Commit Graph

17471 Commits

Author SHA1 Message Date
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
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
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
Harmen Stoppels
5b211c90f5 Bump sirius 7.2.x (#25939) 2021-09-16 15:00:58 +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
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
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
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
Weston Ortiz
56c375743a Add missing mumps TPL commands (#25940) 2021-09-14 20:26:37 +01:00
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
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
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