Clean up a few tests that kill the server.

As noted in MDEV-8841, any test that kills the server must issue
FLUSH TABLES, so that tables of crash-unsafe storage engines will
not be corrupted. Consistently issue this statement after any
call mtr.add_suppression() calls.

Also, do not invoke shutdown_server directly, but use helpers instead.

mysql-test/suite/innodb/r/101_compatibility.result

@@ -2,7 +2,6 @@
 # MDEV-11623 MariaDB 10.1 fails to start datadir created with
 # MariaDB 10.0/MySQL 5.6 using innodb-page-size!=16K
 #
-call mtr.add_suppression("InnoDB: adjusting FSP_SPACE_FLAGS of tablespace");
 CREATE TABLE tr(a INT)ENGINE=InnoDB ROW_FORMAT=REDUNDANT;
 CREATE TABLE tc(a INT)ENGINE=InnoDB ROW_FORMAT=COMPACT;
 CREATE TABLE td(a INT)ENGINE=InnoDB ROW_FORMAT=DYNAMIC;

mysql-test/suite/innodb/r/innodb_bug59641.result

-call mtr.add_suppression("Found 3 prepared XA transactions");
-flush tables;
 CREATE TABLE t(a INT PRIMARY KEY, b INT)ENGINE=InnoDB;
 INSERT INTO t VALUES(2,2),(4,4),(8,8),(16,16),(32,32);
 COMMIT;
@@ -8,20 +6,18 @@ INSERT INTO t VALUES(1,1);
 XA END '123';
 XA PREPARE '123';
 CONNECT  con1,localhost,root,,;
-connection con1;
 XA START '456';
 INSERT INTO t VALUES(3,47),(5,67);
 UPDATE t SET b=2*b WHERE a BETWEEN 5 AND 8;
 XA END '456';
 XA PREPARE '456';
 CONNECT  con2,localhost,root,,;
-connection con2;
 XA START '789';
 UPDATE t SET b=4*a WHERE a=32;
 XA END '789';
 XA PREPARE '789';
 CONNECT  con3,localhost,root,,;
-connection con3;
+# Kill and restart
 SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;
 SELECT * FROM t;
 a	b

mysql-test/suite/innodb/r/xa_recovery.result

@@ -6,8 +6,7 @@ UPDATE t1 set a=2;
 XA END 'x';
 XA PREPARE 'x';
 connection default;
-call mtr.add_suppression("Found 1 prepared XA transactions");
-# Kill the server
+# Kill and restart
 disconnect con1;
 connect  con1,localhost,root;
 SELECT * FROM t1 LOCK IN SHARE MODE;

mysql-test/suite/innodb/t/101_compatibility.test

@@ -9,7 +9,10 @@
 # This is actually testing the opposite: starting the fixed 10.1 with
 # buggy 10.1 files (by manually converting the flags in the files).
 
+--disable_query_log
 call mtr.add_suppression("InnoDB: adjusting FSP_SPACE_FLAGS of tablespace");
+FLUSH TABLES;
+--enable_query_log
 let INNODB_PAGE_SIZE=`select @@innodb_page_size`;
 let MYSQLD_DATADIR=`select @@datadir`;
 

mysql-test/suite/innodb/t/doublewrite.test

@@ -10,14 +10,13 @@
 
 # Slow shutdown and restart to make sure ibuf merge is finished
 SET GLOBAL innodb_fast_shutdown = 0;
---source include/restart_mysqld.inc
-
 --disable_query_log
 call mtr.add_suppression("Header page consists of zero bytes");
 call mtr.add_suppression("Checksum mismatch in datafile");
 call mtr.add_suppression("but the innodb_page_size start-up parameter is");
 call mtr.add_suppression("adjusting FSP_SPACE_FLAGS");
 --enable_query_log
+--source include/restart_mysqld.inc
 
 let INNODB_PAGE_SIZE=`select @@innodb_page_size`;
 let MYSQLD_DATADIR=`select @@datadir`;

mysql-test/suite/innodb/t/innodb_bug59641.test

@@ -2,11 +2,11 @@
 # Bug #59641 Prepared XA transaction causes shutdown hang after a crash
 
 -- source include/not_embedded.inc
-# The server would issue this warning on restart.
-call mtr.add_suppression("Found 3 prepared XA transactions");
 
-# Close tables used by other tests (to not get crashed myisam tables)
-flush tables;
+--disable_query_log
+call mtr.add_suppression("Found 3 prepared XA transactions");
+FLUSH TABLES;
+--enable_query_log
 
 CREATE TABLE t(a INT PRIMARY KEY, b INT)ENGINE=InnoDB;
 INSERT INTO t VALUES(2,2),(4,4),(8,8),(16,16),(32,32);
@@ -17,7 +17,6 @@ XA END '123';
 XA PREPARE '123';
 
 CONNECT (con1,localhost,root,,);
-CONNECTION con1;
 
 XA START '456';
 INSERT INTO t VALUES(3,47),(5,67);
@@ -26,7 +25,6 @@ XA END '456';
 XA PREPARE '456';
 
 CONNECT (con2,localhost,root,,);
-CONNECTION con2;
 
 XA START '789';
 UPDATE t SET b=4*a WHERE a=32;
@@ -34,30 +32,13 @@ XA END '789';
 XA PREPARE '789';
 
 CONNECT (con3,localhost,root,,);
-CONNECTION con3;
 
-# Kill the server without sending a shutdown command
--- exec echo "wait" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
--- shutdown_server 0
--- source include/wait_until_disconnected.inc
-
-# Restart the server.
--- exec echo "restart" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
--- enable_reconnect
--- source include/wait_until_connected_again.inc
+--source include/kill_and_restart_mysqld.inc
 SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;
 SELECT * FROM t;
 COMMIT;
 
-# Shut down the server. This would hang because of the bug.
--- exec echo "wait" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
--- shutdown_server
--- source include/wait_until_disconnected.inc
-
-# Restart the server.
--- exec echo "restart" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
--- enable_reconnect
--- source include/wait_until_connected_again.inc
+--source include/restart_mysqld.inc
 
 SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;
 SELECT * FROM t;

mysql-test/suite/innodb/t/log_file_size.test

@@ -13,6 +13,14 @@ if (`SELECT @@innodb_log_file_size = 1048576`) {
   --skip Test requires innodb_log_file_size>1M.
 }
 
+--disable_query_log
+call mtr.add_suppression("InnoDB: Resizing redo log");
+call mtr.add_suppression("InnoDB: Starting to delete and rewrite log files");
+call mtr.add_suppression("InnoDB: New log files created");
+call mtr.add_suppression("InnoDB: The log sequence numbers [0-9]+ and [0-9]+ in ibdata files do not match the log sequence number [0-9]+ in the ib_logfiles");
+FLUSH TABLES;
+--enable_query_log
+
 CREATE TABLE t1(a INT PRIMARY KEY) ENGINE=InnoDB;
 BEGIN;
 INSERT INTO t1 VALUES (42);
@@ -177,12 +185,5 @@ let SEARCH_PATTERN= InnoDB: Renaming log file .*ib_logfile101 to .*ib_logfile0;
 --let $restart_parameters=
 --source include/start_mysqld.inc
 
---disable_query_log
-call mtr.add_suppression("InnoDB: Resizing redo log");
-call mtr.add_suppression("InnoDB: Starting to delete and rewrite log files");
-call mtr.add_suppression("InnoDB: New log files created");
-call mtr.add_suppression("InnoDB: The log sequence numbers [0-9]+ and [0-9]+ in ibdata files do not match the log sequence number [0-9]+ in the ib_logfiles");
---enable_query_log
-
 SELECT * FROM t1;
 DROP TABLE t1;

mysql-test/suite/innodb/t/xa_recovery.test

-if (`select plugin_auth_version <= "5.6.24" from information_schema.plugins where plugin_name='innodb'`)
-{
-  --skip Not fixed in InnoDB as of 5.6.24 or earlier
-}
 --source include/have_innodb.inc
 # Embedded server does not support restarting.
 --source include/not_embedded.inc
@@ -9,6 +5,7 @@ if (`select plugin_auth_version <= "5.6.24" from information_schema.plugins wher
 # MDEV-8841 - close tables opened by previous tests, 
 # so they don't get marked crashed when the server gets crashed
 --disable_query_log
+call mtr.add_suppression("Found 1 prepared XA transactions");
 FLUSH TABLES;
 --enable_query_log
 
@@ -18,10 +15,7 @@ connect (con1,localhost,root);
 XA START 'x'; UPDATE t1 set a=2; XA END 'x'; XA PREPARE 'x';
 connection default;
 
-call mtr.add_suppression("Found 1 prepared XA transactions");
-
---source include/kill_mysqld.inc
---source include/start_mysqld.inc
+--source include/kill_and_restart_mysqld.inc
 
 disconnect con1;
 connect (con1,localhost,root);