How can I clear my cache?

Question

I'm running a live CD linux distro and I'm getting out of memory exceptions.

>java -version
#Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x0000000646e00000, 264241152, 0) failed; error='Cannot allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (mmap) failed to map 264241152 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /tmp/hs_err_pid50274.log

I ran free -m command and it shows ~250Mb of free RAM and 19Gb used for cache.

>free -m
            total       used       free     shared    buffers     cached
Mem:        24128      23827        301          0         15      18929
-/+ buffers/cache:      4881      19247
Swap:            0          0          0

Here is the memory dump:

---------------  S Y S T E M  ---------------

OS:RapidLinux 20151103

uname:Linux 3.18.22 #1 SMP Fri Oct 9 19:28:11 UTC 2015 x86_64
libc:glibc 2.21 NPTL 2.21 
rlimit: STACK 8192k, CORE infinity, NPROC 96487, NOFILE 4096, AS infinity
load average:2.08 1.73 1.30

/proc/meminfo:
MemTotal:       24708040 kB
MemFree:          307572 kB
MemAvailable:     173696 kB
Buffers:           15612 kB
Cached:         19383916 kB
SwapCached:            0 kB
Active:          3784768 kB
Inactive:       19327244 kB
Active(anon):    3742084 kB
Inactive(anon): 19303520 kB
Active(file):      42684 kB
Inactive(file):    23724 kB
Unevictable:       15016 kB
Mlocked:           15016 kB
SwapTotal:             0 kB
SwapFree:              0 kB
Dirty:                96 kB
Writeback:             0 kB
AnonPages:       3727472 kB
Mapped:            55972 kB
Shmem:          19327344 kB
Slab:             671580 kB
SReclaimable:     116376 kB
SUnreclaim:       555204 kB
KernelStack:       23664 kB
PageTables:        24588 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    12354020 kB
Committed_AS:   28666748 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      738156 kB
VmallocChunk:   34346400260 kB
HardwareCorrupted:     0 kB
AnonHugePages:         0 kB
DirectMap4k:       11748 kB
DirectMap2M:     2072576 kB
DirectMap1G:    23068672 kB

Memory: 4k page, physical 24708040k(307572k free), swap 0k(0k free)

I tried to clear the cache by running sync ; echo 3 | sudo tee /proc/sys/vm/drop_caches as a sanity check and surprise surprise the cache did not go down at all, but the command completed successfully.

There was a ton of old logs that I deleted (from the aufs / which should be in RAM), ran the command to clear the cache - still nothing.

The rest of the file system takes only ~9Gb. How can I force my cache to clear?

Answer 1

You have 19GB of RAM free for programs to use. There is no need to clear the disk cache: the system will reclaim it if it needs the memory for some other purpose such as running a program. The only thing you can do by clearing the disk cache is make your machine slower.

Disk space is irrelevant. Deleting files won't help you.

You have 19GB of RAM and the program claims to fail to allocate 26MB. Do the math: 26MB < 19GB. This is a bug in the program, either in the way it allocates memory or in the way it reports errors. Check /tmp/hs_err_pid50274.log to see if it holds more clues.

Answer 2

Shmem: 19327344 kB

You have 19GB in tmpfs, or some other shared memory object.

It's often tmpfs. Check df -h -t tmpfs.

System V shared memory can be shown by ipcs -m.

Some, but not all, other shared memory can be found by scanning /proc. There is a small python script in my answer here: Can I see the amount of memory which is allocated as GEM buffers?

EDIT: in your case, you might have something holding open a deleted file. This would mean the space usage would show up in df, but not in du. It is possible to scan /proc/ for deleted files... I don't have such a handy script for this, but maybe you can do ls -lR /proc | less, and search for the string (deleted) using the / command of less. It seems possible you would see your deleted log files were still being held open by some process.