Dockerfile for OACIS

Ready-to-run OACIS application in Docker.

Quick Start

0. (prerequisite) install docker & docker compose

• https://docs.docker.com/get-docker/
• https://docs.docker.com/compose/install/

1. Clone oacis_docker_tools

git clone https://github.com/crest-cassia/oacis_docker.git
cd oacis_docker

2. Start OACIS container

$ ./oacis_boot.sh

A container of OACIS launches. It takes some time until the launch completes.

• Visit http://localhost:3000 to access OACIS like the following. You may change the port by specifying -p option.
• Visit http://localhost:8888 to access Jupyter notebook with OACIS API. The port may be changed by -j option.

See OACIS documentation.

3. stopping the container temporarily

$ ./oacis_stop.sh

Even after the server is stopped, the data (including your simulation results) are not deleted. In other words, the virtual machine image still exists. Restart the container by running oacis_start.sh.

$ ./oacis_start.sh

Other commands

stopping the container permanently

When you would like to remove the docker container as well as the docker volumes, run the following command:

$ ./oacis_terminate.sh

Note: The database is deleted. Make sure to make a backup if you want to save your results somewhere.

The simulation output files are stored in Result directory, which is NOT deleted by the above command. To delete all the files, remove Result directory as well.

$ rm -rf Result

making a backup and restoring from it

When we would like to move all the data to other directory or make a backup, run the following command:

$ ./oacis_dump_db.sh

All the data stored in the database running on the container are dumped into Result/db_dump.

After you run the above command, send Result directory to the place you like. For instance, run the following:

$ rsync -avhz --progress Result /path/to/backup

To restore the data from a backup, copy the backup to the Result directory first and then run the restore command. Make sure that OACIS must be running when restoring the DB.

$ rsync -avhz --progress /path/to/backup Result
$ ./oacis_boot.sh                # OACIS must be launched in advance
$ ./oacis_restore_db.sh

logging to the shell

When you would like to login to the shell on the docker container for trouble shooting, run the following command:

$ ./oacis_shell.sh

Set up for the Tutorial

Registering a sample simulator

The following command registers a sample simulator "ns_model" that is used in the tutorial of OACIS. After you add this simulator, Step1 and Step2 of this tutorial are already done. You can start from Step3.

$ ./oacis_shell.sh
# (login to the container)
$ bash ./setup_ns_model.sh
$ exit     # to logout from the container

The source code of this sample simulator can be found at yohm/sim_ns_model.

SSH agent setup

On the container, you can use the SSH agent running on the host OS. (Hereafter, the host on which docker is running is called host OS). If environemnt varialbe SSH_AUTH_SOCK is set in the host OS so that you can connect to remote hosts from OACIS. Here is how to set up SSH agent.

1. Create a key pair and add it to authorized_keys.

OACIS requires an authentication by SSH keys. If you haven't made a SSH key-pair, create one in order to use it for your use.

$ ssh-keygen -t rsa

You may enter a passphrase when making a key-pair. The key pair will be created in ~/.ssh directory.

2. Setup ssh-agent

Set up ssh-agent on your host OS. Launch SSH agent as follows. On macOS, SSH agent is automatically launched so you can skip this step.

$ eval $(ssh-agent)
Agent pid 97280

The information required for SSH connection is determined by this file.

3. Add your key to the agent.

You'll be required to enter the passphrase for this key.

$ ssh-add ~/.ssh/id_rsa

Now you should be able to connect to a remote host wihtout entering a password.

$ ssh my_remote_host

(If you are going to use the host OS as one of the computational hosts for OACIS) Add this key to the list of authorized_keys. Make sure the permission of the authorized_keys is 600 when you make this file for the first time. You should be able to login to the localhost without entering your password.

$ cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
$ chmod 600 authorized_keys
$ ssh localhost     # password should not be required

4. setup xsub in remote hosts

Set up xsub or xsub_py on remote hosts. See README of the repository for the details.

5. Launch OACIS

When these set up are done, launch OACIS.

$ ./oacis_boot.sh

6. Edit .ssh/config on the container

OACIS refers to .ssh/config file when making SSH connections. Run

$ ./oacis_shell.sh

to login to the container. On the container, edit .ssh/config file.

$ vi ~/.ssh/config

Here is an example of the config file. docker-host is the host running the docker. When you want to access a server located in the intranet, use ProxyJump to login via docker-host.

Host my_intra_server
  User my_user
  HostName my_intra_server
  ProxyJump docker-host
Host my_server
  User my_user
  HostName my_server.example.com

6. Register your host OS on OACIS

Go to the page of host list. http://localhost:3000/hosts Select New Host and fill in the host information. You can add hosts that are listed in ~/.ssh/config. See the document for details: How to setup host on OACIS

Add a host with the reserved name "docker-host" to use your host OS as a computational host. You'll be able to run your simulators on your host OS.

synchronizing data with another OACIS

When you would like to copy your data to another OACIS instance in another machine, run a shell script like the following. (Replace your_host_name with your actual host name).

#!/bin/bash

set -eux
./oacis_dump_db.sh
rsync -ahv --progress Result/ your_remote_host:oacis_docker/Result
ssh your_remote_host '~/oacis_docker/oacis_restore_db.sh'

updating OACIS image

Take the following steps to update the docker image of OACIS.

1. ./oacis_dump_db.sh
2. ./oacis_terminate.sh
3. docker pull oacis/oacis_jupyter
4. ./oacis_boot.sh
5. ./oacis_restore_db.sh

License

oacis_docker is a part of OACIS. OACIS is published under the term of the MIT License (MIT). Copyright (c) 2014-2022 RIKEN AICS, RIKEN R-CCS

Note for Developers

available docker images

• oacis
  • A base image, which consists of OACIS and its prerequisites.
• oacis_jupyter
  • On top of the "base" image, Python and Jupyter environments are installed.

running an image built from the source code

When you would like to build an OACIS image from source rather than pulling an image from dockerhub, run oacis_boot.sh with --build-image OACIS_VERSION option. For instance, when you would like to build an OACIS image from develop branch, run the following.

$ ./oacis_boot.sh --build-image develop

Note this command requires some time to build an image.

creating images for a specific version of OACIS

To create images for a specific version of OACIS and push them to dockerhub, edit OACIS_VERSION in "version_tagging.sh" and run it as following.

git pull
# edit "version_tagging.sh"
git commit version_tagging.sh
docker login
./version_tagging.sh
git tag -a ${OACIS_VERSION} -m "version ${OACIS_VERSION}"
git push
git tag --push