Commit graph

24893 commits

Author SHA1 Message Date
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
Valentin Volkl
1b633e1ca4
ocaml: add patch for clang@11: (#25886) 2021-09-14 09:34:57 +02:00
Ben Darwin
2ac9dc76c4
dcmtk: add v3.6.4, v3.6.5, v3.6.6 (#25923) 2021-09-14 09:22:48 +02:00
Weston Ortiz
d7c5aa46fe
trilinos: variant for libx11 (#25823) 2021-09-14 08:53:53 +02:00
Edward Hartnett
f6eb16982a
added new version of parallelio library (#25916) 2021-09-13 18:22:54 -06:00
David Beckingsale
be1c4bc563
Rename camp 'main' version (#25918) 2021-09-13 16:55:55 -06:00
Timothy Brown
998de97091
ESMF, NEMSIO and UFS-UTILS changes. (#25846)
* ESMF and NEMSIO changes.

- Updating ESMF to set the COMM correctly when using Intel oneapi.
- Explicitly setting the CMake MPI Fortran compiler for NEMSIO.

* Update UFS utils CMake to use MPI_<lang>_COMPILER.
2021-09-13 16:13:43 -06:00
Greg Becker
dad69e7d7c
Fix environment reading from lockfile to trust written hashes (#25879)
#22845 revealed a long-standing bug that had never been triggered before, because the
hashing algorithm had been stable for multiple years while the bug was in production. The
bug was that when reading a concretized environment, Spack did not properly read in the
build hashes associated with the specs in the environment. Those hashes were recomputed
(and as long as we didn't change the algorithm, were recomputed identically). Spack's
policy, though, is never to recompute a hash. Once something is installed, we respect its
metadata hash forever -- even if internally Spack changes the hashing method. Put
differently, once something is concretized, it has a concrete hash, and that's it -- forever.

When we changed the hashing algorithm for performance in #22845 we exposed the bug.
This PR fixes the bug at its source, but properly reading in the cached build hash attributes
associated with the specs. I've also renamed some variables in the Environment class
methods to make a mistake of this sort more difficult to make in the future.

* ensure environment build hashes are never recomputed
* add comment clarifying reattachment of env build hashes
* bump lockfile version and include specfile version in env meta
* Fix unit-test for v1 to v2 conversion

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-09-13 15:25:48 -06:00
Satish Balay
9956841331
petsc, petsc4py: add version 3.15.4 (#25912) 2021-09-13 11:49:36 -07:00
Massimiliano Culpo
e9f1cfdaaf
Avoid hidden circular dependencies in spack.architecture (#25873)
* Refactor platform etc. to avoid circular dependencies

All the base classes in spack.architecture have been
moved to the corresponding specialized subpackages,
e.g. Platform is now defined within spack.platforms.

This resolves a circular dependency where spack.architecture
was both:
- Defining the base classes for spack.platforms, etc.
- Collecting derived classes from spack.platforms, etc.
Now it dopes only the latter.

* Move a few platform related functions to "spack.platforms"

* Removed spack.architecture.sys_type()

* Fixup for docs

* Rename Python modules according to review
2021-09-13 11:04:42 -07:00
Chuck Atkins
060582a21d
ci: Add ecp-data-vis-sdk CI pipeline (#22179)
* ci: Add a minimal subset of the ECP Data & Vis SDK CI pipeline

* ci: Expand the ECP Data & Vis SDK pipeline with more variants
2021-09-13 11:34:13 -06:00
Chuck Atkins
c392454125
Disable dvsdk variants (#25889)
* dvsdk: Turn off variants by default

This allows an install to more easily be explicit about which pieces to
turn on as more variants are added

* dvsdk: effectively disable the broken variants
2021-09-13 11:33:55 -06:00
Seth R. Johnson
fca81c2ac8
kokkos: fail gracefully on missing microarch (#25910)
Fall back on known parent microarches (as determined by spack's built-in
archspec knowledge). Clsoes spack/spack#25907 .
2021-09-13 11:07:14 -06:00
Tamara Dahlgren
bafd84e191
Switch http to https where latter exists (#25672)
* Switch http to https where latter exists
* Hopefully restore original permissions
* Add URL updates after include the -L curl option
* Manual corrections to select URL format strings
2021-09-13 09:21:35 -07:00
Desmond Orton
1e08f31e16
New Version: mothur@1.46.1 (#25850) 2021-09-13 10:20:22 -06:00
Seth R. Johnson
1da7839898
trilinos: add conflicts for fortran (#25911) 2021-09-13 16:51:38 +02:00
Harmen Stoppels
a4a22a6926
Add a master branch for gnuconfig (#25866) 2021-09-13 14:17:32 +02:00
Nic McDonald
ceb94bd6ae
Log4cxx add v0.12.0, convert to CMakePackage (#25875) 2021-09-13 05:17:08 -06:00
Tim Gymnich
b745e208a3
ravel: fix missing header file (#25906)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-09-13 04:49:42 -06:00
Harmen Stoppels
6a8383b2a7
Make sure perl doesn't run into recompile with fPIC linker errors (#25834) 2021-09-13 11:29:15 +02:00
Kelly (KT) Thompson
6210e694e1
draco: add v7.11.0 (#24631) 2021-09-13 11:16:57 +02:00
Adam J. Stewart
2f889b045c
py-kornia: add new package (#25844) 2021-09-13 11:10:19 +02:00
Daniel Arndt
bc3b90f6ac
Add SYCL build option to ArborX (#25736) 2021-09-13 11:09:51 +02:00
Harmen Stoppels
1f323d296d
py-glmnet: new package (#25711) 2021-09-13 11:07:59 +02:00
Mikael Simberg
819cd41ee4
hpx, kokkos: add consistent variants for C++ std (#25535)
* Add cuda_constexpr variant to Kokkos package
* Don't require nvcc_wrapper in Kokkos package when using Cray compiler
2021-09-13 10:43:20 +02:00