Commit graph

8364 commits

Author SHA1 Message Date
Douglas Duckworth
ec29461632 added relion 3.0.7 - removed deprecated versions (#12101)
* relion - added v 3.0.7 and removed deprecated versions that have inferior performance

* relion 3.0.7 does require cuda 9 or above
2019-07-23 18:13:00 -05:00
Toyohisa Kameyama
6b07407cd0 isaac-server: Don't add -march=native on ARM and gcc 5.x or before. (#12042) 2019-07-23 16:48:25 -05:00
Toyohisa Kameyama
39139b9db8 nanoflann: Don't add -mtune=native on ARM and gcc 5.x (#12093) 2019-07-23 16:47:28 -05:00
Nichols A. Romero
2b35ad7b22 Quantum Espresso Update 2019 (#12098)
* Add support for QE 6.4.1

* QE 6.3. backports branch no longer relevant.

* List QE develop first.
2019-07-23 16:44:08 -05:00
Jimmie Lin
8095e26ffa Add EFA fabric to libfabric 2019-07-23 12:08:33 -07:00
Pariksheet Nanda
5878b418c5 ioapi: add version 3.2 (#12088)
* ioapi: add version 3.2

* ioapi: unwrap version checksum; it's exempt from line length QA

* ioapi: drop overridden build(); it's the same as the default
2019-07-23 12:10:01 -05:00
Greg Becker
4ff2773704
ncurses: remove TERMINFO from build env (#12086) 2019-07-23 10:13:41 -05:00
Marco Comparato
7ea4e50587 font-util: add missing autoconf automake dependencies (#12053) 2019-07-23 09:41:04 -05:00
Daniel Topa
07f3921838 Add UCX 1.6.0 (#12089)
https://github.com/openucx/ucx/releases/tag/v1.6.0
Released 2019-07-17

Verification builds on LANL Darwin x86_64 and Power9:

dantopa@cn2037:pr-update-ucx.spack $ date
Mon Jul 22 17:04:14 MDT 2019

dantopa@cn2037:pr-update-ucx.spack $ pwd
/scratch/users/dantopa/repos/spack/pr-update-ucx.spack

dantopa@cn2037:pr-update-ucx.spack $ spack find -ldf ucx

==> 2 installed packages
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
w7fp4n6    ucx@1.6.0%gcc
tt2hkol        ^numactl@2.0.12%gcc
srhy7ry        ^rdma-core@20%gcc
kvgvhpv            ^libnl@3.3.0%gcc

-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
cji3ce7    ucx@1.6.0%gcc
pmgndwh        ^numactl@2.0.12%gcc
qymrwx6        ^rdma-core@20%gcc
2263pm5            ^libnl@3.3.0%gcc

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-07-22 21:43:35 -05:00
Matthias Diener
19968a0035 scons: add version 3.1.0 (#12084) 2019-07-22 17:35:40 -05:00
Chuck Atkins
69c302f455 cmake: Move cxx11 flags for fujitsu into the flag_handler method (#12056)
* cmake: Move cxx11 flags for fujitsu into the flag_handler method

* cmake: sanitization and error checking in flag_handler

* cmake: Fix fujitsu flag check from 'fc' to 'fj'
2019-07-22 17:33:40 -05:00
Denis Davydov
8cef81363c gcc: support without command line tools (#11040) 2019-07-22 16:53:50 -05:00
zschulte
db7127c56d openjdk (#10446)
* openjdk

* Removing preferred from latest and adding a few lines for readability.

* Remove bad whitesapce

* removing formatting changes

* stable url for openjdk 1.8

* remove extra blank line

* actual binary
2019-07-22 13:11:45 -05:00
Toyohisa Kameyama
58c84423b1 tealeaf: Don't add -march=native on ARM and gcc 5.x or before. (#12080) 2019-07-22 13:03:43 -05:00
Hironori-Yamaji
8e92409263 jdk: Add JDK 12.0.2_10 (#12081) 2019-07-22 12:40:11 -05:00
Mark W. Krentel
6111758b48 hpctoolkit: add version gpu and variant cuda (#12068)
Add version for 'gpu' and variant for 'cuda'.  These are currently available from the 'master-gpu' branch.

* hpctoolkit: add version gpu and variant cuda
* The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
2019-07-21 22:29:08 -07:00
Toyohisa Kameyama
8ca90e26d9 libsharp: Don't add -march=native on ARM (#12064)
* libsharp: Don't add -march=native on ARM

* Add preferred=True to version 1.0.0.
2019-07-21 21:56:14 -05:00
Mark W. Krentel
930011c124 hpcviewer: add version 2019.07 (#12067)
ibm-java: fix the URL to only use a machine type that ibm-java
supports so that 'spack info' doesn't report a non-existent URL on
platforms that it doesn't support.
2019-07-20 10:07:15 -07:00
Greg Becker
4f9131fdc2 Package inheritance: Find patch files defined in parent classes using MRO (#12051)
Fixes #8908, 11844

Use Python MRO to find patch files from parent classes.
2019-07-19 18:08:05 -07:00
Peter Scheibel
4b6de78062
font-util package: add autoconf/automake build deps (#12071)
Fixes #12026

These are required on some systems
2019-07-19 17:45:22 -07:00
Michael Kuhn
cadff917c7 leveldb: add 1.22 (#12044) 2019-07-19 09:26:09 -05:00
Chris Green
9b763980b6
libxpm: cope with system gettext if configured. (#10881)
* If gettext is installed in the system it won't be in the spec tree.
2019-07-19 08:36:58 -05:00
Gregory Becker
cebf1fd668 stacks: update view management for multiple/combinatorial views
This adds notion of a default view, other views in environments
2019-07-18 19:28:50 -07:00
Matthias Diener
5be1ff83d1 cmake: add version 3.15.0 (#12058) 2019-07-18 18:28:21 -05:00
Adam J. Stewart
032075af74
Add master version to sklearn (#12057) 2019-07-18 15:56:48 -05:00
Matthieu Dorier
6eba9febaa pkg PRRTE: added version 1.0.0 (#12054) 2019-07-18 13:59:39 -05:00
Matthieu Dorier
3120e06359 added version 3.1.3 of PMIx (#12055) 2019-07-18 13:59:02 -05:00
Adam J. Stewart
c96d687c7c
Workaround for #9149 (#12050) 2019-07-18 13:57:37 -05:00
Justin S
620d728aa5 py-mlxtend: new package at 0.16.0 (#12039)
* py-mlxtend: new package at 0.16.0

* py-mlxtend: fix dependencies
2019-07-18 12:25:41 -05:00
Phil Carns
7428fc66f7 update web site and git url for BMI package (#12036) 2019-07-17 21:28:39 -05:00
Jordan Ogas
ada50b968a add charliecloud v0.10 (#12046) 2019-07-17 21:28:02 -05:00
Adam J. Stewart
5d1f965e59
Fix scikit-learn build with Apple clang (#11496)
* Fix scikit-learn build with Apple clang

* Update compiler unit tests

* Fix unit tests

* Fix OpenMP dep

* recursive=True no longer necessary

* Add myself as a maintainer

* Specify which versions require OpenMP

* Typo fixes

* LLVM-OpenMP is the correct dependency, no OMPT

* Flake8 fix

* Undo Apple Clang OpenMP flag change, split into a separate PR
2019-07-17 21:27:16 -05:00
t-karatsu
1269256e25 libjpeg-turbo: set compiler flags with CMake args (#11938)
Later versions of libjpeg-turbo build with CMake; to build with
user-specified cflags, the user must supply these to CMake as
-DCMAKE_C_FLAGS (Spack's typical approach of injecting these flags
into the compiler wrapper invocation is insufficient in this case).

Currently libjpeg-turbo cannot be implemented as a CMakePackage
(and thereby take advantage of the flag_handler implementation it
provides) because not all versions of libjpeg-turbo use CMake, so
this adds a custom implementation of flag_handler and
flags_to_build_system_args to libjpeg-turbo.
2019-07-17 15:37:18 -07:00
Adam J. Stewart
7f3048c8af
Add support for .txz and .tbz2 file extensions (#12048) 2019-07-17 16:23:23 -05:00
Ryan S. Elliott
c9b6c78d3a kim-api 2.1.0 (#12041) 2019-07-17 12:11:34 -05:00
brietzke
0c5ed467ce package opencoarrays: add new version: 2.7.1 (#12043) 2019-07-17 12:11:02 -05:00
t-karatsu
5d9e67d953 Cmake/add option for fujitsu compiler (#11839)
* cmake: change c++ spec when building with Fujitsu compiler.

* cmake: define cxxflags using a Fujitsu compiler's method.

* cmake: Add condition of whether to add cxx11 option.
2019-07-17 12:49:36 -04:00
Shane R. Spencer
1b16be538e Added url_for_version to python/package.py (#12040) 2019-07-16 20:50:43 -05:00
Justin S
267d07e4b9 py-pandas: add 0.24.2 (#12038) 2019-07-16 20:46:17 -05:00
Hironori-Yamaji
c44afdcc80 r: set FPICFLAGS for compilers except 'gcc' (#12033) 2019-07-16 11:56:34 -05:00
brietzke
29d968bd84 package mutationpp: add new version: 1.0.0 (#12035) 2019-07-16 11:55:53 -05:00
Michael Kuhn
ce88cc75ef qt: fix patch checksum (#12024)
It seems that GitHub's output changed slightly for this patch (one more
letter for both short hashes on the index line), probably due to the
number of objects in the repository.
2019-07-15 23:43:02 -05:00
Brian Homerding
36919ba859 binutils: Adding Clang to narrowing conversion error workaround (#12029) 2019-07-15 23:42:02 -05:00
Marc-Andre Hermanns
2cfbde1737 Add JUBE package definition (#12023)
* Add JUBE package definition

* Fixing flake8 errors
2019-07-15 20:58:57 -05:00
Severin Strobl
0ed7204c74 Added HPX version 1.3.0. (#12025) 2019-07-15 20:54:54 -05:00
t-karatsu
e3b513874b boost: use clang toolset when building with Fujitsu compiler. (#11827) 2019-07-15 15:13:04 -07:00
Glenn Johnson
3f83a2a7d8 Add auto-dispatch specification to Intel packages (#11697)
This PR adds the ability to specify the auto-dispatch targets that can
be used by the Intel compilers. The `-ax` flag will be written to the
respective compiler configuration files. This ability is very handy when
wanting to build optimized builds for various architectures. This PR
does not set any optimization flags, however.
2019-07-15 11:37:54 -07:00
Hironori-Yamaji
68ad4caf30 binutils: added '-Wno-narrowing' to CXXFLAGS when using fj compiler via flag_handler (#11922)
FJ compiler fails for older versions w/o '-Wno-narrowing' flag.
2019-07-15 08:50:26 -07:00
Todd Gamblin
a3caf52cac packages: computation.llnl.gov is now computing.llnl.gov (#12013) 2019-07-15 07:32:51 -07:00
Milton Woods
af74c291ed py-basemap: install without egg (#11961)
* py-basemap: avoid creating egg during build, for compatibility with mpl_toolkits

* py-basemap: not ready for py-pyproj@2 onwards
2019-07-15 10:26:13 -04:00