Commit graph

13013 commits

Author SHA1 Message Date
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
Marc Mengel
2cea0633fa allow bootstrap buildcache install of patchelf (#13430)
* allow bootstrap buildcache install of patchelf

* file not path_name on one

* style

* add test for relocating patchelf

* blank lines..
2019-11-01 10:54:55 -05:00
Omar Padron
0f816561db bugfix: spack.util.url.join() now handles absolute paths correctly (#13488)
* fix issue where spack.util.url.join() failed to correctly handle absolute path components
* add url util tests
2019-11-01 03:42:43 -07:00
Gregory Lee
3bdab6f686 sbang: use utf-8 for encoding when patching (#13490)
This fixes a UnicodeDecodeError in the sbang patching function.
2019-11-01 03:39:45 -07:00
Massimiliano Culpo
390ffb80e7 Specs with quoted flags containing spaces are parsed correctly (#13521) 2019-11-01 03:38:11 -07:00
Massimiliano Culpo
42b8355269 targets: print a warning message before downgrading (#13513)
* Make package preferences a soft failure for targets, instead of a hard failure.
* Added unit tests for preferences expressed via packages.yaml
2019-11-01 03:36:28 -07:00
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
Peter Scheibel
6ec39b6c81
Bugfix: BundlePackage staging/installation (#13524)
4af4487 added a mirror_id function to most FetchStrategy
implementations that is used to calculate resource locations in
mirrors. It left out BundleFetchStrategy which broke all packages
making use of BundlePackage (e.g. xsdk). This adds a noop
implementation of mirror_id to BundleFetchStrategy so that the
download/installation of BundlePackages can proceed as normal.
2019-10-31 12:56:38 -07:00
Adam J. Stewart
4b56933643
Docs: unlock requirement versions (#13384) 2019-10-31 14:21:05 -05:00
Adam J. Stewart
536486f0e5
Travis CI: Test Python 3.8 (#13347)
* Travis CI: Test Python 3.8

* Fix use of deprecated cgi.escape method

* Fix version comparison

* Fix flake8 F811 change in Python 3.8

* Make flake8 happy

* Use Python 3.8 for all test categories
2019-10-31 14:20:46 -05:00
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
Greg Becker
a97faeb3c7 Documentation: Database.query methods share docstrings (#13515)
Currently, query arguments in the Spack core are documented on the
Database._query method, where the functionality is defined.

For users of the spack python command, this makes the python builtin
method help less than ideally useful, as help(spack.store.db.query)
and help(spack.store.db.query_local) do not show relevant information.

This PR updates the doc attributes for the Database.query and
Database.query_local arguments to mirror everything after the first
line of the Database._query docstring.
2019-10-30 16:47:48 -07:00
Greg Becker
230c6aa326
cpu: fix clang flags for generic x86_64 (#13491)
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-10-30 17:16:13 -05:00
Massimiliano Culpo
cf1c38162e cuda: fix conflict statements for x86-64 targets (#13472)
* cuda: fix conflict statements for x86-64 targets

fixes #13462

This build system mixin was not updated after the support for specific
targets has been merged.

* Updated the version range of cuda that conflicts with gcc@8:

* Updated the version range of cuda that conflicts with gcc@8: for ppc64le

* Relaxed conflicts for version > 10.1

* Updated versions in conflicts

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
2019-10-30 09:25:46 -07:00
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
Peter Scheibel
c99d367a11 syaml_int type should use int.__repr__ rather than str.__repr__ (#13487) 2019-10-29 13:51:48 -07:00
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
Tamara Dahlgren
3cf21e6edc bugfix: make spack -d test test_changed_files work (#13229)
The `test_changed_files` in `test/cmd/flake8.py` was failing because it calls
`ArgumentParser.parse_args()` without arguments.  Normally that would just
parse `sys.argv` but it seems to fail because of something in either `spack test`
or `pytest`.  Call it with an empty array so that it doesn't try to touch`sys.argv`
at all.

- [x] allow `-d` spack option for `test_changed_files`
2019-10-29 00:25:59 -07:00
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
Adam J. Stewart
b4e027e918
Output directory Spack is looking in for MKL libs (#13465) 2019-10-28 11:46:59 -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