refactor: gohan elasticsearch jvm heap options file

.gitignore

@@ -47,6 +47,10 @@ lib/public/*
 !lib/public/.gitkeep
 !lib/public/docker-compose.public.yaml
 
+# gohan_elasticsearch
+lib/gohan/es_jvm_options/*
+!lib/gohan/es_jvm_options/.gitkeep
+
 # temp test stuff
 etc/tests/*/__pycache__
 etc/tests/*/*/__pycache__

docs/installation.md

@@ -138,6 +138,44 @@ cp ./etc/katsu.config.example.json ./lib/katsu/config.json
 ```
 
 
+### `gohan` configuration
+
+#### Production
+
+When deploying a Bento node that needs to serve variants data, it is recommended to allot larger portions of your 
+compute resources to both `bentov2-gohan-api` and `bentov2-gohan-elasticsearch`.
+Since variants are stored in memory in Elasticsearch, set the `BENTOV2_GOHAN_ES_MEM_LIM` variable to an 
+appropriate value.
+
+
+Alloting additional CPUs with `BENTOV2_GOHAN_API_CPUS` and `BENTOV2_GOHAN_ES_CPUS` will result in shorter ingestion
+times. Consider this option if you need to ingest a large number of VCFs.
+
+Go through the official Elasticsearch 
+[checklist](https://www.elastic.co/guide/en/elasticsearch/reference/current/docker.html#docker-prod-prerequisites) 
+for production deployments on Docker.
+
+The following configurations **MUST** be applied to the host machine deploying the Elasticsearch container:
+* [Set vm.max_map_count](https://www.elastic.co/guide/en/elasticsearch/reference/current/docker.html#_set_vm_max_map_count_to_at_least_262144)
+* [Disable swapping](https://www.elastic.co/guide/en/elasticsearch/reference/current/setup-configuration-memory.html#swappiness)
+
+
+#### Elasticsearch JVM options
+
+In **production**, using the default JVM options provided by Elasticsearch is **recommended**.
+
+In **development**, modifying the JVM heap size could be needed if Elasticsearch's memory limit 
+is low and you are trying to ingest VCFs.
+The heap size can be modified by providing a config file to the `bentov2_gohan-elasticsearch` container:
+
+```bash
+cp ./etc/default.gohan.es.jvm.options ./lib/gohan/es_jvm_options/jvm.options
+```
+
+Set `Xms` and `Xmx` to no more than 50% of the `BENTOV2_GOHAN_ES_MEM_LIM` value.
+For more details, check the official Elasticsearch doc on 
+[heap size](https://www.elastic.co/guide/en/elasticsearch/reference/current/advanced-configuration.html#set-jvm-heap-size).
+
 ## 3. *Development only:* create self-signed TLS certificates 
 
 First, set up your local Bento and Keycloak hostnames (something like `bentov2.local`, `portal.bentov2.local`, and 

etc/bento.env

@@ -357,8 +357,8 @@ BENTOV2_GOHAN_ES_MEM_LIM=4G
 BENTOV2_GOHAN_ES_CPUS=4
 
 # allocate a little bit less memory than what is stated in `mem_limit` ^^
-BENTOV2_GOHAN_ES_JAVA_OPTS="ES_JAVA_OPTS=-Xms3800m -Xmx3800m"
 BENTOV2_GOHAN_ES_DATA_DIR=${BENTOV2_GOHAN_DATA_ROOT}/elasticsearch
+BENTO_GOHAN_ES_JVM_OPTIONS_DIR=${PWD}/lib/gohan/es_jvm_options
 
 # -- API-DRS Bridge
 BENTOV2_GOHAN_API_DRS_BRIDGE_HOST_DIR=${BENTOV2_GOHAN_DATA_ROOT}/api_drs_bridge

etc/default.gohan.es.jvm.options

@@ -0,0 +1,9 @@
+#########################################################
+## FOR DEVELOPMENT ONLY
+## Xms and Xmx MUST have the same value
+## Use no more than 50% of BENTOV2_GOHAN_ES_MEM_LIM
+## Default options assume 'BENTOV2_GOHAN_ES_MEM_LIM=4G'
+#########################################################
+
+-Xms2g
+-Xmx2g

lib/gohan/docker-compose.gohan.yaml

@@ -65,12 +65,12 @@ services:
       - BENTO_UID
       - ELASTIC_USERNAME=${BENTOV2_GOHAN_ES_USERNAME}
       - ELASTIC_PASSWORD=${BENTOV2_GOHAN_ES_PASSWORD}
-      - ${BENTOV2_GOHAN_ES_JAVA_OPTS}
       - xpack.security.enabled=true
       - discovery.type=${BENTOV2_GOHAN_ES_DISC_TYP}
       - ingest.geoip.downloader.enabled=false
     volumes:
       - ${BENTOV2_GOHAN_ES_DATA_DIR}:/usr/share/elasticsearch/data
+      - ${BENTO_GOHAN_ES_JVM_OPTIONS_DIR}:/usr/share/elasticsearch/config/jvm.options.d
     healthcheck:
       test: [ "CMD", "curl", "http://localhost:${BENTOV2_GOHAN_ES_INTERNAL_PORT_1}" ]
       timeout: ${BENTOV2_HEALTHCHECK_TIMEOUT}