Monitoring InnoDB Index Utilization
Instead of using the slow log (which are queries that have finished and logged), you may want to poll mysql for long running queries while they are still running.

You may need to try using mk-query-digest or pt-query-digest and poll the processlist.

I learned how to use mk-query-digest from this youtube video as a replacement for the slow log: http://www.youtube.com/watch?v=GXwg1fiUF68&amp;feature=colike

Here is the script I wrote to run the query digest program

#!/bin/sh

RUNFILE=/tmp/QueriesAreBeingDigested.txt
if [ -f ${RUNFILE} ] ; then exit ; fi

MKDQ=/usr/local/sbin/mk-query-digest
RUNTIME=${1}
COPIES_TO_KEEP=${2}
DBVIP=${3}

WHICH=/usr/bin/which
DATE=`${WHICH} date`
ECHO=`${WHICH} echo`
HEAD=`${WHICH} head`
TAIL=`${WHICH} tail`
AWK=`${WHICH} awk`
SED=`${WHICH} sed`
CAT=`${WHICH} cat`
WC=`${WHICH} wc`
RM=`${WHICH} rm | ${TAIL} -1 | ${AWK} '{print $1}'`
LS=`${WHICH} ls | ${TAIL} -1 | ${AWK} '{print $1}'`

HAS_THE_DBVIP=`/sbin/ip addr show | grep "scope global secondary" | grep -c "${DBVIP}"`
if [ ${HAS_THE_DBVIP} -eq 1 ] ; then exit ; fi

DT=`${DATE} +"%Y%m%d_%H%M%S"`
UNIQUETAG=`${ECHO} ${SSH_CLIENT}_${SSH_CONNECTION}_${DT} | ${SED} 's/\./ /g' | ${SED} 's/ //g'`

cd /root/QueryDigest
OUTFILE=QP_${DT}.txt
HOSTADDR=${DBVIP}
${MKDQ} --processlist h=${HOSTADDR},u=queryprofiler,p=queryprofiler --run-time=${RUNTIME} &gt; ${OUTFILE}

#
# Rotate out Old Copies
#

QPFILES=QPFiles.txt
QPFILES2ZAP=QPFiles2Zap.txt
${LS} QP_[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_[0-9][0-9][0-9][0-9][0-9][0-9].txt &gt; ${QPFILES}

LINECOUNT=`${WC} -l &lt; ${QPFILES}`
if [ ${LINECOUNT} -gt ${COPIES_TO_KEEP} ]
then
        (( DIFF = LINECOUNT - COPIES_TO_KEEP ))
        ${HEAD} -${DIFF} &lt; ${QPFILES} &gt; ${QPFILES2ZAP}
        for QPFILETOZAP in `${CAT} ${QPFILES2ZAP}`
        do
                ${RM} ${QPFILETOZAP}
        done
fi

rm -f ${QPFILES2ZAP}
rm -f ${QPFILES}
rm -f ${RUNFILE}


Make sure


you a user called queryprofiler whose password is queryprofiler and who only has the PROCESS privilege
you put */20 * * * * /root/QueryDigest/ExecQueryDigest.sh 1190s 144 10.64.95.141
 in the crontab to run every 20 minutes (Each profile is 20 min less 10 seconds, Keeps the last 144 copies, and only runs if specfifc DBVIP is present [Alter script to bypass checking for DBVIPs])


The output produces a file with the 20 worst running queries based on the number of times the query was called X avg sec per query.

Here is the sample output of the query profiling summary of mk-query-digest

# Rank Query ID           Response time    Calls   R/Call     Item
# ==== ================== ================ ======= ========== ====
#    1 0x812D15015AD29D33   336.3867 68.5%     910   0.369656 SELECT mt_entry mt_placement mt_category
#    2 0x99E13015BFF1E75E    25.3594  5.2%     210   0.120759 SELECT mt_entry mt_objecttag
#    3 0x5E994008E9543B29    16.1608  3.3%      46   0.351321 SELECT schedule_occurrence schedule_eventschedule schedule_event schedule_eventtype schedule_event schedule_eventtype schedule_occurrence.start
#    4 0x84DD09F0FC444677    13.3070  2.7%      23   0.578567 SELECT mt_entry
#    5 0x377E0D0898266FDD    12.0870  2.5%     116   0.104199 SELECT polls_pollquestion mt_category
#    6 0x440EBDBCEDB88725    11.5159  2.3%      21   0.548376 SELECT mt_entry
#    7 0x1DC2DFD6B658021F    10.3653  2.1%      54   0.191949 SELECT mt_entry mt_placement mt_category
#    8 0x6C6318E56E149036     8.8294  1.8%      44   0.200667 SELECT schedule_occurrence schedule_eventschedule schedule_event schedule_eventtype schedule_event schedule_eventtype schedule_occurrence.start
#    9 0x392F6DA628C7FEBD     8.5243  1.7%       9   0.947143 SELECT mt_entry mt_objecttag
#   10 0x7DD2B294CFF96961     7.3753  1.5%      70   0.105362 SELECT polls_pollresponse
#   11 0x9B9092194D3910E6     5.8124  1.2%      57   0.101973 SELECT content_specialitem content_basecontentitem advertising_product organizations_neworg content_basecontentitem_item_attributes
#   12 0xA909BF76E7051792     5.6005  1.1%      55   0.101828 SELECT mt_entry mt_objecttag mt_tag
#   13 0xEBE07AC48DB8923E     5.5195  1.1%      54   0.102213 SELECT rssfeeds_contentfeeditem
#   14 0x3E52CF0261A7C3FF     4.4676  0.9%      44   0.101536 SELECT schedule_occurrence schedule_occurrence.start
#   15 0x9D0BCD3F6731195B     4.2804  0.9%      41   0.104401 SELECT mt_entry mt_placement mt_category
#   16 0x7961BD4C76277EB7     4.0143  0.8%      18   0.223014 INSERT UNION UPDATE UNION mt_session
#   17 0xD2F486BA41E7A623     3.1448  0.6%      21   0.149754 SELECT mt_entry mt_placement mt_category mt_objecttag mt_tag
#   18 0x3B9686D98BB8E054     2.9577  0.6%      11   0.268885 SELECT mt_entry mt_objecttag mt_tag
#   19 0xBB2443BF48638319     2.7239  0.6%       9   0.302660 SELECT rssfeeds_contentfeeditem
#   20 0x3D533D57D8B466CC     2.4209  0.5%      15   0.161391 SELECT mt_entry mt_placement mt_category


Above this output are histograms of these 20 top worst-performing queries

Example of the first entry's histogram

# Query 1: 0.77 QPS, 0.28x concurrency, ID 0x812D15015AD29D33 at byte 0 __
# This item is included in the report because it matches --limit.
#              pct   total     min     max     avg     95%  stddev  median
# Count         36     910
# Exec time     58    336s   101ms      2s   370ms   992ms   230ms   393ms
# Lock time      0       0       0       0       0       0       0       0
# Users                  1      mt
# Hosts                905 10.64.95.74:54707 (2), 10.64.95.74:56133 (2), 10.64.95.80:33862 (2)... 901 more
# Databases              1     mt1
# Time range 1321642802 to 1321643988
# bytes          1   1.11M   1.22k   1.41k   1.25k   1.26k   25.66   1.20k
# id            36   9.87G  11.10M  11.11M  11.11M  10.76M    0.12  10.76M
# Query_time distribution
#   1us
#  10us
# 100us
#   1ms
#  10ms
# 100ms  ################################################################
#    1s  ###
#  10s+
# Tables
#    SHOW TABLE STATUS FROM `mt1` LIKE 'mt_entry'\G
#    SHOW CREATE TABLE `mt1`.`mt_entry`\G
#    SHOW TABLE STATUS FROM `mt1` LIKE 'mt_placement'\G
#    SHOW CREATE TABLE `mt1`.`mt_placement`\G
#    SHOW TABLE STATUS FROM `mt1` LIKE 'mt_category'\G
#    SHOW CREATE TABLE `mt1`.`mt_category`\G
# EXPLAIN
SELECT `mt_entry`.`entry_id`, `mt_entry`.`entry_allow_comments`, `mt_entry`.`entry_allow_pings`, `mt_entry`.`entry_atom_id`, `mt_entry`.`entry_author_id`, `mt_entry`.`entry_authored_on`, `mt_entry`.`entry_basename`, `mt_entry`.`entry_blog_id`, `mt_entry`.`entry_category_id`, `mt_entry`.`entry_class`, `mt_entry`.`entry_comment_count`, `mt_entry`.`entry_convert_breaks`, `mt_entry`.`entry_created_by`, `mt_entry`.`entry_created_on`, `mt_entry`.`entry_excerpt`, `mt_entry`.`entry_keywords`, `mt_entry`.`entry_modified_by`, `mt_entry`.`entry_modified_on`, `mt_entry`.`entry_ping_count`, `mt_entry`.`entry_pinged_urls`, `mt_entry`.`entry_status`, `mt_entry`.`entry_tangent_cache`, `mt_entry`.`entry_template_id`, `mt_entry`.`entry_text`, `mt_entry`.`entry_text_more`, `mt_entry`.`entry_title`, `mt_entry`.`entry_to_ping_urls`, `mt_entry`.`entry_week_number` FROM `mt_entry` INNER JOIN `mt_placement` ON (`mt_entry`.`entry_id` = `mt_placement`.`placement_entry_id`) INNER JOIN `mt_category` ON (`mt_placement`.`placement_category_id` = `mt_category`.`category_id`) WHERE (`mt_entry`.`entry_status` = 2  AND `mt_category`.`category_basename` IN ('business_review' /*... omitted 3 items ...*/ ) AND NOT (`mt_entry`.`entry_id` IN (53441))) ORDER BY `mt_entry`.`entry_authored_on` DESC LIMIT 4\G


Give it a Try !!!