simstack 2.0.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- simstack/__init__.py +0 -0
- simstack/_version.py +24 -0
- simstack/core/__init__.py +0 -0
- simstack/core/artifacts.py +406 -0
- simstack/core/asnyc_helper.py +14 -0
- simstack/core/config_file.py +60 -0
- simstack/core/context.py +283 -0
- simstack/core/definitions.py +22 -0
- simstack/core/engine.py +115 -0
- simstack/core/find_simstack_modules.py +41 -0
- simstack/core/hash.py +179 -0
- simstack/core/node.py +1137 -0
- simstack/core/node_claim.py +31 -0
- simstack/core/node_runner.py +362 -0
- simstack/core/process_results.py +102 -0
- simstack/core/recompute_artifacts.py +117 -0
- simstack/core/reset_db.py +12 -0
- simstack/core/resource_assignment.py +222 -0
- simstack/core/resources.py +90 -0
- simstack/core/route_table.py +24 -0
- simstack/core/run_docker.py +109 -0
- simstack/core/run_node.py +71 -0
- simstack/core/runner.py +169 -0
- simstack/core/services/__init__.py +11 -0
- simstack/core/services/base_service.py +191 -0
- simstack/core/services/file_transfer_service.py +117 -0
- simstack/core/services/git_restart_service.py +12 -0
- simstack/core/services/git_uv_update_service.py +105 -0
- simstack/core/services/node_execution_service.py +182 -0
- simstack/core/services/resource_branch_monitor_service.py +71 -0
- simstack/core/services/runner_cleanup_service.py +149 -0
- simstack/core/services/runner_manager.py +163 -0
- simstack/core/services/runner_status_service.py +10 -0
- simstack/core/services/slurm_status_service.py +67 -0
- simstack/core/services/stop_check_service.py +27 -0
- simstack/core/services/timeout_restart_service.py +26 -0
- simstack/core/simstack_result.py +39 -0
- simstack/core/submit_node.py +217 -0
- simstack/core/task_id.py +22 -0
- simstack/methods/__init__.py +0 -0
- simstack/methods/archive_files.py +292 -0
- simstack/methods/fire_and_forget_runner.py +113 -0
- simstack/methods/generate_test.py +125 -0
- simstack/methods/get_file.py +26 -0
- simstack/methods/mass_runner.py +154 -0
- simstack/methods/multiple_executor.py +307 -0
- simstack/methods/switch_git.py +16 -0
- simstack/methods/upload_helpers.py +81 -0
- simstack/models/__init__.py +74 -0
- simstack/models/array_list.py +21 -0
- simstack/models/array_storage.py +83 -0
- simstack/models/artifact_models.py +127 -0
- simstack/models/base_lists.py +51 -0
- simstack/models/base_types.py +209 -0
- simstack/models/charts_artifact.py +690 -0
- simstack/models/dataset.py +451 -0
- simstack/models/dataset_metadata.py +390 -0
- simstack/models/datasettuple.py +587 -0
- simstack/models/file_instance.py +150 -0
- simstack/models/file_list.py +45 -0
- simstack/models/files.py +424 -0
- simstack/models/fire_and_forget_result.py +19 -0
- simstack/models/images2d.py +113 -0
- simstack/models/log_entry_model.py +37 -0
- simstack/models/models.py +52 -0
- simstack/models/named_data_reference.py +36 -0
- simstack/models/node_registry.py +96 -0
- simstack/models/pandas_model.py +239 -0
- simstack/models/parameters.py +402 -0
- simstack/models/pickle_models.py +300 -0
- simstack/models/project.py +13 -0
- simstack/models/resource_assignment.py +170 -0
- simstack/models/resource_definition.py +125 -0
- simstack/models/runner_model.py +39 -0
- simstack/models/simple_table.py +79 -0
- simstack/models/simstack_model.py +97 -0
- simstack/models/slurm_info.py +17 -0
- simstack/models/table_artifact.py +87 -0
- simstack/models/tag.py +12 -0
- simstack/models/unused_test_file.py +5 -0
- simstack/simstack_marker.com +1 -0
- simstack/static/docs/.buildinfo +4 -0
- simstack/static/docs/_images/GUI Concept.webp +0 -0
- simstack/static/docs/_modules/index.html +434 -0
- simstack/static/docs/_modules/simstack/core/artifacts.html +743 -0
- simstack/static/docs/_modules/simstack/core/asnyc_helper.html +330 -0
- simstack/static/docs/_modules/simstack/core/config_file.html +379 -0
- simstack/static/docs/_modules/simstack/core/definitions.html +341 -0
- simstack/static/docs/_modules/simstack/core/engine.html +437 -0
- simstack/static/docs/_modules/simstack/core/find_simstack_modules.html +360 -0
- simstack/static/docs/_modules/simstack/core/hash.html +528 -0
- simstack/static/docs/_modules/simstack/core/node.html +1392 -0
- simstack/static/docs/_modules/simstack/core/node_claim.html +347 -0
- simstack/static/docs/_modules/simstack/core/node_runner.html +711 -0
- simstack/static/docs/_modules/simstack/core/process_results.html +418 -0
- simstack/static/docs/_modules/simstack/core/recompute_artifacts.html +433 -0
- simstack/static/docs/_modules/simstack/core/reset_db.html +328 -0
- simstack/static/docs/_modules/simstack/core/resource_assignment.html +553 -0
- simstack/static/docs/_modules/simstack/core/resources.html +424 -0
- simstack/static/docs/_modules/simstack/core/route_table.html +349 -0
- simstack/static/docs/_modules/simstack/core/run_docker.html +425 -0
- simstack/static/docs/_modules/simstack/core/run_node.html +390 -0
- simstack/static/docs/_modules/simstack/core/runner.html +491 -0
- simstack/static/docs/_modules/simstack/core/services/base_service.html +522 -0
- simstack/static/docs/_modules/simstack/core/services/file_transfer_service.html +436 -0
- simstack/static/docs/_modules/simstack/core/services/git_restart_service.html +331 -0
- simstack/static/docs/_modules/simstack/core/services/git_uv_update_service.html +427 -0
- simstack/static/docs/_modules/simstack/core/services/node_execution_service.html +507 -0
- simstack/static/docs/_modules/simstack/core/services/resource_branch_monitor_service.html +390 -0
- simstack/static/docs/_modules/simstack/core/services/runner_cleanup_service.html +468 -0
- simstack/static/docs/_modules/simstack/core/services/runner_manager.html +485 -0
- simstack/static/docs/_modules/simstack/core/services/runner_status_service.html +329 -0
- simstack/static/docs/_modules/simstack/core/services/slurm_status_service.html +386 -0
- simstack/static/docs/_modules/simstack/core/services/stop_check_service.html +346 -0
- simstack/static/docs/_modules/simstack/core/services/timeout_restart_service.html +345 -0
- simstack/static/docs/_modules/simstack/core/simstack_result.html +355 -0
- simstack/static/docs/_modules/simstack/core/submit_node.html +536 -0
- simstack/static/docs/_modules/simstack/core/task_id.html +344 -0
- simstack/static/docs/_modules/simstack/methods/archive_files.html +598 -0
- simstack/static/docs/_modules/simstack/methods/fire_and_forget_runner.html +432 -0
- simstack/static/docs/_modules/simstack/methods/generate_test.html +443 -0
- simstack/static/docs/_modules/simstack/methods/get_file.html +342 -0
- simstack/static/docs/_modules/simstack/methods/mass_runner.html +476 -0
- simstack/static/docs/_modules/simstack/methods/multiple_executor.html +674 -0
- simstack/static/docs/_modules/simstack/methods/switch_git.html +332 -0
- simstack/static/docs/_modules/simstack/methods/upload_helpers.html +403 -0
- simstack/static/docs/_modules/simstack/models/array_list.html +337 -0
- simstack/static/docs/_modules/simstack/models/array_storage.html +417 -0
- simstack/static/docs/_modules/simstack/models/base_lists.html +374 -0
- simstack/static/docs/_modules/simstack/models/base_types.html +588 -0
- simstack/static/docs/_modules/simstack/models/charts_artifact.html +1035 -0
- simstack/static/docs/_modules/simstack/models/dataset.html +866 -0
- simstack/static/docs/_modules/simstack/models/dataset_metadata.html +711 -0
- simstack/static/docs/_modules/simstack/models/datasettuple.html +1005 -0
- simstack/static/docs/_modules/simstack/models/file_instance.html +472 -0
- simstack/static/docs/_modules/simstack/models/file_list.html +367 -0
- simstack/static/docs/_modules/simstack/models/files.html +773 -0
- simstack/static/docs/_modules/simstack/models/fire_and_forget_result.html +335 -0
- simstack/static/docs/_modules/simstack/models/images2d.html +447 -0
- simstack/static/docs/_modules/simstack/models/log_entry_model.html +356 -0
- simstack/static/docs/_modules/simstack/models/models.html +374 -0
- simstack/static/docs/_modules/simstack/models/named_data_reference.html +355 -0
- simstack/static/docs/_modules/simstack/models/node_registry.html +415 -0
- simstack/static/docs/_modules/simstack/models/pandas_model.html +570 -0
- simstack/static/docs/_modules/simstack/models/parameters.html +739 -0
- simstack/static/docs/_modules/simstack/models/pickle_models.html +631 -0
- simstack/static/docs/_modules/simstack/models/project.html +329 -0
- simstack/static/docs/_modules/simstack/models/resource_assignment.html +501 -0
- simstack/static/docs/_modules/simstack/models/resource_definition.html +477 -0
- simstack/static/docs/_modules/simstack/models/runner_model.html +361 -0
- simstack/static/docs/_modules/simstack/models/simple_table.html +413 -0
- simstack/static/docs/_modules/simstack/models/simstack_model.html +416 -0
- simstack/static/docs/_modules/simstack/models/slurm_info.html +333 -0
- simstack/static/docs/_modules/simstack/models/table_artifact.html +406 -0
- simstack/static/docs/_modules/simstack/models/tag.html +328 -0
- simstack/static/docs/_modules/simstack/tables/model_table.html +519 -0
- simstack/static/docs/_modules/simstack/tables/node_children.html +538 -0
- simstack/static/docs/_modules/simstack/tables/node_table.html +854 -0
- simstack/static/docs/_modules/simstack/tables/table_builder.html +642 -0
- simstack/static/docs/_modules/simstack/util/async_zip_utils.html +337 -0
- simstack/static/docs/_modules/simstack/util/b64mixin.html +339 -0
- simstack/static/docs/_modules/simstack/util/cleaned_json_schema.html +336 -0
- simstack/static/docs/_modules/simstack/util/config_reader.html +498 -0
- simstack/static/docs/_modules/simstack/util/custom_model_dump.html +391 -0
- simstack/static/docs/_modules/simstack/util/database_information.html +488 -0
- simstack/static/docs/_modules/simstack/util/db.html +1392 -0
- simstack/static/docs/_modules/simstack/util/db_logger.html +448 -0
- simstack/static/docs/_modules/simstack/util/default_from_dict.html +376 -0
- simstack/static/docs/_modules/simstack/util/directory_iterator.html +553 -0
- simstack/static/docs/_modules/simstack/util/docstring_parser.html +526 -0
- simstack/static/docs/_modules/simstack/util/file_hashing.html +394 -0
- simstack/static/docs/_modules/simstack/util/file_transfer_client.html +791 -0
- simstack/static/docs/_modules/simstack/util/files.html +733 -0
- simstack/static/docs/_modules/simstack/util/find_python_files.html +349 -0
- simstack/static/docs/_modules/simstack/util/generate_ui_schema.html +396 -0
- simstack/static/docs/_modules/simstack/util/generic_list_mixin.html +487 -0
- simstack/static/docs/_modules/simstack/util/get_module_path.html +336 -0
- simstack/static/docs/_modules/simstack/util/git_pull.html +381 -0
- simstack/static/docs/_modules/simstack/util/git_repository_status.html +411 -0
- simstack/static/docs/_modules/simstack/util/import_module.html +377 -0
- simstack/static/docs/_modules/simstack/util/importer.html +637 -0
- simstack/static/docs/_modules/simstack/util/init_data_source.html +357 -0
- simstack/static/docs/_modules/simstack/util/make_graph.html +423 -0
- simstack/static/docs/_modules/simstack/util/make_table.html +1171 -0
- simstack/static/docs/_modules/simstack/util/mappings.html +378 -0
- simstack/static/docs/_modules/simstack/util/minimal_route_finder.html +388 -0
- simstack/static/docs/_modules/simstack/util/mock_db.html +472 -0
- simstack/static/docs/_modules/simstack/util/module_path_checker.html +354 -0
- simstack/static/docs/_modules/simstack/util/object_list_mixin.html +649 -0
- simstack/static/docs/_modules/simstack/util/path_manager.html +566 -0
- simstack/static/docs/_modules/simstack/util/project_root_finder.html +357 -0
- simstack/static/docs/_modules/simstack/util/queue_watcher.html +593 -0
- simstack/static/docs/_modules/simstack/util/resource_config.html +532 -0
- simstack/static/docs/_modules/simstack/util/route_finder.html +390 -0
- simstack/static/docs/_modules/simstack/util/runner_util.html +487 -0
- simstack/static/docs/_modules/simstack/util/runner_utils.html +468 -0
- simstack/static/docs/_modules/simstack/util/safe_code_executor.html +510 -0
- simstack/static/docs/_modules/simstack/util/sample_config.html +414 -0
- simstack/static/docs/_modules/simstack/util/sensitive_content_filter.html +364 -0
- simstack/static/docs/_modules/simstack/util/setup_logging.html +365 -0
- simstack/static/docs/_modules/simstack/util/submit_to_watchdog.html +425 -0
- simstack/static/docs/_modules/simstack/util/toml_reader.html +482 -0
- simstack/static/docs/_modules/simstack/util/transform_file_name.html +357 -0
- simstack/static/docs/_modules/simstack/util/ui_tools.html +541 -0
- simstack/static/docs/_sources/architecture.rst.txt +25 -0
- simstack/static/docs/_sources/array_lists.rst.txt +60 -0
- simstack/static/docs/_sources/ci_pipeline.rst.txt +34 -0
- simstack/static/docs/_sources/data.rst.txt +175 -0
- simstack/static/docs/_sources/database_migrations.rst.txt +310 -0
- simstack/static/docs/_sources/datasets.rst.txt +93 -0
- simstack/static/docs/_sources/developer_guide.rst.txt +25 -0
- simstack/static/docs/_sources/docker_nodes.rst.txt +149 -0
- simstack/static/docs/_sources/files.rst.txt +159 -0
- simstack/static/docs/_sources/fire_and_forget_runner.rst.txt +67 -0
- simstack/static/docs/_sources/index.rst.txt +25 -0
- simstack/static/docs/_sources/installation.rst.txt +213 -0
- simstack/static/docs/_sources/lists.rst.txt +111 -0
- simstack/static/docs/_sources/mass_runner.rst.txt +91 -0
- simstack/static/docs/_sources/misc.rst.txt +106 -0
- simstack/static/docs/_sources/overview.rst.txt +91 -0
- simstack/static/docs/_sources/recovery.rst.txt +38 -0
- simstack/static/docs/_sources/resource_config.rst.txt +141 -0
- simstack/static/docs/_sources/simstack/modules/modules.rst.txt +7 -0
- simstack/static/docs/_sources/simstack/modules/simstack.core.rst.txt +205 -0
- simstack/static/docs/_sources/simstack/modules/simstack.core.services.rst.txt +109 -0
- simstack/static/docs/_sources/simstack/modules/simstack.methods.rst.txt +77 -0
- simstack/static/docs/_sources/simstack/modules/simstack.models.rst.txt +261 -0
- simstack/static/docs/_sources/simstack/modules/simstack.rst.txt +22 -0
- simstack/static/docs/_sources/simstack/modules/simstack.tables.rst.txt +45 -0
- simstack/static/docs/_sources/simstack/modules/simstack.util.rst.txt +381 -0
- simstack/static/docs/_sources/submit.rst.txt +141 -0
- simstack/static/docs/_sources/tables.rst.txt +50 -0
- simstack/static/docs/_sources/testing_complex_nodes.rst.txt +92 -0
- simstack/static/docs/_sources/ui_documentation.rst.txt +272 -0
- simstack/static/docs/_sources/workflows.rst.txt +446 -0
- simstack/static/docs/_static/base-stemmer.js +476 -0
- simstack/static/docs/_static/basic.css +906 -0
- simstack/static/docs/_static/cobalt2-theme.css +1 -0
- simstack/static/docs/_static/debug.css +69 -0
- simstack/static/docs/_static/docs-build-badge.css +51 -0
- simstack/static/docs/_static/docs-build-badge.js +51 -0
- simstack/static/docs/_static/doctools.js +150 -0
- simstack/static/docs/_static/documentation_options.js +13 -0
- simstack/static/docs/_static/english-stemmer.js +1066 -0
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- simstack/static/docs/_static/language_data.js +13 -0
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- simstack/static/docs/_static/scripts/furo.js.LICENSE.txt +7 -0
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- simstack/static/docs/_static/searchtools.js +693 -0
- simstack/static/docs/_static/skeleton.css +296 -0
- simstack/static/docs/_static/sphinx_highlight.js +159 -0
- simstack/static/docs/_static/styles/furo-extensions.css +2 -0
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- simstack/static/docs/_static/styles/furo.css.map +1 -0
- simstack/static/docs/architecture.html +340 -0
- simstack/static/docs/array_lists.html +678 -0
- simstack/static/docs/ci_pipeline.html +385 -0
- simstack/static/docs/data.html +545 -0
- simstack/static/docs/database_migrations.html +652 -0
- simstack/static/docs/datasets.html +1268 -0
- simstack/static/docs/developer_guide.html +359 -0
- simstack/static/docs/docker_nodes.html +503 -0
- simstack/static/docs/files.html +718 -0
- simstack/static/docs/fire_and_forget_runner.html +641 -0
- simstack/static/docs/genindex.html +6390 -0
- simstack/static/docs/index.html +516 -0
- simstack/static/docs/installation.html +553 -0
- simstack/static/docs/lists.html +478 -0
- simstack/static/docs/mass_runner.html +481 -0
- simstack/static/docs/misc.html +454 -0
- simstack/static/docs/objects.inv +0 -0
- simstack/static/docs/overview.html +469 -0
- simstack/static/docs/py-modindex.html +1111 -0
- simstack/static/docs/recovery.html +371 -0
- simstack/static/docs/resource_config.html +590 -0
- simstack/static/docs/search.html +327 -0
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- simstack/static/docs/simstack/modules/modules.html +489 -0
- simstack/static/docs/simstack/modules/simstack.core.html +1883 -0
- simstack/static/docs/simstack/modules/simstack.core.services.html +698 -0
- simstack/static/docs/simstack/modules/simstack.html +3060 -0
- simstack/static/docs/simstack/modules/simstack.methods.html +1150 -0
- simstack/static/docs/simstack/modules/simstack.models.html +13113 -0
- simstack/static/docs/simstack/modules/simstack.tables.html +635 -0
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- simstack/static/docs/submit.html +487 -0
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- simstack/tables/__init__.py +0 -0
- simstack/tables/model_table.py +191 -0
- simstack/tables/node_children.py +219 -0
- simstack/tables/node_table.py +517 -0
- simstack/tables/table_builder.py +314 -0
- simstack/util/__init__.py +0 -0
- simstack/util/async_zip_utils.py +18 -0
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- simstack/util/cleaned_json_schema.py +20 -0
- simstack/util/config_reader.py +179 -0
- simstack/util/custom_model_dump.py +75 -0
- simstack/util/database_information.py +160 -0
- simstack/util/db.py +1013 -0
- simstack/util/db_logger.py +117 -0
- simstack/util/default_from_dict.py +57 -0
- simstack/util/directory_iterator.py +216 -0
- simstack/util/docstring_parser.py +186 -0
- simstack/util/file_hashing.py +72 -0
- simstack/util/file_transfer_client.py +427 -0
- simstack/util/files.py +396 -0
- simstack/util/find_python_files.py +33 -0
- simstack/util/generate_ui_schema.py +80 -0
- simstack/util/generic_list_mixin.py +120 -0
- simstack/util/geometry_utils.py +118 -0
- simstack/util/get_module_path.py +20 -0
- simstack/util/git_pull.py +65 -0
- simstack/util/git_repository_status.py +95 -0
- simstack/util/import_module.py +63 -0
- simstack/util/importer.py +312 -0
- simstack/util/init_data_source.py +41 -0
- simstack/util/make_graph.py +107 -0
- simstack/util/make_table.py +837 -0
- simstack/util/mappings.py +41 -0
- simstack/util/minimal_route_finder.py +72 -0
- simstack/util/mock_db.py +144 -0
- simstack/util/module_path_checker.py +38 -0
- simstack/util/object_list_mixin.py +282 -0
- simstack/util/path_manager.py +223 -0
- simstack/util/project_root_finder.py +41 -0
- simstack/util/queue_watcher.py +262 -0
- simstack/util/resource_config.py +198 -0
- simstack/util/route_finder.py +74 -0
- simstack/util/runner_util.py +166 -0
- simstack/util/runner_utils.py +143 -0
- simstack/util/safe_code_executor.py +194 -0
- simstack/util/sample_config.py +98 -0
- simstack/util/sensitive_content_filter.py +48 -0
- simstack/util/setup_logging.py +49 -0
- simstack/util/submit_to_watchdog.py +106 -0
- simstack/util/toml_reader.py +142 -0
- simstack/util/transform_file_name.py +41 -0
- simstack/util/ui_tools.py +213 -0
- simstack-2.0.1.dist-info/METADATA +454 -0
- simstack-2.0.1.dist-info/RECORD +354 -0
- simstack-2.0.1.dist-info/WHEEL +5 -0
- simstack-2.0.1.dist-info/entry_points.txt +12 -0
- simstack-2.0.1.dist-info/licenses/LICENSE +21 -0
- simstack-2.0.1.dist-info/top_level.txt +1 -0
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<!-- Generated with Sphinx 9.1.0 and Furo 2025.12.19 -->
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<li class="toctree-l1"><a class="reference internal" href="../../../overview.html">Overview</a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../data.html">Persisting and Visualizing Data</a></li>
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<article role="main" id="furo-main-content">
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<h1>Source code for simstack.core.submit_node</h1><div class="highlight"><pre>
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<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">stat</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">subprocess</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">simstack.core.context</span><span class="w"> </span><span class="kn">import</span> <span class="n">context</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">simstack.core.definitions</span><span class="w"> </span><span class="kn">import</span> <span class="n">TaskStatus</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">simstack.models</span><span class="w"> </span><span class="kn">import</span> <span class="n">NodeRegistry</span>
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<span class="kn">from</span><span class="w"> </span><span class="nn">simstack.util.submit_to_watchdog</span><span class="w"> </span><span class="kn">import</span> <span class="n">submit_to_watchdog</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
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<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"submit_node"</span><span class="p">)</span>
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<div class="viewcode-block" id="make_executable">
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<a class="viewcode-back" href="../../../simstack/modules/simstack.core.html#simstack.core.submit_node.make_executable">[docs]</a>
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<span class="k">def</span><span class="w"> </span><span class="nf">make_executable</span><span class="p">(</span><span class="n">file_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">os</span><span class="o">.</span><span class="n">PathLike</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
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<span class="c1"># Get current permissions</span>
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<span class="n">current_permissions</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">stat</span><span class="p">(</span><span class="n">file_path</span><span class="p">)</span><span class="o">.</span><span class="n">st_mode</span>
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<span class="c1"># Add executable bit for user, group and others</span>
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<span class="n">executable_mode</span> <span class="o">=</span> <span class="n">current_permissions</span> <span class="o">|</span> <span class="n">stat</span><span class="o">.</span><span class="n">S_IXUSR</span> <span class="o">|</span> <span class="n">stat</span><span class="o">.</span><span class="n">S_IXGRP</span> <span class="o">|</span> <span class="n">stat</span><span class="o">.</span><span class="n">S_IXOTH</span>
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<span class="c1"># Apply new permissions</span>
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<span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">executable_mode</span><span class="p">)</span></div>
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<div class="viewcode-block" id="submit_node">
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<a class="viewcode-back" href="../../../simstack/modules/simstack.core.html#simstack.core.submit_node.submit_node">[docs]</a>
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<span class="k">async</span> <span class="k">def</span><span class="w"> </span><span class="nf">submit_node</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">:</span> <span class="n">NodeRegistry</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
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<span class="w"> </span><span class="sd">"""Submit a node to the SLURM queue"""</span>
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<span class="n">task_id</span> <span class="o">=</span> <span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span>
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<span class="k">try</span><span class="p">:</span>
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<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Submitting task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> to SLURM queue"</span><span class="p">)</span>
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<span class="c1"># Implement SLURM submission logic here</span>
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<span class="n">base_path</span> <span class="o">=</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">project_root</span>
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<span class="n">python_path</span> <span class="o">=</span> <span class="s2">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="k">for</span> <span class="n">path</span> <span class="ow">in</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">python_paths</span><span class="p">)</span>
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<span class="n">work_dir</span> <span class="o">=</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">workdir</span> <span class="o">/</span> <span class="n">registry_entry</span><span class="o">.</span><span class="n">name</span> <span class="o">/</span> <span class="nb">str</span><span class="p">(</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
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<span class="n">job_name</span> <span class="o">=</span> <span class="n">registry_entry</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"."</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
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<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> workdir </span><span class="si">{</span><span class="n">work_dir</span><span class="si">}</span><span class="s2"> python path </span><span class="si">{</span><span class="n">python_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
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<span class="c1"># write a slurm script that starts a python script "run_node.py" with the node id as an argument</span>
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<span class="n">original_slurm_parameters</span> <span class="o">=</span> <span class="n">registry_entry</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">slurm_parameters</span>
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<span class="k">if</span> <span class="n">original_slurm_parameters</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
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<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Task task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> has no slurm parameters -- failing"</span><span class="p">)</span>
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<span class="n">registry_entry</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">TaskStatus</span><span class="o">.</span><span class="n">FAILED</span>
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<span class="k">await</span> <span class="n">context</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">)</span>
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<span class="k">return</span> <span class="kc">False</span>
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<span class="n">slurm_parameters</span> <span class="o">=</span> <span class="n">original_slurm_parameters</span><span class="o">.</span><span class="n">model_copy</span><span class="p">(</span><span class="n">deep</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">work_dir</span><span class="si">}</span><span class="s2">/%j.out"</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">work_dir</span><span class="si">}</span><span class="s2">/%j.err"</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">job_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">job_name</span><span class="si">}</span><span class="s2">"</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">chdir</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"source ~/.bashrc"</span><span class="p">)</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">environment_start</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
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<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
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<span class="sa">f</span><span class="s2">"export PYTHONPATH=</span><span class="si">{</span><span class="n">python_path</span><span class="si">}</span><span class="s2">:$PYTHONPATH"</span>
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<span class="p">)</span>
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<span class="n">sync_data_start</span> <span class="o">=</span> <span class="s2">"""# 1. Define the rsync function</span>
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<span class="s2"> sync_data() {</span>
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<span class="s2"> echo "=== Time limit approaching! Starting rsync at $(date) ==="</span>
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+
<span class="s2"> # Run rsync safely </span>
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+
<span class="s2"> """</span>
|
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<span class="n">sync_data_end</span> <span class="o">=</span> <span class="s2">"""</span>
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+
<span class="s2"> echo "=== Rsync completed at $(date) ==="</span>
|
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+
<span class="s2"> exit 0</span>
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+
<span class="s2"> } </span>
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349
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+
<span class="s2"> """</span>
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<span class="k">if</span> <span class="n">context</span><span class="o">.</span><span class="n">resource_config</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
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<span class="n">program_config</span> <span class="o">=</span> <span class="n">context</span><span class="o">.</span><span class="n">resource_config</span><span class="o">.</span><span class="n">get_program</span><span class="p">(</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
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<span class="k">else</span><span class="p">:</span>
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+
<span class="n">program_config</span> <span class="o">=</span> <span class="p">{}</span>
|
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+
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> program_config </span><span class="si">{</span><span class="n">program_config</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
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+
<span class="k">if</span> <span class="n">program_config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"use_tmp"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
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+
<span class="n">tmp_dir</span> <span class="o">=</span> <span class="n">context</span><span class="o">.</span><span class="n">resource_config</span><span class="o">.</span><span class="n">tmp_dir</span><span class="p">(</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
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|
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+
|
|
360
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<span class="k">if</span> <span class="ow">not</span> <span class="n">tmp_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">tmp_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
|
|
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+
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
|
|
362
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+
<span class="sa">f</span><span class="s2">"Task task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> tmp_dir </span><span class="si">{</span><span class="n">tmp_dir</span><span class="si">}</span><span class="s2"> does not exist or is not a directory -- failing"</span><span class="p">)</span>
|
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+
<span class="n">registry_entry</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">TaskStatus</span><span class="o">.</span><span class="n">FAILED</span>
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<span class="k">await</span> <span class="n">context</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">)</span>
|
|
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+
<span class="k">return</span> <span class="kc">False</span>
|
|
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+
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|
+
<span class="n">full_sync_data</span> <span class="o">=</span> <span class="n">sync_data_start</span> <span class="o">+</span> <span class="sa">f</span><span class="s1">'cp -a </span><span class="si">{</span><span class="n">tmp_dir</span><span class="si">}</span><span class="s1">/. </span><span class="si">{</span><span class="n">work_dir</span><span class="si">}</span><span class="s1">/recovery</span><span class="se">\n</span><span class="s1">'</span> <span class="o">+</span> <span class="n">sync_data_end</span>
|
|
368
|
+
|
|
369
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> full_sync_data </span><span class="si">{</span><span class="n">full_sync_data</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
|
|
370
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">full_sync_data</span><span class="p">)</span>
|
|
371
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"trap 'sync_data' SIGUSR1"</span><span class="p">)</span>
|
|
372
|
+
|
|
373
|
+
<span class="k">if</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">docker</span><span class="p">:</span>
|
|
374
|
+
<span class="n">external_work_dir</span> <span class="o">=</span> <span class="p">(</span>
|
|
375
|
+
<span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">external_workdir</span>
|
|
376
|
+
<span class="o">/</span> <span class="n">registry_entry</span><span class="o">.</span><span class="n">name</span>
|
|
377
|
+
<span class="o">/</span> <span class="nb">str</span><span class="p">(</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
|
|
378
|
+
<span class="p">)</span>
|
|
379
|
+
|
|
380
|
+
<span class="n">watcher_file</span> <span class="o">=</span> <span class="p">(</span>
|
|
381
|
+
<span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">project_root</span>
|
|
382
|
+
<span class="o">/</span> <span class="s2">"src"</span>
|
|
383
|
+
<span class="o">/</span> <span class="s2">"simstack"</span>
|
|
384
|
+
<span class="o">/</span> <span class="s2">"util"</span>
|
|
385
|
+
<span class="o">/</span> <span class="s2">"queue_watcher.py"</span>
|
|
386
|
+
<span class="p">)</span>
|
|
387
|
+
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">watcher_file</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
|
|
388
|
+
<span class="n">watcher_content</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
|
|
389
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
|
|
390
|
+
<span class="sa">f</span><span class="s2">"cat > watcher.py <<'EOF'</span><span class="se">\n</span><span class="si">{</span><span class="n">watcher_content</span><span class="si">}</span><span class="se">\n</span><span class="s2">EOF"</span>
|
|
391
|
+
<span class="p">)</span>
|
|
392
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"python watcher.py &"</span><span class="p">)</span>
|
|
393
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"WATCHER_PID=$!"</span><span class="p">)</span>
|
|
394
|
+
|
|
395
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"set -euo pipefail"</span><span class="p">)</span>
|
|
396
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
|
|
397
|
+
<span class="s2">"cleanup() { "</span>
|
|
398
|
+
<span class="s1">'if [ -n "$</span><span class="si">{WATCHER_PID:-}</span><span class="s1">" ] && kill -0 "$WATCHER_PID" 2>/dev/null; then '</span>
|
|
399
|
+
<span class="s1">' kill "$WATCHER_PID" 2>/dev/null || true; '</span>
|
|
400
|
+
<span class="s2">" sleep 2; "</span>
|
|
401
|
+
<span class="s1">' kill -9 "$WATCHER_PID" 2>/dev/null || true; '</span>
|
|
402
|
+
<span class="s2">"fi; "</span>
|
|
403
|
+
<span class="s2">"}"</span>
|
|
404
|
+
<span class="p">)</span>
|
|
405
|
+
|
|
406
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"trap cleanup EXIT INT TERM"</span><span class="p">)</span>
|
|
407
|
+
<span class="n">toml_path</span> <span class="o">=</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">project_root</span> <span class="o">/</span> <span class="s2">"simstack_docker.toml"</span>
|
|
408
|
+
<span class="k">if</span> <span class="ow">not</span> <span class="n">toml_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
|
|
409
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
|
|
410
|
+
<span class="sa">f</span><span class="s2">"Task task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> has no simstack.toml file -- failing"</span>
|
|
411
|
+
<span class="p">)</span>
|
|
412
|
+
<span class="n">registry_entry</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">TaskStatus</span><span class="o">.</span><span class="n">FAILED</span>
|
|
413
|
+
<span class="k">await</span> <span class="n">context</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">)</span>
|
|
414
|
+
<span class="k">return</span> <span class="kc">False</span>
|
|
415
|
+
|
|
416
|
+
<span class="n">docker_start</span> <span class="o">=</span> <span class="s2">"udocker run "</span>
|
|
417
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="s2">"-e GIT_TOKEN=XXX"</span>
|
|
418
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"-e NODE_ID=</span><span class="si">{</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s2"> "</span>
|
|
419
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"-e RESOURCE=</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">resource</span><span class="p">)</span><span class="si">}</span><span class="s2"> "</span>
|
|
420
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"-v </span><span class="si">{</span><span class="n">external_work_dir</span><span class="si">}</span><span class="s2">:/home/appuser/simstack "</span>
|
|
421
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="p">(</span>
|
|
422
|
+
<span class="sa">f</span><span class="s2">"-v </span><span class="si">{</span><span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">external_source_dir</span><span class="si">}</span><span class="s2">:/app/simstack-model "</span>
|
|
423
|
+
<span class="p">)</span>
|
|
424
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"-v </span><span class="si">{</span><span class="n">toml_path</span><span class="si">}</span><span class="s2">:/app/simstack-model/simstack.toml "</span>
|
|
425
|
+
<span class="n">docker_start</span> <span class="o">+=</span> <span class="s2">" simstack-runner"</span>
|
|
426
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">docker_start</span><span class="p">)</span>
|
|
427
|
+
<span class="k">else</span><span class="p">:</span>
|
|
428
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
|
|
429
|
+
<span class="sa">f</span><span class="s2">"uv run --directory </span><span class="si">{</span><span class="n">base_path</span><span class="si">}</span><span class="s2"> run_node --node-id </span><span class="si">{</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s2"> --resource </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">resource</span><span class="p">)</span><span class="si">}</span><span class="s2"> &"</span>
|
|
430
|
+
<span class="p">)</span>
|
|
431
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">startup_commands</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"wait"</span><span class="p">)</span>
|
|
432
|
+
<span class="n">slurm_parameters</span><span class="o">.</span><span class="n">signal</span> <span class="o">=</span> <span class="s2">"B:SIGUSR1@60"</span>
|
|
433
|
+
|
|
434
|
+
|
|
435
|
+
<span class="n">slurm_script</span> <span class="o">=</span> <span class="n">slurm_parameters</span><span class="o">.</span><span class="n">to_sbatch_header</span><span class="p">()</span>
|
|
436
|
+
|
|
437
|
+
<span class="c1"># write the script to a file in the work_dir</span>
|
|
438
|
+
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
|
|
439
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> workdir </span><span class="si">{</span><span class="n">work_dir</span><span class="si">}</span><span class="s2"> python path </span><span class="si">{</span><span class="n">python_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
|
|
440
|
+
<span class="n">script_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">work_dir</span><span class="p">,</span> <span class="s2">"slurm_script.sh"</span><span class="p">)</span>
|
|
441
|
+
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">script_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
|
|
442
|
+
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">slurm_script</span><span class="p">)</span>
|
|
443
|
+
|
|
444
|
+
<span class="n">make_executable</span><span class="p">(</span><span class="n">script_path</span><span class="p">)</span>
|
|
445
|
+
<span class="c1"># submit the script to the slurm queue</span>
|
|
446
|
+
<span class="k">if</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">docker</span><span class="p">:</span>
|
|
447
|
+
<span class="n">job_id</span> <span class="o">=</span> <span class="s2">"slurm_"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">registry_entry</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
|
|
448
|
+
<span class="n">queue_dir</span> <span class="o">=</span> <span class="n">context</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">workdir</span> <span class="o">/</span> <span class="s2">"queue"</span>
|
|
449
|
+
<span class="n">result</span> <span class="o">=</span> <span class="n">submit_to_watchdog</span><span class="p">(</span>
|
|
450
|
+
<span class="sa">f</span><span class="s2">"/usr/bin/sbatch </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">external_work_dir</span><span class="p">,</span><span class="w"> </span><span class="s1">'slurm_script.sh'</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
|
|
451
|
+
<span class="n">job_id</span><span class="p">,</span>
|
|
452
|
+
<span class="n">queue_dir</span><span class="p">,</span>
|
|
453
|
+
<span class="p">)</span>
|
|
454
|
+
<span class="k">else</span><span class="p">:</span>
|
|
455
|
+
<span class="n">result</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span>
|
|
456
|
+
<span class="sa">f</span><span class="s2">"/usr/bin/sbatch </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">work_dir</span><span class="p">,</span><span class="w"> </span><span class="s1">'slurm_script.sh'</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
|
|
457
|
+
<span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
|
|
458
|
+
<span class="n">capture_output</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
|
|
459
|
+
<span class="n">text</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
|
|
460
|
+
<span class="n">timeout</span><span class="o">=</span><span class="mi">30</span><span class="p">,</span> <span class="c1"># Add timeout to prevent hanging</span>
|
|
461
|
+
<span class="p">)</span>
|
|
462
|
+
|
|
463
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
|
|
464
|
+
<span class="sa">f</span><span class="s2">"submitting job task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> returns: </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">returncode</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">stdout</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">stderr</span><span class="si">}</span><span class="s2">"</span>
|
|
465
|
+
<span class="p">)</span>
|
|
466
|
+
<span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">returncode</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
|
|
467
|
+
<span class="c1"># Extract job ID using a regex pattern</span>
|
|
468
|
+
<span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">"Submitted batch job (\d+)"</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
|
|
469
|
+
<span class="k">if</span> <span class="n">match</span><span class="p">:</span>
|
|
470
|
+
<span class="n">job_id</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
|
|
471
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
|
|
472
|
+
<span class="sa">f</span><span class="s2">"task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> job successfully submitted with job_id: </span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2">"</span>
|
|
473
|
+
<span class="p">)</span>
|
|
474
|
+
<span class="n">registry_entry</span><span class="o">.</span><span class="n">job_id</span> <span class="o">=</span> <span class="n">job_id</span>
|
|
475
|
+
<span class="k">else</span><span class="p">:</span>
|
|
476
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
|
|
477
|
+
<span class="sa">f</span><span class="s2">"task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> job submitted but could not extract job_id from output: </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">stdout</span><span class="si">}</span><span class="s2">"</span>
|
|
478
|
+
<span class="p">)</span>
|
|
479
|
+
<span class="k">else</span><span class="p">:</span>
|
|
480
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
|
|
481
|
+
<span class="sa">f</span><span class="s2">"error submitting job for task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> return code: </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">returncode</span><span class="si">}</span><span class="s2"> stdout: </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">stdout</span><span class="si">}</span><span class="s2">"</span>
|
|
482
|
+
<span class="p">)</span>
|
|
483
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
|
|
484
|
+
<span class="sa">f</span><span class="s2">"submitting job for task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> stderr: </span><span class="si">{</span><span class="n">result</span><span class="o">.</span><span class="n">stderr</span><span class="si">}</span><span class="s2">"</span>
|
|
485
|
+
<span class="p">)</span>
|
|
486
|
+
<span class="n">registry_entry</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">TaskStatus</span><span class="o">.</span><span class="n">FAILED</span>
|
|
487
|
+
<span class="k">await</span> <span class="n">context</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">)</span>
|
|
488
|
+
<span class="k">return</span> <span class="kc">False</span>
|
|
489
|
+
<span class="n">registry_entry</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">TaskStatus</span><span class="o">.</span><span class="n">SLURM_QUEUED</span>
|
|
490
|
+
<span class="k">await</span> <span class="n">context</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">)</span>
|
|
491
|
+
<span class="k">return</span> <span class="kc">True</span>
|
|
492
|
+
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
|
|
493
|
+
<span class="n">logger</span><span class="o">.</span><span class="n">exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"fatal error in submitting task_id: </span><span class="si">{</span><span class="n">task_id</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
|
|
494
|
+
<span class="n">registry_entry</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">TaskStatus</span><span class="o">.</span><span class="n">FAILED</span>
|
|
495
|
+
<span class="k">await</span> <span class="n">context</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">registry_entry</span><span class="p">)</span>
|
|
496
|
+
<span class="k">return</span> <span class="kc">False</span></div>
|
|
497
|
+
|
|
498
|
+
</pre></div>
|
|
499
|
+
</article>
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|
500
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+
</div>
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501
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+
<footer>
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502
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+
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503
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+
<div class="related-pages">
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504
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505
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+
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506
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+
</div>
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507
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+
<div class="bottom-of-page">
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508
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+
<div class="left-details">
|
|
509
|
+
<div class="copyright">
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|
510
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+
Copyright © 2026, Wolfgang Wenzel
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511
|
+
</div>
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512
|
+
Made with <a href="https://www.sphinx-doc.org/">Sphinx</a> and <a class="muted-link" href="https://pradyunsg.me">@pradyunsg</a>'s
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+
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|
514
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+
<a href="https://github.com/pradyunsg/furo">Furo</a>
|
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515
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+
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516
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+
</div>
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517
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+
<div class="right-details">
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518
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+
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519
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+
</div>
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520
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</div>
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521
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+
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522
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</footer>
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523
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</div>
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524
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+
<aside class="toc-drawer no-toc">
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525
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+
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526
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+
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527
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+
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528
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</aside>
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529
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+
</div>
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530
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</div><script src="../../../_static/documentation_options.js?v=5929fcd5"></script>
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531
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+
<script src="../../../_static/doctools.js?v=fd6eb6e6"></script>
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532
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<script src="../../../_static/sphinx_highlight.js?v=6ffebe34"></script>
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533
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+
<script src="../../../_static/scripts/furo.js?v=46bd48cc"></script>
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534
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+
<script data-docs-built-at="2026-07-17 10:50:10 UTC" src="../../../_static/docs-build-badge.js?v=57cb9fc6"></script>
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535
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