Commit graph

9303 commits

Author SHA1 Message Date
Gregory Lee
7e2e93b787 added archer 2.0.0 and package build fixes (#13577) 2019-11-04 17:39:16 -06:00
Christoph Junghans
dd7ebcf2d9
portage: fix lapack/blas linkage (#13558) 2019-11-04 16:35:28 -07:00
Andreas Baumbach
0f3ffad430 py-colorama: new version 0.4.1 (#13562)
* py-colorama: new version 0.4.1

* add python dependency
2019-11-04 16:46:29 -06:00
Andreas Baumbach
0b93e95049 py-regex: new version 2019.11.1, w/o setuptools (#13563) 2019-11-04 16:45:47 -06:00
Andreas Baumbach
80f63f7f9b py-dataclasses: new package (#13564) 2019-11-04 16:44:11 -06:00
Andreas Baumbach
6b27d87e7a py-tzlocal: add new version 2.0.0 (#13565) 2019-11-04 16:43:15 -06:00
Andreas Baumbach
3bd7d7f211 new package: py-chai (#13567) 2019-11-04 16:41:28 -06:00
Andreas Baumbach
880a8d40ce new package: py-umalqurra (#13568) 2019-11-04 16:40:06 -06:00
Hadrien G
1114ae9375 Add ACTS v0.10.5 (#13556) 2019-11-04 11:43:45 -06:00
Sinan
bbb5284b42 py-astor: specify py-setuptools versions as build fail with latest version (#13533)
* specify py-setuptools dependency as build fail with latest version

* explain

* py-astor builds with setuptools@41.3
2019-11-04 10:21:59 -06:00
Stephen Herbein
19410461b7 Flux v0.11.1 - v0.11.3 (#13199)
* flux: add `url_for_version` to support their C4 repo model

Flux uses a fork of ZeroMQ's Collective Code Construction Contract
(https://github.com/flux-framework/rfc/blob/master/spec_1.adoc).
This model requires a repository fork for every stable release that has
patch releases.  For example, 0.8.0 and 0.9.0 are both tags within the
main repository, but 0.8.1 and 0.9.5 would be releases on the v0.8 and
v0.9 forks, respectively.

* flux: add latest versions

* flux: remove master from `when=@0.X:,master` statements

Now that #1983 has been merged, master > 0.X.0.

* flux-core: remove extraneous `99` patch version in `when` range

Replace `when=@:0.11.99` with `when=@:0.11` since the intention is to
include all patch versions of `0.11`.

* flux-core: fix `setup_build_environment` after changes in #13411

In #13411, `setup_environment` was split into `setup_build_environment`
and `setup_run_environment`, with the `spack_env` and `run_env`
arguments being changed to `env`.  Somehow the flux package was the only
one to not have its `spack_env` references in the function changed to
`env`.

* flux: add runtime environment variables that Flux checks

with older versions of Flux (i.e, 0.0:0.13), FLUX_CONNECTOR_PATH must be
set by spack to prevent failures in certain
scenarios (https://github.com/flux-framework/flux-core/issues/2456).

the flux binary also sets some other environment variables, which can be
listed by running `flux -v start`.  I added a few of those just to be
sure that the Spack-installed paths are used, rather than
system-installed ones.

* flux: add optional testing dependencies to maximize test coverage

Install optional dependencies to ensure that only spack-installed
software is detected and that all tests are run when `spack install
--test` is used.

Flux's test suite will test for the existance of valgrind, jq, and any
MPI installation.  If it detects them (even if they are system-installed
and outside the spack environment), it will run optional tests against
them.  I noticed on my machine that the valgrind tests were running
against the system-install valgrind.

* flux-sched: switch to new `setup_run_environment` API
2019-11-04 09:58:40 -06:00
Adam J. Stewart
903b0071cf Add latest version of py-pybind11 (#13552)
* Add latest version of py-pybind11

* setup_environment -> setup_build_environment
2019-11-04 02:00:02 -08:00
Simon Pintarelli
bcda14f825 Add py-voluptuous (#13457)
Data validation library
2019-11-03 18:48:52 -06:00
Justin S
1d8391a60c r-gstat: new package at 2.0-3 (#13131)
* r-gstat: new package at 2.0-3

* Update var/spack/repos/builtin/packages/r-gstat/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/r-gstat/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-03 18:35:08 -06:00
Ricardo Silva
c42ebb0ccc Polymake: new version and more dependencies (#13399)
* New package: perl-term-readline-gnu

* polymake dependency

* perl-term-readline-gnu: flake8

* New package: perl-xml-libxslt

* polymake dependency

* ppl: new version 1.2

Conflicts:
	var/spack/repos/builtin/packages/ppl/package.py

* polymake: new version and dependencies

Conflicts:
	var/spack/repos/builtin/packages/polymake/package.py

* perl-xml-libxslt: missing dependency
2019-11-03 17:44:34 -06:00
Jannek Squar
9331a943ce New package py-wradlib with new dependencies (#13459)
* New package py-wradlib with new dependencies py-deprecation, py-semver, py-xmltodict

* Adjusted package source source

* Adjusted xarray package to use pypi-source

* Added dependencies

* Added explicit gdal+python dependency

* Concretised dependency versions

* Removed strict version range
2019-11-03 17:38:27 -06:00
Jannek Squar
c175be4420 Added dependencies (#13519)
* Added dependencies

* Adjusted dependency
2019-11-03 17:28:19 -06:00
Jannek Squar
ed037d0c5d Update package saga gis (#13520)
* Improvements of saga-gis package

* Added explicit version ranges for old saga-gis version

* Update var/spack/repos/builtin/packages/saga-gis/package.py

Creative usage of redefinition of getter method

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/saga-gis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/saga-gis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-03 17:26:53 -06:00
Daryl W. Grunau
ed89825557 constexpr_longdouble.patch should be applied to v6 too (#13548) 2019-11-03 16:47:41 -06:00
Adam J. Stewart
e12a738d84
Add latest version of protobuf (#13551) 2019-11-02 15:58:46 -05:00
Adam J. Stewart
573789f067
Add QNNPACK package (#13549) 2019-11-02 14:39:31 -05:00
健美猞猁
c43e6839d4 chgcentre: a new package. (#13500)
* chgcentre: a new package.

* flake8.
2019-11-02 12:58:57 -05:00
Adam J. Stewart
f6e26c402b
Add py-tables 3.6.1 (#13536) 2019-11-01 11:37:04 -05:00
Simon Pintarelli
854f45a136 libxc: update URL / new API (#13471)
- setup_environment -> setup_build_environment
- remove patch
2019-11-01 11:35:30 -05:00
Satish Balay
43b18dada4 hypre: add version 2.18.2 (#13527) 2019-10-31 18:35:13 -05:00
Daniel Topa
93e87474fb dd Open MPI v. 4.0.2 (#13257)
Verification builds on LANL Darwin x86_64, ARM, and, Power9:

x86_64: OPTANE
dantopa@cn733:pr-openmpi-4.0.2.spack $ spack arch
linux-centos7-skylake_avx512

$ spack install openmpi @ 4.0.2 % gcc @ 4.8.5
...
==> Installing openmpi
...
==> Successfully installed openmpi
  Fetch: 2m 15.65s.  Build: 6m 13.17s.  Total: 8m 28.82s.
[+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.0.2-jrypg7vfnk6nl5if2rnzt65wdrjelxsq

NEHALEM
$ spack arch
linux-centos7-nehalem

$ spack install openmpi @ 4.0.2 % gcc @ 4.8.5
...
==> Installing openmpi
...
==> Successfully installed openmpi
  Fetch: 50.48s.  Build: 9m 11.45s.  Total: 10m 1.93s.
[+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-nehalem/gcc-4.8.5/openmpi-4.0.2-4jz3bcwjci44taizt4jqzxqh4y75uswc

ARM
$ spack arch
linux-rhel7-aarch64

$ spack install openmpi @ 4.0.2 % gcc @ 4.8.5
...
==> Installing openmpi
...
==> Successfully installed openmpi
  Fetch: 1m 10.47s.  Build: 11m 41.45s.  Total: 12m 51.92s.
[+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/openmpi-4.0.2-ygr77roadqzdnsdgqz3uactjqnb5nayn

POWER9
$ spack arch
linux-rhel7-power9le

$ spack install openmpi @ 4.0.2 % gcc @ 4.8.5
==> Warning: Using GCC 4.8 to optimize for Power 8 might not work if you are not on Red Hat Enterprise Linux 7, where a custom backport of the feature has been done. Upstream support from GCC starts in version 4.9
...
==> Installing openmpi
...
==> Successfully installed openmpi
  Fetch: 23.95s.  Build: 9m 7.67s.  Total: 9m 31.62s.
[+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-power8le/gcc-4.8.5/openmpi-4.0.2-cid4wfzr2iwgz6ybhkexludwu7koi266

$ spack find -ldf openmpi
==> 4 installed packages
-- linux-centos7-haswell / gcc@4.8.5 ----------------------------
jrypg7v openmpi@4.0.2%gcc
lliismp     hwloc@1.11.11%gcc
7dqpxas         libpciaccess@0.13.5%gcc
viidrh5         libxml2@2.9.9%gcc
yhvj3br         numactl@2.0.12%gcc
pkmj6e7     zlib@1.2.11%gcc

-- linux-centos7-nehalem / gcc@4.8.5 ----------------------------
4jz3bcw openmpi@4.0.2%gcc
pcauu6w     hwloc@1.11.11%gcc
yiqf6bj         libpciaccess@0.13.5%gcc
wpfgqf2         libxml2@2.9.9%gcc
fd2xpnm         numactl@2.0.12%gcc
xguzaxf     zlib@1.2.11%gcc

-- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------
ygr77ro openmpi@4.0.2%gcc
omy3xi2     hwloc@1.11.11%gcc
6a4he35         libpciaccess@0.13.5%gcc
txqo4cc         libxml2@2.9.9%gcc
m5neuus         numactl@2.0.12%gcc
67s2oqn     zlib@1.2.11%gcc

-- linux-rhel7-power8le / gcc@4.8.5 -----------------------------
cid4wfz openmpi@4.0.2%gcc
zcdnwb3     hwloc@1.11.11%gcc
lencfon         libpciaccess@0.13.5%gcc
bve4jop         libxml2@2.9.9%gcc
kajzqwg         numactl@2.0.12%gcc
tjbynt2     zlib@1.2.11%gcc

Thu Oct 17 19:02:50 MDT 2019

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-10-31 14:57:50 -07:00
Nichols A. Romero
14fdaca4b4 Bump up PGMath Library to latest version. More transparent name of the branch, version name equals branch name. (#13511) 2019-10-31 13:00:59 -05:00
Adam J. Stewart
b4a51084ab
Add GRASS 7.8.0 (#13026)
* Add GRASS 7.8.0

* Add new variants/dependencies

* Remove unused dep

* Filter entire libiconv line
2019-10-31 12:48:54 -05:00
Christoph Junghans
a334007808 kokkos: turn host_values into a property (#13518)
* kokkos: turn host_values into a property

* Update package.py

* Update package.py
2019-10-31 12:46:05 -05:00
t-karatsu
e7f574aad5 ipopt: Add condition for 'aarch64' to Ipopt/config.guess (#13499) 2019-10-31 12:38:23 -05:00
Julien Loiseau
738f2e14ce MeshToolKit package (#12870)
* Adding flecsph package

* Correcting header

* Boost version update

* Correcting Flake8 errors

* Correcting headers

* Develop preferred in FleCSI

* Removing FleCSPH branch of FleCSI

* MeshToolKit package

* formatting

* Formatting

* Correcting MSTK package

* Format

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

* Format

* Format

* Correcting package behavior

* Correcting format

* Corrections

* Update var/spack/repos/builtin/packages/mstk/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Multiline
2019-10-31 12:32:54 -05:00
Robert Maynard
3d60c3ec10 VTK-m: Add support for the 1.5 release (#13514) 2019-10-31 12:04:19 -04:00
Christoph Junghans
187706f108
portage: fix lapacke linkage (#13517) 2019-10-31 09:42:18 -06:00
Gregory Lee
4626c28c27 fix openmpi wrappers with libfabric (#13439)
* fix openmpi wrappers with libfabric

* flake8 fix

* flake8 fix

* openmpi fix deprecated API

* openmpi fix deprecated API
2019-10-29 23:09:21 -05:00
t-karatsu
ad6908e35d mumps: Fix compile commands. (#13497) 2019-10-29 23:08:25 -05:00
Justin S
7af668f452 r-bio3d: new package at 2.3-4 (#13496) 2019-10-29 18:09:46 -05:00
Justin S
ccd20c9973 r-fields: new package at 9.9 (#13495) 2019-10-29 18:09:34 -05:00
Justin S
9a0ab3a87a r-spam: new package at 2.3-0.2 (#13494) 2019-10-29 18:09:16 -05:00
Justin S
4d345429ab r-dotcall64: new package at 1.0-0 (#13493)
* r-dotcall64: new package at 1.0-0

* r-dotcall64: break up long line
2019-10-29 18:09:05 -05:00
Justin S
d76ec7b2da r-dada2: new package at 1.14 (#13492)
* r-dada2: new package at 1.14

* r-dada2: add gmake dependency

* Update var/spack/repos/builtin/packages/r-dada2/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-29 18:08:51 -05:00
t-karatsu
e29a6c532c mumps: Add '-DMAIN_COMP' when using Fujitsu compiler. (#13480) 2019-10-29 13:32:36 -05:00
Sinan
944ef2f690 new package: py-scs (#13477)
* new package: py-scs

* rename

* flake8

* Update var/spack/repos/builtin/packages/py-scs/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-29 13:11:31 -05:00
Tiziano Müller
0a5c184a5d CP2K: drop json-fortran dependency and add support for the Nvidia V100 (#13468)
* cp2k: drop json-fortran dep since that's now handled in SIRIUS internally

* cp2k: gained support for Nvidias V100
2019-10-29 14:08:58 +01:00
Simon Pintarelli
aad8ea172c Add SpFFT: sparse 3D FFT library (#13458)
* Add SpFFT: sparse 3D FFT library

SpFFT is required as a dependency for SIRIUS

* cleanup

* add missing dependency
2019-10-28 22:57:07 -05:00
Sinan
bc930f310f new package: py-cvxpy (#13478)
* new package: py-cvxpy

* improve dependency specs
2019-10-28 22:55:08 -05:00
Sinan
95e0d118be new package: py-ecos (#13476)
* new package: py-ecos

* flake8
2019-10-28 20:30:40 -05:00
Sinan
330cd56517 new package: py-osqp (#13475) 2019-10-28 20:28:42 -05:00
Adam J. Stewart
2264e30d99
Update URL parsing regexes and tests (#13411)
* Update URL parsing regexes and tests

* Get rid of no longer used README

* Merge py-udunits and py-cf-units

* netcdf -> netcdf-c

* setup_environment -> setup_*_environment

* Fix doc tests

* Few last minute fixes

* Simplify prefix removal copypasta
2019-10-28 20:27:54 -05:00
Jim Galarowicz
4367e16740 Update the module files for cbtf-krell and openspeedshop (#13400)
* Update the module files for cbtf-krell and openspeedshop adding man paths and needed papi and libmonitor paths.

* Update module files for new API.

* Use the same python for both develop and release branches.
2019-10-28 17:36:12 -05:00
Sinan
e5b1dbf4b4 new Package/scs (#13454)
* new package: SCS

* make flake8 happy

* add missing patch, improve style

* fix typo

* Update var/spack/repos/builtin/packages/scs/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* move filefilter to edit phase
2019-10-28 17:33:32 -05:00