Commit graph

13687 commits

Author SHA1 Message Date
Greg Becker
aa7c229c8f environments: only write when necessary (#13546)
This changes Spack environments so that the YAML file associated with the environment is *only* written when necessary (i.e., if it is changed *by spack*).  The lockfile is still written out as before.

There is a larger question here of which part of Spack should be responsible for setting defaults in config files, and how we can get rid of empty lists and data structures currently cluttering files like `compilers.yaml`.  But that probably requires a rework of the default-setting validator in `spack.config`, as well as the code that uses `spack.config`.  This will at least help for `spack.yaml`.
2019-11-03 15:46:41 -08:00
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
a8228e1aec
spack create: http -> https (#13547) 2019-11-01 17:40:49 -05:00
Peter Scheibel
2e029fc2e5
Bugfix: respect order of mirrors in mirrors.yaml (#13544)
Commands like "spack mirror list" were displaying mirrors in a
different order than what was listed in the corresponding mirrors.yaml
file.

This restores commands to iterate over mirrors in the order that
they appear in the config file.
2019-11-01 14:02:08 -07:00
Greg Becker
24ec9f0ce3
environments: make shell modifications partially unconditional (#13523)
* environments: make shell modifications partially unconditional

* flake

* missing module name

* add regression test

* flake
2019-11-01 12:00:16 -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
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
Todd Gamblin
d670765b97
version bump: 0.13.1 2019-11-01 03:52:04 -07:00
Omar Padron
01a0d554f5
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 03:50:47 -07:00
Gregory Lee
2a9d6b9fbf
sbang: use utf-8 for encoding when patching (#13490)
This fixes a UnicodeDecodeError in the sbang patching function.
2019-11-01 03:50:38 -07:00
Massimiliano Culpo
eb286bb80f
Specs with quoted flags containing spaces are parsed correctly (#13521) 2019-11-01 03:50:26 -07:00
Massimiliano Culpo
1cc69e1ce0
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 03:50:17 -07:00
Adam J. Stewart
338a532e07
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
2019-11-01 03:50:02 -07:00
Greg Becker
30c9609c4e
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.
2019-11-01 03:49:47 -07:00
Massimiliano Culpo
944d7b3d62
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>
2019-11-01 03:49:35 -07:00
Greg Becker
b727f922a4
cpu: fix clang flags for generic x86_64 (#13491)
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-11-01 03:49:16 -07:00
Peter Scheibel
835df4b2e4
syaml_int type should use int.__repr__ rather than str.__repr__ (#13487) 2019-11-01 03:49:00 -07:00
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
eugeneswalker
94de86aeb8 elpa: prefer 2016.05.004 until sse/avx/avx2 issues are resolved (#13530)
- configuration fails on newer versions when enabling sse/avx/avx2
- prefer an older version that will build with these features
2019-10-31 23:56:14 -07:00
Satish Balay
43b18dada4 hypre: add version 2.18.2 (#13527) 2019-10-31 18:35:13 -05:00
eugeneswalker
63afd0d2cf trilinos: temporarily constrain netcdf@:4.7.1 (#13526)
remove this when issues are resolved with `trilinos^netcdf@4.7.2`
2019-10-31 15:53:54 -07:00
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