Commit graph

15488 commits

Author SHA1 Message Date
Antonio Arena
4118a01774
Install gaussian using their scripts (#16723)
* Create VMD recipe

This is a new recipe to install VMD on Spack-managed hosts.

* Fix lint errors.

* Use plain Package

As per peer-review:
- Use Package to build
- Use configure to create a Makefile
- Use install to copy files to prefix directory

* Move VMD package to correct path, duh...

* Restructure description so first short paragraph can be used by module files.

* Add an empty line as suggested by peer-review. That's how you separate paragraphs.

* Remove extra spaces.

* Use setup_build_environment since that's where you're supposed to export OS variblaes. Thanks to peer-review for spotting this.

* Create VMD recipe

This is a new recipe to install VMD on Spack-managed hosts.

* Fix lint errors.

* Use plain Package

As per peer-review:
- Use Package to build
- Use configure to create a Makefile
- Use install to copy files to prefix directory

* Move VMD package to correct path, duh...

* Add Cubist (#16069)

* Add Cubist

* enhance recipe

* Not using OS module anymore

* remove white space

* Fix build shell

* make Flake8 happy

* use bash shell for build

* Convert it To MakefilePackage as per peer-review

* dbcsr: expose all options, check openblas feats (#16034)

* dbcsr: expose all options, check openblas feats

* dbcsr: use Ninja to build, ensure serialized tests

* dbcsr: add myself as maintainer

* MPark.Variant: GCC 7.3.1 Conflict (#16081)

* MPark.Variant: GCC 7.3.1 Conflict

Due to an ICE in this specific patch-release of GCC, compile
errors in downstream packages should be avoided with a clean
conflict.

* Fix superfluous spaces

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

* Fix typo

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

* Move VMD package to correct path, duh...

* Add an empty line as suggested by peer-review. That's how you separate paragraphs.

* New matlab versions (#16086)

* Add new version 1.1.1 (#16087)

* New package bonniepp added (#16091)

* openbabel: fix compilation errors (#16090)

- Disable maeparser as it is broken with CMake
- Added missing dependencies

* singularity: updated maintainer list (#16093)

* New version xrootd-4.11.3 (#16092)

* I added Gaussian 16. I also execute bsd/install to fix scripts instead of filtering them.

* revert VMD so only Gaussian is in my PR.

* revert VMD so only Gaussian is in my PR.

* revert VMD so only Gaussian is in my PR.

* I added myself as a package maintainer.

Co-authored-by: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Co-authored-by: Tiziano Müller <tiziano.mueller@chem.uzh.ch>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Amjad Kotobi <amjadkotbi@gmail.com>
Co-authored-by: athanasio <athanasio@users.noreply.github.com>
Co-authored-by: Carlos Arango Gutierrez <arangogutierrez@gmail.com>
2020-05-20 22:34:03 -05:00
Toyohisa Kameyama
51ff18ef8d
mxnet: Fix dependency and add new version. (#16714)
* mxnet: Fix dependency and add new version.

1. Fix opencv and numpy dependency.
2. Add version 1.6.0.

* typo in patch is fixed.
fixed spec access.
2020-05-20 22:33:31 -05:00
Jeremy
bcd5dd6e3e
add SST packages and dependencies (#16618) 2020-05-20 22:15:02 -05:00
Greg Becker
cfb6f21236
externals: allow package prefs to configure default not buildable (#16735)
Allows `all` to be configured non-buildable in packages.yaml.

The following config would only allow zlib to be built by Spack, all other packages would have to be found as externals.

```
packages:
  all:
    buildable: False
  zlib:
    buildable: True
```
2020-05-20 17:09:07 -07:00
Tamara Dahlgren
92989fbbfd
tests: check presence not equality for rpath changes (#16637)
Fixes #16636
2020-05-20 18:11:26 +02:00
Adam J. Stewart
cc08070da9
py-scikit-learn: add latest version (#16731) 2020-05-19 20:59:11 -05:00
Christoph Junghans
46ab939249
mantevo: update urls to new website (#16732) 2020-05-19 16:19:17 -05:00
Andrew W Elble
7fe6c0945a
py-tensorflow-estimator: new version 2.2.0 (#16726) 2020-05-19 14:29:13 -05:00
Hadrien G
9c16a728fd
Add new Acts release (#16718) 2020-05-19 13:16:57 -05:00
Thomas Madlener
7948344bcd
Introduce version 1.0.0 for py-xenv and remove unreleased development release (#16722)
Problems in 0.0.4 should be fixed for 1.0.0
2020-05-19 13:14:45 -05:00
ddeidda
20f2a6c2e8
update URL and sha256 for aws-parallelcluster 2.7.0 (#16717)
Signed-off-by: ddeidda <ddeidda@amazon.com>
2020-05-19 10:58:46 -05:00
Dr. Christian Tacke
63f09a6662
openssl: Be Explicit About perl Usage (#16721)
The openssl build process can use the wrong perl for
various reasons, including:
* Wrong value in PERL env var
* The build process first looks for `perl5`, which the
  spack system does not provide, but some other
  distributions provide it. That way, the build process can
  end up using the wrong perl.

Stop all of these problems by explicitly setting PERL to
the to be used dependency.
2020-05-19 10:58:04 -05:00
darmac
31ab62fb5e
Add new package: http-post (#16678)
* Add new package: http-post

* refine version name
2020-05-19 10:56:52 -05:00
darmac
05aacb584e
Add new package: http-ping (#16675)
* Add new package: http-ping

* refine version name
2020-05-19 10:56:22 -05:00
Scott Wittenburg
b1f1f5dddb Pipelines: Ensure consistent spack version for entire pipeline
Also retry jobs always, as script failure is not confined to only our
spack ci rebuild command exit code.
2020-05-19 09:40:02 -06:00
vvolkl
31ccf80294
[podio] fix root cxxstd dependency (#16708) 2020-05-18 21:52:18 -05:00
darmac
9d766ae1fa
Add new package: http-load (#16676)
* Add new package: http-load

* refine version format

* fix date/version error
2020-05-18 21:41:00 -05:00
darmac
3f6164053d
Add new package: http-get (#16677)
* Add new package: http-get

* refine version name
2020-05-18 21:40:34 -05:00
Greg Becker
84889ef3a3
move source dir to last cmake arg (#16709) 2020-05-18 16:39:13 -07:00
Adam J. Stewart
cf4c48c37e
TensorFlow: add new versions (#16703) 2020-05-18 16:38:37 -05:00
Justin S
294a91b580
r-decipher: new package at 2.12.0 (#16705) 2020-05-18 16:37:06 -05:00
Justin S
d768b34f17
angsd: add 0.933, add misc programs to install (#16669)
* angsd: add 0.933, add misc programs to install

* angsd: add r variant
2020-05-18 16:07:35 -05:00
Utkarsh Ayachit
154a442817
paraview: use kits by default (#16698)
Adding a variant to enable/disable kits and making the default use kits.
2020-05-18 12:59:40 -05:00
Amjad Kotobi
d957c621ef
r-tensor: New package (#16697) 2020-05-18 11:53:17 -05:00
Amjad Kotobi
864d4a2232
r-goftest: New package (#16699) 2020-05-18 11:51:26 -05:00
Nick Robison
0b37188e4f
Update Apache arrow to 0.17.1 (#16701)
Update Arrow to the latest version.

Also add an additional dependency on `thrift` when building with Parquet support.
2020-05-18 11:49:44 -05:00
darmac
28ef9cad3b
Add new package: hyperscan (#16681)
* Add new package: hyperscan

* hyperscan: remove cmake_args()
2020-05-18 11:36:00 -05:00
archxlith
931932d65d
New package: py-pyeda (#16416)
* New package: py-pyeda

* py-pyeda: added dep for python 3.3 or greater

* [py-pyeda] Added space in depends_on python line
2020-05-18 10:01:59 -05:00
Adam J. Stewart
2d464f69f8
PyYAML: fix linking to libyaml (#16682) 2020-05-18 09:57:51 -05:00
h-denpo
ce8cf5d9b0
revocap-refiner: fixed typo in pic flags (#16694) 2020-05-18 10:04:10 +02:00
Toyohisa Kameyama
ffdd94dd9f
hwloc: Add libudev variant. (#16615)
* hwloc: Add libudev variant.

* typo fix.

* Wrong version for libudev variant is fixed.

* Add maintainers.
2020-05-17 20:00:23 -05:00
Marko Kabic
a4d64402ae
Add new version of COSMA: 2.2.0 (#16672)
* Updated versions of COSMA.

* Added an empty line for formatting.

* Switched to sha256.

* Renamed gpu variant to cuda. Extending the CudaPackage base class.
2020-05-17 12:40:48 -05:00
Amjad Kotobi
045063da7f
r-spatstat-data: New package (#16688) 2020-05-17 12:28:26 -05:00
Amjad Kotobi
d776e52979
r-rms: New package (#16683)
* r-rms: New package

* r-rms: deleted duplicated dependency

* r-rms: deleting comma
2020-05-17 12:27:33 -05:00
Amjad Kotobi
9685792f83
r-spatialpack : New package (#16664)
* r-spatialpack : New package

* r-spatialpack : R dependeny added type

* r-spatialpack: Description was missing
2020-05-17 10:22:52 -05:00
Michael Kuhn
41907639c4
py-scipy: Fix build with gcc@10: (#16687) 2020-05-16 20:55:20 -05:00
Justin S
babfd144ad
py-fastcluster: new package at 1.1.26 (#16588)
* py-fastcluster: new package at 1.1.26

* py-fastcluster: add py-setuptools dep
2020-05-16 16:12:50 -05:00
Amjad Kotobi
5912b8c7cd
r-yaimpute: New package (#16658) 2020-05-16 16:07:58 -05:00
Amjad Kotobi
f71768b1d6
r-envstats: New package (#16659) 2020-05-16 16:07:10 -05:00
h-denpo
a97ce63218
New package frontistr (#16660)
"""Open-Source Large-Scale Parallel FEM Program for
        Nonlinear Structural Analysis"""
2020-05-16 16:06:25 -05:00
Amjad Kotobi
6ca1052999
r-spatstat-utils : New package (#16663) 2020-05-16 16:03:49 -05:00
Mark W. Krentel
b858eebc51
hpctoolkit: add dependency on gotcha (#16670) 2020-05-16 15:59:33 -05:00
Paul
32238391a9
Add Go versions 1.14.3 and 1.13.11 (#16673) 2020-05-16 15:55:51 -05:00
darmac
110b15f20e
Add new package: hiredis (#16679) 2020-05-16 15:51:01 -05:00
darmac
b6498c44af
Add new package: guacamole-server (#16680) 2020-05-16 15:50:24 -05:00
TZ
2ebadbc267
intel-mpi: add libfabrics directory to SPACK_COMPILER_EXTRA_RPATHS (#15214)
workaround for not finding an appropriate libfabrics.so with Intel
MPI 2019+. Fixes #11140 and #12493
2020-05-16 10:40:40 -05:00
Amjad Kotobi
983f05ac41
r-polspline: new package (#16648)
* r-polspline: new package

* r-polspline: updated urls
2020-05-16 09:07:34 -05:00
Omar Padron
97d7ef678d
fix catalyst so that it doesn't depend on a particular spelling of python (#16667) 2020-05-15 15:11:32 -04:00
Greg Becker
32a9adcf60
modules: use projections format for naming schemes (#16629)
* update tcl naming_scheme to use projections

* add projections to lmod modules
2020-05-15 11:12:52 -07:00
Stephen Hudson
955a3db206
py-petsc4py: allow ~mpi variant (#16595)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-15 15:14:06 +02:00