Commit graph

10483 commits

Author SHA1 Message Date
Jon Rood
583617ed67 Hwloc and numactl updates (#9987)
* Adding version 2.0.12 of numactl.

* Adding new versions of hwloc.

* Adding NVML variant to hwloc.

* Adding gl variant to hwloc.

* Updating hwloc numactl dependency and gl dependency.

* Using gl virtual package in hwloc.
2018-12-05 10:26:53 +01:00
Justin Stanley
87bf5296c3 biobloom: new package at 2.2.0 (#10014) 2018-12-04 17:20:24 -06:00
Justin Stanley
68a0305e13 sdsl-lite: new package at 2.1.1 (#10013) 2018-12-04 17:20:10 -06:00
Miles Perry
6020123a0b added bwa runtime dep (#10012) 2018-12-04 17:19:56 -06:00
Matthias Diener
deda7fdd60 ffmpeg: add version 4.1 (#10015) 2018-12-04 17:19:40 -06:00
Denis Davydov
121362383b dealii: do not hardcode prefix.include for BLAS/LAPACK (#10008)
* dealii: do not hardcode prefix.include for BLAS/LAPACK

* dealii: rename lapack_blas -> lapack_blas_libs
2018-12-04 16:55:41 -06:00
HAOCHENG LIU
ce485731bb Remove openmp version guard in vtkm and add precision options (#10005)
Clang 8.0 now supports openmp 4.5 and many commerical compilers also support
openmp >= 4.0. This commit removes the openmp version guard and rely on CMake
to throw errors out when openmp version requirement is not satisified.

It also add options for precision control.
2018-12-04 11:53:17 -08:00
Greg Sjaardema
9f8e445510 CGNS: Add option for 64-bit integers (#9990)
* CGNS: Add option for 64-bit integers

Added the `int64` variant which will build the library using 64-bit integers for certain values.  This gives the capability to have models with more than 2 billion cells and/or nodes.  

Beginning with CGNS-3.1.0, two new typedef variables have been introduced to support 64-bit mode. The `cglong_t` typedef is always a 64-bit integer, and `cgsize_t` will be either a 32-bit or 64-bit integer depending on how the library was built. Many of the C functions in the MLL have been changed to to use `cgsize_t` instead of `int` in the arguments. These functions include any that may exceed the 2Gb limit of an` int`, e.g. zone dimensions, element data, boundary conditions, and connectivity. In Fortran, all integer data is taken to be `integer*4` for 32-bit and `integer*8` for 64-bit builds.
2018-12-04 18:13:49 +01:00
Greg Sjaardema
ec67bbec2f EXODUS: Update version and dependencies (#9971)
* EXODUS: Update version and dependencies

Allow pulling master version from git.  Note that I hope to have better versioning "soon"

Add requirement to use Netcdf-4.6.1 or later as those versions no longer require changing the `maxdims` or `maxvars` defines in the netcdf.h include file.  With these versions, Exodus can use an unmodified NetCDF.  These versions of NetCDF are also better than previous versions (code quality, performance, robustness).

It is still possible to run exodusII with previous NetCDF versions, but I don't know how to specify that the dependency where maxdims/maxvars variants are only needed for versions prior to 4.6.0.  

I also removed the explicit dependency on HDF5 as that dependency should be applied through the NetCDF dependency.

* Remove white-space on blank line
2018-12-04 09:48:15 -06:00
Axel Huebl
427993b951 c-blosc: 1.15.0 (#10009)
Add latest version of c-blosc.
2018-12-04 09:10:08 -06:00
Kelly (KT) Thompson
4d26faac81 Provide a new spackage for py-pint. (#9991)
* Provide a new spackage for py-pint.

Pint is a Python package to define, operate and manipulate physical quantities:
the product of a numerical value and a unit of measurement. It allows arithmetic
operations between them and conversions from and to different
units. https://pint.readthedocs.io/en/latest/

* Switch hash from md5 to sha256.
2018-12-04 08:58:11 -06:00
Greg Sjaardema
b471e2768b MATIO: New versions (#9993)
Add several new versions so that current functionality can be accessed.  Current version is now 1.5.13.

Update `url`, `list_url`, and `list_depth` so spack can find available versions
2018-12-04 08:53:15 -06:00
Oliver Breitwieser
3cf998a5db Add tmux@2.8 (#10010) 2018-12-04 08:37:09 -06:00
Greg Sjaardema
231888f3e9 PNETCDF: Update with current versions (#9982)
* PNETCDF: Update with current versions

Added latest versions. (1.10.0, 1.9.0, 1.8.1)

* PNETCDF: Revert version change in url

Reverted the change in the url variable version since not required.
2018-12-04 08:31:41 -06:00
Greg Sjaardema
6e3b016aa2 NETCDF: Add new versions and update url (#9970)
* NETCDF: Add new versions and update url

Added the 4.6.2 version which was recently released.
Changed the url to point to the official Unidata site and added option to retrieve master version from git.

* NETCDF: checksum and version updates

Reverted back to use of previous URL.  The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0.  Since several installations are still providing 4.4.0, thought it best to go back to previous url.  However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2.  Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
2018-12-04 15:03:25 +01:00
Bert Wesarg
262b3f859e boost: 1.68 also needs boost_1.67.0_pgi.patch (#9980)
Its in upstream with the upcoming 1.69 release though.
2018-12-04 14:49:20 +01:00
Peter Scheibel
34f64f1f3f improved constraint conflict error message (#9975) 2018-12-04 14:19:57 +01:00
Matthias Wolf
e3aa36f4cb fix: adapt junit template to escape std{out,err} (#9935) 2018-12-04 14:05:45 +01:00
George Hartzell
0c3f220fb1 Disallow bcl2fastq2 on OS X (#9966)
* Disallow bcl2fastq2 on OS X

[Illumina's computing requirements][reqs] claim support for RHEL/CentOS and
go on to say:

> May be possible to install and run on other 64-bit Linux distributions or Unix variants.

The sufficient issue is its reliance of malloc.h.  There may be more.

[reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html

* Add an informative msg for the user
2018-12-04 13:44:15 +01:00
Neil Flood
e3d204cb8f Expand dependency on qt to allow qt4 (#9964) 2018-12-04 13:37:37 +01:00
Satish Balay
808c2ea5ce petsc: when petsc is built with fortran [default in spack] its best to use hdf5+fortran (#9986) 2018-12-04 13:32:30 +01:00
Neil Flood
47b7016ea7 r-optparse: new package (#9967) 2018-12-04 13:20:08 +01:00
Nick Forrington
9551b34cb5 pgi: Add checksum for PGI 18.10 (#9985) 2018-12-04 13:12:20 +01:00
Matthias Diener
dfb02fd078 cmake: add version 3.13.1 (#9983) 2018-12-04 13:09:49 +01:00
Levi Baber
27e8fcb945 abyss: new version (#9981) 2018-12-04 13:02:36 +01:00
sknigh
a9695bac50 Added missing libtool dependencies to libvterm and unibilium (#10007) 2018-12-04 13:01:37 +01:00
Robert Maynard
0d033a042c Download CMake sources from the Github releases (#10003)
Now that CMake is providing CMake release artifacts on github,
we should prefer those as they have better download speeds and
uptime.
2018-12-03 12:35:51 -06:00
jthies
3a2045b7c0 Phist 1.7.4 (#9996)
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
2018-12-03 09:40:51 -06:00
HAOCHENG LIU
66a62d82c4 Bump vtkm to version 1.3 and add new features (#9968)
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.

[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
2018-11-30 19:48:22 -08:00
Mark W. Krentel
cc5446f25c hpctoolkit: overhaul to use spack dependencies (#9946)
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.

Remove hpctoolkit-externals since it's no longer needed.
2018-11-30 18:11:12 -08:00
jwallior
930debcf35 New versions for a few python modules (#9969)
* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4
2018-11-28 21:44:15 -06:00
Piotr Luszczek
8375b5b571 Add PLASMA version 18.11.0 and Lua variant (#9689)
* Add PLASMA 18.11.1 with optional Lua and test for headers
2018-11-28 16:59:05 -06:00
Ondřej Čertík
62f1cf3678 Add f18 package (#9183)
* Add f18 package

* Fix flake8 errors

* Install the f18 binary into prefix.bin by hand

* Add spack-build into the path

* Fix the license header
2018-11-28 14:13:30 -06:00
Massimiliano Culpo
e998a399da Injected flags have a consistent order (#9960)
Fixes #9908

Spack was assembling flags in a manner that could in different
orderings for repeated concretizations of the same spec and config
2018-11-28 10:23:38 -08:00
Michael Kuhn
5cea4a75d7 glib: disable SELinux explicitly (#9956) 2018-11-28 10:06:17 +01:00
George Hartzell
e4e980ee97 bcl2fastq2 package: recursively delete after copy (#9959)
Fixes #9944

73c978d replaced a move with a copy, which cased rmdir to fail (as
it expects an empty directory). This switches to use `shutil.rmtree`
instead.
2018-11-27 17:22:14 -08:00
Scott Wittenburg
33b112a60d Expose option to save all dependencies when writing spec.yaml (#9965) 2018-11-27 17:13:39 -08:00
Jon Rood
4c3091b05e Fixing problems with lammps dependencies voropp and latte (#9909)
* Fixing problems with lammps dependencies voropp and latte.

* Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
2018-11-27 16:55:21 -07:00
Matthias Diener
2164181d0a git: add version 2.19.2 (#9961)
Also fixes instructions for new releases
2018-11-27 16:32:22 -06:00
Neil Flood
8a78c9c6bc Rename py-proj to py-pyproj, consistent with Spack's current naming conventions (#9962) 2018-11-27 16:31:30 -06:00
thelfer
2e04f3daab new package: add support for the tfel package (#9930) 2018-11-27 07:16:55 +01:00
Michael Kuhn
16d3e44515 py-pygobject: add missing pkgconfig dependency (#9955) 2018-11-26 21:41:44 -06:00
Axel Huebl
b26c85301d OpenMPI: Prefer Last 3.X (#9945)
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.

Let's wait for some point releases.
2018-11-26 16:46:04 -06:00
Eric
20a6dde10b GATK: Add version 4.0.11.0 (#9953) 2018-11-26 14:54:05 -06:00
Eric
d9046e70c1 minced: Add version 0.1.6 (#9951) 2018-11-26 14:22:17 -06:00
Matthias Diener
bab3d7734a hdf5: add version 1.8.21 (#9952) 2018-11-26 12:56:44 -06:00
Michael Kuhn
7df14134c1 go: add 1.11.2 (#9948) 2018-11-26 11:33:55 -06:00
Eric
5cd8233139 metabat: Add version 2.11.2 (#9950) 2018-11-26 11:32:14 -06:00
Miles Perry
28e93a7a79 Feature/gatk (#9872)
* added 3.8-1 version

* fixed flake8 stuff
2018-11-26 11:30:21 -06:00
Adam J. Stewart
06dcf72f14 Uncomment dependencies previously disallowed by concretizer (#9942) 2018-11-26 09:11:16 +01:00