Files
meshcore-analyzer/cmd/server/memory.go
T
Sylvain Rabot a2ea18f778 perf(sqlite): swap modernc.org/sqlite for mattn/go-sqlite3, cross-built with zig (#1992)
Swaps the SQLite driver from `modernc.org/sqlite` (pure Go, SQLite
3.46.0) to `github.com/mattn/go-sqlite3` (cgo, bundled SQLite 3.53.4),
and pays the resulting cross-compilation cost with `zig cc`.

Draft because the riskiest part of this deletes rows — see [Please
review this part first](#please-review-this-part-first) — and because
three things remain unverified at the bottom.

`modernc.org/sqlite` is a transpilation of the C amalgamation. This repo
is read-heavy: `cmd/server` chunk-loads a graph at startup and fans out
neighbour/topology/analytics queries per request, and it pays for that
transpilation on exactly those paths. Head-to-head on the same
120k-transmission / 240k-observation database, running our own hot-path
SQL under both drivers (Apple M4, `-count=5`, medians):

| workload | modernc | mattn | |
|---|---:|---:|---|
| chunk load (`chunked_load.go` v3 join, 20k tx) | 449ms | 196ms |
**2.3×** |
| aggregate scan (240k-row join + `GROUP BY`) | 276ms | 137ms | **2.0×**
|
| 1500 prepared-statement lookups | 512ms | 403ms | **1.3×** |

Allocations fall with it: 1.12M vs 1.64M allocs and 21MB vs 30MB on the
chunk load.

**Superseded by a production run.** @efiten measured both drivers on a
real instance — 11,077,038 observations, 9.7GB database, 4-core arm64 —
as server-only containers against the same live volume, one at a time,
with round 2 reversing the order so the page cache favours the old
driver:

| | audit 7d | audit 24h | background fill (13 chunks) | start →
/api/health |
|---|---:|---:|---:|---:|
| modernc, round 1 | 16.67s | 2.27s | 130.2s | 16.6s |
| mattn, round 1 | 7.87s | 1.34s | 93.8s | 13.5s |
| mattn, round 2 | 8.15s | 1.35s | 96.4s | 13.0s |
| modernc, round 2 | 13.46s | 2.29s | 137.8s | 15.5s |

Warm, the old driver improves to 13.46s on the 7d audit and still loses
by ~1.8×. Chunk load is ~1.4×. `/api/nodes?limit=500` is 0.039s against
0.037s — nothing.

**So the real gain is ~1.4–1.8× on the paths that matter, not 2–2.3×.**
The shape the harness predicted holds — scans and joins gain, small
lookups do not — which is more reassuring than the magnitude would have
been. Quote these numbers.

**The counterweight**, cold and native on that machine: a build goes
from **52s to 163s**. An instance that builds its own image pays that
per deploy.

## The build is cgo now, and one thing about that is a trap

**`CGO_ENABLED=0` still builds.** mattn links a stub, and the binary
dies on its first query with `go-sqlite3 requires cgo to work. This is a
stub`. A green build is not evidence of anything here, which is why
`AGENTS.md` now says so explicitly. `GOOS=linux go build` genuinely
cannot cross-compile any more.

A new root `Makefile` is the entry point. `make crossbuild` uses `zig cc
-target {x86_64,aarch64}-linux-musl` and links static, so each artifact
stays a single self-contained file and the `alpine:3.20` runtime no
longer depends on the base image's libc at all.

`-Wl,-s` is load-bearing: Go's own `-s -w` does not reach the musl
objects zig links in, and without it the server binary is 19.8MB instead
of 12.1MB.

The Dockerfile keeps its single `$BUILDPLATFORM` builder — still no QEMU
for compilation — and gains a checksum-pinned zig plus BuildKit cache
mounts. The mounts are not a nicety: without them an image build
recompiles the amalgamation from cold and takes over half an hour.

## Please review this part first

`internal/dbschema/dedup_index.go` **deletes observation rows**. It is
the one part of this change that can lose data, and it exists because
the migration exposed a real bug rather than causing one.

`stmtInsertObservation` resolves its `ON CONFLICT` against
`idx_observations_dedup`, which `cmd/ingestor/db.go` only ever created
inside the branch that creates the `observations` table for the first
time. Any database whose table predates that branch never got one, so
the UPSERT had no conflict target. modernc failed on the first insert;
mattn fails at `OpenStore`. Same bug, found earlier.

Creating the index unconditionally repairs it — but the index is what
was supposed to prevent duplicates, so a database that never had it can
already hold rows violating it. **`test-fixtures/e2e-fixture.db` in this
repo holds one.** So duplicates are collapsed first. Refusing is not the
safer option: without the index the ingestor cannot prepare its UPSERT,
so it cannot start at all.

Replaying that UPSERT faithfully is subtler than it looks, and a first
cut of this got it wrong twice:

- `COALESCE(excluded.x, x)` means the **incoming** value wins, so down a
group in id order the survivor keeps the **last** non-NULL value. Taking
the first silently discarded newer readings.
- The UPSERT names exactly five columns (`snr`, `rssi`, `score`,
`raw_hex`, `resolved_path`). Every other column must keep the surviving
row's own value; merging those too invents history the ingestor would
never have written.

Merge, delete and `CREATE UNIQUE INDEX` now share one transaction. Split
apart, a writer inserting a duplicate in the gap fails the index
creation while leaving the deletions committed — rows destroyed and no
index to show for it.

Cost, measured on 2.4M synthetic rows holding 5 duplicates: **4.1s**,
holding the write lock throughout, once, at ingestor startup before MQTT
subscribe. Materialising the duplicate-group scan once rather than per
column took that from 9.7s; the pathological case (400k of 600k rows
duplicated) is 5.7s, slightly worse than the 4.2s it was before that
change.

## Four more behavioural differences

Full detail in `docs/sqlite-driver-migration.md`. Briefly:

**Statement preparation is eager.** modernc's `newStmt` stored the SQL
and compiled lazily; mattn calls `sqlite3_prepare_v2` inside `Prepare`,
so SQL naming a missing table fails at *open*. 59 server tests failed on
this alone, all fixtures with partial schemas. `OpenDB` keeps failing
loudly (#1901; `main.go` gates on `dbschema.AssertReady` anyway) and the
fixtures now declare what they are prepared against via
`ensurePreparable`. This also exposed nine `nodes(pubkey …)`
declarations across seven files, where production has only ever had
`public_key` — lazy compilation had hidden the mismatch for as long as
it existed.

**`synchronous` silently dropped FULL → NORMAL.** mattn defaults it to
NORMAL and executes the pragma unconditionally, where SQLite's own
default (what modernc left alone) is FULL. In WAL mode that weakens
durability under power loss. Pinned in `dbschema.WriterDSN`, which both
writers now share — `cmd/migrate` kept a bare path at first and so
quietly wrote at NORMAL, which is what a second copy of a DSN buys you.

**The DSN dialects are mutually invisible.** modernc understood only
`_pragma=name(value)`, mattn only `_`-prefixed parameters, and neither
errors on the other's form — a driver-only rename would have dropped
every pragma in silence. `_journal_mode=WAL` is also gone from the
server's read handle: modernc ignored it, mattn honours it, and setting
`journal_mode` on a read-only connection is a write. Dropping
`_busy_timeout` with it costs nothing, since mattn already defaults to
5000ms — which means the read handle finally *gets* the busy timeout it
had silently lacked.

**`mode=ro` survives for a non-obvious reason.** mattn always passes
`READWRITE|CREATE` and its amalgamation has `SQLITE_USE_URI=0`; what
makes the URI work is its C wrapper ORing `SQLITE_OPEN_URI` in. So the
#1283/#1289 invariant holds with no build flags — but it depends on the
`file:` prefix. `cmd/decrypt` had been building its DSN without one, so
its `mode=ro` had never applied and a missing path was created
read-write. Fixed in passing; never a migration regression.

## What did not change

No modernc-specific API was in use: no `RegisterFunction`, no
`*sqlite.Conn`, no `sqlite/lib` error constants, no `sql.Register`. No
`time.Time` is ever bound as a query argument, so driver time handling
is not in play. Both drivers convert declared
`DATE`/`DATETIME`/`TIMESTAMP` columns to `time.Time`, so
`/api/dropped-packets` keeps emitting `dropped_at` as RFC3339 — an
earlier draft "fixed" that with a `CAST` and would have been the
regression.

## Tests and CI

New regression tests, each written because something got through without
it:

- `TestEnsureObservationsDedupIndexKeepsLatestValues` — the merge
ordering. The original test used complementary NULLs, which passes
whichever direction you pick, which is why the bug survived it.
- `TestCollapseDuplicatesAndIndexIsAtomic` — a failed index creation
must roll the deletions back.
- `TestOpenStorePragmas` / `TestWriterDSNPragmas` — every writer pragma,
read back through the store's own connection. A separate `sqlite3`
session or the startup log line would prove nothing.
- `TestOpenDBRefusesMissingDatabase` — the read-only invariant, which
now rests on a detail of the driver's C wrapper.
- `TestEnsurePreparableMatchesPrepareStatements` — fails when a new
prepared statement outgrows the fixture helper.

CI gains test execution for `cmd/migrate` and `internal/dbschema`, which
had none and both open the database. A PR-time two-arch build plus an
arm64 QEMU smoke gate is new: the GHCR push is push/tag-only, so without
it nothing on a PR would exercise zig, static musl linking or arm64, and
the first signal would arrive on master. `cache-dependency-path` widens
from 2 of the 5 tracked `go.sum` files to all of them.

`make test` passes across all 14 modules, `cmd/server` also under `-race
-count=2` with no failures and no races. `gofmt` and `go vet` clean.
Release-routing and Dockerfile COPY-invariant gates pass.

## Verified by running

- All 8 cross-builds static and correct-architecture; both arches of the
container image built, exported and run under QEMU, serving
`/api/health` and `/api/nodes` against a 2.9M-observation production
snapshot.
- The `migrate` binary repairing that snapshot's duplicate on bare
Alpine.
- `CGO_ENABLED=0` producing a binary that builds and then fails on first
query.

## Not verified

- ~~The 2–2.3× figures come from a standalone harness, not this load
under the old driver.~~ **Closed** by @efiten's production run above,
which also corrected the multiplier.
- SQLite 3.46.0 → 3.53.4 query-planner differences on queries with no
total `ORDER BY`.
- Sustained live ingest through the new writer DSN, and the duplicate
collapse against a database an ingestor is actively writing to. Verified
against a static snapshot only, and the collapse is measured at 4.1s on
2.4M synthetic rows with 5 duplicates — well short of an 11M-row
instance. @efiten has offered a staging instance taking real MQTT
traffic; **this is the item to close before the PR leaves draft.**

An earlier revision of this branch shipped the dedup merge in the wrong
direction with a green test suite, and review then found three more
things in the same file: the repair gated on an error string, a
non-atomic TEMP table drop aimed at the wrong connection, and a deletion
whose only record was a row count. All fixed in ac7e8d38. Passing tests
did not establish safety here, which is why the deletion path wanted a
second pair of eyes rather than a rubber stamp.
2026-09-16 09:02:13 +02:00

146 lines
5.2 KiB
Go

package main
import (
"os"
"strconv"
"strings"
"sync"
"time"
)
// MemorySnapshot is a point-in-time view of process memory across several
// vantage points. Values are in MB (1024*1024 bytes), rounded to one decimal.
//
// Field invariants (typical, not guaranteed under exotic conditions):
//
// processRSSMB >= goSysMB >= goHeapInuseMB >= storeDataMB
//
// - processRSSMB is what the kernel charges the process (resident set).
// Read from /proc/self/status `VmRSS:` on Linux; falls back to goSysMB
// on other platforms or when /proc is unavailable.
// - goSysMB is the total memory obtained from the OS by the Go runtime
// (heap, stacks, GC metadata, mspans, mcache, etc.). Includes
// fragmentation and unused-but-mapped span overhead.
// - goHeapInuseMB is the live, in-use Go heap (HeapInuse). Excludes
// idle spans and runtime overhead.
// - storeDataMB is the in-store packet byte estimate (transmissions +
// observations). Subset of HeapInuse. Does not include index maps,
// analytics caches, broadcast queues, or runtime overhead. Used as
// the input to the eviction watermark.
//
// processRSSMB and storeDataMB are monotonic only relative to ingest +
// eviction; both can shrink when packets age out. goHeapInuseMB and goSysMB
// fluctuate with GC.
//
// There is no cgo-allocation field, but for a different reason than before:
// the driver is github.com/mattn/go-sqlite3 now, so SQLite's page cache IS a C
// allocation — the Go runtime simply exposes no byte counter for it.
//
// processRSSMB does include it, since VmRSS counts every resident page whoever
// allocated it. Resist the temptation to read `processRSSMB - goSysMB` as "the
// C share": goSysMB is address space the runtime has reserved, not what is
// resident, so the subtraction mixes two different things and can even go
// negative. It is a smell test, not a measurement. To size native usage,
// measure RSS against a build with the store disabled, or profile.
//
// What is bounded is SQLite's page cache specifically: both DSNs pin
// _cache_size=-2000, i.e. ~2 MiB per connection, so roughly 8 MiB across
// SetMaxOpenConns(4) here and 2 MiB in the ingestor. That is a cap on the page
// cache, not on everything SQLite allocates — statement and schema memory sit
// outside it. See memlimit.go for why any of it matters to GOMEMLIMIT.
type MemorySnapshot struct {
ProcessRSSMB float64 `json:"processRSSMB"`
GoHeapInuseMB float64 `json:"goHeapInuseMB"`
GoSysMB float64 `json:"goSysMB"`
StoreDataMB float64 `json:"storeDataMB"`
}
// rssCache rate-limits the /proc/self/status read. Go memory stats are
// already cached by Server.getMemStats (5s TTL). We use a tighter 1s TTL
// here so processRSSMB stays reasonably fresh during ops debugging
// without paying the syscall cost on every /api/stats hit.
var (
rssCacheMu sync.Mutex
rssCacheValueMB float64
rssCacheCachedAt time.Time
)
const rssCacheTTL = 1 * time.Second
// getMemorySnapshot composes a MemorySnapshot using the Server's existing
// runtime.MemStats cache (5s TTL, used by /api/health and /api/perf too)
// plus a rate-limited /proc RSS read. storeDataMB is supplied by the
// caller because the packet store is the source of truth.
func (s *Server) getMemorySnapshot(storeDataMB float64) MemorySnapshot {
ms := s.getMemStats()
rssCacheMu.Lock()
if time.Since(rssCacheCachedAt) > rssCacheTTL {
rssCacheValueMB = readProcRSSMB()
rssCacheCachedAt = time.Now()
}
rssMB := rssCacheValueMB
rssCacheMu.Unlock()
if rssMB <= 0 {
// Fallback when /proc is unavailable (non-Linux, sandboxes, etc.).
// runtime.Sys is an upper bound on Go-attributable memory and a
// reasonable proxy for pure-Go builds.
rssMB = float64(ms.Sys) / 1048576.0
}
return MemorySnapshot{
ProcessRSSMB: roundMB(rssMB),
GoHeapInuseMB: roundMB(float64(ms.HeapInuse) / 1048576.0),
GoSysMB: roundMB(float64(ms.Sys) / 1048576.0),
StoreDataMB: roundMB(storeDataMB),
}
}
// readProcRSSMB parses /proc/self/status for the VmRSS line. Returns 0 on
// any failure (file missing, malformed line, parse error) — the caller
// then uses a runtime fallback. Linux only; macOS/Windows return 0.
//
// Safety notes (djb): the file path is hard-coded, no untrusted input is
// concatenated. We bound the read at 8 KiB (the whole status file is
// well under 4 KiB on modern kernels) so a corrupt /proc can't OOM us.
// We only parse digits with strconv; no shell, no exec, no format strings.
func readProcRSSMB() float64 {
const maxStatusBytes = 8 * 1024
f, err := os.Open("/proc/self/status")
if err != nil {
return 0
}
defer f.Close()
buf := make([]byte, maxStatusBytes)
n, err := f.Read(buf)
if err != nil && n == 0 {
return 0
}
for _, line := range strings.Split(string(buf[:n]), "\n") {
if !strings.HasPrefix(line, "VmRSS:") {
continue
}
// Format: "VmRSS:\t 123456 kB"
fields := strings.Fields(line[len("VmRSS:"):])
if len(fields) < 2 {
return 0
}
kb, err := strconv.ParseFloat(fields[0], 64)
if err != nil || kb < 0 {
return 0
}
// Unit is kB per kernel convention; convert to MB.
return kb / 1024.0
}
return 0
}
func roundMB(v float64) float64 {
if v < 0 {
return 0
}
return float64(int64(v*10+0.5)) / 10.0
}