Commit graph

13381 commits

Author SHA1 Message Date
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
Todd Gamblin
8e5e36dc0b Fix spack flake8 to use Travis's target as base when needed 2019-05-01 04:44:02 +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
ac7f9ef93d Fix handling of MODULEPATH in setup-env.sh (#11274)
Usage of double quotes was preventing word-splitting when parsing
module roots in setup-env.sh, which lead to an error when multiple
module roots are used (in particular when Spack is pointed to use
an upstream module root in addition to its own).
2019-04-24 11:53:25 +09:00
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
Daryl W. Grunau
edca0cde1c _valid_tokens list is missing intended comma (#11271)
* _valid_tokens list is missing a needed comma
2019-04-24 08:55:20 +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
Todd Gamblin
552c9c57fd
Update tutorial page with RIKEN tutorial slides. (#11254)
- Add link to container image, as well as a description of VMs
- Update slide link to point to latest RIKEN tutorial
2019-04-23 01:53:47 +09:00
Greg Becker
5aa4edb939 Fix transitions between tutorial sections (#11251) 2019-04-22 17:14:26 +09:00
Todd Gamblin
0aed3bcea6 spack edit: use execv instead of Executable (#11245)
- `spack edit` previously used `spack.util.executable` `Executable` objects,
  and didn't `exec` the editor like you'd expect it to

- This meant that Spack was still running while your editor was, and
 stdout/stdin were being set up in weird ways

- e.g. on macOS, if you call `spack edit` with `EDITOR` set to the
  builtin `emacs` command, then type `Ctrl-g`, the whole thing dies with
  a `==> Error: Keyboard interrupt`

- Fix all this by changing spack.util.editor to use `os.execv` instead of
  Spack's `Executable` object
2019-04-20 20:51:45 -07:00
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
Adam J. Stewart
7255d5ee3c
Fix detection of LLVM-enabled PGI compilers (#10704)
* Fix detection of LLVM-enabled PGI compilers

* Add unit tests for LLVM-enabled PGI compiler version detection
2019-04-20 17:52:55 -05:00
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
Denis Davydov
95fafb4e44 Move NoLibrariesError/NoHeadersError into error.py (#10997)
Also add constructor to NoLibrariesError which can either take an
error message (like other SpackErrors) or a name and prefix (in
which case the error message is constructed).
2019-04-20 14:08:05 -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
Justin S
6f1fe3904c Fix outdated R packages failing to fetch (#11039)
PR #10758 made a slight change to find_versions_of_archive() which included
archive_url in the search process. While this fixed `spack create` and
`spack checksum` missing command-line arguments, it caused `spack
install` to prefer those URLs over those it found in the scrape process.

As a result, the package url was treated as a list_url causing all R
packages to stop fetching once the package was updated on CRAN.

This patch is more selective about including the archive_url in the
remote versions, explicitly overriding it with matching versions found
by the scraper.
2019-04-19 17:39:13 -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
Greg Becker
141e8b8de3 Fix backwards compatibility for module naming (#11236)
f242f5f8 changed the format strings but maintained backwards
compatibility in all cases except one: The list of valid tokens for
the module naming schemes was not updated properly to contain both
the new and old styles for compilers and package names.

This PR re-adds the old tokens into the list of valid tokens.
2019-04-19 13:20:41 -07:00
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
Peter Scheibel
8a23154755
Spack chain docs: config should go in upstreams.yaml (#11225)
#11152 added documentation for #8772 but some details were based on
an earlier implementation that had changed by the time #8772 was
merged. In particular, #11152 mentioned that upstream Spack instances
were configured in config.yaml, when in fact they should be placed in
a separate upstreams.yaml config file; this PR updates the
documentation accordingly.
2019-04-18 18:57:10 -07:00
Massimiliano Culpo
9cf650d2ab Moved cleanup before raising (the code couldn't be reached before) 2019-04-18 18:41:22 -07:00
Massimiliano Culpo
400aa5fe51 Cleaned get methods of Repo and RepoPath 2019-04-18 18:41:22 -07:00
Massimiliano Culpo
76b5af6bf3 Used functools.wrap for the decorator + reordered imports 2019-04-18 18:41:22 -07:00
Massimiliano Culpo
bbb5d61662 Removed 'namespace' argument from Repo and RepoPath
fixes #11159

The 'namespace' argument to both Repo and RepoPath were used to set the
"super namespace". Currently it seems to be vestigial as the only
"super namespace" allowed for packages is 'spack.pkg' since 39c9bbf
2019-04-18 18:41:22 -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