Question on slow queries

[Michele Quaini]

Hello, I ran a tool on my website and i got these ranking of slow queries. The db engine is INNODB, and i see that the COMMIT and some UPDATES is @ first position. How can i fix this problem? Below i have pasted my my.cnf. May thanks.

# 838.2s user time, 2.2s system time, 113.31M rss, 199.30M vsz
# Current date: Thu May 30 10:09:18 2013
# Hostname: ***
# Files: /var/lib/mysql/mysql-slow.log
# Overall: 3.25M total, 1.11k unique, 64.27 QPS, 0.18x concurrency _______
# Time range: 2013-05-29 19:51:01 to 2013-05-30 09:53:35
# Attribute total min max avg 95% stddev median
# ============ ======= ======= ======= ======= ======= ======= =======
# Exec time 8915s 1us 24s 3ms 1ms 70ms 27us
# Lock time 343s 0 5s 105us 260us 5ms 0
# Rows sent 17.53M 0 151.08k 5.66 19.46 129.22 0
# Rows examine 245.73M 0 151.08k 79.31 28.75 1.47k 0
# Query size 242.82M 5 55.10k 78.28 183.58 101.50 36.69

# Profile
# Rank Query ID Response time Calls R/Call Apdx V/M Item
# ==== ================== =============== ======= ====== ==== ===== ======
# 1 0x813031B8BBC3B329 944.3823 10.6% 14740 0.0641 0.99 1.47 COMMIT
# 2 0x2946F5C805C641F0 731.4449 8.2% 4398 0.1663 0.98 1.80 UPDATE character_stats
# 3 0x06BA864C75EF674B 526.1830 5.9% 1452 0.3624 0.96 1.33 UPDATE users
# 4 0xDD330E911DAEA564 462.8022 5.2% 2205 0.2099 0.98 1.16 UPDATE characters
# 5 0xBD6E40FB34D33F35 407.3738 4.6% 4344 0.0938 0.99 1.47 UPDATE items
# 6 0x401B579DF69F42EC 369.0405 4.1% 240553 0.0015 1.00 1.94 SELECT characters
# 7 0x594F579F62DEA5CF 367.6932 4.1% 1264 0.2909 0.96 1.75 INSERT stats_globals
# 8 0x02744255916D5340 349.9996 3.9% 144223 0.0024 1.00 1.63 SELECT users
# 9 0x1A0E0318A9EB259C 273.7407 3.1% 124777 0.0022 1.00 0.26 SHOW COLUMNS
# 10 0xA35332B856A53F6B 199.9855 2.2% 111913 0.0018 1.00 0.19 SHOW COLUMNS
# 11 0x75B1DBD48BF47623 199.0869 2.2% 129 1.5433 0.74 4.24 INSERT stats_globals
# 12 0x582611CFF1C063BB 183.3514 2.1% 649 0.2825 0.98 0.85 UPDATE characters
# 13 0xDF1FB1A2536CEFBE 173.0813 1.9% 619 0.2796 0.97 0.81 UPDATE messages
# 14 0x754B29BDA72EF43B 168.5860 1.9% 627 0.2689 0.97 0.89 INSERT toplistvotes
# 15 0xE5C6D63541E4E1E2 164.9002 1.8% 1452 0.1136 0.99 1.38 INSERT trace_user_logins
# 16 0x0D2F027A30BDA707 163.3852 1.8% 626 0.2610 0.98 0.79 INSERT messages
# 17 0x076B778757C29A1E 140.1671 1.6% 358 0.3915 0.96 3.75 UPDATE items
# 18 0x8F02E08F358A68AC 119.7538 1.3% 1562 0.0767 1.00 0.51 UPDATE character_actions
# 19 0xC13C4066C2C95AF5 117.0228 1.3% 1562 0.0749 1.00 3.15 SELECT character_actions
# 20 0xB5F7525A5CB371E9 105.5070 1.2% 395 0.2671 0.97 1.63 INSERT character_actions
# 21 0x79136FFAD369F1BA 105.3963 1.2% 354 0.2977 0.97 1.26 INSERT character_actions
# 34 0x7B5B7941028EDE4B 54.0050 0.6% 55 0.9819 0.88 4.13 UPDATE ads
# 57 0x9E7261B3F59F331E 19.2066 0.2% 58 0.3311 0.95 0.67 INSERT character_actions
# 64 0x67A347A2812914DF 16.0391 0.2% 25 0.6416 0.88 3.22 SELECT messages_archive
# 69 0x57A18166A52BD016 14.5479 0.2% 55 0.2645 0.95 4.60 SELECT ad_extras
# 71 0xD350A58013580CAE 14.5026 0.2% 52 0.2789 0.96 0.49 INSERT character_actions
# 73 0xABCD223742501FB1 13.8047 0.2% 22 0.6275 0.89 1.54 UPDATE users
# 83 0xFBB53CDC0C3D2272 10.6655 0.1% 31 0.3440 0.94 0.94 INSERT items
# 98 0x2857E030AF6C119B 8.0144 0.1% 13 0.6165 0.88 1.84 INSERT group_characters
# 107 0x4C61C246A8EE9F3C 6.0430 0.1% 12 0.5036 0.92 0.85 INSERT character_actions
# MISC 0xMISC 2485.5319 27.9% 2590372 0.0010 NS 0.0 <1074 ITEMS>

my.cnf

[mysqlhotcopy]
interactive-timeout

[mysqld]
key_buffer=64M
thread_concurrency=8
max_connections=40
max_user_connections=40

#long_query_time=0
#log_slow_queries="/var/lib/mysql/mysql-slow.log"

read_buffer_size=2M
table_cache=750
tmp_table_size=256M

# InnoDB
# Set buffer pool size to 50-80% of your computer's memory
innodb_buffer_pool_size=640M
innodb_additional_mem_pool_size=20M
# Set the log file size to about 25% of the buffer pool size
innodb_log_file_size=128M
innodb_log_buffer_size=8M
innodb_file_per_table=1
innodb_thread_concurrency=2

wait_timeout=40
skip-external-locking
myisam_sort_buffer_size=64M
connect_timeout=10
max_allowed_packet=1M
server-id=1
thread_cache_size=8
sort_buffer_size=2M
read_rnd_buffer_size=8M
query_cache_size=56M

open_files_limit=2966
[myisamchk]
key_buffer=64M
sort_buffer_size=64M
write_buffer=2M
read_buffer=2M

[mysqldump]
quick
max_allowed_packet=16M
[mysql]
no-auto-rehash