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2019-12-06Spec Header Dirs: Only first include/ (#13991)Axel Huebl3-4/+17
* CUDA HeaderList: Unit Test * Spec Header Dirs: Only first include/ Avoid matching recurringly nested include paths that usually refer to internally shipped libraries in packages. Example in CUDA Toolkit, shipping a libc++ fork internally with libcu++ since 10.2.89: `<prefix>/include/cuda/some/more/details/include/` or `<prefix>/include/cuda/std/detail/libcxx/include` regex: non-greedy first match of include Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com> * CUDA: Re-Enable 10.2.89 as Default
2019-12-06ibm-java: add version 8.0.6.0 (#14003)Mark W. Krentel1-9/+16
* ibm-java: add version 8.0.6.0 Add version 8.0.6.0 and remove 8.0.5.30. IBM is fairly aggressive about removing old versions, and 8.0.5.30 is no longer available from their download site. * Restore version 8.0.5.30, although it is no longer available for download from IBM.
2019-12-06Packages/py-maestrowf (#14010)Francesco Di Natale1-1/+13
* Addition of repository branches to maestrowf. * Addition of 1.1.5dev pre-release. * Correction of a merge conflict. * Addition of Maestro release 1.1.5 * Addition of Maestro release 1.1.6 (removal of 1.1.5) * Sets 1.1.6 to the preferred version. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Tweak to the url to point to latest.
2019-12-06Add py-parameterized package (#14016)Adam J. Stewart1-0/+17
2019-12-06Update py-theano dependencies (#14015)Adam J. Stewart1-3/+4
2019-12-06mesquite: fix build of the no mpi variant. (#14012)nicolas le goff1-3/+8
* mesquite: fix build of the no mpi variant. * mesquite: added the --without-mpi option to configure.
2019-12-06docs: Alphabetize create cmd template options (#13993)Tamara Dahlgren1-1/+2
* Bugfix: Display template options for create command. * Alphabetize "spack create" template options for readability * Revert template choices format; alphabetize list * flake8 fix
2019-12-06Bugfix: spack find -p fails in environment (#13972)Greg Becker3-1/+26
* force spack find -p to print abstract specs without prefixes * hashes have the same issue; improve handling of find -L to match find -l
2019-12-06[Package: HPX] Fix Apex and OTF2 support (#13982)Teodor Nikolov2-1/+89
* Fix Apex and OTF2 support - Comment out apex as a dependncy: it is bundled with HPX. - Apply a patch to v1.3.0 to correctly build with APEX. - Add otf2 as a dependency when APEX is enabled. * Remove depends_on('apex')
2019-12-06augustus: Set compile commands for each compiler and Fix for using 'boost' ↵t-karatsu1-0/+25
on Spack (#13975) * augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack * fix for flake8 * delete 'string' args * Fix args of filter_file func * Fix args of other filter_file func
2019-12-06Add patch to fix issue building current llvm develop master on power9 (#13986)Galen Shipman2-0/+19
* Add patch to fix issue building current llvm develop master on power9 * Conform to proper block commenting Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-06Fastmath: Added required version (#13990)Tamara Dahlgren1-1/+3
* Fastmath: Added required version * Changed the version to 'latest' (per balay).
2019-12-06Ceed: Added required version (#14006)Tamara Dahlgren1-0/+2
2019-12-06sz: Change optimization flags for Fujitsu compiler (#14007)t-karatsu2-0/+15
2019-12-06Specify self for internal setup method (#14008)Paul1-4/+4
2019-12-06Convert llvm Spackage to use the monorepo (#11392)Brian Homerding5-534/+135
* [WIP] Convert llvm spackage to use the monorepo * Correcting python dependencies * Adding develop version for llvm monorepo * Python 2.6 Fix * Build Flang fork in a different root_cmakelists_dir * Formatting Fix * Including flang package changes * Removing explicit llvm dependencies variants * flake8 fix * Updating patches and llvm+flang logic * Updating env setup API * Add top level git * Conflicting flang variant with other variants
2019-12-06Add h5sh python package (#14001)Seth R. Johnson1-0/+25
* Add h5sh package * Fix requirements and update version
2019-12-06docs: Minimal BundlePackage build system doc (#13992)Tamara Dahlgren2-0/+53
* Minimal BundlePackage build system doc * Add link to new bundlepackage file * Fixed link bug and added create command example
2019-12-05hpcviewer: add version 2019.09 (#14004)Mark W. Krentel1-7/+10
Add version 2019.09. Adjust the iteration through versions to eliminate the need for version_list.
2019-12-05Add new TensorFlow package (#13112)Dominik Dold19-43/+978
* add tensorflow Change-Id: Id778c68d148cc42f0b478a9d10a8f937cb54cdc6 * make bazel and tensorflow build Change-Id: Iae9005e8f4dcc8f1ed36ea9337d2430aeebb291f * fix flake8 Change-Id: Ib05529dd796eab4a8855a5d7775cc4efea8e479d * 2nd flake8 attempt Change-Id: I46224be3a374b2a65793048b0c5178ea64adbd78 * replace md5 sums with sha256 * add version 1.13.2 * bazel() -> bazel('build',... * specify versions of bazel dependency * build with CUDA * add TODOs * add more todo"s * improve enum34 dependency * py-future is a dependency as of v1.14 * Update var/spack/repos/builtin/packages/tensorflow/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/tensorflow/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/tensorflow/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/tensorflow/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * enable nccl, cuda by default * explain patches * add todo * remove unnecessary copt_flag * use join * join argument must be an iterable * split long line; use same opts for non-cuda build * without opt flags, configure hangs * introduce build phases; re-arrange * undo mistake * restore unset tmp_path * as of v1.14, nccl_install_path is parsed correctly, hence change ...prefix.lib to ...prefix * now, version 1.14 compiles successfully with cuda * add version 2.1.0 * specify bazel dependency for version 2.1.0-rc0 * account for deprecated bazel opts for v2.1.0-rc0 * disable mkldnn contraction kernel * Flake8 fixes * md5 -> sha256 * Fix TF and TF-estimator version deps * Don't just comment out patch * Add myself as a maintainer * Patch py-astor to support newer py-setuptools * Add more versions and bazel version constraints * Add a build phase * Add note about configure interactivity * dev-build -> build-env * Disable iOS build * Use correct optimization flags * Add variants for all possible features * nccl isn't always a dependency * Specify correct dependency versions for each release * Libs may not be in lib or lib64 * Add py-opt-einsum package * Add newer version of py-protobuf * Add newer version of py-wrapt * Fix Python 2.6 syntax error * Code review * Set more env vars for older versions * Add more env vars, fix bazel versions, add conflicts * Fix config options * Specify version that support --config args * Add py-future dependency for Python 2 * Fix cuda config flag and compute capabilities * Fix installation on macOS, add unit tests * Override cuda variant default to True on non-macOS * Rename tensorflow to py-tensorflow * Has to extend something * Fix os.symlink call * convert cuda_arc values to capabilities * restore nccl prefix path for v1.13.1 * Revert to v2 * Remove extraneous period * Add new version of jdk/openjdk * More stable cuda_arch formatting * Fix bazel unit tests * Fix symlinking * Fix unit tests * +gcp by default until build error figured out
2019-12-05cdash: fix reporting issue with python 3Scott Wittenburg1-1/+4
2019-12-05paraview: Adjust python version constraints (#13999)Chuck Atkins1-2/+2
py-matplotlib: No constraint necessary for py3 but py2 has an upper bound py-numpy: No constraint necessary for py3 but py2 has an upper bound
2019-12-05Added go 1.13.5 and 1.12.14 (#13997)Paul1-0/+2
2019-12-05py-pillow: allow older versions to build with python 3.4 (#14000)Chuck Atkins1-1/+2
2019-12-05eospac: fix url (#13998)Christoph Junghans1-8/+8
2019-12-05New package: swipl (#13978)Alexander Knieps1-0/+71
* New package: swipl * Removed boilerplate, added maintainer * Fixed python 2 incompatibility * Update var/spack/repos/builtin/packages/swipl/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * swipl: Added conflict with intel compiler
2019-12-04patching: do strict version range checking (#13989)Peter Scheibel5-2/+23
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions * add mixed version checks to version comparison tests
2019-12-04Merge tag 'v0.13.2' into developTodd Gamblin1-0/+40
v0.13.2 This release contains major performance improvements for Spack environments, as well as some bugfixes and minor changes. * allow missing modules if they are blacklisted (#13540) * speed up environment activation (#13557) * mirror path works for unknown versions (#13626) * environments: don't try to modify run-env if a spec is not installed (#13589) * use semicolons instead of newlines in module/python command (#13904) * verify.py: os.path.exists exception handling (#13656) * Document use of the maintainers field (#13479) * bugfix with config caching (#13755) * hwloc: added 'master' version pointing at the HEAD of the master branch (#13734) * config option to allow gpg warning suppression (#13744) * fix for relative symlinks when relocating binary packages (#13727) * allow binary relocation of strings in relative binaries (#13724)
2019-12-04update CHANGELOG.md for 0.13.2v0.13.2Todd Gamblin1-0/+40
2019-12-05Add py-matplotlib 3.1.2 (#13994)Adam J. Stewart1-1/+2
2019-12-04Merge branch 'releases/v0.13' into developTodd Gamblin0-0/+0
2019-12-04version bump: 0.13.2Todd Gamblin1-1/+1
2019-12-04version bump: 0.13.2Todd Gamblin1-1/+1
2019-12-04Bugfix: allow missing modules if they are blacklisted (#13540)Peter Scheibel4-30/+115
`spack module loads` and `spack module find` previously failed if any upstream modules were missing. This prevented it from being used with upstreams (or, really, any spack instance) that blacklisted modules. This PR makes module finding is now more lenient (especially for blacklisted modules). - `spack module find` now does not report an error if the spec is blacklisted - instead, it prints a single warning if any modules will be omitted from the loads file - It comments the missing modules out of the loads file so the user can see what's missing - Debug messages are also printed so users can check this with `spack -d...` - also added tests for new functionality
2019-12-04CUDA: Keep 10.1.243 As Preferred (#13983)Axel Huebl1-1/+2
Keep CUDA 10.1.243 as the preferred version until the issue of including implementation details of libcu++ is addressed.
2019-12-04Bugfix: allow missing modules if they are blacklisted (#13540)Peter Scheibel4-30/+115
`spack module loads` and `spack module find` previously failed if any upstream modules were missing. This prevented it from being used with upstreams (or, really, any spack instance) that blacklisted modules. This PR makes module finding is now more lenient (especially for blacklisted modules). - `spack module find` now does not report an error if the spec is blacklisted - instead, it prints a single warning if any modules will be omitted from the loads file - It comments the missing modules out of the loads file so the user can see what's missing - Debug messages are also printed so users can check this with `spack -d...` - also added tests for new functionality
2019-12-04Fix spack test when SPACK_ROOT isn't set (#13980)Adam J. Stewart1-3/+4
2019-12-04Update libensemble to v0.6.0 (#13987)Stephen Hudson1-1/+2
2019-12-04Add latest version of py-scikit-learn (#13979)Adam J. Stewart1-1/+2
2019-12-04Fixed x86-64 optimization flags for clang (#13913)Massimiliano Culpo3-53/+32
* Fixed x86-64 optimization flags for clang * Fixed expected results in unit tests Before the flags used where the one for llc, the underlying compiler from LLVM IR to machine assembly. It turns out that the semantic of `-march`, `-mtune` and `-mcpu` changes from clang front-end to llc. I found no definitive reference for the flags submitted in this PR, but I checked the assembly on a vectorizable function using Godbolt's web-site.
2019-12-04Add Elfutils 0.178 (#13976)Tim Haines1-1/+7
* Add elfutils-0.178 * Disable debuginfod server * Fix flake8
2019-12-04Use correct range check for the version (#13977)Tim Haines1-1/+1
Update to #13893
2019-12-03Release a new version v2.1.8.0 for SZ (#13974)Sheng Di1-1/+4
* Release a new version v2.1.8.0 for SZ * add maintainer * add parallel = False to avoid potential compile issue
2019-12-03mpich: update build requirements (#13966)Rob Latham1-0/+6
To build from git, MPICH will need newer autoconf, automake, and libtool than typically available on many systems.
2019-12-03argobots: consistently use 'master' (#13965)Rob Latham1-4/+4
Commit 71cd91e4 changed "latest from git" to 'master' from former 'develop'. Build dependencies still pointed to @develop, though
2019-12-03new package: Simmetrix SimModSuite (#8730)Cameron Smith1-0/+242
* package for Simmetrix SimModSuite * simmodsuite: passes flake8 * simmetrix: add version, set cmake prefix path A given install will either use the libs built on rhel7 or rhel6. For now, I'm sticking with the non-spack install convention of placing the libraries into sub-directories named according to their build process (os + compiler). * simmetrix: add older version * simmetrix: set build env paths easier to build pumi using CMAKE_PREFIX_PATH * simmetrix: address review comments * simmetrix: add new version and remove old one * simmetrix: flake8 fixes * simmodsuite: oslib var is in self * simmodsuite: update version and checksum * simodsuite: set LD_LIBRARY_PATH for cad kernels * update license * update setup_environment calls * increase indentation for flake8 * python3.8 flake8 fixes * use spack consistent naming Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * sha256 required, update versions and hashes
2019-12-03kaldi: Change process of version analysis when using Fujitsu compiler. (#13960)t-karatsu2-0/+14
2019-12-03fix_cantera_installation (#13962)asmaahassan901-2/+2
For a successful cantera installation, googletest has to be installed with gmock on, and sundials has to be of version less than 3.2
2019-12-03bump libfabric to 1.9.0 (#13964)Phil Carns1-0/+6
2019-12-03Update MrBayes to 3.2.7a and correct MPI variants (#13929)Yuanqi Wang1-13/+10
* Update MrBayes and correct MPI variant * Use tarballs and remove autotools dependencies * MrBayes: remove ISA variants
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