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2019-07-25cmake: Add a patch to revert a findmpi regression (#12129)Chuck Atkins2-0/+33
2019-07-25catch: more versions, new and older. (#12123)Chris Green1-0/+9
New versions 2.9.0, 2.9.1, older versions 2.2.2, 2.2.3, 2.4.1, 2.4.2, 2.7.0, 2.7.1, 2.7.2.
2019-07-25lame & libmad: Added two new packages for sox mp3 support. (#11964)simo-tuomisto4-0/+163
* Added a new package for LAME and a variant in sox for it. * Fixed download url for LAME * libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3. * libmad: Added m4 as a requirement * libmad: Added comment on patch origins * libmad: Added a list_url for alternate download location * libmad: Fixing libmad download url
2019-07-25gdal: added versions 2.4.2 and 3.0.1 (#12125)Sinan1-0/+2
2019-07-25geant4: improvements with respect to building against CLHEP. (#12124)Chris Green2-6/+42
2019-07-24new command: `spack maintainers` queries package maintainersTodd Gamblin5-0/+301
- We don't currently make enough use of the maintainers field on packages, though we could use it to assign reviews. - add a command that allows maintainers to be queried - can ask who is maintaining a package or packages - can ask what packages users are maintaining - can list all maintained or unmaintained packages - add tests for the command
2019-07-24tests: Test install of unconcretized spec (#12099)Tamara Dahlgren1-0/+17
2019-07-24Add py-setuptools as a build dependency for py-absl-py (#12109)Glenn Johnson1-0/+1
I needed to add py-setuptools to get py-absl-py to build.
2019-07-24Add conflicts statement to freetype for icc (#12111)Glenn Johnson1-0/+4
Freetype-2.8 and above use __builtin_shuffle which is not supported by icc.
2019-07-24Perl take in flags (#12112)t-karatsu1-0/+5
* perl: perl package takes in spack cflags. * fix for flake8 test.
2019-07-24nnvm: cmake bug is fixed. (#12113)Toyohisa Kameyama2-0/+21
2019-07-24rapidjson: Don't add -march=native on ARM and gcc 5.x or before. (#12117)Toyohisa Kameyama2-0/+17
2019-07-24QMCPACK Update July 2019 (#12097)Nichols A. Romero1-16/+9
* Add QMCPACK v. 3.8.0 * Remove QE variant conflict for serial QMCPACK installations. * Add support for QE 6.4.1 converter. * FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
2019-07-24Do not build c-blosc test if intel in spec (#12110)Glenn Johnson1-0/+4
While the c-blosc library compiles with icc some of the c-blosc tests do not. Disable the tests so that the spack build can continue.
2019-07-24cmake: fix cxx98flag's name (#12114)t-karatsu1-1/+1
2019-07-24Fixed a name clash in the 'from_environment_diff' function (#12116)Massimiliano Culpo2-12/+18
* Added a unit test reproducing the failure in 12085 * Fixed name clash in the 'from_environment_diff' function The bug reported in #12085 stemmed from a name clash among variables, introduced during the refactor in #10753 and not caught by unit tests and reviews.
2019-07-23rocksdb: Don't add -march=native on ARM and gcc 5.x or before. (#12108)Toyohisa Kameyama1-0/+7
2019-07-23added relion 3.0.7 - removed deprecated versions (#12101)Douglas Duckworth1-7/+2
* relion - added v 3.0.7 and removed deprecated versions that have inferior performance * relion 3.0.7 does require cuda 9 or above
2019-07-23Typo fixes in Spack Environments docs (#12100)Adam J. Stewart1-17/+17
2019-07-23isaac-server: Don't add -march=native on ARM and gcc 5.x or before. (#12042)Toyohisa Kameyama2-0/+19
2019-07-23nanoflann: Don't add -mtune=native on ARM and gcc 5.x (#12093)Toyohisa Kameyama1-0/+4
2019-07-23Quantum Espresso Update 2019 (#12098)Nichols A. Romero1-3/+3
* Add support for QE 6.4.1 * QE 6.3. backports branch no longer relevant. * List QE develop first.
2019-07-23Add EFA fabric to libfabricJimmie Lin1-1/+2
2019-07-23 error messages: include whole spec for "no externals found" message (#12070)Greg Becker1-2/+2
* Provide better error message when matching externals are found for package marked not buildable
2019-07-23ioapi: add version 3.2 (#12088)Pariksheet Nanda1-0/+44
* ioapi: add version 3.2 * ioapi: unwrap version checksum; it's exempt from line length QA * ioapi: drop overridden build(); it's the same as the default
2019-07-23hashing: fix caching of dependency hashes in to_node_dictGregory Becker2-11/+17
2019-07-23ncurses: remove TERMINFO from build env (#12086)Greg Becker1-0/+3
2019-07-23font-util: add missing autoconf automake dependencies (#12053)Marco Comparato1-0/+3
2019-07-22commands: add tests for all subcommands of `spack pkg`Todd Gamblin3-24/+271
2019-07-22commands: add `spack pkg changed` subcommand, better test supportTodd Gamblin1-10/+55
- Add `spack pkg changed` to show changed and added packages for a commit. - Make `spack pkg` support tests better.
2019-07-22Add UCX 1.6.0 (#12089)Daniel Topa1-0/+1
https://github.com/openucx/ucx/releases/tag/v1.6.0 Released 2019-07-17 Verification builds on LANL Darwin x86_64 and Power9: dantopa@cn2037:pr-update-ucx.spack $ date Mon Jul 22 17:04:14 MDT 2019 dantopa@cn2037:pr-update-ucx.spack $ pwd /scratch/users/dantopa/repos/spack/pr-update-ucx.spack dantopa@cn2037:pr-update-ucx.spack $ spack find -ldf ucx ==> 2 installed packages -- linux-centos7-x86_64 / gcc@4.8.5 ----------------------------- w7fp4n6 ucx@1.6.0%gcc tt2hkol ^numactl@2.0.12%gcc srhy7ry ^rdma-core@20%gcc kvgvhpv ^libnl@3.3.0%gcc -- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------ cji3ce7 ucx@1.6.0%gcc pmgndwh ^numactl@2.0.12%gcc qymrwx6 ^rdma-core@20%gcc 2263pm5 ^libnl@3.3.0%gcc Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-07-22scons: add version 3.1.0 (#12084)Matthias Diener1-0/+1
2019-07-22cmake: Move cxx11 flags for fujitsu into the flag_handler method (#12056)Chuck Atkins1-5/+10
* cmake: Move cxx11 flags for fujitsu into the flag_handler method * cmake: sanitization and error checking in flag_handler * cmake: Fix fujitsu flag check from 'fc' to 'fj'
2019-07-22gcc: support without command line tools (#11040)Denis Davydov2-1/+15
2019-07-22Fix version scraping for CRAN packages (#12021)Adam J. Stewart2-20/+20
* Fix version scraping for CRAN packages * Remove set literals
2019-07-22bugfix: env.write() should stringify Spec lists.Todd Gamblin2-2/+8
- Setting specs from lockfiles was not correctly stringifying concretized user specs. - Fix `_set_user_specs_from_lockfile` - Add some validation code to `SpecList` constructor
2019-07-22hashes: consolidate and make hashing logic more consistentPeter Josef Scheibel8-84/+254
Spack has evolved to have three types of hash functions, and it's becoming hard to tell when each one is called. Whlie we aren't yet ready to get rid of them, we can refactor them so that the code is clearer and easier to track. - Add a `hash_types` module with concise descriptors for hashes. - Consolidate hashing logic in a private `Spec._spec_hash()` function. - `dag_hash()`, `build_hash()`, and `full_hash()` all call `_spec_hash()` - `to_node_dict()`, `to_dict()`, `to_yaml()` and `to_json()` now take a `hash` parameter consistent with the one that `_spec_hash()` requires. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2019-07-22env: environments index specs by full DAG w/build depsPeter Josef Scheibel3-30/+257
- ensure that Spec._build_hash attr is defined - add logic to compute _build_hash when it is not already computed (e.g. for specs prior to this PR) - add test to ensure that different instance of a build dep are preserved - test conversion of old env lockfile format to new format - tests: avoid view creation, DAG display in tests using MockPackage - add regression test for more-general bug also fixed by this PR - update lockfile version since the way we are maintaining hashes has changed - write out backup for version-1 lockfiles and test that
2019-07-22openjdk (#10446)zschulte1-2/+18
* openjdk * Removing preferred from latest and adding a few lines for readability. * Remove bad whitesapce * removing formatting changes * stable url for openjdk 1.8 * remove extra blank line * actual binary
2019-07-22tealeaf: Don't add -march=native on ARM and gcc 5.x or before. (#12080)Toyohisa Kameyama1-0/+6
2019-07-22jdk: Add JDK 12.0.2_10 (#12081)Hironori-Yamaji1-0/+2
2019-07-21hpctoolkit: add version gpu and variant cuda (#12068)Mark W. Krentel1-6/+30
Add version for 'gpu' and variant for 'cuda'. These are currently available from the 'master-gpu' branch. * hpctoolkit: add version gpu and variant cuda * The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
2019-07-21libsharp: Don't add -march=native on ARM (#12064)Toyohisa Kameyama3-1/+32
* libsharp: Don't add -march=native on ARM * Add preferred=True to version 1.0.0.
2019-07-20docker: fix builds, remove extra distros, add ci builds (#11621)Omar Padron26-643/+383
* fix docker builds/remove extra builds/add ci builds * preinstall vim in CI builder images * simplify & streamline docker resources * restore os-container-mapping.yaml file
2019-07-20Add OpenMP flag for Apple Clang (#12049)Adam J. Stewart2-5/+3
2019-07-20tests: speed up tests that rely on the database fixture (#12031)Massimiliano Culpo6-61/+95
The database and mutable_database fixtures were installing and uninstalling the same specs multiple times to ensure the database for tests has the correct state. This commit optimizes the procedure by caching the state in an external directory, and copying it in instead of going through the installation or uninstallation again. The database fixture is meant not to be modified by tests. This commit enforces this invariant by making the database read-only before starting the test. * Added missing db markers to tests * Added test for uninstall_by_spec * `database` fixture now returns a read-only database * Tests that modify the DB now use `mutable_database` fixture
2019-07-20hpcviewer: add version 2019.07 (#12067)Mark W. Krentel2-2/+8
ibm-java: fix the URL to only use a machine type that ibm-java supports so that 'spack info' doesn't report a non-existent URL on platforms that it doesn't support.
2019-07-20environment views: refactor stripping build deps (#12069)Greg Becker1-3/+1
2019-07-20compilers: don't raise errors for duplicate compiler definitions (#11910)Greg Becker2-1/+29
Summary: - Allow multiple definitions of compiler in compilers.yaml (use first instance) - Still print debug messages when there are duplicates, to assist users in finding this issue. Merging configs from different scopes can result in multiple compiler being present in the same configuration list. Instead of raising when there are duplicates, take the one with highest precedence. Print a debug message instead of raising, so that we can still diagnose this. We don't have a good way of warning the user about inconsistent configuration *in the same file* -- we'd need to dig into YAML file/line info for that.
2019-07-20environments: add activate/deactivate tests, work wtih `set -u`Todd Gamblin3-15/+143
- [x] Add shell tests to ensure that `spack env activate`, `spack env deactivate`, and `despacktivate` continue to work. - [x] Also ensure that activate and deactivate both work with `set -u`