lsst-ctrl-mpexec 27.0.0 (2024-05-29)

New Features

  • Be more permissive about input/output collection consistency, and provided a --rebase option to pipetask run and pipetask qgraph to force consistency.

    An existing output collection is now considered consistent with a given sequence of input collections if the latter is a contiguous subsequence of the former. When this is not the case, --rebase redefines the output collection such that it will be. (DM-37140)

  • Updated the open-source license to allow for the code to be distributed with either GPLv3 or BSD 3-clause license. (DM-37231)

  • Adde pipeline-graph and task-graph options for pipetask build --show, which provide text-art visualization of pipeline graphs. (DM-39779)

  • Added pipetask report which reads a quantum graph and reports on the outputs of failed, produced and missing quanta. This is a command-line incarnation of QuantumGraphExecutionReport.make_reports in combination with QuantumGraphExecutionReport.write_summary_yaml. (DM-41131)

  • Added --summary option to pipetask qgraph. (DM-41542)

  • Made option to output pipetask report information to the command-line using Astropy tables and set to default. Now unpack a more human-readable dictionary from lsst.pipe.base.QuantumGraphExecutionReports.to_summary_dict and print summary tables of quanta and datasets to the command-line. Can now save error messages and associated data ids to a YAML file in the working directory, or optionally print them to screen as well. (DM-41606)

API Changes

  • SeparablePipelineExecutor.run_pipeline has been modified to take a num_proc parameter to specify how many subprocesses can be used to execute the pipeline. The default is now 1 (no spawning), which is a change from the previous behavior of using 80% of the available cores. (DM-42751)

Bug Fixes

  • Removed shadowing of pipetask build -t by pipetask qgraph -t. -t now means --task (the original meaning) rather than --transfer. (DM-35599)

  • Fixed a storage class bug in registering dataset types in pipetask run.

    Prior to this fix, the presence of multiple storage classes being associated with the same dataset type in a pipeline could cause the registered dataset type’s storage class to be random and nondeterministic in regular pipetask run execution (but not quantum-backed butler execution). It now follows the rules set by PipelineGraph, in which the definition in the task that produces the dataset wins. (DM-41962)

  • Ensured that the implicit threading options for run-qbb is used so that implicit threading can be disabled. (DM-42118)

  • Fixed dump_kwargs TypeError caused by migration to Pydantic 2. (DM-42376)

  • Fixed the --show-errors option in pipetask report.

    Correctly pass the option to the function as a flag. Then, in testing, use the --show-errors option to avoid saving YAML files to disk without adequate cleanup. (DM-43363)

  • Fixed BPS auto-retry functionality broken on DM-43060, by restoring support for repeated execution of already-successful quanta in pipetask run-qbb. (DM-43484)

Other Changes and Additions

  • Dropped support for Pydantic 1.x. (DM-42302)

An API Removal or Deprecation

  • Support for fork option in pipetask run has been removed as unsafe. Default start option now is spawn, and forkserver is also available. The fork option is still present in CLI for compatibility, but is deprecated and replaced by spawn if specified. (DM-41832)

lsst-ctrl-mpexec v26.0.0 (2023-09-23)

New Features

  • Added support for executing quantum graph using Quantum-backed butler. pipetask adds two new commands to support execution with Quantum-backed butler, mostly useful for BPS:

    • pre-exec-init-qbb which runs PreExecInit step of the execution to produce InitOutputs.

    • run-qbb which executes QuantumGraph (or individual quanta) using Quantum-backed butler. (DM-33497)

  • Added --coverage and --cov-packages to pipetask commands to allow for code coverage calculations when running (DM-34420)

  • Added SeparablePipelineExecutor, a pipeline executor midway in capability between SimplePipelineExecutor and CmdLineFwk. SeparablePipelineExecutor is designed to be run from Python, and lets the caller decide when each pipeline processing step is carried out. It also allows certain pipeline steps to be customized by passing alternate implementations of execution strategies (e.g., custom graph builder). (DM-36162)

  • pipetask will now produce QuantumGraph with resolved output references, even with execution butler option. (DM-37582)

  • Added new command update-graph-run to pipetask. It updates existing quantum graph with new output run name and re-generates output dataset IDs. (DM-38780)

  • Added new command line options --cores-per-quantum and --memory-per-quantum. These can be used to pass some execution context into a quantum, allowing that quantum to change how it executes (maybe by using multiple threads). (DM-39661)

  • Made it possible to force failures in mocked pipelines from the command-line. (DM-39672)

  • The output of the pipetask ... --show=graph now includes extended information about dataset references and their related datastore records. (DM-40254)

API Changes

  • Several modification to multiple classes to support execution with Quantum-backed butler:

    • CmdLineFwk class adds two new methods: preExecInitQBB, which only runs PreExecInit step of the execution to produce InitOutputs; and runGraphQBB, which executes QuantumGraph using Quantum-backed butler.

    • Abstract classes QuantumExecutor and QuantumGraphExecutor do not accept Butler instance in their execute() methods.

    • MPGraphExecutor and SingleQuantumExecutor methods updated to reflect above change and support execution with either full Butler or LimitedButler.

    • New class PreExecInitLimited which performs pre-exec-init in case of Quantum-backed butler. The code that it shares with a regular PreExecInit class is now in their common base class PreExecInitBase. (DM-33497)

  • Added new resources parameter to SingleQuantumExecutor, SimplePipelineExecutor, and SeparablePipelineExecutor constructors. This optional parameter is a ExecutionResources object and allows the execution context to be passed into the runQuantum method. (DM-39661)

Bug Fixes

  • Fixed SingleQuantumExecutor class to correctly handle the case with clobberOutputs=True and skipExistingIn=None. Documentation says that complete quantum outputs should be removed in this case, but they were not removed. (DM-38601)

Other Changes and Additions

    • SingleQuantumExecutor has been modified such that it no longer unresolves DatasetRef when putting the non- PipelineTask datasets (such as packages and configs). This has been done so that the refs in the quantum graph are preserved when they are written to a normal Butler.

    • Fixed a race condition when pipetask run creates the graph with a timestamped output run and then executes it. Previously the graph creation and run execution phases calculated their own timestamped output run and it would be possible for the execution output run to be one second later than the graph run. Previously this did not matter (the graph run was being ignored) but with the change to always use the DatasetRef from the graph it becomes critical that they match. (DM-38779)

  • Revive the previously-bitrotted pipeline mocking system.

    Most of the implementation has been moved to pipe_base, and the point at which mocking occurs has moved from execution to just before QuantumGraph generation, which changes which pipetask subcommands the --mock option is valid for. (DM-38952)

  • Updated the directed graph color scheme with an aim towards making node text easier to read. The previous pipeline directed graph nodes used dark gray as their background color. It had been reported that it is difficult to read the black text on the dark gray background. In the process of exploring what color schemes would be optimal to satisfy the aim of this ticket, it emerged that making use of the Rubin visual identity colors may be desirable. This will help to make LSST pipeline graphs more instantly recognizable as Rubin-associated products. Colors: https://rubin.canto.com/g/RubinVisualIdentity (DM-39294)

  • The saveMetadata configuration field is now ignored by executors in this package, metadata is assumed to be saved for each task. (DM-39377)

  • Improved logging and removed some obsolete code paths in SingleQuantumExecutor. (DM-40332)

  • Command line help for pipetask run has been updated to reflect its correct clobbering behavior.

lsst-ctrl-mpexec v25.0.0 (2023-02-28)

New Features

    • Added support for transferring files into execution butler. (DM-35494)

    • Added documentation on how to use --show and --config.

    • A pipeline will now never execute if --show option is used with pipetask run.

    • The --config option can now accept list configuration values (with or without square brackets), for example --config task:listItem=a,b or --config "task:listItem=[a,b]".

    • The --config-file option can now take comma-separated file names for multiple config files. (DM-35917)

    • added additional quanta information to be displayed by the logger, showing number of quanta per task (DM-36145)

  • If pipetask is run with multiple processes and if a butler datastore cache is configured, all subprocesses will now share the same cache. For large numbers of simultaneous processes it may be necessary to significantly increase the number of datasets in the cache to make the cache usable. This can be done by using the $DAF_BUTLER_CACHE_EXPIRATION_MODE environment variable.

    Previously each subprocess would get its own cache and if fork start method was used these cache directories would not be cleaned up. (DM-36412)

  • Always disable implicit threading (e.g. in OpenBLAS) by default in pipetask run, even when not using -j.

    The new --enable-implicit-threading can be used to turn it back on. (DM-36831)

API Changes

  • SimplePipelineExecutor factory methods add bind parameter for bind values to use with the user expression. (DM-36487)

lsst-ctrl-mpexec v24.0.0 (2022-08-26)

New Features

  • Added --dataset-query-constraint option to pipetask qgraph command (and thus downstream commands) that allows a user to control how QuantumGraph creation is constrained by dataset existence. (DM-31769)

  • Builds using setuptools now calculate versions from the Git repository, including the use of alpha releases for those associated with weekly tags. (DM-32408)

  • Added --summary option to pipetask run command, it produces JSON report for execution status of the whole process and individual quanta. (DM-33481)

  • Added pipetask CLI commands purge and cleanup. (DM-33634)

  • Removed dependency on the obs_base and afw packages. Now only depends on pipe_base and daf_butler (along with pex_config and utils). (DM-34105)

  • Replaced the unused --do-raise option with --pdb, which drops the user into the debugger (pdb by default, but --pdb=ipdb also works if you have ipdb installed) on an exception. (DM-34215)

Bug Fixes

  • The click.Path API should mostly be used with keyword arguments, changed from ordered arguments to keyword arguments when calling it. (DM-34261)

  • Fixed a bug where dot graphs of pipelines did not correctly render edges between composite and component dataset types. (DM-34811)

Other Changes and Additions

lsst-ctrl-mpexec v23.0.1 (2022-02-02)

Miscellaneous Changes of Minor Interest

  • Allow pipetask run execution to continue in single-process mode after failure of one or more tasks. Previously execution stopped on an exception from any task. (DM-33339)

lsst-ctrl-mpexec v23.0.0 (2021-12-10)

New Features

  • Several improvements in pipetask execution options:

    • New option --skip-existing-in which takes collection names(s), if output datasets already exist in those collections corresponding quanta is skipped.

    • A --skip-existing option is now equivalent to appending output run collection to the --skip-existing-in list.

    • An --extend-run option implicitly enables --skip-existing option.

    • A --prune-replaced=unstore option only removes regular output datasets; InitOutputs, task configs, and package versions are not removed. (DM-27492)

  • GraphViz dot files generated by pipetask now include more information (RUN collection for datasets, dimensions for tasks, data IDs for quanta). (DM-28111)

  • pipetask qgraph can now generate a standalone “execution butler” which is a SQLite registry with all the expected outputs pre-filled in registry. Using this registry allow pipetask run to execute without touching the main registry whilst still writing file artifacts to the standard location. It is not yet configured to allow a completely detached processing using a local datastore but this can be changed manually after creation to use a chained datastore. (DM-28649)

    • Log messages issued during quantum execution are now collected and stored in butler as tasklabel_log dataset types.

    • New command line options for logging have been added to pipetask. These include --log-file to write log messages to a file and --no-log-tty to disable log output to the terminal. (DM-30977)

    • Add the output run to the log record.

    • Add --log-label option to pipetask command to allow extra information to be injected into the log record. (DM-31884)

Bug Fixes

  • Improve exception handling in ExecFixupDataId (DM-29384)

  • Fix config comparison with --skip-existing. (DM-29580)

  • Include output collection in call to buildExecutionButler. (DM-31691)

  • Fix call to buildExecutionButler when chained input collection. (DM-31711)

Miscellaneous Changes of Minor Interest

  • Add some of the pipetask command line options to QuantumGraph metadata (DM-30702)

lsst-ctrl-mpexec v22.0 (2021-04-01)

New Features

  • pipetask run can now execute a subset of a graph. This allows a single graph file to be created with an entire workflow and then only part of it to be executed. This is very important for large scale workflow execution. [DM-27667]

Performance Enhancement

  • Multi-processing execution performance has been significantly improved for large graphs. [DM-28418]

Other

  • Ignore --input instead of rejecting it if it hasn’t changed. [DM-28101]

  • The graph file format has been changed from a pickle file to a form that can efficiently be accessed from an object store. This new format has a .qgraph file extension. [DM-27784]

  • A full URI can now be used to specify the location of the quantum graph. [DM-27682]