Seismology-Docker

Seismology-Docker is a docker image with seismology-related packages installed.

Requirements

• Docker with BuildKit
• X Server (for GUI support on Windows and macOS)
  • For Windows, VcXsrv or MobaXterm.
  • For Linux, it is installed by default on most of Linux distributions.
  • For macOS, XQuartz.
• xhost
  • For Windows, it is part of VcXsrv.
  • For Arch-based distros, xorg-xhost.
  • For Debian-based distros, x11-server-utils.
  • For macOS, it is part of XQuartz.

Requirements installation guide

Windows

Install VcXsrv (X Server)

Note

If you have MobaXterm installed, you don't need to install VcXsrv.

1. Download and install latest version of VcXsrv.
2. Make sure that Full dropdown selected and click Next.
3. Leave the Destination Folder untouched and click Install.
4. After the installation process successfully completes you may click Close.
5. Configure VcXsrv with the application named XLaunch.
6. Make sure that Multiple windows option selected.
7. Set Display number to 0 and click Next.
8. Make sure that Start no client option selected and click Next.
9. Select Disable access control option and click Next.
10. Click Finish.
11. Now you should see an X icon appears on your taskbar.
    This indicates that the VcXsrv (X Server) is running.

Note

If you killed the X Server or the X icon disappeared from the taskbar, just relaunch XLaunch and follow the configuration steps.

Install Docker Desktop

1. Download and install latest version of Docker Desktop for Windows.
2. Make sure that Use WSL 2 instead of Hyper-V option selected and click Ok.
3. After the installation process successfully completes you may click Close.
4. Reboot the PC.
5. Launch Docker Desktop.
6. Read the terms and conditions completely and click Accept.
7. Click Continue without signing in.
8. Click Skip survey.
9. Now you should see an Docker icon appears on your taskbar.
   This indicates that the Docker Desktop (with Docker Engine) is running.
10. You may close Docker Desktop window when you confirm that Docker Desktop is running on the taskbar icon.

Note

If you killed the Docker Desktop or the Docker icon disappeared from the taskbar, just relaunch Docker Desktop.

macOS

Install XQuartz (X Server)

1. Download and install latest version of XQuartz.
2. Click Continue.
3. Read the information carefully and click Continue.
4. Read the terms and conditions carefully and click Continue.
5. Click Agree.
6. Click Install.
7. After the installation process successfully completes you may click Close.
8. Reboot the PC.
9. Open Terminal.

# Enable Indirect GLX
$ defaults write org.xquartz.X11 enable_iglx -boolean true

# Allow connections from network
$ defaults write org.xquartz.X11 nolisten_tcp -boolean false

10. Reboot the PC.

Installation

Windows

Important

Make sure that the Docker Engine is running before issuing docker command.

1. Run PowerShell.

# Download this repository
PS > iwr 'https://github.com/yurical/seismology-docker/archive/refs/heads/main.zip' -OutFile '.\seismology-docker.zip'
PS > Expand-Archive '.\seismology-docker.zip' .
PS > cd seismology-docker-main

# Go to the directory where you cloned repository or extracted `seismology-docker.zip`.
PS > cd seismology-docker

# Make sure that `Dockerfile` exists in the current directory
PS > Get-ChildItem

    Directory: ...

Mode       LastWriteTime       Length Name
----       -------------       ------ ----
-a---                ...          ... Dockerfile
-a---                ...          ... LICENSE
-a---                ...          ... README.md
-a---                ...          ... requirements.txt

# Build a docker image
PS > docker buildx build . --network host --tag seismology

[+] Building 137.1s (13/13) FINISHED                                                                     docker:default
 => [internal] load build definition from Dockerfile                                                               0.0s
 => [internal] load .dockerignore                                                                                  0.0s
 => [1/7] FROM docker.io/library/python:3.10-slim-bookworm@sha256:e53bad75661571d23d9fd632d10f192b09228f31b14af1f  7.7s
 => [2/7] RUN apt-get update                                                                                       2.8s
 => [3/7] RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q     dbus     pkg-config     libxcb*-dev     l  71.6s
    ...
 => => naming to docker.io/library/seismology                                                                      0.0s

View build details: ...

# Once build finishes, make sure that `seismology` docker image exists
PS > docker image ls

REPOSITORY   TAG      IMAGE ID   CREATED   SIZE
seismology   latest   ...        ...       <about a few GB>

Linux

Important

Make sure that the docker.service is running before issuing docker command.

# Clone this repository
# or you can just download code archive from https://github.com/yurical/seismology-docker/archive/refs/heads/main.zip and extract it.
$ git clone https://github.com/yurical/seismology-docker.git

Cloning into 'seismology-docker'...
remote: Enumerating objects: 8, done.
remote: Counting objects: 100% (8/8), done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 8 (delta 0), reused 8 (delta 0), pack-reused 0
Receiving objects: 100% (8/8), 4.42 KiB | 4.42 MiB/s, done.

# Go to the directory where you extracted `seismology-docker.zip`
$ cd seismology-docker

# Make sure that `Dockerfile` exists in the current directory
$ ls
Dockerfile  LICENSE  README.md  requirements.txt

# Build a docker image
$ docker buildx build . --network host --tag seismology

[+] Building 137.1s (13/13) FINISHED                                                                     docker:default
 => [internal] load build definition from Dockerfile                                                               0.0s
 => [internal] load .dockerignore                                                                                  0.0s
 => [1/7] FROM docker.io/library/python:3.10-slim-bookworm@sha256:e53bad75661571d23d9fd632d10f192b09228f31b14af1f  7.7s
 => [2/7] RUN apt-get update                                                                                       2.8s
 => [3/7] RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q     dbus     pkg-config     libxcb*-dev     l  71.6s
    ...
 => => naming to docker.io/library/seismology                                                                      0.0s

View build details: ...

# Once build finishes, make sure that `seismology` docker image exists
$ docker image ls

REPOSITORY   TAG      IMAGE ID   CREATED   SIZE
seismology   latest   ...        ...       <about a few GB>

Usage

Important

Make sure that the X Server and Docker Engine is running before issuing docker command.

Windows

# Start the docker container with bash entrypoint
PS > docker run -e DISPLAY="host.docker.internal:0.0" --shm-size 4G -it --rm --entrypoint bash seismology

# Now it continues on bash as root
root@67ce68476fdc:/work＃

# Run some applications to confirm GUI works
root@67ce68476fdc:/work＃ geany

# Type exit to quit from container
root@67ce68476fdc:/work＃ exit

PS >

Linux

# Adjust the permissions the X server host
$ xhost +local:docker

# Start the docker container with bash entrypoint
$ docker run -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY --shm-size 4G -it --rm --entrypoint bash seismology

# Now it continues on bash as root
root@67ce68476fdc:/work＃

# Run some applications to confirm GUI works
root@67ce68476fdc:/work＃ geany

# Type exit to quit from container
root@67ce68476fdc:/work＃ exit

$

# You can revert the permissions after you are finished using the container (If you concerned)
$ xhost -local:docker

Troubleshooting

dial unix /var/run/docker.sock: connect: permission denied

# Create a docker group
$ sudo groupadd -f docker

# Add docker group to the current user
$ sudo usermod -aG docker "${USER}"

# Change /var/run/docker.sock owner group
$ sudo chown root:docker /var/run/docker.sock

# Apply the changes to groups
$ newgrp docker

# Restart the docker service
$ sudo systemctl restart docker

E: Failed to fetch http://deb.debian.org/debian/pool/main/*.deb Cannot initiate the connection to deb.debian.org:80. - connect (101: Network is unreachable)

Try the build command again.

TODO

• Add further instructions for macOS