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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>
2020-09-15jemalloc: Use AutotoolsPackage and allow for arbitrary public API prefixes ↵Jason Lee1-14/+16
(#18680) Removed je variant
2020-09-15MatIO: Update repository and add new versions (#18683)Greg Sjaardema1-3/+6
MatIO development has switched to github from sourceforge. Updated the `git` and `url` variables and added the four new versions (1.5.14 -- 1.5.17) that have been released since the last update of this package.
2020-09-15AMD ROCmValidationSuite recipe for 3.5.0 and 3.7.0 (#18678)arjun-raj-kuppala2-0/+85
* AMD ROCmValidationSuite recipe for 3.5.0 and 3.7.0 * Updated the PR comments for rocmvalidationsuite recipe
2020-09-15namd: Added optimization auto-selection for skylake-X+ CPU for 2.14 and ↵Nikolay Simakov1-6/+68
2.15a1 (AVX512 tile) (#18671)
2020-09-15CLAW: update the package (#18673)Sergey Kosukhin2-9/+46
2020-09-15Qbox minor issues 18664 (#18665)Tom Payerle2-5/+121
* qbox: install to correct directory structure * qbox: Have qb executable put in bin rather than src subdir * qbox: Fix python script shebangs to use python from path * qbox: Add dependencies on gnuplot, python2 for utilities * qbox: fix flake8 issue * qbox: Add $prefix/util to PATH
2020-09-15nseg: add return 0; to void functions (#18481)ketsubouchi1-0/+10
2020-09-15fish: add dependencies, patch MacOS (#18526)Adam J. Stewart2-6/+52
2020-09-15py-cmocean: added new package at v2.0 (#18614)Adam J. Stewart1-0/+18
2020-09-15Add setuptools run-time dependency to various Python packages (#18616)Adam J. Stewart13-13/+13
2020-09-15py-jupyterlab-pygments: added new package at v0.1.1 (#18627)Adam J. Stewart1-0/+16
2020-09-15py-nest-asyncio: add new package at v1.4.0 (#18629)Adam J. Stewart1-0/+16
2020-09-15py-ipykernel: added v5.3.4, moved url to PyPI (#18630)Adam J. Stewart1-21/+25
2020-09-15py-ipython: added v7.18.1 (#18631)Adam J. Stewart1-24/+31
2020-09-15py-jupyter-client: added v6.1.7, moved url to PyPI (#18632)Adam J. Stewart1-14/+15
2020-09-15py-jupyter-core: updated the type of the setuptools dependency (#18633)Adam J. Stewart1-2/+1
2020-09-15py-jupyterlab-server: added v1.2.0 (#18634)Adam J. Stewart1-3/+4
2020-09-15py-argon2-cffi: added new package at v20.1.0 (#18626)Adam J. Stewart1-0/+21
2020-09-15py-jupyterlab: added v2.2.7 (#18635)Adam J. Stewart1-9/+6
2020-09-15py-nbformat: add v5.0.7, moved url to PyPI (#18637)Adam J. Stewart1-9/+8
2020-09-15py-terminado: added v0.8.3 (#18639)Adam J. Stewart1-4/+3
2020-09-15py-traitlets: added v5.0.4, moved url to PyPI (#18640)Adam J. Stewart1-12/+15
2020-09-14Added Missing Tag to Cradl Spackage (#18669)Robert Pavel1-0/+2
Added missing proxy apps tag to cradl spackage
2020-09-14CRADL Machine Learning Proxy Spackage (#18668)Robert Pavel3-0/+72
* Initial CRADL Spackage Work Currently resolving ```--single-version-externally-managed``` error * Fixed GPUtil Issues Thanks to Vinay Ramakrishnaiah for overwriting install * Finished CRADL Install Function Finished CRADL install function which is basically copying the scripts to the install directory. Also resolved flake8 issues for PR purposes
2020-09-14SIRIUS: Update dependencies (#18622)Simon Frasch1-1/+12
* sirius: Fixed dependency spfft when build with +rocm * sirius: Added new dependency spla for develop build * sirius: Added maintainer
2020-09-14Make sure each develop pipeline tests associated commitScott Wittenburg1-1/+1
2020-09-14Do not assume we sit in the directory where the env file lives.Scott Wittenburg1-3/+8
2020-09-14Remove :<name> interpolation, add SPACK_VERSION variablesScott Wittenburg3-128/+94
Also fix issues with documentation to reflect changes
2020-09-14Document pipeline keys which can be global but overriddenScott Wittenburg1-6/+108
Update pipelines documentation to describe how 'tags', 'variables', 'image', 'before_script', 'script', and 'after_script' can be supplied at the top level, to be used by any of the runner mappings, and also overridden by any of the runner mappings. Also show an example of capturing the custom spack SHA at pipeline generation time, so all jobs are sure to run with the same version of spack, as a means to illustrate the $env:VARIABLE_NAME syntax.
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