Commit graph

27981 commits

Author SHA1 Message Date
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
Harmen Stoppels
e7b14dd491
database: don't warn adding missing build deps (#33361)
When installing an individual spec `spack --only=package --cache-only /xyz`
from a buildcache, Spack currently issues tons of warnings about
missing build deps (and their deps) in the database.

This PR disables these warnings, since it's fine to have a spec without
its build deps in the db (they are just "missing").
2022-10-17 18:30:19 +02:00
Adam J. Stewart
839cf48352
py-horovod: add v0.26 (#33311)
* py-horovod: add v0.26

* py-petastorm: add v0.12.0
2022-10-17 09:14:55 -07:00
Harmen Stoppels
39105a3a6f
installer.py: traverse_dependencies has local deptype (#33367)
Currently `traverse_dependencies` fixes deptypes to traverse once and
for all in the recursion, but this is incorrect, since deptypes depend
on the node (e.g. if it's a dependency and cache-only, don't follow
build type edges, even if the parent is build from sources and needs
build deps.)
2022-10-17 16:14:12 +00:00
Massimiliano Culpo
9081871966
GnuPG: add v2.3.8 and update stack (#33368) 2022-10-17 10:13:52 -06:00
iarspider
ad430a7504
Add checksum for py-ipykernel 6.15.2 (#33360) 2022-10-17 10:59:21 -05:00
iarspider
db342d8727
Add checksum for py-secretstorage 3.3.3 (#33366) 2022-10-17 10:54:31 -05:00
Carlos Bederián
32761cdb7b
python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (#32623) 2022-10-17 17:47:10 +02:00
Scott Wittenburg
29df7e9be3
Support spackbot rebuilding all specs from source (#32596)
Support spackbot rebuilding all specs from source when asked (with "rebuild everything")

- Allow overriding --prune-dag cli opt with env var
- Use job variable to optionally prevent rebuild jobs early exit behavior
- ci rebuild: Use new install argument to insist deps are always installed from binary, but
package is only installed from source.
- gitlab: fix bug w/ untouched pruning
- ci rebuild: install from hash rather than json file
- When doing a "rebuild everything" pipeline, make sure that each install job only consumes
binary dependencies from the mirror being populated by the current pipeline.  This avoids
using, e.g. binaries from develop, when rebuilding everything on a PR.
- When running a pipeline to rebuild everything, do not die because we generated a hash on
the broken specs list.  Instead only warn in that case.
- bugfix: Replace broken no-args tty.die() with sys.exit(1)
2022-10-17 09:45:09 -06:00
Harmen Stoppels
ea80113d0f
Github Discussions can be used for Q&A (#33364) 2022-10-17 08:38:25 -07:00
Rui Peng Li
4fe53061a8
hypre 2.26.0 (#33299) 2022-10-17 08:31:28 -07:00
iarspider
bfe49222d5
Add checksum for py-prompt-toolkit 3.0.31 (#33362) 2022-10-17 09:02:19 -06:00
iarspider
42a27f3075
Add checksum for py-grpcio-tools 1.48.1 (#33358) 2022-10-17 10:01:22 -05:00
Harmen Stoppels
e882583b01
installer.py: fix/test get_deptypes (#33363)
Fixing an oversight in https://github.com/spack/spack/pull/32537

`get_deptypes` should depend on new `package/dependencies_cache_only`
props.
2022-10-17 08:57:58 -06:00
Scott Wittenburg
1be6506e29
gitlab ci: Do not force protected build jobs to run on aws runners (#33314) 2022-10-17 07:29:56 -07:00
iarspider
25e35c936b
Add checksum for py-astroid 2.12.7, py-astroid 2.12.10, py-setuptools 62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (#32976)
* Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0

* Also add checksum for py-wrapt

* Update package.py

* Update package.py (#57)

* Update package.py

* Update package.py

* Update package.py
2022-10-17 08:09:52 -06:00
Harmen Stoppels
2c802c12a5
installer.py: show timers for binary install (#33305)
Print a message of the form
```
Fetch mm:ss.  Build: mm:ss.  Total: mm:ss
```
when installing from buildcache. 

Previously this only happened for source builds.
2022-10-17 15:54:40 +02:00