Commit Graph

25330 Commits

Author SHA1 Message Date
Vanessasaurus
c2f42a6f09 updating kokkos to 3.4.01 (#26013) 2021-09-19 06:10:55 -06:00
Vanessasaurus
148c7aeb06 updating singularity to 3.8.3 (#26020)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-19 04:20:15 -06:00
jacorvar
4f79a83dd1 Fix R version (#26047)
R version should be `3.0.0`, in contrast to `3.00`.
2021-09-19 12:14:14 +02:00
Alec Scott
2d4d51eb5e Add v1.6.0 to Benchmark (#25996) 2021-09-18 20:59:02 -06:00
Cameron Smith
b14d6d217e omegah: add version 9.34.1 (#25828) 2021-09-18 19:58:44 -06:00
Alec Scott
5b400a69b7 Add v0.935 to Angsd (#25995) 2021-09-18 18:46:55 -06:00
Adam J. Stewart
c0839b14d5 Python: use platform-specific site packages dir (#25998) 2021-09-19 00:37:50 +00:00
Seth R. Johnson
6ff5795342 cmake: allow gcc on macOS for newer versions (#25994) 2021-09-18 17:34:43 -06:00
Michele Martone
60f0d0ac20 librsb: add v1.2.0.10 (#26044) 2021-09-18 17:43:41 -04:00
Axel Huebl
8f3482b2ce FFTW: Fix OpenMP Build on macOS (#26039) 2021-09-18 15:13:47 -06:00
Vanessasaurus
fc79a5da17 updating siesta to 4.0.2 (#26021) 2021-09-18 08:05:02 -06:00
Vanessasaurus
1880db8457 updating universal ctags to 5.2.0.xxxx (#26024) 2021-09-18 07:13:55 -06:00
Vanessasaurus
6538727fb3 updating sparsehash to 2.0.4 (#26023) 2021-09-18 06:52:59 -06:00
Vanessasaurus
f5275fecc5 updating htslib to 1.13 (#26012) 2021-09-18 06:26:00 -06:00
Vanessasaurus
d499309433 updating nco to 5.0.1 (#26014) 2021-09-18 06:23:05 -06:00
Vanessasaurus
c5e2662dea updating graphviz to 2.49.0 (#26011) 2021-09-18 06:19:56 -06:00
Vanessasaurus
7b0a505795 updating veloc to 1.5 and cleaning up spacing (#26025) 2021-09-18 06:10:56 -06:00
Vanessasaurus
e8b86b7ec6 updating cloc to 1.9.0 (#26009) 2021-09-18 05:44:04 -06:00
Vanessasaurus
608a0b1f8f updating poppler (#26016) 2021-09-18 05:10:56 -06:00
Vanessasaurus
abd11cf042 updating raxml to 8.2.12 (#26018) 2021-09-18 04:58:50 -06:00
Vanessasaurus
8ad910d8f1 updating protobuf (Gooooogle!) to 3.18.0 (#26017) 2021-09-18 04:40:49 -06:00
Vanessasaurus
d5c985b888 updating samtools to 1.13 (#26019) 2021-09-18 04:16:51 -06:00
Vanessasaurus
f0443d0327 updating spades to 3.15.3 (#26022) 2021-09-18 03:46:50 -06:00
Vanessasaurus
9af1858bff updating gatk to 4.2.2.0 (#26010) 2021-09-18 10:07:28 +02:00
David Beckingsale
fa3265ea51 Convert RAJA, CHAI and Umpire to CachedCMakePackages (#25788)
* 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
2021-09-17 21:29:41 -07:00
Chris White
79ac572f21 update tutorial version of hdf5 (#25368) 2021-09-17 17:34:56 -07:00
Massimiliano Culpo
b847bb72f0 Bootstrap should search for compilers after switching config scopes (#26029)
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.
2021-09-17 18:28:48 -06:00
Harmen Stoppels
4d36c40cfb Bump reframe (#25970) 2021-09-17 14:23:05 -06:00
Olli Lupton
ae9adba900 Add ccache v4.4.1. (#25957) 2021-09-17 13:37:58 -06:00
Cyrus Harrison
bd415ec841 improve ascent package to use stages and cmake base (#25720)
* improve ascent package to use stages and cmake base

* style

* more style
2021-09-17 10:37:16 -07:00
iarspider
7e7de25aba fmt: add variant for shared library (#25969) 2021-09-17 08:04:55 -06:00
eugeneswalker
730720d50a variant build: openmp_ref should be openmp (#26006) 2021-09-17 06:38:00 -06:00
iarspider
8e486c1e57 gosam: new version 2.1.1 (#25985) 2021-09-17 06:10:41 -06:00
Kurt Sansom
be8e52fbbe GCC: patch for gcc 10.3.0 ICE when using nvcc (#25980)
* fix: patch for gcc 10.3.0 ICE when using nvcc

* fix: use URL reference instead

* fix: add missing sha256sum
2021-09-16 18:43:56 -06:00
Edward Hartnett
f8fae997d3 added package.py for GPTL (#25993) 2021-09-16 17:11:05 -06:00
Massimiliano Culpo
71a3173a32 Filter UserWarning out of test output (#26001) 2021-09-16 14:56:00 -06:00
Miroslav Stoyanov
e027cecff2 workaround a cmake/rocm bug in heffte (#25948) 2021-09-16 13:26:07 -06:00
Alec Scott
bb29c5d674 Add v7.0.2 to Admixtools (#25997) 2021-09-16 12:08:15 -06:00
G-Ragghianti
c4e26ac7c8 Fix for problem with cmake@3.21 (#25989) 2021-09-16 11:52:59 -06:00
AMD Toolchain Support
cf81046bb1 New package: ROMS (#25990)
Co-authored-by: Mohan Babu <mohbabul@amd.com>
2021-09-16 10:34:45 -07:00
Michael Kuhn
2d34acf29e cc: Use parameter expansion instead of basename (#24509)
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.
2021-09-16 16:25:49 +00:00
Michael Kuhn
d73fe19d93 Recommend Git's manyFiles feature (#25977)
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'
```
2021-09-16 09:41:10 -06:00
Harmen Stoppels
5b211c90f5 Bump sirius 7.2.x (#25939) 2021-09-16 15:00:58 +02:00
Massimiliano Culpo
fa6366a7df Add a deprecation warning when using the old concretizer (#25966) 2021-09-16 13:25:24 +02:00
Mikael Simberg
b09ad2cc8c Update HPX package (#25775)
* 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
2021-09-16 13:24:17 +02:00
Harmen Stoppels
ccfdac8402 Improve bootstrapping docs a hair (#25962) 2021-09-16 07:02:31 -04:00
Harmen Stoppels
abb0f6e27c Fix NameError in foreground/background test (#25967) 2021-09-16 10:39:07 +02:00
Harmen Stoppels
3fe9b34362 Inform the user about bootstrapping (#25964) 2021-09-16 09:28:24 +02:00
jacorvar
c0122242ee bedops: Fix checksum for 2.4.40 (#25958)
Fixes #25951
2021-09-15 16:17:40 -07:00
Adam J. Stewart
0015f700b7 py-pybind11: use PythonPackage install method (#25650) 2021-09-15 11:57:33 -07:00