Commit graph

10113 commits

Author SHA1 Message Date
Jennifer Herting
d4d82281d1
[rust] added version 1.41.0 (#14742) 2020-02-04 15:11:36 -06:00
Jennifer Herting
997a0f4207
New version for mariadb and disable dtrace (#14734)
* [mariadb] added version 10.4.8

* [mariadb] disabled dtrace
2020-02-04 15:01:25 -06:00
Rao Garimella
b34e7ad28f
MSTK package: add version 3.3.2 (#14689) 2020-02-04 11:15:45 -08:00
Christoph Junghans
603e2794db
cray-libsci: initial commit (#14709)
* cray-libsci: initial commit
2020-02-04 10:18:20 -07:00
Massimiliano Culpo
1bbe0a1f74
abinit: fix dependency on fftw (#14739)
fixes #14578

Abinit's recipe requires double precision FFTW libraries
2020-02-04 15:29:21 +01:00
Dr. Christian Tacke
0ec9377852
pythia8: added old versions, build depend on rsync (#14740) 2020-02-04 15:27:57 +01:00
Nicolas Richart
19ff3c0f67
akantu: new package at v3.0.0 (#14685) 2020-02-04 11:04:59 +01:00
Andrew W Elble
4accc78409
Git fetching: add option to remove submodules (#14370)
Add an optional 'submodules_delete' field to Git versions in Spack
packages that allows them to remove specific submodules.

For example: the nervanagpu submodule has become unavailable for the
PyTorch project (see issue 19457 at
https://github.com/pytorch/pytorch/issues/). Removing this submodule
allows 0.4.1 to build.
2020-02-03 19:02:45 -08:00
Rob Latham
7d444f08e7
update pmdk to 1.8 (#14733)
new upstream release
- notable in that it has experimental powerpc-le support (e.g. summit)
- required a new patch to disable documentation
2020-02-03 19:15:52 -06:00
Massimiliano Culpo
42633b0869
octave: mkoctfile doesn't use compiler wrappers (#14726)
* Octave: moved the short description in its own paragraph

* Octave: patch mkoctfile.in.cc to avoid using compiler wrappers

* Added a check to ensure mkoctfile works correctly
2020-02-03 15:08:44 -06:00
Adam J. Stewart
74c8f25826
Add new versions of matplotlib (#14731) 2020-02-03 15:07:12 -06:00
albestro
94971d519c
Fix CMake and update libarchive (#14684)
* update libarchive and fix version of libarchive cmake dependency

* (at least) libarchive 3.3.3 dependency from cmake 3.15.0

* cmake depends on libarchive 3.1.0 if not specified differently

currently it is applied to cmake <3.15.0

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-03 11:26:38 -05:00
Andrew W Elble
30dd7ae176
clingo: new versions (#14728)
5.3.0 and 5.4.0
2020-02-03 07:58:34 -06:00
Jean-Paul Pelteret
dcaa50c9d0
deal.II: Add patch for TBB version check (#14724) 2020-02-03 13:04:12 +01:00
Mark W. Krentel
3d9787a8bf
hpcviewer: add version 2020.01 (#14718) 2020-02-02 09:26:21 -06:00
Jean-Paul Pelteret
44f60f9fec
Update package: SymEngine 0.5.0 (#14722) 2020-02-02 09:25:51 -06:00
Adam J. Stewart
0c0aba579a
octave: add maintainer (#14716) 2020-02-01 19:46:35 -06:00
Tim Haines
412c336113
boost: Add versions 1.71.0 and 1.72.0, use Clang toolset on Darwin (#14678)
* boost: Add versions 1.71.0 and 1.72.0

* Remove 'darwin' target

* Add hainest as maintainer
2020-01-31 17:56:40 -06:00
Kelly (KT) Thompson
0c9ac8d8d1
draco: update versions (#14690)
* draco: update versions

+ Added versions 7.3.0 and 7.4.0.
+ Change several variants to be default TRUE since most consumers need these
  variants enabled (eospac, lapack, parmetis, superlu-dist). Change variant name
  for `+superlu_dist` to use hyphen instead of underscore.  This makes the
  variant name consistent with the spackage name for `superlu-dist`.
+ Clean up `depends_on` instructions and avoid specifying `type` when possible.
+ Provide patch files that are necessary for some machines (mostly Cray
  machines).

* Remove trailing whitespace.

* Revert variant name to use underscore.

* add maintainer information.
2020-01-31 14:03:54 -06:00
Themos Tsikas
04e6fd60f3
NAG Fortran Compiler, 6.0 dropped (unavailable), 7.0 added (#14691)
* NAG Fortran Compiler, 6.0 dropped (unavailable), 7.0 added

* Update package.py

* Update package.py
2020-01-31 14:03:31 -06:00
Dr. Christian Tacke
6f4c90378a
[libfabric@1.9.0] Fix C++ header usage (#14703)
Fix from libfabric's git for 1.9.0.

Compiling C++ software against libfabric@1.9.0 doesn't work
without this patch.

See: 2e95b0efd8
2020-01-31 14:01:58 -06:00
Matthieu Dorier
b7ee2d02e4
Fixed DIY package missing MPI dependency (#14704) 2020-01-31 14:01:17 -06:00
Christoph Junghans
d83309493f
superlu-dist: enforce OpenMP=OFF (#14708) 2020-01-31 13:35:46 -06:00
Christoph Junghans
47ee690076
portage: fix compile on icc (#14707) 2020-01-31 13:35:20 -06:00
Andrew W Elble
b072caadec
fix: py-pillow build_ext vs. install (#14666)
Previously, the install stage would compile in things that were
disabled during the build_ext phase. This would also result in the
build pulling in locally installed versions of libraries that were
disabled. The install process doesn't honor the same command-line
flags that build_ext does, but does call build_ext again. Avoid the
whole issue by just writing the options to setup.cfg

Also, add the Imagemagick dependency for tests.
2020-01-30 14:42:48 -06:00
Massimiliano Culpo
1e0408d05a
Updated docstring and version of lmod to v8.3 (#14687) 2020-01-30 12:33:16 -06:00
Adam J. Stewart
ee35d949f9
Add GDAL 3.0.4 (#14688) 2020-01-30 12:08:47 -06:00
Jennifer Herting
a5b2347cfe
[py-joblib] added version 0.11 (#14672) 2020-01-30 02:27:04 -08:00
Jennifer Herting
23a759cda0
[r-manipulatewidget] added versions (#14674) 2020-01-30 02:26:48 -08:00
Jennifer Herting
39035e4517
[r-rgl] added version 0.100.19 (#14675) 2020-01-30 02:26:24 -08:00
Cameron Smith
488e25ea34
pumi: sim version check, meshes via submodule, ctest (#14597)
* pumi: sim version check, meshes via submodule, ctest

* Apply suggestions from code review

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

* pumi: update comment on master version string

* pumi: description of simmodsuite_version_check variant

* pumi: add white space to variant description

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-29 18:29:07 -06:00
Greg Becker
bd60e0f137
fix cycle dependency in libxml+python (#13847)
* fix cycle dependency in libxml+python
* comment why we need these dependencies
2020-01-29 12:39:55 -08:00
noguchi-k
da189b8d1d
Fastx-toolkit package: patch for Fujitsu compiler (#14218)
Specify the scope of pragma pack
2020-01-29 11:45:37 -08:00
Adam J. Stewart
ed4d544e8f
Fix py-pillow tests (#14670) 2020-01-29 13:24:44 -06:00
Robert Pavel
b142914b24
Added MiniAMR@1.4.4 (#14667) 2020-01-29 13:24:22 -06:00
Robert Pavel
30c8e1d8a0
Added xsbench@19 to Version List (#14668) 2020-01-29 13:24:03 -06:00
Jennifer Herting
549aae7f72
[py-griddataformats] added new versions (#14671) 2020-01-29 13:23:22 -06:00
Michael Kuhn
52a7f94d9e
pythia8: add new package (#14665) 2020-01-29 11:40:39 -06:00
Matthias Wolf
4e3617fe1d
py-pyperf: add 1.6.{0,1} (#14662) 2020-01-29 09:00:03 -06:00
Matthias Wolf
1af36f0cdc
flatbuffers: add 1.11.0 (#14663) 2020-01-29 08:58:41 -06:00
Matthias Wolf
53d891a501
py-black: update url, add 19.3b0 (#14664) 2020-01-29 08:56:54 -06:00
Andrew W Elble
9d7e482497
git: add version 2.25.0 and fixup pcre dependency (#14649)
* git: add version 2.25.0 and fixup pcre dependency

pcre2 became optional in 2.14 and the default in 2.18. I noticed this
as git was compiling against the system pcre2 (spack was
specifying pcre as the dependency).

* missed a chunk from my internal repo
2020-01-28 21:01:25 -06:00
Glenn Johnson
e710656310 Set netcdf-fortran to build serially with Intel compiler (#14461)
* Set netcdf-fortran to build serially with Intel compiler

This PR turns off parallel builds when the Intel compiler is used.
Builds with the Intel compiler will fail otherwise.

* Change how parallel build is handled

Use patch from netcdf-fortran project to turn off parallel buildi for
version 4.5.2.
2020-01-28 15:13:51 -06:00
darmac
2b0b340aab racon: support aarch64 and fix install error (#14529)
* racon: support aarch64 and fix install error

* add aarch64 patch for racon
2020-01-28 15:12:40 -06:00
noguchi-k
ea0a549db3 pcma: set return value and change return type of function (#14579) 2020-01-28 15:08:35 -06:00
t-karatsu
492b600d29 diffutils: Changed the handling of undeclared functions from warning … (#14593)
* diffutils: Changed the handling of undeclared functions from warning to error.

* diffutils: Change the handling of warnings or error

* Delete '-Werror=implicit-function-declaration'

* Add '-Qunused-arguments'
2020-01-28 15:06:37 -06:00
Glenn Johnson
0605fc1557 Build graphite2 with Intel compiler (#14636)
This PR sets the definition of REGPARM when building with the Intel
compiler.
2020-01-28 15:03:13 -06:00
Matthias Diener
94def872ee Moreutils: add new package (#14653)
* moreutils: add new package

* fix flake8
2020-01-28 15:02:07 -06:00
Brian Van Essen
f17ce36da2 Fixed path for CEREAL and Protobuf (#14641) 2020-01-28 15:01:50 -06:00
Axel Huebl
2b6106524a openPMD-api: With ADIOS2 by Default (#14643)
Replace the deprecated ADIOS1 backend default with ADIOS2 default.
Disable sz since we do not need it and it conflicts with supported
version ranges between ADIOS2 and ADIOS1 if someone enables both.
2020-01-28 15:01:15 -06:00
noguchi-k
635fc62de0 powerapi: add a space between literal and identifier (#14645) 2020-01-28 14:59:59 -06:00
noguchi-k
da091c0cf5 med: add a space between literal and identifier (#14646) 2020-01-28 14:59:23 -06:00
Ben Morgan
16da648d03 intel-tbb: Fix install names on Darwin (#14650)
* intel-tbb: Fix install names on Darwin

Intel-TBB's libraries on Darwin are installed with "@rpath" prefixed
to their install names. This was found to cause issues building the root
package on Darwin due to libtbb not being found when running some of the
generated tools linking to it.

Follow example from other packages with the same issue and fixup up install
names for intel-tbb post install.

* intel-tbb: fix flake8 errors
2020-01-28 14:57:25 -06:00
iarspider
67c6d99219 Fix for #14148 (#14595)
* Dirty hack to fix #14148

* A better way of checking if a package is taken from system

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

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

* Update qt/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-28 14:15:29 -06:00
Christoph Junghans
12b0340d2f ninja: add v1.10.0 (#14647) 2020-01-28 09:34:31 -08:00
Adam Moody
6ab2c3caa3 mpifileutils: add v0.10 (#14644)
Signed-off-by: Adam Moody <moody20@llnl.gov>
2020-01-27 20:33:26 -08:00
Joe Koning
e01c39019c Add the py-merlinwf package (#14622)
* Add the py-merlinwf package

* Fix importlib-resources package name for spack naming convention.

* Add build to dependencies and add updated versions.

* Remove pytest-runner dependency.

* Fix typo.

* Add the py-tabulate dependency.

* Add sha256 for version 1.0.0

* Change to maestro version 1.1.5.

* Increase to version 1.0.4.

* Bump maestrowf version and prepare for new pypi version.

* Add sha256sum for version 1.1.5

* Add version 1.1.1.
Update maestrowf version to 1.1.7

* Add versions 1.0.5, 1.1.0, 1.1.1 and potential 1.2.0.

* Add version 1.2.0 and when on maestrowf@1.1.6.

* Add version 1.2.2 , remove 1.2.1 and 1.1.0.

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

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

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

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

* Remove mysql variant until new mysql interface module is enabled.
The mysql code may be removed.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-27 17:26:43 -06:00
Erik Schnetter
0f3ae864a5 asdf-cxx: new package (#14637) 2020-01-27 14:50:18 +01:00
Erik Schnetter
b7b27d3862 amrex: Update to version 20.01 (#14635)
Now using Github releases instead of git commits.
2020-01-27 10:07:46 +01:00
Sinan
0e86961b84 pygdal and gdal versions should be in lockstep (#14630) 2020-01-26 18:35:16 -06:00
Adam J. Stewart
71f47b3b26
Add py-vermin package (#14631) 2020-01-26 18:34:56 -06:00
Erik Schnetter
02e077a7fa simulationio: Correct HDF5 dependency bounds (#14626)
The HDF5 dependency bound was inverted. (How did this ever compile? There is a cmake check.)
2020-01-26 17:22:43 -06:00
Erik Schnetter
87c55b79c5 hwloc: New version 2.1.0 (#14627) 2020-01-26 17:22:26 -06:00
Erik Schnetter
06e100d5cc curl: New version 7.68.0 (#14625) 2020-01-26 17:06:38 -06:00
Adam J. Stewart
f8be90cf3f
Add TensorFlow 1.15.2 (#14624) 2020-01-26 15:41:09 -06:00
Erik Schnetter
a26e5caa57 h5cpp: Download from github release instead of git repo (#14573)
* h5cpp: Download from github release instead of git repo

* Correct typo in package description
2020-01-25 18:39:36 -06:00
Adam J. Stewart
cb3f4081a0
Add TensorFlow 2.0.1 (#14623) 2020-01-25 12:45:09 -06:00
Glenn Johnson
c700200959 Get vtk-8.2.0 to build (#14562)
This PR adds some extra dependencies needed for vtk-8.2.0. It also
handles the variable name changes to turn off some of the external
libraries.
2020-01-25 12:44:51 -06:00
Hadrien G
f569577747 acts-core: Add and adapt to ACTS v0.14.0 and v0.15.0 (#14580)
* Add and adapt to ACTS v0.14.0

* Add v0.15.0 too
2020-01-25 12:35:53 -06:00
Brian Homerding
1fd335d654 Removing flang variant from llvm package (#14600) 2020-01-25 12:26:11 -06:00
Adam Moody
1e09de73b7 libcircle: add v0.3 (#14611) 2020-01-25 12:22:21 -06:00
Greg Becker
a57edb7029 configure z3+python to build python libraries in its own prefix (#14604) 2020-01-24 21:16:48 -08:00
Glenn Johnson
71243f3f7b Get py-torch to build caffe2 (#14619)
* Get py-torch to build caffe2

This PR gets the py-torch package to build with caffe2, and closes
issue #14576. If building on a machine with CUDA but no GPU the build
will try to build with all compute capabilities. Older compute
capabilities are not supported so the build will fail. The list of
capabilities can be passed to the build using values set in the
cuda_arch variant. Likewise, conflicts are also set to catch if the
unsupported capabilities are listed in cuda_arch.

This PR also sets version constraints on using an external mkldnn for
newer versions. Currenly, only versions up to 0.4 use an external mkldnn
library. Also, the cuda variant is set to True, which restores
previous behavior.

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

Fix typo.

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

* Adjust conflicts

This commit adjusts the conflicts. There is an issue with the
cuda_arch=20 conflicts directive as there is a conflicting dependency
with any version >=1.1 and a cuda_arch=20 dependency specified in
CudaPackage that gets trapped first.

* Use a common message for conflicts

This commit adds a variable to contain the bulk of the message stringi
for the cuda_arch conflicts. This is used along with a version string
in the conflicts directives messages.

* Fix the strings

- Use a multiline string for the cuda_arch_conflict variable.
- No need for format() in the msg value.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-24 22:57:16 -06:00
Mathew Cleveland
35db2d05b7 py-opppy package: add version 0_1_2 (#14229) 2020-01-24 18:58:22 -08:00
iarspider
bb29932362 py-pygdal package: 2.4.0 depends on gdal 2.4.1 (#14075) 2020-01-24 18:34:37 -08:00
plamborn
f8e0f4251d libhio: remove autoreconf method (#14283)
The autoreconf is not necessary and can cause errors.
2020-01-24 18:20:02 -08:00
健美猞猁
9a6b3b3a07 New package: MBDyn (#14438) 2020-01-24 18:14:14 -08:00
Glenn Johnson
80745128b3 harfbuzz package: add conflict for @2.3.1: with intel compiler (#14386)
harfbuzz 2.3.1 (and presumably all future versions after it) does
not build with the Intel compiler
2020-01-24 18:05:50 -08:00
Sajid Ali
12a261523e New package: p3dfft3 (#14508) 2020-01-24 17:20:36 -08:00
Kevin Huck
33d35768e6 Fixing GCC compiler setting for PDT package 2020-01-24 17:03:52 -08:00
Kevin Manalo
6fd2c66022 IOR package: add version 3.2.1 (#14582) 2020-01-24 16:56:59 -08:00
Jordan Ogas
1c9337a5e4 charliecloud package: add version 0.13; remove older versions (#14591)
* Add version 0.13 and update to use Autotools build system
* Remove all versions prior to 0.13 (which do not use Autotools)
2020-01-24 16:55:55 -08:00
Piotr Luszczek
d646c8d8d5 magma: add new version 2.5.2 2020-01-24 15:27:01 -08:00
Jon Rood
d58390dbf7 Add version 0.6.3 of yaml-cpp. 2020-01-24 15:26:33 -08:00
Brian Van Essen
36fca2c29a Updated and cleaned up the recipe for the LBANN and Hydrogen packages. (#14612)
* Updated and cleaned up the recipe for the LBANN and Hydrogen packages.

* Flake8

* Added type test for catch2
2020-01-24 14:49:05 -06:00
Brian Van Essen
4a5835ef2c Added version for 10.2 compatibility (#14613)
* Added version for 10.2 compatibility

* Updated the preferred version
2020-01-24 09:30:38 -06:00
Seth R. Johnson
ca6e75c9f6 Use Spack target architecture to determine OpenBLAS target (#14380)
Openblas target is now determined automatically upon inspection of
`TargetList.txt`. If the spack target is a generic architecture family
(like x86_64 or aarch64) the DYNAMIC_ARCH setting is used
instead of targeting a specific microarchitecture.
2020-01-24 15:19:05 +01:00
Axel Huebl
b0fce56d5b
openPMD-api: adios_config to run env (#14610)
Popular CMake find-scripts for ADIOS1 search for this binary instead
of looking up `CMAKE_PREFIX_PATH`.
2020-01-23 17:35:45 -08:00
Adam J. Stewart
031fdfd7ca
Add TensorFlow 1.15.1 (#14614) 2020-01-23 16:25:30 -06:00
Hadrien G
80ea96312f ftgl: Move to frankheckenbach fork + CMakePackage (#14221)
* Try to switch to a newer fork of ftgl

* Allow ROOT to be more flexible about ftgl versions

* Turn ftgl into a CMakePackage

* Update ROOT ftgl dep since 2.1.3 isn't a thing anymore

* Please flake8

* Try to bring back the doc variant

* Comment it out instead of removing it
2020-01-23 11:43:11 -06:00
Hadrien G
1a385a5178 root: Fix root+x breakage from #11129 (#14224)
* Fix root+x breakage from #11129

* Separate out +opengl breakage

* Not strictly X11-related, but more breakage from  #11129

* Another X11 breakage found while building 6.08.x

* Don't put system headers in SPACK_INCLUDE_DIRS + deduplicate

* xextproto is only a dependency in +x builds
2020-01-23 11:42:25 -06:00
Mark W. Krentel
5053dfa259 binutils, libiberty: add version 2.33.1 2020-01-22 21:50:10 -08:00
Axel Huebl
910df8cb4e openPMD-api: Default +adios1 (#14599)
Enable the ADIOS1 backend by default.
2020-01-22 15:49:27 -08:00
Axel Huebl
7a0990903f MPark.Variant: Patch NVCC C++14 Build 2 (#14434)
Update the patch to fix builds with NVCC <= 10.2.89 with
the accepted PR for upcoming releases of the library.
2020-01-22 11:29:02 -08:00
Sam Gutiérrez
ffbb0efc81 libquo: Update default version from 1.3 to 1.3.1. (#14585) 2020-01-22 11:14:26 -08:00
Scott Wittenburg
8283d87f6a pipelines: spack ci command with env-based workflow (#12854)
Rework Spack's continuous integration workflow to be environment-based.

- Add the `spack ci` command, which replaces the many scripts in `bin/`

- `spack ci` decouples the CI workflow from the spack instance:
  - CI is defined in a spack environment
  - environment is in its own (single) git repository, separate from Spack
  - spack instance used to run the pipeline is up to the user
  - A new `gitlab-ci` section in environments allows users to configure how
    specs in the environment should be mapped to runners
  - Compilers can be bootstrapped in the new pipeline workflow

- Add extensive documentation on pipelines (see `pipelines.rst` for further details)
- Add extensive tests for pipeline code
2020-01-21 22:35:18 -08:00
Todd Gamblin
4d794d63b5
python: add debug variant to enable pydebug (#14584) 2020-01-21 15:09:41 -08:00
Adam J. Stewart
796722aeee
Add py-scipy 1.2.3 (#14583) 2020-01-21 15:29:50 -06:00
Glenn Johnson
900161d182 Update and fix samtools (#14507)
* Update and fix samtools

This PR adds samtools-1.10 and sets the htlib directory so that the
spack built htslib can be used. This PR also arranges the dependencies
so that the htslib sequence is grouped on its own. Finally, the bzip2
dependency is removed and python and perl run dependencies are added.

* Fix samtools when built with ncurses+termlib

* The CI flake8 tests require lowercase variable

Interestingly, this did not show up when I ran `spack flake8` locally.
2020-01-21 15:24:39 -06:00
Michael Kuhn
54ecc4e504 cmake: Fix patch checksum (#14542)
Add patch locally to make sure checksum cannot change again.
2020-01-21 13:05:42 -06:00
Glenn Johnson
5db5040871 Use CudaPackage mixin for py-theano (#14577)
This PR adds the CudaPackage mixin class to py-theano. This replaces the
`gpu` variant with the `cuda` variant.
2020-01-21 09:27:41 -06:00
Adam J. Stewart
d10505678f
Add new kcov package (#14574)
* Add new kcov package

* Fix linking error and add test
2020-01-20 19:22:05 -06:00
Sean Smith
f23a136d83 Update AWS ParallelCluster to 2.5.1 (#14571)
Signed-off-by: Sean Smith <seaam@amazon.com>
2020-01-20 15:19:28 -06:00
Cyrus Harrison
ca26eb6923 add conduit 0.5.1 release and allow conduit to build against statically linked python (#14559) 2020-01-19 20:22:03 -06:00
Olaf Mersmann
dbb149cd7f capnproto: New package. (#14557)
* capnproto: New package.

* capnproto: Fix flake8 errors.

* Remove characters invalid in Python 2.
2020-01-19 17:20:22 -06:00
Simon Pintarelli
818b00e302 py-voluptuous update versions (#14556) 2020-01-19 10:39:11 -06:00
Howard Pritchard
ba22af0de0 openmpi: swat btl/uct ucx 1.7 bug (#14522)
Unfortunately UCX 1.7.0 is appearing in RPMS before it's officially released.
There's a problem with Open MPI 4.0.x where x < 3 and this version of UCX,
namely that the UCT BTL fails to compile.

See https://github.com/open-mpi/ompi/issues/7128

This patch works around the problem by disabling the build of the UCT BTL
for releases 4.0.0 to 4.0.2.

add hppritcha (me) as maintainer

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2020-01-18 13:52:26 -06:00
Matthieu Dorier
d8b4bee0cd Added py-spdlog package (#14514)
* Added py-spdlog package

* pleasing flake-8

* pleasing flake-8

* addressed some comments from adamjstewart

* changed URL for archive

* replaced with pypi.io url
2020-01-18 13:51:55 -06:00
Martin Pokorny
cacd57d340 Updates to casacore package (#14552)
* Add +cfitsio variant to wcslib dependency

* Replace ncurses dependency with readline dependency

casacore explicitly may depend on readline, not ncurses

* Add workaround for casacore's readline dependency

casacore optionally depends upon readline, but it's CMakeLists.txt provides no
user control over whether or not readline becomes a dependency. As readline is
often present by default on systems, it's better for this package to explicitly
depend on readline in order to prevent linking to whatever system version of the
library happens to be found during the build process. This should be considered
a workaround until casacore's CMakeLists.txt is fixed.

* Apply workaround for casacore's dependency on SOFA

Similar to the issues with casacore's readline dependency, casacore's optional
dependency on SOFA does not provide the user with a means of controlling the
dependency during build time. Unlike the readline library, the SOFA library is
unlikely to exist on most systems by default. As the SOFA dependency is only
optionally used for testing casacore, requiring it by default is not a good
workaround. Until casacore's CMakeLists.txt is fixed, this variant has been
removed to avoid unexpected library dependencies in the installed package.

* Add newer casacore versions

* Add mpokorny to maintainer field
2020-01-17 20:02:51 -06:00
Valentin Reis
c6a6911821 aml: adds 'develop' and 'master' targets. (#14549)
Co-authored-by: mlhardware <57849932+mlhardware@users.noreply.github.com>
2020-01-17 16:38:12 -06:00
Kai Torben Ohlhus
9010d4fce5 suite-sparse: add 5.4.0, 5.5.0, and 5.6.0, GitHub releases (#14547)
- The suite-sparse author publishes new versions starting with 5.5.0 on GitHub, see https://github.com/DrTimothyAldenDavis/SuiteSparse/releases and http://faculty.cse.tamu.edu/davis/SuiteSparse/
  - change spack to download from there
  - updated sha256 checksums from GitHub for all available releases
- For versions 5.4.0, 5.5.0, 5.6.0 there is a slightly different compilation necessary: first `make default` then `make install`.

Summary of the version changes (+ added, -removed [because not available on GitHub]):
```
+ 5.6.0
+ 5.5.0
+ 5.4.0
  5.3.0
  5.2.0
+ 5.1.2
  5.1.0
+ 5.0.0
+ 4.5.6
  4.5.5
- 4.5.4
  4.5.3
- 4.5.1
```
2020-01-17 13:04:53 -06:00
darmac
4bb76cf5e8 add new package : erlang (#14548) 2020-01-17 13:03:08 -06:00
Sajid Ali
c52bcdd080 jdk temporary fix (#14550) 2020-01-17 12:58:58 -06:00
darmac
4d752e63e5 fix hadoop url and update versions (#14530) 2020-01-17 12:56:00 -06:00
Brian Van Essen
94bc6b06b1 Added new hashes for the protobuf and py-protobuf packates. (#14546)
* Added new hashes for the protobuf and py-protobuf packates.

* Fixed flake8
2020-01-16 17:02:50 -06:00
Adam J. Stewart
bdc9b89d86
Don't patch latest version of HDF5 (#14545) 2020-01-16 15:59:26 -06:00
Adam J. Stewart
563e261fa4
Add py-torchvision 0.5.0 (#14544) 2020-01-16 15:46:55 -06:00
Adam J. Stewart
38cd15d0e0
Add py-torch 1.4.0 (#14543) 2020-01-16 15:46:41 -06:00
Adam J. Stewart
7a61d1dbd1
Add include/pythonX.Y to CPATH (#14523) 2020-01-16 15:21:14 -06:00
Cameron Stanavige
0f68ed73c6 unifyfs: new release version (#14527)
This updates the UnifyFS package to account for the latest 0.9.0
version and removes support for version 0.2.0.
2020-01-16 15:16:59 -06:00
Howard Pritchard
876305adf0 mesa: check aarch64 system type as well (#14493)
to disabled use of libunwind.  Without this mesa fails to build
using recent Cray compilers - cce 9 and higher -  on aarch64 systems.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2020-01-16 12:21:34 -06:00
noguchi-k
7319516749 falcon: Set Py_None to return value (#14532) 2020-01-16 12:14:52 -06:00
albestro
c763b68b7c update hpx package for the new release 1.4.0 (#14533) 2020-01-16 12:12:35 -06:00
darmac
f22855f6e7 add new package : geode (#14534)
* add new package : geode

* remove provides for gemfire
2020-01-16 12:11:30 -06:00
darmac
362e79bb3a add new package : ignite (#14539) 2020-01-16 12:04:41 -06:00
Glenn Johnson
5aeab7dbe5 Use CudaPackage mixin for py-torch (#14540)
This PR adds CudaPackage in order to pick up the cuda/compiler conflicts
defined in CudaPackage.
2020-01-16 12:02:53 -06:00
Michael Kuhn
8ad0be96aa perl: Fix binary detection (#14536)
It seems that stable versions of perl also install a `perlX.Y.Z` binary.
However, it seems that this binary can hang if used in conjunction with
Spack's sbang workaround, as observed during automake's build.
2020-01-16 10:11:53 -06:00
Kai Torben Ohlhus
b7f0493563 octave: add 5.1.0 (#14531)
Add version Octave 5.1.0 including sha256.
2020-01-15 22:55:24 -06:00
Glenn Johnson
8b1bf2d613 Update py-csvkit (#14525)
* Update py-csvkit

This PR updates the py-csvkit package. This version requires a python
stack based on agate and this PR includes the new dependency packages.

- py-agate-dbf
- py-agate-excel
- py-agate-sql
- py-agate
- py-dbfread
- py-isodate
- py-leather
- py-parsedatetime
- py-python-slugify
- py-pytimeparse
- py-text-unidecode

* Replace the copy/pasted apostrophes

Python 2 can not process the copy/pasted apostrophes so replace them
with standard single quote character.

* Add version constraints on dependencies
2020-01-15 22:45:04 -06:00
Olaf Mersmann
a48fb69601 Update RocksDB to current version (#14524)
* rocksdb: Fix for rocksdb issue 5303

* rocksdb: Explicitly disable features

* rocksdb: Add TBB variant.

* rocksdb: New version 5.18.3 and 6.5.3
2020-01-15 18:50:24 -06:00
Glenn Johnson
027142bcfc Add version constraint to graphviz patches (#14377)
* Add version contraint to graphviz patches

This PR restricts the graphviz version that the patches for building
with the Intel compiler apply to. The two patches that were needed for
building graphviz-2.40.1 with the Intel compiler are not needed for
graphviz-2.42.2.

* Adjust the qt dependencies

The qt5 patch is only needed for graphviz-2.40.1. However, that version
will only compile with GCC-6 or greater.
2020-01-15 14:14:45 -06:00
Michael Kuhn
c2778d8898 perl: Add 5.30.1 (and 5.31.7) (#14509)
This also fixes actually building the development releases.
2020-01-15 14:12:51 -06:00
Michael Kuhn
e6e06aa2f3 mariadb-c-client: Add 3.1.6 and 3.1.5 (#14510) 2020-01-15 14:10:47 -06:00
Mark W. Krentel
b5d729a829 hpctoolkit: add version 2019.12.28 (#14519)
Add version 2019.12.28 and update the prereqs for the latest master.
2020-01-15 14:04:22 -06:00
Rao Garimella
946a80bd3d New package Jali - unstructured mesh infrastructure for multiphysics applications (#14498)
* add variant for enabling testing

* add variant for enabling testing

* enable tests and clean up other options

* enable tests and clean up other options

* add numbered versions

* add numbered versions

* updates to avoid enable_tests variant; correct versioning

* updates to avoid enable_tests variant; correct versioning

* fixes for style

* appropriate partitioners are enabled if 'all' is specified - so no need to check in spec

* revert accidental change to copyright

* remove erroneously re-introduced line about tests

* new spack recipe for build Jali - unstructured mesh infrastructure for multiphysics applications

* remove the +parallel condition for mstk, update 1.1.1 sha256sum and whitespace cleanup

* reformat description

* cut down description
2020-01-15 12:32:17 -06:00
Robert Mijakovic
a2f961bd6f Adds MPI_THREAD_MULTIPLE support for OpenMPI to the variant with UCX fabrics (#14194)
* Fixes:
1. MPI_THREAD_MULTIPLE problem with OpenMPI and UCX.

Changes:
1. OpenMPI provides two new depends_on options which result in UCX being compiled with multiple threads support. One implicit when OpenMPI 3.x is used, MPI_THREAD_MULTIPLE is enabled by default, and one explicit for OpenMPI <= 2.x, MPI_THREAD_MULTIPLE is disabled by default.
2. Extends UCX package to allow "Enable thread support in UCP and UCT" option.
3. Adds sha256 sums of UCX releases 1.6.1 and 1.2.0.

More details:
Fixes the issue with OpenMPI where programs which use MPI_THREAD_MULTIPLE will fail to execute because UCP worker didn't support it.
During the OpenMPI package installation it's the +thread_multiple spec was not propagated to UCX nor UCX handled it at all.
Now, the OpenMPI package is capable of handling +thread_multiple spec when UCX is request and the UCX package correctly handles +thread_multiple and compiles with the --enable-mt option.
Error message during runtime:
pml_ucx.c:226 Error: UCP worker does not support MPI_THREAD_MULTIPLE

* Adapts check of specs to read better and is the suggested form in the docs.

* Explicitly disables multithreading of UCX if +thread_multiple option is not used.
2020-01-15 12:31:18 -06:00
Glenn Johnson
0232c820ab Rework texlive package to install from source (#14332)
* Rework texlive package to install from source

This PR reworks the texlive package so that it installs from versioned
source distibution files. This is preferred over installing the binary
package for several reasons. For the binary installation:

1. Each component is downloaded, so can not use a spack mirror.
2. Changes in components over time are not reflected in spack hash.
3. Some of the binaries do not run due to glibc issues, depending on OS.

This PR keeps the binary installation as an option but it should be
considered deprecated, and probably rewmoved at some point.

This PR depends on zziplib from PR #14318.

* Fix flake8 issues
2020-01-15 11:35:07 -06:00
Glenn Johnson
f8acb95ad3 Convert encoding of script in interproscan (#14356)
One of the perl scripts was encoded with ISO-8859-1, which caused the
sbang replacement process to fail when spack uses python3. This PR
converts the ps_scan script to UTF-8 encoding.
2020-01-15 11:32:18 -06:00
Glenn Johnson
726a662c2c Change encoding for scripts in repeatmasker (#14358)
This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in
repeatmasker.

- the main RepeatMasker script
- SimpleBatcher.pm
- wublastToCrossmatch.pl

The ISO-8859 encoding prevented the sbang replacement of long paths when
spack uses python3.
2020-01-15 11:31:51 -06:00
Michael Kuhn
b69cf08cfb python: Add 3.7.6 and 3.7.5 (#14497) 2020-01-15 11:24:48 -06:00
Glenn Johnson
e7add79cba Update the icu4c package (#14450)
* Update the icu4c package

This PR makes several changes to the icu4c package

1. add updated version to 65.1
2. modify the default url as project has moved to github
3. set UTF-8 locale to support building from source files in UTF-8
format

Note that the older versions are not available on github so explicit urls
were used. This PR will close #14399.

* Consolidate the urls

Consolidate the URLs in the `version` directives by using an if test in
`url_for_version`.

* Put version and sha256 on same line

* Put top level url back
2020-01-14 22:05:55 -06:00
Glenn Johnson
9f6ac938b7 Update and fix bcftools package (#14505)
* Update and fix bcftools package

This PR updates bcftools to 1.10.2 and is dependent on PR #14504.

This PR also fixes builds of other versions. Versions 1.2-1.4 did not
use autotools so when the packaeg was converted to use autotools with
version 1.6 those older versions could no longer build. Also, those
versions needed to be patched to use an external htsllib. The method of
finding the external htslib is also different for those older versions.

In addition, this PR adds two variants to bcftools:

- libgsl
- perl-filters

Finally, dependencies for perl and python are added, and an unused
dependency for libzip was removed.

* Do not use '@' in variant description

The '@' character in a variant description will cause a problem with
`spack info`.

```
==> Error: Incomplete color format: '@' in
expressions, for @1.8:
```

* Fix error with python2 processing this package
2020-01-14 22:04:47 -06:00
Erik Schnetter
e78f3ed040 Update armadillo (#14499) 2020-01-14 17:49:49 -06:00
Erik Schnetter
ef68791210 Update HDF5 to 1.10.6 (#14500) 2020-01-14 17:49:21 -06:00
Erik Schnetter
8ffb9605d7 h5cpp: New package (#14501) 2020-01-14 17:48:49 -06:00
Justin S
4b1c356a27 trnascan-se: add and configure infernal dependency (#14502)
* trnascan-se: add and configure infernal dep

* trnascan-se: use patch() for infernal config
2020-01-14 17:47:48 -06:00
Erik Schnetter
ae6afaf8e1 mpich: Correct package name in output (#14503) 2020-01-14 17:46:39 -06:00
Glenn Johnson
ed9ab0668f Update htslib and add libcurl variant (#14504)
* Update htslib and add libcurl variant

This PR updates htslib to version 1.10.2 and adds a libcurl variant. The
libcurl variant defaults to True because, while it is optional, it is
highly recommended by the project developers.

Other things done:

- be consistent with quotes

* Change version in variant description

Apparently, `spack info` does not like the `@` character in a variant
description.

```
==> Error: Incomplete color format: '@' in
@1.3:.
```
2020-01-14 17:39:09 -06:00
Justin S
7ddbc9bc87 py-yajl: new package at 0.3.5 (#14278)
* py-yajl: new package at 0.3.5

* py-yajl: use PyPI mirror

* py-yajl: use short PyPI url

* remove py-ujson package

* py-yajl: remove unused imports
2020-01-14 17:23:32 -06:00
Justin S
30694aa501 gapfiller: traverse subdirectories in patch (#14375)
* gapfiller: traverse subdirectories in patch

* gapfiller: revert glob function change

* gapfiller: use more precise glob
2020-01-14 17:22:49 -06:00