This error is most likely due to the fact that the communication with Elasticsearch server has been stopped.
curl -XGET http://[ES server address]:9200
docker-compose restartin the folder where the configuration files of ChemLocator were installed)
If documents are not found when searching check the following:
If indexing is not porgressing after some considerable time it could be possible that some ChemLocator processes have been closed by the host due to insufficient memory (this can be checked by cheking the host logs, e.g. output from command
journalctl | grep "Out of memory": Out of memory: Kill process 19165 (dotnet) score 695 or sacrifice child).
If this is the case an additional check can be performed by running the following command on the Docker host server (replace chemlocator_chemlocator_1 with the one that is running on your server):
docker container top chemlocator_chemlocator_1
The expected output should contain a process with the following command:
dotnet /app/ChemLocator.dll server -r 23.
If this process is missing please restart ChemLocator containers:
docker-compose stop docker-compose start
After the container starts, the indexing process will resume and the documents that previously did not finish indexing will be indexed again.
When the following error occurs during "Substructure search”, you need to start jchem-psql service manually:
Open a command prompt and find the id of jpc-chemlocator container:
$ docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES d5876a3561a1 hub.chemaxon.com/cxn-docker-release/jpc-chemlocator:21.9.0.r13210 "/start-log.sh" 11 days ago Up 11 hours 0.0.0.0:3051->5432/tcp, :::3051->5432/tcp dev_jpc_1 46c128c929ff docker.elastic.co/kibana/kibana:7.6.1 "/usr/local/bin/dumb…" 5 weeks ago Up 9 hours 0.0.0.0:5601->5601/tcp, :::5601->5601/tcp dev_kibana_1 04815b3428bb osixia/openldap:1.2.5 "/container/tool/run…" 5 weeks ago Up 11 hours 0.0.0.0:389->389/tcp, :::389->389/tcp, 0.0.0.0:636->636/tcp, :::636->636/tcp dev_ldap_1 88804b6953de docker.elastic.co/elasticsearch/elasticsearch:7.6.1 "/usr/local/bin/dock…" 5 weeks ago Up 9 hours 0.0.0.0:9200->9200/tcp, :::9200->9200/tcp, 9300/tcp dev_elasticsearch_1
Then enter into the container by issuing the following command:
$ docker exec -it d5876a3561a1 /bin/bash
Check if service is really not running:
$ service –status-all
[ - ] cron [ - ] dbus [ ? ] hwclock.sh [ - ] jchem-psql [ + ] postgresql [ - ] procps [ - ] sysstat [ - ] x11-common
As it looks service is indeed not running, so let’s start it with:
$ service jchem-psql start