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2020-03-25UPC++ 2020.3.0 update (#15623)Dan Bonachea1-9/+100
## Summary This PR updates and improves the Spack package for [UPC++](https://upcxx.lbl.gov). I'm an LBL employee and developer on the UPC++ team, as well as the maintainer of this Spack package. ### Key Improvements: * Adding new 2020.3.0 release and support for use of develop/master branches - Our build infrastructure underwent a major change in this release, switching from a hand-rolled Python2 script to a bash-based autoconf work-alike. - The new build system is NOT using autotools (nor does it support some of the more esoteric autoconf options), but the user interface for common builds is similar. * Add explicit support for an MPI optional dependency - New `mpi` variant enables use of the MPI-based spawner (most relevant on loosely coupled clusters), and the (unofficial) mpi-conduit backend - This variant is OFF by default, since UPC++ works fine without MPI on many systems, increasing the likelihood first-time Spack users get a working build without needing to correctly setup MPI * Add support for post-install testing using the test support deployed in the new build infrastructure * Fix or workaround a few bugs observed during testing ### Status The new package has been validated with a variety of specs across over seven different systems, including: NERSC cori, ALCF Theta, OLCF Summit, an in-house Linux cluster, and macOS laptops (Mojave and Catalina).
2020-03-25WarpX: MPI, Backends, Ascent (#15647)Axel Huebl1-20/+45
Expose serial/parallel build (MPI), CUDA/OpenMP backends, Clang, and Ascent bindings. Interestingly, `warpx +ascent` currently leads to an infinite loop in the Spack concretizer.
2020-03-25provider index: removed import from + refactored a few parts (#15570)Massimiliano Culpo2-130/+179
Removed provider_index use of 'import from' and refactored a few routines to a further subclassing of _IndexBase for implementing user defined bindings of provider specs.
2020-03-25openPMD-api: added v0.11.1 (#15659)Axel Huebl1-0/+1
Add the latest release with HDF5-1.12 compatibility.
2020-03-25mothur: specify version of vsearch (#15661)xfzhao1-1/+1
2020-03-25gitconddb: new package at v0.1.1 (#15651)Ben Morgan1-0/+43
Git-based conditions database for HEP and other experiments. Use latest release version and current master to support Linux and macOS. Add core known dependencies and conflicts related to C++17 support. cxxstd variant added to help transitive dependencies, and for future support for newer standards in future.
2020-03-25ACTS: added v0.19 (#15671)Hadrien G1-0/+1
2020-03-25pocl: add versions up to v1.4.0 (#15672)Sinan1-0/+6
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-03-25julia: added v1.4.0 (#15673)Jeffrey Salmond1-0/+1
2020-03-25libwebp: fix sha256 checksum (#15639)darmac1-1/+1
2020-03-24xz: add version 5.2.5 (#15656)Stephanie Brink1-1/+2
2020-03-24charmpp: add version 6.10.1+cleanupsMatthias Diener1-2/+4
- change URL to http as our server only supports TLSv1.0, which not all HTTPS clients accept anymore - change name of development branch to 'master'
2020-03-24pmix: add version 2.2.3 (#15668)Carson Woods1-0/+1
2020-03-24singularity: add version 3.5.3 (#15669)Carson Woods1-0/+1
2020-03-24spack.repo: remove "import from" statements (#15505)Massimiliano Culpo3-39/+71
spack.repo: remove "import from" statements
2020-03-24workaround for otf2's erroneous python2 configure requirement (#15653)eugeneswalker1-1/+2
2020-03-24r-remotes: added v2.1.1 (#15627)Amjad Kotobi1-1/+2
2020-03-24py-onnx: remove_dllexport_decl. (#15648)Tomoki, Karatsu2-0/+14
2020-03-24spack.relocate: add unit test (#15610)Massimiliano Culpo2-67/+130
* relocate: removed import from statements * relocate: renamed *Exception to *Error This aims at consistency in naming with both the standard library (ValueError, AttributeError, etc.) and other errors in 'spack.error'. Improved existing docstrings * relocate: simplified search function by un-nesting conditionals The search function that searches for patchelf has been refactored to remove deeply nested conditionals. Extended docstring. * relocate: removed a condition specific to unit tests * relocate: added test for _patchelf
2020-03-23automake: Add 1.16.2Michael Kuhn1-0/+1
2020-03-23Bugfix: remove unit tests that install real packages (#15646)Peter Scheibel1-480/+0
Our unit tests run many times. Any unit test which actually installs a package (which involves fetching code on the internet) is a severe bug because it runs an installation many times (i.e. re-downloading the same package for each version of Python that we run unit tests for). This reverts commit 25893f1, which added tests that install real packages.
2020-03-23py-ics: add version 0.7Andreas Baumbach1-0/+1
2020-03-23CMake: add version 3.9.2 (#15644)Carson Woods1-0/+1
2020-03-23lmod: add version 7.8.1 (#15643)Carson Woods1-0/+1
2020-03-23Vendoring: remove dependency on Setuptools from vendored pytest (#15612)Todd Gamblin3-51/+17
If the Python used by Spack does not include Setuptools, then 'spack test' will fail because Spack's vendored pytest dependency imports and uses Setuptools in some of its functions. It turns out that Spack doesn't use the functionality those methods enable, so this PR removes those functions and thereby allows 'spack test' to run without Setuptools.
2020-03-23Bugfix (config): enable "spack test" when in an active environment (#15618)Todd Gamblin1-4/+9
For any Spack test using Spack's YAML configuration, avoid using real Spack configuration that has been cached by other tests and Spack startup logic. Previously this was only done for tests using 'mutable_config' (i.e. those which expected to *change* the configuration of Spack), but in fact all tests that read Spack config should use it. This was an issue when running tests within an environment, because compiler configuration ends up being queried earlier, and the user's real config "leaks" into the cache. Outside an environment, the cache is never set until tests touch it, so we weren't seeing this issue.
2020-03-23xsdk-examples: add new package at version 0.1.0 (#15621)Piotr Luszczek1-0/+39
* xsdk-examples: add new package at version 0.1.0
2020-03-22bugfix: TERM may not be in the environment on Cray (#15630)Todd Gamblin1-3/+7
2020-03-22bugfix: spack test should not output [+] for mock installs (#15609)Todd Gamblin1-3/+2
`spack test` has a spurious '[+] ' in the output: ``` lib/spack/spack/test/install.py .........[+] ...... ``` Output is properly suppressed: ``` lib/spack/spack/test/install.py ............... ```
2020-03-22NCCL: add 1.2.2 (#15628)Adam J. Stewart1-1/+4
2020-03-21WarpX: Update ES and openPMD (#15611)Axel Huebl1-15/+10
Update WarpX for recent developments: - add openPMD I/O (default: ON) - remove electro-static solver option (now a runtime option) - enable tiny profiler by default - depend on new CXX std support in make scripts for C++14 - WarpX only supports 2D and 3D in cartesian dims
2020-03-21davix: add cxxstd variant (#15593)Ben Morgan1-0/+11
* davix: add cxxstd variant Davix is written in C++, so add this variant to allow dependents to specify this so a consistent ABI is used. * davix: fix flake8 errors
2020-03-21Buildcache: attempt to build and install buildcaches in test environment ↵Patrick Gartung1-0/+480
(#15577) * Put bindist.py on it's own branch * Working on SL7 with python 3.6 * Flake8 * Put back clearing of compiler cache
2020-03-21bash: add patches up to 5.0.16 (#15615)Adam J. Stewart1-0/+5
2020-03-21Fix bug in py-dgl installation, add unit tests (#15617)Adam J. Stewart1-2/+36
2020-03-21add new package: nfs-ganesha (#15580)darmac1-0/+29
* add new pacakge: nfs-ganesha * refine package.py * update bison & flex as build depends
2020-03-20Merge branch 'releases/v0.14' into developTodd Gamblin2-1/+13
2020-03-20performance: add a verification file to the database (#14693)Andrew W Elble3-3/+52
Reading the database repeatedly can be quite slow. We need a way to speed up Spack when it reads the DB multiple times, but the DB has not been modified between reads (which is nearly all the time). - [x] Add a file containing a unique uuid that is regenerated at database write time. Use this uuid to suppress re-parsing the database contents if we know a previous uuid and the uuid has not changed. - [x] Fix mutable_database fixture so that it resets the last seen verifier when it resets. - [x] Enable not rereading the database immediately after a write. Make the tests reset the last seen verifier in between tests that use the database fixture. - [x] make presence of uuid module optional
2020-03-20Buildcache: add unit tests for normalized path functions in relocate.py (#15607)Patrick Gartung1-5/+57
2020-03-20fix: change typo dependnecies to dependencies (#15602)Ryan Mast2-2/+2
2020-03-20swig: add version 4.0.1 (#15603)Ryan Mast0-0/+0
2020-03-20py-torchtext: add new package (#15604)Adam J. Stewart1-0/+24
2020-03-20freeipmi: Initial commit (#15576)Matthias Maiterth1-0/+40
* freeipmi: Initial commit Added freeipmi package. Configure and build work fine, install only as root, thus added warning and added reference to issue #4432 . * freeipmi: fixed change requests
2020-03-20Add gmsh v4.5.4 with new options (#15591)Benjamin Fovet1-2/+15
* Add gmsh v4.5.4 with new options This adds OpenCASCADE as an alternative to the oce package. A new variant 'privateapi' is added to enable the gmsh private API. * Make oce conflict with opencascade in gmsh
2020-03-20Add Ceres Solver v1.14.0 with new variants (#15597)Benjamin Fovet1-2/+21
* Add Ceres Solver version 1.14.0 * Add variants for Ceres Solver
2020-03-20Add 33.2.1 version with checksum to lua-luaposix (#15600)Carson Woods1-0/+1
2020-03-20py-sentencepiece: add new package (#15601)Adam J. Stewart1-0/+24
2020-03-20update CHANGELOG.md for 0.14.1v0.14.1Todd Gamblin1-0/+12
2020-03-20version bump: 0.14.1Todd Gamblin1-1/+1
2020-03-20Add version 5.8 and fix sqlite+column_metadata mismatch. (#15450)Dan Lipsa3-3/+3