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2021-09-19Create SECURITY.mdTodd Gamblin1-0/+24
2021-09-19updating kokkos to 3.4.01 (#26013)Vanessasaurus1-1/+2
2021-09-19updating singularity to 3.8.3 (#26020)Vanessasaurus1-3/+3
Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-19Fix R version (#26047)jacorvar1-1/+1
R version should be `3.0.0`, in contrast to `3.00`.
2021-09-18Add v1.6.0 to Benchmark (#25996)Alec Scott1-1/+2
2021-09-18omegah: add version 9.34.1 (#25828)Cameron Smith1-0/+1
2021-09-18Add v0.935 to Angsd (#25995)Alec Scott1-1/+2
2021-09-19Python: use platform-specific site packages dir (#25998)Adam J. Stewart3-3/+3
2021-09-18cmake: allow gcc on macOS for newer versions (#25994)Seth R. Johnson1-5/+4
2021-09-18librsb: add v1.2.0.10 (#26044)Michele Martone1-1/+2
2021-09-18FFTW: Fix OpenMP Build on macOS (#26039)Axel Huebl1-0/+11
2021-09-18updating siesta to 4.0.2 (#26021)Vanessasaurus1-2/+5
2021-09-18updating universal ctags to 5.2.0.xxxx (#26024)Vanessasaurus1-1/+2
2021-09-18updating sparsehash to 2.0.4 (#26023)Vanessasaurus1-1/+2
2021-09-18updating htslib to 1.13 (#26012)Vanessasaurus1-1/+2
2021-09-18updating nco to 5.0.1 (#26014)Vanessasaurus1-1/+2
2021-09-18updating graphviz to 2.49.0 (#26011)Vanessasaurus1-0/+1
2021-09-18updating veloc to 1.5 and cleaning up spacing (#26025)Vanessasaurus1-7/+7
2021-09-18updating cloc to 1.9.0 (#26009)Vanessasaurus1-1/+2
2021-09-18updating poppler (#26016)Vanessasaurus1-1/+2
2021-09-18updating raxml to 8.2.12 (#26018)Vanessasaurus1-1/+2
2021-09-18updating protobuf (Gooooogle!) to 3.18.0 (#26017)Vanessasaurus1-39/+40
2021-09-18updating samtools to 1.13 (#26019)Vanessasaurus1-1/+2
2021-09-18updating spades to 3.15.3 (#26022)Vanessasaurus1-1/+2
2021-09-18updating gatk to 4.2.2.0 (#26010)Vanessasaurus1-73/+21
2021-09-17Convert RAJA, CHAI and Umpire to CachedCMakePackages (#25788)David Beckingsale3-105/+191
* Switch Umpire to CMakeCachedPackage * Fix missing import * Correct tests option in Umpire * Switch RAJA to CachedCMakePackage * Convert CHAI to CachedCMakePackage * Corrections in RAJA * Patches in Umpire & RAJA for BLT target export * Fixup style * Fixup incorrect use of cmake_cache_string
2021-09-17update tutorial version of hdf5 (#25368)Chris White5-117/+417
2021-09-17Bootstrap should search for compilers after switching config scopes (#26029)Massimiliano Culpo6-47/+80
fixes #25992 Currently the bootstrapping process may need a compiler. When bootstrapping from sources the need is obvious, while when bootstrapping from binaries it's currently needed in case patchelf is not on the system (since it will be then bootstrapped from sources). Before this PR we were searching for compilers as the first operation, in case they were not declared in the configuration. This fails in case we start bootstrapping from within an environment. The fix is to defer the search until we have swapped configuration.
2021-09-17Bump reframe (#25970)Harmen Stoppels1-0/+1
2021-09-17Add ccache v4.4.1. (#25957)Olli Lupton1-0/+1
2021-09-17improve ascent package to use stages and cmake base (#25720)Cyrus Harrison1-73/+70
* improve ascent package to use stages and cmake base * style * more style
2021-09-17fmt: add variant for shared library (#25969)iarspider1-1/+5
2021-09-17variant build: openmp_ref should be openmp (#26006)eugeneswalker1-1/+1
2021-09-17gosam: new version 2.1.1 (#25985)iarspider1-4/+8
2021-09-16GCC: patch for gcc 10.3.0 ICE when using nvcc (#25980)Kurt Sansom1-0/+3
* fix: patch for gcc 10.3.0 ICE when using nvcc * fix: use URL reference instead * fix: add missing sha256sum
2021-09-16added package.py for GPTL (#25993)Edward Hartnett1-0/+47
2021-09-16Filter UserWarning out of test output (#26001)Massimiliano Culpo1-0/+2
2021-09-16workaround a cmake/rocm bug in heffte (#25948)Miroslav Stoyanov1-0/+4
2021-09-16Add v7.0.2 to Admixtools (#25997)Alec Scott1-6/+7
2021-09-16Fix for problem with cmake@3.21 (#25989)G-Ragghianti1-0/+3
2021-09-16New package: ROMS (#25990)AMD Toolchain Support1-0/+141
Co-authored-by: Mohan Babu <mohbabul@amd.com>
2021-09-16cc: Use parameter expansion instead of basename (#24509)Michael Kuhn1-1/+1
While debugging #24508, I noticed that we call `basename` in `cc`. The same can be achieved by using Bash's parameter expansion, saving one external process per call. Parameter expansion cannot replace basename for directories in some cases, but is guaranteed to work for executables.
2021-09-16Recommend Git's manyFiles feature (#25977)Michael Kuhn3-3/+3
Git 2.24 introduced a feature flag for repositories with many files, see: https://github.blog/2019-11-03-highlights-from-git-2-24/#feature-macros Since Spack's Git repository contains roughly 8,500 files, it can be worthwhile to enable this, especially on slow file systems such as NFS: ``` $ hyperfine --warmup 3 'cd spack-default; git status' 'cd spack-manyfiles; git status' Benchmark #1: cd spack-default; git status Time (mean ± σ): 3.388 s ± 0.095 s [User: 256.2 ms, System: 625.8 ms] Range (min … max): 3.168 s … 3.535 s 10 runs Benchmark #2: cd spack-manyfiles; git status Time (mean ± σ): 168.7 ms ± 10.9 ms [User: 98.6 ms, System: 126.1 ms] Range (min … max): 144.8 ms … 188.0 ms 19 runs Summary 'cd spack-manyfiles; git status' ran 20.09 ± 1.42 times faster than 'cd spack-default; git status' ```
2021-09-16Bump sirius 7.2.x (#25939)Harmen Stoppels1-0/+2
2021-09-16Add a deprecation warning when using the old concretizer (#25966)Massimiliano Culpo1-0/+8
2021-09-16Update HPX package (#25775)Mikael Simberg2-40/+82
* Add support for C++20 to HPX package * Enable unity builds in HPX package when available * Add support for HIP/ROCm to HPX package * Rearrange and update required versions for HPX package * Add C++20 option to asio package
2021-09-16Improve bootstrapping docs a hair (#25962)Harmen Stoppels2-50/+51
2021-09-16Fix NameError in foreground/background test (#25967)Harmen Stoppels1-2/+4
2021-09-16Inform the user about bootstrapping (#25964)Harmen Stoppels1-0/+3
2021-09-15bedops: Fix checksum for 2.4.40 (#25958)jacorvar1-1/+1
Fixes #25951
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