Commit graph

22566 commits

Author SHA1 Message Date
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
dependabot[bot]
5d23638fdc
build(deps): bump codecov/codecov-action from 2.0.3 to 2.1.0 (#25925)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.0.3 to 2.1.0.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v2.0.3...v2.1.0)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-09-15 16:02:05 +02:00
Tamara Dahlgren
f0b4afe7db
Raise exception when 1+ stand-alone tests fail (#25857) 2021-09-15 08:04:59 -04:00
Ben Corbett
75497537a4
Added LvArray 0.2.2 (#25950) 2021-09-15 01:44:07 -06:00
Massimiliano Culpo
c52426ea7a
Make clingo the default solver (#25502)
Modifications:
- [x] Change `defaults/config.yaml`
- [x] Add a fix for bootstrapping patchelf from sources if `compilers.yaml` is empty
- [x] Make `SPACK_TEST_SOLVER=clingo` the default for unit-tests
- [x] Fix package failures in the e4s pipeline

Caveats:
1. CentOS 6 still uses the original concretizer as it can't connect to the buildcache due to issues with `ssl` (bootstrapping from sources requires a C++14 capable compiler)
1. I had to update the image tag for GitlabCI in e699f14.  
1. libtool v2.4.2 has been deprecated and other packages received some update
2021-09-14 22:44:16 -07:00
Adam J. Stewart
0d0d438c11
Add a __reduce__ method to Environment (#25678)
* Add a __reduce__ method to Environment
* Add unit test
* Convert Path to str
2021-09-14 22:37:36 -07:00
Vanessasaurus
ef5ad4eb34
Adding ability to compare git references to spack install (#24639)
This will allow a user to (from anywhere a Spec is parsed including both name and version) refer to a git commit in lieu of 
a package version, and be able to make comparisons with releases in the history based on commits (or with other commits). We do this by way of:

 - Adding a property, is_commit, to a version, meaning I can always check if a version is a commit and then change some action.
 - Adding an attribute to the Version object which can lookup commits from a git repo and find the last known version before that commit, and the distance
 - Construct new Version comparators, which are tuples. For normal versions, they are unchanged. For commits with a previous version x.y.z, d commits away, the comparator is (x, y, z, '', d). For commits with no previous version, the comparator is ('', d) where d is the distance from the first commit in the repo.
 - Metadata on git commits is cached in the misc_cache, for quick lookup later.
 - Git repos are cached as bare repos in `~/.spack/git_repos`
 - In both caches, git repo urls are turned into file paths within the cache

If a commit cannot be found in the cached git repo, we fetch from the repo. If a commit is found in the cached metadata, we do not recompare to newly downloaded tags (assuming repo structure does not change). The cached metadata may be thrown out by using the `spack clean -m` option if you know the repo structure has changed in a way that invalidates existing entries. Future work will include automatic updates.

# Finding previous versions
Spack will search the repo for any tags that match the string of a version given by the `version` directive. Spack will also search for any tags that match `v + string` for any version string. Beyond that, Spack will search for tags that match a SEMVER regex (i.e., tags of the form x.y.z) and interpret those tags as valid versions as well. Future work will increase the breadth of tags understood by Spack

For each tag, Spack queries git to determine whether the tag is an ancestor of the commit in question or not. Spack then sorts the tags that are ancestors of the commit by commit-distance in the repo, and takes the nearest ancestor. The version represented by that tag is listed as the previous version for the commit.

Not all commits will find a previous version, depending on the package workflow. Future work may enable more tangential relationships between commits and versions to be discovered, but many commits in real world git repos require human knowledge to associate with a most recent previous version. Future work will also allow packages to specify commit/tag/version relationships manually for such situations.

# Version comparisons.
The empty string is a valid component of a Spack version tuple, and is in fact the lowest-valued component. It cannot be generated as part of any valid version. These two characteristics make it perfect for delineating previous versions from distances. For any version x.y.z, (x, y, z, '', _) will be less than any "real" version beginning x.y.z. This ensures that no distance from a release will cause the commit to be interpreted as "greater than" a version which is not an ancestor of it.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-09-14 22:12:34 -07:00
David Beckingsale
c3bc3e61aa
gcc: apply backported fixes to v4.9.3 (#25945) 2021-09-15 07:10:04 +02:00
Satish Balay
148071ac8a
dealii: add version 9.3.1 (#25915) 2021-09-14 15:26:08 -06:00
Scott Wittenburg
bf7c12b4df
Pipelines: (Re)enable E4S on Power stack (#25921)
Pipelines: (Re)enable E4S on Power stack
2021-09-14 14:55:50 -06:00
Weston Ortiz
56c375743a
Add missing mumps TPL commands (#25940) 2021-09-14 20:26:37 +01:00
Vanessasaurus
c6edfa3f31
Update spack monitor to support new spec (#25928)
This PR coincides with tiny changes to spack to support spack monitor using the new spec
the corresponding spack monitor PR is at https://github.com/spack/spack-monitor/pull/31.
Since there are no changes to the database we can actually update the current server
fairly easily, so either someone can test locally or we can just update and then
test from that (and update as needed).

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-14 08:02:04 -06:00
Harmen Stoppels
fc96c49b0b
Add py-pot with patch (#25712) 2021-09-14 15:55:02 +02:00
Harmen Stoppels
ce790a89f2
reframe: set PYTHONPATH at runtime (#25842) 2021-09-14 15:54:14 +02:00