fix(server): don't disable embeddings when macOS misreports 0 MB free

README.md

@@ -100,6 +100,21 @@ with no setup. For the CLI/MCP server it needs a local model directory
 - Distill one from any sentence-transformer (Apache-2.0 Jina-Code by default) in
   ~30 s on CPU: `python scripts/distill_static_model.py`.
 
+#### `CODEGRAPH_SKIP_MEMORY_CHECK` — force the embedding model past the RAM gate
+
+Before loading the ONNX model, the server checks available memory and, if under
+~1.5 GB, skips the model to avoid an OOM-kill (running graph-only instead).
+Set `CODEGRAPH_SKIP_MEMORY_CHECK=1` (also accepts `true`/`yes`) to bypass that
+check and always load the model.
+
+Use it if embeddings are disabled even though the machine has plenty of free
+RAM.
+A reading of `0 MB available` is treated as a detection failure and the model
+loads anyway (macOS parks reclaimable memory in inactive/speculative pages that
+some memory readers do not count as free), so this override is mainly for other
+cases where the reported figure is low but wrong.
+It works in both MCP and one-shot `--run-tool` modes.
+
 #### `--profile` — narrow the MCP tool surface
 
 The full 32-tool surface is convenient but inflates the agent's prompt-context cost. A profile exposes only the slice you need (also settable via the `CODEGRAPH_TOOL_PROFILE` env var):

crates/codegraph-server/src/ai_query/engine.rs

@@ -76,6 +76,15 @@ fn available_memory_mb() -> u64 {
     sys.available_memory() / (1024 * 1024)
 }
 
+/// Whether an available-memory reading counts as real pressure for the embed
+/// loop. A 0 MB reading is a detection failure, not genuine pressure — some
+/// macOS `sysinfo` versions report 0 available because reclaimable memory is
+/// not counted as free (issue #13) — so it must not ratchet the batch size
+/// down or force checkpoints.
+fn embed_memory_pressured(avail_mb: u64) -> bool {
+    avail_mb > 0 && avail_mb < EMBED_LOW_MEM_MB
+}
+
 /// Split an identifier into camelCase/snake_case words (deduped, lowercased),
 /// reusing the BM25 tokenizer: `getUserById` -> "get user by id".
 fn split_identifier_words(name: &str) -> String {
@@ -392,13 +401,13 @@ impl QueryEngine {
             pos = end;
             chunks_done += 1;
 
-            if chunks_done % 10 == 0 && pos < total {
+            if chunks_done.is_multiple_of(10) && pos < total {
                 tracing::info!("[QueryEngine] Embedded {}/{} symbols", pos, total);
             }
 
             // RAM backpressure: shed batch size under memory pressure.
-            let pressured = chunks_done % EMBED_MEM_CHECK_CHUNKS == 0
-                && available_memory_mb() < EMBED_LOW_MEM_MB;
+            let pressured = chunks_done.is_multiple_of(EMBED_MEM_CHECK_CHUNKS)
+                && embed_memory_pressured(available_memory_mb());
             if pressured && chunk_size > 4 {
                 chunk_size = (chunk_size / 2).max(4);
                 tracing::warn!(
@@ -546,8 +555,8 @@ impl QueryEngine {
             pos = end;
             chunks_done += 1;
 
-            let pressured = chunks_done % EMBED_MEM_CHECK_CHUNKS == 0
-                && available_memory_mb() < EMBED_LOW_MEM_MB;
+            let pressured = chunks_done.is_multiple_of(EMBED_MEM_CHECK_CHUNKS)
+                && embed_memory_pressured(available_memory_mb());
             if pressured && chunk_size > 4 {
                 chunk_size = (chunk_size / 2).max(4);
                 tracing::warn!(
@@ -2632,6 +2641,24 @@ mod tests {
         (engine, graph)
     }
 
+    #[test]
+    fn embed_memory_pressured_low_reading_is_pressure() {
+        assert!(embed_memory_pressured(1));
+        assert!(embed_memory_pressured(EMBED_LOW_MEM_MB - 1));
+    }
+
+    #[test]
+    fn embed_memory_pressured_zero_reading_is_detection_failure_not_pressure() {
+        assert!(!embed_memory_pressured(0));
+    }
+
+    #[test]
+    fn embed_memory_pressured_at_or_above_floor_is_not_pressure() {
+        assert!(!embed_memory_pressured(EMBED_LOW_MEM_MB));
+        assert!(!embed_memory_pressured(EMBED_LOW_MEM_MB + 1));
+        assert!(!embed_memory_pressured(64 * 1024));
+    }
+
     #[tokio::test]
     async fn test_engine_creation() {
         let (engine, _) = create_test_engine().await;
@@ -3964,7 +3991,10 @@ mod tests {
 
     #[test]
     fn split_identifier_words_handles_camel_and_snake() {
-        assert_eq!(split_identifier_words("authenticate_user"), "authenticate user");
+        assert_eq!(
+            split_identifier_words("authenticate_user"),
+            "authenticate user"
+        );
         assert_eq!(split_identifier_words("getUserById"), "get user by id");
         // The existing tokenizer keeps acronym+word runs joined (HTML|Parser is
         // NOT split) and drops 1-char tokens — known limitations worth revisiting
@@ -3986,11 +4016,13 @@ mod tests {
         // Enabled: split name words are front-loaded for the static embedder.
         let with_split =
             QueryEngine::build_embed_text(&node, 0, "getUserById", false, true, &graph);
-        assert!(with_split.starts_with("get user by id"), "got: {with_split}");
+        assert!(
+            with_split.starts_with("get user by id"),
+            "got: {with_split}"
+        );
 
         // Disabled (default): original transformer-path text is unchanged.
-        let without =
-            QueryEngine::build_embed_text(&node, 0, "getUserById", false, false, &graph);
+        let without = QueryEngine::build_embed_text(&node, 0, "getUserById", false, false, &graph);
         assert!(without.starts_with("getUserById"), "got: {without}");
         assert!(!without.contains("get user by id"));
     }

crates/codegraph-server/src/mcp/engine.rs

@@ -219,10 +219,24 @@ mod imp {
         let shared_engine = {
             let mut sys = sysinfo::System::new();
             sys.refresh_memory();
-            if sys.available_memory() < 1_500_000_000 {
-                tracing::warn!("Engine: <1.5 GB free — running graph-only (no shared model)");
+            let avail = sys.available_memory();
+            let gate = crate::memory::evaluate_memory_gate(
+                avail,
+                crate::memory::MODEL_MIN_FREE_BYTES,
+                crate::memory::memory_check_bypassed(),
+            );
+            if let crate::memory::MemoryGate::Skip(avail) = gate {
+                tracing::warn!(
+                    "Engine: only {} MB available — skipping shared embedding model to avoid OOM; running graph-only. Set CODEGRAPH_SKIP_MEMORY_CHECK=1 to override.",
+                    avail / 1_000_000
+                );
                 None
             } else {
+                if gate == crate::memory::MemoryGate::ProceedDetectionFailed {
+                    tracing::warn!(
+                        "Engine: available memory read as 0 MB — treating as a detection failure (common on macOS, where reclaimable memory is not counted as free) and proceeding with the shared model load. Set CODEGRAPH_SKIP_MEMORY_CHECK=1 to always bypass this check."
+                    );
+                }
                 match VectorEngine::from_backend(model_cache_dir(), &cfg.embedding_model) {
                     Ok(e) => {
                         tracing::info!("Engine: shared embedding model loaded");

crates/codegraph-server/src/memory.rs

@@ -169,6 +169,62 @@ fn project_data_dir(workspace_path: &Path) -> Result<PathBuf, MemoryError> {
         .join(slug))
 }
 
+/// Minimum available memory to load the ONNX embedding model + runtime
+/// without risking an OOM-kill (a native crash Rust can't catch).
+pub(crate) const MODEL_MIN_FREE_BYTES: u64 = 1_500_000_000; // ~1.5 GB
+
+/// Decision of the pre-model-load RAM gate. Separated from the live sysinfo
+/// reading so the policy is unit-testable.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub(crate) enum MemoryGate {
+    /// Enough available memory (or the check was bypassed) — load the model.
+    Load,
+    /// Genuinely constrained — skip the model and run graph-only. Carries the
+    /// detected byte count for the log/error message.
+    Skip(u64),
+    /// The available-memory reading was 0, which is a detection failure rather
+    /// than a real state: a running process always holds memory, and on macOS
+    /// reclaimable memory is parked in inactive/speculative/purgeable pages
+    /// that some `sysinfo` versions report as 0 available (issue #13). Proceed
+    /// with the load instead of hard-disabling on a number we don't trust.
+    ProceedDetectionFailed,
+}
+
+/// Decide whether to load the embedding model from the available-memory
+/// reading, the minimum threshold, and whether the user forced a bypass.
+///
+/// Pure: no I/O, no env reads — the caller supplies the inputs. This is the
+/// gate policy; keeping it separate lets tests cover the 0-MB detection-failure
+/// path that can't be reproduced by driving `sysinfo` live.
+pub(crate) fn evaluate_memory_gate(
+    available_bytes: u64,
+    min_free_bytes: u64,
+    bypass: bool,
+) -> MemoryGate {
+    if bypass {
+        return MemoryGate::Load;
+    }
+    if available_bytes == 0 {
+        return MemoryGate::ProceedDetectionFailed;
+    }
+    if available_bytes < min_free_bytes {
+        return MemoryGate::Skip(available_bytes);
+    }
+    MemoryGate::Load
+}
+
+/// Whether the user forced the RAM gate off via `CODEGRAPH_SKIP_MEMORY_CHECK`
+/// (`1`/`true`/`yes`, case-insensitive). The escape hatch works in both MCP and
+/// one-shot `--run-tool` modes since it is read at model-load time.
+pub(crate) fn memory_check_bypassed() -> bool {
+    std::env::var("CODEGRAPH_SKIP_MEMORY_CHECK")
+        .map(|v| {
+            let v = v.trim();
+            v == "1" || v.eq_ignore_ascii_case("true") || v.eq_ignore_ascii_case("yes")
+        })
+        .unwrap_or(false)
+}
+
 /// Memory manager for the LSP server
 ///
 /// Opens the database on-demand for each operation and closes it immediately after.
@@ -192,7 +248,10 @@ pub struct MemoryManager {
 impl MemoryManager {
     /// Create a new MemoryManager
     pub fn new(extension_path: Option<PathBuf>) -> Self {
-        Self::with_model(extension_path, codegraph_memory::EmbeddingBackend::default())
+        Self::with_model(
+            extension_path,
+            codegraph_memory::EmbeddingBackend::default(),
+        )
     }
 
     /// Create a new MemoryManager with a specific embedding backend
@@ -284,21 +343,30 @@ impl MemoryManager {
             let mut sys = sysinfo::System::new();
             sys.refresh_memory();
             let avail = sys.available_memory();
-            const MIN_FREE_BYTES: u64 = 1_500_000_000; // ~1.5 GB for model + ort runtime
             tracing::info!(
                 "[MemoryManager::initialize] available memory: {} MB",
                 avail / 1_000_000
             );
-            if avail < MIN_FREE_BYTES {
-                crate::crash_phase::mark("onnx_skipped_lowmem");
-                tracing::warn!(
-                    "[MemoryManager::initialize] only {} MB free — skipping embedding model to avoid OOM; semantic search disabled (graph-only)",
-                    avail / 1_000_000
-                );
-                return Err(MemoryError::Other(format!(
-                    "insufficient memory ({} MB free) to load embedding model; running graph-only",
-                    avail / 1_000_000
-                )));
+            match evaluate_memory_gate(avail, MODEL_MIN_FREE_BYTES, memory_check_bypassed()) {
+                MemoryGate::Skip(avail) => {
+                    crate::crash_phase::mark("onnx_skipped_lowmem");
+                    tracing::warn!(
+                        "[MemoryManager::initialize] only {} MB available — skipping embedding model to avoid OOM; semantic search disabled (graph-only). Set CODEGRAPH_SKIP_MEMORY_CHECK=1 to override.",
+                        avail / 1_000_000
+                    );
+                    return Err(MemoryError::Other(format!(
+                        "insufficient memory ({} MB available) to load embedding model; running graph-only (set CODEGRAPH_SKIP_MEMORY_CHECK=1 to override)",
+                        avail / 1_000_000
+                    )));
+                }
+                MemoryGate::ProceedDetectionFailed => {
+                    // 0 MB is a detection failure (see MemoryGate) — don't
+                    // disable embeddings on a Mac that actually has RAM.
+                    tracing::warn!(
+                        "[MemoryManager::initialize] available memory read as 0 MB — treating as a detection failure (common on macOS, where reclaimable memory is not counted as free) and proceeding with the embedding model load. Set CODEGRAPH_SKIP_MEMORY_CHECK=1 to always bypass this check."
+                    );
+                }
+                MemoryGate::Load => {}
             }
         }
 
@@ -612,6 +680,51 @@ pub use codegraph_memory::{
 mod tests {
     use super::*;
 
+    const MIN: u64 = MODEL_MIN_FREE_BYTES;
+
+    #[test]
+    fn gate_loads_when_ample_memory() {
+        assert_eq!(
+            evaluate_memory_gate(8_000_000_000, MIN, false),
+            MemoryGate::Load
+        );
+    }
+
+    #[test]
+    fn gate_loads_exactly_at_threshold() {
+        // `< min` is the skip condition, so exactly `min` must load.
+        assert_eq!(evaluate_memory_gate(MIN, MIN, false), MemoryGate::Load);
+    }
+
+    #[test]
+    fn gate_skips_when_genuinely_low() {
+        assert_eq!(
+            evaluate_memory_gate(500_000_000, MIN, false),
+            MemoryGate::Skip(500_000_000)
+        );
+    }
+
+    #[test]
+    fn gate_proceeds_on_zero_reading_as_detection_failure() {
+        // The issue-13 case: sysinfo reports 0 available on a healthy Mac.
+        // 0 is never a real state, so proceed rather than disable embeddings.
+        assert_eq!(
+            evaluate_memory_gate(0, MIN, false),
+            MemoryGate::ProceedDetectionFailed
+        );
+    }
+
+    #[test]
+    fn gate_bypass_forces_load_regardless_of_reading() {
+        // CODEGRAPH_SKIP_MEMORY_CHECK=1 overrides even a genuine low reading.
+        assert_eq!(evaluate_memory_gate(0, MIN, true), MemoryGate::Load);
+        assert_eq!(evaluate_memory_gate(1, MIN, true), MemoryGate::Load);
+        assert_eq!(
+            evaluate_memory_gate(500_000_000, MIN, true),
+            MemoryGate::Load
+        );
+    }
+
     #[test]
     fn generation_zero_maps_to_historical_path() {
         let dir = Path::new("/home/u/.codegraph");

mcp-package/README.md

@@ -54,6 +54,11 @@ Pass flags after `--`:
 | `--graph-only` | off | Skip embeddings — graph + structural tools only. No ONNX model load, 10-50× faster indexing. For CI / one-shot graph queries. |
 | `--run-tool <name>` | — | One-shot: index, run a single tool, print result, exit. No MCP handshake. Pair with `--tool-args '<json>'`. |
 
+Before loading the ONNX embedding model, the server checks available memory and runs graph-only if under ~1.5 GB.
+If embeddings are disabled even though the machine has plenty of free RAM, set `CODEGRAPH_SKIP_MEMORY_CHECK=1` (also accepts `true`/`yes`) to bypass the check.
+A reading of `0 MB available` is treated as a detection failure and the model loads anyway (common on macOS).
+Works in both MCP and one-shot `--run-tool` modes.
+
 ### Agent rules (recommended)
 
 Pre-configured rule files that teach your AI agent to use CodeGraph tools before falling back to grep / multi-file reads: