Use standard library foundations

[stanbot8]

Use standard library runtime foundations.

• Core runtime utilities depended on external implementations for standard facilities. Replace those facilities with standard library owners. src/core/environment/uniform_grid_environment.h, src/core/execution_context/execution_context.h, src/core/gpu/cuda_error_chk.h, src/core/gpu/cuda_timer.h, src/core/gpu/opencl_state.h, src/core/interaction_force.cc, src/core/memory/memory_manager.cc, src/core/memory/memory_manager.h, src/core/operation/default_ops.cc, src/core/real_t.h, src/core/util/spinlock.h, src/core/util/thread_info.h, test/unit/core/environment/custom_environment_test.h, test/unit/core/util/thread_info_test.cc
• Runtime behavior depended on dynamically generated type metadata. Replace dynamic metadata with explicit typed definitions. demo/analytic_continuum/src/continuum_model.h, demo/analytic_continuum/src/my_agent.h, demo/analytic_continuum/src/my_behavior.h, demo/cell_division_enhanced/src/cell_division_enhanced.h, demo/flocking/src/boid.h, demo/mars/src/CelestialObjects.h, demo/monolayer_growth/src/behaviours.h, demo/monolayer_growth/src/cell_cell_force.cc, demo/monolayer_growth/src/cycling_cell.h, demo/monolayer_growth/src/evaluate.h, demo/newtons_law_test/src/CelestialObjects.h, demo/parameters/src/parameters.h, demo/pyramidal_cell/src/pyramidal_cell.h, demo/regulatory_networks/src/bdm_ex1.h, demo/regulatory_networks/src/bdm_ex2.h, demo/regulatory_networks/src/lorenz.h, demo/regulatory_networks/src/oscillator.h, demo/regulatory_networks/src/sine.h, demo/sbml_integration/src/sbml_integration.h, demo/solar_system/src/CelestialObjects.h, demo/solar_system/src/solar_system.h, demo/soma_clustering/src/my_cell.h, demo/tumor_concept/src/tumor_concept.h, doc/user_guide/tumor_concept.md, src/core/agent/agent.cc, src/core/agent/agent.h, src/core/agent/agent_handle.h, src/core/agent/agent_pointer.h, src/core/agent/agent_uid.h, src/core/agent/agent_uid_generator.h, src/core/agent/cell.h, src/core/agent/spherical_agent.h, src/core/analysis/reduce.h, src/core/behavior/behavior.h, src/core/behavior/chemotaxis.h, src/core/behavior/gene_regulation.h, src/core/behavior/growth_division.h, src/core/behavior/regulatory_network.h, src/core/behavior/secretion.h, src/core/behavior/stateless_behavior.h, src/core/container/inline_vector.h, src/core/container/parallel_resize_vector.h, src/core/container/shared_data.h, src/core/diffusion/continuum_interface.h, src/core/diffusion/diffusion_grid.h, src/core/diffusion/euler_depletion_grid.h, src/core/diffusion/euler_grid.h, src/core/type_index.cc, src/core/type_index.h, src/core/util/log.h, src/core/util/timing_aggregator.h, src/neuroscience/neurite_element.cc, src/neuroscience/neurite_element.h, src/neuroscience/neuron_soma.cc, src/neuroscience/neuron_soma.h, src/neuroscience/param.h, test/unit/core/agent/agent_pointer_test.h, test/unit/core/agent/agent_test.h, test/unit/core/agent/agent_uid_generator_test.cc, test/unit/core/agent/agent_uid_test.cc, test/unit/core/agent/cell_test.cc, test/unit/core/agent/cell_test.h, test/unit/core/analysis/reduce_test.cc, test/unit/core/behavior/stateless_behavior_test.cc, test/unit/core/container/inline_vector_test.cc, test/unit/core/container/inline_vector_test.h, test/unit/core/container/parallel_resize_vector_test.h, test/unit/core/container/shared_data_test.cc, test/unit/core/container/shared_data_test.h, test/unit/core/diffusion_init_test.cc, test/unit/core/diffusion_init_test.h, test/unit/core/diffusion_test.cc, test/unit/test_util/test_agent.h, src/core/container/math_array.h, src/core/util/random.h
• An allocation escaped the scope that owned its release. Keep the allocation with its matching cleanup path. src/core/execution_context/in_place_exec_ctxt.cc, src/core/execution_context/in_place_exec_ctxt.h, src/core/resource_manager.cc, src/core/resource_manager.h, test/unit/core/resource_manager_test.cc, test/unit/core/resource_manager_test.h, test/unit/core/execution_context/in_place_exec_ctxt_test.cc
• util/valgrind.sh ignored util/valgrind-bdm.supp, so libgomp worker-thread TLS retained until process exit was reported as an application leak. Route Memcheck through --suppressions with only the exact libgomp worker TLS stack. util/valgrind-bdm.supp, util/valgrind.sh
• BDM_REGISTER_OP and BDM_REGISTER_TEMPLATE_OP constructed operation implementations during static initialization, so MechanicalForcesOp and ReductionOp initialized ThreadInfo before simulation runtime. Register OperationImplFactory callbacks and instantiate them in OperationRegistry::NewOperation. src/core/operation/operation_registry.cc, src/core/operation/operation_registry.h
• ReductionOp::Clone shallow-copied two manually owned functor pointers, so multiple destructors could release the same objects. Retain both functors in typed std::shared_ptr owners. src/core/operation/reduction_op.h, test/unit/core/operation/operation_test.cc
• MechanicalForcesOp copied, replaced, and deleted its InteractionForce through a manually owned raw pointer. Retain the force in std::unique_ptr<InteractionForce>. src/core/operation/mechanical_forces_op.h
• Visualization data extraction depended on dynamic runtime services. Replace dynamic extraction with explicit typed data access. cli/view_command.py, paraview_plugin/CMakeLists.txt, paraview_plugin/Plugin/CMakeLists.txt, src/core/visualization/paraview/adaptor.cc, src/core/visualization/paraview/adaptor.h, src/core/visualization/paraview/helper.h, src/core/visualization/paraview/jit_helper.h, src/core/visualization/paraview/mapped_data_array.h, src/core/visualization/paraview/parallel_vti_writer.cc, src/core/visualization/paraview/parallel_vtu_writer.cc, src/core/visualization/paraview/parallel_vtu_writer.h, src/core/visualization/paraview/vtk_agents.cc, src/core/visualization/paraview/vtk_agents.h, src/core/visualization/paraview/vtu_writer.cc, src/core/visualization/paraview/vtu_writer.h, src/core/visualization/visualization_adaptor.cc, test/unit/core/visualization/paraview/adaptor_test.h, test/unit/core/visualization/paraview/integration_test.cc, test/unit/core/visualization/paraview/mapped_data_array_test.cc
• The build still discovered, generated, linked, and packaged an unused dependency. Remove its build, packaging, and setup integration. .devcontainer/Dockerfile, .devcontainer/paraview-wrapper.sh, .github/workflows/README.md, .github/workflows/macos-ci.yml, .github/workflows/macos-system-ci.yml, .github/workflows/repository-checks.yml, .github/workflows/singularity-integration.yml, .github/workflows/ubuntu-ci.yml, .github/workflows/ubuntu-system-ci.yml, CMakeLists.txt, CONTRIBUTING.md, Singularity, cli/config_command.py, cmake/BioDynaMo.cmake, cmake/FindROOT.cmake, cmake/FindTBB.cmake, cmake/Findtcmalloc.cmake, cmake/Installation.cmake, cmake/Notebooks.cmake, cmake/RootUseFile.cmake, cmake/UseBioDynaMo.cmake.in, cmake/Versioning.cmake, cmake/Website.cmake, cmake/bdm-dictionary, cmake/env/bdm-config.in, cmake/env/launcher.sh, cmake/env/sh_functions/paraview, cmake/env/sh_functions/pvbatch, cmake/env/sh_functions/pvpython, cmake/env/sh_functions/root, cmake/env/thisbdm.fish, cmake/env/thisbdm.sh, cmake/external/ParaView.cmake, cmake/external/Qt.cmake, cmake/external/ROOT.cmake, cmake/external/SHA256Digests.cmake, cmake/selection-libVisualizationAdaptor.xml, cmake/selection-libbiodynamo.xml, cmake/selection.xml, cmake/utils.cmake, demo/binding_cells/CMakeLists.txt, demo/binding_cells/analysis.ipynb, demo/binding_cells/bdm.toml, demo/binding_cells/params.json, demo/binding_cells/run.sh, demo/binding_cells/src/agents/monocyte.h, demo/binding_cells/src/agents/t_cell.h, demo/binding_cells/src/binding_cells.cc, demo/binding_cells/src/binding_cells.h, demo/binding_cells/src/biology_modules/connect_within_radius_module.h, demo/binding_cells/src/biology_modules/constant_displacement_module.h, demo/binding_cells/src/biology_modules/inhibitation_module.h, demo/binding_cells/src/biology_modules/physical_bond_module.h, demo/binding_cells/src/biology_modules/random_walk_module.h, demo/binding_cells/src/biology_modules/spring_force_module.h, demo/binding_cells/src/biology_modules/stokes_velocity_module.h, demo/binding_cells/src/macro.C, demo/binding_cells/src/plot_graph.h, demo/epidemiology/CMakeLists.txt, demo/epidemiology/measles.json, demo/epidemiology/optim.json, demo/epidemiology/plot-style.json, demo/epidemiology/render.py, demo/epidemiology/run.sh, demo/epidemiology/src/analytical-solution.cc, demo/epidemiology/src/analytical-solution.h, demo/epidemiology/src/behavior.h, demo/epidemiology/src/epidemiology.cc, demo/epidemiology/src/epidemiology.h, demo/epidemiology/src/evaluate.h, demo/epidemiology/src/person.h, demo/epidemiology/src/sim-param.h, demo/epidemiology/test.sh, demo/epidemiology/visualize.sh, demo/makefile_project/Makefile, demo/makefile_project/README.md, demo/multiple_simulations/src/multiple_simulations.h, doc/dev_guide/build.md, doc/sidebars/userguide.yaml, doc/user_guide/Singularity.md, doc/user_guide/docs/notebooks.md, doc/user_guide/installation.md, doc/user_guide/multi_simulation.md, doc/user_guide/parameter.md, doc/user_guide/prerequisites.md, doc/user_guide/simulation_parameter_tutorial.md, etc/bdm.rootrc, notebook/ST01-model-initializer.ipynb, notebook/ST02-user-defined-random-number-distribution.ipynb, notebook/ST03-agent-reproduction-mortality.ipynb, notebook/ST04-agent-reproduction-with-behaviors.ipynb, notebook/ST05-agent-reproduction-advanced.ipynb, notebook/ST06-environment-search.ipynb, notebook/ST07-multi-scale-simulation.ipynb, notebook/ST08-histograms.ipynb, notebook/ST09-timeseries-plotting-basic.ipynb, notebook/ST10-timeseries-plotting-and-analysis.ipynb, notebook/ST11-multiple-experiments-statistical-analysis.ipynb, notebook/ST12-hierarchical-model.ipynb, notebook/ST13-dynamic-scheduling.ipynb, notebook/ST14-randomize-iteration-order.ipynb, notebook/ST15-replace-interaction-force.ipynb, src/biodynamo.h, src/core/analysis/line_graph.cc, src/core/analysis/line_graph.h, src/core/analysis/style.cc, src/core/analysis/style.h, src/core/analysis/time_series.cc, src/core/analysis/time_series.h, src/core/multi_simulation/algorithm/algorithm.h, src/core/multi_simulation/algorithm/algorithm_registry.cc, src/core/multi_simulation/algorithm/algorithm_registry.h, src/core/multi_simulation/algorithm/parameter_sweep.cc, src/core/multi_simulation/algorithm/particle_swarm.cc, src/core/multi_simulation/database.h, src/core/multi_simulation/dynamic_loop.h, src/core/multi_simulation/experiment.h, src/core/multi_simulation/mpi_helper.h, src/core/multi_simulation/multi_simulation.cc, src/core/multi_simulation/multi_simulation.h, src/core/multi_simulation/multi_simulation_manager.cc, src/core/multi_simulation/multi_simulation_manager.h, src/core/multi_simulation/optimization_param.h, src/core/multi_simulation/optimization_param_type/log_range_param.h, src/core/multi_simulation/optimization_param_type/optimization_param_type.h, src/core/multi_simulation/optimization_param_type/particle_swarm_param.h, src/core/multi_simulation/optimization_param_type/range_param.h, src/core/multi_simulation/optimization_param_type/set_param.h, src/core/param/command_line_options.cc, src/core/param/command_line_options.h, src/core/param/param.cc, src/core/param/param.h, src/core/param/param_group.h, src/core/scheduler.cc, src/core/scheduler.h, src/core/simulation.cc, src/core/simulation.h, src/core/simulation_backup.cc, src/core/simulation_backup.h, src/core/util/io.cc, src/core/util/io.h, src/core/util/jit.cc, src/core/util/jit.h, src/core/util/plot_memory_layout.cc, src/core/util/plot_memory_layout.h, src/core/util/root.cc, src/core/util/root.h, src/core/visualization/root/adaptor.h, src/core/visualization/root/notebook_util.h, test/installation-test.sh, test/system/backup_restore.sh, test/system/backup_restore/CMakeLists.txt, test/system/backup_restore/src/backup_restore.cc, test/system/backup_restore/src/backup_restore.h, test/system/multi_simulation.sh, test/system/multi_simulation/CMakeLists.txt, test/system/multi_simulation/optim.json, test/system/multi_simulation/src/multi_simulation_test.cc, test/system/multi_simulation/src/multi_simulation_test.h, test/system/multi_simulation/src/test_algorithm.cc, test/unit/core/analysis/time_series_test.cc, test/unit/core/command_line_options_test.cc, test/unit/core/multi_simulation/algorithm_test.cc, test/unit/core/multi_simulation/dynamic_loop_test.cc, test/unit/core/multi_simulation/optimization_param_type_test.cc, test/unit/core/param/param_test.cc, test/unit/core/param/test.json, test/unit/core/scheduler_test.cc, test/unit/core/scheduler_test.h, test/unit/core/simulation_backup_test.cc, test/unit/core/simulation_test.cc, test/unit/core/util/io_test.cc, test/unit/test_util/io_test.h, test/util.inc, third_party/OptionParser.h, third_party/cpptoml/cpptoml.h, util/build-third-party/build-all.sh, util/build-third-party/build-paraview.sh, util/build-third-party/build-qt.sh, util/build-third-party/build-root.sh, util/build-third-party/paraview/build.sh, util/build-third-party/paraview/checkout-code.sh, util/build-third-party/paraview/env.sh, util/build-third-party/paraview/make_macos_pvsdk_relocatable.py, util/build-third-party/paraview/package.sh, util/build-third-party/paraview/paraview-superbuild-openmp.v5.9.0.patch, util/build-third-party/paraview/prerequisites.sh, util/build-third-party/qt-silent-install-linux.js, util/build-third-party/qt-silent-install-macos.js, util/build-third-party/third-party-prerequisites.sh, util/clean-build-dir.sh, util/demo_to_notebook.py, util/git/pr_checklist.md, util/install, util/installation/centos-7/Dockerfile, util/installation/osx/package_list_required, util/installation/osx/prerequisites.sh, util/installation/ubuntu-18.04/Dockerfile, util/installation/ubuntu-20.04/Dockerfile, util/installation/ubuntu-22.04/Dockerfile, util/installation/ubuntu-24.04/Dockerfile, util/makefile-build/bdm-code-generation
• CTest could run biodynamo-unit-tests and valgrind_biodynamo-unit-tests concurrently even though both registrations share the suite's output state. Enforce RUN_SERIAL on valgrind_biodynamo-unit-tests. cmake/Testing.cmake