Commit graph

35421 commits

Author SHA1 Message Date
Harmen Stoppels
a0bd53148b
glibc: fix deps, drop pre 2.17 (#39806)
* glibc: add missing deps, drop < 2.17

Building glibc 2.17 requires linking libgcc_{s,eh}.a, which themselves
depend on whatever glibc the current gcc uses for its runtime libraries.

Newer gcc depends on gnu extensions of libdl it seems, so that means you
simply cannot build old glibc with gcc-using-new-glibc.

The relevant fix in glibc is this commit:

commit 95f5a9a866695da4e038aa4e6ccbbfd5d9cf63b7
Author: Joseph Myers <joseph@codesourcery.com>
Date:   Tue Jul 3 19:14:59 2012 +0000

    Avoid use of libgcc_s and libgcc_eh when building glibc.

See also references to that commit in the glibc mailing list.

* update the gmake bound

* add --without-selinux
2023-09-11 10:45:53 -07:00
Massimiliano Culpo
3302b176fd
Update archspec to latest commit (#39920)
- [x] Intel flags for old architectures
- [x] Support for Sapphire Rapids
- [x] Cache the "ancestors" computation
2023-09-11 10:03:35 -07:00
Taillefumier Mathieu
4672346d9c
Support of versions of cp2k below 7 marked as deprecated (#39652)
SIRIUS was introduced in version 7 of cp2k but could be used
in practice in version 9 (input format and functionalities).
SIRIUS with version 6 and below are marked as a dependency
conflict until CP2K version 9.

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
2023-09-11 18:46:52 +02:00
Tom Payerle
4182e97761
elpa: Add --enable-scalapack-tests to configure when +autotune (#39728)
When building elpa +autotune, we apparently need to add
the configure option --enable-scalapack-tests
2023-09-11 18:37:56 +02:00
Seth R. Johnson
5598de88ff
celeritas: add v0.3.2 (#39879) 2023-09-11 12:18:48 -04:00
Simon Pintarelli
d88ecf0af0
sirius: fix cuda_arch flags (#39889) 2023-09-11 12:13:49 -04:00
Scott Wittenburg
516f0461b8
gitlab ci: Use image with awscli for rebuild-index job (#39636)
Instead of pointing to the image on DockerHub, which rate limits us and
causes pipeline failures durying busy times, use the version at ghcr.

And we might as well use the ghcr version everywhere else too.
2023-09-11 18:03:11 +02:00
Alex Richert
b8cf7c3835
w3emc: add develop version and more variants (#39884)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-11 18:02:50 +02:00
Annop Wongwathanarat
707684a7b7
acfl: map rocky9 to RHEL-9 (#39892) 2023-09-11 11:58:45 -04:00
Alex Richert
739aebbd18
sp: add develop version, build precision, and OpenMP support (#39874)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-11 17:41:32 +02:00
Tao Lin
71c053c391
Garfield++: Add the patch to fix the missing headers and Set the environment variable HEED_DATABASE (#39904) 2023-09-11 11:13:22 -04:00
Thomas Gruber
9a0a4eceaf
likwid: search library path for compilation with hwloc (#39659) 2023-09-11 11:03:21 -04:00
kjrstory
19f8e9147d
openfoam-org: zoltan renumbering and decompsition (#39915) 2023-09-11 16:42:50 +02:00
George Young
e99750fd3c
transdecoder: add 5.7.1 (#39916)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-11 16:37:36 +02:00
George Young
33cde87775
gffcompare: new package @0.12.6 (#39917)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-11 16:13:49 +02:00
Annop Wongwathanarat
e63597bf79
wrf: fix patches for 4.2 to 4.4.2 for aarch64 config (#39900) 2023-09-11 16:02:21 +02:00
Robert Cohn
2f63342677
intel-oneapi-mkl: hpcx-mpi support (#39750) 2023-09-11 15:47:52 +02:00
Freifrau von Bleifrei
04eae7316f
DisCoTec: add new package (#35239)
Co-authored-by: Alexander Van Craen <40516079+vancraar@users.noreply.github.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-11 04:18:00 -04:00
Adam Fidel
67d6c086d8
singularity: fix package name in comment (#39822) 2023-09-10 12:33:10 -04:00
Mark (he/his) C. Miller
69370c9c8f
Update package H5Z-ZFP to 1.1.1 (#39740)
* update to 1.1.1

* add maintainers

* add 1.1.0; set default
2023-09-10 09:27:24 -07:00
Rocco Meli
9948785220
spglib: add v2.1.0 (#39910)
* ensure umpire~cuda~rocm when ~cuda~rocm

* update spglib
2023-09-10 08:48:13 -07:00
dependabot[bot]
4047e025e0
build(deps): bump docker/build-push-action from 4.1.1 to 4.2.1 (#39901)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.1 to 4.2.1.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](2eb1c1961a...0a97817b6a)

---
updated-dependencies:
- dependency-name: docker/build-push-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>
2023-09-10 09:52:15 +02:00
dependabot[bot]
783bbdf2db
build(deps): bump actions/upload-artifact from 3.1.2 to 3.1.3 (#39852)
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3.1.2 to 3.1.3.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](0b7f8abb15...a8a3f3ad30)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-08 22:58:55 +02:00
Thomas Madlener
a65f13f79f
root: add latest available tag (#39895) 2023-09-08 14:48:54 -04:00
John W. Parent
fc391d5332
NMake Builder: change property name (#39824)
NMake makefiles are still called makefiles. The corresponding builder
variable was called "nmakefile", which is a bit unintuitive and lead
to a few easy-to-make, hard-to-notice mistakes when creating packages.
This commit renames the builder property to be "makefile"
2023-09-08 11:23:13 -07:00
eugeneswalker
e05f12f18e
veloc: add v1.7 (#39465)
* updates for VELOC 1.6

* veloc: add v1.7

---------

Co-authored-by: Bogdan Nicolae <bogdan.nicolae@acm.org>
2023-09-08 12:57:14 -05:00
John W. Parent
14f248652c
Spack on Windows: fix shell scripts when root contains a space (#39875)
Enclose variable tracking root in quotes.
2023-09-08 13:49:16 -04:00
AMD Toolchain Support
87f99de3fb
Cloverleaf-ref: proposal for a -ref version only (#39894)
* Cloverleaf-ref: proposal for a -ref version only
* Cloverleaf-ref: fixing typo.

---------

Co-authored-by: fpanichi <fpanichi@amd.com>
2023-09-08 10:47:00 -07:00
Dan Lipsa
9e7fe04a77
Windows decompression: fix removal of intermediate file (#38958)
Extensionless archives requiring two-stage decompression and extraction
require intermediate archives to be renamed after decompression/extraction
to prevent collision. Prior behavior attempted to cleanup the intermediate
archive with the original name, this PR ensures the renamed folder is
cleaned instead.

Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
Co-authored-by: John Parent <john.parent@kitware.com>
2023-09-08 10:27:43 -07:00
Todd Gamblin
45d149c7d3
bugfix: only complete aliases for potential aliases (#39887)
Smart alias completion introduced in #39499 wasn't as smart as it needed to be, and
would complete any invalid command prefix and some env names with alias names.

- [x] don't complete aliases if there are no potential completions
      e.g., don't convert `spack isnotacommand` -> `spack concretize`

- [x] don't complete with an aliases if we're not looking at a top-level subcommand.
2023-09-08 12:51:26 +02:00
Anton Kozhevnikov
8250a085b0
BUILD_TESTING is a CMake variable and should not be scoped (#39866) 2023-09-08 10:14:06 +02:00
Massimiliano Culpo
39b9f214a8
Speed-up spack external find execution (#39843)
* Perform external spec detection with multiple workers

The logic to perform external spec detection has been refactored
into classes. These classes use the GoF "template" pattern to account
for the small differences between searching for "executables" and
for "libraries", while unifying the larger part of the algorithm.

A ProcessPoolExecutor is used to parallelize the work.

* Speed-up external find by tagging detectable packages automatically

Querying packages by tag is much faster than inspecting the repository,
since tags are cached. This commit adds a "detectable" tag to every
package that implements the detection protocol, and external detection
uses it to search for packages.

* Pass package names instead of package classes to workers

The slowest part of the search is importing the Python modules
associated with candidate packages. The import is done serially
before we distribute the work to the pool of executors.

This commit pushes the import of the Python module to the job
performed by the workers, and passes just the name of the packages
to the executors.

In this way imports can be done in parallel.

* Rework unit-tests for Windows

Some unit tests were doing a full e2e run of a command
just to check a input handling. Make the test more
focused by just stressing a specific function.

Mark as xfailed 2 tests on Windows, that will be fixed
by a PR in the queue. The tests are failing because we
monkeypatch internals in the parent process, but the
monkeypatching is not done in the "spawned" child
process.
2023-09-08 09:25:50 +02:00
Massimiliano Culpo
7631b5ea14
crosstool-ng: add new package (#39865) 2023-09-08 08:16:39 +02:00
dependabot[bot]
a4d2f8332f
build(deps): bump pytest from 7.4.1 to 7.4.2 in /lib/spack/docs (#39883)
Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.1 to 7.4.2.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.4.1...7.4.2)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-08 08:16:19 +02:00
Tamara Dahlgren
007f02e06a
Docs/Packaging guide: Add BundlePackage (#39691)
* Docs/Packaging guide: Add BundlePackage
* Adjusted version ordering note to reflect convention.
2023-09-07 19:45:51 -07:00
kwryankrattiger
8ec1657136
CI Timing Statistics (#38598)
* Write timing information for installs from cache

* CI: aggregate and upload install_times.json to artifacts

* CI: Don't change root directory for artifact generation

* Flat event based timer variation

Event based timer allows for easily starting and stopping timers without
wiping sub-timer data. It also requires less branching logic when
tracking time.

The json output is non-hierarchical in this version and hierarchy is
less rigidly enforced between starting and stopping.

* Add and write timers for top level install

* Update completion

* remove unused subtimer api

* Fix unit tests

* Suppress timing summary option

* Save timers summaries to user_data artifacts

* Remove completion from fish

* Move spack python to script section

* Write timer correctly for non-cache installs

* Re-add hash to timer file

* Fish completion updates

* Fix null timer yield value

* fix type hints

* Remove timer-summary-file option

* Add "." in front of non-package timer name

---------

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-09-07 15:41:31 -05:00
eflumerf
c5fc794d77
epics-base package: use the Spack compiler wrappers (#39752)
Edit configuration file to use the Spack compiler wrappers.
2023-09-07 16:28:57 -04:00
Sam Reeve
5c409f794a
Make Cabana a Cuda/ROCm package (matching ArborX) (#39809) 2023-09-07 13:36:09 -06:00
Rocco Meli
06b30842e4
Allow to build latest released version of CP2K with CMake (#39782)
* allow to build latest version of cp2k with cmake
* apply black
2023-09-07 12:11:30 -07:00
Niclas Jansson
ebbe63013d
neko: add v0.6.1 and fix package (#39751)
* neko: add v0.6.1 and fix package
* Change to a conditional variant for gslib
2023-09-07 11:30:52 -07:00
David Gardner
3f7f10ca2b
add SUNDIALS v6.6.1 (#39853) 2023-09-07 11:20:54 -07:00
Vanessasaurus
6a5a074150
Automated deployment to update package flux-core 2023-09-07 (#39856)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-09-07 11:18:55 -07:00
Vanessasaurus
c046c61cff
Automated deployment to update package flux-security 2023-09-07 (#39855)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-09-07 11:17:56 -07:00
Harmen Stoppels
7bd95f6ad3
move determine_number_of_jobs into spack.util.cpus, use it in concretize (#37620) 2023-09-07 13:16:51 +02:00
Martin Aumüller
4429e17db0
lua: unzip also required during build (#39802)
Unzip required during build otherwise configuration of luarocks fails during installation of lua@5.3.6 on ubuntu 22.04 w/o system unzip.
2023-09-07 01:48:14 -04:00
Johann Gaebler
65dd6e1196
r-furrr: Add furrr R package. (#39814)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-07 01:08:27 -04:00
Johann Gaebler
a43da48d23
r-functional: Add the functional R package. (#39826)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-07 01:03:45 -04:00
Matheus Henrique
f9c06669ca
Add Figcone Package (#39804)
* Add Figcone Package
* Fix the style
* add url
* fix style removing whitespace of a blanck line
* remove versions
2023-09-07 01:03:31 -04:00
Geoffrey Lentner
11c6431c9a
duckdb: add v0.8.1 (#39851) 2023-09-07 00:58:50 -04:00
Johann Gaebler
1e85a1b227
r-tinytiger: Add tinytiger R package. (#39828)
* r-tinytiger: Add tinytiger R package.
* Fix homepage.

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-07 00:58:36 -04:00