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2019-10-29fix openmpi wrappers with libfabric (#13439)Gregory Lee1-10/+16
* fix openmpi wrappers with libfabric * flake8 fix * flake8 fix * openmpi fix deprecated API * openmpi fix deprecated API
2019-10-29mumps: Fix compile commands. (#13497)t-karatsu1-3/+3
2019-10-29r-bio3d: new package at 2.3-4 (#13496)Justin S1-0/+19
2019-10-29r-fields: new package at 9.9 (#13495)Justin S1-0/+20
2019-10-29r-spam: new package at 2.3-0.2 (#13494)Justin S1-0/+19
2019-10-29r-dotcall64: new package at 1.0-0 (#13493)Justin S1-0/+19
* r-dotcall64: new package at 1.0-0 * r-dotcall64: break up long line
2019-10-29r-dada2: new package at 1.14 (#13492)Justin S1-0/+29
* 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>
2019-10-29mumps: Add '-DMAIN_COMP' when using Fujitsu compiler. (#13480)t-karatsu1-4/+6
2019-10-29new package: py-scs (#13477)Sinan1-0/+43
* 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>
2019-10-29CP2K: drop json-fortran dependency and add support for the Nvidia V100 (#13468)Tiziano Müller1-7/+2
* cp2k: drop json-fortran dep since that's now handled in SIRIUS internally * cp2k: gained support for Nvidias V100
2019-10-28Add SpFFT: sparse 3D FFT library (#13458)Simon Pintarelli1-0/+44
* Add SpFFT: sparse 3D FFT library SpFFT is required as a dependency for SIRIUS * cleanup * add missing dependency
2019-10-28new package: py-cvxpy (#13478)Sinan1-0/+28
* new package: py-cvxpy * improve dependency specs
2019-10-28new package: py-ecos (#13476)Sinan1-0/+21
* new package: py-ecos * flake8
2019-10-28new package: py-osqp (#13475)Sinan1-0/+22
2019-10-28Update URL parsing regexes and tests (#13411)Adam J. Stewart236-740/+581
* 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
2019-10-28Update the module files for cbtf-krell and openspeedshop (#13400)Jim Galarowicz5-86/+97
* 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.
2019-10-28new Package/scs (#13454)Sinan2-0/+55
* 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
2019-10-28update conduit for 0.5.0 release (#13455)Cyrus Harrison2-25/+92
* 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
2019-10-28Fix gcc recipe for RHEL7. (#13460)Kelly (KT) Thompson1-5/+5
* 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'.
2019-10-28Paraview package: add version 5.7.0 and update environment setup (#13255)Jon Rood1-16/+17
Replace setup_environment/setup_dependent_environment with setup__dependent_build_environment and setup_run_environment according to 9ddc98e
2019-10-28Packages: Add cuDNN versions; update LBANN dependencies (#13412)Brian Van Essen2-1/+7
* Add cuDNN version 7.6.3-10.1 (for x86_64 and ppc64le) * Add py-pytest and py-protobuf depenencies to LBANN
2019-10-28Go package: add versions (including 1.13.3) and update environment setup ↵Paul1-9/+18
(#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
2019-10-28Fix PyTorch build with Intel MKL (#13464)Adam J. Stewart1-0/+5
2019-10-28Update emacs to version 26.3 (#13469)Glenn Johnson1-0/+1
2019-10-28scotch: added version 6.0.8 (#13467)Mark Olesen1-0/+1
2019-10-27Add dependency and patch for perl-dbfile (#13261)wenlibin021-0/+5
* Add dependency and patch perl-dbfile There are two problems for the building of `perl-dbfile`: 1) this package depends on the package `berkeley-db` 2) fix the building using a patch, which locates the position of `berkeley-db` and modify the configuration file for the building * Update and reformat the script package.py * Simplify the patch * Update package.py * Update package.py
2019-10-27QE Update Oct 2019 (#13406)Nichols A. Romero1-31/+18
* This filter_file was difficult to maintain and is no longer needed. * Clarify lack of support for HDF5 in serial QE. * Update QE and HDF5 conflicts based on user feedback.
2019-10-27Add Lizard (LZ5) (#13456)Axel Huebl3-8/+109
* Add Lizard (LZ5) Add a new package for Lizard, formerly LZ5, a very fast compressor and decompressor library. * c-blosc2: use external lizard Use an external Lizard (LZ5) dependency and add missing "when="s for other compressor dependents.
2019-10-27Libbeagle fixes (#13463)Glenn Johnson2-8/+9
* Fixes for libbeagle This PR fixes a couple of issues with the libbeagle package. - Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix) - Disable the default of compiling with -march=native as Spack now inserts architecture specific flags - Set BEAST_LIB in the beast1 package not in libbeagle. * Use new setup_run_environment method
2019-10-27new package: py-pandocfilters (#13418)Andreas Baumbach1-0/+15
dependency of py-nbconvert
2019-10-27LLVM code-signing on OSX: link to the offical documentation (#13428)Andreas Baumbach1-7/+8
* LLVM code-signing on OSX: link to the offical documentation * LLVM: update setup_environment method
2019-10-27mariadb: Fix openssl dependencies (#13443)Michael Kuhn1-0/+2
2019-10-27mariadb-c-client: Add 3.1.4 (#13447)Michael Kuhn1-0/+1
2019-10-27new package: ecos (#13453)Sinan1-0/+30
2019-10-27Update PyTorch variable name (#13461)Adam J. Stewart1-1/+1
2019-10-26MPICH: Fix Slurm Find Issue (#13263)Axel Huebl1-0/+9
Set include and library path to slurm explicitly.
2019-10-26Add latest version of py-fiscalyear (#13451)Adam J. Stewart1-2/+4
2019-10-25Add py-twine package (#13449)Adam J. Stewart1-0/+22
2019-10-25Add py-pkginfo package (#13448)Adam J. Stewart1-0/+19
2019-10-25Add latest version of py-tqdm (#13446)Adam J. Stewart1-2/+7
2019-10-25Add latest version of py-requests-toolbelt (#13445)Adam J. Stewart1-2/+3
2019-10-25Add latest version of py-readme-renderer (#13444)Adam J. Stewart1-3/+5
2019-10-25New package: gpu-burn (#13108)Glenn Johnson2-0/+73
2019-10-25py-nbformat package: add version 4.4.0 (#13421)Andreas Baumbach1-0/+1
2019-10-25New package: py-defusedxml (#13419)Andreas Baumbach1-0/+17
2019-10-25New package: OSQP (#13432)Sinan1-0/+22
2019-10-25LIBXSMM package: add version 1.14 (#13436)Hans Pabst1-1/+2
2019-10-25lmdb package: add version 0.9.24 (#13437)Michael Kuhn1-0/+1
2019-10-25sqlite package: add version 3.30.1 (#13438)Michael Kuhn1-0/+1
2019-10-25py-gensim: new package at 3.8.0 (#13136)Justin S1-0/+28
* py-gensim: new package at 3.8.0 * py-gensim: add 3.8.1
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