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* Disable papyrus in the neoverse v1 pipeline
See https://gitlab.spack.io/spack/spack/-/jobs/8983875
The job is hanging on tests for 6 hrs.
* Add papyrus to broken tests instead of removing it
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We have two ways to concretize now:
* `spack concretize` concretizes only the root specs that are not concrete in the environment.
* `spack concretize -f` eliminates all cached concretization data and reconcretizes the *entire* environment.
This PR adds `spack deconcretize`, which eliminates cached concretization data for a spec. This allows
users greater control over what is preserved from their `spack.lock` file and what is reused when not
using `spack concretize -f`. If you want to update a spec installed in your environment, you can call
`spack deconcretize` on it, and that spec and any relevant dependents will be removed from the lock file.
`spack concretize` has two options:
* `--root`: limits deconcretized specs to *specific* roots in the environment. You can use this to
deconcretize exactly one root in a `unify: false` environment. i.e., if `foo` root is a dependent
of `bar`, both roots, `spack deconcretize bar` will *not* deconcretize `foo`.
* `--all`: deconcretize *all* specs that match the input spec. By default `spack deconcretize`
will complain about multiple matches, like `spack uninstall`.
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This changes variant display to use a much more legible format, and to use screen space
much better (particularly on narrow terminals). It also adds color the variant display
to match other parts of `spack info`.
Descriptions and variant value lists that were frequently squished into a tiny column
before now have closer to the full terminal width.
This change also preserves any whitespace formatting present in `package.py`, so package
maintainers can make easer-to-read descriptions of variant values if they want. For
example, `gasnet` has had a nice description of the `conduits` variant for a while, but
it was wrapped and made illegible by `spack info`. That is now fixed and the original
newlines are kept.
Conditional variants are grouped by their when clauses by default, but if you do not
like the grouping, you can display all the variants in order with `--variants-by-name`.
I'm not sure when people will prefer this, but it makes it easier to tell that a
particular variant is/isn't there. I do think grouping by `when` is the better default.
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This reverts commit 4b06862a7f3fee9352cd4834b4de7cb400cd4aa1.
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Currently there's some hacky logic in the AppleClang compiler that makes
it also accept `gfortran` as a fortran compiler if `flang` is not found.
This is guarded by `if sys.platform` checks s.t. it only applies to
Darwin.
But on Linux the feature of detecting mixed toolchains is highly
requested too, cause it's rather annoying to run into a failed build of
`openblas` after dozens of minutes of compiling its dependencies, just
because clang doesn't have a fortran compiler.
In particular in CI where the system compilers may change during system
updates, it's typically impossible to fix compilers in a hand-written
compilers.yaml config file: the config will almost certainly be outdated
sooner or later, and maintaining one config file per target machine and
writing logic to select the correct config is rather undesirable too.
---
This PR introduces a flag `spack compiler find --mixed-toolchain` that
fills out missing `fc` and `f77` entries in `clang` / `apple-clang` by
picking the best matching `gcc`.
It is enabled by default on macOS, but not on Linux, matching current
behavior of `spack compiler find`.
The "best matching gcc" logic and compiler path updates are identical to
how compiler path dictionaries are currently flattened "horizontally"
(per compiler id). This just adds logic to do the same "vertically"
(across different compiler ids).
So, with this change on Ubuntu 22.04:
```
$ spack compiler find --mixed-toolchain
==> Added 6 new compilers to /home/harmen/.spack/linux/compilers.yaml
gcc@13.1.0 gcc@12.3.0 gcc@11.4.0 gcc@10.5.0 clang@16.0.0 clang@15.0.7
==> Compilers are defined in the following files:
/home/harmen/.spack/linux/compilers.yaml
```
you finally get:
```
compilers:
- compiler:
spec: clang@=15.0.7
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
flags: {}
operating_system: ubuntu23.04
target: x86_64
modules: []
environment: {}
extra_rpaths: []
- compiler:
spec: clang@=16.0.0
paths:
cc: /usr/bin/clang-16
cxx: /usr/bin/clang++-16
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
flags: {}
operating_system: ubuntu23.04
target: x86_64
modules: []
environment: {}
extra_rpaths: []
```
The "best gcc" is automatically default system gcc, since it has no
suffixes / prefixes.
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This PR implements the concept of "default environment", which doesn't have to be
created explicitly. The aim is to lower the barrier for adopting environments.
To (create and) activate the default environment, run
```
$ spack env activate
```
This mimics the behavior of
```
$ cd
```
which brings you to your home directory.
This is not a breaking change, since `spack env activate` without arguments
currently errors. It is similar to the already existing `spack env activate --temp`
command which always creates an env in a temporary directory, the difference
is that the default environment is a managed / named environment named `default`.
The name `default` is not a reserved name, it's just that `spack env activate`
creates it for you if you don't have it already.
With this change, you can get started with environments faster:
```
$ spack env activate [--prompt]
$ spack install --add x y z
```
instead of
```
$ spack env create default
==> Created environment 'default in /Users/harmenstoppels/spack/var/spack/environments/default
==> You can activate this environment with:
==> spack env activate default
$ spack env activate [--prompt] default
$ spack install --add x y z
```
Notice that Spack supports switching (but not stacking) environments, so the
parallel with `cd` is pretty clear:
```
$ spack env activate named_env
$ spack env status
==> In environment named_env
$ spack env activate
$ spack env status
==> In environment default
```
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This completes to `spack concretize`:
```
spack conc<tab>
```
but this still gets hung up on the difference between `concretize` and `concretise`:
```
spack -e . conc<tab>
```
We were checking `"$COMP_CWORD" = 1`, which tracks the word on the command line
including any flags and their args, but we should track `"$COMP_CWORD_NO_FLAGS" = 1` to
figure out if the arg we're completing is the first real command.
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This PR adds support for including separate definitions from `spack.yaml`.
Supporting the inclusion of files with definitions enables user to make
curated/standardized collections of packages that can re-used by others.
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Co-authored-by: wspear <wjspear@gmail.com>
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* e4s ci: add exago +cuda, +rocm builds
* exago: rename 5-18-2022-snapshot to snapshot.5-18-2022
* disable exago +rocm for non-external rocm ci install
* note that hiop +rocm fails to find hip libraries when they are spack-installed
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Credits to @ChristianKniep for advocating the idea of OCI image layers
being identical to spack buildcache tarballs.
With this you can configure an OCI registry as a buildcache:
```console
$ spack mirror add my_registry oci://user/image # Dockerhub
$ spack mirror add my_registry oci://ghcr.io/haampie/spack-test # GHCR
$ spack mirror set --push --oci-username ... --oci-password ... my_registry # set login credentials
```
which should result in this config:
```yaml
mirrors:
my_registry:
url: oci://ghcr.io/haampie/spack-test
push:
access_pair: [<username>, <password>]
```
It can be used like any other registry
```
spack buildcache push my_registry [specs...]
```
It will upload the Spack tarballs in parallel, as well as manifest + config
files s.t. the binaries are compatible with `docker pull` or `skopeo copy`.
In fact, a base image can be added to get a _runnable_ image:
```console
$ spack buildcache push --base-image ubuntu:23.04 my_registry python
Pushed ... as [image]:python-3.11.2-65txfcpqbmpawclvtasuog4yzmxwaoia.spack
$ docker run --rm -it [image]:python-3.11.2-65txfcpqbmpawclvtasuog4yzmxwaoia.spack
```
which should really be a game changer for sharing binaries.
Further, all content-addressable blobs that are downloaded and verified
will be cached in Spack's download cache. This should make repeated
`push` commands faster, as well as `push` followed by a separate
`update-index` command.
An end to end example of how to use this in Github Actions is here:
**https://github.com/haampie/spack-oci-buildcache-example**
TODO:
- [x] Generate environment modifications in config so PATH is set up
- [x] Enrich config with Spack's `spec` json (this is allowed in the OCI specification)
- [x] When ^ is done, add logic to create an index in say `<image>:index` by fetching all config files (using OCI distribution discovery API)
- [x] Add logic to use object storage in an OCI registry in `spack install`.
- [x] Make the user pick the base image for generated OCI images.
- [x] Update buildcache install logic to deal with absolute paths in tarballs
- [x] Merge with `spack buildcache` command
- [x] Merge #37441 (included here)
- [x] Merge #39077 (included here)
- [x] #39187 + #39285
- [x] #39341
- [x] Not a blocker: #35737 fixes correctness run env for the generated container images
NOTE:
1. `oci://` is unfortunately taken, so it's being abused in this PR to mean "oci type mirror". `skopeo` uses `docker://` which I'd like to avoid, given that classical docker v1 registries are not supported.
2. this is currently `https`-only, given that basic auth is used to login. I _could_ be convinced to allow http, but I'd prefer not to, given that for a `spack buildcache push` command multiple domains can be involved (auth server, source of base image, destination registry). Right now, no urllib http handler is added, so redirects to https and auth servers with http urls will simply result in a hard failure.
CAVEATS:
1. Signing is not implemented in this PR. `gpg --clearsign` is not the nicest solution, since (a) the spec.json is merged into the image config, which must be valid json, and (b) it would be better to sign the manifest (referencing both config/spec file and tarball) using more conventional image signing tools
2. `spack.binary_distribution.push` is not yet implemented for the OCI buildcache, only `spack buildcache push` is. This is because I'd like to always push images + deps to the registry, so that it's `docker pull`-able, whereas in `spack ci` we really wanna push an individual package without its deps to say `pr-xyz`, while its deps reside in some `develop` buildcache.
3. The `push -j ...` flag only works for OCI buildcache, not for others
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otherwise it detected pre-configured compilers in an potentially different way.
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Update Tcl modulefile template to simplify generated `append-path`,
`prepend-path` and `remove-path` commands and improve their readability.
If path element delimiter is colon character, do not set the `--delim`
option as it is the default delimiter value.
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* ci: don't register detectable compilers
Cause they go out of sync...
* remove intel compiler, it can be detected too
* Do not run spack compiler find since compilers are registered in concretize job already
* trilinos: work around +stokhos +cuda +superlu-dist bug due to EMPTY macro
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* adios2: update variants and dependencies
* adios2: add kokkos rocm|cuda|sycl variant
* e4s oneapi ci stack: add adios2 +sycl
* e4s ci stack: add adios2 +rocm
* [@spackbot] updating style on behalf of vicentebolea
* Apply suggestions from code review
* adios2: fixed cuda variant
* update ecp-data-vis-sdk
* Update share/spack/gitlab/cloud_pipelines/stacks/e4s-power/spack.yaml
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Co-authored-by: vicentebolea <vicentebolea@users.noreply.github.com>
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when verbose (#40634)
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* gromacs +cp2k: build in CI
* libxsmm: x86 only
* attempt to fix dbcsr + new mpich
* use c11 standard
* gromacs: does not depend on dbcsr
* cp2k: build with cmake in CI, s.t. dbcsr is a separate package
* cp2k: cmake patches for config files and C/C++ std
* cp2k: remove unnecessary constraints due to patch
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This adds a `SetupContext` class which is responsible for setting
package.py module globals, and computing the changes to environment
variables for the build, test or run context.
The class uses `effective_deptypes` which takes a list of specs (e.g. single
item of a spec to build, or a list of environment roots) and a context
(build, run, test), and outputs a flat list of specs that affect the
environment together with a flag in what way they do so. This list is
topologically ordered from root to leaf, so that one can be assured that
dependents override variables set by dependencies, not the other way
around.
This is used to replace the logic in `modifications_from_dependencies`,
which has several issues: missing calls to `setup_run_environment`, and
the order in which operations are applied.
Further, it should improve performance a bit in certain cases, since
`effective_deptypes` run in O(v + e) time, whereas `spack env activate`
currently can take up to O(v^2 + e) time due to loops over roots. Each
edge in the DAG is visited once by calling `effective_deptypes` with
`env.concrete_roots()`.
By marking and propagating flags through the DAG, this commit also fixes
a bug where Spack wouldn't call `setup_run_environment` for runtime
dependencies of link dependencies. And this PR ensures that Spack
correctly sets up the runtime environment of direct build dependencies.
Regarding test dependencies: in a build context they are are build-time
test deps, whereas in a test context they are install-time test deps.
Since there are no means to distinguish the build/install type test deps,
they're both.
Further changes:
- all `package.py` module globals are guaranteed to be set before any of the
`setup_(dependent)_(run|build)_env` functions is called
- traversal order during setup: first the group of externals, then the group
of non-externals, with specs in each group traversed topological (dependencies
are setup before dependents)
- modules: only ever call `setup_dependent_run_environment` of *direct* link/run
type deps
- the marker in `set_module_variables_for_package` is dropped, since we should
call the method once per spec. This allows us to set only a cheap subset of
globals on the module: for example it's not necessary to compute the expensive
`cmake_args` and w/e if the spec under consideration is not the root node to be
built.
- `spack load`'s `--only` is deprecated (it has no effect now), and `spack load x`
now means: do everything that's required for `x` to work at runtime, which
requires runtime deps to be setup -- just like `spack env activate`.
- `spack load` no longer loads build deps (of build deps) ...
- `spack env activate` on partially installed or broken environments: this is all
or nothing now. If some spec errors during setup of its runtime env, you'll only
get the unconditional variables + a warning that says the runtime changes for
specs couldn't be applied.
- Remove traversal in upward direction from `setup_dependent_*` in packages.
Upward traversal may iterate to specs that aren't children of the roots
(e.g. zlib / python have hundreds of dependents, only a small fraction is
reachable from the roots. Packages should only modify the direct dependent
they receive as an argument)
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Improve how mirrors are used in gitlab ci, where we have until now thought
of them as only a string.
By configuring ci mirrors ahead of time using the proposed mirror templates,
and by taking advantage of the expressiveness that spack now has for mirrors,
this PR will allow us to easily switch the protocol/url we use for fetching
binary dependencies.
This change also deprecates some gitlab functionality and marks it for
removal in Spack 0.23:
- arguments to "spack ci generate":
* --buildcache-destination
* --copy-to
- gitlab configuration options:
* enable-artifacts-buildcache
* temporary-storage-url-prefix
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Currently `spack env activate --with-view` exists, but is a no-op.
So, it is not too much of a breaking change to make this redundant flag
accept a value `spack env activate --with-view <name>` which activates
a particular view by name.
The view name is stored in `SPACK_ENV_VIEW`.
This also fixes an issue where deactivating a view that was activated
with `--without-view` possibly removes entries from PATH, since now we
keep track of whether the default view was "enabled" or not.
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* Add support for Python 3.12
* Use optimized build of clingo
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* e4s arm stack: duplicate and target both neoverse n1, v1
* remove neoverse_n1 target until issue #40397 is resolved
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* Change 'exit' to 'return' in `setup-env.sh` to avoid losing shell in some cases when sourcing twice.
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* Allow branching out of the "generic build" unification set
For cases like the one in https://github.com/spack/spack/pull/39661
we need to relax rules on unification sets.
The issue is that, right now, nodes in the "generic build" unification
set are unified together with their build dependencies. This was done
out of caution to avoid the risk of circular dependencies, which would
ultimately cause a very slow solve.
For build-tools like Cython, however, the build dependencies is masked
by a long chain of "build, run" dependencies that belong in the
"generic build" unification space.
To allow splitting on cases like this, we relax the rule disallowing
branching out of the "generic build" unification set.
* Fix issue with pure build virtual dependencies
Pure build virtual dependencies were not accounted properly in the
list of possible virtuals. This caused some facts connecting virtuals
to the corresponding providers to not be emitted, and in the end
lead to unsat problems.
* Fixed a few issues in packages
py-gevent: restore dependency on py-cython@3
jsoncpp: fix typo in build dependency
ecp-data-vis-sdk: update spack.yaml and cmake recipe
py-statsmodels: add v0.13.5
* Make dependency on "blt" of type "build"
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This reverts commit bf7f54449ba8ed157c9ee258007e0a7a509600cf.
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* e4s amd64 gcc ci stack: sync with e4s-23.08
* e4s amd64 oneapi ci stack: sync with e4s-23.08
* e4s ppc64 gcc ci stack: sync with e4s-23.08
* add new ci stack: e4s amd64 gcc w/ external rocm
* add new ci stack: e4s arm gcc ci
* updates
* py-scipy: -fvisibility issue is resolved in 2023.1.0: #39464
* paraview oneapi fails
* comment out pkgs that fail to build on power
* fix arm stack name
* fix cabana +cuda specification
* comment out failing spces
* visit fails build on arm
* comment out slepc arm builds due to make issue
* comment out failing dealii arm builds
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This reverts commit 027409120408eb4d41d8bdd82a13c34b3ac7fea9.
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* Implemented +sycl for slate
* style
* style
* add slate +sycl to ci
* slate +sycl: explicitly specify +mpi
* comment out slate+sycl+mpi in e4s oneapi stack
* removing requirement of intel-oneapi-mpi
* Added slate+sycl to e4s oneapi stack
* Removing obsolete comment
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
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* py-scipy: -fvisibility issue is resolved in 2023.1.0:
* e4s oneapi ci: add py-scipy
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* e4s cray sles stack: expand spec list
* remove unnecessary packages:trilinos:one_of
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* e4s ci: add packages: drishti, dxt-explorer
* e4s oneapi ci: comment out dxt-explorer until r%oneapi issue #40257 is resolved
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