Commit graph

7882 commits

Author SHA1 Message Date
Francois Budin
52752efa4d veloc package: add version 1.1 and update master dependencies (#11270)
* Add version 1.1 and set it as preferred
* Add pdsh as a dependency for `master`
2019-05-01 09:44:51 +09:00
Francois Budin
e2825d0ad4 Darshan 3.1.7 and develop versions fpr darshan-runtime and darshan-util (#11269)
* Add version 3.1.7
* Add develop branch (git master)
2019-05-01 09:42:32 +09:00
Thomas Gruber
06ed77bdfa Lua: Fix unresolved symbols in shared library by linking with libdl.so (#11260)
The current lua package.py does not link with libdl.so, so you get
unresolved symbols while linking with lua. This PR adds libdl to fix
the issue.
2019-05-01 08:41:08 +09:00
Greg Becker
7b715564d0 openfoam-com package: build without kahip by default (#11259)
Kahip does not build with clang (conflicts('%clang') in kahip package.
Because of this, openfoam-com %clang fails concretization. Therefore,
this changes the default openfoam-com variant for kahip to False.
2019-05-01 08:26:54 +09:00
Tiziano Müller
d2786ec064 CP2K package: add versions and tests, adjust optimization flags (#11263)
* Remove -ffast-math optimization flag
* Add 'develop' version which points to git repo
* Depend on libint for all versions >= 3.0
* Build directory is different for versions >= 7 (including develop)
* Add "make test" as post install check
2019-05-01 04:52:13 +09:00
Jannek Squar
f41103770d OpenCV: New versions, adjust protobuf dependency (#11243)
* Add versions 3.4.4 through 4.1.0 and 4.1.0-openvino
* Add conflict for gcc version >= 7 when building with +cuda
* Later version of protobuf is required for later versions of OpenCV
* Explicitly remove protobuf dependency with CMake option when not
  building with +dnn
2019-05-01 03:37:47 +09:00
xfzhao
e10dd6f779 Masurca (#11286)
* py-pauvr:new package

* falcon-unzip: new package

* supernova: updating

* masurca: updating

* rm extra files

* modifying available versions and adding url

* fixing deleted supernova
2019-04-30 08:24:12 -05:00
Matthias Diener
c43296e00d git-lfs: add version 2.7.2 (#11311) 2019-04-30 10:20:03 +02:00
Denis Davydov
a11b252a1b remove myself from maintainers of some packages (#11319) 2019-04-30 10:16:53 +02:00
Chuck Atkins
d2a5a10f08 vtk: Use the vendored libharu (#11293)
VTK requires a patched libharu that is not maintained upstream
See https://github.com/libharu/libharu/pull/157
2019-04-30 10:07:29 +02:00
Xavier Delaruelle
1a920ee64f environment-modules: add version 4.2.4 (#11307) 2019-04-27 20:32:57 +02:00
Daryl W. Grunau
c860d743f9 py-dateutil: add missing dependency on py-setuptools-scm (#11282)
Confirmed that versions before 2.7.5 do not require this dependency.
2019-04-26 20:28:35 +09:00
Felix Mayr
a195ffada2 QuantumEspresso package: add version 6.4 (#11302) 2019-04-26 20:25:40 +09:00
Frédéric Simonis
c951d1cb98 precice: add version 1.4.1 (#11276) 2019-04-26 09:49:11 +02:00
Chris Green
1b2817ee0a root: new versions, variants and patches (#11215)
* root: new versions, variants and patches to bring in to line with FNAL's use.

* Support MySQL.
* Patches:
    * Bigger stringbuf.
    * Find MySQL even when it's called mariadb-c-client.
    * Honor external provision of unuran.
    * Properly handle the ROOT7 web GUI for 6.16/00.
* `memstat` variant is now default-OFF due to version-related constraints.
* Add missing dependencies.
* Propagate `python` to `libxml2`.
* Handle external FTGL dependency with X / OpenGL: depends on PR ####
* Force `SPACK_INCLUDE_DIRS` to avoid warning.
* New `gminimal` variant default ON per discussion with Javier Cervantes.

* Style fixes per flake8.

* Remove redundant `PATH_SUFFIX` per https://github.com/root-project/root/pull/1993#discussion_r276840329

* Comment patches per https://github.com/spack/spack/pull/11215#discussion_r276887199.

* Reflect the fact that MariaDB support patch is now upstream.

* Restore ncurses dependency for libtinfo.
2019-04-24 08:48:52 +02:00
Toyohisa Kameyama
3d46dcd6f0 nest: change cmake_options to args. (#11273) 2019-04-24 11:09:49 +09:00
Eric Martin
e6bd4d27ea py-pandas: Add version 0.20.0 (#11264) 2019-04-24 09:01:56 +09:00
George Hartzell
b0080c705c squashfs should depend_on('zlib') (#11265)
Add zlib dependency to squashfs

On my CentOS system it was getting linked in (from Spack, no less)
fortuitously.

On a minimal Ubuntu system it failed until it was added as an explicit
dependency.
2019-04-24 09:01:36 +09:00
Chris Green
597037c9ff ftgl: update to 2.1.3-rc5. (#11214)
* ftgl: update to 2.1.3-rc5.

This updates to the last release (from 2008) with patches required to work with Spack and Root.

* Working 2.1.2 with/without docs, 2.1.3-rc5 without.
2019-04-23 09:42:10 -05:00
Eric Martin
bc080d753c py-umi-tools: Add latest versions (#11256) 2019-04-23 18:23:44 +09:00
George Hartzell
efe62b7d6d Install squashfs exe's into prefix.bin, not prefix (#11246)
The squashfs Makefile's `INSTALL_DIR` args is the path to the `bin` directory, not the top of the install tree.

Adjust accordingly.
2019-04-22 20:16:57 +02:00
Janne Blomqvist
5fb6145f6f OpenBLAS: Allow enabling/disabling AVX2/512 support
Allow specifying whether AVX2 or AVX512 should be enabled or disabled
on x86 targets.

As AVX2 hardware and toolchain support is quite ubiquitous by now,
AVX2 is enabled by default.  Also AVX2 support is not disabled when
building the +virtual_machine variant.

AVX512 is not supported in older but still supported toolchains,
hardware is still expensive, and OpenBLAS AVX512 kernels still have
bugs. Thus AVX512 is disabled by default.
2019-04-20 16:43:11 -07:00
Matthias Diener
a40492172f hdf5: add symbols (#10991) 2019-04-20 15:09:46 -07:00
Adam J. Stewart
f8dc385392 Mercury package: add version 1.0.1 and update dependencies (#10906)
* Add Mercury version 1.0.1
* Remove cci and bmi dependency requirements: these are not currently
  defined in Spack. If +bmi is enabled, the effect is that it may
  use a system install of bmi
* Add a note that fabtests is deprecated and has been folded into the
  libfabric package. Add the fabtests resource to the libfabric
  package
* Add CMake option settings to Mercury based on variant settings
* Mercury: Set OFI testing protocol depending on how libfabric was
  built
* Mercury: add version constraints to dependencies
2019-04-20 15:03:18 -07:00
Satish Balay
39855fbcf8 dealii: add patch for build with boost@1.70.0 (#11239)
Ref: https://github.com/dealii/dealii/issues/7934
2019-04-20 14:00:34 +02:00
Sajid Ali
4a2ec792a6 miniconda 2 and 3 packages: add version 4.6.14 (#11232) 2019-04-19 17:42:02 -07:00
Chris Green
3b34931f68 mysql: 5.7.X versions link boost (#11237)
Fixes #11226

MySQL 5.7.X and Boost 1.59.0 have a closer relationship than
MySQL >= 8.0 and their corresponding Boost versions: 5.7.X needs to
link against boost libraries which is indicated by marking boost as
a link dependency (removing the 'type' reverts to the default, which
includes link and build).
2019-04-19 15:34:55 -07:00
Oliver Breitwieser
56c233b0b7 jdk package: Fix fetching with curl 7.64.0+ (#11108)
Starting with version 7.64.0, curl skips cookies specified with "-H"
(generic custom header specification) when following redirects, which
causes the "accept-license"-cookie for jdk to disappear. The result
is that jdk fails to download. This uses the "-b" option (which is
used specifically for configuring cookies) instead, which is more
permissive.
2019-04-19 14:43:45 -07:00
Satish Balay
e86027d1f8
MUMPS: add version 5.2.0 (#11234) 2019-04-19 15:55:56 -05:00
Satish Balay
1746150f58
hypre: add @osborn9 to maintainers (#11233) 2019-04-19 15:55:35 -05:00
kustowski1
7ee9953dec added libsodium 1.0.16 and 1.0.17 (#11231) 2019-04-19 12:19:51 -07:00
Satish Balay
1eb01e7be5 petsc: fix suitesparse configure options. (#11188)
spec['dep'].libs.ld_flags can return system paths in some cases.
This is a targeted fix for the petsc package when retrieving
suite-sparse dependency libraries.
2019-04-19 11:44:05 -07:00
Massimiliano Culpo
3892b57244
hpx: overhaul of the package recipe (#11194)
* added latest versions + malloc variant
* added a variant to activate different instrumentations
* added a variant to activate or not networking
* added a variant to activate or not cuda and tools
* enforce c++ standard and make it consistent with boost
2019-04-19 16:58:46 +02:00
Harsh Bhatia
3f50dcf6d9 memsurfer: add new package 2019-04-18 19:31:08 -07:00
Harsh Bhatia
1842f9fbd5 vtk: add version 8.1.2 2019-04-18 19:31:08 -07:00
Harsh Bhatia
81f7238743 cgal: add version 4.13 2019-04-18 19:31:08 -07:00
Nichols A. Romero
eb7c79720d QMCPACK CMake fix (#11212)
* cflags and cxxflags from packages.yaml need to be passed into QMCPACK's CMake explictly for now.

* You need the ifcore library from the Intel compler to be manually linked in when you linked against a LAPACK provider that is not MKL.
2019-04-18 20:00:24 +02:00
Daniel Topa
c7725e9ff8 Add Open MPI v3.0.4 (#11221)
tarball posted 2019-04-15
https://www.open-mpi.org/software/ompi/v3.0/

dantopa@cn209:openmpi-3.0.4-5ienfvwpcxky3nz5jt3rygxzxzltkwm4 $ cd lib/

dantopa@cn209:lib $ ls -alh
total 27M
...
lrwxrwxrwx 1 dantopa dantopa   16 Apr 17 10:01 libmpi.so -> libmpi.so.40.0.5

confirmation builds Darwin (LANL):

x86_64
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
5ienfvw    openmpi@3.0.4%gcc
bkkhvej        ^hwloc@1.11.11%gcc
5chyfxo            ^libpciaccess@0.13.5%gcc
bcnjbc3            ^libxml2@2.9.8%gcc
tt2hkol            ^numactl@2.0.12%gcc
64vg6e4        ^zlib@1.2.11%gcc

ARM
-- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------
cq2y6b3    openmpi@3.0.4%gcc
7gqvelc        ^hwloc@1.11.11%gcc
6a4he35            ^libpciaccess@0.13.5%gcc
6a5uzd6            ^libxml2@2.9.8%gcc
m5neuus            ^numactl@2.0.12%gcc
67s2oqn        ^zlib@1.2.11%gcc

Power9
-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
otirvfn    openmpi@3.0.4%gcc
r6cylpu        ^hwloc@1.11.11%gcc
uzm3xdv            ^libpciaccess@0.13.5%gcc
trik6hj            ^libxml2@2.9.8%gcc
pmgndwh            ^numactl@2.0.12%gcc
4v3ticy        ^zlib@1.2.11%gcc

2019-04-18

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-04-18 12:33:26 -05:00
Federico Ficarelli
e64ee7e1be Prevent building llvm@8: with an incompatilble gcc (#11220) 2019-04-18 16:58:41 +02:00
Satish Balay
4571a96a43
xsdk: add/update maintainers to xsdk packages (#11146)
pumi
  slepc
  plasma
  magma
  trilinos
  alquimia
  pflotran
  strumpack
  tasmanian
  amrex
  hypre
  omega-h
  superlu-dist
2019-04-18 08:20:22 -05:00
Stephen Herbein
1dc3744d2c new package: kitty terminal (#9621) 2019-04-18 08:53:52 +02:00
Greg Becker
f242f5f8a9 Features: Improve Spec format strings (#10556)
* Update spec format to simpler syntax, maintain backwards compatibility
* Switch to new spec.format method throughout internals
* update package files for new format strings
* documentation and minor code cleanup. removed nonsensical variant sigils
2019-04-17 18:21:40 -07:00
Veselin Dobrev
49334f006d [WIP] CEED 2.0 (#10903)
* Initial commit for v2.0 of the CEED software suite.

* Update Nek packages and gslib

* Help spack concretize the hypre version for ceed-2.0.

* Fix nekcem install error

* Add support for gfortran v8 in nek5000 and nekcem.

* Split Nek5000 into Nek5000 and Nektools

* Get Nektools to build fine in Theta

* Fix travis failure: remove unused 'import numbers' from nek5000.

* Check for gfortran if it is wrapped

* Tweak the detection of gfortran in nek5000.

* Fix Nek packages to add -std=legacy when FC=gcc

* spack install ceed~petsc works fine on Theta

* Fix flake8 errors

* Fix more flake8 tests

* Fix an import issue

* Tweak the suite-sparse package to avoid interaction with existing system
installations of suite-sparse.

* petsc: update superlu-dist dependency

* Updates in the packages: occa, libceed, and ceed.

* In the libceed package, explicitly tell nvcc which host compiler to use.

* Fix python formatting.

* Simplify the test for gfortran in nek* packages.

* ceed: 2.0 uses petsc@3.11.0

* hpgmg-0.4; use from ceed@2.0.0

* Update the hypre dependency for ceed 2.0.

* Disable the superlu-dist dependency (through hypre) when using a
+quickbuild of ceed 2.0.

* petsc-3.11.0: add xlf fix

* nekcem: has a build dependency on Python 2.7+

* hpgmg: better setting of compiler options and use python for configure

* libceed: use v0.4 tag

* libceed: fix 0.4 release oops (pkgconfig version)

* Add a patch for magma-2.5.0 that brings it up the current 'master'.

* In the mfem package, install the examples, miniapps, and data under
$prefix/share/mfem.

* In the magma package, apply a patch to v2.5.0 that disables
magma_sparse - for testing purposes.

* In the magma package, link the 'magma' library with the
'nvToolsExt' library.

* In the magma package, update the 'magma-2.5.0.patch' with the latest
commits from the magma source repository. Also, remove the library
'nvToolsExt' from the 'magma-2.5.0-cmake.patch' - now it is not
needed.

* In the magma package, disable OpenMP when using v2.5.0 with the
IBM XL compiler.

 Please enter the commit message for your changes. Lines starting

* In the mfem package, add version for the 'laghos-v2.0' tag; also,
prefix the versions `laghos-v*` with their respective development
version numbers -- this way they are properly ordered within spack
relative to the official numbered versions.

* petsc: add version 3.11.1 (#11179)


(cherry picked from commit 1eab6e3c86)

* ceed-2.0: use petsc-3.11.1

* this-is-so-dumb.f -> empty.f
2019-04-17 17:37:41 -07:00
Elsa Gonsiorowski, PhD
a26aec520b mpifileutils v0.9.1 (#11216)
* mpifileutils v0.9.1

* mpifileutils v0.9.1 for realz
2019-04-17 18:11:14 -05:00
Michael Kuhn
b61dd57fdc sublime-text: Miscellaneous improvements (#11154)
- Add 3.2.1
- Reformat versions to include proper upstream version tags
- Add gtk dependency
- Add prefix to PATH so sublime_text can be found
2019-04-17 13:44:34 -07:00
Oliver Breitwieser
f276b3ffa0 ruby: Install certificate for +openssl only (#11184)
If specifying ~openssl, the post-install step will still try to install
the non-existent certificate, leading to an IOError.
2019-04-17 13:03:58 -05:00
Christoph Junghans
c628ca99cf gromacs: added 2019 patch releases (#11211) 2019-04-17 12:48:06 -05:00
Satish Balay
4731041f88
strumpack@3.1.1: add patch for Intel-19 build failure on cori (#11204)
Ref: https://github.com/spack/spack/issues/11202
2019-04-17 12:10:05 -05:00
Justin S
01ada1a3de astral: add 5.6.1 (#11195) 2019-04-17 09:32:50 -05:00
sknigh
e372464611 Add llvm 8.0.0 (#11197) 2019-04-17 09:31:42 -05:00