Commit graph

18680 commits

Author SHA1 Message Date
Wouter Deconinck
7e6a77d907
New package: kassiopeia (#17742)
* [kassiopeia] New package

* [kassiopeia] Remove master branch, update dependencies

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

Unable to test since I do not have a license to intel-parallel-studio, but I see no reason why it would not work if.

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

* [kassiopeia] depends_on mpi

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

* [kassiopeia] cmake_args with self.spec.satisfies and elses

* [kassiopeia] args.extend -> args.append

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-01 17:40:21 -05:00
Simon Pintarelli
75f34126fc
h5py does not correctly recognize hdf5 version on Cray (#17831)
* h5py: explicitly specify version

hdf5@1.10.5 on Cray is wrongly detected as 1.8.4.

* Update var/spack/repos/builtin/packages/py-h5py/package.py

Thanks. Also had this first, then CI was complaining about line length ...

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-01 16:26:41 -05:00
Mark W. Krentel
b0eb771b19
elfutils: add version 0.180 (#17835) 2020-08-01 16:26:13 -05:00
Axel Huebl
7498336f3d
Hotfix: move CUDAHOSTCXX (#17826)
* Hotfix: move CUDAHOSTCXX

Set only in dependent packages.

* dependent compiler
2020-08-01 15:29:17 -05:00
Todd Gamblin
f3cb3a2eb8 license: fix up MIT license so it's an exact match
Before:

```console
$ licensee diff --license mit LICENSE-MIT
Comparing to MIT License:
Input Length:      1092
License length:    1020
Similarity:      92.46%
diff --git a/LICENSE b/LICENSE
index 0ce42af..be0ff1c 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,4 @@
{+spack project developers. see the top-level copyright file for details.+}
permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "software"), to deal in
the software without restriction, including without limitation the rights to
```

After:

```console
$ licensee diff --license mit LICENSE-MIT
Comparing to MIT License:
Input Length:       1020
License length:     1020
Similarity:      100.00%
Exact match!
```

This gets us a 100% license match from GitHub's `licensee` tool.
2020-08-01 10:06:28 -07:00
darmac
3ea9b9a014
Add new package: findbugs (#17825) 2020-08-01 11:46:02 -05:00
darmac
52858be668
Openfst: upgrade version and gcc constraint (#17830)
* openfst: upgrade version and gcc constraint

* refine version format
2020-08-01 11:41:12 -05:00
Todd Gamblin
ff27233e30 bugfix: fix spack buildcache list --allarch
`spack buildcache list` was trying to construct an `Arch` object and
compare it to `arch_for_spec(<spec>)`. for each spec in the buildcache.
`Arch` objects are only intended to be constructed for the machine they
describe. The `ArchSpec` object (part of the `Spec`) is the descriptor
that lets us talk about architectures anywhere.

- [x] Modify `spack buildcache list` and `spack buildcache install` to
      filter with `Spec` matching instead of using `Arch`.
2020-08-01 08:36:12 -07:00
Todd Gamblin
0c48f0a15d architecture: make it easier to get a Spec for the default arch
- [x] Make it easier to get a `Spec` with a proper `ArchSpec` from an
      `Arch` object via new `Arch.to_spec()` method.

- [x] Pull `spack.architecture.default_arch()` out of
      `spack.architecture.sys_type()` so we can get an `Arch` instead of
      a string.
2020-08-01 08:36:12 -07:00
Massimiliano Culpo
c65cde4cf8
Avoid update and upgrades to brew (#17815)
Ci is currently failing on brew update with the error:
```
Error: Cannot install bazelisk because conflicting formulae are installed.
  bazel: because Bazelisk replaces the bazel binary

Please `brew unlink bazel` before continuing.

Unlinking removes a formula's symlinks from /usr/local. You can
link the formula again after the install finishes. You can --force this
install, but the build may fail or cause obscure side effects in the
resulting software.
```
Avoiding:
```
$ brew update
$ brew upgrade
```
solves the issue by preventing the risk of conflicting formulae
2020-08-01 07:45:39 +02:00
Brian Van Essen
5c2b34e43b
cuDNN (package): add version 7.6.5.32-10.2-linux-ppc64le (#17821) 2020-07-31 17:48:03 -07:00
Harmen Stoppels
d4831181ea
Add libxc 5.0.0 (#17807)
With experimental CUDA support and some patches to make it compile.

Currently +shared and +cuda conflict, this has to be fixed upstream.
2020-07-31 18:01:39 -05:00
Michael Kuhn
346977f501
meson: Add 0.55.0 (#17816) 2020-07-31 18:01:12 -05:00
Adam J. Stewart
9d942df352
py-wheel: add new version (#17819) 2020-07-31 15:58:00 -07:00
Adam J. Stewart
89759cc1f1
py-setuptools: add new version (#17818) 2020-07-31 15:57:42 -07:00
Adam J. Stewart
4c35cc1b20
py-pip: add new version (#17817) 2020-07-31 15:57:27 -07:00
Massimiliano Culpo
9dbad500bc
Move Python 2.6 unit tests to Github Actions (#17279)
* Run Python2.6 unit tests on Github Actions
* Skip url tests on Python 2.6 to reduce waiting times
* Skip foreground background tests on Python 2.6 to reduce waiting times
* Removed references to Travis in the documentation
* Deleted install_patchelf.sh (can be installed from repo on CentOS 6)
2020-07-31 15:01:12 -07:00
Adam J. Stewart
4aaa39d091 py-torchvision: add v0.7.0 2020-07-31 14:34:55 -07:00
Adam J. Stewart
58d383877d PyTorch: add v1.6.0 2020-07-31 14:32:56 -07:00
Adam J. Stewart
198ccfae4e Pandas: add v1.1.0 2020-07-31 14:20:17 -07:00
darmac
c2cd728e03
cp2k: support for aarch64 (#17786) 2020-07-31 16:17:31 -05:00
Brian Van Essen
46e7fbe120
LBANN: add versions, update CUDA support and dependencies (#17813)
* Update LBANN, Hydrogen, Aluminum to inherit CudaPackage
* Update CMake constraints: LBANN, Hydrogen, and Aluminum now require
  cmake@3.16.0: (better support for pthreads with nvcc)
* Aluminum: add variants for host-enabled MPI and RMA features in a
  MPI-GPU RDMA-enabled library
* NCCL: add versions 2.7.5-1, 2.7.6-1, and 2.7.8-1
* Hydrogen: add version 1.4.0
* LBANN: add versions 0.99 and 0.100
* Aluminum: add versions 0.4.0 and 0.5.0
2020-07-31 13:53:51 -07:00
Andrew W Elble
d89bc1d998
new package(s): py-gql (#17769)
* new package(s): py-gql

and related dependencies:
py-aiohttp
py-async-timeout
py-graphql-core
py-idna-ssl
py-multidict
py-websockets
py-yarl

new versions:
py-requests

* fixes

Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2020-07-31 14:54:25 -05:00
Rémi Lacroix
0303ef72ac
libxc: Add version 4.3.4. (#17781) 2020-07-31 14:48:48 -05:00
darmac
e938e439b9
Add new package: mongodb-async-driver (#17787) 2020-07-31 14:45:35 -05:00
darmac
8df17d3830
open-iscsi: refine runtime environment (#17789) 2020-07-31 14:43:40 -05:00
Xavier Delaruelle
c7e83a8375
environment-modules: add version 4.5.2 (#17795) 2020-07-31 14:42:08 -05:00
Andrew Gaspar
c436414352
Add Rust versions 1.45.1 and 1.44.1 (#17812) 2020-07-31 14:30:00 -05:00
darmac
b7e0fec5f0
Alluxio (package): update url, add versions (#17805)
* Add versions 2.2.1 and 2.2.0
* Remove version 2.1.0
* Add dependency on Java
2020-07-31 11:25:22 -07:00
Justin S
cab2af9a71
py-mixedhtseq: new package at 0.1.0 (#17702)
* py-mixedhtseq: new package at 0.1.0

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

* py-gpy: remove unneeded dep

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

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

* nwchem 6.8.1 breaks with gcc 10 and later

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

* changes for flake8

* url fixed

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

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

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

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

This allows properly setting the rpaths.

* Ferret: Add support for versions 7.3 to 7.6.

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

* Ferret: Define some useful runtime environnement variables.

* Ferret: Fix flake8.

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

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

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

* [podio] add new version and update env vars

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

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

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

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

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

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

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

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

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

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

* added license header and changed url_for_version to just url

* removed unused imports, addressed comments

* removed trailing whitespace on line 14

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

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

* py-uvw: added py-setuptools as dependency
2020-07-30 21:52:17 -05:00
Dr Owain Kenway
8b515f3ba0
flang: make sure to find libstdc++ if needed (#17480) 2020-07-30 14:55:16 +02:00
Adam J. Stewart
d512537417
Python: added v3.8.4, v3.8.5, v3.7.7, v3.7.8, v3.6.11 (#17775)
Also added older version in the 3.6 and 3.5 series
2020-07-30 14:49:01 +02:00
G-Ragghianti
2f5e4e1664
MAGMA isn't compatible with CUDA 11 (#17753)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-30 11:24:21 +02:00