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2020-08-08package/cmake: add versions 1.18.0 and 1.18.1 (#17945)Sinan0-0/+0
* package/cmake: add versions 1.18.0 and 1.18.1 * fix shasums Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-08-07Feature/raja chai umpire update (#17665)Adrien Bernede4-8/+102
* Changing raja, chai, and umpire packages so all will compile with each other. * Need a CUDA version of CHAI when compiling with raja+cuda+chai * Updating checks for commit. * Adding comments explaining why chai+umpire tests were disabled * Reactivating tests for CHAI and Umpire * reordering versions * Unified handling of Cuda Arch * Adding latest versions * Unused/Untested: removed * Aesthetic and test mode in Chai * Unified handling of Cuda Arch * Using 'ON' consistently, instead of 'On' * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fix, suggestion and patch: Chai depends on RAJA, not the other way. Apply suggested master-main version mapping. Add Umpire version 3.0.0 and patch. Co-authored-by: Robert Blake <blake14@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-07conduit: dont use cmake >= 3.18 because of FindHDF5 bug (#17937)eugeneswalker1-1/+1
2020-08-07New package - REDItools (#17703)Glenn Johnson6-0/+1042
* New package - REDItools This PR adds the REDItools package, along with a new package dependency, py-fisher. This contains a patch generated from the python 2to3 script as well as some other fixes. I am not sure if the project is ready to support python-3 yet but I submitted the other patches upstream. * Update var/spack/repos/builtin/packages/reditools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-07py-inference-schema: add new package (#17912)Adam J. Stewart1-0/+33
2020-08-07Fujitsu compiler: Accept alphabet as version. (#17890)Tomoki, Karatsu2-7/+7
* Fujitsu compiler: Accept alphabet as version. * Fujitsu copiler: Updated test pattern.
2020-08-07gromacs: new version 2020.3; variant nosuffix and mkl support (#17908)g-mathias1-6/+38
* new version 2020.3; new variants nosuffix and fft; version selections for plumed * fixed too long lines * fixed whitespaces * revised fft interface according to @haampie 's suggestions Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-08-06activeharmony: add version 4.6.0 (#17867)darmac2-4/+52
2020-08-06py-rasterio: add v1.1.5Adam J. Stewart1-6/+9
2020-08-06New package: ProfugusMC (#17914)Robert Pavel1-0/+24
Added spackage for profugusMC
2020-08-06hpctoolkit: fix commit hash for version 2020.08.03 (#17920)Mark W. Krentel1-1/+1
2020-08-06Wonton (package): Fix sha 256 sum for version (#17916)Rao Garimella1-1/+1
2020-08-06stacks (package): add version 2.53 (#17915)Justin S1-0/+1
2020-08-06isescan: new package at 1.7.2.1 (#16589)Justin S1-0/+71
* isescan: new package at 1.7.2.1 * isescan: update external program paths * isescan: use spack compiler
2020-08-06New Package Wonton (#17882)Rao Garimella1-0/+127
* new package Wonton * remove the flecsi variant because flecsi-sp does not have a spackage * fix url, clean up whitespaces * formatting * put in explicit else clauses for variants in CMake section because CMake's behavior is system-dependent Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2020-08-06Bazel: relax Java dependency (#17734)Adam J. Stewart1-11/+1
* Bazel: relax Java dependency * Flake8 fix
2020-08-06New package: HDFView (#17707)Julius-Plehn3-0/+64
* HDFView * adds support for version 3.1.1
2020-08-05bugfix: fix spack -V with releases/latest and shallow clones (#17884)Todd Gamblin1-2/+2
`spack -V` stopped working when we added the `releases/latest` tag to track the most recent release. It started just reporting the version, even on a `develop` checkout. We need to tell it to *only* search for tags that start with `v`, so that it will ignore `releases/latest`. `spack -V` also would print out unwanted git eror output on a shallow clone. - [x] add `--match 'v*'` to `git describe` arguments - [x] route error output to `os.devnull`
2020-08-05GPI-2 new package (#17875)Robert Mijakovic1-0/+79
* update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote. * Fixes a typo with one of the sha256 checksum.. * Adds version entries for new versions of Intel packages. * Adds hashes for new versions of Intel packages. * Adds missing hash of Intel compiler. * Adds the newest version of Intel MPI 2019.8. * Fixes hash for intel-parallel-studio and intel-tbb. * Fixes version number of Intel MPI. * Adds GPI-2 package. * Fixes flake8 noticed issues. * Second try to fix flake8 comment * Fixes some issues adamjstewart noticed. * Fixes package according to flake8 complains. * Fixes flake8 issue. * Renames next version to master and removes master. * Adds maintainer into gpi-2 and returns master branch for the git repository. Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
2020-08-05Variant with fortran for likwid package (#17889)carlabguillen1-0/+16
* Option to build likwid with fortran interface * Removing white spaces * Flake8 conform
2020-08-05add depends_on('zlib', type='link') (#17887)h-denpo1-0/+1
2020-08-05bcache:add pkg-config to find blkid.h in linux-utils (#17888)darmac1-0/+1
2020-08-05remove hypre variant from mfem and all references to it (#17885)Greg Becker3-9/+3
2020-08-05nodejs: add version 8.11.4 (#17824)darmac1-1/+5
* nodejs: add version 8.11.4 * node-js: refine configure() for different version
2020-08-05charmpp: added v6.10.2 (#17886)Ronak Buch1-0/+1
2020-08-04[py-smart-open] fixing dependencies (#17640)Jen Herting1-1/+2
* version 1.8.4 requires py-boto at 2.3.2: * google-cloud-storage only in newer versions
2020-08-04[bowtie] added version 1.3.0. Patch fixed for new version (#17744)Jen Herting2-1/+14
2020-08-04Dyninst: 10.2 release (#17847)Tim Haines1-1/+8
* Dyninst: 10.2 release * Use 'elf' instead of 'elfutils' * Use v10.2.0 tag * Change minimum elfutils to 0.173 * Move STERILE_BUILD option to correct cmake_args * make a sacrifice to the flake8 gods * Add maintainer * Revert to using elf@1 for elfutils
2020-08-04Renamed the aluminum variant for thhe intra-node RMA functions. (#17861)Brian Van Essen3-6/+6
2020-08-04ParaView: Allow all ParaView versions to depend on Python 2 (#17484)Ethan Stam1-3/+16
* Allow all ParaView versions to depend on Python 2 * Keep conflict for 5.9 and up with python 2 * Fix line too long * Don't use backslash * Try fixing indent * Clean logic for python cmake flags * Try fixing indent
2020-08-04yorick: avoid hang to fputest on aarch64. (#17865)Toyohisa Kameyama1-3/+5
2020-08-04Added new package: spla (#17868)Simon Frasch1-0/+47
2020-08-04Prefer dynamic linking for Python in vim when +python (#17870)Robert Underwood1-2/+2
Previously the python package for vim used static linking, and depending on what system libraries were available and linked against could cause symbol conflicts for python leading to segfaults in loading c modules in the standard library (i.e. heapq). This patch address this issue by dynamically linking them.
2020-08-04Add openssh runtime dependency to git (#17872)Robert Underwood1-0/+1
If you use git to clone a repository ssh, git transfers control the ssh binary available on your path, if that ssh binary was built with contradictory version of openssl/kerberos, then your git commands will fail.
2020-08-04py-keras-preprocessing: add new version (#17735)Adam J. Stewart1-9/+10
2020-08-04abyss 2.1.4: fails to build with GCC 8 (#17614)t-nojiri2-3/+25
* abyss 2.1.4: fails to build with GCC 8 * abyss 2.1.4: fails to build with GCC 8 * abyss 2.1.4: Revise the points indicated by the review.
2020-08-04[delphes] pythia8 variant and cleanup (#17664)vvolkl1-8/+9
* [delphes] new version * [delphes] pythia8 variant * [delphes] flake8
2020-08-04Add Espanso Package and its xdotool Dependency (#17586)Zicklag2-0/+67
2020-08-04sirius (new versions, fixes), q-e-sirius (new package), nlcglib (new ↵Simon Pintarelli3-4/+399
package) (#17844) * sirius, update versions, fixes, add missing options - sirius/spfft: depend on fftw-api - cleanup +shared option - sirius add option for memory pool - sirius add version 6.5.3 and 6.5.4 - sirius: add spfft dependency for @master, @develop * add nlcglib package Robust wave function optimization for SIRIUS. * add q-e-sirius package based on q-e package * Update var/spack/repos/builtin/packages/q-e-sirius/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * nlcglib: pass nvcc_wrapper to cmake * Add 6.5.6 * Make flake8 happy Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2020-08-04hpctoolkit: add v2020.08.03 (#17860)Mark W. Krentel1-5/+2
Add version 2020.08.03. Adjust the cuda args. The --with-cupti arg was redundant, even for old versions of hpctoolkit.
2020-08-04AWS ParallelCluster: added v2.8.1 (#17866)Enrico Usai1-1/+2
2020-08-04Added versions for cuDNN 8.0.2. (#17862)Brian Van Essen1-0/+14
2020-08-04subread: extend support for aarch64 to v2.0.0 (#17864)t-nojiri1-1/+1
2020-08-03new plumed versions 2.5.5 and 2.6.1; bumped default to 2.5.5 (#17850)g-mathias1-1/+3
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-08-03HPX: fix wrong method name and use define/define_from_variant methods (#17851)albestro1-65/+31
* bug fix: wrong method name * refactoring using define_from_variant and define * flake8 style fix * revert change string format
2020-08-03Bump cmake (#17852)Harmen Stoppels1-0/+1
2020-08-03Fix typo: yaml -> json (#17854)Harmen Stoppels1-1/+1
2020-08-03amrex:: new version 20.08 (#17856)mic841-0/+1
2020-08-03canu: fix depends issue & using java instead of jdk (#17599)darmac1-1/+3
* canu: fix depends issue & using java instead of jdk * Update var/spack/repos/builtin/packages/canu/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-08-03Add new package: ycsb (#17788)darmac1-0/+35
* Add new package: ycsb * refine mongodb-async-driver jar path
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