If anyone can help me understand why my cluster is hung I would appreciate 
it.

jstack output:

https://gist.github.com/anonymous/075c862cb211ae249707

I am able to query the cluster and health is good but I can't DELETE or 
CLOSE index as it is unresponsive.

mlockall is set to true

iostat:

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           2.00    0.05    0.30    0.08    0.00   97.57

Device:            tps   Blk_read/s   Blk_wrtn/s   Blk_read   Blk_wrtn
sdb               7.40         0.00       939.20          0       4696
sda               0.40         0.00         4.80          0         24
dm-0              0.60         0.00         4.80          0         24
dm-1              0.00         0.00         0.00          0          0
dm-2            117.40         0.00       939.20          0       4696

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           2.93    0.03    0.23    0.08    0.00   96.74

Device:            tps   Blk_read/s   Blk_wrtn/s   Blk_read   Blk_wrtn
sdb               6.80         0.00       776.00          0       3880
sda               0.80         0.00        20.80          0        104
dm-0              2.60         0.00        20.80          0        104
dm-1              0.00         0.00         0.00          0          0
dm-2             97.00         0.00       776.00          0       3880

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           1.20    0.03    0.25    0.10    0.00   98.42

Device:            tps   Blk_read/s   Blk_wrtn/s   Blk_read   Blk_wrtn
sdb              11.40         0.00      1312.00          0       6560
sda               0.80         0.00        22.40          0        112
dm-0              2.80         0.00        22.40          0        112
dm-1              0.00         0.00         0.00          0          0
dm-2            164.00         0.00      1312.00          0       6560

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           7.07    0.03    0.50    0.08    0.00   92.33

Device:            tps   Blk_read/s   Blk_wrtn/s   Blk_read   Blk_wrtn
sdb              20.40         0.00      5064.00          0      25320
sda               1.00         0.00        25.60          0        128
dm-0              3.20         0.00        25.60          0        128
dm-1              0.00         0.00         0.00          0          0
dm-2            633.00         0.00      5064.00          0      25320

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           1.23    0.05    0.33    0.10    0.00   98.30

Device:            tps   Blk_read/s   Blk_wrtn/s   Blk_read   Blk_wrtn
sdb              15.20         0.00      2604.80          0      13024
sda               2.40         0.00        38.40          0        192
dm-0              4.80         0.00        38.40          0        192
dm-1              0.00         0.00         0.00          0          0
dm-2            325.60         0.00      2604.80          0      13024


vmstat:

-bash-4.1$ vmstat 5
procs -----------memory---------- ---swap-- -----io---- --system-- 
-----cpu-----
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id 
wa st
 0  0      0 141532 163140 1955776    0    0    19    80    2    0  2  0 96 
 2  0
 0  0      0 140664 163156 1956428    0    0     0   801  776  719  3  0 97 
 0  0
 0  0      0 138880 163164 1958264    0    0     0   776  770  765  2  0 98 
 0  0
 0  0      0 133820 163192 1963364    0    0     0  1570 1174  825  4  0 95 
 0  0
 1  0      0 129984 163200 1967036    0    0     0  1422 1026  836  4  0 95 
 0  0


-bash-4.1$ lsof -u elasticsearch | wc -l
3004


/etc/security/limits.conf:elasticsearch hard nofile 65536
/etc/security/limits.conf:elasticsearch soft nofile 65536
/etc/security/limits.conf:elasticsearch - memlock unlimited



top - 18:15:25 up 18 days, 14:36,  1 user,  load average: 0.23, 0.32, 0.32
Tasks: 190 total,   1 running, 189 sleeping,   0 stopped,   0 zombie
Cpu(s):  0.5%us,  0.2%sy,  0.0%ni, 99.3%id,  0.0%wa,  0.0%hi,  0.0%si, 
 0.0%st
Mem:   8060812k total,  7928472k used,   132340k free,   164384k buffers
Swap:        0k total,        0k used,        0k free,  1963024k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
26117 elastics  20   0 55.0g 5.2g 327m S  4.3 68.1   1836:21 java
 1358 logstash  39  19 5078m 257m  11m S  0.7  3.3 183:28.43 java

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