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I notices that applications use almost all memory on my ubuntu 14.04 server.

Can you look into my htop screen and let me know whether this situation is normal?

Ubuntu server memory usage

There are many processes for two java application, for both of them all related threads use 3.7% and 4.8% of memory. Is it for each thread or only for root process 3.7%?

How can I see in percentage which process use this percentage of memory and how many? I have 60 processes with 3.7% so it is much more than 100%

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All threads in a Java process share almost all memory. Each thread will have a local stack which is usually less than a megabyte. As you see all the relate threads show the same memory utilization. The 60 related processes showing 3.7% memory utilization might be using 3.8% of available memory.

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