ca-specific-schema.sql: add index on RealisationsRefs(referrer) and (outputPath)

For a typical desktop system (~2K packages) we can easily get 100K
entries in RealisationsRefs. Without indices query for RealisationsRefs
requires linear scan.

RealisationsRefs(referrer)
--------------------------

Inefficiency is seen as a 100% CPU load of nix-daemon for the following
scenario:

    $ nix edit -f . bash # add unused environment variable, like FOO="1"
    # populate RealisationsRefs, build fresh system
    $ nix build -f nixos system --arg config '{ contentAddressedByDefault = true; }'
    $ nix edit -f . bash # add unused environment variable, like FOO="2"
    $ time nix build -f nixos system --arg config '{ contentAddressedByDefault = true; }'

In this case `bash `will be rebuilt a few times and then rest of CPU
time is spent on scanning RealisationsRefs table (about 5 CPU-minutes
on my machine).

Before the change:

    $ time nix build -f nixos system ... # step 4 above
    real    34m3,613s
    user    0m5,232s
    sys     0m0,758s

Of all this time about 29.5 minutes are taken by nix-daemon's CPU time.

After the change:

    $ time nix build -f nixos system ... # step 4 above
    real    4m50,061s
    user    0m5,038s
    sys     0m0,677s

Of all this time about 1 minute is taken by nix-daemon's CPU time.
Most of the time is spent polling for non-existent realisations on
cache-nixos.org.

Realisations(outputPath)
------------------------

After running CA system for two weeks I got ~1M entries in Realisations
table. `nix-collect-garbage` became very slow (seemingly 100 path deletions
per second). It happens due to a slow cascading delete from Realisations
triggered by deletion from ValidPaths.

The fix is to add an index on primary key from ValidPaths(id) that
triggers cascading deletions.

Before the change:
    $ time nix-collect-garbage -d --max-freed 100G
    <interrupted before finish, took too long>
    real    23m32.411s
    user    17m49.679s
    sys     4m50.609s

Most of time was spent in re-scanning Realisations table on each path deletion.

After the change:
    $ time nix-collect-garbage -d --max-freed 100G

    real    8m43.226s
    user    6m16.317s
    sys     1m40.188s

Time is spent scanning sqlite indices and in kernel when unlinking directories.

2 files changed, 17 insertions, 1 deletions

diff --git a/src/libstore/ca-specific-schema.sql b/src/libstore/ca-specific-schema.sql
index 08af0cc1f..64cc97fde 100644
--- a/src/libstore/ca-specific-schema.sql
+++ b/src/libstore/ca-specific-schema.sql
@@ -19,3 +19,8 @@ create table if not exists RealisationsRefs (
     foreign key (referrer) references Realisations(id) on delete cascade,
     foreign key (realisationReference) references Realisations(id) on delete restrict
 );
+
+-- used by QueryRealisationReferences
+create index if not exists IndexRealisationsRefs on RealisationsRefs(referrer);
+-- used by cascade deletion when ValidPaths is deleted
+create index if not exists IndexRealisationsRefsOnOutputPath on Realisations(outputPath);
diff --git a/src/libstore/local-store.cc b/src/libstore/local-store.cc
index eecd407f5..fcddd1f8e 100644
--- a/src/libstore/local-store.cc
+++ b/src/libstore/local-store.cc
@@ -79,7 +79,7 @@ int getSchema(Path schemaPath)
 
 void migrateCASchema(SQLite& db, Path schemaPath, AutoCloseFD& lockFd)
 {
-    const int nixCASchemaVersion = 2;
+    const int nixCASchemaVersion = 3;
     int curCASchema = getSchema(schemaPath);
     if (curCASchema != nixCASchemaVersion) {
         if (curCASchema > nixCASchemaVersion) {
@@ -130,6 +130,17 @@ void migrateCASchema(SQLite& db, Path schemaPath, AutoCloseFD& lockFd)
             txn.commit();
         }
 
+        if (curCASchema < 3) {
+            SQLiteTxn txn(db);
+            // Apply new indices added in this schema update.
+            db.exec(R"(
+                -- used by QueryRealisationReferences
+                create index if not exists IndexRealisationsRefs on RealisationsRefs(referrer);
+                -- used by cascade deletion when ValidPaths is deleted
+                create index if not exists IndexRealisationsRefsOnOutputPath on Realisations(outputPath);
+            )");
+            txn.commit();
+        }
         writeFile(schemaPath, fmt("%d", nixCASchemaVersion));
         lockFile(lockFd.get(), ltRead, true);
     }