Commit graph

8435 commits

Author SHA1 Message Date
Adam J. Stewart
07fefea52d Add Python 3.7.4 (#12142) 2019-07-26 09:18:46 +02:00
Oliver Breitwieser
867ba9d7fe googletest: Fix reversed +pthreads option (#12128)
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.

If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.

Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
2019-07-25 19:50:23 -05:00
Justin S
94af6cad5f interproscan: new package at 5.36-75.0 (#12130) 2019-07-25 19:49:42 -05:00
Matthias Diener
7cc1292202 git-lfs: add version 2.8.0 (#12131) 2019-07-25 19:46:03 -05:00
Glenn Johnson
7ad8061cbb Patches for graphviz (#12133)
- patch to build with qt5, enabling gvedit to build
- two patches to compile graphviz with icc
2019-07-25 19:45:10 -05:00
Satish Balay
7bd3b66f6e
xsdk: phist has a conflict with gcc version <= gcc-4.9.1 (#11946)
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds

This is triggered by #11677

* fix typo
2019-07-25 14:01:00 -05:00
Chuck Atkins
e614d4b481 cmake: Add a patch to revert a findmpi regression (#12129) 2019-07-25 10:23:01 -07:00
Chris Green
c20c153d16
catch: more versions, new and older. (#12123)
New versions 2.9.0, 2.9.1, older versions 2.2.2, 2.2.3, 2.4.1, 2.4.2, 2.7.0, 2.7.1, 2.7.2.
2019-07-25 11:33:03 -05:00
simo-tuomisto
4c7ee8b7c8 lame & libmad: Added two new packages for sox mp3 support. (#11964)
* Added a new package for LAME and a variant in sox for it.

* Fixed download url for LAME

* libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3.

* libmad: Added m4 as a requirement

* libmad: Added comment on patch origins

* libmad: Added a list_url for alternate download location

* libmad: Fixing libmad download url
2019-07-25 10:40:50 -05:00
Sinan
9ace419aa5 gdal: added versions 2.4.2 and 3.0.1 (#12125) 2019-07-25 17:14:37 +02:00
Chris Green
4190f302e5 geant4: improvements with respect to building against CLHEP. (#12124) 2019-07-25 08:58:13 -05:00
Todd Gamblin
b0abbfecb8 new command: spack maintainers queries package maintainers
- We don't currently make enough use of the maintainers field on
  packages, though we could use it to assign reviews.

- add a command that allows maintainers to be queried
  - can ask who is maintaining a package or packages
  - can ask what packages users are maintaining
  - can list all maintained or unmaintained packages

- add tests for the command
2019-07-24 14:10:08 -07:00
Glenn Johnson
8bb745325d Add py-setuptools as a build dependency for py-absl-py (#12109)
I needed to add py-setuptools to get py-absl-py to build.
2019-07-24 12:33:45 -05:00
Glenn Johnson
642d3345f6 Add conflicts statement to freetype for icc (#12111)
Freetype-2.8 and above use __builtin_shuffle which is not supported by
icc.
2019-07-24 12:33:24 -05:00
t-karatsu
0f98cf0398 Perl take in flags (#12112)
* perl: perl package takes in spack cflags.

* fix for flake8 test.
2019-07-24 12:32:49 -05:00
Toyohisa Kameyama
bbc689ae38 nnvm: cmake bug is fixed. (#12113) 2019-07-24 12:31:49 -05:00
Toyohisa Kameyama
cb62b1ff85 rapidjson: Don't add -march=native on ARM and gcc 5.x or before. (#12117) 2019-07-24 12:30:32 -05:00
Nichols A. Romero
63813fa9c0 QMCPACK Update July 2019 (#12097)
* Add QMCPACK v. 3.8.0

* Remove QE variant conflict for serial QMCPACK installations.

* Add support for QE 6.4.1 converter.

* FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
2019-07-24 12:28:35 -05:00
Glenn Johnson
42c3782f7e Do not build c-blosc test if intel in spec (#12110)
While the c-blosc library compiles with icc some of the c-blosc tests do
not. Disable the tests so that the spack build can continue.
2019-07-24 11:17:11 -05:00
t-karatsu
0d690edfb2 cmake: fix cxx98flag's name (#12114) 2019-07-24 11:28:22 -04:00
Toyohisa Kameyama
a8b12f0cb6 rocksdb: Don't add -march=native on ARM and gcc 5.x or before. (#12108) 2019-07-23 22:33:05 -05:00
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
Matthias Diener
9be127890f gdb: add version 8.3 (#12018) 2019-07-14 16:45:55 -05:00
Reinhard Prix
9e7eae0e2f make cfitsio explicitly depend on curl (#12016)
- currently would revert to using system-curl instead, pulling in
  unwanted system dependencies and lib-paths
2019-07-14 14:40:09 -05:00
Michael Kuhn
d7b76df5ac bzip2: Add 1.0.8 (#12017)
Update URLs to official ones.
2019-07-14 14:25:20 -05:00
Adam J. Stewart
0bff0c2d0d
Make JDK version more specific (#12008) 2019-07-13 09:05:48 -05:00
Adam J. Stewart
452021398a
Add py-jsonschema 2.6.0 (#12009) 2019-07-13 09:05:17 -05:00
Tim Fuller
5bc15b2d9a find_libraries searches lib and lib64 before prefix (#11958)
The default library search for a package checks the lib/ and lib64/
directories for libraries before the root prefix, in order to save
time when searching for libraries provided by externals (which e.g.
may have '/usr/' as their root).

This moves that logic into the "find_libraries" utility method so
packages implementing their own custom library search logic can
benefit from it.

This also updates packages which appear to be replicating this logic
exactly, replacing it with a single call to "find_libraries".
2019-07-12 17:46:47 -07:00
xfzhao
f1ce1dd163 New package: Nim (#11649) 2019-07-12 17:03:26 -07:00
Justin S
9b361bea5a r package: add rmath variant for standalone rmath library (#11693) 2019-07-12 16:50:04 -07:00
egreen77
d01d79eb5d new package: umap (#12000) 2019-07-12 15:26:24 -05:00
Hironori-Yamaji
505ad8960e jdk: Add the 'provides' call (#11997) 2019-07-12 09:45:19 -07:00
Stephen Hudson
cdc72963d1 Update libensemble (#11990) 2019-07-12 10:36:44 -05:00
Phil Tooley
52e0f47a3f update scalasca to latest version, simplify recipe (#11999)
add list_url for use with spack checksum
2019-07-12 10:30:07 -05:00
Glenn Johnson
42c7d24075 Modifications to r package (#11957)
This PR has several modifications for the r package.

- The tk package is always depended on but this pulls in X11, making the
  'X' variant non-functional. This PR sets a dependency of tk on '+X'.
- There is a missing dependency on libxmu when '+X' is set.
- The libraries for R wind up in a non-standard location and are thus
  left out of the RPATH settings. This PR adds that directory to RPATH.
- The MKL integer interface for gfortran is not in the BLAS libs. This
  PR replaces the intel interface with the gfortran interface if needed.
- Use the `LibraryList` `ld_flags` method for blas as that is more in
  line with th R Installation and Administration manual.

Note that this PR depends on PR #11956. This PR closes #8642.
2019-07-11 22:22:37 -05:00
Glenn Johnson
909c5f5019 Add variants for tk package (#11956)
TK can be built with support for libXft and X Screensaver. Both of these
are turned on in the Tk configure script. That means the system
libraries will get picked up if they are on the system and nothing is
specified in the package. Since the default for both of them is 'True' I
set the default value for the variants to 'True'.
2019-07-11 22:21:17 -05:00
Toyohisa Kameyama
4288dac35b bowtie2: Add version 2.5.3.1 and fix to build on ARM (#11974)
* bowtie2: Add version 2.5.3.1 and fix to build on ARM

1. Add version 2.5.3.1.
2. Add simde for ARM.
3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM.
4. Add Makefile option POPCNT_CAPABILITY=0 for ARM.

* flake8.
2019-07-11 22:04:22 -05:00
Toyohisa Kameyama
ea9ac3ee52 velvet: remove -m64 on aarch64. (#11984) 2019-07-11 21:59:24 -05:00
Nick Forrington
ff728bd06c Boost: Compile with toolset=clang for Arm compiler (#11992)
Bootstraps with gcc, but compiles with clang
2019-07-11 21:53:54 -05:00
Toyohisa Kameyama
0dfa5a467c megahit package: add patch to build on ARM. (#11963) 2019-07-11 17:40:00 -07:00
Phil Tooley
14271331f9 New package: dimemas (#11979) 2019-07-11 13:55:43 -07:00
Mark Olesen
138226e038 OpenFOAM package: update download url (#11973) 2019-07-11 13:45:38 -07:00
Phil Carns
3a4d37d6d6 libfabric package: add support for tcp provider (#11965) 2019-07-11 13:43:38 -07:00
Toyohisa Kameyama
6a731b4d8f luit package: use autotools. (#11962) 2019-07-11 13:34:50 -07:00
Tamara Dahlgren
e3299e6923 Rename build logs and make names consistent (#11806)
Fixes #11781

* Rename build log to spack-build-log.txt
* Rename environment variables file to spack-build-env.txt
* The name of the log and env files is now the same during the build
  and after the build completes
* Update packages which referred to the build log/env files
* For packages installed before this commit using older names for the
  build and env files, search for the older names
2019-07-11 13:32:06 -07:00
Michael Kuhn
d3be42fcca mpich: Add 3.3.1 (#11976) 2019-07-10 20:41:23 -05:00
Michael Kuhn
975b9a611a bzip2: Add 1.0.7 (#11975) 2019-07-10 18:37:16 -05:00
Reinhard
ea431be4b0 py-astropy: added latest version 3.2.1 (#11967)
- correctly installs under python@3.5:3.7.3
- (partially) fixes https://github.com/spack/spack/issues/11966
2019-07-09 21:19:38 -04:00
Carson Woods
2838aa772d package: Add powerapi package (#11845)
* Add powerapi package

* Fix flake8 formatting

* Fix download URL

* Update powerapi version line

* Fix how configure arguments are selected to improve readability

* Bug Fixes

* Fix trailing whitespace

* Bug fixes

* Remove incorrect configure flag
2019-07-09 09:57:53 -04:00
Milton Woods
d0b2c77cd1 Ferret: add version 7.2 and adjust dependencies (#11921)
* ferret: use libx11 from spack

* ferret: use mpi library with or without fortran support

* ferret: add version 7.2

* ferret: no need to specify ~mpi

* ferret: creating symlinks may fail for external packages; set include/lib paths instead
2019-07-09 09:33:07 -04:00
Toyohisa Kameyama
dab3026f2f diffsplice package: remove -m64 on ARM. (#11899) 2019-07-08 17:13:49 -07:00