ViSUS Docker Deployment

Quick start

Start your Docker and login into your account. If you don't have installed follow these instructions: Docker Documentation

To log in from your terminal:

docker login
Username: your_username
Password: XXXX

Now pull the ViSUS image:

docker pull visus/visus

This image contains:

• the ViSUS Server
• configuration files (see ViSUS configuration file)
• a simple 2D web viewer
• some tools to convert data (see [[ViSUS Convert]).

Run the image:

docker run -it --rm -p 8080:80 visus/visus

Check if the server is running:

curl -v "http://localhost:8080/mod_visus?action=list"

You will get a list of the current datasets on the server.

Content of the image

This image contains folders that contains configuration and utilities. Those folder are under /home/visus:

• config, it contains the visus server.config (see ViSUS configuration file)
• apache2, it contains the apache2 config files that you can use for security settings (see ViSUS Server)
• visus, it contains visus tool (see ViSUS Convert) to convert data to IDX format

The user can map those folders locally and edit them adding:

-v local_directory:docker_directory

when you run you docker image. Your run command to mount all the folders to local directories will become as following:

docker run -d -p 8080:80 -v $PWD/config:/home/visus/config -v $PWD/apache2:/home/visus/apache2 -v $PWD/viewer:/home/visus/viewer visus/visus

Web Viewer

You can preview and navigate you data on the server using the webviewer using your browser at the URL: http://localhost:8080

Here is a picture of the viewer:

With the commands on the bottom bar you can:

• change server
• set a slice (if using a 3D dataset)
• set a timestep
• set palettes and min-max range
• choose a field of the selected dataset

Example of using precompiled mod_visus

Create 'server.config' file (replace 2kbit1 with your dataset name):

cat <<EOF > server.config
<?xml version="1.0" ?>
<visus>
  <dataset name='2kbit1' url='file:///home/visus/dataset/2kbit1/visus.idx' permissions='public'/>
</visus>
EOF

Create Dockerfile:

cat <<EOF > Dockerfile
FROM visus/mod_visus
COPY server.config /home/visus/server.config
EOF

Build mod_visus docker image:

docker build -t visus/my-server .

Run the image mounting a host volume:

docker run -it --rm -p 8080:80 --volume="c:/visus_dataset/2kbit1:/home/visus/dataset/2kbit1" visus/my-server 

Test if it works:

wget "http://localhost:8080/mod_visus?action=readdataset&dataset=2kbit1"

Use ViSUS convert from docker

The ViSUS tools executables (see ViSUS Convert) are contained in the image under /usr/local/visus/bin.

For example, if you want to use the tools to convert a raw dataset using your docker deployment you can do it as follow.

Mount a folder that contains your raw data and your converted idx data as follow:

docker run -d -p 8080:80 -v /full/path/to/your/raw/:/home/visus/datasets/raw -v /full/path/to/your/idx/:/home/visus/datasets/idx visus/visus

Check that your container is running correctly (using docker ps) and take note of the Container ID.

Now run a bash session on this container using:

docker exec -it <id_from_docker_ps> /bin/bash

From this bash session you can use your ViSUS converter to convert your data (just mounted in the container) as described in ViSUS Convert.

Example of creating a test david_subsampled server

Create 'server.config' file:

cat <<EOF > server.config
<?xml version="1.0" ?>
<visus>
  <dataset name='david_subsampled' url='file:///home/visus/dataset/david_subsampled/visus.idx' permissions='public'/>
</visus>
EOF

Create Dockerfile:

cat <<EOF > Dockerfile
FROM visus/mod_visus
COPY server.config /home/visus/server.config
RUN set -x \
  && apt update \
  && apt install -y curl \
  && cd /home/visus/dataset \
  && curl http://atlantis.sci.utah.edu/download/david_subsampled.tar.gz -o temp.tar.gz \
  && tar xvzf temp.tar.gz \
  && rm -f temp.tar.gz \
  && chown -R www-data /home/visus/dataset \
  && chmod -R a+rX  /home/visus/dataset  
EOF

Build mod_visus docker image:

docker build -t visus/david_subsampled .

Run the image mounting a host volume:

docker run -it --rm -p 8080:80 visus/david_subsampled 

Test if it works:

wget "http://localhost:8080/mod_visus?action=readdataset&dataset=david_subsampled"

Some tricks

To debug mod_visus (example: to check Apache log files):

docker run -ti -p 8080:80 --entrypoint=/bin/bash visus/mod_visus -s
/usr/local/bin/httpd-foreground.sh

To run an interactive 'clean' ubuntu (or whatever):

docker run -ti -p 8080:80 --entrypoint=/bin/bash ubuntu:16.04 -s

If you want to remove all old docker images and containers (and you know what you are doing!)

docker rm  -f $(docker ps  -a -q)
docker rmi -f $(docker images -q)