* AMReX: 23.06+ Multi-Dim Support
This updated the Spack package to allow to install AMReX, modules of
AMReX in E4S deployments and dependent packages with support for
multiple dimensions. Due to an upstream change in AMReX, we do not
longer need to ship three, binary incompatible package variants.
* [E4S] oneAPI AMReX < 23.06 Variant
Work-around the auto-concretization to the multi-dim of `dimensions`,
which only in 23.06+ became a multi-variant.
* e4s cray rhel ci: temporarily disable amrex build until spurious ci failure can be resolved
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Refactor gitlab ci configs so that mac and cray jobs can reuse as much higher level
configuration as possible.
* CI: remove redundant sections
* CI: Include base linux CI configs in cray stacks
Relocation and runner mapping is consistent between cray and linux runners.
* Export user cache path in before script
* CI: add GPG root for mac runners
* Disable user configs
Metal runners share a ~ directory
* Disable user config and add configs in activate env
* ci: run spack list in power ci
Let's see if Spack itself is the bottleneck in CI...
* rebuild curl in CI
* more of the same please!
* drop the profiler
* undo rebuildme test in ci variant
* add comment for posterity
* enable profiling
* trigger CI
* See how it goes now that perf regressions are fixed on develop
* try shorter poll intervals
* Revert "try shorter poll intervals"
This reverts commit d60c34ad3eceead0c13a5277cf8e783fd42b7458.
* Remove spec.format call in Database._get_matching_spec_key
* once more in ci please
* undo irrelevant changes
* run spack list in before script
* test in ci
* -:
* Undo CI testing
* openssl: prefer 3.x
This PR is not intended to be merged immediately, but it would be good
to see what packages fail to build in CI so that we can get proper
version constraints on openssl (before all packages update and support
both openssl 1 and 3)
* Disable assembly for 3.x %oneapi
* cmake: depend on spack curl, to deal with curl - openssl compat
* also make zlib external
* remove overly strict & unsafe requirement on py-cryptographty patch version number
* update openssl compat bounds in py-cryptography
* smaller diff
* Make libssh2 an autotools/cmake package
* fix weird upperbound in libssh2 as there is not openssl v2
* libssh2: pc file lists plain -lssl -lcrypto w/o leading -L flag, confusing libgit2 parsing of pkg-config output
* Actually fix the issue in libssh2: its pc file looks broken
* WarpX 23.06
Update WarpX and related Python packages to the lastest releases.
WarpX 23.06 introduces multi-dimension support in a single package,
which will ease deployment in E4S et al. that can ship now a single,
full-feature module/package that is NOT incompatible with itself
anymore.
* e4s ci stacks: multiple specs for each dim variant no longer required
* [@spackbot] updating style on behalf of ax3l
* WarpX: Update CMake CLI and Test/Check
* Add Missing `build-directory`
* [@spackbot] updating style on behalf of ax3l
* Remove `build_directory` again
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Co-authored-by: ax3l <ax3l@users.noreply.github.com>
The pcluster image has am internal buildcache without an index.
Also, we need to force reuse to avoid rebuilding GCC, since the default is
to only reuse dependencies - and that is subject to changes in the GCC
recipe.
* e4s oneapi ci: use official intel oneapi-derived runner image
* update oneapi image
* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
* e4s cray ci stack
* e4s ci: add cray
* add zen4 tag
* WIP: new defintions just for cray
* updates
* remove ci signing job overrride, not necessary
* echo $PATH and show modules loaded
* add mirror
* add external def for cray-libsci
* comment out quantum-espresso
* use /etc/protected-runner as key path
* cray ci stack: do not remove tags: [spack, public]
* make cray stack composable
* generate job should run on public tagged runner, override default config:install_tree:root
* CI: Use relative path in default script
* CI: Use relative includes paths for shell runners
* Use concrete_env_dir for relpath
* ml-darwin-aarch64-mps: jax has bazel codesign issue
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
* llvm: replace +omp_as_runtime with omp=runtime
* llvm: fetch 'libomp-libflags-as-list.patch' from upstream repo
* llvm: replace 'llvm14-hwloc-ompd.patch' with the official fix from upstream repo
* llvm: fix-up for the black reformatting
* llvm: fetch 'constexpr_longdouble.patch' from upstream repo
* llvm: optionally build libcxx as a runtime
* llvm: fetch 'llvm5-sanitizer-ustat.patch' from upstream repo
* llvm: update 'sanitizer-ipc_perm_mode.patch'
* llvm: refactor compiler conflicts when libcxx=project
* llvm: fetch 'llvm_python_path.patch' from upstream repo
* llvm: update comments and condition for 'xray_buffer_queue-cstddef.patch'
* llvm: optionally build compiler-rt as a runtime
* llvm: fetch 'lldb_external_ncurses-10.patch' from upstream repo
* llvm: fetch 'llvm_py37.patch' from upstream repo
* llvm: rename variant 'internal_unwind' to 'libunwind'
* llvm: optionally build libunwind as a runtime
* llvm: extend the list of maintainers
* llvm: allow for explicit '~clang~flang~libomptarget~lldb~omp_debug~z3'
* llvm: fetch 'llvm5-lld-ELF-Symbols.patch' from FreeBSD port repo
* llvm: fetch most of 'missing-includes.patch' from upstream repo and reuse 'llvm-gcc11.patch'
* llvm: regroup patches for missing include directives and drop compiler constraints for them
* llvm: fetch 'llvm-gcc11.patch' from upstream repo
* llvm: fetch 'no_cyclades.patch' from upstream repo
* llvm: update comments and condition for 'no_cyclades9.patch'
* llvm: rename variant 'omp' to 'openmp'
* llvm: constrain and rename variant 'omp_tsan' to 'libomp_tsan'
* llvm: rename variant 'omp_debug' to 'libomptarget_debug'
* llvm: do not apply same patch twice
* llvm: constrain and document the '*-thread.patch' patches
* llvm: document the '~lld+libomptarget' conflict
* llvm: update comments for the 'D133513.diff' patch
* Add macOS ML CI stacks
* torchmeta is no longer maintained and requires ancient PyTorch
* Add MXNet
* update darwin aarch64 stacks
* add darwin-aarch64 scoped config.yaml
* remove unnecessary cleanup job
* fix specifications
* fix labels
* fix labels
* fix indent on tags specification
* no tags for trigger jobs
* try overriding tags in stack spack.yaml
* do not use CI_STACK_CONFIG_SCOPES
* incorporate config:install_tree:root: overrides and compiler defs
* copy relevant ci-scoped config settings directly into stack spack.yaml
* remove build-job-remove
* spack ci generate: add debug flag
* include cdash config directly in stack spack.yaml
* customize build-job script section to avoid absolute paths
* add any-job specification
* tags: use aarch64-macos instead of aarch64
* generate tags: use aarch64-macos instead of aarch64
* do not add morepadding
* use shared mirror; comment out known failures
* remove any-job
* nproc || true
* comment out specs failing due to bazel from cache codesign issue
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
* [pcluster pipeline] Use local buildcache instead of upstream spack
Spack currently does not relocate compiler references from upstream spack
installations. When using a buildcache we don't need an upstream spack.
* gcc needs to be installed via postinstall to get correct deps
* quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1
* Force gitlab to pull the new container
* Revert "Force gitlab to pull the new container"
This reverts commit 3af5f4cd88.
Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml
* Gitlab keeps picking up wrong container. Renaming
* Update containers once more after failed build
Add aws-plcuster[-aarch64] stacks. These stacks build packages defined in
https://github.com/spack/spack-configs/tree/main/AWS/parallelcluster
They use a custom container from https://github.com/spack/gitlab-runners which
includes necessary ParallelCluster software to link and build as well as an
upstream spack installation with current GCC and dependencies.
Intel and ARM software is installed and used during the build stage but removed
from the buildcache before the signing stage.
Files `configs/linux/{arch}/ci.yaml` select the necessary providers in order to
build for specific architectures (icelake, skylake, neoverse_{n,v}1).
* CI: Expand E4S ROCm stack to include missing DaV packages
Ascent: Fixup for VTK-m with Kokkos backend
* DaV SDK: Removed duplicated openmp variant for ascent
* Drop visit and add conflict for Kokkos
* E4S: Drop ascent from CUDA builds
Ensure that requirements `packages:*:require:@x` and preferences `packages:*:version:[x]`
fail concretization when no version defined in the package satisfies `x`. This always holds
except for git versions -- they are defined on the fly.
* gitlab ci: release fixes and improvements
- use rules to reduce boilerplate in .gitlab-ci.yml
- support copy-only pipeline jobs
- make pipelines for release branches rebuild everything
- make pipelines for protected tags copy-only
* gitlab ci: remove url changes used in testing
* gitlab ci: tag mirrors need public key
Make sure that mirrors associated with release branches and tags
contain the public key needed to verify the signed binaries. This
also ensures that when stack-specific mirror contents are copied
to the root, the root mirror has the public key as well.
* review: be more specific about tags, curl flags
* Make the check in ci.yaml consistent with the .gitlab-ci.yml
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
The flags --mirror-name / --mirror-url / --directory were deprecated in
favor of just passing a positional name, url or directory, and letting spack
figure it out.
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
* DaV SDK: Enable ParaView raytracing with in SDK
* CI: Drop swr testing from Data Vis SDK
* ISPC: extend LLVM requirement to main
* DaV SDK: Disallow concretizing develop unifyfs
No longer needed after mochi-margo patch
* CI: Fixup docs for bootstrap.
* CI: Add compatibility shim
* Add an update method for CI
Update requires manually renaming section to `ci`. After
this patch, updating and using the deprecated `gitlab-ci` section
should be possible.
* Fix typos in generate warnings
* Fixup CI schema validation
* Add unit tests for legacy CI
* Add deprecated CI stack for continuous testing
* Allow updating gitlab-ci section directly with env update
* Make warning give good advice for updating gitlab-ci
* Fix typo in CI name
* Remove white space
* Remove unneeded component of deprected-ci
* ECP-SDK: enable hdf5 VOL adapters
- When +hdf5, enable VOL adapters suitable for the SDK.
- Each VOL package must prepend to the HDF5_PLUGIN_PATH.
- hdf5: 1.13.3 will break existing VOL packages, constrain
VOLs related to SDK and add note to keep 1.13.2 available.
- hdf5-vol-async:
- Do not set HDF5_VOL_CONNECTOR, consumers must opt-in.
- Enforce DAG constraints on MPI to require threaded version.
- Depend on an explicit version of argbots to relax
concretization issues in other spack environments.
- paraview: fix compiler flag usage for the 110 ABI (followup to #33617).
* ECP Data and ViS: Add constraits for HDF5 VOLS
* CI: HDF5 1.14 builds without VisIt
* hdf5-vol-async: Update docs string
---------
Co-authored-by: Stephen McDowell <stephen.mcdowell@kitware.com>
* py-pytorch-lightning: add v2.0.0
* py-lightning-utilities: add v0.8.0
* Update all PyTorch packages
* Open-CE does not yet have patches for PyTorch 2 on ppc64le
* ci: version bump for ghcr.io/spack/e4s-amazonlinux-2
This new image comes with GnuPG v2.4.0
* py-cython: upperbounds for Python versions
* fix py-gevent nonsense
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* CI configuration boilerplate reduction and refactor
Configuration:
- New notation for list concatenation (prepend/append)
- New notation for string concatenation (prepend/append)
- Break out configuration files for: ci.yaml, cdash.yaml, view.yaml
- Spack CI section refactored to improve self-consistency and
composability
- Scripts are now lists of lists and/or lists of strings
- Job attributes are now listed under precedence ordered list that are
composed/merged using Spack config merge rules.
- "service-jobs" are identified explicitly rather than as a batch
CI:
- Consolidate common, platform, and architecture configurations for all CI stacks into composable configuration files
- Make padding consistent across all stacks (256)
- Merge all package -> runner mappings to be consistent across all
stacks
Unit Test:
- Refactor CI module unit-tests for refactor configuration
Docs:
- Add docs for new notations in configuration.rst
- Rewrite docs on CI pipelines to be consistent with refactored CI
workflow
* Script verbose environ, dev bootstrap
* Port #35409
By setting the traversal depth to 1, only specs matching the changed
package and direct dependents of those (and of course all dependencies
of that set) are removed from pruning candidacy.
* e4s: restore builds builds
* gitlab ci: allow UO to build protected binaries for signing
* use newer image; comment out failing builds
* gitlab-ci: Some tweaks for e4s power builds
- fix tags (no longer require generate jobs to run on aws)
- fix resource requests for generation jobs resource requests
- remove SPACK_SIGNING_KEY from protected power build jobs
- update UO signing key path
- change the CDash build group to reflect stack name
- retry pipeline generation jobs *always*
* correct double packages: section
* gitlab-ci:script: modernize
* remove new gnu make, not for ppc64le
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
* paraview: add `rocm` variant
This conflicts with CUDA and requires at least ParaView 5.11.0. More
dependencies are also needed.
* E4S: Add ParaView for ROCm and CUDA stacks
* DAV SDK: Update ParaView version and GPU variants
* Verify using hipcc vs amdclang++ for newer hip
Co-authored-by: Ben Boeckel <ben.boeckel@kitware.com>
Gitlab does not merge lists when a job extends two other definitions
that include the same list (e.g. tags). Also, it merges dictionaries
as long as the keys are distinct, but just takes the last mentioned
value when there are key collisions.
This change makes sure that when different tags are needed by a
pipeline, the ones we want are actually provided. It also changes
the example stack to better follow this pattern so we do not lead
developers astray in the future.
* ML CI: Linux x86_64
* Update comments
* Rename again
* Rename comments
* Update to match other arches
* No compiler
* Compiler was wrong anyway
* Faster TF
* CI: Update Data and Vis SDK Stack
* Update image to match target deployments (E4S)
* Enable all packages
* Test supported variants of ParaView and VisIt
* Sensei: Update Python hint for newer cmake
* Sensei: add Python3 hint
This commit extends the DSL that can be used in packages
to allow declaring that a package uses different build-systems
under different conditions.
It requires each spec to have a `build_system` single valued
variant. The variant can be used in many context to query, manipulate
or select the build system associated with a concrete spec.
The knowledge to build a package has been moved out of the
PackageBase hierarchy, into a new Builder hierarchy. Customization
of the default behavior for a given builder can be obtained by
coding a new derived builder in package.py.
The "run_after" and "run_before" decorators are now applied to
methods on the builder. They can also incorporate a "when="
argument to specify that a method is run only when certain
conditions apply.
For packages that do not define their own builder, forwarding logic
is added between the builder and package (methods not found in one
will be retrieved from the other); this PR is expected to be fully
backwards compatible with unmodified packages that use a single
build system.
When we lose a running pod (possibly loss of spot instance) or encounter
some other infrastructure-related failure of this job, we need to retry
it. This retries the job the maximum number of times in those cases.
`reuse` and `when_possible` concretization broke the invariant that
`spec[pkg_name]` has unique keys. This invariant is relied on in tons of
places, such as when setting up the build environment.
When using `when_possible` concretization, one may end up with two or
more `perl`s or `python`s among the transitive deps of a spec, because
concretization does not consider build-only deps of reusable specs.
Until the code base is fixed not to rely on this broken property of
`__getitem__`, we should disable reuse in CI.
Currently "spack ci generate" chooses the first matching entry in
gitlab-ci:mappings to fill attributes for a generated build-job,
requiring that the entire configuration matrix is listed out
explicitly. This unfortunately causes significant problems in
environments with large configuration spaces, for example the
environment in #31598 (spack.yaml) supports 5 operating systems,
3 architectures and 130 packages with explicit size requirements,
resulting in 1300 lines of configuration YAML.
This patch adds a configuraiton option to the gitlab-ci schema called
"match_behavior"; when it is set to "merge", all matching entries
are applied in order to the final build-job, allowing a few entries
to cover an entire matrix of configurations.
The default for "match_behavior" is "first", which behaves as before
this commit (only the runner attributes of the first match are used).
In addition, match entries may now include a "remove-attributes"
configuration, which allows matches to remove tags that have been
aggregated by prior matches. This only makes sense to use with
"match_behavior:merge". You can combine "runner-attributes" with
"remove-attributes" to effectively override prior tags.
Basic stack of ML packages we would like to test and generate binaries for in CI.
Spack now has a large CI framework in GitLab for PR testing and public binary generation.
We should take advantage of this to test and distribute optimized binaries for popular ML
frameworks.
This is a pretty extensive initial set, including CPU, ROCm, and CUDA versions of a core
`x96_64_v4` stack.
### Core ML frameworks
These are all popular core ML frameworks already available in Spack.
- [x] PyTorch
- [x] TensorFlow
- [x] Scikit-learn
- [x] MXNet
- [x] CNTK
- [x] Caffe
- [x] Chainer
- [x] XGBoost
- [x] Theano
### ML extensions
These are domain libraries and wrappers that build on top of core ML libraries
- [x] Keras
- [x] TensorBoard
- [x] torchvision
- [x] torchtext
- [x] torchaudio
- [x] TorchGeo
- [x] PyTorch Lightning
- [x] torchmetrics
- [x] GPyTorch
- [x] Horovod
### ML-adjacent libraries
These are libraries that aren't specific to ML but are still core libraries used in ML pipelines
- [x] numpy
- [x] scipy
- [x] pandas
- [x] ONNX
- [x] bazel
Co-authored-by: Jonathon Anderson <17242663+blue42u@users.noreply.github.com>
PR #32615 deprecated Python versions up to 3.6.X. Since
the "build-systems" pipeline requires Python 3.6.15 to
build "tut", it will fail on the first rebuild that
involves Python.
The "tut" package is meant to perform an end-to-end
test of the "Waf" build-system, which is scarcely
used. The fix therefore is just to remove it from
the pipeline.
amazon linux 2 ships a glibc that is too old to work with cuda toolkit
for aarch64.
For example:
`libcurand.so.10.2.10.50` requires the symbol `logf@@GLIBC_2.27`, but
glibc is at 2.26.
So, these specs are removed.
Move the copying of the buildcache to a root job that runs after all the child
pipelines have finished, so that the operation can be coordinated across all
child pipelines to remove the possibility of race conditions during potentially
simlutandous copies. This lets us ensure the .spec.json.sig and .spack files
for any spec in the root mirror always come from the same child pipeline
mirror (though which pipeline is arbitrary). It also allows us to avoid copying
of duplicates, which we now do.
This support requires adding the '--tests' option to 'spack ci rebuild'.
Packages whose stand-alone tests are broken (in the CI environment) can
be configured in gitlab-ci to be skipped by adding them to
broken-tests-packages.
Highlights include:
- Restructured 'spack ci' help to provide better subcommand summaries;
- Ensured only one InstallError (i.e., installer's) rather than allowing
build_environment to have its own; and
- Refactored CI and CDash reporting to keep CDash-related properties and
behavior in a separate class.
This allows stand-alone tests from `spack ci` to run when the `--tests`
option is used. With `--tests`, stand-alone tests are run **after** a
**successful** (re)build of the package. Test results are collected
and report(able) using CDash.
This PR adds the following features:
- Adds `-t` and `--tests` to `spack ci rebuild` to run stand-alone tests;
- Adds `--fail-fast` to stop stand-alone tests after the first failure;
- Ensures a *single* `InstallError` across packages
(i.e., removes second class from build environment);
- Captures skipping tests for externals and uninstalled packages
(for CDash reporting);
- Copies test logs and outputs to the CI artifacts directory to facilitate
debugging;
- Parses stand-alone test results to report outputs from each `run_test` as
separate test parts (CDash reporting);
- Logs a test completion message to allow capture of timing of the last
`run_test` part;
- Adds the runner description to the CDash site to better distinguish entries
in CDash tables;
- Adds `gitlab-ci` `broken-tests-packages` to CI configuration to skip
stand-alone testing for packages with known issues;
- Changes `spack ci --help` so description of each subcommand is a single line;
- Changes `spack ci <subcommand> --help` to provide the full description of
each command (versus no description); and
- Ensures `junit` test log file ends in an `.xml` extension (versus default where
it does not).
Tasks:
- [x] Include the equivalent of the architecture information, or at least the host target, in the CDash output
- [x] Upload stand-alone test results files as `test` artifacts
- [x] Confirm tests are run in GitLab
- [x] Ensure CDash results are uploaded as artifacts
- [x] Resolve issues with CDash build-and test results appearing on same row of the table
- [x] Add unit tests as needed
- [x] Investigate why some (dependency) packages don't have test results (e.g., related from other pipelines)
- [x] Ensure proper parsing and reporting of skipped tests (as `not run`) .. post- #28701 merge
- [x] Restore the proper CDash URLand or mirror ONCE out-of-band testing completed
