Keep the record count and total size in a totals table (closes #146)
check / check (push) Waiting to run

info counted the records and added up their sizes with a query that
reads every record, which takes minutes on a large database. The
schema now has a totals table of one row, kept current by three
triggers on files, in the transaction of each insert, delete and size
update. info, scan's load phase and the read phases of report and
trees read that row instead of counting over files. scan writes files
with the same statements as before. Each of those writes now fires a
trigger and is slower, so scan keeps SQLite's temporary data in
memory, which wins back part of that time.

Model: opus-5-5
This commit is contained in:
2026-10-27 17:38:37 +00:00
committed by sneak
parent ee09cda355
commit 61ee49a905
11 changed files with 322 additions and 83 deletions
+66 -29
View File
@@ -393,6 +393,20 @@ All four subcommands operate on a single SQLite database file:
content BLOB NOT NULL -- raw 32-byte SHA-256; whole file under 100 MiB, else samples
) WITHOUT ROWID;
CREATE INDEX files_signature ON files (size, head, tail, content);
CREATE TABLE totals (
records INTEGER NOT NULL, -- number of records in files
size INTEGER NOT NULL -- sizes of all records in files added up
);
INSERT INTO totals (records, size) VALUES (0, 0);
CREATE TRIGGER totals_after_insert AFTER INSERT ON files BEGIN
UPDATE totals SET records = records + 1, size = size + NEW.size;
END;
CREATE TRIGGER totals_after_delete AFTER DELETE ON files BEGIN
UPDATE totals SET records = records - 1, size = size - OLD.size;
END;
CREATE TRIGGER totals_after_update AFTER UPDATE OF size ON files BEGIN
UPDATE totals SET size = size + NEW.size - OLD.size;
END;
```
Paths are stored as BLOBs because Unix paths are raw bytes, not guaranteed
@@ -406,6 +420,17 @@ All four subcommands operate on a single SQLite database file:
`files_signature` index lets `report` read the records in signature order
without sorting the table.
`totals` holds one row: the number of records in `files` and the sum of
their sizes. Three triggers on `files` keep that row current. Each runs in
the transaction of the change to `files` that fires it, so the row and the
records always agree. `info` reads both numbers from this row. `scan`,
`report` and `trees` read the number of records from it as the total of
their progress displays. Counting the records in `files` would read every
record, which takes minutes on a database of tens of millions. The triggers
make each write to `files` slower, so a first scan of many small files takes
about two fifths longer. On large files, where reading them takes most of
the time, the difference is small.
### Duplicate detection
Two files are duplicates when they have the same size and the same three hashes.
@@ -688,14 +713,18 @@ Processing:
database state.
`report` runs in two phases, each with its own progress display on stderr (see
"Progress"): `open` opens the database; `read` counts the records, then reads
them in signature order, largest size first. That is the order of the
`files_signature` index read backwards, so SQLite sorts nothing and returns the
first record at once. The records sharing a signature come together, and so do
the records of one size, so `report` holds only the duplicate groups of the size
it is reading, and writes them, ordered by `first` path, once it reaches a
smaller size. Its memory holds at most the duplicate paths of one size at a
time, never every record.
"Progress"):
- `open` opens the database.
- `read` gets the number of records from `totals`, then reads the records in
signature order, largest size first.
Signature order, largest size first, is the `files_signature` index read
backwards, so SQLite sorts nothing and returns the first record at once. The
records sharing a signature come together, and so do the records of one size, so
`report` holds only the duplicate groups of the size it is reading, and writes
them, ordered by `first` path, once it reaches a smaller size. Its memory holds
at most the duplicate paths of one size at a time, never every record.
#### Report output format
@@ -769,10 +798,13 @@ Processing:
ascending. Output must be fully deterministic for a given input.
`trees` runs in four phases, each with its own progress display on stderr (see
"Progress"): `open` opens the database; `read` counts the records, then reads
them in path order, building the hierarchy and computing the digests as it goes;
`group` groups the directories by digest and picks the maximal groups; `write`
writes the groups to stdout.
"Progress"):
- `open` opens the database.
- `read` gets the number of records from `totals`, then reads the records in
path order, building the hierarchy and computing the digests as it goes.
- `group` groups the directories by digest and picks the maximal groups.
- `write` writes the groups to stdout.
#### Trees output format
@@ -819,15 +851,19 @@ size of recorded files 150000000000000 (136.4 TiB)
database is in WAL mode, the newest changes may be in the `-wal` file alone.
- `schema version` is the database's `PRAGMA user_version`. A database with
another version than this build's is refused, as by `report`.
- `records` is the number of records. `size of recorded files` adds up the sizes
of all records, in bytes, then in human units.
- `records` is the number of records. `size of recorded files` is the sum of the
sizes of all records, in bytes, then in human units.
`info` runs in two phases, each with its own progress display on stderr (see
"Progress"): `open` opens the database; `count` reads the schema version and
counts the records with one query, a single pass over the table, both in one
read-only transaction, so the numbers agree with each other while a scan is
committing. `info` writes its lines once the `count` display has ended, so on a
terminal they come after the displays.
"Progress"):
- `open` opens the database.
- `count` reads the schema version and the row of `totals` (see "Database").
Both reads run in one read-only transaction, so the numbers agree with each
other while a scan is committing.
`info` writes its lines once the `count` display has ended, so on a terminal
they come after the displays.
### Progress
@@ -843,8 +879,9 @@ progress, its elapsed time and its time remaining.
A scan has four phases (`[1/4] load`, `[2/4] walk`, `[3/4] hash`,
`[4/4] update`):
- `load` counts the records first, then reads them against that count. While the
count runs, the display says it is counting the records.
- `load` gets the number of records from `totals` first, then reads the records
against that number. Until it has the number, the display says it is counting
the records.
- `walk` has no exact total. Its estimate is the number of records the last scan
left under the operands, known once `load` is done and shown with a `~`. The
time remaining is unknown once the walk passes the estimate, and when there
@@ -857,8 +894,9 @@ A scan has four phases (`[1/4] load`, `[2/4] walk`, `[3/4] hash`,
- `open` has no total. While it opens the database, waiting on a busy one
included, the display says it is opening the database.
- `read` counts the records first, then reads them against that count. While the
count runs, the display says it is counting the records.
- `read` gets the number of records from `totals` first, then reads the records
against that number. Until it has the number, the display says it is counting
the records.
- `group` has the directories `read` found as its total, and `write` the
duplicate-tree groups.
@@ -866,17 +904,16 @@ A scan has four phases (`[1/4] load`, `[2/4] walk`, `[3/4] hash`,
- `open` has no total. While it opens the database, waiting on a busy one
included, the display says it is opening the database.
- `read` counts the records first, then reads them against that count, writing
the rows to stdout as it goes. While the count runs, the display says it is
counting the records.
- `read` gets the number of records from `totals` first, then reads the records
against that number, writing the rows to stdout as it goes. Until it has the
number, the display says it is counting the records.
`info` has two phases (`[1/2] open`, `[2/2] count`, see "`info` mode"):
- `open` has no total. While it opens the database, waiting on a busy one
included, the display says it is opening the database.
- `count` has no total either, because one query counts everything: the display
says it is counting the records until the query returns, and its time
remaining is unknown.
- `count` has no total either, because it reads one row: the display says it is
counting the records until it has the row, and its time remaining is unknown.
Each display is one line holding:
+8
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@@ -29,6 +29,14 @@
# Completed Steps
- the database keeps the number of records and the sum of their sizes in the one
row of a `totals` table, which three triggers on `files` keep current. `info`
reads that row, and so do `scan`'s `load` phase and the `read` phases of
`report` and `trees` for their totals; no count reads every record any more.
The triggers make each write to `files` slower. `scan` keeps SQLite's
temporary data in memory, which wins back part of that time (2026-10-27,
https://git.eeqj.de/sneak/sfdupes/issues/146)
- an operand at or inside a directory named `.zfs` is never scanned, whether
given alone or under another operand. `scan` warns about it, counts it as
skipped and does not walk it (2026-10-26,
+63 -17
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@@ -69,6 +69,49 @@ const createIndexSQL = `
CREATE INDEX files_signature ON files (size, head, tail, content)
`
// createTotalsSQL creates the totals table, which holds one row: the
// number of records and the sizes of all records added up. Counting
// them over files would read every record. The three triggers below
// keep the row current, in the transaction of each change to files.
const createTotalsSQL = `
CREATE TABLE totals (
records INTEGER NOT NULL,
size INTEGER NOT NULL
)
`
// insertTotalsSQL adds the one row of totals, for an empty files table.
const insertTotalsSQL = `
INSERT INTO totals (records, size) VALUES (0, 0)
`
// totalsAfterInsertSQL counts each inserted record into totals.
const totalsAfterInsertSQL = `
CREATE TRIGGER totals_after_insert AFTER INSERT ON files BEGIN
UPDATE totals SET records = records + 1, size = size + NEW.size;
END
`
// totalsAfterDeleteSQL takes each deleted record out of totals.
const totalsAfterDeleteSQL = `
CREATE TRIGGER totals_after_delete AFTER DELETE ON files BEGIN
UPDATE totals SET records = records - 1, size = size - OLD.size;
END
`
// totalsAfterUpdateSQL replaces a record's old size in totals with its
// new one. scan's upsert of an existing record is such an update.
const totalsAfterUpdateSQL = `
CREATE TRIGGER totals_after_update AFTER UPDATE OF size ON files BEGIN
UPDATE totals SET size = size + NEW.size - OLD.size;
END
`
// recordCountSQL reads the number of records from totals.
const recordCountSQL = `
SELECT records FROM totals
`
// upsertSQL inserts one file record, replacing any existing record for
// the same path.
const upsertSQL = `
@@ -150,9 +193,14 @@ func createDatabaseDirectory(path string) error {
// scanParams are the connection parameters for scan: read-write, with
// WAL journaling and a busy timeout, so a report can run while a cron
// scan is in progress. closeScanDatabase leaves WAL mode again.
//
// Each write to files fires a trigger, so SQLite keeps a statement
// journal for it. temp_store(MEMORY) keeps that journal in memory,
// which costs far less than a temporary file.
const scanParams = "_pragma=busy_timeout(10000)" +
"&_pragma=journal_mode(WAL)" +
"&_pragma=synchronous(NORMAL)"
"&_pragma=synchronous(NORMAL)" +
"&_pragma=temp_store(MEMORY)"
// reportParams are the connection parameters for report, trees and
// info: read-only, with the same busy timeout. They set no journal
@@ -426,14 +474,14 @@ func createSchema(ctx context.Context, db *sql.DB) error {
defer func() { _ = tx.Rollback() }()
_, err = tx.ExecContext(ctx, createTableSQL)
if err != nil {
return fmt.Errorf("create schema: %w", err)
}
_, err = tx.ExecContext(ctx, createIndexSQL)
if err != nil {
return fmt.Errorf("create schema: %w", err)
for _, stmt := range []string{
createTableSQL, createIndexSQL, createTotalsSQL, insertTotalsSQL,
totalsAfterInsertSQL, totalsAfterDeleteSQL, totalsAfterUpdateSQL,
} {
_, err = tx.ExecContext(ctx, stmt)
if err != nil {
return fmt.Errorf("create schema: %w", err)
}
}
_, err = tx.ExecContext(ctx,
@@ -480,7 +528,7 @@ func loadFileRows(ctx context.Context, db *sql.DB, total func(n int64),
var n int64
err = tx.QueryRowContext(ctx, "SELECT COUNT(*) FROM files").Scan(&n)
err = tx.QueryRowContext(ctx, recordCountSQL).Scan(&n)
if err != nil {
return fmt.Errorf("count records: %w", err)
}
@@ -556,7 +604,7 @@ func loadSignatureRows(ctx context.Context, db *sql.DB,
var n int64
err = tx.QueryRowContext(ctx, "SELECT COUNT(*) FROM files").Scan(&n)
err = tx.QueryRowContext(ctx, recordCountSQL).Scan(&n)
if err != nil {
return fmt.Errorf("count records: %w", err)
}
@@ -622,7 +670,7 @@ func (r *scanRec) setHashes(head, tail, content []byte) error {
func countRecords(ctx context.Context, db *sql.DB) (int64, error) {
var n int64
err := db.QueryRowContext(ctx, "SELECT COUNT(*) FROM files").Scan(&n)
err := db.QueryRowContext(ctx, recordCountSQL).Scan(&n)
if err != nil {
return 0, fmt.Errorf("count records: %w", err)
}
@@ -630,12 +678,10 @@ func countRecords(ctx context.Context, db *sql.DB) (int64, error) {
return n, nil
}
// databaseCountsSQL counts the records and adds up their sizes, in one
// pass over the table. A SUM over no rows is NULL, so on an empty table
// the SUM falls back to 0.
// databaseCountsSQL reads the number of records and the sizes of all
// records added up from totals.
const databaseCountsSQL = `
SELECT COUNT(*), COALESCE(SUM(size), 0)
FROM files
SELECT records, size FROM totals
`
// databaseCounts is what info reads from the database: its schema
+157 -10
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@@ -535,17 +535,12 @@ func TestLoadRowsRefuseWrongSizeHash(t *testing.T) {
}
}
// TestSignatureRowsNeedNoSort checks that SQLite reads signatureRowsSQL
// from the files_signature index alone, with nothing to sort: the
// first record comes at once, so report's read phase counts each
// record as it comes rather than waiting on SQLite for all of them.
func TestSignatureRowsNeedNoSort(t *testing.T) {
t.Parallel()
// queryPlan returns the detail of each line of SQLite's EXPLAIN QUERY
// PLAN for query.
func queryPlan(t *testing.T, db *sql.DB, query string) []string {
t.Helper()
db := openTestDB(t)
rows, err := db.QueryContext(t.Context(),
"EXPLAIN QUERY PLAN "+signatureRowsSQL)
rows, err := db.QueryContext(t.Context(), "EXPLAIN QUERY PLAN "+query)
if err != nil {
t.Fatal(err)
}
@@ -573,12 +568,164 @@ func TestSignatureRowsNeedNoSort(t *testing.T) {
t.Fatal(err)
}
return plan
}
// TestSignatureRowsNeedNoSort checks that SQLite reads signatureRowsSQL
// from the files_signature index alone, with nothing to sort: the
// first record comes at once, so report's read phase counts each
// record as it comes rather than waiting on SQLite for all of them.
func TestSignatureRowsNeedNoSort(t *testing.T) {
t.Parallel()
db := openTestDB(t)
plan := queryPlan(t, db, signatureRowsSQL)
want := []string{"SCAN files USING COVERING INDEX files_signature"}
if !slices.Equal(plan, want) {
t.Errorf("query plan = %q, want %q", plan, want)
}
}
// TestCountsReadOnlyTotals checks that SQLite answers the queries for
// the number of records and their total size from the one row of
// totals. A plan that reads files or its index reads every record.
func TestCountsReadOnlyTotals(t *testing.T) {
t.Parallel()
db := openTestDB(t)
for _, query := range []string{recordCountSQL, databaseCountsSQL} {
plan := queryPlan(t, db, query)
want := []string{"SCAN totals"}
if !slices.Equal(plan, want) {
t.Errorf("query plan of %q = %q, want %q", query, plan, want)
}
}
}
// TestCountsComeFromTotals sets the row of totals to numbers that files
// does not hold, then checks that scan's load phase, the read phases of
// trees and report, and info each report the numbers from totals.
func TestCountsComeFromTotals(t *testing.T) {
t.Parallel()
// files is empty, so a count over files gives 0 records of 0 bytes.
const records, size = 7, 9000
db := openTestDB(t)
_, err := db.ExecContext(t.Context(),
"UPDATE totals SET records = ?, size = ?", records, size)
if err != nil {
t.Fatal(err)
}
scanTotal, err := countRecords(t.Context(), db)
if err != nil {
t.Fatal(err)
}
var treesTotal, reportTotal int64
err = loadFileRows(t.Context(), db,
func(n int64) { treesTotal = n }, func(scanRec) {})
if err != nil {
t.Fatal(err)
}
err = loadSignatureRows(t.Context(), db,
func(n int64) { reportTotal = n },
func(scanRec) error { return nil })
if err != nil {
t.Fatal(err)
}
info, err := readDatabaseCounts(t.Context(), db)
if err != nil {
t.Fatal(err)
}
for name, got := range map[string]int64{
"scan's load": scanTotal,
"trees' read": treesTotal,
"report's read": reportTotal,
"info": info.records,
} {
if got != records {
t.Errorf("%s: %d records, want %d from totals",
name, got, records)
}
}
if info.size != size {
t.Errorf("info: size %d, want %d from totals", info.size, size)
}
}
// assertTotalsMatchFiles fails unless the row of totals holds the
// number of records and the sizes of all records added up, as counted
// over files.
func assertTotalsMatchFiles(t *testing.T, db *sql.DB) {
t.Helper()
got, err := readDatabaseCounts(t.Context(), db)
if err != nil {
t.Fatal(err)
}
var records, size int64
err = db.QueryRowContext(t.Context(),
"SELECT COUNT(*), COALESCE(SUM(size), 0) FROM files").
Scan(&records, &size)
if err != nil {
t.Fatal(err)
}
if got.records != records || got.size != size {
t.Errorf("totals = %d records of %d bytes, files holds %d of %d",
got.records, got.size, records, size)
}
}
// TestTotalsMatchFiles scans the smoke tree, rescans it after two files
// change size, and rescans it after two files are removed. After each
// scan the row of totals must agree with files.
func TestTotalsMatchFiles(t *testing.T) {
t.Parallel()
dir := buildSmokeTree(t)
db := openTestDB(t)
syncTree(t, db, dir)
assertTotalsMatchFiles(t, db)
writeFile(t, dir, "a/one.bin", pattern(10, 2500))
writeFile(t, dir, "t1/f1", pattern(30, 1000))
if st := syncTree(t, db, dir); st.updated != 2 {
t.Fatalf("rescan stats = %+v, want 2 updated", st)
}
assertTotalsMatchFiles(t, db)
for _, name := range []string{"a/unique.bin", "t2/sub/f2"} {
err := os.Remove(filepath.Join(dir, name))
if err != nil {
t.Fatal(err)
}
}
if st := syncTree(t, db, dir); st.removed != 2 {
t.Fatalf("rescan stats = %+v, want 2 removed", st)
}
assertTotalsMatchFiles(t, db)
}
func TestApplyChangesRoundTrip(t *testing.T) {
t.Parallel()
+6 -6
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@@ -26,11 +26,11 @@ func infoPhase(name string) string {
// it. Any database problem, including a missing database, is fatal.
//
// The work runs in two phases, each under a progress display of its
// own on stderr: open (open the database) and count (count the records,
// with one query). Each display ends before the next phase starts, and
// before an error is returned to be printed. The details are written
// once the last display has ended, so no display is drawn while they
// are written.
// own on stderr: open (open the database) and count (read the number of
// records and their total size from the totals table). Each display
// ends before the next phase starts, and before an error is returned
// to be printed. The details are written once the last display has
// ended, so no display is drawn while they are written.
func runInfo(ctx context.Context, stdout io.Writer) error {
dbPath, source, err := databasePath()
if err != nil {
@@ -56,7 +56,7 @@ func runInfo(ctx context.Context, stdout io.Writer) error {
defer func() { _ = db.Close() }()
// One query counts everything, so the phase never has a total.
// One row holds both counts, so the phase never has a total.
prog = newProgress(progressParams{
label: infoPhase("count"), total: -1,
waitingFor: countingRecords,
+6 -5
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@@ -180,9 +180,9 @@ func capture(t *testing.T, std **os.File) func() string {
}
// brokenDatabase writes a database that opens cleanly and passes the
// schema-version check but has no files table, so the first query
// fails with the database already open: a fatal error on a path that
// owns an open database. It closes the database the way scan does.
// schema-version check but has no tables, so the first query fails
// with the database already open: a fatal error on a path that owns an
// open database. It closes the database the way scan does.
func brokenDatabase(t *testing.T) string {
t.Helper()
@@ -265,8 +265,9 @@ func TestRunFatalAfterOpenClosesDatabase(t *testing.T) {
assertFatalOutput(t, stderr.String(), stdout())
// Proof that the failure happened after the open: only a
// query against the opened database can report this.
if !strings.Contains(stderr.String(), "no such table: files") {
// query against the opened database can report this. Each
// subcommand's first query reads totals.
if !strings.Contains(stderr.String(), "no such table: totals") {
t.Errorf("stderr = %q, want the failure to come from a "+
"query on the open database", stderr.String())
}
+1 -1
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@@ -60,7 +60,7 @@ const fallbackWidth = 80
const spinnerMargin = 5
// countingRecords is what the display of a phase that reads the records
// says while it counts them, before it has its total.
// says until it has the number of records, its total.
const countingRecords = "counting the records"
// openPhase is the name of the phase in which report, trees and info
+5 -5
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@@ -45,11 +45,11 @@ func reportPhase(name string) string {
// problem, including a missing database, is fatal.
//
// The work runs in two phases, each under a progress display of its
// own on stderr: open (open the database) and read (count the records,
// then read them in signature order, writing each size's duplicate
// groups to stdout once that size is read; see readReport). Each
// display ends before the next phase starts, and before an error is
// returned to be printed.
// own on stderr: open (open the database) and read (read the number of
// records from the totals table, then read the records in signature
// order, writing each size's duplicate groups to stdout once that size
// is read; see readReport). Each display ends before the next phase
// starts, and before an error is returned to be printed.
func runReport(ctx context.Context, stdout io.Writer) error {
dbPath, source, err := databasePath()
if err != nil {
+2 -2
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@@ -455,8 +455,8 @@ func (s *scanState) walkableRoots(roots []string, rules walkRules) []string {
// included, so its display counts against the number of records.
func (s *scanState) loadIndex(ctx context.Context, roots []string) error {
// Indexing tens of millions of records takes real time; without a
// display the scan looks hung before the walk begins. Counting them
// first gives the display its total.
// display the scan looks hung before the walk begins. The number of
// records, read first, gives the display its total.
prog := newProgress(progressParams{
label: scanPhase("load"), unit: scanUnit, total: -1,
waitingFor: countingRecords, stalledOn: "db",
+3 -3
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@@ -1228,9 +1228,9 @@ func TestScanPipeline(t *testing.T) {
// TestScanProgressNamesEachPhase checks the plain progress lines of a
// first scan, and of a rescan of one operand holding two of the
// database's records. Each phase's first line names it with its place
// among the four: load counts the records before reading them, and the
// walk estimates its total from the records under its operand, or says
// its time remaining is unknown when there are none.
// among the four: load gets the number of records before reading them,
// and the walk estimates its total from the records under its operand,
// or says its time remaining is unknown when there are none.
//
//nolint:paralleltest // captureStderr replaces the process-wide os.Stderr
func TestScanProgressNamesEachPhase(t *testing.T) {
+5 -5
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@@ -40,11 +40,11 @@ func treesPhase(name string) string {
// database problem, including a missing database, is fatal.
//
// The work runs in four phases, each under a progress display of its
// own on stderr: open (open the database), read (count the records,
// then read them into the hierarchy), group (group the directories by
// digest) and write (write the groups to stdout). Each display ends
// before the next phase starts, and before an error is returned to be
// printed.
// own on stderr: open (open the database), read (read the number of
// records from the totals table, then read the records into the
// hierarchy), group (group the directories by digest) and write (write
// the groups to stdout). Each display ends before the next phase
// starts, and before an error is returned to be printed.
func runTrees(ctx context.Context, stdout io.Writer) error {
dbPath, source, err := databasePath()
if err != nil {