Merge lp:~percona-toolkit-dev/percona-toolkit/pt-osc-metadata-lock-bug-1113301 into lp:percona-toolkit/2.2

[Daniel Nichter]

[lp:~percona-toolkit-dev/percona-toolkit/pt-osc-metadata-lock-bug-1113301]

536. By Daniel Nichter on 2013-03-01

Retry rebuilding fk constraints. Update --retries docs.

537. By Daniel Nichter on 2013-03-01

Fix typo.

538. By Daniel Nichter on 2013-03-01

Fix --stats sample for < MySQL 5.5.

539. By Daniel Nichter on 2013-03-01

Fix bug 968596: rename NibbleIterator::chunk_size() to limit() and update ptc and pt-osc.

540. By Daniel Nichter on 2013-03-02

Fix t/pt-table-checksum/replication_filters.t again, better.

[Daniel Nichter (daniel-nichter)]

review: Approve

[lp:~percona-toolkit-dev/percona-toolkit/pt-osc-metadata-lock-bug-1113301]

541. By Daniel Nichter on 2013-03-02

Fix t/pt-table-checksum/replication_filters.t again because my Mac is the odd ball.

542. By Daniel Nichter on 2013-03-04

Merge enhanced-set-vars.

543. By Daniel Nichter on 2013-03-04

Update DSNParser in all tools.

544. By Daniel Nichter on 2013-03-04

New, simpler RISKS section. Fix spelling errors.

[Daniel Nichter (daniel-nichter)]

All pt-osc tests are passing, in all 20 envs.

=== modified file 'bin/pt-archiver'
--- bin/pt-archiver	2013-02-27 00:01:17 +0000
+++ bin/pt-archiver	2013-03-04 18:10:28 +0000
@@ -712,6 +712,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1695,6 +1696,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2397,7 +2437,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2412,13 +2452,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2493,6 +2528,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -5335,7 +5421,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    # Frequently used options.
    $src             = $o->get('source');
@@ -7094,12 +7180,22 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.
-
-Specify any variables you want to be set immediately after connecting to MySQL.
-These will be included in a C<SET> command.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the default
+value of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --share-lock
 

=== modified file 'bin/pt-config-diff'
--- bin/pt-config-diff	2013-02-26 23:57:02 +0000
+++ bin/pt-config-diff	2013-03-04 18:10:28 +0000
@@ -712,6 +712,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1695,6 +1696,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1986,7 +2026,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2001,13 +2041,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2082,6 +2117,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -4984,7 +5070,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    if ( !$o->get('help') ) {
       if ( @ARGV < 1 ) {
@@ -5325,10 +5411,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-deadlock-logger'
--- bin/pt-deadlock-logger	2013-02-28 02:23:08 +0000
+++ bin/pt-deadlock-logger	2013-03-04 18:10:28 +0000
@@ -67,6 +67,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1050,6 +1051,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2330,7 +2370,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2345,13 +2385,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2426,6 +2461,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -4254,7 +4340,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    my $src;
    if ( my $src_dsn_string = shift @ARGV ) {
@@ -5116,10 +5202,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-duplicate-key-checker'
--- bin/pt-duplicate-key-checker	2013-02-27 00:01:17 +0000
+++ bin/pt-duplicate-key-checker	2013-03-04 18:10:28 +0000
@@ -875,7 +875,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -890,13 +890,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -971,6 +966,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1003,6 +1049,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1986,6 +2033,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -4662,7 +4748,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    $o->usage_or_errors();
 
@@ -5144,10 +5230,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-find'
--- bin/pt-find	2013-02-27 00:01:17 +0000
+++ bin/pt-find	2013-03-04 18:10:28 +0000
@@ -309,7 +309,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -324,13 +324,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -405,6 +400,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -437,6 +483,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1420,6 +1467,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -3719,7 +3805,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    # Make sure OptionParser understands that these options are used.
    # cmin ctime empty kmin ktime mmin mtime exec printf 
@@ -4263,10 +4349,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-fk-error-logger'
--- bin/pt-fk-error-logger	2013-02-28 02:23:08 +0000
+++ bin/pt-fk-error-logger	2013-03-04 18:10:28 +0000
@@ -62,6 +62,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1045,6 +1046,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1487,7 +1527,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -1502,13 +1542,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -1583,6 +1618,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -3721,7 +3807,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    my $src;
    if ( my $src_dsn_string = shift @ARGV ) {
@@ -4127,10 +4213,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-heartbeat'
--- bin/pt-heartbeat	2013-02-27 00:01:17 +0000
+++ bin/pt-heartbeat	2013-03-04 18:10:28 +0000
@@ -797,6 +797,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1780,6 +1781,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2071,7 +2111,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2086,13 +2126,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2167,6 +2202,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -4641,7 +4727,7 @@
 
    my $dp = $o->DSNParser;
    $dp->prop('dbidriver', $o->get('dbi-driver'));
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    if ( !$o->get('help') ) {
       my @frames = $o->get('frames') =~ m/(\d+[smhd])/g;
@@ -5737,10 +5823,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --skew
 

=== modified file 'bin/pt-index-usage'
--- bin/pt-index-usage	2013-02-22 17:47:57 +0000
+++ bin/pt-index-usage	2013-03-04 18:10:28 +0000
@@ -319,7 +319,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -334,13 +334,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -415,6 +410,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -598,6 +644,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1581,6 +1628,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -6112,7 +6198,7 @@
    $o->get_specs();
    $o->get_opts();
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
    $o->set('progress', undef) if $o->get('q');
 
    if ( !$o->got('help') ) {
@@ -7159,10 +7245,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this
-string will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-kill'
--- bin/pt-kill	2013-02-27 00:01:17 +0000
+++ bin/pt-kill	2013-03-04 18:10:28 +0000
@@ -72,6 +72,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1055,6 +1056,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1990,7 +2030,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2005,13 +2045,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2086,6 +2121,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -6371,7 +6457,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    if ( !$o->got('busy-time') ) {
       $o->set('interval', 30) unless $o->got('interval');
@@ -7383,10 +7469,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-online-schema-change'
--- bin/pt-online-schema-change	2013-02-27 00:01:17 +0000
+++ bin/pt-online-schema-change	2013-03-04 18:10:28 +0000
@@ -23,7 +23,6 @@
       VersionParser
       DSNParser
       Daemon
-      ReportFormatter
       Quoter
       TableNibbler
       TableParser
@@ -80,6 +79,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1063,6 +1063,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2193,7 +2232,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2208,13 +2247,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2289,6 +2323,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2506,427 +2591,6 @@
 # ###########################################################################
 
 # ###########################################################################
-# ReportFormatter package
-# This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
-#   lib/ReportFormatter.pm
-#   t/lib/ReportFormatter.t
-# See https://launchpad.net/percona-toolkit for more information.
-# ###########################################################################
-{
-package ReportFormatter;
-
-use Lmo;
-use English qw(-no_match_vars);
-use constant PTDEBUG => $ENV{PTDEBUG} || 0;
-
-use List::Util qw(min max);
-use POSIX qw(ceil);
-
-eval { require Term::ReadKey };
-my $have_term = $EVAL_ERROR ? 0 : 1;
-
-
-has underline_header => (
-   is      => 'ro',
-   isa     => 'Bool',
-   default => sub { 1 },
-);
-has line_prefix => (
-   is      => 'ro',
-   isa     => 'Str',
-   default => sub { '# ' },
-);
-has line_width => (
-   is      => 'ro',
-   isa     => 'Int',
-   default => sub { 78 },
-);
-has column_spacing => (
-   is      => 'ro',
-   isa     => 'Str',
-   default => sub { ' ' },
-);
-has extend_right => (
-   is      => 'ro',
-   isa     => 'Bool',
-   default => sub { '' },
-);
-has truncate_line_mark => (
-   is      => 'ro',
-   isa     => 'Str',
-   default => sub { '...' },
-);
-has column_errors => (
-   is      => 'ro',
-   isa     => 'Str',
-   default => sub { 'warn' },
-);
-has truncate_header_side => (
-   is      => 'ro',
-   isa     => 'Str',
-   default => sub { 'left' },
-);
-has strip_whitespace => (
-   is      => 'ro',
-   isa     => 'Bool',
-   default => sub { 1 },
-);
-has title => (
-   is        => 'rw',
-   isa       => 'Str',
-   predicate => 'has_title',
-);
-
-
-has n_cols => (
-   is      => 'rw',
-   isa     => 'Int',
-   default => sub { 0 },
-   init_arg => undef,
-);
-
-has cols => (
-   is       => 'ro',
-   isa      => 'ArrayRef',
-   init_arg => undef,
-   default  => sub { [] },
-   clearer  => 'clear_cols',
-);
-
-has lines => (
-   is       => 'ro',
-   isa      => 'ArrayRef',
-   init_arg => undef,
-   default  => sub { [] },
-   clearer  => 'clear_lines',
-);
-
-has truncate_headers => (
-   is       => 'rw',
-   isa      => 'Bool',
-   default  => sub { undef },
-   init_arg => undef,
-   clearer  => 'clear_truncate_headers',
-);
-
-sub BUILDARGS {
-   my $class = shift;
-   my $args  = $class->SUPER::BUILDARGS(@_);
-
-   if ( ($args->{line_width} || '') eq 'auto' ) {
-      die "Cannot auto-detect line width because the Term::ReadKey module "
-         . "is not installed" unless $have_term;
-      ($args->{line_width}) = GetTerminalSize();
-      PTDEBUG && _d('Line width:', $args->{line_width});
-   }
-
-   return $args;
-}
-
-sub set_columns {
-   my ( $self, @cols ) = @_;
-   my $min_hdr_wid = 0;  # check that header fits on line
-   my $used_width  = 0;
-   my @auto_width_cols;
-
-   for my $i ( 0..$#cols ) {
-      my $col      = $cols[$i];
-      my $col_name = $col->{name};
-      my $col_len  = length $col_name;
-      die "Column does not have a name" unless defined $col_name;
-
-      if ( $col->{width} ) {
-         $col->{width_pct} = ceil(($col->{width} * 100) / $self->line_width());
-         PTDEBUG && _d('col:', $col_name, 'width:', $col->{width}, 'chars =',
-            $col->{width_pct}, '%');
-      }
-
-      if ( $col->{width_pct} ) {
-         $used_width += $col->{width_pct};
-      }
-      else {
-         PTDEBUG && _d('Auto width col:', $col_name);
-         $col->{auto_width} = 1;
-         push @auto_width_cols, $i;
-      }
-
-      $col->{truncate}        = 1 unless defined $col->{truncate};
-      $col->{truncate_mark}   = '...' unless defined $col->{truncate_mark};
-      $col->{truncate_side} ||= 'right';
-      $col->{undef_value}     = '' unless defined $col->{undef_value};
-
-      $col->{min_val} = 0;
-      $col->{max_val} = 0;
-
-      $min_hdr_wid        += $col_len;
-      $col->{header_width} = $col_len;
-
-      $col->{right_most} = 1 if $i == $#cols;
-
-      push @{$self->cols}, $col;
-   }
-
-   $self->n_cols( scalar @cols );
-
-   if ( ($used_width || 0) > 100 ) {
-      die "Total width_pct for all columns is >100%";
-   }
-
-   if ( @auto_width_cols ) {
-      my $wid_per_col = int((100 - $used_width) / scalar @auto_width_cols);
-      PTDEBUG && _d('Line width left:', (100-$used_width), '%;',
-         'each auto width col:', $wid_per_col, '%');
-      map { $self->cols->[$_]->{width_pct} = $wid_per_col } @auto_width_cols;
-   }
-
-   $min_hdr_wid += ($self->n_cols() - 1) * length $self->column_spacing();
-   PTDEBUG && _d('min header width:', $min_hdr_wid);
-   if ( $min_hdr_wid > $self->line_width() ) {
-      PTDEBUG && _d('Will truncate headers because min header width',
-         $min_hdr_wid, '> line width', $self->line_width());
-      $self->truncate_headers(1);
-   }
-
-   return;
-}
-
-sub add_line {
-   my ( $self, @vals ) = @_;
-   my $n_vals = scalar @vals;
-   if ( $n_vals != $self->n_cols() ) {
-      $self->_column_error("Number of values $n_vals does not match "
-         . "number of columns " . $self->n_cols());
-   }
-   for my $i ( 0..($n_vals-1) ) {
-      my $col   = $self->cols->[$i];
-      my $val   = defined $vals[$i] ? $vals[$i] : $col->{undef_value};
-      if ( $self->strip_whitespace() ) {
-         $val =~ s/^\s+//g;
-         $val =~ s/\s+$//;
-         $vals[$i] = $val;
-      }
-      my $width = length $val;
-      $col->{min_val} = min($width, ($col->{min_val} || $width));
-      $col->{max_val} = max($width, ($col->{max_val} || $width));
-   }
-   push @{$self->lines}, \@vals;
-   return;
-}
-
-sub get_report {
-   my ( $self, %args ) = @_;
-
-   $self->_calculate_column_widths();
-   if ( $self->truncate_headers() ) {
-      $self->_truncate_headers();
-   }
-   $self->_truncate_line_values(%args);
-
-   my @col_fmts = $self->_make_column_formats();
-   my $fmt      = $self->line_prefix()
-                . join($self->column_spacing(), @col_fmts);
-   PTDEBUG && _d('Format:', $fmt);
-
-   (my $hdr_fmt = $fmt) =~ s/%([^-])/%-$1/g;
-
-   my @lines;
-   push @lines, $self->line_prefix() . $self->title() if $self->has_title();
-   push @lines, $self->_truncate_line(
-         sprintf($hdr_fmt, map { $_->{name} } @{$self->cols}),
-         strip => 1,
-         mark  => '',
-   );
-
-   if ( $self->underline_header() ) {
-      my @underlines = map { '=' x $_->{print_width} } @{$self->cols};
-      push @lines, $self->_truncate_line(
-         sprintf($fmt, map { $_ || '' } @underlines),
-         mark  => '',
-      );
-   }
-
-   push @lines, map {
-      my $vals = $_;
-      my $i    = 0;
-      my @vals = map {
-            my $val = defined $_ ? $_ : $self->cols->[$i++]->{undef_value};
-            $val = '' if !defined $val;
-            $val =~ s/\n/ /g;
-            $val;
-      } @$vals;
-      my $line = sprintf($fmt, @vals);
-      if ( $self->extend_right() ) {
-         $line;
-      }
-      else {
-         $self->_truncate_line($line);
-      }
-   } @{$self->lines};
-
-   $self->clear_cols();
-   $self->clear_lines();
-   $self->clear_truncate_headers();
-
-   return join("\n", @lines) . "\n";
-}
-
-sub truncate_value {
-   my ( $self, $col, $val, $width, $side ) = @_;
-   return $val if length $val <= $width;
-   return $val if $col->{right_most} && $self->extend_right();
-   $side  ||= $col->{truncate_side};
-   my $mark = $col->{truncate_mark};
-   if ( $side eq 'right' ) {
-      $val  = substr($val, 0, $width - length $mark);
-      $val .= $mark;
-   }
-   elsif ( $side eq 'left') {
-      $val = $mark . substr($val, -1 * $width + length $mark);
-   }
-   else {
-      PTDEBUG && _d("I don't know how to", $side, "truncate values");
-   }
-   return $val;
-}
-
-sub _calculate_column_widths {
-   my ( $self ) = @_;
-
-   my $extra_space = 0;
-   foreach my $col ( @{$self->cols} ) {
-      my $print_width = int($self->line_width() * ($col->{width_pct} / 100));
-
-      PTDEBUG && _d('col:', $col->{name}, 'width pct:', $col->{width_pct},
-         'char width:', $print_width,
-         'min val:', $col->{min_val}, 'max val:', $col->{max_val});
-
-      if ( $col->{auto_width} ) {
-         if ( $col->{min_val} && $print_width < $col->{min_val} ) {
-            PTDEBUG && _d('Increased to min val width:', $col->{min_val});
-            $print_width = $col->{min_val};
-         }
-         elsif ( $col->{max_val} &&  $print_width > $col->{max_val} ) {
-            PTDEBUG && _d('Reduced to max val width:', $col->{max_val});
-            $extra_space += $print_width - $col->{max_val};
-            $print_width  = $col->{max_val};
-         }
-      }
-
-      $col->{print_width} = $print_width;
-      PTDEBUG && _d('print width:', $col->{print_width});
-   }
-
-   PTDEBUG && _d('Extra space:', $extra_space);
-   while ( $extra_space-- ) {
-      foreach my $col ( @{$self->cols} ) {
-         if (    $col->{auto_width}
-              && (    $col->{print_width} < $col->{max_val}
-                   || $col->{print_width} < $col->{header_width})
-         ) {
-            $col->{print_width}++;
-         }
-      }
-   }
-
-   return;
-}
-
-sub _truncate_headers {
-   my ( $self, $col ) = @_;
-   my $side = $self->truncate_header_side();
-   foreach my $col ( @{$self->cols} ) {
-      my $col_name    = $col->{name};
-      my $print_width = $col->{print_width};
-      next if length $col_name <= $print_width;
-      $col->{name}  = $self->truncate_value($col, $col_name, $print_width, $side);
-      PTDEBUG && _d('Truncated hdr', $col_name, 'to', $col->{name},
-         'max width:', $print_width);
-   }
-   return;
-}
-
-sub _truncate_line_values {
-   my ( $self, %args ) = @_;
-   my $n_vals = $self->n_cols() - 1;
-   foreach my $vals ( @{$self->lines} ) {
-      for my $i ( 0..$n_vals ) {
-         my $col   = $self->cols->[$i];
-         my $val   = defined $vals->[$i] ? $vals->[$i] : $col->{undef_value};
-         my $width = length $val;
-
-         if ( $col->{print_width} && $width > $col->{print_width} ) {
-            if ( !$col->{truncate} ) {
-               $self->_column_error("Value '$val' is too wide for column "
-                  . $col->{name});
-            }
-
-            my $callback    = $args{truncate_callback};
-            my $print_width = $col->{print_width};
-            $val = $callback ? $callback->($col, $val, $print_width)
-                 :             $self->truncate_value($col, $val, $print_width);
-            PTDEBUG && _d('Truncated val', $vals->[$i], 'to', $val,
-               '; max width:', $print_width);
-            $vals->[$i] = $val;
-         }
-      }
-   }
-   return;
-}
-
-sub _make_column_formats {
-   my ( $self ) = @_;
-   my @col_fmts;
-   my $n_cols = $self->n_cols() - 1;
-   for my $i ( 0..$n_cols ) {
-      my $col = $self->cols->[$i];
-
-      my $width = $col->{right_most} && !$col->{right_justify} ? ''
-                : $col->{print_width};
-
-      my $col_fmt  = '%' . ($col->{right_justify} ? '' : '-') . $width . 's';
-      push @col_fmts, $col_fmt;
-   }
-   return @col_fmts;
-}
-
-sub _truncate_line {
-   my ( $self, $line, %args ) = @_;
-   my $mark = defined $args{mark} ? $args{mark} : $self->truncate_line_mark();
-   if ( $line ) {
-      $line =~ s/\s+$// if $args{strip};
-      my $len  = length($line);
-      if ( $len > $self->line_width() ) {
-         $line  = substr($line, 0, $self->line_width() - length $mark);
-         $line .= $mark if $mark;
-      }
-   }
-   return $line;
-}
-
-sub _column_error {
-   my ( $self, $err ) = @_;
-   my $msg = "Column error: $err";
-   $self->column_errors() eq 'die' ? die $msg : warn $msg;
-   return;
-}
-
-sub _d {
-   my ($package, undef, $line) = caller 0;
-   @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
-        map { defined $_ ? $_ : 'undef' }
-        @_;
-   print STDERR "# $package:$line $PID ", join(' ', @_), "\n";
-}
-
-no Lmo;
-1;
-}
-# ###########################################################################
-# End ReportFormatter package
-# ###########################################################################
-
-# ###########################################################################
 # Quoter package
 # This package is a copy without comments from the original.  The original
 # with comments and its test file can be found in the Bazaar repository at,
@@ -5617,9 +5281,9 @@
    return $self->{one_nibble};
 }
 
-sub chunk_size {
+sub limit {
    my ($self) = @_;
-   return $self->{limit} + 1;
+   return $self->{limit};
 }
 
 sub set_chunk_size {
@@ -7870,6 +7534,7 @@
 use Percona::Toolkit;
 use constant PTDEBUG => $ENV{PTDEBUG} || 0;
 
+use List::Util qw(max);
 use Time::HiRes qw(time sleep);
 use Data::Dumper;
 $Data::Dumper::Indent    = 1;
@@ -7905,7 +7570,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    # The original table, i.e. the one being altered, must be specified
    # on the command line via the DSN.
@@ -8010,37 +7675,7 @@
    # ########################################################################
    my $set_on_connect = sub {
       my ($dbh) = @_;
-
-      # See the same code in pt-table-checksum.
-      my $lock_wait_timeout = $o->get('lock-wait-timeout');
-      my $set_lwt = "SET SESSION innodb_lock_wait_timeout=$lock_wait_timeout";
-      PTDEBUG && _d($set_lwt);
-      eval {
-         $dbh->do($set_lwt);
-      };
-      if ( $EVAL_ERROR ) {
-         PTDEBUG && _d($EVAL_ERROR);
-         # Get the server's current value.
-         my $sql = "SHOW SESSION VARIABLES LIKE 'innodb_lock_wait_timeout'";
-         PTDEBUG && _d($dbh, $sql);
-         my (undef, $curr_lwt) = $dbh->selectrow_array($sql);
-         PTDEBUG && _d('innodb_lock_wait_timeout on server:', $curr_lwt);
-         if ( !defined $curr_lwt ) {
-            PTDEBUG && _d('innodb_lock_wait_timeout does not exist;',
-               'InnoDB is probably disabled');
-         }
-         elsif ( $curr_lwt > $lock_wait_timeout ) { 
-            warn "Failed to $set_lwt: $EVAL_ERROR\n"
-               . "The current innodb_lock_wait_timeout value "
-               . "$curr_lwt is greater than the --lock-wait-timeout "
-               . "value $lock_wait_timeout and the variable cannot be "
-               . "changed.  innodb_lock_wait_timeout is only dynamic when "
-               . "using the InnoDB plugin.  To prevent this warning, either "
-               . "specify --lock-wait-time=$curr_lwt, or manually set "
-               . "innodb_lock_wait_timeout to a value less than or equal "
-               . "to $lock_wait_timeout and restart MySQL.\n";
-         }
-      }
+      return;
    };
 
    # Do not call "new Cxn(" directly; use this sub so that set_on_connect
@@ -8051,7 +7686,7 @@
    # and it might be good to just make a convention of it.
    my $make_cxn = sub {
       my (%args) = @_;
-      my $cxn = new Cxn(
+      my $cxn = Cxn->new(
          %args,
          DSNParser    => $dp,
          OptionParser => $o,
@@ -8064,7 +7699,8 @@
       return $cxn;
    };
 
-   my $cxn = $make_cxn->(dsn => $dsn);
+   my $cxn     = $make_cxn->(dsn => $dsn);
+   my $aux_cxn = $make_cxn->(dsn => $dsn, prev_dsn => $dsn);
 
    my $cluster = Percona::XtraDB::Cluster->new;
    if ( $cluster->is_cluster_node($cxn) ) {
@@ -8110,6 +7746,32 @@
    my $lock_in_share_mode = $server_version < '5.1' ? 0 : 1;
 
    # ########################################################################
+   # Create --plugin.
+   # ########################################################################   
+   my $plugin;
+   if ( my $file = $o->get('plugin') ) {
+      die "--plugin file $file does not exist\n" unless -f $file;
+      eval {
+         require $file;
+      };
+      die "Error loading --plugin $file: $EVAL_ERROR" if $EVAL_ERROR;
+      eval {
+         $plugin = pt_online_schema_change_plugin->new(
+            cxn     => $cxn,
+            aux_cxn => $aux_cxn,
+            alter   => $o->get('alter'),
+            execute => $o->get('execute'),
+            dry_run => $o->get('dry-run'),
+            print   => $o->get('print'),
+            quiet   => $o->get('quiet'),
+            Quoter  => $q,
+         );
+      };
+      die "Error creating --plugin: $EVAL_ERROR" if $EVAL_ERROR;
+      print "Created plugin from $file.\n";
+   }
+
+   # ########################################################################
    # Setup lag and load monitors.
    # ########################################################################   
    my $slaves;         # all slaves that are found or specified
@@ -8290,7 +7952,7 @@
          ],
       );
    }
-   
+
    # ########################################################################
    # Setup and check the original table.
    # ########################################################################
@@ -8452,6 +8114,21 @@
       return;
    };
 
+   # The 2nd to last cleanup task is printing the --statistics which
+   # may reveal something about the failure.
+   if ( $o->get('statistics') ) {
+      push @cleanup_tasks, sub {
+         my $n = max( map { length $_ } keys %stats );
+         my $fmt = "# %-${n}s %5s\n";
+         printf $fmt, 'Event', 'Count';
+         printf $fmt, ('=' x $n),'=====';
+         foreach my $event ( sort keys %stats ) {
+            printf $fmt,
+               $event, (defined $stats{$event} ? $stats{$event} : '?');
+         }
+      };
+   }
+
    # ########################################################################
    # Check the --alter statement.
    # ########################################################################
@@ -8491,9 +8168,30 @@
       $daemon->make_PID_file();
    }
 
+   # ########################################################################
+   # Init the --plugin.
+   # ########################################################################   
+
+   # --plugin hook
+   if ( $plugin && $plugin->can('init') ) {
+      $plugin->init(
+         orig_tbl       => $orig_tbl,
+         child_tables   => $child_tables,
+         renamed_cols   => $renamed_cols,
+         slaves         => $slaves,
+         slave_lag_cxns => $slave_lag_cxns,
+      );
+   }
+
    # #####################################################################
    # Step 1: Create the new table.
    # #####################################################################
+
+   # --plugin hook
+   if ( $plugin && $plugin->can('before_create_new_table') ) {
+      $plugin->before_create_new_table();
+   }
+
    my $new_tbl;
    eval {
       $new_tbl = create_new_table(
@@ -8564,10 +8262,25 @@
                       );
    }
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('after_create_new_table') ) {
+      $plugin->after_create_new_table(
+         new_tbl => $new_tbl,
+      );
+   }
+
    # #####################################################################
    # Step 2: Alter the new, empty table.  This should be very quick,
    # or die if the user specified a bad alter statement.
    # #####################################################################
+
+   # --plugin hook
+   if ( $plugin && $plugin->can('before_alter_new_table') ) {
+      $plugin->before_alter_new_table(
+         new_tbl => $new_tbl,
+      );
+   }
+
    if ( my $alter = $o->get('alter') ) {
       print "Altering new table...\n";
       my $sql = "ALTER TABLE $new_tbl->{name} $alter";
@@ -8679,22 +8392,43 @@
          'columns', @$del_cols);
    }
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('after_alter_new_table') ) {
+      $plugin->after_alter_new_table(
+         new_tbl => $new_tbl,
+         del_tbl => $del_tbl,
+      );
+   }
+
    # ########################################################################
    # Step 3: Create the triggers to capture changes on the original table and
    # apply them to the new table.
    # ########################################################################
 
+   my $retry = new Retry();
+
    # Drop the triggers.  We can save this cleanup task before
    # adding the triggers because if adding them fails, this will be
    # called which will drop whichever triggers were created.
    push @cleanup_tasks, sub {
       PTDEBUG && _d('Clean up triggers');
+      # --plugin hook
+      if ( $plugin && $plugin->can('before_drop_triggers') ) {
+         $plugin->before_drop_triggers(
+            oktorun           => $oktorun,
+            drop_trigger_sqls => \@drop_trigger_sqls,
+         );
+      }
+
       if ( $oktorun ) {
          drop_triggers(
             tbl          => $orig_tbl,
             Cxn          => $cxn,
             Quoter       => $q,
             OptionParser => $o,
+            Retry        => $retry,
+            retries      => $o->get('retries'),
+            stats        => \%stats,
          );
       }
       else {
@@ -8704,6 +8438,11 @@
       }
    };
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('before_create_triggers') ) {
+      $plugin->before_create_triggers();
+   }
+
    my @trigger_names = eval {
       create_triggers(
          orig_tbl     => $orig_tbl,
@@ -8713,12 +8452,20 @@
          Cxn          => $cxn,
          Quoter       => $q,
          OptionParser => $o,
+         Retry        => $retry,
+         retries      => $o->get('retries'),
+         stats        => \%stats,
       );
    };
    if ( $EVAL_ERROR ) {
       die "Error creating triggers: $EVAL_ERROR\n";
    };
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('after_create_triggers') ) {
+      $plugin->after_create_triggers();
+   }
+
    # #####################################################################
    # Step 4: Copy rows.
    # #####################################################################
@@ -8730,7 +8477,6 @@
    my $total_rows = 0;
    my $total_time = 0;
    my $avg_rate   = 0;  # rows/second
-   my $retry      = new Retry();  # for retrying to exec the copy statement
    my $limit      = $o->get('chunk-size-limit');  # brevity
    my $chunk_time = $o->get('chunk-time');        # brevity
 
@@ -8850,7 +8596,7 @@
          my $expl = explain_statement(
             tbl  => $tbl,
             sth  => $sth->{explain_upper_boundary},
-            vals => [ @{$boundary->{lower}}, $nibble_iter->chunk_size() ],
+            vals => [ @{$boundary->{lower}}, $nibble_iter->limit() ],
          );
          if (lc($expl->{key} || '') ne lc($nibble_iter->nibble_index() || '')) {
             my $msg
@@ -8865,7 +8611,7 @@
                . $sth->{upper_boundary}->{Statement}
                . " with values "
                . join(", ", map { defined $_ ? $_ : "NULL" }
-                      (@{$boundary->{lower}}, $nibble_iter->chunk_size()))
+                      (@{$boundary->{lower}}, $nibble_iter->limit()))
                . "\n";
             die $msg;
          } 
@@ -8896,10 +8642,10 @@
          # Exec and time the chunk checksum query.
          $tbl->{nibble_time} = exec_nibble(
             %args,
-            Retry        => $retry,
-            Quoter       => $q,
-            OptionParser => $o,
-            stats        => \%stats,
+            retries => $o->get('retries'),
+            Retry   => $retry,
+            Quoter  => $q,
+            stats   => \%stats,
          );
          PTDEBUG && _d('Nibble time:', $tbl->{nibble_time});
 
@@ -9031,6 +8777,11 @@
       );
    }
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('before_copy_rows') ) {
+      $plugin->before_copy_rows();
+   }
+
    # Start copying rows.  This may take awhile, but --progress is on
    # by default so there will be progress updates to stderr.
    eval {
@@ -9071,6 +8822,11 @@
       }
    }
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('after_copy_rows') ) {
+      $plugin->after_copy_rows();
+   }
+
    # #####################################################################
    # XXX
    # Step 5: Rename tables: orig -> old, new -> orig
@@ -9079,6 +8835,12 @@
    # state the tables are left in.
    # XXX
    # #####################################################################
+
+   # --plugin hook
+   if ( $plugin && $plugin->can('before_swap_tables') ) {
+      $plugin->before_swap_tables();
+   }
+
    my $old_tbl;
    if ( $o->get('swap-tables') ) {
       eval {
@@ -9089,22 +8851,38 @@
             Cxn          => $cxn,
             Quoter       => $q,
             OptionParser => $o,
+            Retry        => $retry,
+            retries      => $o->get('retries'),
+            stats        => \%stats,
          );
       };
       if ( $EVAL_ERROR ) {
-         die "Error swapping the tables: $EVAL_ERROR\n"
-           . "Verify that the original table $orig_tbl->{name} has not "
-           . "been modified or renamed to the old table $old_tbl->{name}.  "
-           . "Then drop the new table $new_tbl->{name} if it exists.\n";
+         # TODO: one of these values can be undefined
+         die "Error swapping tables: $EVAL_ERROR\n"
+           . "To clean up, first verify that the original table "
+           . "$orig_tbl->{name} has not been modified or renamed, "
+           . "then drop the new table $new_tbl->{name} if it exists.\n";
       }
    }
    $orig_tbl->{swapped} = 1;  # flag for cleanup tasks
    PTDEBUG && _d('Old table:', Dumper($old_tbl));
 
+   # --plugin hook
+   if ( $plugin && $plugin->can('after_swap_tables') ) {
+      $plugin->after_swap_tables(
+         old_tbl => $old_tbl,
+      );
+   }
+
    # #####################################################################
    # Step 6: Update foreign key constraints if there are child tables.
    # #####################################################################
    if ( $child_tables ) {
+      # --plugin hook
+      if ( $plugin && $plugin->can('before_update_foreign_keys') ) {
+         $plugin->before_update_foreign_keys();
+      }
+
       eval {
          if ( $alter_fk_method eq 'none' ) {
             # This shouldn't happen, but in case it does we should know.
@@ -9121,6 +8899,8 @@
                Cxn          => $cxn,
                TableParser  => $tp,
                stats        => \%stats,
+               Retry        => $retry,
+               retries      => $o->get('retries'),
             );
          }
          elsif ( $alter_fk_method eq 'drop_swap' ) {
@@ -9129,6 +8909,9 @@
                new_tbl      => $new_tbl,
                Cxn          => $cxn,
                OptionParser => $o,
+               stats        => \%stats,
+               Retry        => $retry,
+               retries      => $o->get('retries'),
             );
          }
          elsif ( !$alter_fk_method
@@ -9147,6 +8930,11 @@
          # TODO: improve error message and handling.
          die "Error updating foreign key constraints: $EVAL_ERROR\n";
       }
+
+      # --plugin hook
+      if ( $plugin && $plugin->can('after_update_foreign_keys') ) {
+         $plugin->after_update_foreign_keys();
+      }
    }
 
    # ########################################################################
@@ -9160,6 +8948,11 @@
          print "Not dropping old table because --no-swap-tables was specified.\n";
       }
       else {
+         # --plugin hook
+         if ( $plugin && $plugin->can('before_drop_old_table') ) {
+            $plugin->before_drop_old_table();
+         }
+
          print "Dropping old table...\n";
 
          if ( $alter_fk_method eq 'none' ) {
@@ -9182,32 +8975,25 @@
             die "Error dropping the old table: $EVAL_ERROR\n";
          }
          print "Dropped old table $old_tbl->{name} OK.\n";
+
+         # --plugin hook
+         if ( $plugin && $plugin->can('after_drop_old_table') ) {
+            $plugin->after_drop_old_table();
+         }
       }
    }
-   
+
    # ########################################################################
    # Done.
    # ########################################################################
    $orig_tbl->{success} = 1;  # flag for cleanup tasks
    $cleanup = undef;          # exec cleanup tasks
 
-   if ( $o->get('statistics') ) {
-      my $report = new ReportFormatter(
-         line_width => 74,
-      );
-      $report->set_columns(
-         { name => 'Event',                    },
-         { name => 'Count', right_justify => 1 },
-      );
-
-      foreach my $event ( sort keys %stats ) {
-         $report->add_line(
-            $event,
-            $stats{$event},
-         );
-      }
-
-      print $report->get_report();
+   # --plugin hook
+   if ( $plugin && $plugin->can('before_exit') ) {
+      $plugin->before_exit(
+         exit_status => $exit_status,
+      );
    }
 
    return $exit_status;
@@ -9424,7 +9210,7 @@
    return 1; # safe
 }
 
-sub create_new_table{
+sub create_new_table {
    my (%args) = @_;
    my @required_args = qw(orig_tbl Cxn Quoter OptionParser TableParser);
    foreach my $arg ( @required_args ) {
@@ -9514,15 +9300,16 @@
 
 sub swap_tables {
    my (%args) = @_;
-   my @required_args = qw(orig_tbl new_tbl Cxn Quoter OptionParser);
+   my @required_args = qw(orig_tbl new_tbl Cxn Quoter OptionParser Retry retries stats);
    foreach my $arg ( @required_args ) {
       die "I need a $arg argument" unless $args{$arg};
    }
-   my ($orig_tbl, $new_tbl, $cxn, $q, $o) = @args{@required_args};
+   my ($orig_tbl, $new_tbl, $cxn, $q, $o, $retry, $retries, $stats) = @args{@required_args};
 
-   my $prefix     = '_';
-   my $table_name = $orig_tbl->{tbl} . ($args{suffix} || '');
-   my $tries      = 10;  # don't try forever
+   my $prefix       = '_';
+   my $table_name   = $orig_tbl->{tbl} . ($args{suffix} || '');
+   my $tries        = 10;  # don't try forever
+   my $table_exists = qr/table.+?already exists/i;
 
    # This sub only works for --execute.  Since the options are
    # mutually exclusive and we return in the if case, the elsif
@@ -9538,10 +9325,10 @@
    }
    elsif ( $o->get('execute') ) {
       print "Swapping tables...\n";
-      
+
       while ( $tries-- ) {
          $table_name = $prefix . $table_name;
-         
+
          if ( length($table_name) > 64 ) {
             my $truncated_table_name = substr($table_name, 0, 64);
             PTDEBUG && _d($table_name, 'is over 64 characters long, truncating to',
@@ -9552,22 +9339,36 @@
          my $sql     = "RENAME TABLE $orig_tbl->{name} "
                      . "TO " . $q->quote($orig_tbl->{db}, $table_name)
                      . ", $new_tbl->{name} TO $orig_tbl->{name}"; 
-         PTDEBUG && _d($sql); 
+
          eval {
-            $cxn->dbh()->do($sql);
+            osc_retry(
+               Cxn     => $cxn,
+               Retry   => $retry,
+               retries => $retries,
+               stats   => $stats,
+               code    => sub {
+                  PTDEBUG && _d($sql);
+                  $cxn->dbh()->do($sql);
+               },
+               ignore_errors => [
+                  # Ignore this error because if multiple instances of the tool
+                  # are running, or previous runs failed and weren't cleaned up,
+                  # then there will be other similarly named tables with fewer
+                  # leading prefix chars.  Or, in rare cases, the db happens
+                  # to have a similarly named table created by the user for
+                  # other purposes.
+                  $table_exists,
+               ],
+            );
          };
-         if ( $EVAL_ERROR ) {
-            # Ignore this error because if multiple instances of the tool
-            # are running, or previous runs failed and weren't cleaned up,
-            # then there will be other similarly named tables with fewer
-            # leading prefix chars.  Or, in rarer cases, the db just happens
-            # to have a similarly named table created by the user for other
-            # purposes.
-            next if $EVAL_ERROR =~ m/table.+?already exists/i;
-
-            # Some other error happened.  Let caller catch it.
-            die $EVAL_ERROR;
+         if ( my $e = $EVAL_ERROR ) {
+            if ( $e =~ $table_exists ) {
+               PTDEBUG && _d($e);
+               next;
+            }
+            die $e;
          }
+
          print $sql, "\n" if $o->get('print');
          print "Swapped original and new tables OK.\n";
          return { # success
@@ -9728,11 +9529,12 @@
 sub rebuild_constraints {
    my ( %args ) = @_;
    my @required_args = qw(orig_tbl old_tbl child_tables stats
-                          Cxn Quoter OptionParser TableParser);
+                          Cxn Quoter OptionParser TableParser
+                          Retry retries);
    foreach my $arg ( @required_args ) {
       die "I need a $arg argument" unless $args{$arg};
    }
-   my ($orig_tbl, $old_tbl, $child_tables, $stats, $cxn, $q, $o, $tp)
+   my ($orig_tbl, $old_tbl, $child_tables, $stats, $cxn, $q, $o, $tp, $retry, $retries)
       = @args{@required_args};
 
    # MySQL has a "feature" where if the parent tbl is in the same db,
@@ -9807,9 +9609,17 @@
               . join(', ', @rebuilt_constraints);
       print $sql, "\n" if $o->get('print');
       if ( $o->get('execute') ) {
-         PTDEBUG && _d($sql);
-         $cxn->dbh()->do($sql);
-         $stats->{rebuilt_constraint}++;
+         osc_retry(
+            Cxn     => $cxn,
+            Retry   => $retry,
+            retries => $retries,
+            stats   => $stats,
+            code    => sub {
+               PTDEBUG && _d($sql);
+               $cxn->dbh()->do($sql);
+               $stats->{rebuilt_constraint}++;
+            },
+         );
       }
    }
 
@@ -9822,11 +9632,11 @@
 
 sub drop_swap {
    my ( %args ) = @_;
-   my @required_args = qw(orig_tbl new_tbl Cxn OptionParser);
+   my @required_args = qw(orig_tbl new_tbl Cxn OptionParser stats Retry retries);
    foreach my $arg ( @required_args ) {
       die "I need a $arg argument" unless $args{$arg};
    }
-   my ($orig_tbl, $new_tbl, $cxn, $o) = @args{@required_args};
+   my ($orig_tbl, $new_tbl, $cxn, $o, $stats, $retry, $retries) = @args{@required_args};
 
    if ( $o->get('dry-run') ) {
       print "Not drop-swapping tables because this is a dry run.\n";
@@ -9843,8 +9653,19 @@
 
    foreach my $sql ( @sqls ) {
       PTDEBUG && _d($sql);
-      print $sql, "\n"      if $o->get('print');
-      $cxn->dbh()->do($sql) if $o->get('execute');
+      print $sql, "\n" if $o->get('print');
+      if ( $o->get('execute') ) {
+         osc_retry(
+            Cxn     => $cxn,
+            Retry   => $retry,
+            retries => $retries,
+            stats   => $stats,
+            code    => sub {
+               PTDEBUG && _d($sql);
+               $cxn->dbh()->do($sql);
+            },
+         );
+      }
    }
 
    if ( $o->get('execute') ) {
@@ -9856,11 +9677,11 @@
 
 sub create_triggers {
    my ( %args ) = @_;
-   my @required_args = qw(orig_tbl new_tbl del_tbl columns Cxn Quoter OptionParser);
+   my @required_args = qw(orig_tbl new_tbl del_tbl columns Cxn Quoter OptionParser Retry retries stats);
    foreach my $arg ( @required_args ) {
       die "I need a $arg argument" unless $args{$arg};
    }
-   my ($orig_tbl, $new_tbl, $del_tbl, $cols, $cxn, $q, $o) = @args{@required_args};
+   my ($orig_tbl, $new_tbl, $del_tbl, $cols, $cxn, $q, $o, $retry, $retries, $stats) = @args{@required_args};
 
    # This sub works for --dry-run and --execute.  With --dry-run it's
    # only interesting if --print is specified, too; then the user can
@@ -9928,9 +9749,16 @@
       my ($name, $sql) = @$trg;
       print $sql, "\n" if $o->get('print');
       if ( $o->get('execute') ) {
-         # Let caller catch errors.
-         PTDEBUG && _d($sql);
-         $cxn->dbh()->do($sql);
+         osc_retry(
+            Cxn     => $cxn,
+            Retry   => $retry,
+            retries => $retries,
+            stats   => $stats,
+            code    => sub {
+               PTDEBUG && _d($sql);
+               $cxn->dbh()->do($sql);
+            },
+         );
       }
       # Only save the trigger once it has been created
       # (or faked to be created) so if the 2nd trigger
@@ -9950,11 +9778,11 @@
 
 sub drop_triggers {
    my ( %args ) = @_;
-   my @required_args = qw(tbl Cxn Quoter OptionParser);
+   my @required_args = qw(tbl Cxn Quoter OptionParser Retry retries stats);
    foreach my $arg ( @required_args ) {
       die "I need a $arg argument" unless $args{$arg};
    }
-   my ($tbl, $cxn, $q, $o) = @args{@required_args};
+   my ($tbl, $cxn, $q, $o, $retry, $retries, $stats) = @args{@required_args};
 
    # This sub works for --dry-run and --execute, although --dry-run is
    # only interesting with --print so the user can see the drop trigger
@@ -9970,9 +9798,17 @@
    foreach my $sql ( @drop_trigger_sqls ) {
       print $sql, "\n" if $o->get('print');
       if ( $o->get('execute') ) {
-         PTDEBUG && _d($sql);
          eval {
-            $cxn->dbh()->do($sql);
+            osc_retry(
+               Cxn     => $cxn,
+               Retry   => $retry,
+               retries => $retries,
+               stats   => $stats,
+               code    => sub {
+                  PTDEBUG && _d($sql);
+                  $cxn->dbh()->do($sql);
+               },
+            );
          };
          if ( $EVAL_ERROR ) {
             warn "Error dropping trigger: $EVAL_ERROR\n";
@@ -9995,15 +9831,93 @@
    return;
 }
 
+sub error_event {
+   my ($error) = @_;
+   return 'undefined_error' unless $error;
+   my $event
+      = $error =~ m/Lock wait timeout/         ? 'lock_wait_timeout'
+      : $error =~ m/Deadlock found/            ? 'deadlock'
+      : $error =~ m/execution was interrupted/ ? 'query_killed'
+      : $error =~ m/server has gone away/      ? 'lost_connection'
+      : $error =~ m/Lost connection/           ? 'connection_killed'
+      :                                          'unknown_error';
+   return $event;
+}
+
+sub osc_retry {
+   my (%args) = @_;
+   my @required_args = qw(Cxn Retry retries code stats);
+   foreach my $arg ( @required_args ) {
+      die "I need a $arg argument" unless $args{$arg};
+   }
+   my $cxn           = $args{Cxn};
+   my $retry         = $args{Retry};
+   my $retries       = $args{retries};
+   my $code          = $args{code};
+   my $stats         = $args{stats};
+   my $ignore_errors = $args{ignore_errors};
+
+   return $retry->retry(
+      tries => $retries,
+      wait  => sub { sleep 0.25; return; },
+      try   => $code,
+      fail => sub {
+         my (%args) = @_;
+         my $error = $args{error};
+         PTDEBUG && _d('Retry fail:', $error);
+
+         if ( $ignore_errors ) {
+            return 0 if grep { $error =~ $_ } @$ignore_errors;
+         }
+
+         # The query failed/caused an error.  If the error is one of these,
+         # then we can possibly retry.
+         if (   $error =~ m/Lock wait timeout exceeded/
+             || $error =~ m/Deadlock found/
+             || $error =~ m/Query execution was interrupted/
+         ) {
+            # These errors/warnings can be retried, so don't print
+            # a warning yet; do that in final_fail.
+            $stats->{ error_event($error) }++;
+            return 1;  # try again
+         }
+         elsif (   $error =~ m/MySQL server has gone away/
+                || $error =~ m/Lost connection to MySQL server/
+         ) {
+            # The 1st pattern means that MySQL itself died or was stopped.
+            # The 2nd pattern means that our cxn was killed (KILL <id>).
+            $stats->{ error_event($error) }++;
+            $cxn->connect();  # connect or die trying
+            return 1;  # reconnected, try again
+         }
+
+         $stats->{retry_fail}++;
+
+         # At this point, either the error/warning cannot be retried,
+         # or we failed to reconnect.  Don't retry; call final_fail.
+         return 0;
+      },
+      final_fail => sub {
+         my (%args) = @_;
+         my $error = $args{error};
+         # This die should be caught by the caller.  Copying rows and
+         # the tool will stop, which is probably good because by this
+         # point the error or warning indicates that something is wrong.
+         $stats->{ error_event($error) }++;
+         die $error;
+      }
+   );
+}
+
 sub exec_nibble {
    my (%args) = @_;
-   my @required_args = qw(Cxn tbl stats NibbleIterator Retry Quoter OptionParser);
+   my @required_args = qw(Cxn tbl stats retries Retry NibbleIterator Quoter);
    foreach my $arg ( @required_args ) {
       die "I need a $arg argument" unless $args{$arg};
    }
-   my ($cxn, $tbl, $stats, $nibble_iter, $retry, $q, $o)= @args{@required_args};
+   my ($cxn, $tbl, $stats, $retries, $retry, $nibble_iter, $q)
+      = @args{@required_args};
 
-   my $dbh         = $cxn->dbh();
    my $sth         = $nibble_iter->statements();
    my $boundary    = $nibble_iter->boundaries();
    my $lb_quoted   = $q->serialize_list(@{$boundary->{lower}});
@@ -10035,10 +9949,12 @@
       },
    );
 
-   return $retry->retry(
-      tries => $o->get('retries'),
-      wait  => sub { sleep 0.25; return; },
-      try   => sub {
+   return osc_retry(
+      Cxn     => $cxn,
+      Retry   => $retry,
+      retries => $retries,
+      stats   => $stats,
+      code    => sub {
          # ###################################################################
          # Start timing the query.
          # ###################################################################
@@ -10067,7 +9983,7 @@
          # Check if query caused any warnings.
          my $sql_warn = 'SHOW WARNINGS';
          PTDEBUG && _d($sql_warn);
-         my $warnings = $dbh->selectall_arrayref($sql_warn, { Slice => {} } );
+         my $warnings = $cxn->dbh->selectall_arrayref($sql_warn, {Slice => {}});
          foreach my $warning ( @$warnings ) {
             my $code    = ($warning->{code} || 0);
             my $message = $warning->{message};
@@ -10087,7 +10003,7 @@
                         ? $warn_code{$code}->{message}
                         : $message)
                      . "\nThis MySQL error is being ignored ";
-                  if ( $o->get('statistics') ) {
+                  if ( get('statistics') ) {
                      $err .= "but further occurrences will be reported "
                            . "by --statistics when the tool finishes.\n";
                   }
@@ -10114,54 +10030,6 @@
          # Success: no warnings, no errors.  Return nibble time.
          return $t_end - $t_start;
       },
-      fail => sub {
-         my (%args) = @_;
-         my $error = $args{error};
-         PTDEBUG && _d('Retry fail:', $error);
-
-         # The query failed/caused an error.  If the error is one of these,
-         # then we can possibly retry.
-         if (   $error =~ m/Lock wait timeout exceeded/
-             || $error =~ m/Deadlock found/
-             || $error =~ m/Query execution was interrupted/
-         ) {
-            # These errors/warnings can be retried, so don't print
-            # a warning yet; do that in final_fail.
-            my $event
-               = $error =~ m/Lock wait timeout/         ? 'lock_wait_timeout'
-               : $error =~ m/Deadlock found/            ? 'deadlock'
-               : $error =~ m/execution was interrupted/ ? 'query_killed'
-               :                                          'unknown1';
-            $stats->{$event}++;
-            return 1;  # try again
-         }
-         elsif (   $error =~ m/MySQL server has gone away/
-                || $error =~ m/Lost connection to MySQL server/
-         ) {
-            # The 1st pattern means that MySQL itself died or was stopped.
-            # The 2nd pattern means that our cxn was killed (KILL <id>).
-            my $event
-               = $error =~ m/server has gone away/ ? 'lost_connection'
-               : $error =~ m/Lost connection/      ? 'connection_killed'
-               :                                     'unknown2';
-            $stats->{$event}++;
-            $dbh = $cxn->connect();  # connect or die trying
-            return 1;  # reconnected, try again
-         }
-
-         $stats->{retry_fail}++;
-
-         # At this point, either the error/warning cannot be retried,
-         # or we failed to reconnect.  Don't retry; call final_fail.
-         return 0;
-      },
-      final_fail => sub {
-         my (%args) = @_;
-         # This die should be caught by the caller.  Copying rows and
-         # the tool will stop, which is probably good because by this
-         # point the error or warning indicates that something is wrong.
-         die $args{error};
-      }
    );
 }
 
@@ -10249,23 +10117,21 @@
 
 =head1 RISKS
 
-The following section is included to inform users about the potential risks,
-whether known or unknown, of using this tool.  The two main categories of risks
-are those created by the nature of the tool (e.g. read-only tools vs. read-write
-tools) and those created by bugs.
-
-pt-online-schema-change modifies data and structures. You should be careful with
-it, and test it before using it in production.  You should also ensure that you
-have recoverable backups before using this tool.
-
-At the time of this release, we know of no bugs that could cause harm to users.
-
-The authoritative source for updated information is always the online issue
-tracking system.  Issues that affect this tool will be marked as such.  You can
-see a list of such issues at the following URL:
-L<http://www.percona.com/bugs/pt-online-schema-change>.
-
-See also L<"BUGS"> for more information on filing bugs and getting help.
+Percona Toolkit is mature, proven in the real world, and well tested,
+but all database tools can pose a risk to the system and the database
+server.  Before using this tool, please:
+
+=over
+
+=item * Read the tool's documentation
+
+=item * Review the tool's known L<"BUGS">
+
+=item * Test the tool on a non-production server
+
+=item * Backup your production server and verify the backups
+
+=back
 
 =head1 DESCRIPTION
 
@@ -10329,9 +10195,10 @@
 
 =item *
 
-The tool sets its lock wait timeout to 1 second so that it is more likely to be
-the victim of any lock contention, and less likely to disrupt other
-transactions. See L<"--lock-wait-timeout"> for details.
+The tool sets C<innodb_lock_wait_timeout=1> and (for MySQL 5.5 and newer)
+C<lock_wait_timeout=60> so that it is more likely to be the victim of any
+lock contention, and less likely to disrupt other transactions.  These
+values can be changed by specifying L<"--set-vars">.
 
 =item *
 
@@ -10409,7 +10276,7 @@
 C<DROP FOREIGN KEY constraint_name> requires specifying C<_constraint_name>
 rather than the real C<constraint_name>.  Due to a limitation in MySQL,
 pt-online-schema-change adds a leading underscore to foreign key constraint
-names when creating the new table.  For example, to drop this contraint:
+names when creating the new table.  For example, to drop this constraint:
 
   CONSTRAINT `fk_foo` FOREIGN KEY (`foo_id`) REFERENCES `bar` (`foo_id`)
 
@@ -10798,18 +10665,6 @@
 
 Connect to host.
 
-=item --lock-wait-timeout
-
-type: int; default: 1
-
-Set the session value of C<innodb_lock_wait_timeout>.  This option helps guard
-against long lock waits if the data-copy queries become slow for some reason.
-Setting this option dynamically requires the InnoDB plugin, so this works only
-on newer InnoDB and MySQL versions.  If the setting's current value is greater
-than the specified value, and the tool cannot set the value as desired, then it
-prints a warning. If the tool cannot set the value but the current value is less
-than or equal to the desired value, there is no error.
-
 =item --max-lag
 
 type: time; default: 1s
@@ -10874,6 +10729,18 @@
 tool will overwrite the PID file with the current PID.  The PID file is
 removed automatically when the tool exits.
 
+=item --plugin
+
+type: string
+
+Perl module file that defines a C<pt_online_schema_change_plugin> class.
+A plugin allows you to write a Perl module that can hook into many parts
+of pt-online-schema-change.  This requires a good knowledge of Perl and
+Percona Toolkit conventions, which are beyond this scope of this
+documentation.  Please contact Percona if you have questions or need help.
+
+See L<"PLUGIN"> for more information.
+
 =item --port
 
 short form: -P; type: int
@@ -10949,18 +10816,64 @@
 
 =item --retries
 
-type: int; default: 3
-
-Retry a chunk this many times when there is a nonfatal error.  Nonfatal errors
-are problems such as a lock wait timeout or the query being killed. This option
-applies to the data copy operation.
+type: int; default: 10
+
+Retry critical operations and recover from non-fatal errors.  The tool
+retries these operations:
+
+   Creating triggers
+   Dropping triggers
+   Copying chunks
+   Swapping tables
+   Rebuilding foreign key constraints
+
+For creating and dropping triggers, the number of retries applies to each
+C<CREATE TRIGGER> and C<DROP TRIGGER> statement for each trigger.
+For copying chunks, the number of retries applies to each chunk, not the
+entire table.  For swapping tables, the number of retries usually applies
+once because there is usually only one C<RENAME TABLE> statement.
+For rebuilding foreign key constraints, the number of retries applies to
+each statement (C<ALTER> statements for the C<rebuild_constraints>
+L<"--alter-foreign-keys-method">; other statements for the C<drop_swap>
+method).
+
+The tool retries each operation if these errors occur:
+
+   Lock wait timeout (innodb_lock_wait_timeout and lock_wait_timeout)
+   Deadlock found
+   Query is killed (KILL QUERY <thread_id>)
+   Connection is killed (KILL CONNECTION <thread_id>)
+   Lost connection to MySQL
+
+In the case of lost and killed connections, the tool will automatically
+reconnect.
+
+To alter extremely busy tables, it may be necessary to increase L<"--retries">,
+and also C<innodb_lock_wait_timeout> and (for MySQL 5.5 and newer)
+C<lock_wait_timeout> by specifying higher values with L<"--set-vars">.
+
+Failures and retries are recorded in the L<"--statistics">.
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+   innodb_lock_wait_timeout=1
+   lock_wait_timeout=60
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the default
+value of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 
@@ -11014,6 +10927,52 @@
 
 =back
 
+=head1 PLUGIN
+
+The file specified by L<"--plugin"> must define a class (i.e. a package)
+called C<pt_online_schema_change_plugin> with a C<new()> subroutine.
+The tool will create an instance of this class and call any hooks that
+it defines.  No hooks are required, but a plugin isn't very useful without
+them.
+
+These hooks, in this order, are called if defined:
+
+   init
+   before_create_new_table
+   after_create_new_table
+   before_alter_new_table
+   after_alter_new_table
+   before_create_triggers
+   after_create_triggers
+   before_copy_rows
+   after_copy_rows
+   before_swap_tables
+   after_swap_tables
+   before_update_foreign_keys
+   after_update_foreign_keys
+   before_drop_old_table
+   after_drop_old_table
+   before_drop_triggers
+   before_exit
+
+Each hook is passed different arguments.  To see which arguments are passed
+to a hook, search for the hook's name in the tool's source code, like:
+
+   # --plugin hook
+   if ( $plugin && $plugin->can('init') ) {
+      $plugin->init(
+         orig_tbl       => $orig_tbl,
+         child_tables   => $child_tables,
+         renamed_cols   => $renamed_cols,
+         slaves         => $slaves,
+         slave_lag_cxns => $slave_lag_cxns,
+      );
+   }
+
+The comment C<# --plugin hook> precedes every hook call.
+
+Please contact Percona if you have questions or need help.
+
 =head1 DSN OPTIONS
 
 These DSN options are used to create a DSN.  Each option is given like

=== modified file 'bin/pt-query-advisor'
--- bin/pt-query-advisor	2013-02-27 00:01:17 +0000
+++ bin/pt-query-advisor	2013-03-04 18:10:28 +0000
@@ -969,7 +969,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -984,13 +984,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -1065,6 +1060,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1097,6 +1143,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2080,6 +2127,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -8078,7 +8164,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    my $review_dsn = $o->get('review');
    my $groupby    = lc $o->get('group-by');
@@ -9150,10 +9236,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --[no]show-create-table
 

=== modified file 'bin/pt-query-digest'
--- bin/pt-query-digest	2013-02-28 02:23:08 +0000
+++ bin/pt-query-digest	2013-03-04 18:10:28 +0000
@@ -981,7 +981,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -996,13 +996,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -1077,6 +1072,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1260,6 +1306,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2243,6 +2290,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -12394,7 +12480,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    # Frequently used options.
    my $review_dsn = $o->get('review'); 
@@ -15408,10 +15494,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this
-string will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --shorten
 

=== modified file 'bin/pt-show-grants'
--- bin/pt-show-grants	2013-02-27 00:01:17 +0000
+++ bin/pt-show-grants	2013-03-04 18:10:28 +0000
@@ -37,6 +37,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1020,6 +1021,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1311,7 +1351,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -1326,13 +1366,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -1407,6 +1442,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1654,7 +1740,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    $o->usage_or_errors();
 
@@ -2119,10 +2205,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this
-string will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-slave-delay'
--- bin/pt-slave-delay	2013-02-27 00:01:17 +0000
+++ bin/pt-slave-delay	2013-03-04 18:10:28 +0000
@@ -65,6 +65,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1048,6 +1049,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1983,7 +2023,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -1998,13 +2038,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2079,6 +2114,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -3981,7 +4067,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    my $dsn_defaults = $dp->parse_options($o);
    my $slave_dsn  = @ARGV ? $dp->parse(shift @ARGV, $dsn_defaults)
@@ -4505,10 +4591,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-slave-find'
--- bin/pt-slave-find	2013-02-27 00:01:17 +0000
+++ bin/pt-slave-find	2013-03-04 18:10:28 +0000
@@ -45,6 +45,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1028,6 +1029,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1963,7 +2003,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -1978,13 +2018,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2059,6 +2094,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -3584,7 +3670,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    if ( $o->get('ask-pass') ) {
       $o->set('password', OptionParser::prompt_noecho("Enter password: "));
@@ -4047,10 +4133,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this
-string will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-slave-restart'
--- bin/pt-slave-restart	2013-02-27 00:01:17 +0000
+++ bin/pt-slave-restart	2013-03-04 18:10:28 +0000
@@ -217,6 +217,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1200,6 +1201,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2329,7 +2369,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2344,13 +2384,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2425,6 +2460,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -4636,7 +4722,7 @@
    $o->get_opts();
 
    $dp = $o->DSNParser(); 
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    $o->set('verbose', 0) if $o->get('quiet');
 
@@ -5386,10 +5472,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this string
-will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --skip-count
 

=== modified file 'bin/pt-table-checksum'
--- bin/pt-table-checksum	2013-02-28 02:23:08 +0000
+++ bin/pt-table-checksum	2013-03-04 18:10:28 +0000
@@ -1555,7 +1555,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -1570,13 +1570,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -1651,6 +1646,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -1683,6 +1729,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2666,6 +2713,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -6055,9 +6141,9 @@
    return $self->{one_nibble};
 }
 
-sub chunk_size {
+sub limit {
    my ($self) = @_;
-   return $self->{limit} + 1;
+   return $self->{limit};
 }
 
 sub set_chunk_size {
@@ -8613,7 +8699,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    # Add the --replicate table to --ignore-tables.
    my %ignore_tables = (
@@ -8754,43 +8840,7 @@
             . "level to REPEATABLE-READ.\n";
       }
 
-      # We set innodb_lock_wait_timeout=1 (the option's default value)
-      # so that if this tool happens to cause some locking, it will more
-      # likely be the victim than other connections and thus avoid disrupting
-      # the server.  The var is only dynamic with the InnoDB plugin, so
-      # if setting it fails we only warn if the server's value is greater
-      # than the desired value.  E.g. if user does --lock-wait-timeout 5
-      # and the set fails but the server's value is 1, then that's ok, but
-      # if the server's value is 10, then that's not ok.
-      my $lock_wait_timeout = $o->get('lock-wait-timeout');
-      my $set_lwt = "SET SESSION innodb_lock_wait_timeout=$lock_wait_timeout";
-      PTDEBUG && _d($dbh, $set_lwt);
-      eval {
-         $dbh->do($set_lwt);
-      };
-      if ( $EVAL_ERROR ) {
-         PTDEBUG && _d($EVAL_ERROR);
-         # Get the server's current value.
-         $sql = "SHOW SESSION VARIABLES LIKE 'innodb_lock_wait_timeout'";
-         PTDEBUG && _d($dbh, $sql);
-         my (undef, $curr_lwt) = $dbh->selectrow_array($sql);
-         PTDEBUG && _d('innodb_lock_wait_timeout on server:', $curr_lwt);
-         if ( !defined $curr_lwt ) {
-            PTDEBUG && _d('innodb_lock_wait_timeout does not exist;',
-               'InnoDB is probably disabled');
-         }
-         elsif ( $curr_lwt > $lock_wait_timeout ) { 
-            warn "Failed to $set_lwt: $EVAL_ERROR\n"
-               . "The current innodb_lock_wait_timeout value "
-               . "$curr_lwt is greater than the --lock-wait-timeout "
-               . "value $lock_wait_timeout and the variable cannot be "
-               . "changed.  innodb_lock_wait_timeout is only dynamic when "
-               . "using the InnoDB plugin.  To prevent this warning, either "
-               . "specify --lock-wait-time=$curr_lwt, or manually set "
-               . "innodb_lock_wait_timeout to a value less than or equal "
-               . "to $lock_wait_timeout and restart MySQL.\n";
-         }
-      }
+      return;
    };
 
    # Do not call "new Cxn(" directly; use this sub so that set_on_connect
@@ -9533,7 +9583,7 @@
          my $expl = explain_statement(
             tbl  => $tbl,
             sth  => $sth->{explain_upper_boundary},
-            vals => [ @{$boundary->{lower}}, $nibble_iter->chunk_size() ],
+            vals => [ @{$boundary->{lower}}, $nibble_iter->limit() ],
          );
          if (   lc($expl->{key} || '')
              ne lc($nibble_iter->nibble_index() || '') ) {
@@ -11553,18 +11603,6 @@
 
 Ignore tables whose names match the Perl regex.
 
-=item --lock-wait-timeout
-
-type: int; default: 1
-
-Set the session value of C<innodb_lock_wait_timeout> on the master host.
-This option helps guard against long lock waits if the checksum queries
-become slow for some reason.  Setting this option dynamically requires the
-InnoDB plugin, so this works only on newer InnoDB and MySQL versions.  If
-setting the value fails and the current server value is greater than the
-specified value, then a warning is printed; else, if the current server
-value is less than or equal to the specified value, no warning is printed.
-
 =item --max-lag
 
 type: time; default: 1s; group: Throttle
@@ -11824,10 +11862,22 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000; group: Connection
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this
-string will be appended to SET and executed.
+type: Array; group: Connection
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+   innodb_lock_wait_timeout=1
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-table-sync'
--- bin/pt-table-sync	2013-02-27 00:01:17 +0000
+++ bin/pt-table-sync	2013-03-04 18:10:28 +0000
@@ -80,6 +80,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1063,6 +1064,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -2149,7 +2189,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -2164,13 +2204,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -2245,6 +2280,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -9476,7 +9562,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    if ( $o->get('replicate') || $o->get('sync-to-master') ) {
       $o->set('wait', 60) unless $o->got('wait');
@@ -12137,10 +12223,21 @@
 
 =item --set-vars
 
-type: string; default: wait_timeout=10000
-
-Set these MySQL variables.  Immediately after connecting to MySQL, this
-string will be appended to SET and executed.
+type: Array
+
+Set the MySQL variables in this comma-separated list of C<variable=value> pairs.
+
+By default, the tool sets:
+
+=for comment ignore-pt-internal-value
+MAGIC_set_vars
+
+   wait_timeout=10000
+
+Variables specified on the command line override these defaults.  For
+example, specifying C<--set-vars wait_timeout=500> overrides the defaultvalue of C<10000>.
+
+The tool prints a warning and continues if a variable cannot be set.
 
 =item --socket
 

=== modified file 'bin/pt-table-usage'
--- bin/pt-table-usage	2013-02-28 02:23:08 +0000
+++ bin/pt-table-usage	2013-03-04 18:10:28 +0000
@@ -300,7 +300,7 @@
 
       if ( my ($charset) = $cxn_string =~ m/charset=([\w]+)/ ) {
          $sql = qq{/*!40101 SET NAMES "$charset"*/};
-         PTDEBUG && _d($dbh, ':', $sql);
+         PTDEBUG && _d($dbh, $sql);
          eval { $dbh->do($sql) };
          if ( $EVAL_ERROR ) {
             die "Error setting NAMES to $charset: $EVAL_ERROR";
@@ -315,13 +315,8 @@
          }
       }
 
-      if ( my $var = $self->prop('set-vars') ) {
-         $sql = "SET $var";
-         PTDEBUG && _d($dbh, ':', $sql);
-         eval { $dbh->do($sql) };
-         if ( $EVAL_ERROR ) {
-            die "Error setting $var: $EVAL_ERROR";
-         }
+      if ( my $vars = $self->prop('set-vars') ) {
+         $self->set_vars($dbh, $vars);
       }
 
       $sql = 'SET @@SQL_QUOTE_SHOW_CREATE = 1'
@@ -396,6 +391,57 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $vars) = @_;
+
+   return unless $vars;
+
+   foreach my $var ( sort keys %$vars ) {
+      my $val = $vars->{$var}->{val};
+
+      (my $quoted_var = $var) =~ s/_/\\_/;
+      my ($var_exists, $current_val);
+      eval {
+         ($var_exists, $current_val) = $dbh->selectrow_array(
+            "SHOW VARIABLES LIKE '$quoted_var'");
+      };
+      my $e = $EVAL_ERROR;
+      if ( $e ) {
+         PTDEBUG && _d($e);
+      }
+
+      if ( $vars->{$var}->{default} && !$var_exists ) {
+         PTDEBUG && _d('Not setting default var', $var,
+            'because it does not exist');
+         next;
+      }
+
+      if ( $current_val && $current_val eq $val ) {
+         PTDEBUG && _d('Not setting var', $var, 'because its value',
+            'is already', $val);
+         next;
+      }
+
+      my $sql = "SET SESSION $var=$val";
+      PTDEBUG && _d($dbh, $sql);
+      eval { $dbh->do($sql) };
+      if ( my $set_error = $EVAL_ERROR ) {
+         chomp($set_error);
+         $set_error =~ s/ at \S+ line \d+//;
+         my $msg = "Error setting $var: $set_error";
+         if ( $current_val ) {
+            $msg .= "  The current value for $var is $current_val.  "
+                  . "If the variable is read only (not dynamic), specify "
+                  . "--set-vars $var=$current_val to avoid this warning, "
+                  . "else manually set the variable and restart MySQL.";
+         }
+         warn $msg . "\n\n";
+      }
+   }
+
+   return; 
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -428,6 +474,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -449,7 +496,6 @@
       'default'    => 1,
       'cumulative' => 1,
       'negatable'  => 1,
-      'value_is_optional' => 1,
    );
 
    my $self = {
@@ -691,10 +737,9 @@
             $opt->{short} = undef;
          }
 
-         $opt->{is_negatable}   = $opt->{spec} =~ m/!/        ? 1 : 0;
-         $opt->{is_cumulative}  = $opt->{spec} =~ m/\+/       ? 1 : 0;
-         $opt->{optional_value} = $opt->{spec} =~ m/:/        ? 1 : 0;
-         $opt->{is_required}    = $opt->{desc} =~ m/required/ ? 1 : 0;
+         $opt->{is_negatable}  = $opt->{spec} =~ m/!/        ? 1 : 0;
+         $opt->{is_cumulative} = $opt->{spec} =~ m/\+/       ? 1 : 0;
+         $opt->{is_required}   = $opt->{desc} =~ m/required/ ? 1 : 0;
 
          $opt->{group} ||= 'default';
          $self->{groups}->{ $opt->{group} }->{$long} = 1;
@@ -830,7 +875,7 @@
    if ( $opt->{is_cumulative} ) {
       $opt->{value}++;
    }
-   elsif ( !($opt->{optional_value} && !$val) ) {
+   else {
       $opt->{value} = $val;
    }
    $opt->{got} = 1;
@@ -1210,7 +1255,7 @@
             $desc .= ".  Optional suffix s=seconds, m=minutes, h=hours, "
                    . "d=days; if no suffix, $s is used.";
          }
-         $desc = join("\n$rpad", grep { $_ } $desc =~ m/(.{0,$rcol})(?:\s+|$)/g);
+         $desc = join("\n$rpad", grep { $_ } $desc =~ m/(.{0,$rcol}(?!\W))(?:\s+|(?<=\W)|$)/g);
          $desc =~ s/ +$//mg;
          if ( $short ) {
             $usage .= sprintf("  --%-${maxs}s -%s  %s\n", $long, $short, $desc);
@@ -1371,12 +1416,11 @@
 sub _parse_attribs {
    my ( $self, $option, $attribs ) = @_;
    my $types = $self->{types};
-   my $eq    = $attribs->{'value_is_optional'} ? ':' : '=';
    return $option
       . ($attribs->{'short form'} ? '|' . $attribs->{'short form'}   : '' )
       . ($attribs->{'negatable'}  ? '!'                              : '' )
       . ($attribs->{'cumulative'} ? '+'                              : '' )
-      . ($attribs->{'type'}       ? $eq . $types->{$attribs->{type}} : '' );
+      . ($attribs->{'type'}       ? '=' . $types->{$attribs->{type}} : '' );
 }
 
 sub _parse_synopsis {
@@ -1414,6 +1458,45 @@
    );
 };
 
+sub set_vars {
+   my ($self, $file) = @_;
+   $file ||= $self->{file} || __FILE__;
+
+   my %user_vars;
+   my $user_vars = $self->has('set-vars') ? $self->get('set-vars') : undef;
+   if ( $user_vars ) {
+      foreach my $var_val ( @$user_vars ) {
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $user_vars{$var} = {
+            val     => $val,
+            default => 0,
+         };
+      }
+   }
+
+   my %default_vars;
+   my $default_vars = $self->read_para_after($file, qr/MAGIC_set_vars/);
+   if ( $default_vars ) {
+      %default_vars = map {
+         my $var_val = $_;
+         my ($var, $val) = $var_val =~ m/([^\s=]+)=(\S+)/;
+         die "Invalid --set-vars value: $var_val\n" unless $var && $val;
+         $var => {
+            val     => $val,
+            default => 1,
+         };
+      } split("\n", $default_vars);
+   }
+
+   my %vars = (
+      %default_vars, # first the tool's defaults
+      %user_vars,    # then the user's which overwrite the defaults
+   );
+   PTDEBUG && _d('--set-vars:', Dumper(\%vars));
+   return \%vars;
+}
+
 sub _d {
    my ($package, undef, $line) = caller 0;
    @_ = map { (my $temp = $_) =~ s/\n/\n# /g; $temp; }
@@ -6398,7 +6481,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());