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Answered
I'M Trying To Set Up Clearml Server On A New Vm But The Elasticsearch Container Is Erroring With The Following:

I'm trying to set up clearml server on a new vm but the elasticsearch container is erroring with the following:
Attaching to clearml-elastic clearml-elastic | Exception in thread "main" java.lang.RuntimeException: starting java failed with [1] clearml-elastic | output: clearml-elastic | [0.000s][error][logging] Error opening log file 'logs/gc.log': Permission denied clearml-elastic | [0.000s][error][logging] Initialization of output 'file=logs/gc.log' using options 'filecount=32,filesize=64m' failed. clearml-elastic | error: clearml-elastic | Invalid -Xlog option '-Xlog:gc*,gc+age=trace,safepoint:file=logs/gc.log:utctime,pid,tags:filecount=32,filesize=64m', see error log for details. clearml-elastic | Error: Could not create the Java Virtual Machine. clearml-elastic | Error: A fatal exception has occurred. Program will exit. clearml-elastic | at org.elasticsearch.tools.launchers.JvmOption.flagsFinal(JvmOption.java:119) clearml-elastic | at org.elasticsearch.tools.launchers.JvmOption.findFinalOptions(JvmOption.java:81) clearml-elastic | at org.elasticsearch.tools.launchers.JvmErgonomics.choose(JvmErgonomics.java:38) clearml-elastic | at org.elasticsearch.tools.launchers.JvmOptionsParser.jvmOptions(JvmOptionsParser.java:135) clearml-elastic | at org.elasticsearch.tools.launchers.JvmOptionsParser.main(JvmOptionsParser.java:86) clearml-elastic | Exception in thread "main" java.lang.RuntimeException: starting java failed with [1]I tried deleting everything and starting from scratch, but I always end up in this state. Can anyone help with this issue? Thanks

  
  
Posted one year ago
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Answers 11


Thanks AppetizingMouse58 . I managed to fix it by removing docker completely and reinstalling it.

  
  
Posted one year ago

Hi WittyOwl57 , there is a chance that the reason is in this setting: Xlog:gc*,gc+age=trace,safepoint:file=logs/gc.log ...
First it say says about invalid log option that may require further investigation. Second the file that it tries to write to is logs/gc.log and it is not under the $clearml folder where you give the write permissions to the ES user. I would try cancelling JVM logging at all or specifying the full path to the file so that it would be under the folder that has 1000:1000 owner. Please see more here:
https://www.elastic.co/guide/en/elasticsearch/reference/current/important-settings.html#gc-logging

  
  
Posted one year ago

I didn't add that to the script since the effect is persistent (i.e. it only needs to be done once, right?) In any case, I checked that multiple times and it was as expected.

  
  
Posted one year ago

WittyOwl57 what about? vm.max_map_count echo "vm.max_map_count=262144" > /tmp/99-clearml.conf
sudo mv /tmp/99-clearml.conf /etc/sysctl.d/99-clearml.conf
sudo sysctl -w vm.max_map_count=262144
sudo service docker restart `https://clear.ml/docs/latest/docs/deploying_clearml/clearml_server_linux_mac (5)

  
  
Posted one year ago

Hi SuccessfulKoala55 ,yes, I am running as sudo. It's not my first time setting this up either. Just that on this vm (which is a particularly large instance) I get this issue which has me stumped.

  
  
Posted one year ago

WittyOwl57 maybe you have a filesystem permissions issue? Are you running this as root (or using sudo)?
Error opening log file 'logs/gc.log': Permission denied

  
  
Posted one year ago

WittyOwl57 not much info here but since it seems to fail on the Java options, I suspect AgitatedDove14 is correct and the most likely cause is not enough RAM?

  
  
Posted one year ago

WittyOwl57 could it be the EC2 instance is too small (i.e. not enough storage / memory) ?

  
  
Posted one year ago

I actually put all the commands in a script. The failure mode is exactly the same. I have no idea what to do next.
` #!/bin/bash

clearml_root=$1

if [[ $# -gt 0 ]]; then
echo Using "$1" as root
else
echo No root argument was provided, using /datadrive1
clearml_root=/datadrive1
fi

clearml="$clearml_root/clearml"

rm -R "$clearml"

mkdir -p "$clearml"/data/elastic_7
mkdir -p "$clearml"/data/mongo_4/db
mkdir -p "$clearml"/data/mongo_4/configdb
mkdir -p "$clearml"/data/redis
mkdir -p "$clearml"/logs
mkdir -p "$clearml"/config
mkdir -p "$clearml"/data/fileserver

dc_yaml="$clearml"/docker-compose.yaml

curl -o "$dc_yaml"
sed -i 's#/opt/clearml#'"$clearml"'#g' "$dc_yaml"

chown -R 1000:1000 "$clearml"

docker-compose -f "$dc_yaml" down
docker-compose -f "$dc_yaml" up -d `

  
  
Posted one year ago

Hi AgitatedDove14 , I deleted everything in /opt/clearml as per the docs. Should I delete anything else?

  
  
Posted one year ago

Hi WittyOwl57
Are you starting a new server from scratch or is it running on previously stored data?

  
  
Posted one year ago
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11 Answers
one year ago
one year ago
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