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2019-11-14Config option to allow gpg warning suppression (#13743)Greg Becker4-3/+17
Add a configuration option to suppress gpg warnings during binary package verification. This only suppresses warnings: a gpg failure will still fail the install. This allows users who have already explicitly trusted the gpg key they are using to avoid seeing repeated warnings that it is self-signed.
2019-11-14xsdk@0.5.0 (#13682)Satish Balay3-25/+86
Update: hypre@2.18.2 mfem@4.0.1-xsdk superlu-dist@6.1.1 trilinos@12.18.1 - dtk-3.1 petsc@3.12.1 dealii@9.1.1 pflotran@xsdk-0.5.0 alquimia@xsdk-0.5.0 sundials@5.0.0 plasma@19.8.1 magma@2.5.1 amrex@19.08 slepc@3.12.0 omega-h@9.29.0 strumpack@3.3.0 pumi@2.2.1 tasmanian@7.0 phist@1.8.0 New: ginkgo@1.1.0 py-libensemble@0.5.2 precice@1.6.1 butterflypack@1.1.0 Add variants: ginkgo libensemble precice butterflypack strumpack trilinos tasmanian: use ~openmp only on OSX precice: disable on OSX enable sundials+superlu-dist sundials+superlu-dist requires OpenMP 4.5+ (so enable only for gcc@6.1+) enable mfem+sundials enable sundials+petsc+superlu_dist remove hypre~internal-superlu petsc: build with +batch on cray precice: use ~petsc on cray libensemble: add as runtime dependency for PYTHONPATH
2019-11-14z3: bugfix about python dependency and fallthrough annotation. (#13713)t-karatsu3-2/+30
* z3: * Fixed python dependency to always be required. * bugfix about fallthrough annotation. * z3: Add patch for before ver.4.4.1. * Update var/spack/repos/builtin/packages/z3/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-14Mark conflicts between newer packages and Intel 14 compilers (#13729)Seth R. Johnson4-0/+11
* Mark compiler/version conflict for CMake Intel 14 lacks some C++11 features needed to compile new versions of cmake. ``` /tmp/s3j/spack-stage/spack-stage-cmake-3.15.5-46lgp4ybhopy2p4rr66rxnew5iaddvmg/spack-src/Source/ cm_static_string_view.hxx(28): error: expected an operator friend static_string_view operator"" _s(const char* data, size_t ^ ``` * Mark compiler/version conflict for icu4c With Intel 14.0.4 on Linux for icu4c 60.1 and higher: ``` locid.cpp(1156): error #1140: a using-declaration may not name a constructor or destructor using KeywordEnumeration::KeywordEnumeration; ``` * Mark compiler/version conflict for nasm Error installing `nasm@2.14.02%intel@14.0.4`: ``` In file included from nasmlib/crc64.c(35): ./include/nasmlib.h(116): error: expected a ";" fatal_func nasm_assert_failed(const char *, int, const char *); ``` * Mark compiler/version conflict for bison Installing `bison@3.4.2%intel@14.0.4`: ``` In file included from /tmp/s3j/spack-stage/spack-stage-bison-3.4.2- uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/quotearg.c(33): /tmp/s3j/spack-stage/spack-stage-bison-3.4.2-uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/ xalloc.h(51): warning #303: explicit type is missing ("int" assumed) extern _Noreturn void xalloc_die (void); ``` * Mark compiler/version conflict for icu4c With `icu4c@60.1%intel@16.0.4` and `icu4c@64.1%intel@16.0.4`: ``` In file included from ucurr.cpp(26): static_unicode_sets.h(130): error #913: invalid multibyte character sequence {POUND_SIGN, u'£'}, ^ ``` * Change conflict comments into messages
2019-11-14py-matplotlib only needs backports when ^python@:2 (#13712)George Hartzell3-3/+3
* py-matplotlib only needs backports when ^python@:2 This implements @scheibelp's suggestion in #13711. py-matplotlib should only depends_on py-backports-functools-lru-cache when it's using a python that actually *needs* it. See #13711 for details. * Don't depend_ons py-enum34 unless python@:3.3 * Tighten up enum34 dependency @adamjstewart cracked open the setup.py files and suggested a tighter dependency for py-enum34. 1.4 and 1.5 only require it for pythons before 3.4, 1.3 requires it unconditionally. So...., we'll do the same. * Remove conflict on python 3.4 from enum34 at @adamjstewart's request see PR notes
2019-11-14add boost dependency to stat package (#13735)Gregory Lee1-0/+2
2019-11-14update to v0.6.4 (#13737)xfzhao1-0/+3
2019-11-14Update DMTCP package to v2.6.0 (#13739)Emir İşman1-1/+2
2019-11-14Removed github repository and develop version from dataspaces package as it ↵Nicholas Sly1-2/+0
is no longer present/accessible. (#13740)
2019-11-14update vsearch (#13736)xfzhao1-0/+2
2019-11-14hwloc: added 'master' version pointing at the HEAD of the master branch (#13731)Massimiliano Culpo1-4/+6
2019-11-14new package Qscintilla (with python bindings via py-pyqt ) (#12793)Sinan3-3/+188
* qscintilla_with_python_bindings_disabled * pyqt5 with variant +qsci to compile qscintilla python bindings * fix a dyn linking issue for Qsci python module * fix a bug * fix bug: use sip provided by py-pyqt5 * fix typo * tidy up, make designer * tidy up * fix designer build issue, set env for designer plugin * tidy up * tidy up * minor improvements * improve style * build Qscintilla python bindings here * make qsci config option variant dependent * get rid of commented out code * improvements: add resource for qscintilla, improve config_args * flake8: spaces, blank lines etc * flake8: fix long lines * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * dont install source tree under prefix * remove duplicate line * use os.path.join instead of + * separate build and run environment setups * flake8 * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * fix rsrc path * use python_include_dir * use "with working_dir" * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * flake8
2019-11-14package/geopm: Added versions 1.0.0 and 1.1.0 (#13721)Matthias Maiterth1-17/+28
* package/geopm: Added versions 1.0.0 and 1.1.0 Added changes for 1.1.0 and 1.0.0 in this patch. Patch for 1.0.0 was previously not merged. variant for hwloc removed since that is not a dependency since 0.5.1 and variant('hwloc', when=:0.5.1 is not supported afaik. made depends_on versions more explicit. * package/geopm: removed 1.0.0 release candidates 1 and 2.
2019-11-14Adding final bug-releases for the gromacs-2016 and -2018 and Plumed (#13715)Hector Martinez-Seara2-3/+12
* Adding final bug-releases for the gromacs-2016 and -2018 * Added newer versions of plumed and libmatheval not a dependency >v2.5 * plumed package: chamge name git branch to master
2019-11-14Fix libbsd on Intel compilers (#13720)Seth R. Johnson2-0/+13
Libbsd assumes GCC-defined compiler macros: ``` In file included from nlist.c(44): local-elf.h(238): catastrophic error: #error directive: Unknown ELF machine type #error Unknown ELF machine type ^ ``` The `__amd64__` and `__x86_64__` macros should be equivalent, but the latter is defined by intel.
2019-11-13symlink relativization: determine target relative to the link directory (#13710)Peter Scheibel1-3/+3
when making a package relative, relocate links relative to link directory rather than the full link path (which includes the file name) because `os.path.relpath` expects a directory.
2019-11-13Added "file" package and added missing depenency to VIM (#13705)sknigh6-0/+63
* Added "file" package and added missing depenency to Vim * added which and grep * Added gzip * added missing dependency to gmake
2019-11-13Add Caliper v2.2.0 and v2.1.1 (#13723)David Böhme1-5/+12
* Add Caliper v2.2.0 and v2.1.1 * Add conflict for adiak when for versions <2.2 * Trim trailing whitespace
2019-11-13Allow binary relocation of strings in relative binaries (#13725)Greg Becker2-15/+25
Binaries with relative RPATHS currently do not relocate strings hard-coded in binaries This PR extends the best-effort relocation of strings hard-coded in binaries to those whose RPATHs have been relativized.
2019-11-13Papi components (#13706)G-Ragghianti1-2/+23
* Added support for papi components. * Restored sha256 hashes to package files.
2019-11-13rnaz: new package at 2.1 (#13707)Justin S1-0/+15
2019-11-13Fix mgis package dependency on boost/numpy (#13717)thelfer1-1/+1
2019-11-13Docs update for deprecated `spack sha256` (#13701)William F Godoy1-2/+2
* Docs update for deprecated `spack sha256` * Added macOS shasum * Update lib/spack/docs/packaging_guide.rst Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-13new package: sfcgal (#12624)Sinan1-0/+32
* new package: sfcgal * improve meta information * add variant and optional dependencies * add cmake options for building with viewer * improve dependency type * improve viewer variant * improve viewer variant * specify dependency versions * add ref * remove depricated variant
2019-11-13Update MVAPICH2 package for 2.3.2 release (#13236)Hari Subramoni1-4/+9
* Update MVAPICH2 package for 2.3.2 release Update default build from psm to mrail * Update different provides for older versions based on feedback from Todd Gamblin * Simplify rule so one rule covers 2.1 and 2.2 * Add support for disabling rpath based on feedback from Dr. Shende * Add colon based on comment * Address review comment by Adam Stewart * Add declaration of the wrapperpath variant. - Thanks to Massimiliano Culpo for the comment
2019-11-13superlu_dist: fix build with xl compilers (#13702)Satish Balay2-0/+33
* superlu_dist: fix build with xl compilers * fix link error ../SRC/libsuperlu_dist.so.6.1.1: undefined reference to `ztrtri_' * Fixed the ordering of the spec on the xl-611 patch. * fix flake8 error
2019-11-12root: relax libxml2 requirements when ~python. (#13657)Chris Green1-21/+24
* Relax libxml2 requirements when ~python. Per https://github.com/spack/spack/issues/13637#issuecomment-552026561 * Satisfy package_sanity.py::test_prs_update_old_api.
2019-11-12strumpack: revert default to ~shared [i.e behavior before this variant was ↵Satish Balay1-1/+1
added] as +shared fails on multiple builds (#13703)
2019-11-12docs: use nicer looking code blocks in docs (#13708)Todd Gamblin1-1/+19
- [x] Use higher contrast terminal output font - [x] Use higher contrast code block background color than default - [x] Use a noticeable prompt character See also https://github.com/spack/spack-tutorial/pull/10.
2019-11-12add new version for py-ranger-fm (formerly py-ranger) (#13681)Simon Pintarelli2-18/+17
- download from pypi, drop 1.7.2 - drop 1.7.2, it is not available from pypi
2019-11-12Add missing dependencies to flex. (#13692)sknigh1-0/+2
2019-11-12 Fixed url. url="https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") ↵h-denpo1-1/+1
(#13693)
2019-11-12damselfly: Add mpi dependency. (#13694)t-karatsu1-0/+1
2019-11-12Fixing Fortran MPI compiler reference in mpt package (#13699)Adrian Jackson1-3/+3
2019-11-12Update nlopt package to add Python bindings to PYTHONPATH (#13688)Stephen Hudson1-4/+5
* Update nlopt package to add Python bindings to PYTHONPATH * Use extends for nlopt/python fix * nlopt - change develop to master and add python dep qualifiers
2019-11-12athena, mvapich2, spectrum-mpi: use new API to setup environment (#13677)Massimiliano Culpo3-66/+65
* athena: updated api call to setup build environment * mvapich2: updated api call to setup build and run environment * spectrum-mpi: updated api call to setup build and run environment
2019-11-12precice: enable petsc by default (#13696)Frédéric Simonis1-1/+1
2019-11-12trilinos: add version 12.18.1 with dtk-3.1 (#13690)Satish Balay1-1/+8
2019-11-12sundial: add patch for build failure on cori/theta (#13665)Satish Balay2-0/+70
2019-11-11verify.py: os.path.exists exception handling (#13656)Daryl W. Grunau1-14/+16
2019-11-11SIRIUS: add new version, add magma support (#13680)Simon Pintarelli1-7/+30
- depends on spfft starting from 6.4.0 - add magma variant - avoid setting cuda_arch to none - add python dependencies - use release as default build type
2019-11-11added lcov package (#13687)sknigh1-0/+21
2019-11-11Add HPE MPT package (#13616)Adrian Jackson1-0/+77
* Adding in HMPT package for HPE MPI libraries * Updating copyright dates * Renaming HPE MPI package * Fixing error in package file * Tidying up defintions and linting * liniting * Adding in library setup so packages that want to manually add mpi libraries can do so (i.e. npb) * Linting * Linting * Investigating old API errors * Investigating api errors * Investigating api errors * Investigating api errors * Investigating api errors * Investigating api errors: adding back in functions to see when the build fails * Investigating api errors: adding back in functions to see when the build fails * Investigating api errors: adding back in functions to see when the build fails * Investigating api errors: adding back in functions to see when the build fails * Investigating api errors: adding back in functions to see when the build fails * Linting * Linting * Fixing * Fixing
2019-11-11cuDNN: add new versions (#13668)Adam J. Stewart1-33/+171
* cuDNN: add new versions * cuDNN 9.0 can build against CUDA 9.1 * Undo version format change
2019-11-11Add new version of Intel MKL-DNN (#13669)Adam J. Stewart2-10/+34
* Add new version of Intel MKL-DNN * Get OpenMP build working * lomp is also needed for linking * http -> https * Add myself as maintainer
2019-11-11py-scikit-learn: update OpenMP flag (#13683)Adam J. Stewart1-1/+1
2019-11-11new CDO release 1.9.8 (#13674)Brian Spilner1-0/+1
2019-11-11Update ButterflyPACK and STRUMPACK (#13661)Pieter Ghysels2-5/+20
* Add new strumpack version (3.2.0), with new dependency on ButterflyPACK. * add ButterflyPACK version 1.1.0 * Add strumpack version 3.3.0, add dependency on ButterflyPACK 1.1.0 * Sort ButterflyPACk versions from newest to oldest * Add a shared variant for STRUMPACK * Also allow possible newer versions of ButterflyPACK
2019-11-11pmdk: fix x86_64 arch check (#13676)Phil Carns1-2/+1
2019-11-11environments: don't try to modify run-env if a spec is not installed (#13589)Adam J. Stewart1-2/+2
Fixes #13529 Fixes #13509
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