Commit graph

9290 commits

Author SHA1 Message Date
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
Cyrus Harrison
1b3f546ba4 update conduit for 0.5.0 release (#13455)
* add support for static (via ~shared) and use vtk-m 1.2

* updating vtkh package to output cmake configure file and pinning it to vtkm 1.2

* trying a different cmake for vtkh

* removing problematic b

* making conduit respect ~python

* fixing ascent python logic

* update ascent package

* consistant cmake usage

* conditionally add tbb in ascent if vtkh

* applying becker fix

* adding vtkh tag

* fixing vtkh tagged version

* updating ascent and conduit for static builds

* enabling openmp

* reverting files that should not have been changed

* ascent updates

* more robust handling of variants

* fixing ascent package typo

* ascent: add optional support for mfem

* enable mfem conduit support for ascent

* add optional adios dep to conduit

* remove ver req from conduit

* ascent: remove confusing comment

* tweaks to conduit and ascent pkg recipes

* fix typo in conduit package

* pref conduit master

* fixing mfem typo for ascent

* reverting files

* adding mirror for bzip

* changing mfem to depend on conduit@master to get updated relay

* restore use of conduit 0.3.1 or greater for mfem

* set master as prefered conduit version

* allow mfem to use conduit master

* adding rover package and editing ascent

* updating vtkm cmake dep

* updates from axom

* guard ascent python support on +shared

* removing rover to simply ascent package

* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified

* fix fortran compiler check so it can work on cray systems

* working towards cuda fix for vtkm lagrange filter

* update ascent package with more variants, and patch to avoid nvcc issue

* hdf5 flags fix for BGQ

* flake8

* extra guards for cuda patch

* conduit and ascent fortran fix

* fix patch for non cuda case

* add test variant to conduit, tweak ascent pkg

* change min ver of cmake used for ascent

* h5z-zfp package: unset FC when ~fortran

* conform to expected upstream solution

* pinning vtkm

* going back to vtkm master

* add back vtk-m variant for shared libs

* update ascent and vtkh packages

* wire up option to run tests during install

* add post install test

* add testing to ascent

* tweak for blueos xl

* add ctest output on error for run_tests

* enable ctest output on error for run_tests

* add testing of the using-with-make example

* update using-with-make examples

* typo in ascent using-with-cmake test

* fix ascent using test exe names

* more fixes, less sleep

* more fixes, less sleep ...

* remove unwired up version

* improvments suggested on review

* adding new cmake

* Update package.py

* Update package.py

* changes post cori os update

* fix cray hack

* Update package.py

Fixing 'fix'. Inconsistent variable names in conduit package

* type in spack recipes

* add zfp support to conduit

* fix indent error in conduit pkg

* move to use build phases, add sphinx rtd as dep, fix ex names in tests

* add conduit 0.5.0 release

* flake8

* remove old cray hack

* incorp feedback from review

* fix to use proper build env sig
2019-10-28 17:32:16 -05:00
Kelly (KT) Thompson
ffb4e02a53 Fix gcc recipe for RHEL7. (#13460)
* Fix gcc recipe for RHEL7.

+ It appears that macOS related changes to the gcc recipe broke gcc on RHEL7.
  This bug manifests as `libstdc++.so: undefined reference to libiconv` when gcc
  is used.
+ Fixes #13452 by moving
  `--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix)` into the darwin
  OS section of the configuration.
+ Change qualification of `depends_on(libiconv)` to limit dependency to macOS.

* Replace deprecated 'setup_environment' with 'setup_run_environment'.

* Fix cut and paste error.

* Rename 'run_env' to just 'env'.
2019-10-28 17:31:23 -05:00
Jon Rood
8786cb468a Paraview package: add version 5.7.0 and update environment setup (#13255)
Replace setup_environment/setup_dependent_environment with
setup__dependent_build_environment and setup_run_environment
according to 9ddc98e
2019-10-28 14:55:08 -07:00
Brian Van Essen
802c3c0c51 Packages: Add cuDNN versions; update LBANN dependencies (#13412)
* Add cuDNN version 7.6.3-10.1 (for x86_64 and ppc64le)
* Add py-pytest and py-protobuf depenencies to LBANN
2019-10-28 13:24:50 -07:00
Paul
f4e6f28e6d Go package: add versions (including 1.13.3) and update environment setup (#13254)
* Add versinos 1.13.3, 1.13.2, 1.12.12, and 1.12.11
* Replace setup_environment/setup_dependent_environment with
  setup_build_environment and setup_dependent_{build, run}_environment
  according to 9ddc98e
2019-10-28 13:19:14 -07:00
Adam J. Stewart
33a34f9619
Fix PyTorch build with Intel MKL (#13464) 2019-10-28 11:47:21 -05:00
Glenn Johnson
283b3e601c Update emacs to version 26.3 (#13469) 2019-10-28 11:46:27 -05:00
Mark Olesen
cacd0fb139 scotch: added version 6.0.8 (#13467) 2019-10-28 15:58:25 +01:00
wenlibin02
ba69ebc5f7 Add dependency and patch for perl-dbfile (#13261)
* Add dependency and patch perl-dbfile

There are two problems for the building of `perl-dbfile`:

1) this package depends on the package `berkeley-db`
2) fix the building using a patch, which locates the position of `berkeley-db` and modify the configuration file for the building

* Update and reformat the script package.py

* Simplify the patch

* Update package.py

* Update package.py
2019-10-27 22:31:10 -05:00
Nichols A. Romero
c11c3f2710 QE Update Oct 2019 (#13406)
* This filter_file was difficult to maintain and is no longer needed.

* Clarify lack of support for HDF5 in serial QE.

* Update QE and HDF5 conflicts based on user feedback.
2019-10-27 22:27:55 -05:00
Axel Huebl
7b86251bef Add Lizard (LZ5) (#13456)
* Add Lizard (LZ5)

Add a new package for Lizard, formerly LZ5, a very fast compressor
and decompressor library.

* c-blosc2: use external lizard

Use an external Lizard (LZ5) dependency and add missing
"when="s for other compressor dependents.
2019-10-27 22:24:27 -05:00
Glenn Johnson
1d760e79a6 Libbeagle fixes (#13463)
* Fixes for libbeagle

This PR fixes a couple of issues with the libbeagle package.

- Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix)
- Disable the default of compiling with -march=native as Spack now
  inserts architecture specific flags
- Set BEAST_LIB in the beast1 package not in libbeagle.

* Use new setup_run_environment method
2019-10-27 22:24:06 -05:00
Andreas Baumbach
c0a2e8651b new package: py-pandocfilters (#13418)
dependency of py-nbconvert
2019-10-27 22:22:25 -05:00