Firstly, see this post for reference.

Secondly, I have found that the innodb logfiles constantly get corrupted when the mysql service shuts down. An ugly (but useful) hack is to remove the logfiles when starting the service:

# ugly hack for innodb (logfiles constantly get corrupted)
sed -i s"|  'start')|  'start')\n        # ugly hack for innodb logfile corruption\n        rm -f /var/lib/mysql/ib_logfile*|" /etc/init.d/mysql

Note: I have not used this hack in a production environment, but in my testing it works without any unforeseen issues.

when I referred to start, i didn't mean at the "start" of the file, but rather after the 'start') code - it should look something like this:

BEFORE
------

case "${1:-''}" in
  'start')
        sanity_checks;
        # Start daemon
        log_daemon_msg "Starting MySQL database server" "mysqld"

AFTER
-----

case "${1:-''}" in
  'start')
        # ugly hack for innodb logfile corruption
        rm -f /var/lib/mysql/ib_logfile*
        sanity_checks;
        # Start daemon
        log_daemon_msg "Starting MySQL database server" "mysqld"

Regarding storage_engine.cnf, you can use your favourite editor (vim, nano, etc.) to create the file, or just do this:

cat >/etc/mysql/conf.d/storage_engine.cnf<<EOF
[mysqld]
default-storage-engine = InnoDB
EOF

BTW, why do you want to use InnoDB in the first place??

No problem, just keep experimenting and learning, and you'll get there.

You are right that you need to edit my.cnf, which is what we did although indirectly. my.cnf imports all configuration in /etc/mysql/conf.d/

I'm out of tips, so I will need to perform the changes locally and see if I can replicate the issues you are having. I'll try get to it later in the day and report back my findings...

Ok, so I found some time to do some testing, and have sketched out the exact steps I used to enable InnoDB as the default storage engine of MySQL.
Please note the GOTCHA in the PHPMyAdmin section.

Steps to enabled InnoDB as default storage engine

Stop MySQL

/etc/init.d/mysql stop

Ugly hack for innodb (logfiles constantly get corrupted)

sed -i "s|  'start')|  'start')\n        # ugly hack for innodb logfile corruption\n        rm -f /var/lib/mysql/ib_logfile*|" /etc/init.d/mysql

Start MySQL

/etc/init.d/mysql start

Display supported/default engines

mysql -uroot -pPASSWORD
> show engines;
 MyISAM     | DEFAULT
 InnoDB     | YES
 ...
> quit;

Configure default storage engine

cat > /etc/mysql/conf.d/storage_engine.cnf <<EOF
[mysqld]
default-storage-engine = InnoDB
EOF

Restart mysql for changes to take effect

/etc/init.d/mysql restart

 Display supported/default engines

mysql -uroot -pPASSWORD
> show engines;
 MyISAM     | ENABLED
 InnoDB     | DEFAULT
 ...
> quit;

Testing with PHPMyAdmin

Connect to phpmyadmin with your browser: https://appliance_ip:12322
Click "storage engines" -> "InnoDB"
  This will display InnoDB's configuration and that it is the default storage engine

GOTCHA: Do not be confused by the description of MyISAM
        MyISAM       Default engine as of MySQL 3.23 with great performance

        It is just the description, it is not the engine status

Create a test database with test tables, notice that the default is InnoDB.

 

Enjoy!

In my previous post I recommended using an ugly hack to remove the innodb logfiles pre mysql start as they "contantly get corrupted".

In theory, this should not happen and if it does the sysadmin should remedy the problem by shutting down mysql (without errors), manually remove the logfiles and restart mysql to avoid data loss.

I hacked together a patch to the mysql init script to be a little less forceful. It only takes into account the default innodb configuration, so if you tweaked it this might not work for you.

My patch is in bold:

#!/bin/bash
#
### BEGIN INIT INFO
# Provides:          mysql
# Required-Start:    $remote_fs $syslog mysql-ndb
# Required-Stop:     $remote_fs $syslog mysql-ndb
# Should-Start:      $network $named $time
# Should-Stop:       $network $named $time
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: Start and stop the mysql database server daemon
# Description:       Controls the main MySQL database server daemon "mysqld"
#                    and its wrapper script "mysqld_safe".
### END INIT INFO
#
set -e
set -u
${DEBIAN_SCRIPT_DEBUG:+ set -v -x}

test -x /usr/sbin/mysqld || exit 0

. /lib/lsb/init-functions

SELF=$(cd $(dirname $0); pwd -P)/$(basename $0)
CONF=/etc/mysql/my.cnf
MYADMIN="/usr/bin/mysqladmin --defaults-file=/etc/mysql/debian.cnf"

# priority can be overriden and "-s" adds output to stderr
ERR_LOGGER="logger -p daemon.err -t /etc/init.d/mysql -i"

# Safeguard (relative paths, core dumps..)
cd /
umask 077

# mysqladmin likes to read /root/.my.cnf. This is usually not what I want
# as many admins e.g. only store a password without a username there and
# so break my scripts.
export HOME=/etc/mysql/

## Fetch a particular option from mysql's invocation.
#
# Usage: void mysqld_get_param option
mysqld_get_param() {
    /usr/sbin/mysqld --print-defaults \
        | tr " " "\n" \
        | grep -- "--$1" \
        | tail -n 1 \
        | cut -d= -f2
}

## Do some sanity checks before even trying to start mysqld.
sanity_checks() {
  # check for config file
  if [ ! -r /etc/mysql/my.cnf ]; then
    log_warning_msg "$0: WARNING: /etc/mysql/my.cnf cannot be read. See README.Debian.gz"
    echo                "WARNING: /etc/mysql/my.cnf cannot be read. See README.Debian.gz" | $ERR_LOGGER
  fi

  # check for diskspace shortage
  datadir=`mysqld_get_param datadir`
  if LC_ALL=C BLOCKSIZE= df --portability $datadir/. | tail -n 1 | awk '{ exit ($4>4096) }'; then
    log_failure_msg "$0: ERROR: The partition with $datadir is too full!"
    echo                "ERROR: The partition with $datadir is too full!" | $ERR_LOGGER
    exit 1
  fi
}

## Checks if there is a server running and if so if it is accessible.
#
# check_alive insists on a pingable server
# check_dead also fails if there is a lost mysqld in the process list
#
# Usage: boolean mysqld_status [check_alive|check_dead] [warn|nowarn]
mysqld_status () {
    ping_output=`$MYADMIN ping 2>&1`; ping_alive=$(( ! $? ))

    ps_alive=0
    pidfile=`mysqld_get_param pid-file`
    if [ -f "$pidfile" ] && ps `cat $pidfile` >/dev/null 2>&1; then ps_alive=1; fi
   
    if [ "$1" = "check_alive"  -a  $ping_alive = 1 ] ||
       [ "$1" = "check_dead"   -a  $ping_alive = 0  -a  $ps_alive = 0 ]; then
    return 0 # EXIT_SUCCESS
    else
      if [ "$2" = "warn" ]; then
          echo -e "$ps_alive processes alive and '$MYADMIN ping' resulted in\n$ping_output\n" | $ERR_LOGGER -p daemon.debug
    fi
      return 1 # EXIT_FAILURE
    fi
}

delete_innodb_logfiles () {
    # remove innodb logfiles if they differ in size
    datadir=`mysqld_get_param datadir`

    ibsize0=$(du $datadir/ib_logfile0 | cut -f 1)
    ibsize1=$(du $datadir/ib_logfile1 | cut -f 1)
    if [ "$ibsize0" != "$ibsize1" ]; then
        rm -f $datadir/ib_logfile*
        return 0
    fi
    return 1
}

#
# main()
#

case "${1:-''}" in
  'start')
    sanity_checks;
    # Start daemon
    log_daemon_msg "Starting MySQL database server" "mysqld"
    if mysqld_status check_alive nowarn; then
       log_progress_msg "already running"
       log_end_msg 0
    else
          /usr/bin/mysqld_safe > /dev/null 2>&1 &
        # 6s was reported in #352070 to be too few when using ndbcluster
        for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14; do
                sleep 1
            if mysqld_status check_alive nowarn ; then break; fi
        log_progress_msg "."
        done
        if mysqld_status check_alive warn; then
                log_end_msg 0
            # Now start mysqlcheck or whatever the admin wants.
            output=$(/etc/mysql/debian-start)
        [ -n "$output" ] && log_action_msg "$output"
        else
            log_end_msg 1
        log_failure_msg "Please take a look at the syslog"
        fi
    fi

    # Some warnings
        if $MYADMIN variables | egrep -q have_bdb.*YES; then
            echo "BerkeleyDB is obsolete, see /usr/share/doc/mysql-server-5.0/README.Debian.gz" | $ERR_LOGGER -p daemon.info
        fi
        if [ -f /etc/mysql/debian-log-rotate.conf ]; then
            echo "/etc/mysql/debian-log-rotate.conf is obsolete, see /usr/share/doc/mysql-server-5.0/NEWS.Debian.gz" | $ERR_LOGGER -p daemon.info
        fi
    ;;

  'stop')
    # * As a passwordless mysqladmin (e.g. via ~/.my.cnf) must be possible
    # at least for cron, we can rely on it here, too. (although we have
    # to specify it explicit as e.g. sudo environments points to the normal
    # users home and not /root)
    log_daemon_msg "Stopping MySQL database server" "mysqld"
    if ! mysqld_status check_dead nowarn; then
        set +e
        shutdown_out=`$MYADMIN shutdown 2>&1`; r=$?
        set -e
        if [ "$r" -ne 0 ]; then
            log_end_msg 1
            [ "$VERBOSE" != "no" ] && log_failure_msg "Error: $shutdown_out"
            log_daemon_msg "Killing MySQL database server by signal" "mysqld"
            killall -15 mysqld
            server_down=
            for i in 1 2 3 4 5 6 7 8 9 10; do
                sleep 1
                if mysqld_status check_dead nowarn; then server_down=1; break; fi
            done
            if test -z "$server_down"; then killall -9 mysqld; fi
        fi
    fi

    if ! mysqld_status check_dead warn; then
        log_end_msg 1
        log_failure_msg "Please stop MySQL manually and read /usr/share/doc/mysql-server-5.0/README.Debian.gz!"
        exit -1
    else
        #its safe to clean delete logfiles if mysql has shutdown without errors
        delete_innodb_logfiles || true
        log_end_msg 0
    fi
    ;;

  'restart')
    set +e; $SELF stop; set -e
    $SELF start
    ;;

  'reload'|'force-reload')
      log_daemon_msg "Reloading MySQL database server" "mysqld"
    $MYADMIN reload
    log_end_msg 0
    ;;

  'status')
    if mysqld_status check_alive nowarn; then
      log_action_msg "$($MYADMIN version)"
    else
      log_action_msg "MySQL is stopped."
      exit 3
    fi
      ;;

  'delete-innodb-logfiles')
    # remove innodb logfiles if they differ in size
    # do not remove the logfiles if mysql is not stopped
    if mysqld_status check_alive nowarn; then
      log_action_msg "MySQL is not stopped, refusing to delete innodb logfiles"
      exit 4
    fi
    if delete_innodb_logfiles; then
      log_action_msg "InnoDB logfiles deleted"
    else
      log_action_msg "InnoDB logfiles not deleted as they do not differ in size"
    fi
    ;;
  *)
    echo "Usage: $SELF start|stop|restart|reload|force-reload|status|delete-innodb-logfiles"
    exit 1
    ;;
esac