First of all, yes, I have read LinuxAteMyRAM, which doesn't explain my situation.

# free -tm
         total       used       free     shared    buffers     cached
Mem:         48149      43948       4200          0          4         75
-/+ buffers/cache:      43868       4280
Swap:        38287          0      38287
Total:       86436      43948      42488
#

As shown above, the -/+ buffers/cache: line shows indicates the used memory rate is very high. However, from output of top, I don't see any process used more than 100MB of memory.

So, what used the memory?

PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
28078 root      18   0  327m  92m  10m S    0  0.2   0:25.06 java
31416 root      16   0  250m  28m  20m S    0  0.1  25:54.59 ResourceMonitor
21598 root     -98   0 26552  25m 8316 S    0  0.1  80:49.54 had
24580 root      16   0 24152  10m  760 S    0  0.0   1:25.87 rsyncd
 4956 root      16   0 62588  10m 3132 S    0  0.0  12:36.54 vxconfigd
26703 root      16   0  139m 7120 2900 S    1  0.0   4359:39 hrmonitor
21873 root      15   0 18764 4684 2152 S    0  0.0  30:07.56 MountAgent
21883 root      15   0 13736 4280 2172 S    0  0.0  25:25.09 SybaseAgent
21878 root      15   0 18548 4172 2000 S    0  0.0  52:33.46 NICAgent
21887 root      15   0 12660 4056 2168 S    0  0.0  25:07.80 SybaseBkAgent
17798 root      25   0 10652 4048 1160 S    0  0.0   0:00.04 vxconfigbackupd

This is an x86_64 machine (not a common-brand server) running x84_64 Linux, not a container in a virtual machine. Kernel (uname -a):

Linux 2.6.16.60-0.99.1-smp #1 SMP Fri Oct 12 14:24:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

Content of /proc/meminfo:

MemTotal:     49304856 kB
MemFree:       4066708 kB
Buffers:         35688 kB
Cached:         132588 kB
SwapCached:          0 kB
Active:       26536644 kB
Inactive:     17296272 kB
HighTotal:           0 kB
HighFree:            0 kB
LowTotal:     49304856 kB
LowFree:       4066708 kB
SwapTotal:    39206624 kB
SwapFree:     39206528 kB
Dirty:             200 kB
Writeback:           0 kB
AnonPages:      249592 kB
Mapped:          52712 kB
Slab:          1049464 kB
CommitLimit:  63859052 kB
Committed_AS:   659384 kB
PageTables:       3412 kB
VmallocTotal: 34359738367 kB
VmallocUsed:    478420 kB
VmallocChunk: 34359259695 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
Hugepagesize:     2048 kB

df reports no large consumption of memory from tmpfs filesystems.