You have a variety of tools at your fingertips to help work out the cause of a problem. Over time you will expand what is in your toolbelt, but to start with you must know how to use each of these:
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top,vmstat,iostat,systat,sar,mpstathelp you see the current state of the system - what is running, what is using cpu, memory? Is the disk being heavily used? There is a great deal of information, and knowing how these tools work will help you pick out the bits you should focus on. -
tcpdump,ngrepIf you suspect you have a network-related problem,tcpdumpandngrepcan help you confirm it.