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Author SHA1 Message Date
Chris Green
c124b1f471 postgresql package: build enhancements. (#10877) 
We add new variants to handle readline vs libedit, a client-only
build and install, and bindings to TCL, Python and Perl. We also add
new versions and the ability to detect remote versions not otherwise
dealt with.
 2019-03-25 19:51:51 -05:00
simo-tuomisto
6478a32598 New package: elmer-fem (#10860) 
Elmer finite element method solver; builds Elmer, ElmerICE and
contributed solvers with MPI support.
 2019-03-25 19:47:15 -05:00
Omar Padron
bf03edb51b LLVM package: disable CUDA (#10858) 
This avoids using a system-installed CUDA package. In the future a
variant can be added to allow using Spack-installed CUDA, but for
now CUDA support is always disabled.
 2019-03-25 19:43:18 -05:00
Brian Van Essen
a88b540723 Conduit package: add option to build with hdf5 versions > 1.8 (#10913) 
Added a variant to allow conduit to build with newer versions of
HDF5.  Set the default for the variant to prefer compatibility mode
with HDF5 v1.8
 2019-03-25 12:26:30 -05:00
Satish Balay
365c17a3d5
xsdk: enable sundials@4.1.0 for xsdk@develop (#10989) 
- disable sundials varaiant for dealii and mfem - as they are incomatible with sundials@4.1.0
 2019-03-24 22:17:20 -05:00
Satish Balay
8c165494f2
hypre: add superlu-dist variant (#10985) 
- add a patch to fix build error with superlu-dist
 2019-03-24 22:16:47 -05:00
Satish Balay
d7e984bcf8
amrex: current @develop - and future releases require cmake@3.13 or higher (#10953) 2019-03-24 22:15:49 -05:00
Navdeep Rana
fb946e51a4 Added a package for chapel. (#11002) 
* Added a package for chapel.

* flake8 compliance.
 2019-03-24 17:18:19 -05:00
Xavier Delaruelle
95a0e9c693 environment-modules: add version 4.2.3 (#11003) 2019-03-24 17:17:50 -05:00
Denis Davydov
64acce557d petsc: workaround xcode stub-out-of-sync issue (#10999) 2019-03-24 10:38:40 -05:00
Daryl W. Grunau
7081dba9ee Packages/zoltan (#10432) 
* serialize the F90 interface build

* serialize the F90 interface build
 2019-03-23 13:38:29 +01:00
Stephen McDowell
878b122f45 add ninja v1.9.0 (#10994) 2019-03-22 10:05:14 -05:00
Eric Martin
ec45c22808 netgen: update broken URL (#10882) 
* netgen: update broken URL

* netgen: fix url_for_version URL
 2019-03-22 10:01:07 -05:00
Michael Kuhn
b6185d4ad7 openfoam-com: Fix flex dependency (#10956) 
openfoam-com needs flex's FlexLexer.h, which can only be found if flex
is also a link dependency.
 2019-03-22 12:46:53 +01:00
Eric Martin
ba5f37ee26 vdt: Add version 0.4.3 (#10982) 2019-03-22 11:57:30 +01:00
Michael Kuhn
ea227b9974 py-hpccm: New package (#10957) 2019-03-22 11:39:10 +01:00
Eric Martin
1599dce2ae canu: Add versions 1.8 and 1.7 (#10978) 2019-03-22 11:27:36 +01:00
Eric Martin
563e573b13 megahit: Add version 1.1.4 (#10979) 2019-03-22 11:19:28 +01:00
Eric Martin
d9eaad80c3 racon: Add versions 1.3.2 and 1.3.1 (#10980) 2019-03-22 11:19:13 +01:00
Eric Martin
487fa5713c trimgalore: Add versions 0.6.0 and 0.6.1 (#10981) 2019-03-22 11:18:45 +01:00
Eric Martin
46e0ad3269 bowtie: Add missing zlib dependency (#10984) 2019-03-22 11:17:16 +01:00
Matthias Diener
133d4ca9ce gdb: add version 8.2.1 (#10988) 2019-03-22 11:00:28 +01:00
Hadrien G
cc8a086082 ACTS: add version 0.8.2 (#10974) 2019-03-22 10:59:45 +01:00
Denis Davydov
6d971c4493 add ginkgo package, use it in dealii along with symengine (#10917) 2019-03-22 10:58:48 +01:00
Stephen McDowell
7bc899d9ca add eigen v3.3.7 (#10955) 2019-03-21 12:16:26 -05:00
Patrick Schratz
bffe3a605f update R to v3.5.3 (#10928) 
* update R to v3.5.3
 2019-03-20 13:06:57 -05:00
Michael Kuhn
e02eb3633e mpich: Do not use libfabric@1.7: with ch3 ofi netmod (#10919) 2019-03-20 10:01:39 -07:00
Michael Kuhn
c66a24f22d pkgconf: add 1.6.0 (#10942) 2019-03-20 14:10:11 +01:00
bfovet
81f699eca3 Update GMSH to 4.2.2 with OpenMP variant (#10914) 2019-03-20 05:12:57 +01:00
Patrick Schratz
f51bce5636 saga-gis: new versions up to 7.3.0 (#10922) 2019-03-20 05:03:14 +01:00
Denis Davydov
de3ff1a96b gettext: fix dependency type of xz (#10935) 2019-03-20 04:57:08 +01:00
sknigh
e717230bf8 added yara (#10901) 2019-03-20 04:55:02 +01:00
fcannini
9a8c4cf071 gromacs: make sure cuda support is disabled when cuda=False (#10936) 
* abinit: Fix building with hdf5/netcdf.

* gromacs: Fix attempt to build with cuda support when 'cuda=False'

If for some reason there's a cuda toolkit installed by other means,
(i.e. not by spack) cmake will still try to build with cuda support,
even though 'cuda=False' is the default of the spec.

* Revert "abinit: Fix building with hdf5/netcdf."

This reverts commit e16f725e37b91193fe519b1821446c76ab551928.

This should not be here.
 2019-03-20 04:54:03 +01:00
Michael Kuhn
1db5a3e0a3 libfabric: add 1.6.2 (#10918) 2019-03-20 04:52:50 +01:00
Matthias Diener
d935048982 git: add version 2.21.0 (#10937) 2019-03-20 04:49:47 +01:00
Michael Kuhn
b48a6f22be strace: add 5.0 (#10940) 2019-03-20 04:48:13 +01:00
Michael Kuhn
09d57d8cee libeatmydata: new package (#10941) 2019-03-20 04:47:45 +01:00
Kelly (KT) Thompson
a1eeeadfd8 Branson: provide new versions. (#10926) 
* Branson: provide new versions.

+ Also update dependencies (newer version have fewer dependencies).

* fix style issue
 2019-03-19 08:49:58 -06:00
Kelly (KT) Thompson
29ce8eb892 Draco: add variants (#10925) 
* Draco: add variants

+ This package has many optional build dependencies that were not registered in
  older versions of this recipe.  I've added (and tested) this more complete
  list of optional dependencies: parmetis, superlu-dist, qt.

* fix style issues
 2019-03-19 08:49:30 -06:00
Owen Solberg
3618d405b1 added checksum for new bowtie2 version (#10930) 2019-03-19 15:14:25 +01:00
Christoph Junghans
a6ccd99054
cabana: cuda backend (#10660) 2019-03-18 14:02:28 -06:00
Massimiliano Culpo
4aead5e35b
redis: new package (#10915) 
Added versions from 4.0.11 to 5.0.3

closes #9180
 2019-03-16 14:47:11 +01:00
Mark W. Krentel
e811e23f2e hpcviewer: new package (#10878) 
* hpcviewer: new package

Add binary package for hpcviewer and hpctraceviewer for the Rice
hpctoolkit on Linux x86_64, ppc64 and ppc64le.

* ibm-java: add property 'home' so that spec['java'].home will work.

* Flake

* More flake.

* Test that the version, machine type pair exists before using it in the
sha dictionaries so that 'spack info' doesn't crash on unsupported
configurations.
 2019-03-15 15:47:22 -05:00
Chris Green
6de6d5396c New package: mariadb-c-client (#7729) 
* mariadb-c-client is a new package using the distinct, LGPL,
  MySQL-compatible client library from mariadb.com. It provides the
  virtual package mariadb-client
* mariadb is recorded as a provider of the mariadb-client virtual
* The mysql-client virtual package is also added, and mariadb-c-client
  is recorded as a provider for it
 2019-03-15 14:12:30 -05:00
Adam J. Stewart
82e3380049
Add latest version and missing dependencies of MySQL (#10904) 
* Add latest version and missing dependencies of MySQL

* m4 only needed on solaris
 2019-03-15 14:01:54 -05:00
Christoph Junghans
4baf3d9d02 py-espressopp: add v2.0.2 (#10909) 2019-03-15 12:59:23 -05:00
Matthias Diener
dd09ab697b cmake: add version 3.14.0 (#10908) 2019-03-15 11:49:59 -05:00
Adam J. Stewart
cba5a8058e
Add ladot package (#10905) 2019-03-15 01:13:25 -05:00
Adam J. Stewart
4e6285a19b
Ensure that every package has a description (#10896) 2019-03-14 20:49:07 -05:00
Jordan Ogas
1d73868333 charliecloud: added version 0.9.8 (#10900) 2019-03-14 20:36:53 +01:00
Chris Green
6a9f02c96f cppunit: support cxxstd. (#10888) 2019-03-14 16:17:31 +01:00
Elizabeth Fischer
f15f3076db libxaw: added version 1.0.12 (#10591) 2019-03-14 12:55:56 +01:00
Levi Baber
a71664a42d py-pybigwig: needs curl at link time (#10892) 2019-03-14 11:07:50 +01:00
Cody Balos
4025ec9508 sundials: add new version (4.1.0) (#10890) 2019-03-14 11:00:22 +01:00
Nichols A. Romero
ec5bf38245 QMCPACK More CUDA Fixes (#10864) 
* Throw InstallError if more than one GPU architecture is passed to cuda_arch. Previous cuda_arch test was not actually working because comparison with none string was on the cuda_arch list instead of the first entry of the list.

* Removing redundant cuda_arch statement.
 2019-03-13 16:03:28 -05:00
Eric Martin
2bca687605 py-treehash: Create new package (#10872) 2019-03-13 16:03:09 -05:00
Levi Baber
39c40ee3fc revbayes: new version (#10873) 2019-03-13 21:36:13 +01:00
Michael Kuhn
d3365e4356 libplist, libusbmuxd: Fix pkgconfig dependency (#10876) 
pkgconfig is the correct virtual provider.
 2019-03-13 14:55:23 -05:00
Michael Kuhn
db79317eb9 cubelib, cubew: Add missing pkgconfig dependency (#10875) 2019-03-13 20:15:02 +01:00
Michael Kuhn
3019068e0c mpich: Add patch to fix node list parsing (#10870) 
mpich@3.3 introduced a new regex-based function for node list parsing
that does not recognize hostnames without a dash properly.
 2019-03-13 10:58:05 -07:00
Eric Martin
358226b946 py-biomine: new package (#10868) 2019-03-13 15:17:06 +01:00
Eric Martin
6a87b6215f help2man: Add version 1.47.8 and perl runtime dependency (#10862) 2019-03-13 15:11:45 +01:00
Eric Martin
7d50567423 py-advancedhtmlparser: new package (#10867) 2019-03-13 15:06:01 +01:00
Eric Martin
ffbc4f199e fqtrim: Create new package (#10861) 2019-03-12 21:30:30 -05:00
David Hows
c629a6f780 Fix mysqldb1 (#9978) 
* Update package.py

* Add MYSQL Package file

* Fixes for linter
 2019-03-12 20:57:29 -05:00
Elizabeth Fischer
82e9c01b5c New package: py-mysql-connector (#10327) 
* New package: py-mysql-connector

* Fixed docstring

* 1. Determined that py-setuptools was not needed at all, so removed.
2. Added py-protobuf.  Docs seem to imply that only C protobuf library is required; however, the Python setup.py says differently, and some Python code seems to reference protobuf too.  I don't know why this worked for me, but it looks like including py-protobuf is the right thing to do.

* Applied solution detailed in:

https://github.com/mysql/mysql-connector-python/pull/9

Uncommenting this patch will make `error: option --single-version-externally-managed not recognized`  reappear.

* Clean up / reorder lines

* flake8
 2019-03-12 20:52:43 -05:00
Eric Martin
3d7164c13f varscan: set VARSCAN_HOME variable to jar file location (#10744) 2019-03-12 20:29:48 -05:00
Eric Martin
0ebd81bd15 py-pytables: Add hdf5 1.10.x support for versions above 3.4.0 (#10746) 2019-03-12 20:29:24 -05:00
David Poliakoff
d5c3ce790f Update caliper package (#10750) 
* Updating Caliper package with a shared lib option

* Tightened version bounds on Caliper package

* Removed testing. Loosened version constraints

* Add Caliper 2.0.1, cleanup dependency specs
 2019-03-12 20:28:13 -05:00
Rob Latham
da28b592fc "Werror" too strict for recent compilers (#10802) 
rapidjson gives warnings with gcc-7.3 and branch fall through
 2019-03-12 20:10:51 -05:00
Michael Kuhn
65f37746af qt: Use more system dependencies and fix build with new gcc versions (#10817) 
qt currently falls back to bundled versions of sqlite, harfbuzz, pcre,
double-conversion and xcb. This adds the appropriate dependencies and
configure arguments. A new variant adds multibyte support to pcre and
pcre2, which is required by qt.

Additionally, newer versions of gcc (starting with @8.3.0) cause build
failures. This adds a patch to fix the problem.

The changes have been tested with all versions of qt currently available
in Spack. 5.2 and 5.3 do not build for reasons that seem to be unrelated
to these changes, though.
 2019-03-12 20:04:11 -05:00
健美猞猁
a79230c832 casacore does not support fftw+mpi . (#10839) 2019-03-12 19:59:48 -05:00
健美猞猁
d32a342fc6 Aoflagger: a new package. (#10840) 
* A new package: aoflagger.

* aoflagger does not support boost>1.66.0 .

* Add fftw~mpi dependency.

* flake8.

* Flake8.

* Update package heder.

* md5 -> sha256.
 2019-03-12 19:59:24 -05:00
Axel Huebl
fd6d3f6b8c openPMD-api: shared variant (#10847) 
Add a variant to control shared/static builds (one at a time) and
make shared the default.
 2019-03-12 19:58:44 -05:00
Alberto Chiusole
46fb6ed5b6 Revert to manual flag enabling, due to RegCM bug in configure. (#10863) 
The configure of RegCM treats --disable-FEATURE as --enable-FEATURE,
so we cannot use enable_or_disable.
 2019-03-12 19:48:45 -05:00
Owen Solberg
dc5b16a8e9 added checksum for 20190222 release of gnu parallel (#10865) 2019-03-12 19:40:29 -05:00
Eric Martin
50193229ea py-llvmlite: Add versions 0.26.0 and 0.27.1 (#10866) 2019-03-12 19:40:01 -05:00
Mark W. Krentel
3ed6e78338 New package: ibm-java (#10777) 
* Add binary package of the IBM Java SDK for big and little-endian
  powerpc (power7, 8 and 9).  The jdk and openjdk packages only install
  on x86_64.
* Add ibm-java as a java provider
* The jdk and openjdk packages only install on x86_64. Add conflicts
  for ppc64 and ppc64le to jdk and openjdk.
 2019-03-12 18:05:47 -05:00
wspear
e1e5eb29d2 Elfutils package: add m4 dependency and version 0.176 (#10834) 
* Elfutils requires m4 to build
* Add version 0.176
 2019-03-12 17:35:59 -05:00
Robert Pavel
1450fe72fa New package: Draco (#10844) 2019-03-11 20:57:00 -05:00
Matthias Diener
5e68af5a78 scons package: add missing dependency to py-setuptools (#10856) 2019-03-11 20:30:12 -05:00
Jiawei Zhuang
74b33e9f82 OpenMPI: v4.0.0 + Slurm installation error (#10853) 
shmemrun and oshrun do not exist in OpenMPI v4.0.0
(ref: https://www.open-mpi.org/doc/v4.0/)

The Spack OpenMPI package was failing the install by trying to
remove them. This guards the removal of several scripts when
using the Slurm scheduler to handle the case where they don't exist.
 2019-03-11 20:18:50 -05:00
Michael Kuhn
1e6b13d335 Fix URLs for VI-HPS projects (#10821) 
URLs for the opari2, otf2, and scorep packages have changed (although
the checksums are the same)
 2019-03-11 20:12:44 -05:00
Stas Sergienko
9ffd508d7c mpich: add psm2 fabric support (#10814) 
psm2 is only supported for versions 2.2 and up, so a conflict is
added for earlier versions
 2019-03-11 20:10:02 -05:00
健美猞猁
888bb76758 New package: cotter (#10838) 2019-03-11 19:46:40 -05:00
Eric Martin
1d51cdf824 STAR: Add versions 2.7.0d and 2.7.0e (#10831) 2019-03-11 19:44:54 -05:00
Eric Martin
23b73ca982 py-chardet: Add version 3.0.2 (#10827) 2019-03-11 19:44:30 -05:00
Eric Martin
2e47b45d9f py-urllib3: Add version 1.21.1 (#10826) 2019-03-11 19:44:07 -05:00
Greg Sjaardema
204063e21a cgns package: add version 3.4.0 and update hdf5 dependency (#10803) 
* Add version 3.4.0
* Update checksums for older versions to sha256
* Require hdf5~mpi when building with ~mpi
 2019-03-11 19:43:16 -05:00
Eric Martin
dc0b6a0613 samtools package: Add version 1.5 and htslib 1.5 dependency (#10825) 2019-03-11 19:29:29 -05:00
Alberto Chiusole
2b591653fa hdf5 package: add version 1.10.5 (#10794) 2019-03-11 15:15:03 -05:00
Justin Stanley
46466381b8 py-crossmap: new package at 0.3.3 (#10854) 2019-03-11 15:13:02 -05:00
Michael Kuhn
9425075a23 flex: Apply 2.6.4 patch regardless of gcc version (#10841) 
It seems that this is actually a glibc problem and while 2.6.4 builds
without the patch on newer versions of gcc (@8:), it still sometimes
segfaults (as observed during the doxygen build).
 2019-03-11 15:12:28 -05:00
Ce Qin
43525d3445 mpich: remove libpciaccess dependency for MacOS (#10795) 2019-03-11 15:06:49 -05:00
Gregory Lee
1fd01af773
added intel 19.0.3 packages (#10835) 
* added intel 19.0.3 packages

* added intel 19.0.3 packages
 2019-03-11 07:03:24 -07:00
Chris Green
1931bc8b40
Add 2019.{3,4} and patches for pedantic warnings. (#10836) 2019-03-11 09:03:19 -05:00
Chris Green
7e22fdfa21
boost: patch for problem with warnings for 1.69.0. (#10820) 2019-03-11 09:02:50 -05:00
Eric Martin
43b45f4140 breseq package: Add version 0.33.2 and zlib dependency (#10747) 
For zlib, also update the `CFLAGS`/`LDFLAGS`
 2019-03-08 20:57:00 -06:00
Denis Davydov
c81e68030a intel: add 2019.3 (#10843) 2019-03-08 14:50:58 -08:00
Christoph Junghans
0d07dea2eb
snap: overwrite flags (#10832) 2019-03-07 14:53:04 -07:00
Christoph Junghans
c11e745421
cloverleaf3d: overwrite flags (#10830) 2019-03-07 14:08:52 -07:00
Christoph Junghans
2f7589adc4
cloverleaf: overwrite flags (#10829) 2019-03-07 14:08:36 -07:00
Levi Baber
016945f67a
autofact: fix dependency (#10818) 2019-03-07 13:51:40 -06:00
Eric Martin
e750c5af66 trimmomatic package: restrict java dependency to version 8 (#10741) 2019-03-07 13:49:57 -06:00
Tristan Carel
dd6e91fcb6 Nix package: update dependencies (#10646) 
* Add 'fiber' as a default library for boost
* Add autoconf/automake etc. dependencies to libseccomp package
* New package: brotli
* New package: editline
* Add brotli, editline, boost dependencies to Nix
 2019-03-07 13:32:55 -06:00
Matthias Maiterth
23822e9717 GEOPM package: add version 1.0.0-rc2 (#10737) 2019-03-07 13:18:05 -06:00
Eric Martin
d072a1e0e3 py-sip package: Add version 4.19.3 (#10742) 2019-03-07 13:16:54 -06:00
Eric Martin
435db9d1a5 seqtk package: Add version 1.3 (#10743) 2019-03-07 13:16:20 -06:00
Michael Kuhn
3fb75e1206 flex package: patch for building 2.6.4 with gcc 7 (#10754) 
Remove 2.6.3 as preferred version (but keep it available for
building). The latest version (currently 2.6.4) is now preferred
(according to Spack's defaults).
 2019-03-07 13:15:47 -06:00
Eric Martin
49e307398b py-certifi: Add version 2017.4.17 (#10828) 2019-03-07 13:09:26 -06:00
Michael Kuhn
2fed84058d py-flake8: Add missing dependencies for @3.7.7 (#10796) 
* Update dependencies for py-flake8 when building version 3.7.7
* Add FIXME comment for an example dependency constraint which causes
  concretization to hang
* Add py-entrypoints version 0.3
* Add py-pycodestyle version 2.5.0
 2019-03-07 12:50:30 -06:00
健美猞猁
42633e34ab CMake package: update libuv dependency constraints (#10824) 
* Add libuv version 1.10.0
* CMake versions before 3.12.0 do not build with libuv version
  1.25.0, so a constraint is added to build earlier versions of
  CMake with libuv version 1.10.x
 2019-03-07 12:42:24 -06:00
prs513rosewood
32bbffc869 thrust: add versions 1.9.0-1.9.4 (#10823) 2019-03-07 14:36:59 +01:00
Eric Martin
efdeb860d1 transdecoder package: Add version 5.5.0 and fix up url and installation paths (#10745) 
* Add version 5.5.0 and fix installation locations
* URL format has changed as of version 5.5.0
* Update paths created for installation
 2019-03-06 20:58:50 -06:00
Eric Martin
45856c3660 bsseeker2 package: Add versions 2.1.8 and 2.1.5 (#10748) 
As of version 2.1.8, the url format changed, so also update that
 2019-03-06 20:55:06 -06:00
Jeongseok Lee
0e22a94f81 Eigen package: support Spack-external builds using Eigen (#10751) 
Update CPATH in setup_environment for Eigen, so that the
Spack-generated module for Eigen will help builds outside of Spack
use the appropriate include prefix for Eigen headers 
(<install_prefix>/include/eigen3/ rather than <install_prefix>/include/)
Note that this only updates the run-time environment, rather than the
build-time environment, so Spack builds depending on Eigen that use
pkgconfig will not be confused by the presence of the Eigen include
directory in CPATH.
 2019-03-06 20:48:38 -06:00
Matthias Diener
836f40e30f scons: add version 3.0.4, cleanup URLs (#10806) 2019-03-06 20:39:39 -06:00
HAOCHENG LIU
a3a8ed7234 vtk-m package: turn off mpi support by default (#10755) 2019-03-06 20:34:49 -06:00
健美猞猁
9d880b8838 New package: dysco (#10767) 2019-03-06 20:25:06 -06:00
Greg Sjaardema
c19df8be5d NetCDF package: update constraints on hdf5 mpi support (#10788) 
Update NetCDF to require building hdf5 without mpi when NetCDF itself
is built without mpi support.
 2019-03-06 20:20:16 -06:00
Satish Balay
35daaa440f omega-h: add version 9.22.2 and update gcc 8 conflict (#10776) 
* Versions before 9.22.2 compiler with gcc 8.3 or later
* Added version 9.22.2, which compiles with all gcc 8.x versions
  (including those before 8.3)
 2019-03-06 20:10:47 -06:00
Ryan S. Elliott
39467e4d67 Update kim-api package and add openkim-models-v2 (#10780) 
* Replace kim-api package with kim-api-v2, which has different
  versions and removes the 'cmake_args' method
* Add openkim-models-v2 as an extension package
 2019-03-06 19:23:05 -06:00
Mark W. Krentel
edecdc3ace libelf: move url to fossies.org (#10815) 
* libelf: move url to fossies.org

Libelf is no longer maintained and the original mr511.de web site no
longer exists.  The final release, 0.8.13 from Nov 2009 is still
archived at fossies.org.

Fixes #10757.

* Change the homepage to the FSF entry.
 2019-03-06 11:42:44 -08:00
Gregory Lee
10b0251af0 added python 2.7.16 (#10805) 2019-03-06 11:05:32 -08:00
Gregory Lee
86a1230a60 build fixes for util-linux (#10811) 2019-03-06 11:04:53 -08:00
Cameron Stanavige
9f734e0cfd unifycr: dependency changes and new version (#10722) 
New release of UnifyCR. Remove unsupported pre-1.0 versions

UnifyCR has had a few dependency changes to make the backend more
efficient. A new pre-release version has been released as well to
mark these changes. Prior versions are no longer supported.
 2019-03-06 10:56:20 -08:00
Owen Solberg
ff7cd40ca1 update package rsem (#10813) 2019-03-06 14:57:54 +01:00
Isaac Whitfield
1605368148 libusbmuxd: new package (#10726) 2019-03-06 10:10:02 +01:00
健美猞猁
c5573e660c intel-parallel-studio package: add version cluster.2019.2 (#10782) 2019-03-05 18:08:00 -06:00
健美猞猁
40d66e34d3 New package: pal (#10766) 2019-03-05 17:41:54 -06:00
健美猞猁
063f5b63da New package: erfa (#10763) 2019-03-05 17:40:39 -06:00
Greg Sjaardema
4c493b065c NetCDF package: add version 4.6.3 and update naming (#10786) 
* Add NetCDF version 4.6.3
* Naming scheme for artifacts >= 4.6.2 has changed. Add a
  url_for_version function to generate the appropriate URLs
 2019-03-05 17:33:47 -06:00
clellsolomon
b72715ed7c Add fzf utility package (#10778) 
* Add fzf utility package

* Fix "style checks" errors

- var/spack/repos/builtin/packages/fzf/package.py:32:
  [E226] missing whitespace around arithmetic operator
 2019-03-05 17:17:48 -06:00
Michael Kuhn
5758e49c80 gcc package: Add 8.3.0 (#10772) 2019-03-05 17:15:57 -06:00
Gregory Lee
7bd8689f06 openss package: allow all 2.7.x versions (#10807) 
Originally the version constraint range had an upper bound of 2.7.15
This allows all 2.7.x versions
 2019-03-05 17:14:32 -06:00
Alberto Chiusole
63e172d2ac RegCM: intel FC 'hint', 4.7.0 intel warning, fcflags, fix extensions. (#10797) 
This should fix and improve #9934, which was messed up by a fetch from develop
 2019-03-05 21:30:53 +01:00
Gregory Lee
bad485a221 various package version updates and build fixes (#10775) 
* various package version updates and build fixes
 2019-03-05 11:59:47 -08:00
Matthias Diener
c939e36ed9 cantera: make sundials dependency optional (#10764) 2019-03-05 19:58:00 +01:00
Michael Kuhn
c717f56359 ncl: Add 6.6.2 (#10800) 2019-03-05 17:13:51 +01:00
Michael Kuhn
21fb7dadb3 openssl: Add 1.1.1b, 1.1.0j and 1.0.2r (#10779) 2019-03-05 16:26:18 +01:00
Matthias Diener
9ba4d4e2af git-lfs: add version 2.7.1 (#10770) 2019-03-05 16:25:20 +01:00
Greg Sjaardema
d580d2a033 seacas: Update NetCDF version requirement (#10787) 
Modified NetCDF requirement to allow NetCDF-4.6.2 and subsequent versions.
 2019-03-05 14:05:52 +01:00
Justin Stanley
f19a214a19 libbeagle: add 3.1.2 (#10789) 2019-03-05 14:02:52 +01:00
Peter Scheibel
af4a36c4d9
Header subdirectories for Python and Eigen (#10773) 
Fixes #10769 

This updates the .headers property to include header subdirectories
for Python and Eigen (as is recommended by these packages).

#10623 updated the default behavior of .headers.directories to
exclude subdirectories (since this can cause clashes with system
headers). This broke some packages which depended on the old behavior
of .headers.directories: for example if you had
<package-prefix>/include/subdir/ex1.h, .headers.directories would
include <package-prefix>/include/subdir.
 2019-03-04 12:36:51 -06:00
Brian Van Essen
0ce1500376 Package Updates for ECP CANDLE Supervisor (#10760) 
* Add EQ-R package
* Add Fansi, Pillar, UTF8 (R) packages
* Add new versions for py-mdanalysis, r-cli, r-dplyr, r-pkgconfig,
  r-rlang, r-tibble, stc, and turbine packages
* Add hdf5 support for turbine
* Specify configure directory for stc package
 2019-03-01 14:46:13 -06:00
Justin Stanley
c8557ba7d8 blast2go: new package at 5.2.5 (#10725) 
* blast2go: new package at 5.2.5

* blast2go: remove redundant url
 2019-03-01 12:36:00 -06:00
Matthias Diener
ee5e5ce3c6 new package: intel-pin (#10546) 2019-03-01 12:29:01 -06:00
Justin Stanley
1a8161a982 r-bfastspatial: new package at 0.6.2 (#10734) 2019-03-01 10:18:14 -06:00
Justin Stanley
cbc6a2070a r-bfast: new package at 1.5.7 (#10733) 2019-03-01 10:17:37 -06:00
Justin Stanley
94357a274c bedops: avoid static linking with glibc (#10456) 2019-03-01 10:17:01 -06:00
Justin Stanley
165d8da0c2 blast-legacy: new package at 2.2.26 (#10610) 
* blast-legacy: new package at 2.2.26

* blast-legacy: compile from source

* blast-legacy: add missing os.symlink import

* blast-legacy: fix build script interpreter
 2019-03-01 10:14:37 -06:00
Justin Stanley
f9947333ca bridger: new package at 2014-12-01 (#10611) 2019-03-01 10:09:23 -06:00
Justin Stanley
c4aba6a204 r-spatial: new package at 7.3-11 (#10728) 2019-03-01 09:57:59 -06:00
Justin Stanley
16af5f31d9 r-nortest: new package at 1.0-4 (#10729) 2019-03-01 09:55:30 -06:00
Justin Stanley
4f1044a072 r-xts: add 0.11-2 (#10730) 2019-03-01 09:54:26 -06:00
Justin Stanley
104a8a1422 r-gdalutils: new package at 2.0.1.14 (#10731) 2019-03-01 09:53:30 -06:00
Justin Stanley
0766e7fbbb r-rgdal: add 1.3-9 (#10732) 2019-03-01 09:52:07 -06:00
Justin Stanley
89f59f7ab0 hyphy: new package at 2.3.14 (#10759) 2019-03-01 09:31:46 -06:00
Jiawei Zhuang
433cc4a972 Fix sha256 sum for IOR (#10765) 2019-03-01 09:59:36 +01:00
Sajid Ali
6d20e938da petsc: add +knl variant 2019-02-28 11:07:04 -06:00
Satish Balay
f8da8dbd0e
Trilinos: add release 12.14.1 (#10740) 
xsdk: switch from 12.14.0-rc1 to 12.14.1
 2019-02-28 11:05:05 -06:00
Eric Martin
4e80977506 py-tetoolkit: Add version 2.0.3 (#10749) 2019-02-28 12:59:30 +01:00
Owen Solberg
fac2dbda07 git-lfs: patch Makefile for v2.7.0 (#10720) 
Fixes #10702

Same fix merged upstream in git-lfs/git-lfs#3545 -- it may appear
in future release v2.7.2 according to package maintainer.
 2019-02-27 16:02:25 -06:00
Justin Stanley
2f4f828b45 wtdbg2: new package (#10639) 
* wtdbg2: new package at 2.3

* wtdbg2: flake8 fix
 2019-02-27 13:27:45 -06:00
Michael Kuhn
b1a04b7699 mpich: Improve package (#10643) 
- Add missing pkg-config, libpciaccess and libxml2 dependencies
- Add slurm variant for nodelist parsing
- Add missing configure flag for libfabric
- Unset F90 and F90FLAGS
- Allow selecting different PMI interfaces
 2019-02-27 13:13:44 -06:00
Paschalis Korosoglou
ab499a958d otf2 package: fix download URL (#10735) 2019-02-27 12:47:56 -06:00
Gregory Lee
d60106a3f6 Add newer versions for 51 Python packages (#10738) 2019-02-27 12:45:28 -06:00
Massimiliano Culpo
7eec038690
Update environment-modules package (#10717) 
The environment modules package has been updated to include 
versions up to 4.0.0. The url of the package and the homepage
have been updated accordingly.

The `spack bootstrap` command now builds version 3.2.10 of
the environment-modules package, and will do until #10708 
is fixed.
 2019-02-27 14:00:46 +01:00
Isaac Whitfield
5efff5d2fc new package: libusb (#10682) 2019-02-26 20:52:47 -06:00
Isaac Whitfield
938939b7e4 new package: libtasn1 (#10681) 2019-02-26 20:52:04 -06:00
Nichols A. Romero
d9b7c1faea QMCPACK package: cuda/hdf5 fixes (#10701) 
* Make use of new QE multi-valued HDF5 variant interface
* Remove explicit CUDA dependency (which is handled by inheriting
  from CudaPackage)
* Update cuda_arch unset variant check
 2019-02-26 20:50:32 -06:00
Satish Balay
c11f598e0b petsc: add version 3.10.4 (#10724) 2019-02-26 20:41:33 -06:00
Justin Stanley
cbecf9f555 new package: phred (#10700) 
Part of the software collection introduced in #10529. Developers must
be contacted via email to receive the source code.
 2019-02-26 19:14:58 -06:00
Isaac Whitfield
fbdbed1180 new package: libplist (#10680) 
Dependency of Google's Flutter toolchain.
 2019-02-26 19:12:41 -06:00
Justin Stanley
df4b77f120 libbeagle package: add cuda support (#10650) 
libbeagle compiles against CUDA by default but no there is no mention
of it in the package recipe. This PR adds explicit cuda paths and
variants, and fixes the target architecture as well (for those who
don't have compute_13)
 2019-02-26 18:50:08 -06:00
Michael Kuhn
0adf1b5405 vampirtrace: patch for new mpich and openmpi versions (#10665) 2019-02-26 18:48:14 -06:00
Phil Tooley
018ae371d6 new package: routino (#10679) 2019-02-26 18:41:44 -06:00
Janne Blomqvist
312122f169 Don't try to build TARGET=PILEDRIVER on aarch64 
Piledriver is a codename for an AMD x86-64 processor, it can't
possibly make sense to compile for that if the architecture is
aarch64.
 2019-02-26 18:40:39 -06:00
Neil Flood
2831184e41 kealib package: add version 1.4.11 (#10706) 2019-02-26 18:39:27 -06:00
Daryl W. Grunau
ecd98d1953 eospac package: add version 6.4.0 (#10718) 2019-02-26 18:38:52 -06:00
Justin Stanley
ba2ed96513 beast2 package: add version 2.5.2 (#10723) 2019-02-26 18:38:21 -06:00
Nichols A. Romero
5aa6cbf437 Quantum ESPRESSO package: Serial HDF5 Bug Fix (#10689) 
Serial HDF5 in serial QE only works in develop version. This adds
a conflict to the QE package to prevent Spack from trying to build
specs which don't satisfy this constraint.
 2019-02-26 18:36:50 -06:00
Massimiliano Culpo
42386dbe94 Use Package.headers for -I options (#10623) 
This restores the use of Package.headers when computing -I options
for building a package that was added in #8136 and reverted in
#10604. #8136 used utility logic that located all header files in
an installation prefix, and calculated the -I options as the
immediate roots containing those header files.

In some cases, for a package containing a directory structure like

  prefix/
    include/
	  ex1.h
	  subdir/
	    ex2.h

dependents may expect to include ex2.h relative to 'include', and
adding 'prefix/include/subdir' as a -I was causing errors,
in particular if ex2.h has the same name as a system header.

This updates header utility logic to by default return the base
"include" directory when it exists, rather than subdirectories.
It also makes it possible for package implementers to override
Package.headers to return the subdirectory when it is required
(for example with libxml2).
 2019-02-26 12:42:30 -06:00
Justin Stanley
ad25e7f3b0 r-vfs: new package at 1.0.2 (#10697) 2019-02-26 12:21:12 -06:00
Justin Stanley
68318ab076 r-nleqslv: new package at 3.3.2 (#10696) 2019-02-26 12:19:48 -06:00
Daniel Topa
c832479c65 Add libhio v1.4.1.3, 1.4.1.1 (#10699) 
- Switch all libhio tarball listings to sha256 checksums
- Correct typo in alert message in /lib/spack/spack/util/module_cmd.py: fucntion -> function

https://github.com/hpc/libhio/releases
Released 2019-02-01

Verification builds on LANL Darwin:

**Intel Xeon**
Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                40
On-line CPU(s) list:   0-39
Thread(s) per core:    2
Core(s) per socket:    10
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 63
Model name:            Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
Stepping:              2
CPU MHz:               1198.779
CPU max MHz:           3300.0000
CPU min MHz:           1200.0000
BogoMIPS:              5193.70
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              25600K
NUMA node0 CPU(s):     0-9,20-29
NUMA node1 CPU(s):     10-19,30-39
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm abm cpuid_fault epb invpcid_single pti intel_ppin tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc dtherm ida arat pln pts
`
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.3-s4fnmesfp65trhks5qi3it5p73ssfpsp
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.2-fkgh5vqpijvwqywffmokgmsglqxwfrtl
`

**Arm**
Architecture:          aarch64
Byte Order:            Little Endian
CPU(s):                256
On-line CPU(s) list:   0-255
Thread(s) per core:    4
Core(s) per socket:    32
Socket(s):             2
NUMA node(s):          2
Model:                 0
BogoMIPS:              400.00
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              32768K
NUMA node0 CPU(s):     0-127
NUMA node1 CPU(s):     128-255
Flags:                 fp asimd evtstrm aes pmull sha1 sha2 crc32 atomics cpuid asimdrdm
`
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.3-q6nnwiy6bi7ktnghdsngwamom23zpmgy
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.2-y6nwovff3qbdy242zc4x2toloz6xpcvm
`

2019-02-25

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2019-02-26 09:56:20 +01:00
Stephen Hudson
7c38dc06dc libEnsemble package: add v0.4.1 (#10688) 
Also add v0.4.0 and remove version lower bound on petsc4py
 2019-02-25 14:37:51 -06:00
Michael Kuhn
385d108b5d slurm: Add PMI support (#10683) 
- Add support for pmix (optional)
- Install pmi2 header and library
 2019-02-25 13:05:31 -06:00
Elsa Gonsiorowski, PhD
d85a0bae8f mpiFileUtils v0.9 (#10676) 
* working on updating to cmake

* generic package, any ver of cmake

* install for autotools or cmake
 2019-02-25 09:24:52 -08:00
Hadrien G
236180c109 ACTS: new package (#10600) 2019-02-25 11:11:01 +01:00
Sinan
691a2f4b71 py-unicycler: new package (#7727) 2019-02-25 09:44:05 +01:00
Denis Davydov
2851b3f57c dealii: fix default of cuda_arch (#10690) 2019-02-24 08:53:13 +01:00
Adam J. Stewart
b43e8fcaa7
Python: optional dependencies and post-installation tests (#10335) 
* Add post-installation tests to Python package

* libbsd does not build on macOS

* Make Python dependencies optional

* Add readline dep, remove ncurses patch, fix autoreconf
 2019-02-23 12:36:26 -06:00
Justin Stanley
68af6148d1 beast-tracer: new package at 1.7.1 (#10652) 2019-02-22 19:22:30 -06:00
Levi Baber
0e7b19adf4 stacks package: add version 2.3b (#10653) 2019-02-22 19:16:44 -06:00
Brian Spilner
ba70d6e706 cdo package: add version 1.9.6 (#10654) 2019-02-22 18:38:35 -06:00
Geoffrey Oxberry
219c17a340 automake package: add version 1.13.4 (#10662) 
Also replace MD5 hashes with SHA256 hashes for older versions
 2019-02-22 18:38:00 -06:00
Eric Martin
49f56cb49c gmap-gsnap package: Add version 2019-02-15 (#10677) 2019-02-22 18:36:40 -06:00
Axel Huebl
7bd960ba86 ADIOS package: add version 2.3.1 (#10666) 
Update older md5 checksums to sha256. Require CMake >= 3.6.0 (updated
from 3.5.0). Remove some third-party depends_on statements (which
were commented out before).
 2019-02-22 18:36:04 -06:00
Hadrien G
510a28d156 Gaudi package: new version + xenv bugfix (#10668) 
Extract implicit xenv dependency into a new package and add it as an
explicit dependency. Update Gaudi to explicitly depend on older
versions of xenv rather than the latest develop because that
conflicts with Spack's compiler wrappers.
 2019-02-21 19:04:03 -06:00