Stabilize preflight, runners, and ERF artifacts (#55)

* sync ERF dependency pin and startup readiness docs
* add first-run readiness red tests and integration clone coverage
* Implement Phase 5 startup readiness preflight logic
* Rebuild ERF FAISS artifacts and refresh schema rename outputs
* Set default FAISS embedding model to lbl/nomic-embed-text
* Add startup preflight hook in main with TTY/non-TTY coverage
* Improve preflight mismatch remediation guidance and non-TTY hint
* Improve interactive preflight UX for ERF mismatch and repo selection
* Refactor executable discovery policy and runner fallbacks
* Prefer case-derived solver over default in runners
* Refactor solver compile flow to use config policy
* Stream and log preflight clone progress with SSH fallback
* Resolve local submit executable via solver build policy
* Use solver policy for superfacility executable selection
* Add interactive development+rebuild path for ERF commit mismatch
* Propagate interactive repo selection and rerun preflight checks
* Add tracked ERF first-run auto-setup matrix script
* Add continue+rebuild option and progress logs for ERF mismatch
* Make rebuild check optional and avoid repeated interactive rebuild loops
* Waive same-run ERF mismatch after successful rebuild
* Prefer runner run directory in visualization node
* restore post-merge test contracts and clean ERF schema artifact
* Remove scripts and local outputs
* Added additional skips for spurious tests
* Added preflight stubs to CLI integration tests
* Implement code-gated viz mapping with clarification disambiguation
* Gate solver-dependent viz tests and assert catalog hard-fail

Author: jmsexton03

.dependencies.json

@@ -18,7 +18,7 @@
     "erf": {
       "url": "https://github.com/erf-model/ERF.git",
       "branch": "development",
-      "commit": "1df48173da427f57a8201e157518afa7fd2e73ee"
+      "commit": "5613ec3943a33d5f0b4f954e34c4e3ff5559a945"
     },
     "remora": {
       "url": "https://github.com/AMReX-Codes/REMORA.git",

database/configs/amrex_config.py

@@ -52,3 +52,11 @@ class AMReXConfig(BaseAMReXConfig):
     priority_cases = [
         "Tests/Amr/Advection_AmrCore",
     ]
+
+    @classmethod
+    def get_plotfile_period_param(cls) -> str | None:
+        return "amr.plot_per"
+
+    @classmethod
+    def get_plotfile_step_interval_param(cls) -> str | None:
+        return "amr.plot_int"

database/configs/base_amrex_config.py

@@ -172,6 +172,32 @@ class BaseAMReXConfig:
 
     default_exec_pattern: ClassVar[str | None] = None
     """Glob pattern for default executable within default_exec_repo_path."""
+    build_system_preference: ClassVar[str] = "gnumake"
+    """Preferred build system for executable discovery (e.g., gnumake, cmake)."""
+    executable_search_path_templates: ClassVar[list[str]] = ["{central_build_dir}"]
+    """Ordered executable search templates used by runtime runner fallbacks."""
+    cmake_executable_names: ClassVar[list[str]] = []
+    """Executable filenames emitted by CMake workflows (e.g., erf_exec)."""
+    cmake_executable_ignores_accel_suffix: ClassVar[bool] = False
+    """If True, CMake executables are treated as feature-agnostic names."""
+    gnumake_executable_globs: ClassVar[list[str]] = ["*.ex"]
+    """Executable glob patterns emitted by GNUmake workflows."""
+    cmake_source_dir_template: ClassVar[str] = "{repo_root}"
+    """CMake source directory template for compile orchestration."""
+    cmake_build_dir_template: ClassVar[str] = "{repo_root}/build"
+    """CMake build directory template for compile orchestration."""
+    cmake_install_prefix_template: ClassVar[str | None] = None
+    """Optional CMake install prefix template."""
+    cmake_configure_args: ClassVar[list[str]] = []
+    """Additional args for `cmake -S ... -B ...`."""
+    cmake_build_args: ClassVar[list[str]] = []
+    """Additional args for `cmake --build ...`."""
+    cmake_install_args: ClassVar[list[str]] = []
+    """Additional args for `cmake --install ...`."""
+    gnumake_clean_targets: ClassVar[list[str]] = ["realclean"]
+    """GNUmake clean targets executed before build."""
+    gnumake_build_args: ClassVar[list[str]] = ["USE_MPI=TRUE", "DEBUG=FALSE"]
+    """GNUmake build flag defaults."""
 
     # === Solver Heuristics (Config-Driven) ===
     selection_keywords: ClassVar[list[str]] = []
@@ -2076,6 +2102,68 @@ def resolve_default_inputs_path(cls, repo_root: Path | None) -> Path | None:
             return base / "inputs"
         return None
 
+    @classmethod
+    def get_build_system_preference(cls) -> str:
+        return str(getattr(cls, "build_system_preference", "gnumake")).strip().lower()
+
+    @classmethod
+    def get_executable_search_path_templates(cls) -> list[str]:
+        templates = getattr(cls, "executable_search_path_templates", [])
+        return [str(item) for item in templates]
+
+    @classmethod
+    def get_cmake_executable_names(cls) -> list[str]:
+        names = getattr(cls, "cmake_executable_names", [])
+        return [str(item) for item in names]
+
+    @classmethod
+    def cmake_ignores_accel_suffix(cls) -> bool:
+        return bool(getattr(cls, "cmake_executable_ignores_accel_suffix", False))
+
+    @classmethod
+    def get_gnumake_executable_globs(cls) -> list[str]:
+        globs = getattr(cls, "gnumake_executable_globs", [])
+        return [str(item) for item in globs] if globs else ["*.ex"]
+
+    @classmethod
+    def get_cmake_source_dir_template(cls) -> str:
+        return str(getattr(cls, "cmake_source_dir_template", "{repo_root}"))
+
+    @classmethod
+    def get_cmake_build_dir_template(cls) -> str:
+        return str(getattr(cls, "cmake_build_dir_template", "{repo_root}/build"))
+
+    @classmethod
+    def get_cmake_install_prefix_template(cls) -> str | None:
+        value = getattr(cls, "cmake_install_prefix_template", None)
+        return None if value is None else str(value)
+
+    @classmethod
+    def get_cmake_configure_args(cls) -> list[str]:
+        return [str(item) for item in getattr(cls, "cmake_configure_args", [])]
+
+    @classmethod
+    def get_cmake_build_args(cls) -> list[str]:
+        return [str(item) for item in getattr(cls, "cmake_build_args", [])]
+
+    @classmethod
+    def get_cmake_install_args(cls) -> list[str]:
+        return [str(item) for item in getattr(cls, "cmake_install_args", [])]
+
+    @classmethod
+    def get_gnumake_clean_targets(cls) -> list[str]:
+        targets = getattr(cls, "gnumake_clean_targets", None)
+        if targets is None:
+            return ["realclean"]
+        return [str(item) for item in targets] or ["realclean"]
+
+    @classmethod
+    def get_gnumake_build_args(cls) -> list[str]:
+        args = getattr(cls, "gnumake_build_args", None)
+        if args is None:
+            args = getattr(cls, "gnumake_flags", ["USE_MPI=TRUE", "DEBUG=FALSE"])
+        return [str(item) for item in args]
+
     @classmethod
     def get_slurm_metadata(cls) -> dict[str, str]:
         """
@@ -2296,6 +2384,68 @@ def get_viz_variable_catalog(cls, repo_root: Path | None = None) -> list[dict[st
         return []
 
     @classmethod
+    def get_viz_tier1_intents(cls) -> dict[str, dict[str, Any]]:
+        """
+        Return canonical semantic visualization intents (Tier 1).
+        """
+        return {
+            "temperature": {"aliases": ["temperature", "temp", "thermal"]},
+            "velocity": {"aliases": ["velocity", "speed"]},
+            "vertical_velocity": {
+                "aliases": [
+                    "vertical velocity",
+                    "vertical_velocity",
+                    "w-velocity",
+                    "w velocity",
+                    "updraft",
+                    "downdraft",
+                ]
+            },
+            "pressure": {"aliases": ["pressure", "pres"]},
+            "density": {"aliases": ["density", "rho"]},
+            "vorticity": {"aliases": ["vorticity", "vort"]},
+            "cloud_water": {
+                "aliases": [
+                    "cloud water",
+                    "cloud_water",
+                    "liquid water",
+                    "cloud liquid",
+                    "qc",
+                ]
+            },
+        }
+
+    @classmethod
+    def build_viz_tier2_candidates(cls, repo_root: Path | None = None) -> dict[str, list[dict[str, Any]]]:
+        """
+        Build solver candidates (Tier 2) from live source catalog.
+        """
+        catalog = cls.get_viz_variable_catalog(repo_root=repo_root)
+        if not catalog:
+            return {}
+
+        intents = cls.get_viz_tier1_intents()
+        candidates: dict[str, list[dict[str, Any]]] = {}
+        for token, spec in intents.items():
+            aliases = {token.lower()}
+            for alias in spec.get("aliases", []) or []:
+                aliases.add(str(alias).strip().lower())
+            token_candidates: list[dict[str, Any]] = []
+            for entry in catalog:
+                if not isinstance(entry, dict):
+                    continue
+                name = str(entry.get("name", "")).strip()
+                if not name:
+                    continue
+                entry_aliases = {name.lower()}
+                for alias in entry.get("aliases", []) or []:
+                    entry_aliases.add(str(alias).strip().lower())
+                if aliases.intersection(entry_aliases):
+                    token_candidates.append(dict(entry))
+            if token_candidates:
+                candidates[token] = token_candidates
+        return candidates
+
     def get_default_slice_axis(cls) -> str | None:
         """
         Return preferred default slice-normal axis for visualization.
@@ -2304,6 +2454,50 @@ def get_default_slice_axis(cls) -> str | None:
         """
         return None
 
+    @classmethod
+    def get_plotfile_var_param(cls) -> str:
+        """
+        Return solver-specific parameter key for plot variable selection.
+        """
+        return "amr.plot_vars"
+
+    @classmethod
+    def get_plot_var_param_candidates(cls) -> list[str]:
+        """
+        Return ordered plot-var ParmParse candidate keys (primary first).
+        """
+        return [cls.get_plotfile_var_param()]
+
+    @classmethod
+    def get_plotfile_period_param(cls) -> str | None:
+        """
+        Return solver-specific time-based plot cadence parameter, if supported.
+        """
+        return None
+
+    @classmethod
+    def get_plotfile_step_interval_param(cls) -> str | None:
+        """
+        Return solver-specific step-based plot interval parameter, if supported.
+        """
+        return None
+
+    @classmethod
+    def supports_physical_time_cadence(cls) -> bool:
+        """
+        Return whether solver time-based cadence can be interpreted from seconds.
+        """
+        return True
+
+    @classmethod
+    def convert_plot_cadence_prompt_seconds_to_solver_time(cls, seconds: float) -> float | None:
+        """
+        Convert prompt seconds into solver-time cadence units.
+
+        Default behavior assumes solver time is seconds (identity transform).
+        """
+        return float(seconds)
+
     @classmethod
     def _resource_bytes_per_cell(cls, config: dict[str, Any]) -> int:
         return 200

database/configs/erf_config.py

@@ -29,6 +29,22 @@ def get_default_slice_axis(cls) -> str | None:
         """
         return "y"
 
+    @classmethod
+    def get_plotfile_var_param(cls) -> str:
+        return "erf.plot_vars_1"
+
+    @classmethod
+    def get_plotfile_period_param(cls) -> str | None:
+        return "erf.plot_per_1"
+
+    @classmethod
+    def get_plotfile_step_interval_param(cls) -> str | None:
+        return "erf.plot_int_1"
+
+    @classmethod
+    def get_plot_var_param_candidates(cls) -> list[str]:
+        return ["erf.plot_vars_1", "amr.plot_vars", "plot_vars"]
+
     # === Registry Metadata ===
     github_org = "erf-model"
     github_repo = "ERF"
@@ -38,6 +54,29 @@ def get_default_slice_axis(cls) -> str | None:
     default_inputs_path = "Exec/RegTests/Bubble/inputs"
     default_exec_repo_path = "Exec/RegTests/Bubble"
     default_exec_pattern = "ERF*ex"
+    build_system_preference = "cmake"
+    preferred_build_system = "cmake"
+    executable_search_path_templates = [
+        "{repo_root}/build/Exec",
+        "{repo_root}/Build/Exec",
+        "{repo_root}/install/bin",
+        "{central_build_dir}",
+    ]
+    cmake_executable_names = ["erf_exec"]
+    cmake_executable_ignores_accel_suffix = True
+    gnumake_executable_globs = ["ERF*ex"]
+    cmake_source_dir_template = "{repo_root}"
+    cmake_build_dir_template = "{repo_root}/build"
+    cmake_install_prefix_template = None
+    cmake_configure_args = [
+        "-DCMAKE_BUILD_TYPE=Release",
+        "-DERF_ENABLE_MPI=ON",
+    ]
+    cmake_build_args = []
+    cmake_install_args = []
+    gnumake_clean_targets = ["realclean"]
+    gnumake_build_args = ["USE_MPI=TRUE", "DEBUG=FALSE"]
+    gnumake_flags = ["USE_MPI=TRUE", "DEBUG=FALSE"]
 
     selection_keywords = [
         "abl",

database/configs/pelelmex_config.py

@@ -167,6 +167,22 @@ class PeleLMeXConfig(BaseAMReXConfig):
         "prompt": "What {section}.atol and {section}.rtol should I use for PeleLMeX with a QSSA mechanism?",
     }
 
+    @classmethod
+    def get_plotfile_var_param(cls) -> str:
+        return "peleLM.derive_plot_vars"
+
+    @classmethod
+    def get_plot_var_param_candidates(cls) -> list[str]:
+        return ["peleLM.derive_plot_vars", "amr.plot_vars", "plot_vars"]
+
+    @classmethod
+    def get_plotfile_period_param(cls) -> str | None:
+        return "amr.plot_per"
+
+    @classmethod
+    def get_plotfile_step_interval_param(cls) -> str | None:
+        return "amr.plot_int"
+
     prompt_templates: ClassVar[dict[str, Any]] = {
         "misc": {
             "schema_scan": """Identify requested concepts from the case description that do not map to known baseline or schema parameters.

database/configs/remora_config.py

@@ -29,6 +29,14 @@ def get_default_slice_axis(cls) -> str | None:
         """
         return "y"
 
+    @classmethod
+    def get_plotfile_period_param(cls) -> str | None:
+        return "remora.plot_int_time"
+
+    @classmethod
+    def get_plotfile_step_interval_param(cls) -> str | None:
+        return "remora.plot_int"
+
     # === Registry Metadata ===
     github_org = "AMReX-Codes"
     github_repo = "REMORA"

database/faiss/cborg/build_session_manifest.json

@@ -1,5 +1,32 @@
 {
+  "build_script": "build_all_indices.py",
   "entries": [
+    {
+      "build_script": "build_all_indices.py",
+      "dependencies_commit": null,
+      "embedding_dimension": null,
+      "embedding_model": "lbl/nomic-embed-text",
+      "embedding_provider": "cborg",
+      "generated_at": "2026-03-18T14:44:08.389712+00:00",
+      "level": "0",
+      "manifest_path": "level0/faiss_provenance.json",
+      "repo_commit": null,
+      "solver": null,
+      "version": "1"
+    },
+    {
+      "build_script": "build_all_indices.py",
+      "dependencies_commit": "5613ec3943a33d5f0b4f954e34c4e3ff5559a945",
+      "embedding_dimension": null,
+      "embedding_model": "lbl/nomic-embed-text",
+      "embedding_provider": "cborg",
+      "generated_at": "2026-03-18T14:45:12.017072+00:00",
+      "level": "1",
+      "manifest_path": "level1/erf_faiss_provenance.json",
+      "repo_commit": "5613ec3943a33d5f0b4f954e34c4e3ff5559a945",
+      "solver": "erf",
+      "version": "1"
+    },
     {
       "build_script": "build_all_indices.py",
       "dependencies_commit": "99914444329f6be784c6a153581c53bc60ae8937",
@@ -26,6 +53,19 @@
       "solver": "erf",
       "version": "1"
     },
+    {
+      "build_script": "build_all_indices.py",
+      "dependencies_commit": "5613ec3943a33d5f0b4f954e34c4e3ff5559a945",
+      "embedding_dimension": null,
+      "embedding_model": "lbl/nomic-embed-text",
+      "embedding_provider": "cborg",
+      "generated_at": "2026-03-18T14:58:05.501994+00:00",
+      "level": "2",
+      "manifest_path": "level2/erf_faiss_provenance.json",
+      "repo_commit": "5613ec3943a33d5f0b4f954e34c4e3ff5559a945",
+      "solver": "erf",
+      "version": "1"
+    },
     {
       "build_script": "build_all_indices.py",
       "dependencies_commit": "a6b4dff152c2cad2cf0edee58099eefffd2ba328",
@@ -66,5 +106,6 @@
       "version": "1"
     }
   ],
+  "generated_at": "2026-03-18T14:58:05.507710+00:00",
   "version": "1"
 }