Commit graph

29097 commits

Author SHA1 Message Date
Satish Balay
93db654b8d
intel-tbb: add in versions 2021.7.0, 2021.6.0 (#33445)
2021.7.0 fixes build on linux-ubuntu20.04-skylake / oneapi@2022.2.0
2022-10-21 06:34:18 -04:00
Massimiliano Culpo
abf3a696bd
Remove "spack buildcache copy" in v0.19.0 (#33437) 2022-10-21 12:17:53 +02:00
eugeneswalker
1e4732d5fe
e4s ci: add raja +rocm (#32505) 2022-10-20 14:26:18 -07:00
Luke Diorio-Toth
9621b2bb3b
replaced package shortbred with py-shortbred (#33404)
* fixed version numbers to python 2 and old biopython

* changed shortbred pacakge to pypi, removed python 2 version

* added package description

* re-added shortbred package with depreciated flag

* fixed style and removed unnecessary python dep (it can't build with python 2 anyway)

* removed whitespace and readded the python2.7.9+ dep

* fixed style
2022-10-20 15:44:57 -05:00
Mikael Simberg
ee721f9c91
Add Boost 1.80.0 (#32879)
* Add Boost 1.80.0
* Add conflict for Boost 1.80.0 and dealii
* Add conflict for Boost 1.80 and %oneapi
2022-10-20 13:32:25 -07:00
eugeneswalker
e981ab9b65
hiop: add v0.7.0 (#33441)
* hiop: add v0.7.0

* Update var/spack/repos/builtin/packages/hiop/package.py

Co-authored-by: Cameron Rutherford <cameron.rutherford@me.com>

Co-authored-by: Cameron Rutherford <cameron.rutherford@me.com>
2022-10-20 20:21:43 +00:00
Cody Balos
e60e743843
kokkos and kokkos-kernels: add new versions (#33301)
* kokkos: add version 3.7.00
* kokkos-kernels: add versions 3.6.01 and 3.7.00
* add correct kokkos dependence
2022-10-20 11:50:59 -07:00
Satish Balay
70e369086c
butterflypack: add version 2.2.2 and openmp variant (#33416)
- add conflcit with gcc < 7
- fails with MacOS sed - so add in (gnu) sed as build dependency
2022-10-20 11:20:45 -07:00
Jon Rood
cd015b8498
Update OpenFAST package file (#33438)
* Update OpenFAST package file.
* Add comment.
2022-10-20 11:04:55 -07:00
SoniaScard
69e66f57a9
ophidia-primitives: new package at v1.7 (#33434)
* ophidia-primitives: new package at v1.7
* ophidia-primitives: Add mantainers
* ophidia-primitives: Fix style

Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
2022-10-20 10:56:53 -07:00
Adam J. Stewart
0b873be13c
py-rasterio: add v1.3.3 (#33428) 2022-10-20 10:12:59 -07:00
Rémi Lacroix
b3e04e8cd2
spdlog: Add version 1.10.0 (#33431) 2022-10-20 10:12:02 -07:00
Scott Wittenburg
9a1957c881
gitlab: Do not use root_spec['pkg_name'] anymore (#33403)
* gitlab: Do not use root_spec['pkg_name'] anymore

For a long time it was fine to index a concrete root spec with the name
of a dependency in order to access the concrete dependency spec.  Since
pipelines started using `--use-buildcache dependencies:only,package:never`
though, it has exposed a scheduling issue in how pipelines are
generated.  If a concrete root spec depends on two different hashes of
`openssl` for example, indexing that root with just the package name
is ambiguous, so we should no longer depend on that approach when
scheduling jobs.

* env: make sure exactly one spec in env matches hash
2022-10-20 10:33:18 -06:00
G-Ragghianti
af5d6295d5
Change scalapack to test-only dependency (#33433) 2022-10-20 08:42:52 -07:00
eugeneswalker
3e1db75372
arpack-ng %cce: add -hnopattern to fflags (#33424) 2022-10-20 08:09:35 -07:00
Luke Diorio-Toth
70d2556f4b
py-bakta: new package (#33417) 2022-10-20 08:22:59 -05:00
Massimiliano Culpo
89cf5004db
FIX CI after git update (#33429)
Add `protocol.file.allow always` to git configuration in CI
2022-10-20 09:46:04 +02:00
eugeneswalker
8aac0d09d4
e4s ci: add umpire +rocm (#32504) 2022-10-19 17:05:45 -06:00
Richard Berger
0934c4d602
singularity-eos: new version 1.6.2 (#33415) 2022-10-19 14:06:44 -07:00
Harmen Stoppels
e1344067fd
depfile: buildcache support (#33315)
When installing some/all specs from a buildcache, build edges are pruned
from those specs. This can result in a much smaller effective DAG. Until
now, `spack env depfile` would always generate a full DAG.

Ths PR adds the `spack env depfile --use-buildcache` flag that was
introduced for `spack install` before. This way, not only can we drop
build edges, but also we can automatically set the right buildcache
related flags on the specific specs that are gonna get installed.

This way we get parallel installs of binary deps without redundancy,
which is useful for Gitlab CI.
2022-10-19 13:57:06 -07:00
Jon Rood
ae7999d7a1
Simplify TIOGA package (#33396)
* Update TIOGA package.

* Add comment.

* Remove cuda variant and MPI_ROOT.

* Style.
2022-10-19 13:33:01 -07:00
Adam J. Stewart
4b0832d3bc
py-pandas: add v1.5.1 (#33412) 2022-10-19 14:18:00 -06:00
Sergey Kosukhin
ef872cc64b
mpich: enable building when @3.4~cuda (#33325) 2022-10-19 13:04:32 -07:00
eugeneswalker
1f0751defe
patch std::filesystem check as done in llnl/umpire pr#784 (#33250) 2022-10-19 14:14:46 -05:00
eugeneswalker
fa30f74e0c
umpire +rocm: use hipcc as CMAKE_CXX_COMPILER (#33377) 2022-10-19 12:53:58 -06:00
eugeneswalker
6b45e2fef1
raja +rocm: use hipcc as CMAKE_CXX_COMPILER (#33375) 2022-10-19 13:43:51 -05:00
Luke Diorio-Toth
5cce66be75
pilercr: new package (#33251)
* new package
* fixed style
* actually building now
2022-10-19 11:41:39 -07:00
eugeneswalker
9f89926980
axom: python only reliably available when +python, +devtools (#33414) 2022-10-19 11:41:52 -06:00
Massimiliano Culpo
7ad7fde09c
Add a command to bootstrap Spack right now (#33407) 2022-10-19 19:25:20 +02:00
Stephen Sachs
25cbb34579
Relocate "run" type dependencies too (#33191)
When downloading from binary cache not only replace RPATHs to dependencies, but
also text references to dependencies.

Example:
`autoconf@2.69` contains a text reference to the executable of its dependency
`perl`:

```
$ grep perl-5 /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/autoconf-2.69-q3lo/bin/autoreconf
eval 'case $# in 0) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0";; *) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0" "$@";; esac'
```

These references need to be replace or any package using `autoreconf` will fail
as it cannot find the installed `perl`.

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-10-19 17:37:07 +02:00
Jonathon Anderson
a423dc646a
Update the binary index before attempting direct fetches (#32137)
"spack install" will not update the binary index if given a concrete
spec, which causes it to fall back to direct fetches when a simple
index update would have helped. For S3 buckets in particular, this
significantly and needlessly slows down the install process.

This commit alters the logic so that the binary index is updated
whenever a by-hash lookup fails. The lookup is attempted again with
the updated index before falling back to direct fetches. To avoid
updating too frequently (potentially once for each spec being
installed), BinaryCacheIndex.update now includes a "cooldown"
option, and when this option is enabled it will not update more
than once in a cooldown window (set in config.yaml).

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-19 09:36:27 -06:00
Tamara Dahlgren
3ec7304699
spack checksum: warn if version is deprecated (#32438)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-18 22:51:38 +00:00
Robert Cohn
7bb4b58b8b
intel-oneapi-compilers: do not pass -Wno-unused-command-line-argument to icc + refactor (#33389) 2022-10-18 16:17:50 -06:00
Tamara Dahlgren
13356f3bfa
Docs: Spack info option updates (#33376) 2022-10-18 21:11:21 +02:00
Harmen Stoppels
c6c5e56ec1
Reusable --use-buildcache with better validation (#33388)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-18 18:52:28 +00:00
Bernhard Kaindl
1ae32ff62c
go,gcc: Support external go compilers for Go bootstrap (#27769)
For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64)
2022-10-18 10:18:49 -07:00
Howard Pritchard
d95f14084e
papi: fix for Intel OneAPI compiler (#33225)
Without this patch one hits this error trying to compiler papi with Intel OneAPI:

icx: error: Note that use of '-g' without any optimization-level option will turn off most compiler optimizations similar to use of '-O0' [-Werror,-Wdebug-disables-optimization]

Signed-off-by: Howard Pritchard <howardp@lanl.gov>

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-10-18 11:18:04 -06:00
snehring
b44c83429c
vsearch: add v2.22.1 (#33327) 2022-10-18 08:59:38 -06:00
snehring
8e8d6e5adb
mothur: add v1.48.0 and variants (#33326) 2022-10-18 08:54:23 -06:00
dependabot[bot]
b21e54dffa
build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (#33384)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](95cb08cb26...c74574e6c8)

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

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-10-18 10:22:30 +02:00
Massimiliano Culpo
fe2656f182
intel-oneapi-compilers: fix Python 2.7 compliance (#33383) 2022-10-18 07:19:25 +02:00
Adam J. Stewart
0b014ff9cd
py-fiona: add v1.8.22 (#33372) 2022-10-17 22:33:50 -06:00
eugeneswalker
dd003f66a8
e4s ci stack: add trilinos +rocm (#31601) 2022-10-17 21:04:31 +00:00
Michael Kuhn
9d11b96e4b
lz4: add 1.9.4 (#33334) 2022-10-17 14:42:03 -06:00
Brian Van Essen
47bfc60845
Bugfix HIP and aluminum rocm build (#33344)
* Fixed two bugs in the HIP package recipe.  The first is that the
HIP_PATH was being set to the actual spec, and not the spec prefix.

The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip
but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and
/opt/rocm-x.y.z/lib.  This means that the external detection logic may
find it in either and it turns out that some modules only expose one
of those two locations.  Logic is added to ensure that the internal
HIP_PATH and associated ROCM_PATH are correctly set in both cases.

* Added support for Aluminum to use the libfabric plugin with either
RCCL or NCCL.
2022-10-17 13:07:27 -07:00
Mosè Giordano
9b87b4c8cd
grid: reference fftw-api instead of fftw (#33374)
This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`.
2022-10-17 14:06:15 -06:00
snehring
c0361168a5
New packages: libbigwig, methyldackel (#33273)
* libbigwig: adding new package libbigwig
* methyldackel: adding new package methyldackel
* libbigwig: tighten up curl variant
2022-10-17 12:40:01 -07:00
Robert Underwood
da6aeaad44
Initial contribution of LibPressio ecosystem (#32630)
* Add libpressio and dependencies; some of these packages are
  maintained as forks of the original repositories and in those
  cases the docstring mentions this.
* Add optional dependency in adios2 on libpressio
* cub package: set CUB_DIR environment variable for dependent
  installations
* Clear R_HOME/R_ENVIRON before Spack installation (avoid sources
  outside of Spack from affecting the installation in Spack)
* Rename dlib to dorian3d-dlib and update dependents; add new dlib
  implementation. Pending an official policy on how to handle
  packages with short names, reviewer unilaterally decided that
  the rename was acceptable given that the new Spack dlib package
  is referenced more widely (by orders of magnitude) than the
  original

Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
2022-10-17 13:30:54 -06:00
Luke Diorio-Toth
fb090a69f4
py-xopen: version bump to 1.6.0 (#33231)
* version bump to 1.6.0

* added py-isal, updated URL
2022-10-17 19:16:09 +00:00
Stephen Sachs
2e55812417
Classic Intel compilers do not support gcc-toolchain (#33281)
* Classic Intel compilers do not support gcc-toolchain

This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel
compilers. AFAIK this option is only supported for Clang based compilers.

This lead to an issue when installing cmake. Reproducer:
```
spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt
build_type=Release arch=linux-amzn2-skylake_avx512
```

Tagging maintainer @rscohn2

* Add `-gcc-name` for icc

.. and `-gxx-name` for icpc.

AFAIK this is used for modern C++ support, so we can ignore `ifort`.

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-10-17 10:46:11 -06:00