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2020-09-21util-linux: fix bash completion install errors. (#18696)Robert Blake2-2/+17
* Disable bash completion by default. * flake8 * Adding explicit dependence on libuuid * Adding explicit dependence on cryptsetup This way we don't pick up host crypto packages by mistake. * Fixing the completion directory. * Update var/spack/repos/builtin/packages/util-linux/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * flake8 * Removing libuuid linkage according to @michaelkuhn on #18696 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-09-21nut: fix install (#18848)Christoph Junghans1-2/+2
* nut: fix install * flake8
2020-09-21fix spack-build usages (#18846)Christoph Junghans3-3/+3
2020-09-21typo (#18845)Greg Becker1-1/+1
2020-09-21add groff and ghostscript (#18803)Joseph Wang1-0/+3
Without these packages, graphviz will set groff/ghostscript to false which will cause the build to fail.
2020-09-20libksba: add new version (#18798)Adam J. Stewart1-0/+3
2020-09-19readline: simplify linking to ncurses (#18801)Adam J. Stewart1-9/+1
2020-09-19SciPy: add patch to fix XCode 12 build (#18800)Adam J. Stewart1-0/+4
2020-09-19ncurses: fix libs method (#18799)Adam J. Stewart1-5/+5
2020-09-19graphviz: fix build with Apple Clang 12.0.0 (#18797)Adam J. Stewart2-0/+18
2020-09-19fish: relax ncurses dependency constraints (#18796)Adam J. Stewart1-1/+4
2020-09-19Ensure variant defaults are parsable from CLI. (#18661)Massimiliano Culpo3-21/+33
- Add a unit test to check if there are unparsable defaults - Fix 'rust' and 'nsimd' variants
2020-09-18Hdf5 1.10.7 (#18712)Larry Knox2-4/+6
* Update hdf5/package.py for HDF5 1.10.7 release and obsolete home url. Add maintainer to hdf/package.py. * remove stray space. * Remove unnecessary /diplay/support from homepage urls.
2020-09-18bedtools2: Add missing python build dependency (#18744) (#18746)Tom Payerle1-0/+1
Makefile invokes python to build some scripts See #18744
2020-09-18popt: Add missing libiconv dependency (#18731)Michael Kuhn1-0/+2
Without this dependency, the build fails due to undefined references.
2020-09-18py-notebook: add new version (#18638)Adam J. Stewart1-28/+16
2020-09-18do out of source builds in hashed directories (#18574)Greg Becker1-1/+2
2020-09-18trigger ascent e4s pipeline on merge to spack develop (#18655)Shahzeb Siddiqui1-0/+6
* trigger ascent e4s pipeline on merge to spack develop * change pipeline name ecpcitest/e4s is the pipeline that will be triggered for merge on develop its the E4S use-case.
2020-09-18Add mumax-3.10 release version (#18740)Glenn Johnson1-5/+27
This PR adds the current release version of mumax and tweaks the install of the previous beta version. - Set the url parameter to reflect the release version over the beta version. Hopefully, this will be consistent going forward. - Set an explicit url for the previous beta version. - Accept values for `cuda_arch`. The previous version had its own list but the release version does not. - Replace the built in cuda compute capabilities list with the one provided by Spack for the 3.10beta version.
2020-09-18swig: add version 4.0.2 and 4.0.2-fortran (#18741)Seth R. Johnson1-3/+9
2020-09-18env view failures: print underlying error message (#18713)Greg Becker2-1/+13
2020-09-18[py-pyarrow] added variant cuda (#18716)Jen Herting1-1/+2
* [py-pyarrow] added variant cuda * [py-pyarrow] simplifying variant dependencies
2020-09-18util-linux: fix build error (#18647)darmac1-0/+3
* util-linux: fix build error * refine install stage
2020-09-18Add new package: shiro (#18541)darmac1-0/+23
* Add new package: shiro * refine description and dependencies
2020-09-18ocaml: support 4.11 (#18705)ketsubouchi1-2/+10
2020-09-18iwyu: Require llvm+all_targets on non-x86_64 systems (#18710)Toyohisa Kameyama1-0/+10
2020-09-18py-recommonmark: fix URL and docutils version (#18714)Axel Huebl1-2/+2
2020-09-18py-breathe: added v4.21.0 (#18722)Axel Huebl1-0/+1
2020-09-17libpfm4: add version 4.11.0 (#18720)Mark W. Krentel1-0/+2
Add version 4.11.0 for libpfm4. Add myself as maintainer.
2020-09-17[arrow] added cuda variant (#18715)Jen Herting1-1/+3
2020-09-17Add bart-0.6.00 (#18717)Glenn Johnson3-1/+110
This PR adds version 0.6.00 of bart.
2020-09-17py-nbconvert: add new version (#18636)Adam J. Stewart1-27/+25
2020-09-17py-nbclient: add new package (#18628)Adam J. Stewart1-0/+23
2020-09-17py-matplotlib: add v3.2.2 (#18681)Adam J. Stewart1-2/+3
2020-09-17bowtie : Fix for aarch64 (#18709)t-nojiri2-5/+5
2020-09-17gpu-burn: allow to build with non-gcc compilers (#18707)Glenn Johnson1-2/+2
This PR modifies the patch to use $(CXX) rather than g++ to allow the spack compiler to be used.
2020-09-17Update libbeagle (#18703)Glenn Johnson1-4/+12
This PR fixes a couple of things with the libbeagle package. - libbeagle can only be built for one GPU type. Add a test for that. - version 2 had the arch statement in libhmsbeagle/GPU/kernels/Makefile.am but version 3 has it in configure.ac. Put the variant specified value in configure.ac for consistency.
2020-09-17Rocm 3.7 miopen, miopengemm, rocalution and rocm-opencl (#18690)Ganesh Kumar5-17/+32
* ROCm 3.5 miopen recipe * fixing flake8 issues * cmake variant fix * min support fix * variant possible values * rocm3.7 change for miopen, rocalution and rocm-opencl * review comments
2020-09-17aws-parallelcluster: add 2.9.1 and 2.9.0 releases (#18676)Enrico Usai1-6/+24
Checked all the third party dependencies for all the versions.
2020-09-16Hipify clang with AMD rocm 3.7.0 update (#18672)arjun-raj-kuppala1-2/+3
* Hipify clang with rocm 3.7.0 update * Update var/spack/repos/builtin/packages/hipify-clang/package.py Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2020-09-16seacas: Force use of non-mpi-enabled hdf5 (#18702)Greg Sjaardema1-0/+1
Due to recent changes in the `netcdf-c` package, it is now necessary to explicitly request a non-mpi-enabled hdf5 build if building a non-mpi-enabled seacas.
2020-09-16lustre: Adding external support. Closing #18698 (#18700)Robert Blake1-0/+9
2020-09-16spla: Add version 1.1.1 and fix cmake flag when build with +cuda (#18699)Simon Frasch1-4/+2
2020-09-16bump CGAL version (#18693)Sajid Ali1-13/+44
* bump CGAL version * Address reviewer comments * flake8 fix * Address reviewer comments * Address reviewer comments
2020-09-16[dd4hep]: add variant lcio (#18691)Andre Sailer1-0/+3
2020-09-16libvdwxc: unbreak concretization, request fftw-api (#18688)Tiziano Müller2-26/+6
* libvdwxc: unbreak concretization, request fftw-api mixing both fftw and fftw-api in a dependency tree can trigger the following: ``` $ spack spec cp2k@master +sirius ==> [2020-09-16-12:36:06.552981] sirius applying constraint gsl ==> [2020-09-16-12:36:06.554270] sirius applying constraint openblas@0.3.10%gcc@7.5.0~consistent_fpcsr~ilp64+pic+shared threads=none arch=linux-opensuse_leap15-sandybridge Traceback (most recent call last): File "./bin/spack", line 64, in <module> sys.exit(spack.main.main()) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/main.py", line 762, in main return _invoke_command(command, parser, args, unknown) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/main.py", line 490, in _invoke_command return_val = command(parser, args) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/cmd/spec.py", line 103, in spec spec.concretize() File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2228, in concretize user_spec_deps=user_spec_deps), File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2716, in normalize visited, all_spec_deps, provider_index, tests) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2654, in _normalize_helper dep, visited, spec_deps, provider_index, tests) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2613, in _merge_dependency visited, spec_deps, provider_index, tests) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2654, in _normalize_helper dep, visited, spec_deps, provider_index, tests) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2554, in _merge_dependency provider = self._find_provider(dep, provider_index) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2489, in _find_provider providers = provider_index.providers_for(vdep) File "/data/tiziano/debug-spack/spack2/lib/spack/spack/provider_index.py", line 80, in providers_for return sorted(s.copy() for s in result) File "/data/tiziano/debug-spack/spack2/lib/spack/llnl/util/lang.py", line 249, in <lambda> lambda s, o: o is not None and s._cmp_key() < o._cmp_key()) TypeError: '<' not supported between instances of 'str' and 'NoneType' ``` while at the same point disallowing MKL as a fftw provider. Solving both issues by depending on `fftw-api@3` instead and adding a conflict on `^fftw~mpi` when using `+mpi` (thanks to alalazo). * cp2k: use conflicts instead of runtime checks for fftw/openblas variants
2020-09-16fraggenescan: Modify build_targets for aarch64 (#18687)t-nojiri1-1/+1
2020-09-16environment-modules: add version 4.6.0 (#18686)Xavier Delaruelle1-1/+2
2020-09-16Added spackage for cosmoflow-benchmark proxy app (#18685)Robert Pavel1-0/+38
* Initial Draft of Cosmoflow Spackage Need to add in logic to streamline cpu/gpu builds * Added ~cuda logic to cosmoflow spackage Added logic to support a ~cuda build for cosmoflow * Requested Changes to Cosmoflow Spackage Made requested changes to cosmoflow spackage
2020-09-16Likwid versions >= 5.0.0 depend on Lua 5.2. (#18675)Severin Strobl1-1/+2
* Likwid versions >= 5.0.0 depend on Lua 5.2. According to https://github.com/RRZE-HPC/likwid/issues/324 recent versions of Likwid require Lua 5.2. * Update var/spack/repos/builtin/packages/likwid/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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