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Teach me how to optimize my dedicated server

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I

igordr

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22
2012
1
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Hello,

I am Igor, have 19 years, live in Serbia.
I own dedicated server with about 20 sites on it, but just two of them have traffic - all together 10 000 unique visitors daily.

My server details:

Code: 
HDD     2x 500 GB SATA
RAM     6 GB DDR2-RAM
CPU     AMD Athlon 64 X2 3400+, Dual-Core
CentOS 6.3
I also use licensed version of WHM/Cpanel, regularly updated.
Have SHH access, root.

My problem: Server load is enormous, taking too long to respond [30+ seconds].

When i run TOP in shh:

Code: 
top - 14:48:30 up 8 days, 22:35,  1 user,  load average: 80.32, 86.56, 76.90
Tasks: 377 total,  44 running, 330 sleeping,   1 stopped,   2 zombie
Cpu(s): 70.7%us, 21.9%sy,  0.0%ni,  0.0%id,  0.0%wa,  0.0%hi,  7.4%si,  0.0%st
Mem:   5733840k total,  4201196k used,  1532644k free,   159604k buffers
Swap:  2097136k total,   182140k used,  1914996k free,   768072k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 4389 mysql     20   0  633m  75m 4484 S 24.3  1.3   0:51.67 mysqld
  617 nobody    20   0 43900  472  264 S  2.0  0.0 288:42.78 perl
 3209 nobody    20   0  138m  32m 4084 R  1.6  0.6   0:03.53 httpd
 4484 nobody    20   0  129m  22m 3736 R  1.6  0.4   0:01.31 httpd
 4523 nobody    20   0  127m  21m 3624 R  1.6  0.4   0:00.92 httpd
 4710 nobody    20   0  119m  11m 3168 S  1.6  0.2   0:00.09 httpd
 2348 nobody    20   0  140m  33m 3976 R  1.4  0.6   0:04.03 httpd
 2825 nobody    20   0  141m  35m 4060 R  1.4  0.6   0:04.07 httpd
 2833 nobody    20   0  140m  34m 3968 R  1.4  0.6   0:02.32 httpd
 3004 nobody    20   0  140m  34m 3848 S  1.4  0.6   0:03.17 httpd
 3277 nobody    20   0  118m  12m 3624 R  1.4  0.2   0:01.54 httpd
 3348 nobody    20   0  142m  36m 3860 R  1.4  0.6   0:03.51 httpd
 3893 nobody    20   0 52904  10m 1344 R  1.4  0.2 384:43.25 perl
 3895 nobody    20   0 54236  11m 1024 S  1.4  0.2   0:07.77 perl
 3897 nobody    20   0 54580  11m 1024 R  1.4  0.2   0:07.71 perl
 3899 nobody    20   0 54232  11m 1024 R  1.4  0.2   0:07.71 perl
 3902 nobody    20   0 54312  11m 1024 R  1.4  0.2   0:07.75 perl
Current my.cnf looks like:

Code: 
[mysqld]
max_connections = 500
key_buffer = 32M
myisam_sort_buffer_size = 32M
join_buffer_size = 1M
read_buffer_size = 1M
sort_buffer_size = 2M
table_cache = 4000
thread_cache_size = 286
interactive_timeout = 25
wait_timeout = 7000
connect_timeout = 10
max_allowed_packet = 16M
max_connect_errors = 10
query_cache_limit = 2M
query_cache_size = 24M
query_cache_type = 1
tmp_table_size = 32M
skip-innodb
[mysqld_safe]
open_files_limit = 8192
[mysqldump]
quick
max_allowed_packet = 16M
[myisamchk]
key_buffer = 64M
sort_buffer = 64M
read_buffer = 16M
write_buffer = 16M
[mysqlhotcopy]
interactive-timeout
Default my.cnf which i have changed according to this tutorial [http://www.firemakerhosting.com/ser...timizing-mysql-for-whm-dedicated-server-vps/] was looking:

Code: 
[mysqld]
set-variable = max_connections=500
query_cache_limit       = 2M
query_cache_size        = 32M
table_cache = 400
thread_cache_size = 286
log-slow-queries
safe-show-database
After running mysqltuner.pl with current my.cnf settings i get:

Code: 
root@bravo612 [~]# ./mysqltuner.pl

 >>  MySQLTuner 1.2.0 - Major Hayden <major@mhtx.net>
 >>  Bug reports, feature requests, and downloads at http://mysqltuner.com/
 >>  Run with '--help' for additional options and output filtering

-------- General Statistics --------------------------------------------------
[--] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.1.63-cll
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: +Archive -BDB -Federated -InnoDB -ISAM -NDBCluster
[--] Data in MyISAM tables: 172M (Tables: 715)
[!!] Total fragmented tables: 29

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

-------- Performance Metrics -------------------------------------------------
[--] Up for: 9m 29s (32K q [57.963 qps], 990 conn, TX: 64M, RX: 2M)
[--] Reads / Writes: 92% / 8%
[--] Total buffers: 72.0M global + 4.5M per thread (300 max threads)
[OK] Maximum possible memory usage: 1.4G (25% of installed RAM)
[OK] Slow queries: 0% (86/32K)
[OK] Highest usage of available connections: 24% (74/300)
[OK] Key buffer size / total MyISAM indexes: 32.0M/52.8M
[OK] Key buffer hit rate: 99.7% (2M cached / 5K reads)
[OK] Query cache efficiency: 49.1% (12K cached / 25K selects)
[OK] Query cache prunes per day: 0
[OK] Sorts requiring temporary tables: 2% (23 temp sorts / 1K sorts)
[!!] Temporary tables created on disk: 38% (379 on disk / 979 total)
[OK] Thread cache hit rate: 92% (74 created / 990 connections)
[OK] Table cache hit rate: 97% (292 open / 299 opened)
[OK] Open file limit used: 5% (459/8K)
[OK] Table locks acquired immediately: 95% (14K immediate / 14K locks)

-------- Recommendations -----------------------------------------------------
General recommendations:
    Run OPTIMIZE TABLE to defragment tables for better performance
    MySQL started within last 24 hours - recommendations may be inaccurate
    Enable the slow query log to troubleshoot bad queries
    When making adjustments, make tmp_table_size/max_heap_table_size equal
    Reduce your SELECT DISTINCT queries without LIMIT clauses
Variables to adjust:
    tmp_table_size (> 16M)
    max_heap_table_size (> 16M)
Also, i need to mention, i have installed VNC service with GNOME desktop environment on current server, but i don't use it regularly.
Also, i have spotted, when i clean seass_ files server is faster, but just minute or two, after that, it's the same...

If you need any additional details, please ask me.

I won't sleep tonight until my web server start to load faster, so please, reply me, i am ready to teach HOW TO... =)

Greetings,
Igor

---------- Post added 22nd Jul 2012 at 01:11 PM ---------- Previous post was 21st Jul 2012 at 01:47 PM ----------

Still no reply. May somebody help me, please?
 
4 comments
Disable those sites temporarily. Create a temp landing page.

Then google for server optimization guides, there are plenty of guides on the web.
Check those of Bharat, posted here.
 
Well at the first you can try tuning mysql :-

Code: 
wget http://mysqltuner.com/mysqltuner.pl
chmod +x mysqltuner.pl
./mysqltuner.pl

Then , check the instructions which is listed by this script on your ssh panel.

then try changing the web server , install nginx or lighttpd .

Also from here you can get some guides .

http://www.wjunction.com/13-tutorials-guides/148113-tutorials-servers-server-management.html

Let me know , if anything else needed . Probably i can help in decreasing some loads .
 
I assume you run php as suPHP(default cPanel setup?). If so, I'd highly recommend you running FCGID instead. FCGID, if configured properly, will do a lot of difference(preventing one account from using all resources, reducing resource usage, improving loading speeds etc).

With FCGID you can also run PHP opcode cache systems such as eAccelerator(recommended!), XCache etc

You may also want to run nginx or Varnish in front of Apache for serving/static content. It is also very important optimization step on the server end.

I realize this may be too complicated for a beginner so I'd suggest you hiring someone to do the above right. Otherwise, my suggestions won't do any good if configured badly.
 
Thanks everyone.

Especially thanks to my new friend Bharat, which helped me to resolve all issue on the server.

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