I am trying to run single node Elasticsearch instance on a HPC cluster. To do this, I am converting the Elasticsearch docker container as a singularity container. When I launch the container itself I get the following error:
$ singularity exec --overlay overlay.img elastic.sif /usr/share/elasticsearch/bin/elasticsearch
Could not create auto-configuration directory
Exception in thread "main" java.lang.RuntimeException: starting java failed with [1]
output:
[0.000s][error][logging] Error opening log file 'logs/gc.log': Permission denied
[0.000s][error][logging] Initialization of output 'file=logs/gc.log' using options 'filecount=32,filesize=64m' failed.
error:
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.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
at org.elasticsearch.server.cli.JvmOption.flagsFinal(JvmOption.java:113)
at org.elasticsearch.server.cli.JvmOption.findFinalOptions(JvmOption.java:80)
at org.elasticsearch.server.cli.MachineDependentHeap.determineHeapSettings(MachineDependentHeap.java:59)
at org.elasticsearch.server.cli.JvmOptionsParser.jvmOptions(JvmOptionsParser.java:132)
at org.elasticsearch.server.cli.JvmOptionsParser.determineJvmOptions(JvmOptionsParser.java:90)
at org.elasticsearch.server.cli.ServerProcess.createProcess(ServerProcess.java:211)
at org.elasticsearch.server.cli.ServerProcess.start(ServerProcess.java:106)
at org.elasticsearch.server.cli.ServerProcess.start(ServerProcess.java:89)
at org.elasticsearch.server.cli.ServerCli.startServer(ServerCli.java:213)
at org.elasticsearch.server.cli.ServerCli.execute(ServerCli.java:90)
at org.elasticsearch.common.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:54)
at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:85)
at org.elasticsearch.cli.Command.main(Command.java:50)
at org.elasticsearch.launcher.CliToolLauncher.main(CliToolLauncher.java:64)
If I understand correctly, Elasticsearch is trying to create a logfile in /var/log/elasticsearch but does not have the correct permissions. So I created the following recipe to create the folders and set the permission such that any process can write into the log directory. My recipe is the following:
Bootstrap: docker
From: elasticsearch:8.3.1
%files
elasticsearch.yml /usr/share/elasticsearch/config/
%post
mkdir -p /var/log/elasticsearch
chown -R elasticsearch:elasticsearch /var/log/elasticsearch
chmod -R 777 /var/log/elasticsearch
mkdir -p /var/data/elasticsearch
chown -R elasticsearch:elasticsearch /var/data/elasticsearch
chmod -R 777 /var/data/elasticsearch
The elasticsearch.yml file has the following content:
cluster.name: "docker-cluster"
network.host: 0.0.0.0
discovery.type: single-node
ingest.geoip.downloader.enabled: false
After building this recipe the directory /var/log/elasticsearch seems to get created correctly:
$ singularity exec elastic.sif ls -alh /var/log/
total 569K
drwxr-xr-x 4 root root 162 Jul 8 14:43 .
drwxr-xr-x 12 root root 172 Jul 8 14:43 ..
-rw-r--r-- 1 root root 7.7K Jun 29 17:29 alternatives.log
drwxr-xr-x 2 root root 69 Jun 29 17:29 apt
-rw-r--r-- 1 root root 58K May 31 11:43 bootstrap.log
-rw-rw---- 1 root utmp 0 May 31 11:43 btmp
-rw-r--r-- 1 root root 187K Jun 29 17:30 dpkg.log
drwxrwxrwx 2 elasticsearch elasticsearch 3 Jul 8 14:43 elasticsearch
-rw-r--r-- 1 root root 32K Jun 29 17:30 faillog
-rw-rw-r-- 1 root utmp 286K Jun 29 17:30 lastlog
-rw-rw-r-- 1 root utmp 0 May 31 11:43 wtmp
But when I launch the container I get the permission denied error listed above.
What is missing here? What permissions is Elasticsearch expecting?
The following workaround seems to be working for me now:
When launching the singularity container, the elasticsearch process is executed inside the container with the same UID as my own UID (the user that is launching the singularity container with singularity exec). The elasticsearch container is configured to run elasticsearch with the a separate user elasticsearch that exists inside the container. The issue is that singularity (unlike docker) will run every process inside the container with my own UID and not the elasticsearch UID, resulting in the error above.
To work around this, I created a base ubuntu singularity image and then installed elasticsearch into the container following these installation instructions (https://www.elastic.co/guide/en/elasticsearch/reference/current/targz.html). Because the installation was performed with my system user and UID, the entire elasticsearch installation belongs to my system user and not a separate elasticsearch user. Then I can launch the elasticsearch service inside the container.
Related
How does docker create a file system for a Linux container? And how are permissions set up on the root file system?
I encountered a situation when starting a docker container on a particular machine with Ubuntu Server. For some reason, /tmp in the container doesn't have write permissions:
$ docker run -it python:3.11-slim-buster /bin/bash
root#5d5fefe9b9a2:/# ls -la /tmp
total 8
drwxr-xr-t 1 root root 4096 Jan 26 06:58 .
drwxr-xr-x 1 root root 4096 Jan 29 04:31 ..
Note that this has 755 permissions.
However, when I start the same docker image as a container on WSL, I get 777:
$ docker run -it python:3.11-slim-buster /bin/bash
root#201dfe147e5a:/# ls -la /tmp
total 8
drwxrwxrwt 1 root root 4096 Nov 16 06:56 .
drwxr-xr-x 1 root root 4096 Jan 29 04:36 ..
This was fine a few weeks ago on the Ubuntu machine. I recently moved all the files from /var/lib/ubuntu to /ubuntu because the partition mounted at /var was full. Would this have caused the behavior with the permissions of /tmp inside a container? If so, why? And how do I fix it? If not, what else would cause this and...how do I fix it?
Docker uses a so-called union file system for a running container. The recommended driver on Linux is called overlay2. The files and directories for each layer of an image are stored under /var/lib/docker/overlay2, assuming the default config. The directory structure for each layer is combined to create the final file system for the container. See https://docs.docker.com/storage/storagedriver/overlayfs-driver/ for more details.
As for the permissions for the files in the container, they are derived from the permissions of the files in this directory in the host file system. When I copied the files from /var/lib/docker to /docker, I failed to preserve ownership and permissions. My best guess is that umask was applied as each new file was created.
This question relates to this repository with the most relevant Travis job here.
The repository is for static site built from Jupyter notebooks. The notebooks are converted using build/build.py which, for each post, builds a Docker image, starts a corresponding container with the post notebook directory mounted, and uses nbconvert to convert the notebook to Markdown. One step of nbconvert's conversion involves creating a supporting file directory. This fails on Travis due to a permission issue.
In attempting to debug this problem, I found that the ownership and permissions of the repo are the same on my local machine and Travis (with my username switched for travis) before running Docker. Despite this, inside the mounted volume of the Docker container, the ownerships are different:
Local:
drwxrwxr-x 3 jovyan 1000 4096 Dec 10 19:56 .
drwsrwsr-x 1 jovyan users 4096 Dec 3 21:51 ..
-rw-rw-r-- 1 jovyan 1000 105 Dec 7 09:57 Dockerfile
drwxr-xr-x 2 jovyan 1000 4096 Dec 10 12:09 .ipynb_checkpoints
-rw-r--r-- 1 jovyan 1000 154229 Dec 10 12:28 post.ipynb
Travis:
drwxrwxr-x 2 2000 2000 4096 Dec 10 19:58 .
drwsrwsr-x 1 jovyan users 4096 Nov 8 16:37 ..
-rw-rw-r-- 1 2000 2000 101 Dec 10 19:58 Dockerfile
-rw-rw-r-- 1 2000 2000 35271 Dec 10 19:58 post.ipynb
Both my local machine and Travis are running Ubuntu 20.04, have the same version of Docker, and all other tools come from Conda so should behave the same. I am struggling to understand where this difference in ownership is coming from.
Try running the docker again with this command, so the uid outside the container is propagated inside:
docker run -u `id -u`
alternative, as pointed by #anemyte:
docker run -u $(id -u)
This should involve the creation of the new files inside the docker to be owned by "jovyan".
If you are able to guess that mounting points will exist, you could also pre-create them so the ownership of the files inside is also correct:
docker run -v /path/on/host:/path/in/container ...
If you set the permissions of your local path (/path/on/host) as 777, that will also be propagated to the mounting point: no permission error will be thrown regardless of the user that docker uses to create those files.
After that, you'll be free to restore permissions, if needed.
I have an executable written in Golang, it starts and runs fine when started from the Linux-prompt. As you can see, the executable needs an XML file when started. But when started inside a Docker environment, I get error message:
standard_init_linux.go:190: exec user process caused "no such file or directory"
Let me tell you what I tried. First, this is my Dockerfile:
FROM alpine:latest
MAINTAINER Bert Verhees "xxxxx"
ADD archibold_ucum_service /archibold_ucum_service
ADD data/ucum-essence.xml /data/ucum-essence.xml
ENTRYPOINT ["/archibold_ucum_service", "-ucumfile=/data/ucum-essence.xml"]
I build it in this way:
docker build -t=ucum_micro_service .
Then I start it in this way
docker run --name=ucum_micro_service -i -t ucum_micro_service /bin/sh
When I do this, I get the error-message, as displayed above. Then I tried commenting out the ENTRYPOINT line, and then it builds OKAY and it starts the linux prompt, so I can query what is inside.
The executable is in it, and the data-file also. And the executable also has the right attributes (it is executable inside the docker-container)
Then I try to start the executable from the linux-prompt, inside the started container, and then I get again a message that the file is not found:
/ # ./archibold_ucum_service
/bin/sh: ./archibold_ucum_service: not found
For completeness, here is partly the directory-structure in the container:
/ # ls -l
total 17484
-rwxrwxr-x 1 root root 17845706 Aug 3 13:21 archibold_ucum_service
drwxr-xr-x 2 root root 4096 Jul 5 14:47 bin
drwxr-xr-x 2 root root 4096 Aug 3 14:29 data
drwxr-xr-x 5 root root 360 Aug 4 20:27 dev
drwxr-xr-x 15 root root 4096 Aug 4 20:27 etc
drwxr-xr-x 2 root root 4096 Jul 5 14:47 home
drwxr-xr-x 5 root root ........
.......
So, what can be the problem. I am trying to solve this for over a day now. Thanks for support.
Is there a way to associate existing docker volumes (located in /etc/docker/volumes) to containers?
One way to do this is to use docker inspect :conatiner_id but this assumes that the container exists. How can you find to which container the volume belonged to, in the scenario that the container does no longer exist?
Check docker volumes
$ ls -l /var/lib/docker/volumes/
total 72
drwxr-xr-x 3 root root 4096 Nov 14 14:27 0f801819cf76b04b6794163b65df5d649bd795e23f4fc778f78db9ac60a0180d
drwxr-xr-x 3 root root 4096 Nov 29 14:29 my-jenkins
For more info about your volume you can perform docker volume inspect but this tells you nothing about what's really inside your volume. The only way to know this is by going inside the volume-folder and check.
So I'll check "unamed" volume:
$ ls -l /var/lib/docker/volumes/0f801819cf76b04b6794163b65df5d649
bd795e23f4fc778f78db9ac60a0180d/_data
...
drwx------ 2 999 ping 4096 Nov 14 14:27 pg_tblspc
drwx------ 2 999 ping 4096 Nov 14 14:27 pg_twophase
drwx------ 3 999 ping 4096 Nov 14 14:27 pg_xlog
-rw------- 1 999 ping 88 Nov 14 14:27 postgresql.auto.conf
-rw------- 1 999 ping 20791 Nov 14 14:27 postgresql.conf
-rw------- 1 999 ping 37 Nov 14 14:27 postmaster.opts
Normally you should be able to link your volume to the old container you've used. You can check everything what's inside. There isn't a better way at the moment. This is actually the answer on your question but I'll give some more explanation to make it easier in the future.
The best way is to create named volumes. After deleting your container the volume will remain easy to recognize:
docker volume create --name my-jenkins
So in /var/lib/docker/volumes you'll see my-jenkins.
Now I start my jenkins container and link it with my named volume.
Everything which is in /var/jenkins_home will be stored in the named volume.
docker run -d -p 8080:8080 -v my-jenkins:/var/jenkins_home jenkins
I'll create a job in jenkins with the name firstjob. You'll see this job in my named docker volume.
$ ls -l /var/lib/docker/volumes/my-jenkins/_data/jobs/
total 4
drwxr-xr-x 3 dockrema dockrema 4096 Nov 29 14:47 firstjob
Now I will delete my container (id = fa1003894dbc). The container is gone:
$ docker rm -fv fa1003894dbc
I'm a bit later. I want to reuse the named docker volume which still exists to start a new jenkins container which will immediatly container the job "firstjob".
$ docker run -d -p 8080:8080 -v my-jenkins:/var/jenkins_home jenkins
If you have an unnamed docker volume (created automatically with name 0f8018x9cf76b04x163b6xdf) you can use
docker run -d -v 0f8018x9cf76b04x163b6xdf:/var/jenkins_home jenkins
Now your jenkins will use everything which is inside that volume (it's only not a named volume, what makes it more difficult to see with which type of container it was linked. But by accessing the volume folder you will find it in most cases.)
This question is a minimal failing version of this other one:
How to get contents generated by a docker container on the local fileystem
I have the following files:
./test
-rw-r--r-- 1 miqueladell staff 114 Jan 21 15:24 Dockerfile
-rw-r--r-- 1 miqueladell staff 90 Jan 21 15:23 docker-compose.yml
drwxr-xr-x 3 miqueladell staff 102 Jan 21 15:25 html
./test/html:
-rw-r--r-- 1 miqueladell staff 0 Jan 21 15:22 file_from_local_filesystem
DockerFile
FROM php:7.0.2-apache
RUN touch /var/www/html/file_generated_inside_the_container
VOLUME /var/www/html/
docker-compose.yml
test:
image: test
volumes:
- ./html:/var/www/html/
After running a container built from the image defined in the Dockerfile what I want is having:
./html
-- file_from_local_filesystem
-- file_generated_inside_the_container
Instead of this I get the following:
build the image
$ docker build --no-cache -t test .
Sending build context to Docker daemon 4.096 kB
Step 1 : FROM php:7.0.2-apache
---> 2f16964f48ba
Step 2 : RUN touch /var/www/html/file_generated_inside_the_container
---> Running in b957cc9d7345
---> 5579d3a2d3b2
Removing intermediate container b957cc9d7345
Step 3 : VOLUME /var/www/html/
---> Running in 6722ddba76cc
---> 4408967d2a98
Removing intermediate container 6722ddba76cc
Successfully built 4408967d2a98
run a container with previous image
$ docker-compose up -d
Creating test_test_1
list files on the local machine filesystem
$ ls -al html
total 0
drwxr-xr-x 3 miqueladell staff 102 Jan 21 15:25 .
drwxr-xr-x 5 miqueladell staff 170 Jan 21 14:20 ..
-rw-r--r-- 1 miqueladell staff 0 Jan 21 15:22 file_from_local_filesystem
list files from the container
$ docker exec -i -t test_test_1 ls -alR /var/www/html
/var/www/html:
total 4
drwxr-xr-x 1 1000 staff 102 Jan 21 14:25 .
drwxr-xr-x 4 root root 4096 Jan 7 18:05 ..
-rw-r--r-- 1 1000 staff 0 Jan 21 14:22 file_from_local_filesystem
The volume from the local filesystem gets mounted on the container file system replacing the contents of it.
This is contrary at what I understand in the section "Permissions and Ownership" of this guide Understanding volumes
How could I get the desired output?
Thanks
EDIT: As is said in the accepted answer I did not understand volumes when asking the question. Volumes, as mountponint, replace the container content with the local filesystem that is mounted.
The solution I needed was to use ENTRYPOINT to run the necessary commands to initialize the contents of the mounted volume once the container is running.
The code that originated the question can be seen working here:
https://github.com/MiquelAdell/composed_wordpress/tree/1.0.0
This is from the guide you've pointed to
This won’t happen if you specify a host directory for the volume
Volumes you share from other containers or host filesystem replace directories from container.
If you need to add some files to volume, you should do it after you start container. You can do an entrypoint for example which does touch and then runs your main process.
Yep, pretty sure it should be the full path:
docker-compose.yml
test:
image: test
volumes:
- ./html:/var/www/html/
./html should be /path/to/html
Edit
Output after changing to full path and running test.sh:
$ docker exec -ti dockervolumetest_test_1 bash
root#c0bd7a722b63:/var/www/html# ls -la
total 8
drwxr-xr-x 2 1000 adm 4096 Jan 21 15:19 .
drwxr-xr-x 3 root root 4096 Jan 7 18:05 ..
-rw-r--r-- 1 1000 adm 0 Jan 21 15:19 file_from_local_filesystem
Edit 2
Sorry, I misunderstood the entire premise of the question :)
So you're trying to get file_generated_inside_the_container (which is created inside your docker image only) mounted to some location on your host machine - like a "reverse mount".
This isn't possible to do with any docker commands, but if all you're after is access to your VOLUMEs files on your host, you can find the files in the docker root directory (normally /var/lib/docker). To find the exact location of the files, you can use docker inspect [container_id], or in the latest versions use the docker API.
See cpuguy's answer in this github issue: https://github.com/docker/docker/issues/12853#issuecomment-123953258 for more details.