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I'm running low on memory here:

$ free -h
             total       used       free     shared    buffers     cached
Mem:          1.9G       1.9G        83M         0B        28M       394M
-/+ buffers/cache:       1.4G       506M
Swap:         2.9G       705M       2.2G

Yet Top is showing that the only high-memory process running was java (Netbeans): (I used f key to select fields, sort by mem%)

%Cpu(s):  1.0 us,  1.0 sy,  0.0 ni, 96.2 id,  1.7 wa,  0.0 hi,  0.2 si,  0.0 st
KiB Mem:   2031108 total,  1946956 used,    84152 free,    29080 buffers
KiB Swap:  3063548 total,   722128 used,  2341420 free,   404272 cached

  PID USER      PR  NI  VIRT  RES  SHR S  %CPU %MEM    TIME+  COMMAND                                                                                                                 
12825 username  20   0 2309m 704m  18m S   0.0 35.5  19:18.90 java                                                                                                                    
 1488 root      20   0  339m  54m  19m S   0.3  2.7  25:32.13 Xorg                                                                                                                    
 3442 username  20   0 1098m  45m 8416 S   0.7  2.3   6:08.10 unity-panel-ser                                                                                                         
22568 www-data  20   0  353m  32m  24m S   0.0  1.7   0:00.82 apache2                                                                                                                 
22855 www-data  20   0  353m  31m  23m S   0.0  1.6   0:00.34 apache2                                                                              

So what could be taking up memory here? on Ubuntu 13.04.

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From what I see in your ps list java is using 704MB physical RAM. Kill the PID using kill -9 12825.

You can also use ps -eo pid,rss,cmd --sort -rss | head to list processes by RES to see which PID is using the most RAM.

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