Difference between revisions of "ViSUS Docker Deployment"

From
Jump to: navigation, search
(Before starting)
(Use ViSUS convert from the Docker container)
(31 intermediate revisions by the same user not shown)
Line 1: Line 1:
== Before starting ==
+
== Quick start ==
  
 
Start your Docker and login into your account.  
 
Start your Docker and login into your account.  
 +
If you don't have installed follow these instructions: [https://docs.docker.com Docker Documentation]
 +
 +
To log in from your terminal:
 +
<syntaxhighlight lang="bash">
 +
docker login
 +
Username: your_username
 +
Password: XXXX
 +
</syntaxhighlight>
  
Open a docker shell and make sure you are logged:
+
Now pull the ViSUS image:
 +
<syntaxhighlight lang="bash">
 +
docker pull visus/visus
 +
</syntaxhighlight>
  
<pre>docker login
+
This image contains:
Username: your_username
+
* the ViSUS Server
Password: XXXX</pre>
+
* configuration files (see [[ViSUS configuration file]])
 +
* a simple 2D web viewer
 +
* some tools to convert data (see [[ViSUS Convert]]).
 +
 
 +
Run the image:
 +
<syntaxhighlight lang="bash">
 +
docker run -it --rm -p 8080:80 visus/visus
 +
</syntaxhighlight>
 +
 
 +
Check if the server is running:
 +
<syntaxhighlight lang="bash">
 +
curl -v "http://localhost:8080/mod_visus?action=list"
 +
</syntaxhighlight>
 +
 
 +
You will get a list of the current datasets on the server.
 +
 
 +
=== Content of the image ===
 +
 
 +
This image contains folders with configuration files and utilities.
 +
The folders of interest are under /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:
 +
 
 +
<syntaxhighlight lang="bash">
 +
-v local_directory:docker_directory
 +
</syntaxhighlight>
 +
 
 +
when you run you docker image.
  
If you don't have installed follow these instructions: [https://docs.docker.com Docker Documentation]
+
== How to customize the list of datasets on your server ==
 +
The list of dataset that the server exposes are contained in the [[ViSUS configuration file]].
  
== Example of using precompiled mod_visus ==
+
If you have already a [[ViSUS configuration file]] that you want to use, you can run the container as following:
 +
<syntaxhighlight lang="bash">
 +
docker run -d -p 8080:80 -v $PWD/config:/visus/config visus/visus
 +
</syntaxhighlight>
  
Create 'server.config' file (replace 2kbit1 with your dataset name):
+
and edit the '''visus.config''' file (see [[ViSUS configuration file]]).
  
<pre>cat &lt;&lt;EOF &gt; server.config
+
'''Note''': The server needs to be able to read and write the configuration file, so make sure that your ''server.config'' has the right privileges. For example:
&lt;?xml version=&quot;1.0&quot; ?&gt;
+
<syntaxhighlight lang="bash">
&lt;visus&gt;
+
chmod 766 /path/to/your/server.config
  &lt;dataset name='2kbit1' url='file:///home/visus/dataset/2kbit1/visus.idx' permissions='public'/&gt;
+
</syntaxhighlight>
&lt;/visus&gt;
 
EOF</pre>
 
Create Dockerfile:
 
  
<pre>cat &lt;&lt;EOF &gt; Dockerfile
+
Making the configuration file writable will allow to add datasets dynamically using the action ''add_dataset'' (see [[ViSUS Server]]).
FROM visus/mod_visus
 
COPY server.config /home/visus/server.config
 
EOF</pre>
 
Build mod_visus docker image:
 
  
<pre>docker build -t visus/my-server .</pre>
+
If you also want to customize the apache security (e.g. change the users) you can run the command to mount also the apache2 directory as following:
Run the image mounting a host volume:
+
<syntaxhighlight lang="bash">
 +
docker run -d -p 8080:80 -v $PWD/config:/visus/config -v $PWD/apache2:/visus/apache2 visus/visus
 +
</syntaxhighlight>
  
<pre>docker run -it --rm -p 8080:80 --volume=&quot;c:/visus_dataset/2kbit1:/home/visus/dataset/2kbit1&quot; visus/my-server </pre>
+
== Convert your data in IDX using the Docker deployment ==
Test if it works:
 
  
<pre>wget &quot;http://localhost:8080/mod_visus?action=readdataset&amp;dataset=2kbit1&quot;</pre>
+
The ViSUS tools executables (see [[ViSUS Convert]]) are contained in the container under <code>/usr/local/visus/bin</code>.
== Example of creating a test david_subsampled server ==
 
  
Create 'server.config' file:
+
For example, if you want to use the tools to convert a raw dataset using your docker deployment you can do it as follow.
  
<pre>cat &lt;&lt;EOF &gt; server.config
+
Mount a folder that contains your ''raw'' data and your converted ''idx'' data as follow:
&lt;?xml version=&quot;1.0&quot; ?&gt;
+
<syntaxhighlight lang="bash">
&lt;visus&gt;
+
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
  &lt;dataset name='david_subsampled' url='file:///home/visus/dataset/david_subsampled/visus.idx' permissions='public'/&gt;
+
</syntaxhighlight>
&lt;/visus&gt;
 
EOF</pre>
 
Create Dockerfile:
 
  
<pre>cat &lt;&lt;EOF &gt; Dockerfile
+
Check that your container is running correctly (using <code>docker ps</code>) and take note of the ''Container ID''.
FROM visus/mod_visus
 
COPY server.config /home/visus/server.config
 
RUN set -x \
 
  &amp;&amp; apt update \
 
  &amp;&amp; apt install -y curl \
 
  &amp;&amp; cd /home/visus/dataset \
 
  &amp;&amp; curl http://atlantis.sci.utah.edu/download/david_subsampled.tar.gz -o temp.tar.gz \
 
  &amp;&amp; tar xvzf temp.tar.gz \
 
  &amp;&amp; rm -f temp.tar.gz \
 
  &amp;&amp; chown -R www-data /home/visus/dataset \
 
  &amp;&amp; chmod -R a+rX  /home/visus/dataset 
 
EOF</pre>
 
Build mod_visus docker image:
 
  
<pre>docker build -t visus/david_subsampled .</pre>
+
Now run a bash session on this container using:
Run the image mounting a host volume:
+
<syntaxhighlight lang="bash">
 +
docker exec -it <id_from_docker_ps> /bin/bash
 +
</syntaxhighlight>
  
<pre>docker run -it --rm -p 8080:80 visus/david_subsampled </pre>
+
From this bash session you can use your ViSUS converter to convert your data (just mounted in the container) as described in [[ViSUS Convert]].
Test if it works:
 
  
<pre>wget &quot;http://localhost:8080/mod_visus?action=readdataset&amp;dataset=david_subsampled&quot;</pre>
+
== Experimental: Web Viewer ==
== Some tricks ==
 
  
To debug mod_visus (example: to check Apache log files):
+
You can preview and navigate you data on the server using the webviewer using your browser at the URL: http://localhost:8080
  
<pre>docker run -ti -p 8080:80 --entrypoint=/bin/bash visus/mod_visus -s
+
Here is a picture of the viewer:
/usr/local/bin/httpd-foreground.sh</pre>
+
[[File:2dwebviewer.png|300px]]
To run an interactive 'clean' ubuntu (or whatever):
 
  
<pre>docker run -ti -p 8080:80 --entrypoint=/bin/bash ubuntu:16.04 -s</pre>
+
With the commands on the bottom bar you can:
If you want to remove all old docker images and containers (and you know what you are doing!)
+
* 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
  
<pre>docker rm  -f $(docker ps  -a -q)
+
Note: this component is experimental and under development.
docker rmi -f $(docker images -q)</pre>
 

Revision as of 18:40, 5 June 2018

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:

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 with configuration files and utilities. The folders of interest are under /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.

How to customize the list of datasets on your server

The list of dataset that the server exposes are contained in the ViSUS configuration file.

If you have already a ViSUS configuration file that you want to use, you can run the container as following:

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

and edit the visus.config file (see ViSUS configuration file).

Note: The server needs to be able to read and write the configuration file, so make sure that your server.config has the right privileges. For example:

chmod 766 /path/to/your/server.config

Making the configuration file writable will allow to add datasets dynamically using the action add_dataset (see ViSUS Server).

If you also want to customize the apache security (e.g. change the users) you can run the command to mount also the apache2 directory as following:

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

Convert your data in IDX using the Docker deployment

The ViSUS tools executables (see ViSUS Convert) are contained in the container 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.

Experimental: 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: 2dwebviewer.png

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

Note: this component is experimental and under development.