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Author SHA1 Message Date
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