TDB concurrent usage error

[jtrugman]

Hi,

I ran into a weird error while running stain/jena-fuseki using Docker Compose. Whenever I run:

version: '3'
services:
  fuseki:
    image: stain/jena-fuseki:latest
    environment:
      - ADMIN_PASSWORD=enter1234
    ports:
      - "5050:3030" 

It works the first time, when stain/jena-fuseki cannot be found locally and has to be fetched from the internet. However, when I run it again after stopping the container/killing the docker process I get an error like this:

Server     ERROR Exception in initialization: Process ID 7 can't open database at location /fuseki/system/ because it is already locked by the process with PID 8. TDB databases do not permit concurrent usage across JVMs so in order to prevent possible data corruption you cannot open this location from the JVM that does not own the lock for the dataset
fuseki_1  | [2020-03-11 16:44:57] WebAppContext WARN  Failed startup of context o.e.j.w.WebAppContext@1a28aef1{Apache Jena Fuseki Server,/,file:///jena-fuseki/webapp/,UNAVAILABLE}
fuseki_1  | org.apache.jena.tdb.TDBException: Process ID 7 can't open database at location /fuseki/system/ because it is already locked by the process with PID 8. TDB databases do not permit concurrent usage across JVMs so in order to prevent possible data corruption you cannot open this location from the JVM that does not own the lock for the dataset

This is making me think that some processes are not cleaning up fully when they are stopped or something similar to that. Especially since when I remove all of the containers (docker rm container_id) and remove the docker image (docker rmi stain/jena-fuseki) and rerun it, it works.

More than happy to help debug the issue too! Just let me know.

Cheers, Justin

[infinite-dao]

I have a similar problem I did:

1. create a data container for permanent data, I named it fuseki-data
2. create a container fuseki-app, stop it
3. do a loading of data with a named container fuseki-loadsh-use-fuseki-data into a brand new dataset
4. stop the loading container after successful load
5. restart container fuseki-app
6. then it fails as docker logs fuseki-app shows (see below in bash # commends)

Here the commands I executed:

docker run --detach --name fuseki-data --volume /fuseki busybox # data container

docker run --detach --name fuseki-app -p 3030:3030 \
  -e ADMIN_PASSWORD=pw123 \
  --volumes-from fuseki-data stain/jena-fuseki
docker logs fuseki-app
# OK
docker stop fuseki-app
docker ps --all
# CONTAINER ID        IMAGE               COMMAND                  CREATED              STATUS                                PORTS               NAMES
# 6f6af0faad44        stain/jena-fuseki   "/docker-entrypoint.…"   About a minute ago   Exited (137) Less than a second ago                       fuseki-app
# 6591645f4ee6        busybox             "sh"                     About a minute ago   Exited (0) About a minute ago                             fuseki-data
# try to load into a brand new cetaf-test20200312-1205
docker run  --name fuseki-loadsh-use-fuseki-data \
  --volumes-from fuseki-data \
  --volume /home/aplank/sandbox/staging:/staging \
  stain/jena-fuseki \
  ./load.sh cetaf-test20200312-1205 Thread-2_herbarium.bgbm.org.rdf
# OK
docker ps --all
# CONTAINER ID        IMAGE               COMMAND                  CREATED              STATUS                       PORTS               NAMES
# 65bd64c29a01        stain/jena-fuseki   "/docker-entrypoint.…"   About a minute ago   Up About a minute            3030/tcp            fuseki-loadsh-use-fuseki-data
# 6f6af0faad44        stain/jena-fuseki   "/docker-entrypoint.…"   4 minutes ago        Exited (137) 3 minutes ago                       fuseki-app
# 6591645f4ee6        busybox             "sh"                     4 minutes ago        Exited (0) 4 minutes ago                         fuseki-data
docker stop fuseki-loadsh-use-fuseki-data
docker ps --all
# CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS                        PORTS               NAMES
# 65bd64c29a01        stain/jena-fuseki   "/docker-entrypoint.…"   3 minutes ago       Exited (137) 22 seconds ago                       fuseki-loadsh-use-fuseki-data
# 6f6af0faad44        stain/jena-fuseki   "/docker-entrypoint.…"   6 minutes ago       Exited (137) 4 minutes ago                        fuseki-app
# 6591645f4ee6        busybox             "sh"                     6 minutes ago       Exited (0) 6 minutes ago                          fuseki-data
docker start fuseki-app
docker logs fuseki-app
# TDB        WARN  Your platform does not support checking process liveness so TDB disk locations cannot be reliably locked to prevent possible corruption due to unsafe multi-JVM usage
# java.io.IOException: Cannot run program "ps": error=2, No such file or directory
# [2020-03-12 11:09:54] Server     ERROR Exception in initialization: caught: Process ID 8 can’t open database at location /fuseki/databases/cetaf-test20200312/ because it is already locked by the process with PID 9. TDB databases do not permit concurrent usage across JVMs so in order to prevent possible data corruption you cannot open this location from the JVM that does not own the lock for the dataset
# [2020-03-12 11:09:54] WebAppContext WARN  Failed startup of context o.e.j.w.WebAppContext@859ea42{Apache Jena Fuseki Server,/,file:///jena-fuseki/webapp/,UNAVAILABLE}
# org.apache.jena.assembler.exceptions.AssemblerException: caught: Process ID 8 can’t open database at location /fuseki/databases/cetaf-test20200312/ because it is already locked by the process with PID 9. TDB databases do not permit concurrent usage across JVMs so in order to prevent possible data corruption you cannot open this location from the JVM that does not own the lock for the dataset
# [2020-03-12 11:09:54] Server     INFO  Started 2020/03/12 11:09:54 UTC on port 3030

… and the server is broken.

I guess the ps utility should be included into the Dockerfile to minimise Java errors java.io.IOException: Cannot run program "ps": error=2, No such file or directory it seems located in the procps package or so.

Update: later, when I was starting my named containers fuseki-app and fuseki-loadsh-use-fuseki-data I installed at first in those containers procps. I guess in my case it is related, because in ProcessUtils.java it uses this ps command, so better have it available in the container too. This time I got no errors after stopping fuseki-loadsh-use-fuseki-data and restarting fuseki-app. The step of install in the container was:

docker exec -it fuseki-app bash # run in the container named “fuseki-app”
root@7fc3133f5863:/jena-fuseki#
  apt-get update;
  apt-get install -y --no-install-recommends procps
  exit
docker start fuseki-app
# proceed with normal usage

[tonicebrian]

Same problem here, after a docker restart fuseki the lock is preventing fuseki from start. Any ideas about how to solve that?

[daxid]

The bug is still there on the latest Docker Hub image...

[AnaKostovska]

I have the same problem. Could you tell me how you solved the issue?

[daxid]

@AnaKostovska

You can try to build your docker image frome the Dockerfile in this repo (I didn't try). It seems that this bus has been fixed here in Master but that it also made the automatic build of Docker Hub image fail.

You could also try a different image from Docker Hub. I'm running since yesterday with the following docker-compose.yml :

version: '2'
services:
    fuseki:
        hostname: fuseki
        image: zacanbot/fuseki
        environment:
            JVM_ARGS: -Xmx4g
        volumes:
            - /home/daxid/DEV/fuseki/data:/data/fuseki
        ports:
            - "127.0.0.1:3030:3030"```

[leroykim]

So, I followed @infinite-dao and it worked.

Here's what I did:

1. docker run --name fuseki-data -v /fuseki busybox
2. docker run -d --name fuseki -p 3030:3030 --volumes-from fuseki-data stain/jena-fuseki
3. NO DATA UPLOADING BEFORE RUNNING COMMANDS BELOW
4. Run the commands:

   
   docker exec -it fuseki bash

root@7fc3133f5863:/jena-fuseki# apt-get update root@7fc3133f5863:/jena-fuseki# apt-get install -y procps root@7fc3133f5863:/jena-fuseki# exit

5. Run `docker restart fuseki` to see if it throws errors.
6. Upload data (I uploaded the pizza ontology)
7. Run `docker restart fuseki` again to see if it throws errors.

Here's the result I got - no errors:

[2021-05-24 08:59:28] Server INFO Apache Jena Fuseki 3.14.0 [2021-05-24 08:59:28] Config INFO FUSEKI_HOME=/jena-fuseki [2021-05-24 08:59:28] Config INFO FUSEKI_BASE=/fuseki [2021-05-24 08:59:28] Config INFO Shiro file: file:///fuseki/shiro.ini [2021-05-24 08:59:28] Config INFO Configuration file: /fuseki/config.ttl [2021-05-24 08:59:29] Config INFO Load configuration: file:///fuseki/configuration/pizza.ttl [2021-05-24 08:59:29] Config INFO Register: /pizza [2021-05-24 08:59:29] Server INFO Started 2021/05/24 08:59:29 UTC on port 3030

[SimonBin]

for anyone else running into this, we had some success by using docker run --init to enable the tini init system

[milkbread]

So, I followed @infinite-dao and it worked.

Here's what I did:

1. docker run --name fuseki-data -v /fuseki busybox
2. docker run -d --name fuseki -p 3030:3030 --volumes-from fuseki-data stain/jena-fuseki
3. NO DATA UPLOADING BEFORE RUNNING COMMANDS BELOW
4. Run the commands:

docker exec -it fuseki bash

root@7fc3133f5863:/jena-fuseki# apt-get update
root@7fc3133f5863:/jena-fuseki# apt-get install -y procps
root@7fc3133f5863:/jena-fuseki# exit

5. Run docker restart fuseki to see if it throws errors.
6. Upload data (I uploaded the pizza ontology)
7. Run docker restart fuseki again to see if it throws errors.

Here's the result I got - no errors:

[2021-05-24 08:59:28] Server INFO Apache Jena Fuseki 3.14.0
[2021-05-24 08:59:28] Config INFO FUSEKI_HOME=/jena-fuseki
[2021-05-24 08:59:28] Config INFO FUSEKI_BASE=/fuseki
[2021-05-24 08:59:28] Config INFO Shiro file: file:///fuseki/shiro.ini
[2021-05-24 08:59:28] Config INFO Configuration file: /fuseki/config.ttl
[2021-05-24 08:59:29] Config INFO Load configuration: file:///fuseki/configuration/pizza.ttl
[2021-05-24 08:59:29] Config INFO Register: /pizza
[2021-05-24 08:59:29] Server INFO Started 2021/05/24 08:59:29 UTC on port 3030

This workaround worked for me even after a rebuild!