglez
49f0e9640d
cuda: add installation workaround for version 10.1.243 on ppc64le (#21200)
Fixes #21170
2021-01-22 14:27:14 -08:00
arjun-raj-kuppala
cdb9b10e27
Bump up rocm version 4.0.0: rocm-gdb and mivisionx (#21137) 2021-01-22 18:04:01 +01:00
ketsubouchi
2d6fea86d6
py-pygit2, libgit2: add new versions (#21160) 2021-01-22 09:59:01 -06:00
Chuck Atkins
14f6d64edf
adios2: Fix dependency issues (#21211)
- Typo in the SZ version (:ver should have been ver:)
- Patch to fix python dependency when testing is disabled
2021-01-22 10:31:21 -05:00
René Widera
1026eb2186
isaac-server: add v1.5.1 and v1.5.2 (#21217)
Add latest releases of isaac-server and adjust jansson requirements.
2021-01-22 15:30:57 +01:00
Adam J. Stewart
99e36bcef6
py-scikit-learn: add v0.24.1 (#21158) 2021-01-22 14:32:23 +01:00
Adam J. Stewart
551105749b
py-pandas: add v1.2.1 (#21176) 2021-01-22 14:28:24 +01:00
Adam J. Stewart
ccb5cc50f7
TensorFlow: add v2.4.1 (#21205) 2021-01-22 14:12:37 +01:00
Dr. Christian Tacke
1961dc5f51
xrootd: add v4.12.6, v5.0.3; drop preferred (#21199)
Add version 4.12.6, 5.0.3

I think, the preferred was there to keep version 4.
But that's why we have spack, because people can install
whatever version they want.

And root has a properly versioned dependency.
2021-01-22 14:10:54 +01:00
Jen Herting
f50f67f4db
py-memprof: new package (#20730) 2021-01-22 14:07:16 +01:00
Jen Herting
3b38e4345f
py-filterpy: new package (#20747) 2021-01-22 14:06:34 +01:00
Tomoyasu Nojiri
f6db2f4da4
cnvnator: add -lcrypto to Makefile. (#21209) 2021-01-22 13:50:05 +01:00
René Widera
4b466d06f4
isaac: add v1.5.1 and v1.5.2 (#21216) 2021-01-22 13:11:28 +01:00
arjun-raj-kuppala
f41317d8b2
AMD ROCm: Bump rocm-tensile with 3.9.0, 3.10.0, 4.0.0 releases (#20439) 2021-01-22 13:07:36 +01:00
Dominik Gresch
ec7caefc69
Add Quantum ESPRESSO version 6.7. (#21192) 2021-01-22 09:58:30 +01:00
Harmen Stoppels
d42d9a619a
add patch for not linking to clang rt bulitin lib, and apply patches to 3.9.0 too (#20937) 2021-01-22 09:55:46 +01:00
Tom Payerle
f7064fa181
mumps: Fix for problematic src/makefile patch (#20590) (#20758)
* mumps: Fix for problematic src/makefile patch (#20590)

Minor change in src/Makefile between 5.2.0 and 5.3.3 causing patch to
break.  Split into 2 patchfiles

* mumps: Additional patch for fixing #20590

This is to fix issue wherein build fails on Ubuntu due to undefined
symbols, despite symbols being included in other libraries referenced
on the compilation line.  I believe the issue is that the inclusion
of libsmumps.so was (due to my original patch) causing
libmumps_common.so to be automatically loaded, but since libpords.so
was not also required, the error was occuring.  I have added libpords.so
along with libmumps_common.so to be explicit dependencies of
libsmumps.so, etc., which seems to resolve the issue.
2021-01-21 20:41:11 -08:00
mic84
9ed4eb7a9a
amrex: fix missing hdf5 dependency (#20714)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-01-21 16:16:55 -08:00
Kurt Sansom
06f65afdd5
hdf: build with gcc10 (#20773) 2021-01-21 17:07:28 -06:00
Chuck Atkins
3d54ca4d5a
ecp-data-vis-sdk: Disable broken cinema variant (#21204) 2021-01-21 15:42:25 -05:00
Baptiste Jonglez
af1eda5359
miniconda3: add ppc64le package version (#21196)
It requires reorganizing version definitions to facilitate adding new architectures.

This is inspired from the cuda package.
2021-01-21 14:36:36 -06:00
Omar Padron
b76d21710b
Add develop versions of faodel and zfp (#21201)
* add master version of faodel

* add develop version of zfp
2021-01-21 14:12:21 -05:00
Sreenivasa Murthy Kolam
85ea52acd1
fix build failure due to #20759 change (#21185) 2021-01-21 18:13:28 +01:00
Tomoyasu Nojiri
6e258ca6ca
catalyst: Fix for aarch64 (#21187) 2021-01-21 10:50:08 -06:00
Brian Van Essen
d3a078c7da
Add support for building with an FFT layer in LBANN. Updated the (#21184)
HWLOC requirements to properly include CUDA and NVML variants as
appropriate.
2021-01-21 10:49:53 -06:00
arjun-raj-kuppala
90a7c846f6
install lib/headers option support (#21186) 2021-01-21 10:47:55 -06:00
Tomoki, Karatsu
2957f76cb1
abinit: add version 8.10.2. (#21188) 2021-01-21 10:46:12 -06:00
vvolkl
2c6c6756a8
[assimp] add new version 5.0.1 (#21191) 2021-01-21 10:45:21 -06:00
Harmen Stoppels
0cf0be588b
Always set SPLA_OMP and SPLA_STATIC (#21195) 2021-01-21 10:43:57 -06:00
Gerasimos Chourdakis
1ceab34fc8
precice: Add version 2.2.0 (#21166) 2021-01-21 09:38:53 -06:00
Jen Herting
d9a8ff455e
[py-numba] added version 0.51.1 (#21182)
* [py-numba] added version 0.51.1

* [py-numba] updated llvmlite dependencies
2021-01-21 09:38:35 -06:00
Rémi Lacroix
afa536fc1d
Plumed: Add a new ArrayFire variant. (#20624) 2021-01-21 09:29:11 -06:00
Rémi Lacroix
6f166283ca
ArrayFire improvements (#20615)
* ArrayFire: Add version 3.7.2.

* ArrayFire: Allow using MKL as the FFTW provider.

* ArrayFire: Ensure the libraries are properly found.

The required backend(s) can be specified in the library query.
2021-01-21 09:29:00 -06:00
Simon Frasch
10baa48d95
spfft: add version 1.0.1 (#21193) 2021-01-21 15:23:01 +01:00
Scott McMillan
fcf99be939
openssl: remove preprocessor flags incompatible with NVIDIA HPC SDK (#21180)
* openssl: remove preprocessor flags incompatible with NVIDIA HPC SDK

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

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

Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-20 21:42:53 -06:00
Toyohisa Kameyama
c5ed46e026
libcap-ng: fix detect python. (#21162)
* libcap-ng: fix detect python.

- add python variant.
- add --with-python and --with-python3 configure option.

* fix style.

* - Add python variant.
- change - to --
2021-01-20 21:42:36 -06:00
Tomoyasu Nojiri
bf3fb8428d
util-linux: Add ncurses depend (#21165) 2021-01-20 21:40:03 -06:00
Tomoyasu Nojiri
644b8b52e2
systemtap: Add depend (#21163)
* systemtap: Add depend

* systemtap: Fix depend
2021-01-20 21:31:04 -06:00
Scott McMillan
2ea336e6aa
libevent: Remove compiler flags incompatible with NVIDIA HPC SDK (#21181)
Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2021-01-20 17:38:34 -06:00
Greg Sjaardema
6ecc3fc06f
SEACAS: New version v2021-01-20 (#21178)
Added a new version due to new application `nas2exo` and also adding the build of `slice` if `+applications` is specified.
2021-01-20 17:07:38 -06:00
Jen Herting
69bfdb0843
[py-statsmodels] added version 0.12.1 and updated dependencies accord… (#21175)
* [py-statsmodels] added version 0.12.1 and updated dependencies accordingly

* [py-statsmodels] added python requirements for new version and fixed formatting for readability
2021-01-20 17:07:10 -06:00
Sergei Shudler
a95bf8df43
Mirror current E4S hypre test suite test as a smoke test (#20484) 2021-01-20 15:05:25 -08:00
bryanherman
a6ea16ded5
Fix PVM dependencies (#20951)
* added m4 dep to PVM recipe

* added libtirpc dep to PVM recipe

* decode str or bytestr string to unicode

* Resolved comments from @adamjstewart on setup_build_environment
2021-01-20 15:52:22 -06:00
Robert Brunner
966f6bc2d2
Propagate SCR resource_manager flag to libyogrt dependency (#21168)
* When the SCR spec specifies a resource_manager=SLURM or LSF flag, propagate the spec through to
the libyogrt scheduler=slurm or lsf

* Use libyogrt default scheduler option when the SCR spec does not specify LSF or SLURM
2021-01-20 15:51:46 -06:00
Scott McMillan
0e2fa561f3
Perl: NVIDIA HPC SDK updates (#21177)
* Perl: NVIDIA HPC SDK updates

* fix indentation

Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2021-01-20 15:51:06 -06:00
Rémi Lacroix
bef250535a
Plumed: Ensure the Python interfaces are also built with Spack's wrappers. (#20625) 2021-01-20 14:12:27 -06:00
Rémi Lacroix
23181d24a2
PETSc: Add a new ptscotch variant. (#20699)
Currently the Parmetis wrapper is disabled which means nested dissection cannot be used with PTScotch.
2021-01-20 14:11:23 -06:00
Evan Bollig
2d9e36c4f0
updated relion package for new versions (#21155)
* updated relion for new versions

* Switched to checksum versions

* Enabled spack tracking for MKL and TBB when CPU optimizations are enabled

* Added variants to control MKL FFT and Ppatent feature

* Replaced tags with sha256 for older versions an and switched to virtual packages
2021-01-20 13:53:59 -06:00
Andrew-Dunning-NNL
28c0f20214
py-funcy: new recipe (#21136)
* py-funcy: new recipe

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

add build and run python dependencies

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-20 13:53:13 -06:00
Tomoyasu Nojiri
085360ec0b
qwt: Fix qt depend (#21161) 2021-01-20 13:47:03 -06:00
Erik Schnetter
d11ba90198
z3: New version 4.8.9 (#21167) 2021-01-20 13:36:46 -06:00
Baptiste Jonglez
95b974707b
openjdk: Add ppc64le package (#21173) 2021-01-20 13:30:39 -06:00
Omar Padron
43935b4917
fix an issue where some variants were not being concatenated correctly (#21174) 2021-01-20 13:27:41 -06:00
darmac
6f3027b9fb
py-iminuit: update version to fix test error (#21143)
* py-iminuit: update version to fix test error

* py-iminuit: update py-numpy limitation

* py-iminuit: fix dependency mistake
2021-01-20 13:22:35 -06:00
Tomoyasu Nojiri
a187b2fb09
py-mikado: Add version 1.2.4 (#20678)
* py-pysam: Add version 0.15.3

* py-biopython: Add version 1.78

* py-mikado: Add version 1.2.4

* py-mikado: Reflection of review points.

* py-biopython: Add python depend

* py-mikado: Fix depend

* py-mikado: Add py-tabulate depend
2021-01-20 13:21:59 -06:00
Nathan Hanford
ebc871abbf
[WIP] relocate.py: parallelize test replacement logic (#19690)
* sbang pushed back to callers;
star moved to util.lang

* updated unit test

* sbang test moved; local tests pass

Co-authored-by: Nathan Hanford <hanford1@llnl.gov>
2021-01-20 09:17:47 -08:00
Tomoyasu Nojiri
c63f680d2a
r-farver: Fix checksum for 2.0.1 (#20897) 2021-01-19 17:45:51 -08:00
Omar Padron
49141f9528
fix typo in ec-data-vis-sdk package (#21156) 2021-01-19 17:09:42 -06:00
mlawsonca
881ca8406c
fixing outdated metis link (#21003)
* fixing outdated metis link

* updated url to the official website since the previous url was a GitHub repo that is an unofficial mirror that only contains the latest version
2021-01-19 16:58:38 -06:00
Andrew-Dunning-NNL
8a92ebd504
py-pyjnius: new recipie (#21150) 2021-01-19 16:57:10 -06:00
Andrew-Dunning-NNL
c6cb0d7869
py-dictdiffer: new recipe (#21151)
* py-dictdiffer: new recipie

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

add correct setuptools dependency

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-19 16:56:53 -06:00
Andrew-Dunning-NNL
6de193fd27
py-pytest-arraydiff: new recipie (#21152) 2021-01-19 16:56:38 -06:00
Andrew-Dunning-NNL
7a913582f2
py-phonenumbers: new recipie (#21153) 2021-01-19 16:56:24 -06:00
Andrew-Dunning-NNL
d3b04f7704
py-pygtrie: new recipie (#21154) 2021-01-19 16:56:09 -06:00
Erik Schnetter
0c5602dc4e
amrex: remove build_type variant (#20938)
This variant is already provided by CMakePackage.
2021-01-19 19:17:37 +01:00
William Downs
35a51760a8
esmf: Add versions 8.0.0 and 8.0.1 (#21147) 2021-01-19 10:52:47 -06:00
Harmen Stoppels
034debeba5
Always set cmake args because defaults change across versions (#21146) 2021-01-19 09:57:12 -06:00
ketsubouchi
8a6e7c8687
cpmd: new package (#21138) 2021-01-19 09:02:09 -06:00
Tomoyasu Nojiri
ab83b6689e
sortmerna: Fix for aarch64 (#21126) 2021-01-19 09:01:16 -06:00
yellowhat
89b9d07efa
gromacs: add v2020.5 (#21144) 2021-01-19 10:26:35 +01:00
Robert Brunner
91f65b9772
libyogrt: add lsf scheduler support, create yogrt.conf file (#19960)
Tell the libyogrt installer to create a yogrt.conf file, specifying whatever 
scheduler was specified in the scheduler=XXX parameter.
2021-01-19 10:01:48 +01:00
Adam J. Stewart
86e9d93859
libidn2:use http for download (#21001)
This is needed since libidn is used to bootstrap curl
2021-01-19 09:54:25 +01:00
Pramod Kumbhar
908528f2f1
NEURON: add v7.8.2, move to CMake and remove all old versions (#20582)
* Update NEURON simulator package
  - update recipe to support autoconf as well as cmake
  - new versions >=7.8 support cmake
  - remove old variants
  - added patch for latest bug fix release 7.8.2

Co-authored-by: Kumbhar Pramod Shivaji <kumbhar@bbpv1.epfl.ch>
Co-authored-by: Kumbhar Pramod Shivaji <kumbhar@bb-c02vf1h0hv2r.epfl.ch>
2021-01-19 09:42:50 +01:00
Thomas Madlener
a92bb5400e
lcio, sio: add sio dependency, update versions and expose zlib version for sio (#20839) 2021-01-19 09:20:43 +01:00
Glenn Johnson
82b10583f9
r-grbase: added v1.8-6.7 (#21033) 2021-01-19 09:10:21 +01:00
Tomoki, Karatsu
5033250140
specfem3d-globe: add new package (#20830) 2021-01-19 08:55:18 +01:00
h-denpo
f781fd1878
universal-ctags: added link dependency on libiconv (#21141) 2021-01-19 08:47:26 +01:00
darmac
a567b73108
py-numexpr: added v2.7.2 (#21142) 2021-01-19 08:42:16 +01:00
yellowhat
83eec2d170
NAMD: FIX build +cuda and mpi ~smp (#20778)
* NAMD: FIX build +cuda

Hi,
If I try to compile NAMD with CUDA support, it fails because cannot file the file "{self.arch}.cuda" because it is undet the "arch" folder.

* NAMD: FIX mpi ~smp

Fix `spack install namd ^charmpp backend=mpi ~smp`
2021-01-18 23:12:06 -06:00
Rao Garimella
a36c40b61d
Update versions of Wonton and Tangram packages (#20813) 2021-01-18 23:06:26 -06:00
Michael Kuron
2e299c5008
siesta: fix build with gfortran (#20840)
Avoid Error: Line truncated at (1) [-Werror=line-truncation]
2021-01-18 22:59:53 -06:00
Erik Schnetter
a2d8023e2a
ssht: New version 1.3.4 (#20880)
* ssht: New version 1.3.4

ssht changed configuration mechanism from "home-grown" to "cmake. The previously current version 1.2b1 (a beta release) is thus unfortunately not available any more.

* ssht: Don't set build type

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-18 22:57:53 -06:00
Vicente Bolea
94f1e838b2
ParaView: add new ParaView-5.9.0-RC4 release (#21132)
* ParaView: add new ParaView-5.9.0-RC4 release

Signed-off-by: Vicente Adolfo Bolea Sanchez <vicente.bolea@kitware.com>

* ParaView: add official maintainer @vicentebolea

Signed-off-by: Vicente Adolfo Bolea Sanchez <vicente.bolea@kitware.com>
2021-01-18 22:53:17 -06:00
Toyohisa Kameyama
3143222d87
salmon-tddft: add eigenexa variant (#21140) 2021-01-18 22:52:50 -06:00
Thomas Madlener
d1174bd40f
Make sure sio library is properly propagated (#20940) 2021-01-18 22:52:27 -06:00
darmac
fe32d256d2
ceres-solver: add v2.0.0 (#21005) 2021-01-18 22:51:57 -06:00
Harmen Stoppels
1dab789504
Don't use CUDA for hipblas (#20935)
* Don't use CUDA for hipblas

* old versions use TRY_CUDA

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-18 22:49:59 -06:00
Glenn Johnson
85838e98fb
add version 2.2-2 to r-gwmodel (#21121)
* add version 2.2-2 to r-gwmodel

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

Fix comma, space issue.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-18 16:59:05 -06:00
Glenn Johnson
c7d3651356
add version 0.3.17 to r-inline (#21053)
* add version 0.3.17 to r-inline

* Drop R version constraint

A really old version of R was specified in the 0.3.14 and 0.3.15
versions of r-inline. This constraint was dropped in the 0.3.17 version.
Drop it from the spack recipe as well.
2021-01-18 16:58:08 -06:00
Michael Kuron
cec784bb10
vasp: fix build with gfortran 10 and add version 6.1.1 (#20900)
* vasp: fix build with gfortran 10

Avoid Error: Type mismatch between actual argument at (1) and actual argument at (2)

* vasp: add version 6.1.1

* vasp 6: allow building without CUDA
2021-01-18 16:54:52 -06:00
kuramoto-fj
bd51f81e20
Mapsplice2: Add new package (#20901) 2021-01-18 16:53:50 -06:00
Thomas Madlener
e960721c65
Use shared=True to find libraries, since this is the default (#20907)
package also does not expose a shared variant
2021-01-18 16:51:44 -06:00
Atsushi Hori
777901843f
New Package: Process-in-Process (PiP) -- 2nd trial (#20925)
* Adding PiP recipe

* pip@1 recipe (it seems working)

* change install dir hierarchy

* installing PiP man pages

* add pip-glibc & pip-gdb

* fix configure option designations, fix dependency types

* fix dependency type of pip

* use AutotoolsPackage in pip recipe

* add patch for pip-glibc & pip-gdb to enable 'disable-werror'

* change glibc install directory

* add linux distro check to pip-gdb

* create process-in-process package

* use flag_handler and join_path

* add gcc version constraint, change install-test to check-installed

* fix gcc version designations on conflicts()

* add constraint of target cpu, fix flake8 warnings

* add version constraint to resource()

* Some fixes to adapt the current version
	not to execute 'piplnlibs'
	change documentation install command

* Update
	new branch name of PiP-gdb
	adapting PiP-Testsuite

* update pip-gdb github urls

* The very first commit of Process-in-Process (PiP)
	details can be found at https://github.com/RIKEN-SysSoft/PiP

* Fix comment style issues

* New Package: Process-in-Process (PiP) -- 2nd trial

* fix style issue

* change inline comments style (required to have two spaces)

Co-authored-by: Daiki Matsunaga <daikim@axe.bz>
2021-01-18 16:50:48 -06:00
Tomoyasu Nojiri
b7badf2447
gengetopt: Add texinfo depend (#20929) 2021-01-18 16:40:34 -06:00
bryanherman
c500ea80c3
Add SVN extension to Git (#20939)
* added package for svn extension to perl

* added svn variant to git recipe
2021-01-18 16:39:56 -06:00
takanori-ihara
a5963d686c
eigenexa: new package. (#20934) 2021-01-18 23:37:09 +01:00
G-Ragghianti
335c5ed5cb
Updated with requirements for openblas dependency (#20956)
* Updated with requirements for openblas dependency

* Python style fixes
2021-01-18 16:34:21 -06:00
Simon Frasch
e91ff86882
spfft: add version 1.0.0 (#20959) 2021-01-18 16:33:18 -06:00
Glenn Johnson
699df81a95
add version 1.2-9 to r-aer (#20965) 2021-01-18 12:57:28 -06:00
Glenn Johnson
5fb647d17c
The latest version of imagemagick needs libtool linking (#20969)
Imagemagick-7.0.8 needs to link against libltdl. Otherwise, the build will fail with:

```
2 errors found in build log:
     503    checking for libltdl...
     504    checking ltdl.h usability... no
     505    checking ltdl.h presence... no
     506    checking for ltdl.h... no
     507    checking for lt_dlinit in -lltdl... no
     508    checking if libltdl package is complete... no
  >> 509    configure: error: in `/tmp/gpjohnsn/spack-stage/spack-stage-imagemagick-7.0.8-7-4y44gaklhhciiwjzhfpxjfwdj5q
            ltjp3/spack-src':
  >> 510    configure: error: libltdl is required for modules and OpenCL builds
     511    See `config.log' for more details
```
2021-01-18 12:57:15 -06:00
Glenn Johnson
8f5651e63e
add version 3.3.3 to r-ggplot2 (#21021) 2021-01-18 12:56:36 -06:00
Glenn Johnson
e879c4176d
add version 0.6-2 to r-gmp (#21028) 2021-01-18 12:56:21 -06:00
Glenn Johnson
bd404d8ff8
add version 0.5-1 to r-gridgraphics (#21034) 2021-01-18 12:56:06 -06:00
Glenn Johnson
7f7f9a7bfb
add version 3.8.2 to r-gtools (#21038)
* add version 3.8.2 to r-gtools

* Improve formatting of description

In case the list gets formatted as a non-list:
- added semicolons to end of list items
- replaced dashes with [#]
2021-01-18 12:55:51 -06:00
Glenn Johnson
415cff5061
add version 1.30 to r-knitr (#21061)
* add version 1.30 to r-knitr

* Fix version constraints

- r-digest
- r-formatr

The version constraints on those packages should actually be in the `when`
clause.
2021-01-18 12:55:33 -06:00
Glenn Johnson
91fcd49484
add version 1.0-6 to r-libcoin (#21075) 2021-01-18 12:55:18 -06:00
Glenn Johnson
978f74eac7
add version 1.2.0 to r-gh (#21112) 2021-01-18 12:55:04 -06:00
Glenn Johnson
2c3550ae18
add version 1.1.2 to r-tidyr (#21113) 2021-01-18 12:54:51 -06:00
Glenn Johnson
b424dbfead
new package: r-rcppdate (#21114)
'date' is a C++ header library offering extensive date and time
functionality for the C++11, C++14 and C++17 standards written by Howard
Hinnant and released under the MIT license. A slightly modified version
has been accepted (along with 'tz.h') as part of C++20. This package
regroups all header files from the upstream repository by Howard Hinnant
so that other R packages can use them in their C++ code. At present, few
of the types have explicit 'Rcpp' wrapper though these may be added as
needed.
2021-01-18 12:54:35 -06:00
Glenn Johnson
563d939804
add version 2.0.2 to r-mnormt (#21115) 2021-01-18 12:54:22 -06:00