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From: Eric Wong <e@yhbt.net>
To: meta@public-inbox.org
Subject: [PATCH 5/7] index: v2: --sequential-shard option
Date: Fri,  7 Aug 2020 01:14:04 +0000	[thread overview]
Message-ID: <20200807011406.12285-6-e@yhbt.net> (raw)
In-Reply-To: <20200807011406.12285-1-e@yhbt.net>

This gives better page cache utilization for Xapian indexing on
slow storage by improving locality for random I/O activity on
the Xapian DB.

Instead of doing a single-pass to index both SQLite and Xapian;
this indexes them separately.  The first pass is identical to
indexlevel=basic: it indexes both over.sqlite3 and msgmap.sqlite3.

Subsequent passes only operate on a single Xapian shard for
documents belonging to that shard.  Given enough shards, each
individual shard can be made small enough to fit into the kernel
page cache and avoid HDD seeks for read activity.

Doing rough tests with a busy system with a 7200 RPM HDD with ext4,
full indexing of LKML (9 epochs) goes from ~80 hours (-j0) to
~30 hours (-j8) with 16GB RAM with 7 shards configured and fsync(2)
disabled (--no-sync) and `--batch-size=10m'.
---
 Documentation/public-inbox-config.pod    |  6 +++
 Documentation/public-inbox-index.pod     | 53 ++++++++++++++++++++++-
 Documentation/public-inbox-v2-format.pod | 11 +++--
 lib/PublicInbox/Config.pm                |  9 ++--
 lib/PublicInbox/V2Writable.pm            | 55 ++++++++++++++++++++++--
 lib/PublicInbox/WatchMaildir.pm          |  2 +-
 script/public-inbox-index                | 22 +++++++++-
 t/config.t                               |  6 +--
 t/v2mirror.t                             | 14 ++++++
 9 files changed, 161 insertions(+), 17 deletions(-)

diff --git a/Documentation/public-inbox-config.pod b/Documentation/public-inbox-config.pod
index e6108c35..05b84819 100644
--- a/Documentation/public-inbox-config.pod
+++ b/Documentation/public-inbox-config.pod
@@ -139,6 +139,10 @@ allow for searching for phrases using quoted text.
 
 Default: C<full>
 
+=item publicinbox.<name>.indexSequentialShard
+
+See L<public-inbox-index(1)/publicInbox.indexSequentialShard>
+
 =item publicinbox.<name>.httpbackendmax
 
 If a digit, the maximum number of parallel
@@ -291,6 +295,8 @@ or /usr/share/cgit/
 See L<public-inbox-edit(1)>
 
 =item publicinbox.indexMaxSize
+=item publicinbox.indexBatchSize
+=item publicinbox.indexSequentialShard
 
 See L<public-inbox-index(1)>
 
diff --git a/Documentation/public-inbox-index.pod b/Documentation/public-inbox-index.pod
index aeb1b3a3..f525ba54 100644
--- a/Documentation/public-inbox-index.pod
+++ b/Documentation/public-inbox-index.pod
@@ -34,12 +34,16 @@ normal search functionality.
 
 =item --jobs=JOBS, -j
 
-Control the number of Xapian indexing jobs in a
+Influences the number of Xapian indexing shards in a
 (L<public-inbox-v2-format(5)>) inbox.
 
 C<--jobs=0> is accepted as of public-inbox 1.6.0 (PENDING)
 to disable parallel indexing.
 
+If the inbox has not been indexed, C<JOBS - 1> shards
+will be created (one job is always needed for indexing
+the overview and article number mapping).
+
 Default: the number of existing Xapian shards
 
 =item --compact / -c
@@ -120,6 +124,14 @@ and Xapian.  This is only effective with Xapian 1.4+.
 
 Available in public-inbox 1.6.0 (PENDING).
 
+=item --sequential-shard
+
+Sets or overrides L</publicinbox.indexSequentialShard> on a
+per-invocation basis.  See L</publicinbox.indexSequentialShard>
+below.
+
+Available in public-inbox 1.6.0 (PENDING).
+
 =back
 
 =head1 FILES
@@ -167,6 +179,45 @@ inbox with 3 shards will flush every 3 megabytes by default.
 
 Default: 1m (one megabyte)
 
+=item publicinbox.indexBatchSize
+
+Flushes changes to the filesystem and releases locks after
+indexing the given number of bytes.  The default value of C<1m>
+(one megabyte) is low to minimize memory use and reduce
+contention with parallel invocations of L<public-inbox-mda(1)>,
+L<public-inbox-learn(1)>, and L<public-inbox-watch(1)>.
+
+Increase this value on powerful systems to improve throughput at
+the expense of memory use.  The reduction of lock granularity
+may not be noticeable on fast systems.
+
+This option is available in public-inbox 1.6 or later.
+public-inbox 1.5 and earlier used the current default, C<1m>.
+
+For L<public-inbox-v2-format(5)> inboxes, this value is
+multiplied by the number of Xapian shards.  Thus a typical v2
+inbox with 3 shards will flush every 3 megabytes by default.
+
+Default: 1m (one megabyte)
+
+=item publicinbox.indexSequentialShard
+=item publicinbox.<inbox_name>.indexSequentialShard
+
+For L<public-inbox-v2-format(5)> inboxes, setting this to C<true>
+allows indexing Xapian shards in multiple passes.  This speeds up
+indexing on rotational storage with high seek latency by allowing
+individual shards to fit into the kernel page cache.
+
+Using a higher-than-normal number of C<--jobs> with
+L<public-inbox-init(1)> may be required to ensure individual
+shards are small enough to fit into cache.
+
+Available in public-inbox 1.6.0 (PENDING).
+
+This is ignored on L<public-inbox-v1-format(5)> inboxes.
+
+Default: false, shards are indexed in parallel
+
 =back
 
 =head1 ENVIRONMENT
diff --git a/Documentation/public-inbox-v2-format.pod b/Documentation/public-inbox-v2-format.pod
index 9e284a75..6876989c 100644
--- a/Documentation/public-inbox-v2-format.pod
+++ b/Documentation/public-inbox-v2-format.pod
@@ -113,9 +113,14 @@ improved with high-quality and high-quantity solid-state storage.
 Issuing TRIM commands with L<fstrim(8)> was necessary to maintain
 consistent performance while developing this feature.
 
-Rotational storage devices are NOT recommended for indexing of
-large mail archives; but are fine for backup and usable for
-small instances.
+Rotational storage devices perform significantly worse than
+solid state storage for indexing of large mail archives; but are
+fine for backup and usable for small instances.
+
+As of public-inbox 1.6.0, the C<--sequential-shard> option of
+L<public-inbox-index(1)> may be used with a high shard count
+to ensure individual shards fit into page cache when the entire
+Xapian DB cannot.
 
 Our use of the L</OVERVIEW DB> requires Xapian document IDs to
 remain stable.  Using L<public-inbox-compact(1)> and
diff --git a/lib/PublicInbox/Config.pm b/lib/PublicInbox/Config.pm
index 67199bb3..f9184bd2 100644
--- a/lib/PublicInbox/Config.pm
+++ b/lib/PublicInbox/Config.pm
@@ -369,8 +369,8 @@ sub _fill_code_repo {
 	$git;
 }
 
-sub _git_config_bool ($) {
-	my ($val) = @_;
+sub git_bool {
+	my ($val) = $_[-1]; # $_[0] may be $self, or $val
 	if ($val =~ /\A(?:false|no|off|[\-\+]?(?:0x)?0+)\z/i) {
 		0;
 	} elsif ($val =~ /\A(?:true|yes|on|[\-\+]?(?:0x)?[0-9]+)\z/i) {
@@ -386,7 +386,8 @@ sub _fill {
 
 	foreach my $k (qw(inboxdir filter newsgroup
 			watch httpbackendmax
-			replyto feedmax nntpserver indexlevel)) {
+			replyto feedmax nntpserver
+			indexlevel indexsequentialshard)) {
 		my $v = $self->{"$pfx.$k"};
 		$ibx->{$k} = $v if defined $v;
 	}
@@ -400,7 +401,7 @@ sub _fill {
 	foreach my $k (qw(obfuscate)) {
 		my $v = $self->{"$pfx.$k"};
 		defined $v or next;
-		if (defined(my $bval = _git_config_bool($v))) {
+		if (defined(my $bval = git_bool($v))) {
 			$ibx->{$k} = $bval;
 		} else {
 			warn "Ignoring $pfx.$k=$v in config, not boolean\n";
diff --git a/lib/PublicInbox/V2Writable.pm b/lib/PublicInbox/V2Writable.pm
index f98afa61..7bc24592 100644
--- a/lib/PublicInbox/V2Writable.pm
+++ b/lib/PublicInbox/V2Writable.pm
@@ -875,7 +875,8 @@ sub reindex_checkpoint ($$) {
 
 	$self->{ibx}->git->cleanup; # *async_wait
 	${$sync->{need_checkpoint}} = 0;
-	$sync->{mm_tmp}->atfork_prepare;
+	my $mm_tmp = $sync->{mm_tmp};
+	$mm_tmp->atfork_prepare if $mm_tmp;
 	$self->done; # release lock
 
 	if (my $pr = $sync->{-opt}->{-progress}) {
@@ -884,7 +885,7 @@ sub reindex_checkpoint ($$) {
 
 	# allow -watch or -mda to write...
 	$self->idx_init; # reacquire lock
-	$sync->{mm_tmp}->atfork_parent;
+	$mm_tmp->atfork_parent if $mm_tmp;
 }
 
 sub index_oid { # cat_async callback
@@ -1085,7 +1086,10 @@ sub sync_prepare ($$$) {
 		}
 		$all->cat_async_wait;
 	}
-	return 0 if (!$regen_max && !keys(%{$self->{unindex_range}}));
+	if (!$regen_max && !keys(%{$self->{unindex_range}})) {
+		$sync->{-regen_fmt} = "%u/?\n";
+		return 0;
+	}
 
 	# reindex should NOT see new commits anymore, if we do,
 	# it's a problem and we need to notice it via die()
@@ -1177,6 +1181,36 @@ sub sync_ranges ($$$) {
 	$ranges;
 }
 
+sub index_xap_only { # git->cat_async callback
+	my ($bref, $oid, $type, $size, $smsg) = @_;
+	my $self = $smsg->{v2w};
+	my $idx = idx_shard($self, $smsg->{num} % $self->{shards});
+	$idx->begin_txn_lazy;
+	$idx->add_message(PublicInbox::Eml->new($bref), $smsg);
+	$self->{transact_bytes} += $size;
+}
+
+sub index_seq_shard ($$$) {
+	my ($self, $sync, $off) = @_;
+	my $ibx = $self->{ibx};
+	my $max = $ibx->mm->max or return;
+	my $all = $ibx->git;
+	my $over = $ibx->over;
+	my $batch_bytes = $PublicInbox::SearchIdx::BATCH_BYTES;
+	if (my $pr = $sync->{-opt}->{-progress}) {
+		$pr->("Xapian indexlevel=$ibx->{indexlevel} % $off\n");
+	}
+	for (my $num = $off; $num <= $max; $num += $self->{shards}) {
+		my $smsg = $over->get_art($num) or next;
+		$smsg->{v2w} = $self;
+		$all->cat_async($smsg->{blob}, \&index_xap_only, $smsg);
+		if ($self->{transact_bytes} >= $batch_bytes) {
+			${$sync->{nr}} = $num;
+			reindex_checkpoint($self, $sync);
+		}
+	}
+}
+
 sub index_epoch ($$$) {
 	my ($self, $sync, $i) = @_;
 
@@ -1218,6 +1252,11 @@ sub index_sync {
 	my $epoch_max;
 	my $latest = git_dir_latest($self, \$epoch_max);
 	return unless defined $latest;
+
+	my $seq = $opt->{sequentialshard};
+	my $idxlevel = $self->{ibx}->{indexlevel};
+	local $self->{ibx}->{indexlevel} = 'basic' if $seq;
+
 	$self->idx_init($opt); # acquire lock
 	fill_alternates($self, $epoch_max);
 	$self->{over}->rethread_prepare($opt);
@@ -1252,6 +1291,16 @@ sub index_sync {
 		$pr->('all.git '.sprintf($sync->{-regen_fmt}, $$nr)) if $pr;
 	}
 
+	if ($seq) { # deal with Xapian shards sequentially
+		my $end = $self->{shards} - 1;
+		$self->{ibx}->{indexlevel} = $idxlevel;
+		delete $sync->{mm_tmp};
+		$self->idx_init($opt); # re-acquire lock
+		index_seq_shard($self, $sync, $_) for (0..$end);
+		$self->{ibx}->git->cat_async_wait;
+		$self->done;
+	}
+
 	# reindex does not pick up new changes, so we rerun w/o it:
 	if ($opt->{reindex}) {
 		my %again = %$opt;
diff --git a/lib/PublicInbox/WatchMaildir.pm b/lib/PublicInbox/WatchMaildir.pm
index 142118bd..2ba10a9e 100644
--- a/lib/PublicInbox/WatchMaildir.pm
+++ b/lib/PublicInbox/WatchMaildir.pm
@@ -285,7 +285,7 @@ sub cfg_intvl ($$$) {
 sub cfg_bool ($$$) {
 	my ($cfg, $key, $url) = @_;
 	my $orig = $cfg->urlmatch($key, $url) // return;
-	my $bool = PublicInbox::Config::_git_config_bool($orig);
+	my $bool = $cfg->git_bool($orig);
 	warn "W: $key=$orig for $url is not boolean\n" unless defined($bool);
 	$bool;
 }
diff --git a/script/public-inbox-index b/script/public-inbox-index
index 5a0ceab7..be518134 100755
--- a/script/public-inbox-index
+++ b/script/public-inbox-index
@@ -16,7 +16,8 @@ use PublicInbox::Xapcmd;
 my $compact_opt;
 my $opt = { quiet => -1, compact => 0, maxsize => undef, sync => 1 };
 GetOptions($opt, qw(verbose|v+ reindex rethread compact|c+ jobs|j=i prune sync!
-		indexlevel|L=s maxsize|max-size=s batchsize|batch-size=s))
+		indexlevel|L=s maxsize|max-size=s batchsize|batch-size=s
+		sequentialshard|seq-shard|sequential-shard))
 	or die "bad command-line args\n$usage";
 die "--jobs must be >= 0\n" if defined $opt->{jobs} && $opt->{jobs} < 0;
 
@@ -46,6 +47,15 @@ if (my $bs = $opt->{batchsize} // $cfg->{lc('publicInbox.indexBatchSize')}) {
 	$PublicInbox::SearchIdx::BATCH_BYTES = $bs;
 }
 
+my $s = $opt->{sequentialshard} //
+			$cfg->{lc('publicInbox.indexSequentialShard')};
+if (defined $s) {
+	my $v = $cfg->git_bool($s);
+	defined($v) or
+		die "`publicInbox.indexSequentialShard=$s' not boolean\n";
+	$opt->{sequentialshard} = $v;
+}
+
 my $mods = {};
 foreach my $ibx (@ibxs) {
 	# XXX: users can shoot themselves in the foot, with opt->{indexlevel}
@@ -63,6 +73,14 @@ for my $ibx (@ibxs) {
 		PublicInbox::Xapcmd::run($ibx, 'compact', $compact_opt);
 	}
 	$ibx->{-no_sync} = 1 if !$opt->{sync};
-	PublicInbox::Admin::index_inbox($ibx, undef, $opt);
+
+	my $ibx_opt = $opt;
+	if (defined(my $s = $ibx->{indexsequentialshard})) {
+		defined(my $v = $cfg->git_bool($s)) or die <<EOL;
+publicInbox.$ibx->{name}.indexSequentialShard not boolean
+EOL
+		$ibx_opt = { %$opt, sequentialshard => $v };
+	}
+	PublicInbox::Admin::index_inbox($ibx, undef, $ibx_opt);
 	PublicInbox::Xapcmd::run($ibx, 'compact', $compact_opt) if $compact_opt;
 }
diff --git a/t/config.t b/t/config.t
index d7fd9446..ee51c6cc 100644
--- a/t/config.t
+++ b/t/config.t
@@ -220,18 +220,18 @@ EOF
 
 {
 	for my $t (qw(TRUE true yes on 1 +1 -1 13 0x1 0x12 0X5)) {
-		is(PublicInbox::Config::_git_config_bool($t), 1, "$t is true");
+		is(PublicInbox::Config::git_bool($t), 1, "$t is true");
 		is(xqx([qw(git -c), "test.val=$t",
 			qw(config --bool test.val)]),
 			"true\n", "$t matches git-config behavior");
 	}
 	for my $f (qw(FALSE false no off 0 +0 +000 00 0x00 0X0)) {
-		is(PublicInbox::Config::_git_config_bool($f), 0, "$f is false");
+		is(PublicInbox::Config::git_bool($f), 0, "$f is false");
 		is(xqx([qw(git -c), "test.val=$f",
 			qw(config --bool test.val)]),
 			"false\n", "$f matches git-config behavior");
 	}
-	is(PublicInbox::Config::_git_config_bool('bogus'), undef,
+	is(PublicInbox::Config::git_bool('bogus'), undef,
 		'bogus is undef');
 }
 
diff --git a/t/v2mirror.t b/t/v2mirror.t
index b24528fe..a4ac682d 100644
--- a/t/v2mirror.t
+++ b/t/v2mirror.t
@@ -4,6 +4,7 @@ use strict;
 use warnings;
 use Test::More;
 use PublicInbox::TestCommon;
+use File::Path qw(remove_tree);
 use Cwd qw(abs_path);
 require_git(2.6);
 local $ENV{HOME} = abs_path('t');
@@ -189,6 +190,19 @@ is($mibx->git->check($to_purge), undef, 'unindex+prune successful in mirror');
 	is(scalar($mset->items), 0, '1@example.com no longer visible in mirror');
 }
 
+if ('sequential-shard') {
+	$mset = $mibx->search->query('m:15@example.com', {mset => 1});
+	is(scalar($mset->items), 1, 'large message not indexed');
+	remove_tree(glob("$tmpdir/m/xap*"), glob("$tmpdir/m/msgmap.*"));
+	my $cmd = [ qw(-index -j9 --sequential-shard), "$tmpdir/m" ];
+	ok(run_script($cmd), '--sequential-shard works');
+	my @shards = glob("$tmpdir/m/xap*/?");
+	is(scalar(@shards), 8, 'got expected shard count');
+	PublicInbox::InboxWritable::cleanup($mibx);
+	$mset = $mibx->search->query('m:15@example.com', {mset => 1});
+	is(scalar($mset->items), 1, 'search works after --sequential-shard');
+}
+
 if ('max size') {
 	$mime->header_set('Message-ID', '<2big@a>');
 	my $max = '2k';

  parent reply	other threads:[~2020-08-07  1:14 UTC|newest]

Thread overview: 8+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2020-08-07  1:13 [PATCH 0/7] index: --sequential-shard and other stuff Eric Wong
2020-08-07  1:14 ` [PATCH 1/7] xapcmd: quietly no-op on indexlevel=basic Eric Wong
2020-08-07  1:14 ` [PATCH 2/7] xapcmd: remove redundant searchidx require Eric Wong
2020-08-07  1:14 ` [PATCH 3/7] xapcmd: drop outdated comment Eric Wong
2020-08-07  1:14 ` [PATCH 4/7] v2writable: fix rethread cleanup Eric Wong
2020-08-07  1:14 ` Eric Wong [this message]
2020-08-07  1:14 ` [PATCH 6/7] index: support --xapian-only switch Eric Wong
2020-08-07  1:14 ` [PATCH 7/7] index+xcpdb: rename `--no-sync' to `--no-fsync' Eric Wong

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