My Rig settings

DirectAdmin roughly running 72 accounts, most of them are lightweight php based websites, 1 is really heavy Joomla website, with forums, gallery, messaging system, lots of users. So a lot of MySQL queries.

DirectAdmin settings:
cat directadmin.conf
SSL=0
addip=/usr/local/directadmin/scripts/addip
admin_helper=admin.site-helper.com
admindir=./data/admin
apache_public_html=0
apache_ver=2.0
apachecert=/etc/httpd/conf/ssl.crt/server.crt
apacheconf=/etc/httpd/conf/extra/directadmin-vhosts.conf
apacheips=/etc/httpd/conf/ips.conf
apachekey=/etc/httpd/conf/ssl.key/server.key
apachelogdir=/var/log/httpd/domains
apachemimetypes=/etc/mime.types
backup_hard_link_check=0
brute_force_log_scanner=0
brute_force_time_limit=120
brutecount=10
bruteforce=1
cacert=/usr/local/directadmin/conf/cacert.pem
cakey=/usr/local/directadmin/conf/cakey.pem
check_partitions=2
check_subdomain_owner=1
clear_blacklist_ip_time=700
clear_brute_log_entry_time=3
clear_brute_log_time=24
cloud_cache=0
cluster=0
demodocsroot=./data/skins/enhanced
docsroot=./data/skins/enhanced
dovecot=1
emailspoolvirtual=/var/spool/virtual
emailvirtual=/etc/virtual
enforce_difficult_passwords=0
ethernet_dev=venet0:0
exempt_local_block=1
filemanager_du=1
fm_dir_permissons=755
fm_file_permissions=644
fm_owners=|USER|:|GROUP|
frontpage_on=0
ftpconfig=/etc/proftpd.conf
ftppasswd=/etc/proftpd.passwd
ftpvhosts=/etc/proftpd.vhosts.conf
ip_brutecount=1000
license=/usr/local/directadmin/conf/license.key
log_rotate_size=5
logdir=/var/log/directadmin
logger=/usr/local/directadmin/logger
loghostname=0
login_history=10
logs_to_keep=5
lost_password=0
max_username_length=10
maxfilesize=104857600
mysqlconf=/usr/local/directadmin/conf/mysql.conf
namedconfig=/etc/bind/named.conf
nameddir=/etc/bind
nginx=0
nginx_proxy=0
numservers=5
owsadm=/usr/local/frontpage/version5.0/bin/owsadm.exe
partition_usage_threshold=90
pureftp=1
purge_spam_days=0
quota_partition=/
quota_update_interval=10
removeip=/usr/local/directadmin/scripts/removeip
reseller_helper=reseller.site-helper.com
secure_access_group=access
servername=vps51.lithost.lt
serverpath=/usr/local/directadmin
session_minutes=60
skinsdir=./data/skins
sshdconfig=/etc/ssh/sshd_config
ssl_cipher=SSLv3
taskqueue=/usr/local/directadmin/data/task.queue
templates=/usr/local/directadmin/data/templates
ticketsdir=/usr/local/directadmin/data/tickets
timeout=60
tmpdir=../../../home/tmp
unified_ftp_password_file=1
user_brutecount=1000
user_can_select_skin=1
user_helper=www.site-helper.com
userdata=./data/users

MySQL current configs:

[mysqld]
max_connections=40
join_buffer_size = 4M
tmp_table_size = 300M
max_heap_table_size = 300M
query_cache_size = 128M
query_cache_limit = 20M
key_buffer=64M
key_buffer_size = 1G
thread_cache_size = 16K
open_files_limit = 10000
table_cache = 14k
table_open_cache = 14k
table_definition_cache = 44k
innodb_buffer_pool_size = 1024M
slow_query_log
local-infile=0
low_priority_updates=1
concurrent_insert=ALWAYS
long_query_time = 5
innodb_file_per_table=1
connect_timeout = 14400
interactive_timeout = 14400

#innodb_optimize_fulltext_only=1
#innodb_ft_num_word_optimize=2000
#log-bin=/home/mysql/
log-bin-index=/usr/local/mysql/data/
#performance schema = 'ON' #sitas gali po restarto mysql startuoti, dar nebandytas.
read_buffer_size = 256K

log_queries_not_using_indexes =1
long_query_time = 2

# INNODB #
#innodb_flush_method            = O_DIRECT
#innodb_log_files_in_group      = 2
#innodb_log_file_size            = 128M
#innodb_flush_log_at_trx_commit  = 2
#innodb_file_per_table          = 1
#innodb_buffer_pool_size        = 2G

#skip-host-cache
#skip-name-resolve

mysqltuner.pl

 >>  MySQLTuner 1.3.0 - Major Hayden <major@mhtx.net>
 >>  Bug reports, feature requests, and downloads at http://mysqltuner.com/
 >>  Run with '--help' for additional options and output filtering
[OK] Currently running supported MySQL version 5.5.37-log
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: +ARCHIVE +BLACKHOLE +CSV -FEDERATED +InnoDB +MRG_MYISAM
[--] Data in MyISAM tables: 1G (Tables: 3314)
[--] Data in InnoDB tables: 775M (Tables: 1391)
[--] Data in PERFORMANCE_SCHEMA tables: 0B (Tables: 17)
[--] Data in MEMORY tables: 0B (Tables: 4)
[!!] Total fragmented tables: 285

-------- Security Recommendations  -------------------------------------------
[OK] All database users have passwords assigned

-------- Performance Metrics -------------------------------------------------
[--] Up for: 39d 18h 30m 19s (3B q [954.863 qps], 10M conn, TX: 3898B, RX: 192B)
[--] Reads / Writes: 77% / 23%
[--] Total buffers: 2.4G global + 6.8M per thread (40 max threads)
[OK] Maximum possible memory usage: 2.7G (44% of installed RAM)
[OK] Slow queries: 0% (6M/3B)
[!!] Highest connection usage: 100%  (41/40)
[OK] Key buffer size / total MyISAM indexes: 1.0G/361.7M
[OK] Key buffer hit rate: 100.0% (333M cached / 53K reads)
[OK] Query cache efficiency: 99.6% (3B cached / 3B selects)
[!!] Query cache prunes per day: 180004
[OK] Sorts requiring temporary tables: 0% (10K temp sorts / 3M sorts)
[!!] Joins performed without indexes: 444369
[!!] Temporary tables created on disk: 33% (1M on disk / 4M total)
[OK] Thread cache hit rate: 99% (41 created / 10M connections)
[!!] Table cache hit rate: 1% (8K open / 495K opened)
[OK] Open file limit used: 32% (9K/28K)
[OK] Table locks acquired immediately: 99% (18M immediate / 18M locks)
[OK] InnoDB buffer pool / data size: 1.0G/775.8M
[OK] InnoDB log waits: 0
-------- Recommendations -----------------------------------------------------
General recommendations:
    Run OPTIMIZE TABLE to defragment tables for better performance
    Reduce or eliminate persistent connections to reduce connection usage
    Adjust your join queries to always utilize indexes
    Temporary table size is already large - reduce result set size
    Reduce your SELECT DISTINCT queries without LIMIT clauses
    Increase table_cache gradually to avoid file descriptor limits
    Read this before increasing table_cache over 64: http://bit.ly/1mi7c4C
Variables to adjust:
    max_connections (> 40)
    wait_timeout (< 28800)
    interactive_timeout (< 14400)
    query_cache_size (> 128M)
    join_buffer_size (> 4.0M, or always use indexes with joins)
    table_cache (> 14336)

./tuning-primer.sh

        -- MYSQL PERFORMANCE TUNING PRIMER --
             - By: Matthew Montgomery -

MySQL Version 5.5.37-log x86_64

Uptime = 39 days 18 hrs 41 min 53 sec
Avg. qps = 954
Total Questions = 3281825174
Threads Connected = 1

Server has been running for over 48hrs.
It should be safe to follow these recommendations

To find out more information on how each of these
runtime variables effects performance visit:
http://dev.mysql.com/doc/refman/5.5/en/server-system-variables.html
Visit http://www.mysql.com/products/enterprise/advisors.html
for info about MySQL's Enterprise Monitoring and Advisory Service

SLOW QUERIES
The slow query log is enabled.
Current long_query_time = 2.000000 sec.
You have 6936462 out of 3281825195 that take longer than 2.000000 sec. to complete
Your long_query_time seems to be fine

BINARY UPDATE LOG
The binary update log is NOT enabled.
You will not be able to do point in time recovery
See http://dev.mysql.com/doc/refman/5.5/en/point-in-time-recovery.html

WORKER THREADS
Current thread_cache_size = 16384
Current threads_cached = 40
Current threads_per_sec = 0
Historic threads_per_sec = 0
Your thread_cache_size is fine

MAX CONNECTIONS
Current max_connections = 40
Current threads_connected = 1
Historic max_used_connections = 41
The number of used connections is 102% of the configured maximum.
You should raise max_connections

INNODB STATUS
Current InnoDB index space = 263 M
Current InnoDB data space = 775 M
Current InnoDB buffer pool free = 0 %
Current innodb_buffer_pool_size = 1.00 G
Depending on how much space your innodb indexes take up it may be safe
to increase this value to up to 2 / 3 of total system memory

MEMORY USAGE
Max Memory Ever Allocated : 2.41 G
Configured Max Per-thread Buffers : 270 M
Configured Max Global Buffers : 2.14 G
Configured Max Memory Limit : 2.40 G
Physical Memory : 6.00 G
Max memory limit seem to be within acceptable norms

KEY BUFFER
Current MyISAM index space = 361 M
Current key_buffer_size = 1.00 G
Key cache miss rate is 1 : 6249
Key buffer free ratio = 77 %
Your key_buffer_size seems to be fine

QUERY CACHE
Query cache is enabled
Current query_cache_size = 128 M
Current query_cache_used = 111 M
Current query_cache_limit = 20 M
Current Query cache Memory fill ratio = 87.11 %
Current query_cache_min_res_unit = 4 K
However, 7159732 queries have been removed from the query cache due to lack of memory
Perhaps you should raise query_cache_size
MySQL won't cache query results that are larger than query_cache_limit in size

SORT OPERATIONS
Current sort_buffer_size = 2 M
Current read_rnd_buffer_size = 256 K
Sort buffer seems to be fine

JOINS
Current join_buffer_size = 4.00 M
You have had 443748 queries where a join could not use an index properly
You have had 713 joins without keys that check for key usage after each row
join_buffer_size >= 4 M
This is not advised
You should enable "log-queries-not-using-indexes"
Then look for non indexed joins in the slow query log.

OPEN FILES LIMIT
Current open_files_limit = 28722 files
The open_files_limit should typically be set to at least 2x-3x
that of table_cache if you have heavy MyISAM usage.
Your open_files_limit value seems to be fine

TABLE CACHE
Current table_open_cache = 14336 tables
Current table_definition_cache = 45056 tables
You have a total of 4750 tables
You have 8106 open tables.
The table_cache value seems to be fine

TEMP TABLES
Current max_heap_table_size = 300 M
Current tmp_table_size = 300 M
Of 3008164 temp tables, 33% were created on disk
Perhaps you should increase your tmp_table_size and/or max_heap_table_size
to reduce the number of disk-based temporary tables
Note! BLOB and TEXT columns are not allow in memory tables.
If you are using these columns raising these values might not impact your
ratio of on disk temp tables.

TABLE SCANS
Current read_buffer_size = 256 K
Current table scan ratio = 4577 : 1
You have a high ratio of sequential access requests to SELECTs
You may benefit from raising read_buffer_size and/or improving your use of indexes.

TABLE LOCKING
Current Lock Wait ratio = 1 : 23492
Your table locking seems to be fine

Host machine hardware:
node1
    description: Rack Mount Chassis
    product: PowerEdge 2950
    vendor: Dell Inc.
    serial: 249N5D1
    width: 64 bits
    capabilities: smbios-2.5 dmi-2.5 vsyscall64 vsyscall32
    configuration: boot=normal chassis=rackmount uuid=44454C4C-3400-1039-804E-B2C04F354431
  *-core
       description: Motherboard
       product: 0DT021
       vendor: Dell Inc.
       physical id: 0
       version: A02
       serial: ..CN1374074P006Q.
     *-firmware
          description: BIOS
          vendor: Dell Inc.
          physical id: 0
          version: 2.7.0 (10/30/2010)
          size: 64KiB
          capacity: 960KiB
          capabilities: isa pci pnp upgrade shadowing escd cdboot bootselect edd int13floppytoshiba int13floppy360 int13floppy1200 int13floppy720 int5printscreen int9keyboard int14serial int17printer int10video acpi usb biosbootspecification netboot
     *-cpu:0
          description: CPU
          product: Intel(R) Xeon(R) CPU           E5345  @ 2.33GHz
          vendor: Intel Corp.
          physical id: 400
          bus info: cpu@0
          version: Intel(R) Xeon(R) CPU           E5345  @ 2.33GHz
          slot: CPU1
          size: 2333MHz
          capacity: 3600MHz
          width: 64 bits
          clock: 1333MHz
          capabilities: fpu fpu_exception wp vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx x86-64 constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm tpr_shadow
        *-cache:0
             description: L1 cache
             physical id: 700
             size: 128KiB
             capacity: 128KiB
             capabilities: internal write-back data
        *-cache:1
             description: L2 cache
             physical id: 701
             size: 8MiB
             capacity: 8MiB
             capabilities: internal write-back unified
     *-cpu:1
          description: CPU
          product: Intel(R) Xeon(R) CPU           E5345  @ 2.33GHz
          vendor: Intel Corp.
          physical id: 401
          bus info: cpu@1
          version: Intel(R) Xeon(R) CPU           E5345  @ 2.33GHz
          slot: CPU2
          size: 2333MHz
          capacity: 3600MHz
          width: 64 bits
          clock: 1333MHz
          capabilities: fpu fpu_exception wp vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx x86-64 constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm tpr_shadow
        *-cache:0
             description: L1 cache
             physical id: 703
             size: 128KiB
             capacity: 128KiB
             capabilities: internal write-back data
        *-cache:1
             description: L2 cache
             physical id: 704
             size: 8MiB
             capacity: 8MiB
             capabilities: internal write-back unified
     *-memory
          description: System Memory
          physical id: 1000
          slot: System board or motherboard
          size: 32GiB
        *-bank:0
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 0
             serial: 02291806
             slot: DIMM1
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:1
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 1
             serial: 0229100E
             slot: DIMM2
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:2
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 2
             serial: 02291604
             slot: DIMM3
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:3
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 3
             serial: 02291206
             slot: DIMM4
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:4
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 4
             serial: 0229190D
             slot: DIMM5
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:5
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 5
             serial: 02291905
             slot: DIMM6
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:6
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 6
             serial: 0229130D
             slot: DIMM7
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
        *-bank:7
             description: FB-DIMM DDR2 FB-DIMM Synchronous 667 MHz (1.5 ns)
             product: HYMP151F72CP8D5-Y5
             vendor: 80AD7FB380AD
             physical id: 7
             serial: 02291006
             slot: DIMM8
             size: 4GiB
             width: 64 bits
             clock: 667MHz (1.5ns)
     *-pci:0
          description: Host bridge
          product: 5000X Chipset Memory Controller Hub
          vendor: Intel Corporation
          physical id: 100
          bus info: pci@0000:00:00.0
          version: 12
          width: 32 bits
          clock: 33MHz
        *-pci:0
             description: PCI bridge
             product: 5000 Series Chipset PCI Express x4 Port 2
             vendor: Intel Corporation
             physical id: 2
             bus info: pci@0000:00:02.0
             version: 12
             width: 32 bits
             clock: 33MHz
             capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:88 memory:f2000000-f7ffffff
           *-pci:0
                description: PCI bridge
                product: 6311ESB/6321ESB PCI Express Upstream Port
                vendor: Intel Corporation
                physical id: 0
                bus info: pci@0000:06:00.0
                version: 01
                width: 32 bits
                clock: 33MHz
                capabilities: pci pciexpress pm normal_decode bus_master cap_list
                resources: memory:f4000000-f7ffffff
              *-pci:0
                   description: PCI bridge
                   product: 6311ESB/6321ESB PCI Express Downstream Port E1
                   vendor: Intel Corporation
                   physical id: 0
                   bus info: pci@0000:07:00.0
                   version: 01
                   width: 32 bits
                   clock: 33MHz
                   capabilities: pci pciexpress msi pm normal_decode bus_master cap_list
                   resources: memory:f4000000-f7ffffff
                 *-pci
                      description: PCI bridge
                      product: EPB PCI-Express to PCI-X Bridge
                      vendor: Broadcom
                      physical id: 0
                      bus info: pci@0000:08:00.0
                      version: c3
                      width: 32 bits
                      clock: 33MHz
                      capabilities: pci pciexpress pcix pm normal_decode bus_master cap_list
                      resources: memory:f4000000-f7ffffff
                    *-network
                         description: Ethernet interface
                         product: NetXtreme II BCM5708 Gigabit Ethernet
                         vendor: Broadcom Corporation
                         physical id: 0
                         bus info: pci@0000:09:00.0
                         logical name: eth1
                         version: 12
                         serial: 00:19:b9:ca:f3:0f
                         size: 100MB/s
                         capacity: 1GB/s
                         width: 64 bits
                         clock: 66MHz
                         capabilities: pcix pm vpd msi bus_master cap_list ethernet physical tp 10bt 10bt-fd 100bt 100bt-fd 1000bt-fd autonegotiation
                         configuration: autonegotiation=on broadcast=yes driver=bnx2 driverversion=2.2.3f duplex=full firmware=7.4.8 bc 5.0.4 UMP 1.1.9 latency=64 link=yes mingnt=64 multicast=yes port=twisted pair speed=100MB/s
                         resources: irq:97 memory:f4000000-f5ffffff
              *-pci:1
                   description: PCI bridge
                   product: 6311ESB/6321ESB PCI Express Downstream Port E2
                   vendor: Intel Corporation
                   physical id: 1
                   bus info: pci@0000:07:01.0
                   version: 01
                   width: 32 bits
                   clock: 33MHz
                   capabilities: pci pciexpress msi pm normal_decode bus_master cap_list
           *-pci:1
                description: PCI bridge
                product: 6311ESB/6321ESB PCI Express to PCI-X Bridge
                vendor: Intel Corporation
                physical id: 0.3
                bus info: pci@0000:06:00.3
                version: 01
                width: 32 bits
                clock: 33MHz
                capabilities: pci pciexpress pm pcix normal_decode bus_master cap_list
        *-pci:1
             description: PCI bridge
             product: 5000 Series Chipset PCI Express x4 Port 3
             vendor: Intel Corporation
             physical id: 3
             bus info: pci@0000:00:03.0
             version: 12
             width: 32 bits
             clock: 33MHz
             capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:89 memory:fc300000-fc5fffff ioport:d8000000(size=1048576)
           *-pci:0
                description: PCI bridge
                product: 80333 Segment-A PCI Express-to-PCI Express Bridge
                vendor: Intel Corporation
                physical id: 0
                bus info: pci@0000:01:00.0
                version: 00
                width: 32 bits
                clock: 33MHz
                capabilities: pci pciexpress msi pm pcix normal_decode bus_master cap_list
                resources: memory:fc400000-fc5fffff ioport:d8000000(size=1048576)
              *-storage
                   description: RAID bus controller
                   product: PowerEdge Expandable RAID controller 5
                   vendor: Dell
                   physical id: e
                   bus info: pci@0000:02:0e.0
                   logical name: scsi0
                   version: 00
                   width: 32 bits
                   clock: 66MHz
                   capabilities: storage pm msi pcix bus_master cap_list rom
                   configuration: driver=megaraid_sas latency=32 mingnt=128
                   resources: irq:78 memory:d80f0000-d80fffff(prefetchable) memory:fc5c0000-fc5dffff memory:fc400000-fc407fff(prefetchable)
                 *-enclosure UNCLAIMED
                      description: SCSI Enclosure
                      product: BACKPLANE
                      vendor: DP
                      physical id: 0.8.0
                      bus info: scsi@0:0.8.0
                      version: 1.05
                      configuration: ansiversion=5
                 *-disk
                      description: SCSI Disk
                      product: PERC 5/i
                      vendor: DELL
                      physical id: 2.0.0
                      bus info: scsi@0:2.0.0
                      logical name: /dev/sda
                      version: 1.03
                      serial: 0042ea21f3f5000b19003f503cb08801
                      size: 836GiB (898GB)
                      capabilities: partitioned partitioned:dos
                      configuration: ansiversion=5 signature=000cabab
                    *-volume:0
                         description: EXT3 volume
                         vendor: Linux
                         physical id: 1
                         bus info: scsi@0:2.0.0,1
                         logical name: /dev/sda1
                         logical name: /boot
                         version: 1.0
                         serial: 033481e1-2b94-47b0-80ae-1774e090697b
                         size: 511MiB
                         capacity: 511MiB
                         capabilities: primary bootable journaled extended_attributes recover ext3 ext2 initialized
                         configuration: created=2013-04-25 00:49:29 filesystem=ext3 modified=2013-08-22 04:02:29 mount.fstype=ext3 mount.options=rw,relatime,errors=continue,barrier=0,data=ordered mounted=2013-08-22 04:02:29 state=mounted
                    *-volume:1
                         description: Linux LVM Physical Volume partition
                         physical id: 2
                         bus info: scsi@0:2.0.0,2
                         logical name: /dev/sda2
                         serial: HjTyL5-OnVm-vpKQ-XWok-rS3w-eV3J-AXdZG6
                         size: 836GiB
                         capacity: 836GiB
                         capabilities: primary multi lvm2
           *-pci:1
                description: PCI bridge
                product: 80333 Segment-B PCI Express-to-PCI Express Bridge
                vendor: Intel Corporation
                physical id: 0.2
                bus info: pci@0000:01:00.2
                version: 00
                width: 32 bits
                clock: 33MHz
                capabilities: pci pciexpress msi pm pcix normal_decode bus_master cap_list
        *-pci:2
             description: PCI bridge
             product: 5000 Series Chipset PCI Express x8 Port 4-5
             vendor: Intel Corporation
             physical id: 4
             bus info: pci@0000:00:04.0
             version: 12
             width: 32 bits
             clock: 33MHz
             capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:90
        *-pci:3
             description: PCI bridge
             product: 5000 Series Chipset PCI Express x4 Port 5
             vendor: Intel Corporation
             physical id: 5
             bus info: pci@0000:00:05.0
             version: 12
             width: 32 bits
             clock: 33MHz
             capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:91
        *-pci:4
             description: PCI bridge
             product: 5000 Series Chipset PCI Express x8 Port 6-7
             vendor: Intel Corporation
             physical id: 6
             bus info: pci@0000:00:06.0
             version: 12
             width: 32 bits
             clock: 33MHz
             capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:92
        *-pci:5
             description: PCI bridge
             product: 5000 Series Chipset PCI Express x4 Port 7
             vendor: Intel Corporation
             physical id: 7
             bus info: pci@0000:00:07.0
             version: 12
             width: 32 bits
             clock: 33MHz
             capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:93
        *-generic
             description: System peripheral
             product: 5000 Series Chipset DMA Engine
             vendor: Intel Corporation
             physical id: 8
             bus info: pci@0000:00:08.0
             version: 12
             width: 64 bits
             clock: 33MHz
             capabilities: pm msi pciexpress bus_master cap_list
             configuration: driver=ioatdma latency=0
             resources: irq:95 memory:fc600400-fc6007ff
        *-pci:6
             description: PCI bridge
             product: 631xESB/632xESB/3100 Chipset PCI Express Root Port 1
             vendor: Intel Corporation
             physical id: 1c
             bus info: pci@0000:00:1c.0
             version: 09
             width: 32 bits
             clock: 33MHz
             capabilities: pci pciexpress msi pm normal_decode bus_master cap_list
             configuration: driver=pcieport
             resources: irq:94 memory:f8000000-fbffffff
           *-pci
                description: PCI bridge
                product: EPB PCI-Express to PCI-X Bridge
                vendor: Broadcom
                physical id: 0
                bus info: pci@0000:04:00.0
                version: c3
                width: 64 bits
                clock: 33MHz
                capabilities: pci pciexpress pcix pm normal_decode bus_master cap_list
                resources: iomemory:220001f10-220001f0f memory:f8000000-fbffffff
              *-network
                   description: Ethernet interface
                   product: NetXtreme II BCM5708 Gigabit Ethernet
                   vendor: Broadcom Corporation
                   physical id: 0
                   bus info: pci@0000:05:00.0
                   logical name: eth0
                   version: 12
                   serial: 00:19:b9:ca:f3:0d
                   size: 100MB/s
                   capacity: 1GB/s
                   width: 64 bits
                   clock: 66MHz
                   capabilities: pcix pm vpd msi bus_master cap_list ethernet physical tp 10bt 10bt-fd 100bt 100bt-fd 1000bt-fd autonegotiation
                   configuration: autonegotiation=on broadcast=yes driver=bnx2 driverversion=2.2.3f duplex=full firmware=7.4.8 bc 5.0.4 UMP 1.1.9 latency=32 link=yes mingnt=64 multicast=yes port=twisted pair speed=100MB/s
                   resources: irq:96 memory:f8000000-f9ffffff
        *-usb:0
             description: USB controller
             product: 631xESB/632xESB/3100 Chipset UHCI USB Controller #1
             vendor: Intel Corporation
             physical id: 1d
             bus info: pci@0000:00:1d.0
             version: 09
             width: 32 bits
             clock: 33MHz
             capabilities: uhci bus_master
             configuration: driver=uhci_hcd latency=0
             resources: irq:21 ioport:dce0(size=32)
        *-usb:1
             description: USB controller
             product: 631xESB/632xESB/3100 Chipset UHCI USB Controller #2
             vendor: Intel Corporation
             physical id: 1d.1
             bus info: pci@0000:00:1d.1
             version: 09
             width: 32 bits
             clock: 33MHz
             capabilities: uhci bus_master
             configuration: driver=uhci_hcd latency=0
             resources: irq:20 ioport:dcc0(size=32)
        *-usb:2
             description: USB controller
             product: 631xESB/632xESB/3100 Chipset UHCI USB Controller #3
             vendor: Intel Corporation
             physical id: 1d.2
             bus info: pci@0000:00:1d.2
             version: 09
             width: 32 bits
             clock: 33MHz
             capabilities: uhci bus_master
             configuration: driver=uhci_hcd latency=0
             resources: irq:21 ioport:dca0(size=32)
        *-usb:3
             description: USB controller
             product: 631xESB/632xESB/3100 Chipset EHCI USB2 Controller
             vendor: Intel Corporation
             physical id: 1d.7
             bus info: pci@0000:00:1d.7
             version: 09
             width: 32 bits
             clock: 33MHz
             capabilities: pm debug ehci bus_master cap_list
             configuration: driver=ehci_hcd latency=0
             resources: irq:21 memory:fc600000-fc6003ff
        *-pci:7
             description: PCI bridge
             product: 82801 PCI Bridge
             vendor: Intel Corporation
             physical id: 1e
             bus info: pci@0000:00:1e.0
             version: d9
             width: 32 bits
             clock: 33MHz
             capabilities: pci subtractive_decode bus_master cap_list
             resources: ioport:e000(size=4096) memory:fc100000-fc2fffff ioport:d0000000(size=134217728)
           *-display
                description: VGA compatible controller
                product: ES1000
                vendor: Advanced Micro Devices [AMD] nee ATI
                physical id: d
                bus info: pci@0000:10:0d.0
                version: 02
                width: 32 bits
                clock: 33MHz
                capabilities: pm vga_controller bus_master vga_palette cap_list rom
                configuration: driver=radeon latency=32 mingnt=8
                resources: irq:19 memory:d0000000-d7ffffff(prefetchable) ioport:ec00(size=256) memory:fc2d0000-fc2dffff memory:fc100000-fc11ffff(prefetchable)
        *-isa
             description: ISA bridge
             product: 631xESB/632xESB/3100 Chipset LPC Interface Controller
             vendor: Intel Corporation
             physical id: 1f
             bus info: pci@0000:00:1f.0
             version: 09
             width: 32 bits
             clock: 33MHz
             capabilities: isa bus_master
             configuration: latency=0
     *-pci:1
          description: Host bridge
          product: 5000 Series Chipset FSB Registers
          vendor: Intel Corporation
          physical id: 101
          bus info: pci@0000:00:10.0
          version: 12
          width: 32 bits
          clock: 33MHz
          configuration: driver=i5000_edac
          resources: irq:0
     *-pci:2
          description: Host bridge
          product: 5000 Series Chipset FSB Registers
          vendor: Intel Corporation
          physical id: 102
          bus info: pci@0000:00:10.1
          version: 12
          width: 32 bits
          clock: 33MHz
     *-pci:3
          description: Host bridge
          product: 5000 Series Chipset FSB Registers
          vendor: Intel Corporation
          physical id: 103
          bus info: pci@0000:00:10.2
          version: 12
          width: 32 bits
          clock: 33MHz
     *-pci:4
          description: Host bridge
          product: 5000 Series Chipset Reserved Registers
          vendor: Intel Corporation
          physical id: 104
          bus info: pci@0000:00:11.0
          version: 12
          width: 32 bits
          clock: 33MHz
     *-pci:5
          description: Host bridge
          product: 5000 Series Chipset Reserved Registers
          vendor: Intel Corporation
          physical id: 105
          bus info: pci@0000:00:13.0
          version: 12
          width: 32 bits
          clock: 33MHz
     *-pci:6
          description: Host bridge
          product: 5000 Series Chipset FBD Registers
          vendor: Intel Corporation
          physical id: 106
          bus info: pci@0000:00:15.0
          version: 12
          width: 32 bits
          clock: 33MHz
     *-pci:7
          description: Host bridge
          product: 5000 Series Chipset FBD Registers
          vendor: Intel Corporation
          physical id: 107
          bus info: pci@0000:00:16.0
          version: 12
          width: 32 bits
          clock: 33MHz
  *-scsi:0
       physical id: 1
       bus info: scsi@4
       logical name: scsi4
       capabilities: scsi-host
       configuration: driver=usb-storage
  *-scsi:1
       physical id: 2
       bus info: scsi@5
       logical name: scsi5
       capabilities: scsi-host
       configuration: driver=usb-storage
  *-scsi:2
       physical id: 3
       bus info: scsi@6
       logical name: scsi6
       capabilities: scsi-host
       configuration: driver=usb-storage

Virtual Machine which has MySQL hosted on settings on OpenVZ:

PHYSPAGES="0:1572864"
SWAPPAGES="0:1572864"
KMEMSIZE="2927624192:3221225472"
DCACHESIZE="1463812096:1610612736"
LOCKEDPAGES="786432"
PRIVVMPAGES="unlimited"
SHMPAGES="unlimited"
NUMPROC="unlimited"
VMGUARPAGES="0:unlimited"
OOMGUARPAGES="0:unlimited"
NUMTCPSOCK="unlimited"
NUMFLOCK="unlimited"
NUMPTY="unlimited"
NUMSIGINFO="unlimited"
TCPSNDBUF="unlimited"
TCPRCVBUF="unlimited"
OTHERSOCKBUF="unlimited"
DGRAMRCVBUF="unlimited"
NUMOTHERSOCK="unlimited"
NUMFILE="unlimited"
NUMIPTENT="unlimited"

# Disk quota parameters (in form of softlimit:hardlimit)
DISKSPACE="314572800:346030080"
DISKINODES="60000000:66000000"
QUOTATIME="9223372036854775807"
QUOTAUGIDLIMIT="6144"

# CPU fair scheduler parameter
CPUUNITS="1000"
CPUS="4"
VE_ROOT="/var/lib/vz/root/$VEID"
VE_PRIVATE="/var/lib/vz/private/2001"
OSTEMPLATE="debian-7.0-standard_7.0-2_amd64"

ORIGIN_SAMPLE="2001"
DISK_QUOTA="yes"
CAPABILITY="CHOWN:on FOWNER:on FS_MASK:on"

Very frequent Anturis reports on mySQL:

Heavy join rate value 64.9895178197 % should be less than 20.0 %
Heavy join rate value 64.9895178197 % should be less than 10.0 %
On-disk temporary table rate value 37.0 % should be less than 20.0 %
On-disk temporary table rate value 37.0 % should be less than 10.0 %
Innodb buffer pool usage value 99.7085526818 % should be less than 90.0 %
Innodb buffer pool usage value 99.7085526818 % should be less than 80.0 %