I'm trying to run the Hetionet v1.0 docker container mentioned in this SO post.
I've setup a digitalocean droplet with Docker
I ran docker pull dhimmel/hetionet and it worked
Now I run docker run dhimmel/hetionet and the following happens (and never returns to the interactive shell prompt).
If that completed successfully I think the last thing I'm supposed to do is run sh ~/run-docker.sh. Furthermore nothing is live at my droplet's ip_address:7474.
The error in the screenshot above looks a lot like it could be related to some redundant #Path("/") annotation, as described in this SO post's comment, buried in the docker container but I'm not sure.
Is the output from running docker run dhimmel/hetionet supposed to hang my shell? I'm running a 2 GB Memory / 40 GB Disk Droplet on Ubuntu 16.04 with Docker 1.12.5.
Thanks for your interest in the Hetionet Docker.
The output in 3 is expected. It looks like a Docker container successfully launched, downloaded the Hetionet database, and launched the Neo4j server. I'll look into fixing the warnings, but they're not errors, as Neo4j is still launching.
For production, we use a more advanced Docker run command. Depending on your use case, you may want to use the development docker run command:
docker run \
--publish=7474:7474 \
--publish=7687:7687 \
--volume=$HOME/neo4j/hetionet-data:/data \
--volume=$HOME/neo4j/hetionet-logs:/var/lib/neo4j/logs \
dhimmel/hetionet
Both the production and development command map ports. This will make it so the Neo4j server running inside your Docker container is available at http://localhost:7474/. This is most likely what you want. If you're doing this on DigitalOcean, you would replace http://localhost with the IP address of your droplet.
For an interactive shell session in a dhimmel/hetionet container, you can use:
docker run --interactive --tty dhimmel/hetionet bash
However, that command does not launch the Neo4j server -- it just let's you explore the image.
Does this clear things up?
Related
Sometimes the Docker container where Memgraph is running just stops working or says that the process was aborted with exit code 137. How can I fix this?
You should check the Memgraph logs, where you'll probably find the reason why the process was aborted.
Since you said that you're using Memgraph with Docker, there are two options:
If you run Memgraph with Docker using the volume for logs, that is with
-v mg_log:/var/log/memgraph, then mg_log folder usually can be found at \\wsl$\docker-desktop-data\version-pack-data\community\docker\volumes\ (Windows) or /var/lib/docker/volumes/ (Linux and macOS).
If you run Memgraph without using the volume for logs, then you need to enter the Docker container. In order to do that, first you have to find out the container ID by running docker ps. Then you have to copy the container ID and run docker exec -it <containerID> bash. For example, if container ID is 83d76fe4df5a, then you run docker exec -it 83d76fe4df5a bash. Next, you need find the folder where logs are located. You can do that by running cd /var/log/memgraph. To read the logs, run cat <memgraph_date>.log, that is, if you have log file memgraph_2022-03-02.log located inside the log folder, then run cat memgraph_2022-03-02.log.
Hopefully, when you read the logs, you'll be able to fix your problem.
I try to run docker in bash ubuntu on windows. But every time I get this message
"Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?". If i run it in powershell - it work. Can somebody help?
Connecting to the docker deamon requires some privilidges that you don't have when starting the bash terminal.
You can however use the docker command terminal which will allow you to interact with the docker deamon.
Found the solution on this post: https://blog.jayway.com/2017/04/19/running-docker-on-bash-on-windows/
Connect Docker on WSL to Docker on Windows
Running docker against an engine on a different machine is actually quite easy, as Docker can expose a TCP endpoint which the CLI can attach to.
This TCP endpoint is turned off by default; to activate it, right-click the Docker icon in your taskbar and choose Settings, and tick the box next to “Expose daemon on tcp://localhost:2375 without TLS”.
With that done, all we need to do is instruct the CLI under Bash to connect to the engine running under Windows instead of to the non-existing engine running under Bash, like this:
$ docker -H tcp://0.0.0.0:2375 images
REPOSITORY TAG IMAGE ID CREATED SIZE
There are two ways to make this permanent – either add an alias for the above command, or better yet, export an environment variable which instructs Docker where to find the host engine:
$ echo "export DOCKER_HOST='tcp://0.0.0.0:2375'" >> ~/.bashrc
$ source ~/.bashrc
Now, running docker commands from Bash works just like they’re supposed to.
$ docker run hello-world
Hello from Docker!This message shows that your installation appears to be working correctly.
I'm very new to kubernetes and trying to conceptualize it as well as set it up locally in order to try developing something on it.
There's a confound though that I am running on a windows machine.
Their "getting started" documentation in github says you have to run Linux to use kubernetes.
As docker runs on windows, I was wondering if it was possible to create a kubernetes instance as a container in windows docker and use it to manage the rest of the cluster in the same windows docker instance.
From reading the setup instructions, it seems like docker, kubernetes, and something called etcd all have to run "in parallel" on a single host operating system... But part of me thinks it might be possible to
Start docker, boot 'default' machine.
Create kubernetes container - configure to communicate with the existing docker 'default' machine
Use kubernetes to manage existing docker.
Pipe dream? Wrongheaded foolishness? I see there are some options around running it in a vagrant instance. Does that mean docker, etcd, & kubernetes together in a single VM (which in turn creates a cluster of virtual machines inside it?)
I feel like I need to draw a picture of what this all looks like in terms of physical hardware and "memory boxes" to really wrap my head around this.
With Windows, you need docker-machine and boot2docker VMs to run anything docker related.
There is no (not yet) "docker for Windows".
Note that issue 7428 mentioned "Can't run kubernetes within boot2docker".
So even when you follow instructions (from a default VM created with docker-machine), you might still get errors:
➜ workspace docker run --net=host -d -v /var/run/docker.sock:/var/run/docker.sock gcr.io/google_containers/hyperkube:v0.14.2 /hyperkube kubelet --api_servers=http://localhost:8080 --v=2 --address=0.0.0.0 --enable_server --hostname_override=127.0.0.1 --config=/etc/kubernetes/manifests
ee0b490f74f6bc9b70c1336115487b38d124bdcebf09b248cec91832e0e9af1d
➜ workspace docker logs -f ee0b490f74f6bc9b70c1336115487b38d124bdcebf09b248cec91832e0e9af1d
W0428 09:09:41.479862 1 server.go:249] Could not load kubernetes auth path: stat : no such file or directory. Continuing with defaults.
I0428 09:09:41.479989 1 server.go:168] Using root directory: /var/lib/kubelet
The alternative would be to try on a full-fledge Linux VM (like the latest Ubuntu), instead of a boot2docker-like VM (based on a TinyCore distro).
All k8s components can be raised up with hyperkube, which helps you bring up a containerized one.
If you're able to run docker on windows, it would probably work. I haven't tried it on windows personally.
I am trying to push some image to my registry, but when i tried to do:
sudo docker push myreg:5000\image
i got some error that told me that i need to start docker daemon with
docker -d --insecure-registry myreg:5000
So i stopped the docker service, and started it using the command above, once i do that the current shell window(ssh) is stuck with docker output, and if i close it the docker service is stopped.
I know this is an easy one, and i searched for hours and couldn't find anything.
Thank you
The problem is that when i run the command, i get all the docker output to the shell, and if i close it, the docker service stopped, usually the -d should take care of it, but it wont work
I think there's a confusion here; the top-level -d (docker -d) flag starts docker in daemon mode, in the foreground. This is different from the docker run -d <image> flag, which means "start a container from <image>, in detached mode". What you're seeing on your screen, is the daemon output / logs, waiting for connections from a docker client.
Back to your original issue;
The instructions to run docker -d --insecure-registry myreg:5000 could be clearer, but they illustrate that you should change the daemon options of your docker service to include the --insecure-registry myreg:5000 option.
Depending on the process manager your system users (e.g., upstart or systemd), this means you'll have to edit the /etc/default/docker file (see the documentation), or adding a "drop-in" file to override the default systemd service options; see SystemD custom daemon options
Some notes;
The top-level -d option is deprecated in docker 1.8 in favor of the new docker daemon command
Using --insecure-registry is discouraged for security reasons as it allows both unencrypted and untrustworthy communication with the registry. It's preferable to add your CA to the trusted list of your system.
I installed boot2docker as explained on the docker website. Here are some command runs to show that I have things installed correctly:
$$:~ kv$ boot2docker start
Waiting for VM and Docker daemon to start...
...................ooo
Started.
Writing /Users/kvantum/.boot2docker/certs/boot2docker-vm/ca.pem
Writing /Users/kvantum/.boot2docker/certs/boot2docker-vm/cert.pem
Writing /Users/kvantum/.boot2docker/certs/boot2docker-vm/key.pem
Your environment variables are already set correctly.
$$:~ kv$ docker images
REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE
ubuntu 14.04 b39b81afc8ca 11 days ago 188.3 MB
hello-world latest e45a5af57b00 3 weeks ago 910 B
After this, I ran the following command:
docker run -t -i ubuntu:14.04 /bin/bash
Inside the container, I installed zeromq, and started a zeromq server on port 5555 using tcp.
My questions are following:
If I exit out of the container, will it save all the work I do inside it?
I have no idea how to connect to the server running on port 5555. I read something about exposing a port, but I am not sure how to go about doing that. I did an ifconfig inside the container, and tried to connect to the server from the host like this:
$$:~ kv$ ./zmq_client tcp://container_ip:5555
This did not work. Can someone please lists the steps I need to take in order to connect to the server running within the container.
For completion sake, I am providing the list of my environment variables:
TERM_PROGRAM=Apple_Terminal
TERM=xterm-256color
SHELL=/bin/bash
TMPDIR=/var/folders/km/5kbpdx4s7cg4rmyc6d5q9l9r0000gq/T/
DOCKER_HOST=tcp://192.168.109.103:2376
Apple_PubSub_Socket_Render=/tmp/launch-1tWMHJ/Render
TERM_PROGRAM_VERSION=326
OLDPWD=/Users
TERM_SESSION_ID=262CBC8B-0A74-4B70-9F28-D9FA51FF713C
USER=kv
SSH_AUTH_SOCK=/tmp/launch-ZTWNGL/Listeners
__CF_USER_TEXT_ENCODING=0x1F7:0:0
DOCKER_TLS_VERIFY=1
__CHECKFIX1436934=1
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
PWD=/Users/kv
DOCKER_CERT_PATH=/Users/kv/.boot2docker/certs/boot2docker-vm
HOME=/Users/kv
SHLVL=1
LOGNAME=kv
LC_CTYPE=UTF-8
DISPLAY=/tmp/launch-rco9zt/org.macosforge.xquartz:0
_=/usr/bin/env
One last question I have is about code performance. So within my Mac OS X, I have a docker container running (which runs Ubuntu). If I run the application, like a zeromq based server inside the container, will it not be slower as compared to running it on Mac OS X directly. Please explain the benefits of using docker in such a scenario..
You should really do some more reading and research before turning to SO, then ask about anything you can't figure out. But:
No. If the container is "exited" you can restart it and your files will still be there, but once it is removed your files are gone. You can use docker commit to save them to an image, but the best bet is to use a Dockerfile.
docker run -p 5000:8000 image will expose port 8000 in the container as port 5000 on the host.
Yes, it will be slower due to the boot2docker VM. It would not be slower if you were running on a Linux host. The advantage is that zeromq is now running in an isolated container with all its dependencies.