Merge lp:~percona-toolkit-dev/percona-toolkit/enhanced-set-vars-for-bug-1113301 into lp:~percona-toolkit-dev/percona-toolkit/pt-osc-metadata-lock-bug-1113301

[Daniel Nichter]

This branch was branched from lp:~percona-toolkit-dev/percona-toolkit/pt-osc-metadata-lock-bug-1113301 to update all the other tools' --set-vars and remove --lock-wait-timeout from pt-table-checksum.

[lp:~percona-toolkit-dev/percona-toolkit/enhanced-set-vars-for-bug-1113301]

545. By Daniel Nichter on 2013-03-02

Fix tests to work with new --set-vars, and change --lock-wait-timeout to --set-vars innodb_lock_wait_timeout in tests.

546. By Daniel Nichter on 2013-03-02

Fix more tests for set-vars.

547. By Daniel Nichter on 2013-03-02

Don't set innodb_lock_wait_timeout in tests because it generates a warning on 5.0 and 5.1 that the tests don't suppress.

548. By Daniel Nichter on 2013-03-02

Pass file to OptionParser->new() in tests so OptionParser::get_vars() works.

549. By Daniel Nichter on 2013-03-02

Fix t/lib/Percona/XtraDB/Cluster-no-PXC.t.

550. By Daniel Nichter on 2013-03-03

Truly fix t[/pt-fifo-split/pt-fifo-split.t.

551. By Daniel Nichter on 2013-03-03

Fix error in t/lib/DSNParser.t.

552. By Daniel Nichter on 2013-03-03

Make t/lib/KeySize.t flexible because EXPLAIN plans differ slightly.

553. By Daniel Nichter on 2013-03-03

Skip t/pt-archiver/check_slave_lag.t on MySQL 5.6 because the trick doesn't work.

[Daniel Nichter (daniel-nichter)]

Tests are passing again.

review: Approve

=== modified file 'bin/pt-archiver'
--- bin/pt-archiver	2013-02-27 00:01:17 +0000
+++ bin/pt-archiver	2013-03-03 15:43:19 +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 +2528,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +5419,7 @@
    $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 +7178,22 @@
 
 =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	2013-03-03 15:43:19 +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 +2117,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +5068,7 @@
    $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 +5409,21 @@
 
 =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	2013-03-03 15:43:19 +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 +2461,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +4338,7 @@
    $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 +5200,21 @@
 
 =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	2013-03-03 15:43:19 +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 +966,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +1047,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1986,6 +2031,45 @@
    );
 };
 
+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 +4746,7 @@
    $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 +5228,21 @@
 
 =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	2013-03-03 15:43:19 +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 +400,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +481,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1420,6 +1465,45 @@
    );
 };
 
+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 +3803,7 @@
    $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 +4347,21 @@
 
 =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	2013-03-03 15:43:19 +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 +1618,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +3805,7 @@
    $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 +4211,21 @@
 
 =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	2013-03-03 15:43:19 +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 +2202,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +4725,7 @@
 
    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 +5821,21 @@
 
 =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	2013-03-03 15:43:19 +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 +410,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +642,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1581,6 +1626,45 @@
    );
 };
 
+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 +6196,7 @@
    $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 +7243,21 @@
 
 =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	2013-03-03 15:43:19 +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 +2121,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +6455,7 @@
    $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 +7467,21 @@
 
 =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-query-advisor'
--- bin/pt-query-advisor	2013-02-27 00:01:17 +0000
+++ bin/pt-query-advisor	2013-03-03 15:43:19 +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 +1060,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +1141,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2080,6 +2125,45 @@
    );
 };
 
+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 +8162,7 @@
    $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 +9234,21 @@
 
 =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	2013-03-03 15:43:19 +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 +1072,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +1304,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2243,6 +2288,45 @@
    );
 };
 
+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 +12478,7 @@
    $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 +15492,21 @@
 
 =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	2013-03-03 15:43:19 +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 +1442,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +1738,7 @@
    $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 +2203,21 @@
 
 =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	2013-03-03 15:43:19 +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 +2114,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +4065,7 @@
    $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 +4589,21 @@
 
 =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	2013-03-03 15:43:19 +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 +2094,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +3668,7 @@
    $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 +4131,21 @@
 
 =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	2013-03-03 15:43:19 +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 +2460,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +4720,7 @@
    $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 +5470,21 @@
 
 =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	2013-03-01 02:26:04 +0000
+++ bin/pt-table-checksum	2013-03-03 15:43:19 +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 +1646,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +1727,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2666,6 +2711,45 @@
    );
 };
 
+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; }
@@ -8613,7 +8697,7 @@
    $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 +8838,7 @@
             . "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
@@ -11553,18 +11601,6 @@
 
 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 +11860,22 @@
 
 =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	2013-03-03 15:43:19 +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 +2280,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +9560,7 @@
    $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 +12221,21 @@
 
 =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	2013-03-03 15:43:19 +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 +391,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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 +472,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -449,7 +494,6 @@
       'default'    => 1,
       'cumulative' => 1,
       'negatable'  => 1,
-      'value_is_optional' => 1,
    );
 
    my $self = {
@@ -691,10 +735,9 @@
             $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 +873,7 @@
    if ( $opt->{is_cumulative} ) {
       $opt->{value}++;
    }
-   elsif ( !($opt->{optional_value} && !$val) ) {
+   else {
       $opt->{value} = $val;
    }
    $opt->{got} = 1;
@@ -1210,7 +1253,7 @@
             $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 +1414,11 @@
 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 +1456,45 @@
    );
 };
 
+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 +6479,7 @@
    $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();
 
@@ -7245,10 +7326,21 @@
 
 =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-upgrade'
--- bin/pt-upgrade	2013-02-27 00:01:17 +0000
+++ bin/pt-upgrade	2013-03-03 15:43:19 +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 +1072,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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; }
@@ -1671,6 +1715,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -2654,6 +2699,45 @@
    );
 };
 
+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; }
@@ -12296,7 +12380,7 @@
    $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 ) {
@@ -13522,10 +13606,21 @@
 
 =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-variable-advisor'
--- bin/pt-variable-advisor	2013-02-27 00:01:17 +0000
+++ bin/pt-variable-advisor	2013-03-03 15:43:19 +0000
@@ -69,6 +69,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -1052,6 +1053,45 @@
    );
 };
 
+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; }
@@ -1987,7 +2027,7 @@
 
       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";
@@ -2002,13 +2042,8 @@
          }
       }
 
-      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'
@@ -2083,6 +2118,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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; }
@@ -4885,7 +4969,7 @@
    $o->get_opts();
 
    my $dp = $o->DSNParser();
-   $dp->prop('set-vars', $o->get('set-vars'));
+   $dp->prop('set-vars', $o->set_vars());
 
    my $vars_from         = $o->get('source-of-variables');
    # my $status_from       = lc $o->get('source-of-status');
@@ -5766,10 +5850,21 @@
 
 =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-visual-explain'
--- bin/pt-visual-explain	2013-02-27 00:01:17 +0000
+++ bin/pt-visual-explain	2013-03-03 15:43:19 +0000
@@ -711,6 +711,7 @@
 
 use List::Util qw(max);
 use Getopt::Long;
+use Data::Dumper;
 
 my $POD_link_re = '[LC]<"?([^">]+)"?>';
 
@@ -732,7 +733,6 @@
       'default'    => 1,
       'cumulative' => 1,
       'negatable'  => 1,
-      'value_is_optional' => 1,
    );
 
    my $self = {
@@ -974,10 +974,9 @@
             $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;
@@ -1113,7 +1112,7 @@
    if ( $opt->{is_cumulative} ) {
       $opt->{value}++;
    }
-   elsif ( !($opt->{optional_value} && !$val) ) {
+   else {
       $opt->{value} = $val;
    }
    $opt->{got} = 1;
@@ -1493,7 +1492,7 @@
             $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);
@@ -1654,12 +1653,11 @@
 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 {
@@ -1697,6 +1695,45 @@
    );
 };
 
+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; }
@@ -1988,7 +2025,7 @@
 
       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";
@@ -2003,13 +2040,8 @@
          }
       }
 
-      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'
@@ -2084,6 +2116,55 @@
    return \%new_dsn;
 }
 
+sub set_vars {
+   my ($self, $dbh, $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; }
@@ -2329,7 +2410,7 @@
    $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();
 
@@ -2966,10 +3047,21 @@
 
 =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 'lib/DSNParser.pm'
--- lib/DSNParser.pm	2013-02-28 01:47:00 +0000
+++ lib/DSNParser.pm	2013-03-03 15:43:19 +0000
@@ -448,6 +448,8 @@
 sub set_vars {
    my ($self, $dbh, $vars) = @_;
 
+   return unless $vars;
+
    foreach my $var ( sort keys %$vars ) {
       my $val = $vars->{$var}->{val};
 

=== modified file 't/lib/Cxn.t'
--- t/lib/Cxn.t	2013-02-26 23:34:48 +0000
+++ t/lib/Cxn.t	2013-03-03 15:43:19 +0000
@@ -29,10 +29,22 @@
    plan skip_all => 'Cannot connect to sandbox master';
 }
 
-my $o  = new OptionParser(description => 'Cxn');
+my $o = new OptionParser(
+   description => 'Cxn',
+   file        => "$trunk/bin/pt-table-checksum",
+);
 $o->get_specs("$trunk/bin/pt-table-checksum");
 $o->get_opts();
-$dp->prop('set-vars', $o->get('set-vars'));
+
+# In 2.1, these tests did not set innodb_lock_wait_timeout because
+# it was not a --set-vars default but rather its own option handled
+# by/in the tool.  In 2.2, the var is a --set-vars default, which
+# means it will cause a warning on 5.0 and 5.1, so we remoe the var
+# to remove the warning.
+my $set_vars = $o->set_vars();
+delete $set_vars->{innodb_lock_wait_timeout};
+delete $set_vars->{lock_wait_timeout};
+$dp->prop('set-vars', $set_vars);
 
 sub make_cxn {
    my (%args) = @_;

=== modified file 't/lib/DSNParser.t'
--- t/lib/DSNParser.t	2012-12-03 03:43:10 +0000
+++ t/lib/DSNParser.t	2013-03-03 15:43:19 +0000
@@ -439,7 +439,7 @@
    $dbh->disconnect();
 
    $dp = new DSNParser(opts => $opts);
-   $dp->prop('set-vars', 'wait_timeout=1000');
+   $dp->prop('set-vars', { wait_timeout => { val => 1000, default => 1}});
    $d  = $dp->parse('h=127.0.0.1,P=12345,A=utf8,u=msandbox,p=msandbox');
    my $dbh2 = $dp->get_dbh($dp->get_cxn_params($d), {mysql_use_result=>1});
    sleep 2;
@@ -560,8 +560,14 @@
    "get_dbh dies with an unknown charset"
 );
 
-$dp->prop('set-vars', "time_zoen='UTC'");
-($out, undef) = full_output(sub { $dp->get_dbh($dp->get_cxn_params($dsn), {}) });
+$dp->prop('set-vars',  { time_zoen => { val => 'UTC' }});
+$out = output(
+   sub {
+      my $dbh = $dp->get_dbh($dp->get_cxn_params($dsn), {});
+      $dbh->disconnect();
+   },
+   stderr => 1,
+);
 
 like(
    $out,
@@ -575,7 +581,7 @@
 # https://bugs.launchpad.net/percona-toolkit/+bug/1078887
 # #############################################################################
 
-$dp->prop('set-vars', "sql_mode=ANSI_QUOTES");
+$dp->prop('set-vars', { sql_mode => { val=>'ANSI_QUOTES' }});
 my $sql_mode_dbh = $dp->get_dbh($dp->get_cxn_params($dsn), {});
 
 my (undef, $sql_mode) = $sql_mode_dbh->selectrow_array(q{SHOW VARIABLES LIKE 'sql\_mode'});
@@ -628,4 +634,4 @@
 # Done.
 # #############################################################################
 done_testing;
-   
\ No newline at end of file
+   

=== modified file 't/lib/KeySize.t'
--- t/lib/KeySize.t	2012-06-03 17:54:32 +0000
+++ t/lib/KeySize.t	2013-03-03 15:43:19 +0000
@@ -144,18 +144,18 @@
    '',
    'No error (issue 364)'
 );
-is(
+like(
    $ks->explain(),
-   "extra: Using where; Using index
+   qr/^extra: Using where; Using index
 id: 1
 key: BASE_KID_ID
 key_len: 17
 possible_keys: BASE_KID_ID
 ref: NULL
-rows: 176
+rows: 17[1-9]
 select_type: SIMPLE
 table: issue_364
-type: index",
+type: index\Z/,
    'EXPLAIN plan (issue 364)'
 );
 is(

=== modified file 't/lib/Percona/XtraDB/Cluster-no-PXC.t'
--- t/lib/Percona/XtraDB/Cluster-no-PXC.t	2012-11-21 20:04:42 +0000
+++ t/lib/Percona/XtraDB/Cluster-no-PXC.t	2013-03-03 15:43:19 +0000
@@ -43,10 +43,22 @@
    plan skip_all => 'Cannot connect to sandbox master';
 }
 
-my $o  = new OptionParser(description => 'Cxn');
+my $o = new OptionParser(
+   description => 'Cxn',
+   file        => "$trunk/bin/pt-table-checksum",
+);
 $o->get_specs("$trunk/bin/pt-table-checksum");
 $o->get_opts();
-$dp->prop('set-vars', $o->get('set-vars'));
+
+# In 2.1, these tests did not set innodb_lock_wait_timeout because
+# it was not a --set-vars default but rather its own option handled
+# by/in the tool.  In 2.2, the var is a --set-vars default, which
+# means it will cause a warning on 5.0 and 5.1, so we remoe the var
+# to remove the warning.
+my $set_vars = $o->set_vars();
+delete $set_vars->{innodb_lock_wait_timeout};
+delete $set_vars->{lock_wait_timeout};
+$dp->prop('set-vars', $set_vars);
 
 sub make_cxn {
    my (%args) = @_;

=== modified file 't/lib/Percona/XtraDB/Cluster.t'
--- t/lib/Percona/XtraDB/Cluster.t	2012-11-21 20:04:42 +0000
+++ t/lib/Percona/XtraDB/Cluster.t	2013-03-03 15:43:19 +0000
@@ -44,10 +44,22 @@
    plan skip_all => "PXC-only test";
 }
 
-my $o  = new OptionParser(description => 'Cxn');
+my $o  = new OptionParser(
+   description => 'Cxn',
+   file        => "$trunk/bin/pt-table-checksum",
+);
 $o->get_specs("$trunk/bin/pt-table-checksum");
 $o->get_opts();
-$dp->prop('set-vars', $o->get('set-vars'));
+
+# In 2.1, these tests did not set innodb_lock_wait_timeout because
+# it was not a --set-vars default but rather its own option handled
+# by/in the tool.  In 2.2, the var is a --set-vars default, which
+# means it will cause a warning on 5.0 and 5.1, so we remoe the var
+# to remove the warning.
+my $set_vars = $o->set_vars();
+delete $set_vars->{innodb_lock_wait_timeout};
+delete $set_vars->{lock_wait_timeout};
+$dp->prop('set-vars', $set_vars);
 
 sub make_cxn {
    my (%args) = @_;

=== modified file 't/lib/ReplicaLagWaiter.t'
--- t/lib/ReplicaLagWaiter.t	2011-10-19 17:27:19 +0000
+++ t/lib/ReplicaLagWaiter.t	2013-03-03 15:43:19 +0000
@@ -41,10 +41,22 @@
 }
 
 my $dp = new DSNParser(opts=>$dsn_opts);
-my $o  = new OptionParser(description => 'Cxn');
+my $o  = new OptionParser(
+   description => 'Cxn',
+   file        => "$trunk/bin/pt-table-checksum",
+);
 $o->get_specs("$trunk/bin/pt-table-checksum");
 $o->get_opts();
-$dp->prop('set-vars', $o->get('set-vars'));
+
+# In 2.1, these tests did not set innodb_lock_wait_timeout because
+# it was not a --set-vars default but rather its own option handled
+# by/in the tool.  In 2.2, the var is a --set-vars default, which
+# means it will cause a warning on 5.0 and 5.1, so we remoe the var
+# to remove the warning.
+my $set_vars = $o->set_vars();
+delete $set_vars->{innodb_lock_wait_timeout};
+delete $set_vars->{lock_wait_timeout};
+$dp->prop('set-vars', $set_vars);
 
 my $r1 = new Cxn(dsn=>{n=>'slave1'}, dbh=>1, DSNParser=>$dp, OptionParser=>$o);
 my $r2 = new Cxn(dsn=>{n=>'slave2'}, dbh=>2, DSNParser=>$dp, OptionParser=>$o);

=== modified file 't/pt-archiver/check_slave_lag.t'
--- t/pt-archiver/check_slave_lag.t	2013-02-12 16:23:45 +0000
+++ t/pt-archiver/check_slave_lag.t	2013-03-03 15:43:19 +0000
@@ -29,13 +29,10 @@
 elsif ( $sb->is_cluster_mode ) {
    plan skip_all => 'Not for PXC',
 }
-else {
-   plan tests => 7;
+elsif ( $sandbox_version ge '5.6' ) {
+   plan skip_all => 'Slave trick does not work on MySQL 5.6+';
 }
 
-$sb->wipe_clean($dbh);
-$sb->wipe_clean($dbh2);
-
 my $output;
 my $sql;
 my $cnf = "/tmp/12345/my.sandbox.cnf";
@@ -44,6 +41,7 @@
 # #############################################################################
 # Issue 758: Make mk-archiver wait for a slave
 # #############################################################################
+
 $sb->load_file('master', 't/pt-archiver/samples/issue_758.sql');
 
 is_deeply(
@@ -52,11 +50,9 @@
    'Table not purged yet (issue 758)'
 );
 
-# TODO: MySQL 5.6 is no longer tricked by this method.
-
 # Once this goes through repl, the slave will sleep causing
 # seconds behind master to increase > 0.
-system('/tmp/12345/use -e "insert into issue_758.t select sleep(2)"');
+system('/tmp/12345/use -e "insert into issue_758.t select sleep(3)"');
 
 # Slave seems to be lagging now so the first row should get purged
 # immediately, then the script should wait about 2 seconds until
@@ -70,14 +66,11 @@
    'No changes on slave yet (issue 758)'
 );
 
-TODO: {
-   local $::TODO = "Timing-related test, may fail";
-   is_deeply(
-      $dbh->selectall_arrayref('select * from issue_758.t'),
-      [[0],[2]],
-      'First row purged (issue 758)'
-   );
-}
+is_deeply(
+   $dbh->selectall_arrayref('select * from issue_758.t'),
+   [[0],[2]],
+   'First row purged (issue 758)'
+);
 
 # The script it waiting for slave lag so no more rows should be purged yet.
 sleep 1;
@@ -106,6 +99,5 @@
 # Done.
 # #############################################################################
 $sb->wipe_clean($dbh);
-$sb->wipe_clean($dbh2);
 ok($sb->ok(), "Sandbox servers") or BAIL_OUT(__FILE__ . " broke the sandbox");
-exit;
+done_testing;

=== modified file 't/pt-fifo-split/pt-fifo-split.t'
--- t/pt-fifo-split/pt-fifo-split.t	2013-02-28 05:24:57 +0000
+++ t/pt-fifo-split/pt-fifo-split.t	2013-03-03 15:43:19 +0000
@@ -11,7 +11,8 @@
 use English qw(-no_match_vars);
 use Test::More;
 use File::Temp qw(tempfile);
-use IO::File;
+use Data::Dumper;
+use Time::HiRes qw(sleep);
 
 use PerconaTest;
 require "$trunk/bin/pt-fifo-split";
@@ -27,24 +28,60 @@
 my ($fh, $filename) = tempfile("pt-fifo-split-data.XXXXXXXXX", OPEN => 1, TMPDIR => 1, UNLINK => 1);
 $fh->autoflush(1);
 print { $fh } "$_\n" for 1..9;
+close $fh;
+
+# WARNING: This can "deadlock" if not done correctly.  First, for Perl open():
+# "When you open a fifo, the program will block until there's something on
+# the other end."  So pt-fifo-split needs to mkfifo and open() it first,
+# then we open it.  That's ok, but the problem is: after we read everything,
+# pt-fifo-split will close, rm, mkfifo, and open() it again.  That can take
+# a few microseconds longer than the test closing and trying to read the
+# fifo again.  In fact, the test can close, -p $fifo, and open() before
+# pt-fifo-split has done rm (unlink).  When this happens, the test holds
+# open the fifo it just read, then pt-fifo-split creates a new fifo and
+# open()s it and blocks because there's no program on the other end--
+# because the test is reading a phantom fifo.  Rather make the tool sleep
+# some arbitrary time before re-open()ing the fifo, we check for a new
+# file inode which ensures the fifo is new.
+sub read_fifo {
+   my ($n_reads) = @_;
+   my $last_inode = 0;
+   my @data;
+   for (1..$n_reads) {
+      PerconaTest::wait_until(sub {
+         my $inode;
+         (undef, $inode) = stat($fifo) if -p $fifo;
+         if ( $inode && $inode != $last_inode ) {
+            $last_inode = $inode;
+            return 1;
+         }
+         return;
+      });
+      open my $read_fifo_fh, '<', $fifo
+         or die "Cannot open $fifo: $OS_ERROR";
+      my $data = '';
+      while ( <$read_fifo_fh> ) {
+         $data .= $_;
+      }
+      close $read_fifo_fh;
+      push @data, $data;
+   }
+   return \@data;
+}
 
 local $SIG{CHLD} = 'IGNORE';
 my $pid = fork();
 die "Cannot fork: $OS_ERROR" unless defined $pid;
 if ( !$pid ) {
    exec { $cmd } $cmd, qw(--lines 2), $filename;
-   exit 1;
-}
-
-PerconaTest::wait_until(sub { -p $fifo });
-my @fifo;
-while (kill 0, $pid) {
-   push @fifo, slurp_file($fifo) if -e $fifo;
-}
+}
+
+my $data = read_fifo(5);
+
 waitpid($pid, 0);
 
 is_deeply(
-   \@fifo,
+   $data,
    [
       "1\n2\n",
       "3\n4\n",
@@ -53,53 +90,53 @@
       "9\n",
    ],
    "--lines=2 with 9 lines works as expected"
-);
+) or diag(Dumper($data));
 
 $pid = fork();
 die "Cannot fork: $OS_ERROR" unless defined $pid;
 if ( !$pid ) {
    exec { $cmd } $cmd, qw(--lines 15), $filename;
-   exit 1;
-}
-PerconaTest::wait_until(sub { -p $fifo });
-
-@fifo = ();
-while (kill 0, $pid) {
-   push @fifo, slurp_file($fifo) if -e $fifo;
-}
+}
+
+$data = read_fifo(1);
+
 waitpid($pid, 0);
 
 is_deeply(
-   \@fifo,
-   [
-      "1\n2\n3\n4\n5\n6\n7\n8\n9\n",
-   ],
+   $data,
+   [ "1\n2\n3\n4\n5\n6\n7\n8\n9\n" ],
    "--lines=15 with 9 lines works as expected"
-);
-
-close $fh or die "Cannot close $filename: $OS_ERROR";
+) or diag(Dumper($data));
 
 system("($cmd --lines 10000 $trunk/bin/pt-fifo-split > /dev/null 2>&1 < /dev/null)&");
-PerconaTest::wait_until(sub { -p $fifo });
-
-my $contents  = slurp_file($fifo);
+
+$data = read_fifo(1);
+
 my $contents2 = load_file('bin/pt-fifo-split');
 
-is($contents, $contents2, 'I read the file');
+is_deeply(
+   $data,
+   [ $contents2 ],
+   'I read the file'
+);
 
 system("($cmd $trunk/t/pt-fifo-split/samples/file_with_lines --offset 2 > /dev/null 2>&1 < /dev/null)&");
-PerconaTest::wait_until(sub { -p $fifo });
-
-$contents = slurp_file($fifo);
-
-is($contents, <<EOF
+
+$data = read_fifo(1);
+
+is_deeply(
+   $data,
+   [
+<<EOF
      2	hi
      3	there
      4	b
      5	c
      6	d
 EOF
-, 'Offset works');
+   ],
+   'Offset works'
+);
 
 # #########################################################################
 # Issue 391: Add --pid option to all scripts

=== modified file 't/pt-online-schema-change/ansi_quotes.t'
--- t/pt-online-schema-change/ansi_quotes.t	2013-02-28 01:47:00 +0000
+++ t/pt-online-schema-change/ansi_quotes.t	2013-03-03 15:43:19 +0000
@@ -29,7 +29,8 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the
+# tool will die.
 my $master_dsn = 'h=127.1,P=12348,u=msandbox,p=msandbox';
 my @args       = (qw(--set-vars innodb_lock_wait_timeout=3));
 my $output;

=== modified file 't/pt-online-schema-change/bugs.t'
--- t/pt-online-schema-change/bugs.t	2013-02-28 01:47:00 +0000
+++ t/pt-online-schema-change/bugs.t	2013-03-03 15:43:19 +0000
@@ -30,7 +30,8 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the
+# tool will die.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
 my @args       = (qw(--set-vars innodb_lock_wait_timeout=3));
 my $output;

=== modified file 't/pt-online-schema-change/check_alter.t'
--- t/pt-online-schema-change/check_alter.t	2013-02-28 01:47:00 +0000
+++ t/pt-online-schema-change/check_alter.t	2013-03-03 15:43:19 +0000
@@ -30,7 +30,8 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the
+# tool will die.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
 my @args       = (qw(--set-vars innodb_lock_wait_timeout=3));
 my $output;

=== modified file 't/pt-online-schema-change/privs.t'
--- t/pt-online-schema-change/privs.t	2013-02-28 01:47:00 +0000
+++ t/pt-online-schema-change/privs.t	2013-03-03 15:43:19 +0000
@@ -40,7 +40,8 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the
+# tool will die.
 my $master_dsn = 'h=127.1,P=12345,p=msandbox';
 my @args       = (qw(--set-vars innodb_lock_wait_timeout=3));
 my $row;

=== modified file 't/pt-online-schema-change/pxc.t'
--- t/pt-online-schema-change/pxc.t	2013-02-28 01:47:00 +0000
+++ t/pt-online-schema-change/pxc.t	2013-03-03 15:43:19 +0000
@@ -46,8 +46,6 @@
    plan skip_all => "PXC tests";
 }
 
-# The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
 my $node1_dsn = $sb->dsn_for('node1');
 my $output;
 my $exit;

=== modified file 't/pt-online-schema-change/rename_columns.t'
--- t/pt-online-schema-change/rename_columns.t	2013-02-28 01:47:00 +0000
+++ t/pt-online-schema-change/rename_columns.t	2013-03-03 15:43:19 +0000
@@ -30,7 +30,8 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout-3 else the
+# tool will die.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
 my @args       = (qw(--set-vars innodb_lock_wait_timeout=3));
 my $output;

=== modified file 't/pt-table-checksum/basics.t'
--- t/pt-table-checksum/basics.t	2013-02-28 02:44:37 +0000
+++ t/pt-table-checksum/basics.t	2013-03-03 15:43:19 +0000
@@ -40,9 +40,9 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3));
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3));
 my $row;
 my $output;
 my $exit_status;
@@ -351,7 +351,7 @@
 $output = output(
    sub { $exit_status =  pt_table_checksum::main(
    qw(--user msandbox --pass msandbox),
-   qw(-S /tmp/12345/mysql_sandbox12345.sock --lock-wait-timeout 3)) },
+   qw(-S /tmp/12345/mysql_sandbox12345.sock --set-vars innodb_lock_wait_timeout=3)) },
    stderr => 1,
 );
 

=== modified file 't/pt-table-checksum/bugs.t'
--- t/pt-table-checksum/bugs.t	2013-02-19 20:01:58 +0000
+++ t/pt-table-checksum/bugs.t	2013-03-03 15:43:19 +0000
@@ -40,9 +40,9 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3));
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3));
 my $output;
 my $exit_status;
 my $sample  = "t/pt-table-checksum/samples/";

=== modified file 't/pt-table-checksum/char_chunking.t'
--- t/pt-table-checksum/char_chunking.t	2013-02-18 20:54:25 +0000
+++ t/pt-table-checksum/char_chunking.t	2013-03-03 15:43:19 +0000
@@ -27,10 +27,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 
 $sb->create_dbs($master_dbh, ['test']);
 $sb->load_file('master', "t/lib/samples/char-chunking/ascii.sql", 'test');

=== modified file 't/pt-table-checksum/chunk_index.t'
--- t/pt-table-checksum/chunk_index.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/chunk_index.t	2013-03-03 15:43:19 +0000
@@ -27,10 +27,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3 --explain --chunk-size 3), '--max-load', '');
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3 --explain --chunk-size 3), '--max-load', '');
 my $output;
 my $out        = "t/pt-table-checksum/samples/";
 
@@ -110,7 +110,7 @@
 $output = output(sub {
    $exit_status = pt_table_checksum::main(
       $master_dsn, '--max-load', '',
-      qw(--lock-wait-timeout 3 --chunk-size 5 -t ALL_UC.T)
+      qw(--set-vars innodb_lock_wait_timeout=3 --chunk-size 5 -t ALL_UC.T)
    ) },
    stderr => 1,
 );
@@ -164,7 +164,7 @@
 $output = output(sub {
    $exit_status = pt_table_checksum::main(
       $master_dsn, '--max-load', '',
-      qw(--lock-wait-timeout 3 --chunk-size 10 -t bad_plan.t)
+      qw(--set-vars innodb_lock_wait_timeout=3 --chunk-size 10 -t bad_plan.t)
    ) },
    stderr => 1,
 );
@@ -190,7 +190,7 @@
       sub {
          pt_table_checksum::main(
             $master_dsn, '--max-load', '',
-            qw(--lock-wait-timeout 3 --chunk-size 5000  -t sakila.rental),
+            qw(--set-vars innodb_lock_wait_timeout=3 --chunk-size 5000  -t sakila.rental),
             qw(--chunk-index rental_date --chunk-index-columns 2),
             qw(--explain --explain));
       },
@@ -203,7 +203,7 @@
    sub {
       $exit_status = pt_table_checksum::main(
          $master_dsn, '--max-load', '',
-         qw(--lock-wait-timeout 3 --chunk-size 1000  -t sakila.film_actor),
+         qw(--set-vars innodb_lock_wait_timeout=3 --chunk-size 1000  -t sakila.film_actor),
          qw(--chunk-index PRIMARY --chunk-index-columns 9),
       );
    },
@@ -220,7 +220,7 @@
    sub {
       $exit_status = pt_table_checksum::main(
          $master_dsn, '--max-load', '',
-         qw(--lock-wait-timeout 3 --chunk-size 1000 -t sakila.film_actor),
+         qw(--set-vars innodb_lock_wait_timeout=3 --chunk-size 1000 -t sakila.film_actor),
          qw(--chunk-index-columns 1 --chunk-size-limit 3),
       );
    },

=== modified file 't/pt-table-checksum/chunk_size.t'
--- t/pt-table-checksum/chunk_size.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/chunk_size.t	2013-03-03 15:43:19 +0000
@@ -28,10 +28,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 
 my $row;
 my $output;

=== modified file 't/pt-table-checksum/create_replicate_table.t'
--- t/pt-table-checksum/create_replicate_table.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/create_replicate_table.t	2013-03-03 15:43:19 +0000
@@ -31,10 +31,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 
 my $output;
 my $row;

=== modified file 't/pt-table-checksum/error_handling.t'
--- t/pt-table-checksum/error_handling.t	2013-02-19 20:01:58 +0000
+++ t/pt-table-checksum/error_handling.t	2013-03-03 15:43:19 +0000
@@ -30,10 +30,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 my $exit_status;
 
@@ -189,7 +189,7 @@
 $output = output(
    sub { $exit_status = pt_table_checksum::main(
       "h=127.1,u=ro_checksum_user,p=msandbox,P=12345",
-      qw(--lock-wait-timeout 3 -t mysql.user)) },
+      qw(--set-vars innodb_lock_wait_timeout=3 -t mysql.user)) },
    stderr => 1,
 );
 

=== modified file 't/pt-table-checksum/filters.t'
--- t/pt-table-checksum/filters.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/filters.t	2013-03-03 15:43:19 +0000
@@ -28,10 +28,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 
 
 # ############################################################################

=== modified file 't/pt-table-checksum/float_precision.t'
--- t/pt-table-checksum/float_precision.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/float_precision.t	2013-03-03 15:43:19 +0000
@@ -27,10 +27,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 
 $sb->load_file('master', "t/pt-table-checksum/samples/float_precision.sql");

=== modified file 't/pt-table-checksum/fnv_64.t'
--- t/pt-table-checksum/fnv_64.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/fnv_64.t	2013-03-03 15:43:19 +0000
@@ -24,10 +24,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $sample     = "t/pt-table-checksum/samples/";
 my $row;
 my $output;

=== modified file 't/pt-table-checksum/ignore_columns.t'
--- t/pt-table-checksum/ignore_columns.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/ignore_columns.t	2013-03-03 15:43:19 +0000
@@ -31,10 +31,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 
 $sb->create_dbs($master_dbh, [qw(test)]);

=== modified file 't/pt-table-checksum/issue_388.t'
--- t/pt-table-checksum/issue_388.t	2012-12-14 19:14:12 +0000
+++ t/pt-table-checksum/issue_388.t	2013-03-03 15:43:19 +0000
@@ -27,10 +27,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 
 # #############################################################################

=== modified file 't/pt-table-checksum/issue_47.t'
--- t/pt-table-checksum/issue_47.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/issue_47.t	2013-03-03 15:43:19 +0000
@@ -27,10 +27,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 my $row;
 

=== modified file 't/pt-table-checksum/issue_602.t'
--- t/pt-table-checksum/issue_602.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/issue_602.t	2013-03-03 15:43:19 +0000
@@ -27,10 +27,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 
 $sb->load_file('master', 't/pt-table-checksum/samples/issue_602.sql');

=== modified file 't/pt-table-checksum/option_sanity.t'
--- t/pt-table-checksum/option_sanity.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/option_sanity.t	2013-03-03 15:43:19 +0000
@@ -57,11 +57,11 @@
    "Default --host=localhost"
 );
 
-like(
-   $output,
-   qr/^  --lock-wait-timeout\s+1$/m,
-   "Default --lock-wait-timeout=1"
-);
+#like(
+#   $output,
+#   qr/^  --lock-wait-timeout\s+1$/m,
+#   "Default --lock-wait-timeout=1"
+#);
 
 like(
    $output,

=== modified file 't/pt-table-checksum/privs.t'
--- t/pt-table-checksum/privs.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/privs.t	2013-03-03 15:43:19 +0000
@@ -41,9 +41,9 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 my $master_dsn = 'h=127.1,P=12345';
-my @args       = (qw(--lock-wait-timeout 3));
+my @args       = (qw(--set-vars innodb_lock_wait_timeout=3));
 my $row;
 my $output;
 my $exit_status;

=== modified file 't/pt-table-checksum/progress.t'
--- t/pt-table-checksum/progress.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/progress.t	2013-03-03 15:43:19 +0000
@@ -41,13 +41,13 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables. Setting
 # --chunk-size may help prevent the tool from running too fast and finishing
 # before the TEST_WISHLIST job below finishes. (Or, it might just make things
 # worse. This is a random stab in the dark. There is a problem either way.)
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3),
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3),
                   '--progress', 'time,1', '--max-load', '', '--chunk-size', '500'); 
 my $output;
 my $row;

=== modified file 't/pt-table-checksum/pxc.t'
--- t/pt-table-checksum/pxc.t	2012-11-30 18:14:06 +0000
+++ t/pt-table-checksum/pxc.t	2013-03-03 15:43:19 +0000
@@ -42,9 +42,9 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 my $node1_dsn = $sb->dsn_for('node1');
-my @args      = ($node1_dsn, qw(--lock-wait-timeout 3));
+my @args      = ($node1_dsn, qw(--set-vars innodb_lock_wait_timeout=3));
 my $output;
 my $exit_status;
 my $sample  = "t/pt-table-checksum/samples/";

=== modified file 't/pt-table-checksum/replication_filters.t'
--- t/pt-table-checksum/replication_filters.t	2013-03-02 01:31:31 +0000
+++ t/pt-table-checksum/replication_filters.t	2013-03-03 15:43:19 +0000
@@ -48,10 +48,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', '');
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', '');
 my $output;
 my $row;
 

=== modified file 't/pt-table-checksum/resume.t'
--- t/pt-table-checksum/resume.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/resume.t	2013-03-03 15:43:19 +0000
@@ -31,10 +31,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $row;
 my $output;
 

=== modified file 't/pt-table-checksum/run_time.t'
--- t/pt-table-checksum/run_time.t	2012-12-20 23:18:15 +0000
+++ t/pt-table-checksum/run_time.t	2013-03-03 15:43:19 +0000
@@ -29,10 +29,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 my $exit_status;
 

=== modified file 't/pt-table-checksum/skip_innodb.t'
--- t/pt-table-checksum/skip_innodb.t	2013-02-19 20:01:58 +0000
+++ t/pt-table-checksum/skip_innodb.t	2013-03-03 15:43:19 +0000
@@ -39,10 +39,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12348,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', ''); 
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', ''); 
 my $output;
 my $retval;
 

=== modified file 't/pt-table-checksum/standard_options.t'
--- t/pt-table-checksum/standard_options.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/standard_options.t	2013-03-03 15:43:19 +0000
@@ -31,9 +31,9 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
-my @args     = (qw(--lock-wait-timeout 3 --explain --tables sakila.country),
+my @args     = (qw(--set-vars innodb_lock_wait_timeout=3 --explain --tables sakila.country),
                 '--max-load', ''); 
 my $cnf      = "/tmp/12345/my.sandbox.cnf";
 my $pid_file = "/tmp/mk-table-checksum-test.pid";

=== modified file 't/pt-table-checksum/throttle.t'
--- t/pt-table-checksum/throttle.t	2012-11-21 16:58:40 +0000
+++ t/pt-table-checksum/throttle.t	2013-03-03 15:43:19 +0000
@@ -41,10 +41,10 @@
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
-# so we need to specify --lock-wait-timeout=3 else the tool will die.
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
 # And --max-load "" prevents waiting for status variables.
 my $master_dsn = 'h=127.1,P=12345,u=msandbox,p=msandbox';
-my @args       = ($master_dsn, qw(--lock-wait-timeout 3), '--max-load', '',
+my @args       = ($master_dsn, qw(--set-vars innodb_lock_wait_timeout=3), '--max-load', '',
                   '--progress', 'time,1');
 my $output;
 my $row;

=== modified file 't/pt-table-sync/basics.t'
--- t/pt-table-sync/basics.t	2013-02-19 20:01:58 +0000
+++ t/pt-table-sync/basics.t	2013-03-03 15:43:19 +0000
@@ -172,7 +172,7 @@
 
 # pt-table-checksum waits for all checksums to replicate to all slaves,
 # so no need to call $sb->wait_for_slaves() after this.
-`$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --max-load '' --lock-wait 3 --chunk-size 50 --chunk-index idx_actor_last_name -t sakila.actor --quiet`;
+`$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --max-load '' --set-vars innodb_lock_wait_timeout=3 --chunk-size 50 --chunk-index idx_actor_last_name -t sakila.actor --quiet`;
 
 $slave_dbh->do("update percona.checksums set this_crc='' where db='sakila' and tbl='actor' and chunk=3");
 $slave_dbh->do("update sakila.actor set last_name='' where actor_id=30");
@@ -192,7 +192,7 @@
    "--replicate with char index col (bug 911996)"
 );
 
-$output = `$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --max-load '' --lock-wait 3 --chunk-size 50 --chunk-index idx_actor_last_name -t sakila.actor`;
+$output = `$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --max-load '' --set-vars innodb_lock_wait_timeout=3 --chunk-size 50 --chunk-index idx_actor_last_name -t sakila.actor`;
 is(
    PerconaTest::count_checksum_results($output, 'diffs'),
    0,
@@ -205,7 +205,7 @@
 
 # pt-table-checksum waits for all checksums to replicate to all slaves,
 # so no need to call $sb->wait_for_slaves() after this.
-`$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --max-load '' --lock-wait 3 --chunk-size 2 -t test.t --quiet`;
+`$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --max-load '' --set-vars innodb_lock_wait_timeout=3 --chunk-size 2 -t test.t --quiet`;
 
 $output = output(
    sub {

=== modified file 't/pt-table-sync/bugs.t'
--- t/pt-table-sync/bugs.t	2012-06-07 16:43:18 +0000
+++ t/pt-table-sync/bugs.t	2013-03-03 15:43:19 +0000
@@ -46,7 +46,7 @@
 $slave_dbh->do("DELETE FROM test.aaa WHERE STOP_ARCHIVE IN (5,6,7)");
 $slave_dbh->do("UPDATE test.zzz SET c='x' WHERE id IN (44,45,46)");
 
-$output = `$trunk/bin/pt-table-checksum $master_dsn --lock-wait-timeout 3 --max-load '' -d test --chunk-size 10 2>&1`;
+$output = `$trunk/bin/pt-table-checksum $master_dsn --set-vars innodb_lock_wait_timeout=3 --max-load '' -d test --chunk-size 10 2>&1`;
 
 is(
    PerconaTest::count_checksum_results($output, 'diffs'),
@@ -112,7 +112,7 @@
 $slave_dbh->do("DELETE FROM test.aaa WHERE STOP_ARCHIVE IN (5,6,7)");
 $slave_dbh->do("UPDATE test.zzz SET c='x' WHERE id IN (44,45,46)");
 
-$output = `$trunk/bin/pt-table-checksum $master_dsn --lock-wait-timeout 3 --max-load '' -d test --chunk-size 10 2>&1`;
+$output = `$trunk/bin/pt-table-checksum $master_dsn --set-vars innodb_lock_wait_timeout=3 --max-load '' -d test --chunk-size 10 2>&1`;
 
 is(
    PerconaTest::count_checksum_results($output, 'diffs'),

=== modified file 't/pt-table-sync/filters.t'
--- t/pt-table-sync/filters.t	2012-07-11 18:21:47 +0000
+++ t/pt-table-sync/filters.t	2013-03-03 15:43:19 +0000
@@ -110,7 +110,7 @@
 # Checksum the filter tables.
 $master_dbh->do("DROP DATABASE IF EXISTS percona");
 $sb->wait_for_slaves();
-diag(`$trunk/bin/pt-table-checksum $master_dsn -d d1,d2,d3 --chunk-size 100 --quiet --lock-wait-timeout 3 --max-load ''`);
+diag(`$trunk/bin/pt-table-checksum $master_dsn -d d1,d2,d3 --chunk-size 100 --quiet --set-vars innodb_lock_wait_timeout=3 --max-load ''`);
 
 my $rows = $master_dbh->selectall_arrayref("SELECT CONCAT(db, '.', tbl) FROM percona.checksums ORDER BY db, tbl");
 is_deeply(
@@ -180,7 +180,7 @@
 $slave_dbh->do("INSERT INTO test.empty_it VALUES (null,11,11,'eleven')");
 
 # Create the checksums.
-diag(`$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox -d test --quiet --quiet --lock-wait-timeout 3 --max-load ''`);
+diag(`$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox -d test --quiet --quiet --set-vars innodb_lock_wait_timeout=3 --max-load ''`);
 
 # Make sure all the tables were checksummed.
 $rows = $master_dbh->selectall_arrayref("SELECT DISTINCT db, tbl FROM percona.checksums ORDER BY db, tbl");

=== modified file 't/pt-table-sync/issue_560.t'
--- t/pt-table-sync/issue_560.t	2012-06-07 14:25:44 +0000
+++ t/pt-table-sync/issue_560.t	2013-03-03 15:43:19 +0000
@@ -40,7 +40,7 @@
 $slave_dbh->do('UPDATE issue_560.buddy_list SET buddy_id=0 WHERE player_id IN (333,334)');
 $slave_dbh->do('UPDATE issue_560.buddy_list SET buddy_id=0 WHERE player_id=486');
 
-$output = `$trunk/bin/pt-table-checksum --replicate issue_560.checksum h=127.1,P=12345,u=msandbox,p=msandbox  -d issue_560 --chunk-size 50 --lock-wait-time 3`;
+$output = `$trunk/bin/pt-table-checksum --replicate issue_560.checksum h=127.1,P=12345,u=msandbox,p=msandbox  -d issue_560 --chunk-size 50 --set-vars innodb_lock_wait_timeout=3`;
 
 is(
    PerconaTest::count_checksum_results($output, 'diffs'),

=== modified file 't/pt-table-sync/issue_627.t'
--- t/pt-table-sync/issue_627.t	2012-06-03 17:54:32 +0000
+++ t/pt-table-sync/issue_627.t	2013-03-03 15:43:19 +0000
@@ -48,7 +48,7 @@
 $slave_dbh->do('UPDATE issue_375.t SET foo="zz" WHERE id=100');
 
 # Checksum and replicate.
-diag(`$trunk/bin/pt-table-checksum --create-replicate-table --replicate issue_375.checksum h=127.1,P=12345,u=msandbox,p=msandbox -d issue_375 -t t --lock-wait-time 3 > /dev/null`);
+diag(`$trunk/bin/pt-table-checksum --create-replicate-table --replicate issue_375.checksum h=127.1,P=12345,u=msandbox,p=msandbox -d issue_375 -t t --set-vars innodb_lock_wait_timeout=3 > /dev/null`);
 
 # And now sync using the replicated checksum results/differences.
 $output = output(

=== modified file 't/pt-table-sync/issue_996.t'
--- t/pt-table-sync/issue_996.t	2012-06-03 17:54:32 +0000
+++ t/pt-table-sync/issue_996.t	2013-03-03 15:43:19 +0000
@@ -33,7 +33,7 @@
 my $output;
 my @args = ('--sync-to-master', 'h=127.1,P=12346,u=msandbox,p=msandbox',
             qw(-d issue_375 --replicate issue_375.checksums --print));
-my $pt_table_checksum = "$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox -d issue_375 --chunk-size 20 --chunk-size-limit 0 --lock-wait-time 3";
+my $pt_table_checksum = "$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox -d issue_375 --chunk-size 20 --chunk-size-limit 0 --set-vars innodb_lock_wait_timeout=3";
 
 # #############################################################################
 # Issue 996: might not chunk inside of mk-table-checksum's boundaries

=== modified file 't/pt-table-sync/triggers.t'
--- t/pt-table-sync/triggers.t	2012-07-11 19:46:54 +0000
+++ t/pt-table-sync/triggers.t	2013-03-03 15:43:19 +0000
@@ -44,7 +44,7 @@
 $sb->load_file('master', 't/pt-table-sync/samples/issue_37.sql');
 $sb->use('master', '-e "SET SQL_LOG_BIN=0; INSERT INTO test.issue_37 VALUES (1), (2);"');
 
-`$trunk/bin/pt-table-checksum h=127.0.0.1,P=12345,u=msandbox,p=msandbox --replicate test.checksum -d test --lock-wait-time 3 2>&1 > /dev/null`;
+`$trunk/bin/pt-table-checksum h=127.0.0.1,P=12345,u=msandbox,p=msandbox --replicate test.checksum -d test --set-vars innodb_lock_wait_timeout=3 2>&1 > /dev/null`;
 
 $output = `$trunk/bin/pt-table-sync --no-check-slave --execute u=msandbox,p=msandbox,h=127.0.0.1,P=12345,D=test,t=issue_37 h=127.1,P=12346 2>&1`;
 like($output,
@@ -103,7 +103,7 @@
 $slave_dbh->do('DELETE FROM db2.t1 WHERE i > 4');
 
 # Replicate checksum of db2.t1.
-$output = `$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --replicate db1.checksum --create-replicate-table --databases db1,db2 --lock-wait-time 3 2>&1`;
+$output = `$trunk/bin/pt-table-checksum h=127.1,P=12345,u=msandbox,p=msandbox --replicate db1.checksum --create-replicate-table --databases db1,db2 --set-vars innodb_lock_wait_timeout=3 2>&1`;
 like(
    $output,
    qr/db2.t1/,