Elasticsearch service hang and kills while data insertion jvm heap - elasticsearch

Question

I am using elasticsearch 5.6.13 version, I need some experts configurations for the elasticsearch. I have 3 nodes in the same system (node1,node2,node3) where node1 is master and else 2 data nodes. I have number of indexes around 40, I created all these indexes with default 5 primary shards and some of them have 2 replicas.
What I am facing the issue right now, My data (scraping) is growing day by day and I have 400GB of the data in my one of index. similarly 3 other indexes are also very loaded.
From some last days I am facing the issue while insertion of data my elasticsearch hangs and then the service is killed which effect my processing. I have tried several things. I am sharing the system specs and current ES configuration + logs. Please suggest some solution.
The System Specs:
RAM: 160 GB,
CPU: AMD EPYC 7702P 64-Core Processor,
Drive: 2 TB SSD (The drive in which the ES installed still have 500 GB left)
ES Configuration JVM options:
-Xms26g,
-Xmx26g
(I just try this but not sure what is the perfect heap size for my scenario)
I just edit this above lines and the rest of the file is as defult. I edit this on all three nodes jvm.options files.
ES LOGS
[2021-09-22T12:05:17,983][WARN ][o.e.m.j.JvmGcMonitorService] [sashanode1] [gc][170] overhead, spent [7.1s] collecting in the last [7.2s]
[2021-09-22T12:05:21,868][WARN ][o.e.m.j.JvmGcMonitorService] [sashanode1] [gc][171] overhead, spent [3.7s] collecting in the last [1.9s]
[2021-09-22T12:05:51,190][WARN ][o.e.m.j.JvmGcMonitorService] [sashanode1] [gc][172] overhead, spent [27.7s] collecting in the last [23.3s]
[2021-09-22T12:06:54,629][WARN ][o.e.m.j.JvmGcMonitorService] [cluster_name] [gc][173] overhead, spent [57.5s] collecting in the last [1.1m]
[2021-09-22T12:06:56,536][WARN ][o.e.m.j.JvmGcMonitorService] [cluster_name] [gc][174] overhead, spent [1.9s] collecting in the last [1.9s]
[2021-09-22T12:07:02,176][WARN ][o.e.m.j.JvmGcMonitorService] [cluster_name] [gc][175] overhead, spent [5.4s] collecting in the last [5.6s]
[2021-09-22T12:06:56,546][ERROR][o.e.i.e.Engine ] [cluster_name] [index_name][3] merge failed
java.lang.OutOfMemoryError: Java heap space
[2021-09-22T12:06:56,548][ERROR][o.e.b.ElasticsearchUncaughtExceptionHandler] [cluster_name] fatal error in thread [elasticsearch[cluster_name][bulk][T#25]], exiting
java.lang.OutOfMemoryError: Java heap space
Some more logs
[2021-09-22T12:10:06,526][INFO ][o.e.n.Node ] [cluster_name] initializing ...
[2021-09-22T12:10:06,589][INFO ][o.e.e.NodeEnvironment ] [cluster_name] using [1] data paths, mounts [[(D:)]], net usable_space [563.3gb], net total_space [1.7tb], spins? [unknown], types [NTFS]
[2021-09-22T12:10:06,589][INFO ][o.e.e.NodeEnvironment ] [cluster_name] heap size [1.9gb], compressed ordinary object pointers [true]
[2021-09-22T12:10:07,239][INFO ][o.e.n.Node ] [cluster_name] node name [sashanode1], node ID [2p-ux-OXRKGuxmN0efvF9Q]
[2021-09-22T12:10:07,240][INFO ][o.e.n.Node ] [cluster_name] version[5.6.13], pid[57096], build[4d5320b/2018-10-30T19:05:08.237Z], OS[Windows Server 2019/10.0/amd64], JVM[Oracle Corporation/Java HotSpot(TM) 64-Bit Server VM/1.8.0_261/25.261-b12]
[2021-09-22T12:10:07,240][INFO ][o.e.n.Node ] [cluster_name] JVM arguments [-Xms2g, -Xmx2g, -XX:+UseConcMarkSweepGC, -XX:CMSInitiatingOccupancyFraction=75, -XX:+UseCMSInitiatingOccupancyOnly, -XX:+AlwaysPreTouch, -Xss1m, -Djava.awt.headless=true, -Dfile.encoding=UTF-8, -Djna.nosys=true, -Djdk.io.permissionsUseCanonicalPath=true, -Dio.netty.noUnsafe=true, -Dio.netty.noKeySetOptimization=true, -Dio.netty.recycler.maxCapacityPerThread=0, -Dlog4j.shutdownHookEnabled=false, -Dlog4j2.disable.jmx=true, -Dlog4j.skipJansi=true, -XX:+HeapDumpOnOutOfMemoryError, -Delasticsearch, -Des.path.home=D:\Databases\ES\elastic and kibana 5.6.13\es_node_1, -Des.default.path.logs=D:\Databases\ES\elastic and kibana 5.6.13\es_node_1\logs, -Des.default.path.data=D:\Databases\ES\elastic and kibana 5.6.13\es_node_1\data, -Des.default.path.conf=D:\Databases\ES\elastic and kibana 5.6.13\es_node_1\config, exit, -Xms2048m, -Xmx2048m, -Xss1024k]
Also in my ES folder there are so many files with the random names (java_pid197036.hprof)
Further details can be shared please suggest any further configurations.
Thanks
The output for _cluster/stats?pretty&human is
{ "_nodes": { "total": 3, "successful": 3, "failed": 0 }, "cluster_name": "cluster_name", "timestamp": 1632375228033, "status": "red", "indices": { "count": 42, "shards": { "total": 508, "primaries": 217, "replication": 1.3410138248847927, "index": { "shards": { "min": 2, "max": 60, "avg": 12.095238095238095 }, "primaries": { "min": 1, "max": 20, "avg": 5.166666666666667 }, "replication": { "min": 1.0, "max": 2.0, "avg": 1.2857142857142858 } } }, "docs": { "count": 107283077, "deleted": 1047418 }, "store": { "size": "530.2gb", "size_in_bytes": 569385384976, "throttle_time": "0s", "throttle_time_in_millis": 0 }, "fielddata": { "memory_size": "0b", "memory_size_in_bytes": 0, "evictions": 0 }, "query_cache": { "memory_size": "0b", "memory_size_in_bytes": 0, "total_count": 0, "hit_count": 0, "miss_count": 0, "cache_size": 0, "cache_count": 0, "evictions": 0 }, "completion": { "size": "0b", "size_in_bytes": 0 }, "segments": { "count": 3781, "memory": "2gb", "memory_in_bytes": 2174286255, "terms_memory": "1.7gb", "terms_memory_in_bytes": 1863786029, "stored_fields_memory": "105.6mb", "stored_fields_memory_in_bytes": 110789048, "term_vectors_memory": "0b", "term_vectors_memory_in_bytes": 0, "norms_memory": "31.9mb", "norms_memory_in_bytes": 33527808, "points_memory": "13.1mb", "points_memory_in_bytes": 13742470, "doc_values_memory": "145.3mb", "doc_values_memory_in_bytes": 152440900, "index_writer_memory": "0b", "index_writer_memory_in_bytes": 0, "version_map_memory": "0b", "version_map_memory_in_bytes": 0, "fixed_bit_set": "0b", "fixed_bit_set_memory_in_bytes": 0, "max_unsafe_auto_id_timestamp": 1632340789677, "file_sizes": { } } }, "nodes": { "count": { "total": 3, "data": 3, "coordinating_only": 0, "master": 1, "ingest": 3 }, "versions": [ "5.6.13" ], "os": { "available_processors": 192, "allocated_processors": 96, "names": [ { "name": "Windows Server 2019", "count": 3 } ], "mem": { "total": "478.4gb", "total_in_bytes": 513717497856, "free": "119.7gb", "free_in_bytes": 128535437312, "used": "358.7gb", "used_in_bytes": 385182060544, "free_percent": 25, "used_percent": 75 } }, "process": { "cpu": { "percent": 5 }, "open_file_descriptors": { "min": -1, "max": -1, "avg": 0 } }, "jvm": { "max_uptime": "1.9d", "max_uptime_in_millis": 167165106, "versions": [ { "version": "1.8.0_261", "vm_name": "Java HotSpot(TM) 64-Bit Server VM", "vm_version": "25.261-b12", "vm_vendor": "Oracle Corporation", "count": 3 } ], "mem": { "heap_used": "5gb", "heap_used_in_bytes": 5460944144, "heap_max": "5.8gb", "heap_max_in_bytes": 6227755008 }, "threads": 835 }, "fs": { "total": "1.7tb", "total_in_bytes": 1920365228032, "free": "499.1gb", "free_in_bytes": 535939969024, "available": "499.1gb", "available_in_bytes": 535939969024 }, "plugins": [ ], "network_types": { "transport_types": { "netty4": 3 }, "http_types": { "netty4": 3 } } } }
The jvm.options file.
## JVM configuration
################################################################
## IMPORTANT: JVM heap size
################################################################
##
## You should always set the min and max JVM heap
## size to the same value. For example, to set
## the heap to 4 GB, set:
##
## -Xms4g
## -Xmx4g
##
## See https://www.elastic.co/guide/en/elasticsearch/reference/current/heap-size.html
## for more information
##
################################################################
# Xms represents the initial size of total heap space
# Xmx represents the maximum size of total heap space
-Xms26g
-Xmx26g
################################################################
## Expert settings
################################################################
##
## All settings below this section are considered
## expert settings. Don't tamper with them unless
## you understand what you are doing
##
################################################################
## GC configuration
-XX:+UseConcMarkSweepGC
-XX:CMSInitiatingOccupancyFraction=75
-XX:+UseCMSInitiatingOccupancyOnly
## optimizations
# pre-touch memory pages used by the JVM during initialization
-XX:+AlwaysPreTouch
## basic
# force the server VM (remove on 32-bit client JVMs)
-server
# explicitly set the stack size (reduce to 320k on 32-bit client JVMs)
-Xss1m
# set to headless, just in case
-Djava.awt.headless=true
# ensure UTF-8 encoding by default (e.g. filenames)
-Dfile.encoding=UTF-8
# use our provided JNA always versus the system one
-Djna.nosys=true
# use old-style file permissions on JDK9
-Djdk.io.permissionsUseCanonicalPath=true
# flags to configure Netty
-Dio.netty.noUnsafe=true
-Dio.netty.noKeySetOptimization=true
-Dio.netty.recycler.maxCapacityPerThread=0
# log4j 2
-Dlog4j.shutdownHookEnabled=false
-Dlog4j2.disable.jmx=true
-Dlog4j.skipJansi=true
## heap dumps
# generate a heap dump when an allocation from the Java heap fails
# heap dumps are created in the working directory of the JVM
-XX:+HeapDumpOnOutOfMemoryError
# specify an alternative path for heap dumps
# ensure the directory exists and has sufficient space
#-XX:HeapDumpPath=${heap.dump.path}
## GC logging
#-XX:+PrintGCDetails
#-XX:+PrintGCTimeStamps
#-XX:+PrintGCDateStamps
#-XX:+PrintClassHistogram
#-XX:+PrintTenuringDistribution
#-XX:+PrintGCApplicationStoppedTime
# log GC status to a file with time stamps
# ensure the directory exists
#-Xloggc:${loggc}
# By default, the GC log file will not rotate.
# By uncommenting the lines below, the GC log file
# will be rotated every 128MB at most 32 times.
#-XX:+UseGCLogFileRotation
#-XX:NumberOfGCLogFiles=32
#-XX:GCLogFileSize=128M
# Elasticsearch 5.0.0 will throw an exception on unquoted field names in JSON.
# If documents were already indexed with unquoted fields in a previous version
# of Elasticsearch, some operations may throw errors.
#
# WARNING: This option will be removed in Elasticsearch 6.0.0 and is provided
# only for migration purposes.
#-Delasticsearch.json.allow_unquoted_field_names=true
and the elasticsearch.yml (master node)
cluster.name: cluster_name
node.name: node1
node.master : true
network.host: 0.0.0.0
discovery.zen.ping.unicast.hosts: ["192.168.11.159", "192.168.11.157"]

Answer 1

My issue is solved, It is due to the heap size issue, actually I am running the ES as service and the heap size is by default 2 GB and it is not reflecting.
I just install the new service with the updated options.jvm file with heap size of 10 GB, and then run my cluster. It reflect the heap size from 2 GB to 10 GB.
And my problem is solved. Thanks for the suggestions.
to check your heap size use this command.
http://localhost:9200/_cat/nodes?h=heap*&v