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.
Files changed (354) hide show
  1. simstack/__init__.py +0 -0
  2. simstack/_version.py +24 -0
  3. simstack/core/__init__.py +0 -0
  4. simstack/core/artifacts.py +406 -0
  5. simstack/core/asnyc_helper.py +14 -0
  6. simstack/core/config_file.py +60 -0
  7. simstack/core/context.py +283 -0
  8. simstack/core/definitions.py +22 -0
  9. simstack/core/engine.py +115 -0
  10. simstack/core/find_simstack_modules.py +41 -0
  11. simstack/core/hash.py +179 -0
  12. simstack/core/node.py +1137 -0
  13. simstack/core/node_claim.py +31 -0
  14. simstack/core/node_runner.py +362 -0
  15. simstack/core/process_results.py +102 -0
  16. simstack/core/recompute_artifacts.py +117 -0
  17. simstack/core/reset_db.py +12 -0
  18. simstack/core/resource_assignment.py +222 -0
  19. simstack/core/resources.py +90 -0
  20. simstack/core/route_table.py +24 -0
  21. simstack/core/run_docker.py +109 -0
  22. simstack/core/run_node.py +71 -0
  23. simstack/core/runner.py +169 -0
  24. simstack/core/services/__init__.py +11 -0
  25. simstack/core/services/base_service.py +191 -0
  26. simstack/core/services/file_transfer_service.py +117 -0
  27. simstack/core/services/git_restart_service.py +12 -0
  28. simstack/core/services/git_uv_update_service.py +105 -0
  29. simstack/core/services/node_execution_service.py +182 -0
  30. simstack/core/services/resource_branch_monitor_service.py +71 -0
  31. simstack/core/services/runner_cleanup_service.py +149 -0
  32. simstack/core/services/runner_manager.py +163 -0
  33. simstack/core/services/runner_status_service.py +10 -0
  34. simstack/core/services/slurm_status_service.py +67 -0
  35. simstack/core/services/stop_check_service.py +27 -0
  36. simstack/core/services/timeout_restart_service.py +26 -0
  37. simstack/core/simstack_result.py +39 -0
  38. simstack/core/submit_node.py +217 -0
  39. simstack/core/task_id.py +22 -0
  40. simstack/methods/__init__.py +0 -0
  41. simstack/methods/archive_files.py +292 -0
  42. simstack/methods/fire_and_forget_runner.py +113 -0
  43. simstack/methods/generate_test.py +125 -0
  44. simstack/methods/get_file.py +26 -0
  45. simstack/methods/mass_runner.py +154 -0
  46. simstack/methods/multiple_executor.py +307 -0
  47. simstack/methods/switch_git.py +16 -0
  48. simstack/methods/upload_helpers.py +81 -0
  49. simstack/models/__init__.py +74 -0
  50. simstack/models/array_list.py +21 -0
  51. simstack/models/array_storage.py +83 -0
  52. simstack/models/artifact_models.py +127 -0
  53. simstack/models/base_lists.py +51 -0
  54. simstack/models/base_types.py +209 -0
  55. simstack/models/charts_artifact.py +690 -0
  56. simstack/models/dataset.py +451 -0
  57. simstack/models/dataset_metadata.py +390 -0
  58. simstack/models/datasettuple.py +587 -0
  59. simstack/models/file_instance.py +150 -0
  60. simstack/models/file_list.py +45 -0
  61. simstack/models/files.py +424 -0
  62. simstack/models/fire_and_forget_result.py +19 -0
  63. simstack/models/images2d.py +113 -0
  64. simstack/models/log_entry_model.py +37 -0
  65. simstack/models/models.py +52 -0
  66. simstack/models/named_data_reference.py +36 -0
  67. simstack/models/node_registry.py +96 -0
  68. simstack/models/pandas_model.py +239 -0
  69. simstack/models/parameters.py +402 -0
  70. simstack/models/pickle_models.py +300 -0
  71. simstack/models/project.py +13 -0
  72. simstack/models/resource_assignment.py +170 -0
  73. simstack/models/resource_definition.py +125 -0
  74. simstack/models/runner_model.py +39 -0
  75. simstack/models/simple_table.py +79 -0
  76. simstack/models/simstack_model.py +97 -0
  77. simstack/models/slurm_info.py +17 -0
  78. simstack/models/table_artifact.py +87 -0
  79. simstack/models/tag.py +12 -0
  80. simstack/models/unused_test_file.py +5 -0
  81. simstack/simstack_marker.com +1 -0
  82. simstack/static/docs/.buildinfo +4 -0
  83. simstack/static/docs/_images/GUI Concept.webp +0 -0
  84. simstack/static/docs/_modules/index.html +434 -0
  85. simstack/static/docs/_modules/simstack/core/artifacts.html +743 -0
  86. simstack/static/docs/_modules/simstack/core/asnyc_helper.html +330 -0
  87. simstack/static/docs/_modules/simstack/core/config_file.html +379 -0
  88. simstack/static/docs/_modules/simstack/core/definitions.html +341 -0
  89. simstack/static/docs/_modules/simstack/core/engine.html +437 -0
  90. simstack/static/docs/_modules/simstack/core/find_simstack_modules.html +360 -0
  91. simstack/static/docs/_modules/simstack/core/hash.html +528 -0
  92. simstack/static/docs/_modules/simstack/core/node.html +1392 -0
  93. simstack/static/docs/_modules/simstack/core/node_claim.html +347 -0
  94. simstack/static/docs/_modules/simstack/core/node_runner.html +711 -0
  95. simstack/static/docs/_modules/simstack/core/process_results.html +418 -0
  96. simstack/static/docs/_modules/simstack/core/recompute_artifacts.html +433 -0
  97. simstack/static/docs/_modules/simstack/core/reset_db.html +328 -0
  98. simstack/static/docs/_modules/simstack/core/resource_assignment.html +553 -0
  99. simstack/static/docs/_modules/simstack/core/resources.html +424 -0
  100. simstack/static/docs/_modules/simstack/core/route_table.html +349 -0
  101. simstack/static/docs/_modules/simstack/core/run_docker.html +425 -0
  102. simstack/static/docs/_modules/simstack/core/run_node.html +390 -0
  103. simstack/static/docs/_modules/simstack/core/runner.html +491 -0
  104. simstack/static/docs/_modules/simstack/core/services/base_service.html +522 -0
  105. simstack/static/docs/_modules/simstack/core/services/file_transfer_service.html +436 -0
  106. simstack/static/docs/_modules/simstack/core/services/git_restart_service.html +331 -0
  107. simstack/static/docs/_modules/simstack/core/services/git_uv_update_service.html +427 -0
  108. simstack/static/docs/_modules/simstack/core/services/node_execution_service.html +507 -0
  109. simstack/static/docs/_modules/simstack/core/services/resource_branch_monitor_service.html +390 -0
  110. simstack/static/docs/_modules/simstack/core/services/runner_cleanup_service.html +468 -0
  111. simstack/static/docs/_modules/simstack/core/services/runner_manager.html +485 -0
  112. simstack/static/docs/_modules/simstack/core/services/runner_status_service.html +329 -0
  113. simstack/static/docs/_modules/simstack/core/services/slurm_status_service.html +386 -0
  114. simstack/static/docs/_modules/simstack/core/services/stop_check_service.html +346 -0
  115. simstack/static/docs/_modules/simstack/core/services/timeout_restart_service.html +345 -0
  116. simstack/static/docs/_modules/simstack/core/simstack_result.html +355 -0
  117. simstack/static/docs/_modules/simstack/core/submit_node.html +536 -0
  118. simstack/static/docs/_modules/simstack/core/task_id.html +344 -0
  119. simstack/static/docs/_modules/simstack/methods/archive_files.html +598 -0
  120. simstack/static/docs/_modules/simstack/methods/fire_and_forget_runner.html +432 -0
  121. simstack/static/docs/_modules/simstack/methods/generate_test.html +443 -0
  122. simstack/static/docs/_modules/simstack/methods/get_file.html +342 -0
  123. simstack/static/docs/_modules/simstack/methods/mass_runner.html +476 -0
  124. simstack/static/docs/_modules/simstack/methods/multiple_executor.html +674 -0
  125. simstack/static/docs/_modules/simstack/methods/switch_git.html +332 -0
  126. simstack/static/docs/_modules/simstack/methods/upload_helpers.html +403 -0
  127. simstack/static/docs/_modules/simstack/models/array_list.html +337 -0
  128. simstack/static/docs/_modules/simstack/models/array_storage.html +417 -0
  129. simstack/static/docs/_modules/simstack/models/base_lists.html +374 -0
  130. simstack/static/docs/_modules/simstack/models/base_types.html +588 -0
  131. simstack/static/docs/_modules/simstack/models/charts_artifact.html +1035 -0
  132. simstack/static/docs/_modules/simstack/models/dataset.html +866 -0
  133. simstack/static/docs/_modules/simstack/models/dataset_metadata.html +711 -0
  134. simstack/static/docs/_modules/simstack/models/datasettuple.html +1005 -0
  135. simstack/static/docs/_modules/simstack/models/file_instance.html +472 -0
  136. simstack/static/docs/_modules/simstack/models/file_list.html +367 -0
  137. simstack/static/docs/_modules/simstack/models/files.html +773 -0
  138. simstack/static/docs/_modules/simstack/models/fire_and_forget_result.html +335 -0
  139. simstack/static/docs/_modules/simstack/models/images2d.html +447 -0
  140. simstack/static/docs/_modules/simstack/models/log_entry_model.html +356 -0
  141. simstack/static/docs/_modules/simstack/models/models.html +374 -0
  142. simstack/static/docs/_modules/simstack/models/named_data_reference.html +355 -0
  143. simstack/static/docs/_modules/simstack/models/node_registry.html +415 -0
  144. simstack/static/docs/_modules/simstack/models/pandas_model.html +570 -0
  145. simstack/static/docs/_modules/simstack/models/parameters.html +739 -0
  146. simstack/static/docs/_modules/simstack/models/pickle_models.html +631 -0
  147. simstack/static/docs/_modules/simstack/models/project.html +329 -0
  148. simstack/static/docs/_modules/simstack/models/resource_assignment.html +501 -0
  149. simstack/static/docs/_modules/simstack/models/resource_definition.html +477 -0
  150. simstack/static/docs/_modules/simstack/models/runner_model.html +361 -0
  151. simstack/static/docs/_modules/simstack/models/simple_table.html +413 -0
  152. simstack/static/docs/_modules/simstack/models/simstack_model.html +416 -0
  153. simstack/static/docs/_modules/simstack/models/slurm_info.html +333 -0
  154. simstack/static/docs/_modules/simstack/models/table_artifact.html +406 -0
  155. simstack/static/docs/_modules/simstack/models/tag.html +328 -0
  156. simstack/static/docs/_modules/simstack/tables/model_table.html +519 -0
  157. simstack/static/docs/_modules/simstack/tables/node_children.html +538 -0
  158. simstack/static/docs/_modules/simstack/tables/node_table.html +854 -0
  159. simstack/static/docs/_modules/simstack/tables/table_builder.html +642 -0
  160. simstack/static/docs/_modules/simstack/util/async_zip_utils.html +337 -0
  161. simstack/static/docs/_modules/simstack/util/b64mixin.html +339 -0
  162. simstack/static/docs/_modules/simstack/util/cleaned_json_schema.html +336 -0
  163. simstack/static/docs/_modules/simstack/util/config_reader.html +498 -0
  164. simstack/static/docs/_modules/simstack/util/custom_model_dump.html +391 -0
  165. simstack/static/docs/_modules/simstack/util/database_information.html +488 -0
  166. simstack/static/docs/_modules/simstack/util/db.html +1392 -0
  167. simstack/static/docs/_modules/simstack/util/db_logger.html +448 -0
  168. simstack/static/docs/_modules/simstack/util/default_from_dict.html +376 -0
  169. simstack/static/docs/_modules/simstack/util/directory_iterator.html +553 -0
  170. simstack/static/docs/_modules/simstack/util/docstring_parser.html +526 -0
  171. simstack/static/docs/_modules/simstack/util/file_hashing.html +394 -0
  172. simstack/static/docs/_modules/simstack/util/file_transfer_client.html +791 -0
  173. simstack/static/docs/_modules/simstack/util/files.html +733 -0
  174. simstack/static/docs/_modules/simstack/util/find_python_files.html +349 -0
  175. simstack/static/docs/_modules/simstack/util/generate_ui_schema.html +396 -0
  176. simstack/static/docs/_modules/simstack/util/generic_list_mixin.html +487 -0
  177. simstack/static/docs/_modules/simstack/util/get_module_path.html +336 -0
  178. simstack/static/docs/_modules/simstack/util/git_pull.html +381 -0
  179. simstack/static/docs/_modules/simstack/util/git_repository_status.html +411 -0
  180. simstack/static/docs/_modules/simstack/util/import_module.html +377 -0
  181. simstack/static/docs/_modules/simstack/util/importer.html +637 -0
  182. simstack/static/docs/_modules/simstack/util/init_data_source.html +357 -0
  183. simstack/static/docs/_modules/simstack/util/make_graph.html +423 -0
  184. simstack/static/docs/_modules/simstack/util/make_table.html +1171 -0
  185. simstack/static/docs/_modules/simstack/util/mappings.html +378 -0
  186. simstack/static/docs/_modules/simstack/util/minimal_route_finder.html +388 -0
  187. simstack/static/docs/_modules/simstack/util/mock_db.html +472 -0
  188. simstack/static/docs/_modules/simstack/util/module_path_checker.html +354 -0
  189. simstack/static/docs/_modules/simstack/util/object_list_mixin.html +649 -0
  190. simstack/static/docs/_modules/simstack/util/path_manager.html +566 -0
  191. simstack/static/docs/_modules/simstack/util/project_root_finder.html +357 -0
  192. simstack/static/docs/_modules/simstack/util/queue_watcher.html +593 -0
  193. simstack/static/docs/_modules/simstack/util/resource_config.html +532 -0
  194. simstack/static/docs/_modules/simstack/util/route_finder.html +390 -0
  195. simstack/static/docs/_modules/simstack/util/runner_util.html +487 -0
  196. simstack/static/docs/_modules/simstack/util/runner_utils.html +468 -0
  197. simstack/static/docs/_modules/simstack/util/safe_code_executor.html +510 -0
  198. simstack/static/docs/_modules/simstack/util/sample_config.html +414 -0
  199. simstack/static/docs/_modules/simstack/util/sensitive_content_filter.html +364 -0
  200. simstack/static/docs/_modules/simstack/util/setup_logging.html +365 -0
  201. simstack/static/docs/_modules/simstack/util/submit_to_watchdog.html +425 -0
  202. simstack/static/docs/_modules/simstack/util/toml_reader.html +482 -0
  203. simstack/static/docs/_modules/simstack/util/transform_file_name.html +357 -0
  204. simstack/static/docs/_modules/simstack/util/ui_tools.html +541 -0
  205. simstack/static/docs/_sources/architecture.rst.txt +25 -0
  206. simstack/static/docs/_sources/array_lists.rst.txt +60 -0
  207. simstack/static/docs/_sources/ci_pipeline.rst.txt +34 -0
  208. simstack/static/docs/_sources/data.rst.txt +175 -0
  209. simstack/static/docs/_sources/database_migrations.rst.txt +310 -0
  210. simstack/static/docs/_sources/datasets.rst.txt +93 -0
  211. simstack/static/docs/_sources/developer_guide.rst.txt +25 -0
  212. simstack/static/docs/_sources/docker_nodes.rst.txt +149 -0
  213. simstack/static/docs/_sources/files.rst.txt +159 -0
  214. simstack/static/docs/_sources/fire_and_forget_runner.rst.txt +67 -0
  215. simstack/static/docs/_sources/index.rst.txt +25 -0
  216. simstack/static/docs/_sources/installation.rst.txt +213 -0
  217. simstack/static/docs/_sources/lists.rst.txt +111 -0
  218. simstack/static/docs/_sources/mass_runner.rst.txt +91 -0
  219. simstack/static/docs/_sources/misc.rst.txt +106 -0
  220. simstack/static/docs/_sources/overview.rst.txt +91 -0
  221. simstack/static/docs/_sources/recovery.rst.txt +38 -0
  222. simstack/static/docs/_sources/resource_config.rst.txt +141 -0
  223. simstack/static/docs/_sources/simstack/modules/modules.rst.txt +7 -0
  224. simstack/static/docs/_sources/simstack/modules/simstack.core.rst.txt +205 -0
  225. simstack/static/docs/_sources/simstack/modules/simstack.core.services.rst.txt +109 -0
  226. simstack/static/docs/_sources/simstack/modules/simstack.methods.rst.txt +77 -0
  227. simstack/static/docs/_sources/simstack/modules/simstack.models.rst.txt +261 -0
  228. simstack/static/docs/_sources/simstack/modules/simstack.rst.txt +22 -0
  229. simstack/static/docs/_sources/simstack/modules/simstack.tables.rst.txt +45 -0
  230. simstack/static/docs/_sources/simstack/modules/simstack.util.rst.txt +381 -0
  231. simstack/static/docs/_sources/submit.rst.txt +141 -0
  232. simstack/static/docs/_sources/tables.rst.txt +50 -0
  233. simstack/static/docs/_sources/testing_complex_nodes.rst.txt +92 -0
  234. simstack/static/docs/_sources/ui_documentation.rst.txt +272 -0
  235. simstack/static/docs/_sources/workflows.rst.txt +446 -0
  236. simstack/static/docs/_static/base-stemmer.js +476 -0
  237. simstack/static/docs/_static/basic.css +906 -0
  238. simstack/static/docs/_static/cobalt2-theme.css +1 -0
  239. simstack/static/docs/_static/debug.css +69 -0
  240. simstack/static/docs/_static/docs-build-badge.css +51 -0
  241. simstack/static/docs/_static/docs-build-badge.js +51 -0
  242. simstack/static/docs/_static/doctools.js +150 -0
  243. simstack/static/docs/_static/documentation_options.js +13 -0
  244. simstack/static/docs/_static/english-stemmer.js +1066 -0
  245. simstack/static/docs/_static/file.png +0 -0
  246. simstack/static/docs/_static/language_data.js +13 -0
  247. simstack/static/docs/_static/minus.png +0 -0
  248. simstack/static/docs/_static/plus.png +0 -0
  249. simstack/static/docs/_static/pygments.css +250 -0
  250. simstack/static/docs/_static/scripts/furo-extensions.js +0 -0
  251. simstack/static/docs/_static/scripts/furo.js +3 -0
  252. simstack/static/docs/_static/scripts/furo.js.LICENSE.txt +7 -0
  253. simstack/static/docs/_static/scripts/furo.js.map +1 -0
  254. simstack/static/docs/_static/searchtools.js +693 -0
  255. simstack/static/docs/_static/skeleton.css +296 -0
  256. simstack/static/docs/_static/sphinx_highlight.js +159 -0
  257. simstack/static/docs/_static/styles/furo-extensions.css +2 -0
  258. simstack/static/docs/_static/styles/furo-extensions.css.map +1 -0
  259. simstack/static/docs/_static/styles/furo.css +2 -0
  260. simstack/static/docs/_static/styles/furo.css.map +1 -0
  261. simstack/static/docs/architecture.html +340 -0
  262. simstack/static/docs/array_lists.html +678 -0
  263. simstack/static/docs/ci_pipeline.html +385 -0
  264. simstack/static/docs/data.html +545 -0
  265. simstack/static/docs/database_migrations.html +652 -0
  266. simstack/static/docs/datasets.html +1268 -0
  267. simstack/static/docs/developer_guide.html +359 -0
  268. simstack/static/docs/docker_nodes.html +503 -0
  269. simstack/static/docs/files.html +718 -0
  270. simstack/static/docs/fire_and_forget_runner.html +641 -0
  271. simstack/static/docs/genindex.html +6390 -0
  272. simstack/static/docs/index.html +516 -0
  273. simstack/static/docs/installation.html +553 -0
  274. simstack/static/docs/lists.html +478 -0
  275. simstack/static/docs/mass_runner.html +481 -0
  276. simstack/static/docs/misc.html +454 -0
  277. simstack/static/docs/objects.inv +0 -0
  278. simstack/static/docs/overview.html +469 -0
  279. simstack/static/docs/py-modindex.html +1111 -0
  280. simstack/static/docs/recovery.html +371 -0
  281. simstack/static/docs/resource_config.html +590 -0
  282. simstack/static/docs/search.html +327 -0
  283. simstack/static/docs/searchindex.js +1 -0
  284. simstack/static/docs/simstack/modules/modules.html +489 -0
  285. simstack/static/docs/simstack/modules/simstack.core.html +1883 -0
  286. simstack/static/docs/simstack/modules/simstack.core.services.html +698 -0
  287. simstack/static/docs/simstack/modules/simstack.html +3060 -0
  288. simstack/static/docs/simstack/modules/simstack.methods.html +1150 -0
  289. simstack/static/docs/simstack/modules/simstack.models.html +13113 -0
  290. simstack/static/docs/simstack/modules/simstack.tables.html +635 -0
  291. simstack/static/docs/simstack/modules/simstack.util.html +3320 -0
  292. simstack/static/docs/submit.html +487 -0
  293. simstack/static/docs/tables.html +539 -0
  294. simstack/static/docs/testing_complex_nodes.html +458 -0
  295. simstack/static/docs/ui_documentation.html +788 -0
  296. simstack/static/docs/workflows.html +766 -0
  297. simstack/tables/__init__.py +0 -0
  298. simstack/tables/model_table.py +191 -0
  299. simstack/tables/node_children.py +219 -0
  300. simstack/tables/node_table.py +517 -0
  301. simstack/tables/table_builder.py +314 -0
  302. simstack/util/__init__.py +0 -0
  303. simstack/util/async_zip_utils.py +18 -0
  304. simstack/util/b64mixin.py +23 -0
  305. simstack/util/cleaned_json_schema.py +20 -0
  306. simstack/util/config_reader.py +179 -0
  307. simstack/util/custom_model_dump.py +75 -0
  308. simstack/util/database_information.py +160 -0
  309. simstack/util/db.py +1013 -0
  310. simstack/util/db_logger.py +117 -0
  311. simstack/util/default_from_dict.py +57 -0
  312. simstack/util/directory_iterator.py +216 -0
  313. simstack/util/docstring_parser.py +186 -0
  314. simstack/util/file_hashing.py +72 -0
  315. simstack/util/file_transfer_client.py +427 -0
  316. simstack/util/files.py +396 -0
  317. simstack/util/find_python_files.py +33 -0
  318. simstack/util/generate_ui_schema.py +80 -0
  319. simstack/util/generic_list_mixin.py +120 -0
  320. simstack/util/geometry_utils.py +118 -0
  321. simstack/util/get_module_path.py +20 -0
  322. simstack/util/git_pull.py +65 -0
  323. simstack/util/git_repository_status.py +95 -0
  324. simstack/util/import_module.py +63 -0
  325. simstack/util/importer.py +312 -0
  326. simstack/util/init_data_source.py +41 -0
  327. simstack/util/make_graph.py +107 -0
  328. simstack/util/make_table.py +837 -0
  329. simstack/util/mappings.py +41 -0
  330. simstack/util/minimal_route_finder.py +72 -0
  331. simstack/util/mock_db.py +144 -0
  332. simstack/util/module_path_checker.py +38 -0
  333. simstack/util/object_list_mixin.py +282 -0
  334. simstack/util/path_manager.py +223 -0
  335. simstack/util/project_root_finder.py +41 -0
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+ <section id="creating-docker-containers-for-simstack-nodes">
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+ <span id="docker-nodes"></span><h1>Creating Docker Containers for SimStack Nodes<a class="headerlink" href="#creating-docker-containers-for-simstack-nodes" title="Link to this heading">¶</a></h1>
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+ <p>This document explains the mechanism for creating Docker containers for SimStack nodes, using the <cite>psi4_node</cite> as a practical example.</p>
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+ <section id="mechanism-overview">
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+ <h2>Mechanism Overview<a class="headerlink" href="#mechanism-overview" title="Link to this heading">¶</a></h2>
286
+ <p>SimStack nodes can be containerized to ensure a consistent execution environment, especially when complex dependencies like quantum chemistry codes (e.g., Psi4) are involved.</p>
287
+ <p>The general approach involves:
288
+ 1. Creating a <cite>Dockerfile</cite> that sets up the environment and installs necessary software.
289
+ 2. Including SimStack and its core running mechanism in the container.
290
+ 3. Defining an <cite>ENTRYPOINT</cite> that calls the SimStack node runner.</p>
291
+ </section>
292
+ <section id="example-psi4-node">
293
+ <h2>Example: Psi4 Node<a class="headerlink" href="#example-psi4-node" title="Link to this heading">¶</a></h2>
294
+ <p>The <cite>psi4_node</cite> is part of the <cite>molecular_qm_psi4</cite> package. It requires <cite>psi4</cite> and <cite>crest</cite> which are best installed via <cite>micromamba</cite> (a fast alternative to conda).</p>
295
+ <section id="node-implementation">
296
+ <h3>Node Implementation<a class="headerlink" href="#node-implementation" title="Link to this heading">¶</a></h3>
297
+ <p>The node is defined in <cite>molecular_qm_psi4/psi4_node.py</cite>. It uses the <cite>&#64;node</cite> decorator and interacts with SimStack’s <cite>node_runner</cite>.</p>
298
+ <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
299
+ <span class="k">try</span><span class="p">:</span>
300
+ <span class="kn">import</span><span class="w"> </span><span class="nn">psi4</span>
301
+ <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
302
+ <span class="n">psi4</span> <span class="o">=</span> <span class="kc">None</span>
303
+
304
+ <span class="kn">from</span><span class="w"> </span><span class="nn">simstack.core.node</span><span class="w"> </span><span class="kn">import</span> <span class="n">node</span>
305
+ <span class="kn">from</span><span class="w"> </span><span class="nn">simstack.core.simstack_result</span><span class="w"> </span><span class="kn">import</span> <span class="n">SimstackResult</span>
306
+ <span class="kn">from</span><span class="w"> </span><span class="nn">molecular_qm_models</span><span class="w"> </span><span class="kn">import</span> <span class="n">QMInput</span><span class="p">,</span> <span class="n">QMResult</span><span class="p">,</span> <span class="n">Molecule</span><span class="p">,</span> <span class="n">Atom</span><span class="p">,</span> <span class="n">MoleculeList</span>
307
+
308
+ <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="vm">__name__</span><span class="p">)</span>
309
+
310
+ <span class="k">def</span><span class="w"> </span><span class="nf">qminput_to_psi4_molecule</span><span class="p">(</span><span class="n">molecule</span><span class="p">:</span> <span class="n">Molecule</span><span class="p">,</span> <span class="n">charge</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">multiplicity</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
311
+ <span class="w"> </span><span class="sd">&quot;&quot;&quot;Converts a Simstack Molecule to a Psi4 molecule string.&quot;&quot;&quot;</span>
312
+ <span class="n">mol_str</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">charge</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">multiplicity</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span>
313
+ <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">molecule</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
314
+ <span class="n">mol_str</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">atom</span><span class="o">.</span><span class="n">element</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">atom</span><span class="o">.</span><span class="n">x</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">atom</span><span class="o">.</span><span class="n">y</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">atom</span><span class="o">.</span><span class="n">z</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span>
315
+ <span class="k">return</span> <span class="n">mol_str</span>
316
+
317
+ <span class="nd">@node</span>
318
+ <span class="k">async</span> <span class="k">def</span><span class="w"> </span><span class="nf">psi4_calculator</span><span class="p">(</span><span class="n">qm_input</span><span class="p">:</span> <span class="n">QMInput</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SimstackResult</span><span class="p">:</span>
319
+ <span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
320
+ <span class="sd"> Psi4 node implementation using Python bindings.</span>
321
+ <span class="sd"> &quot;&quot;&quot;</span>
322
+ <span class="n">node_runner</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;node_runner&quot;</span><span class="p">)</span>
323
+
324
+ <span class="k">if</span> <span class="n">psi4</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
325
+ <span class="k">return</span> <span class="n">node_runner</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="s2">&quot;Psi4 is not installed in the current environment.&quot;</span><span class="p">)</span>
326
+
327
+ <span class="k">try</span><span class="p">:</span>
328
+ <span class="c1"># Set up Psi4 molecule</span>
329
+ <span class="n">mol_str</span> <span class="o">=</span> <span class="n">qminput_to_psi4_molecule</span><span class="p">(</span><span class="n">qm_input</span><span class="o">.</span><span class="n">molecule</span><span class="p">,</span> <span class="n">qm_input</span><span class="o">.</span><span class="n">charge</span><span class="p">,</span> <span class="n">qm_input</span><span class="o">.</span><span class="n">multiplicity</span><span class="p">)</span>
330
+ <span class="n">psi4</span><span class="o">.</span><span class="n">geometry</span><span class="p">(</span><span class="n">mol_str</span><span class="p">)</span>
331
+
332
+ <span class="c1"># ... (configuration and execution logic) ...</span>
333
+
334
+ <span class="c1"># Execute calculation</span>
335
+ <span class="k">if</span> <span class="n">qm_input</span><span class="o">.</span><span class="n">optimization</span><span class="p">:</span>
336
+ <span class="n">energy</span><span class="p">,</span> <span class="n">wfn</span> <span class="o">=</span> <span class="n">psi4</span><span class="o">.</span><span class="n">optimize</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">return_wfn</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
337
+ <span class="c1"># ...</span>
338
+ <span class="k">else</span><span class="p">:</span>
339
+ <span class="n">energy</span><span class="p">,</span> <span class="n">wfn</span> <span class="o">=</span> <span class="n">psi4</span><span class="o">.</span><span class="n">energy</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">return_wfn</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
340
+
341
+ <span class="n">qm_result</span> <span class="o">=</span> <span class="n">QMResult</span><span class="p">()</span>
342
+ <span class="n">qm_result</span><span class="o">.</span><span class="n">final_energy</span> <span class="o">=</span> <span class="n">energy</span>
343
+ <span class="c1"># ...</span>
344
+
345
+ <span class="n">node_runner</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Psi4 calculation finished successfully&quot;</span><span class="p">)</span>
346
+ <span class="n">node_runner</span><span class="o">.</span><span class="n">psi4_result</span> <span class="o">=</span> <span class="n">qm_result</span>
347
+ <span class="k">return</span> <span class="n">node_runner</span><span class="o">.</span><span class="n">succeed</span><span class="p">()</span>
348
+
349
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
350
+ <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">&quot;Psi4 calculation failed: </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">&quot;</span><span class="p">)</span>
351
+ <span class="k">return</span> <span class="n">node_runner</span><span class="o">.</span><span class="n">fail</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Psi4 execution failed: </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">&quot;</span><span class="p">)</span>
352
+ <span class="k">finally</span><span class="p">:</span>
353
+ <span class="k">if</span> <span class="n">psi4</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
354
+ <span class="n">psi4</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">clean</span><span class="p">()</span>
355
+ </pre></div>
356
+ </div>
357
+ </section>
358
+ <section id="dockerfile-configuration">
359
+ <h3>Dockerfile Configuration<a class="headerlink" href="#dockerfile-configuration" title="Link to this heading">¶</a></h3>
360
+ <p>The <cite>Dockerfile</cite> for this node is located at <cite>molecular_qm_psi4/Dockerfile</cite>. It uses <cite>micromamba</cite> for environment management and <cite>uv</cite> for fast Python package installation.</p>
361
+ <div class="highlight-dockerfile notranslate"><div class="highlight"><pre><span></span><span class="c"># Use a base image with micromamba (conda replacement)</span>
362
+ <span class="k">FROM</span><span class="w"> </span><span class="s">mambaorg/micromamba:latest</span>
363
+
364
+ <span class="k">USER</span><span class="w"> </span><span class="s">root</span>
365
+
366
+ <span class="c"># Install git and other build essentials</span>
367
+ <span class="k">RUN</span><span class="w"> </span>apt-get<span class="w"> </span>update<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span>apt-get<span class="w"> </span>install<span class="w"> </span>-y<span class="w"> </span>--no-install-recommends<span class="w"> </span><span class="se">\</span>
368
+ <span class="w"> </span>git<span class="w"> </span><span class="se">\</span>
369
+ <span class="w"> </span>ca-certificates<span class="w"> </span><span class="se">\</span>
370
+ <span class="w"> </span>curl<span class="w"> </span><span class="se">\</span>
371
+ <span class="w"> </span>build-essential<span class="w"> </span><span class="se">\</span>
372
+ <span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span>rm<span class="w"> </span>-rf<span class="w"> </span>/var/lib/apt/lists/*
373
+
374
+ <span class="c"># Fix for _distutils_hack error: explicitly install setuptools</span>
375
+ <span class="k">RUN</span><span class="w"> </span>micromamba<span class="w"> </span>install<span class="w"> </span>-y<span class="w"> </span>-n<span class="w"> </span>base<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>setuptools<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="se">\</span>
376
+ <span class="w"> </span>micromamba<span class="w"> </span>clean<span class="w"> </span>--all<span class="w"> </span>--yes
377
+
378
+ <span class="c"># Install uv</span>
379
+ <span class="k">RUN</span><span class="w"> </span>curl<span class="w"> </span>-LsSf<span class="w"> </span>https://astral.sh/uv/install.sh<span class="w"> </span><span class="p">|</span><span class="w"> </span>sh
380
+ <span class="k">ENV</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span><span class="s2">&quot;/opt/conda/bin:/root/.local/bin:</span><span class="nv">$PATH</span><span class="s2">&quot;</span>
381
+
382
+ <span class="c"># Set up work directory</span>
383
+ <span class="k">WORKDIR</span><span class="w"> </span><span class="s">/app</span>
384
+
385
+ <span class="c"># Install Psi4 and crest from conda</span>
386
+ <span class="k">RUN</span><span class="w"> </span>micromamba<span class="w"> </span>install<span class="w"> </span>-y<span class="w"> </span>-n<span class="w"> </span>base<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>psi4<span class="w"> </span>crest<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="se">\</span>
387
+ <span class="w"> </span>micromamba<span class="w"> </span>clean<span class="w"> </span>--all<span class="w"> </span>--yes
388
+
389
+ <span class="c"># Copy the repositories/directories</span>
390
+ <span class="k">COPY</span><span class="w"> </span>molecular_qm_models<span class="w"> </span>/app/molecular_qm_models
391
+ <span class="k">COPY</span><span class="w"> </span>molecular_qm_psi4<span class="w"> </span>/app/molecular_qm_psi4
392
+ <span class="k">COPY</span><span class="w"> </span>molecular_qm_psi4/README.md<span class="w"> </span>/app/README.md
393
+ <span class="k">COPY</span><span class="w"> </span>simstack.toml<span class="w"> </span>/app/simstack.toml
394
+
395
+ <span class="k">ENV</span><span class="w"> </span><span class="nv">PYTHONPATH</span><span class="o">=</span><span class="s2">&quot;/app:/app/molecular_qm_psi4&quot;</span>
396
+ <span class="k">ENV</span><span class="w"> </span><span class="nv">UV_PYTHON</span><span class="o">=</span>/opt/conda/bin/python
397
+ <span class="k">ENV</span><span class="w"> </span><span class="nv">UV_PROJECT_ENVIRONMENT</span><span class="o">=</span>/opt/conda
398
+ <span class="k">ENV</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span><span class="s2">&quot;/opt/conda/bin:/root/.local/bin:</span><span class="nv">$PATH</span><span class="s2">&quot;</span>
399
+
400
+ <span class="c"># Install dependencies directly</span>
401
+ <span class="k">RUN</span><span class="w"> </span>uv<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>--system<span class="w"> </span><span class="s2">&quot;simstack @ git+https://github.com/simstack/simstack.git@feature-test-generation&quot;</span><span class="w"> </span><span class="s2">&quot;setuptools&gt;=80.9.0&quot;</span>
402
+
403
+ <span class="c"># Entrypoint: call the module directly</span>
404
+ <span class="k">ENTRYPOINT</span><span class="w"> </span><span class="p">[</span><span class="s2">&quot;python&quot;</span><span class="p">,</span><span class="w"> </span><span class="s2">&quot;-m&quot;</span><span class="p">,</span><span class="w"> </span><span class="s2">&quot;simstack.core.run_node&quot;</span><span class="p">]</span>
405
+ </pre></div>
406
+ </div>
407
+ </section>
408
+ </section>
409
+ <section id="key-components-for-containerization">
410
+ <h2>Key Components for Containerization<a class="headerlink" href="#key-components-for-containerization" title="Link to this heading">¶</a></h2>
411
+ <ol class="arabic simple">
412
+ <li><p><strong>Base Image</strong>: Use a lightweight and appropriate base image (e.g., <cite>micromamba</cite> for scientific software).</p></li>
413
+ <li><p><strong>Environment Setup</strong>: Install all non-Python dependencies (compilers, libraries, etc.).</p></li>
414
+ <li><p><strong>Python Environment</strong>: Install Python and required packages. The use of <cite>uv</cite> is recommended for performance.</p></li>
415
+ <li><p><strong>Code Integration</strong>: Copy your node code and its local dependencies into the container.</p></li>
416
+ <li><p><strong>PYTHONPATH</strong>: Ensure that the <cite>PYTHONPATH</cite> is set correctly so that SimStack can find your node and models.</p></li>
417
+ <li><p><strong>SimStack Installation</strong>: Install the <cite>simstack</cite> package itself.</p></li>
418
+ <li><p><strong>Entrypoint</strong>: The <cite>ENTRYPOINT [“python”, “-m”, “simstack.core.run_node”]</cite> is crucial as it tells SimStack how to execute the node within the container.</p></li>
419
+ </ol>
420
+ </section>
421
+ </section>
422
+
423
+ </article>
424
+ </div>
425
+ <footer>
426
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+ <div class="toc-tree-container">
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+ <ul>
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+ <li><a class="reference internal" href="#">Creating Docker Containers for SimStack Nodes</a><ul>
479
+ <li><a class="reference internal" href="#mechanism-overview">Mechanism Overview</a></li>
480
+ <li><a class="reference internal" href="#example-psi4-node">Example: Psi4 Node</a><ul>
481
+ <li><a class="reference internal" href="#node-implementation">Node Implementation</a></li>
482
+ <li><a class="reference internal" href="#dockerfile-configuration">Dockerfile Configuration</a></li>
483
+ </ul>
484
+ </li>
485
+ <li><a class="reference internal" href="#key-components-for-containerization">Key Components for Containerization</a></li>
486
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