Visualization: Difference between revisions

= Visualization on the new Compute Canada systems = <!--T:6-->

Frequently, it may be useful to start up graphical user interfaces for various software packages like Matlab. Doing so over X-forwarding can result in a very slow connection to the server, one useful alternative to X-forwarding is using VNC to start and connect to a remote desktop.  

For more information, please see the article on [[VNC]].

Click Ok and wait for VisIt's engine to start. If you selected rendering on a compute node, it may take some time for your job to get started. Once your dataset appears in the Active source in the main VisIt window, the VisIt's engine is running, and you can proceed with creating and drawing your plot.

=== Software Available ===

We have installed the latest versions of the open source visualization suites: VMD, VisIt and ParaView.

Notice that for using ParaView you need to explicitly specify one of the mesa flags in order to avoid trying to use openGL, i.e.,

after loading the paraview module, use the following command:

Notice that Niagara does not have specialized nodes nor specially designated hardware for visualization, so if you want to perform interactive visualization or exploration of your data you will need to submit an interactive job (debug job, see [[https://docs.scinet.utoronto.ca/index.php/Niagara_Quickstart#Testing]]).

For the same reason you won't be able to request or use GPUs for rendering as there are none!

Runtime is limited on the login nodes, so you will need to request a testing job in order to have more time for exploring and visualizing your data.

Additionally by doing so, you will have access to the 40 cores of each of the nodes requested.

<li> ssh into niagara.scinet.utoronto.ca with the -X/-Y flag for x-forwarding

<li> request an interactive job, ie.</li>

   debugjob

this will connect you to a node, let's say for the argument "niaXYZW"

<li> run your favourite visualization program, eg. VisIt/ParaView </li>

   visit

   paraview --mesa-swr

<li> exit the debug session.

</ol>

You can use any of the remote visualization protocols supported for both VisIt and ParaView.

Both, VisIt and ParaView, support "remote visualization" protocols.

This includes:

</ul>

For allowing VisIt connect to the Niagara cluster you need to set up a "Host Configuration".

Choose *one* of the methods bellow:

You can just download the Niagara host file, right click on the following link [https://support.scinet.utoronto.ca/~mponce/viz/host_niagara.xml host_niagara.xml] and select save as...  

Depending on the OS you are using on your local machine:

</ul>

Restart VisIt and check that the niagara profile should be available in your hosts.

If you prefer to set up the verser yourself, instead of the configuration file from the previous section, just follow along these steps.

Open VisIt in your computer, go to the 'Options' menu, and click on "Host profiles..."

Then click on 'New Host' and select:

  Remote host name = niagara.scinet.utoronto.ca

  Username = Enter_Your_OWN_username_HERE

  Path to VisIt installation = /scinet/niagara/software/2018a/opt/base/visit/2.13.1

Click on the "<code>Tunnel data connections through SSH</code>", and then hit Apply!

{| align="center"

| [[File:Visit_niagara-01.png|480px|]]

Now on the top of the window click on 'Launch Profiles' tab.

You will have to create two profiles:

Then click on the Parallel tab and set the "Launch parallel engine"

For the slurm profile, you will need to set the parameters as seen below:

<br style="clear:both" />

{| align="center"

<br style="clear:both" />

Finally, after you are done with these changes, go to the "Options" menu and select "Save settings", so that your changes are saved and available next time you relaunch VisIt.

Similarly to VisIt you will need to start a <code>debugjob</code> in order to use a compute node to files and compute resources.

Here are the steps to follow:

<li> Launch an interactive job (debugjob) on Niagara,</li>

<li> After getting a compute node, let's say niaXYZW, load the ParaView module and start a ParaView server,</li>

   pvserver --mesa-swr-ax2

The <code>--mesa-swr-avx2</code> flag has been reported to offer faster software rendering using the OpenSWR library.

<li> Now, you have to wait a few seconds for the server to be ready to accept client connections.</li>

   Connection URL: cs://niaXYZW.scinet.local:11111

   Accepting connection(s): niaXYZW.scinet.local:11111

<li> Open a new terminal without closing your debugjob, and ssh into Niagara using the following command,</li>

this will establish a tunnel mapping the port 11111 in your computer (<code>localhost</code>) to the port 11111 on the Niagara's compute node, <code>niaXYZW</code>, where the ParaView server will be waiting for connections.

<li> Start ParaView on your local computer, go to "File -> Connect" and click on 'Add Server'.

You will need to point ParaView to your local port <code>11111</code>, so you can do something like</li>

then click Configure, select <code>Manual</code> and click Save.

<li> Once the remote server is added to the configuration, simply select the server from the list and click Connect.

The first terminal window that read <code>Accepting connection...</code> will now read <code>Client connected</code>.

<li> Open a file in ParaView (it will point you to the remote filesystem) and visualize it as usual.

</ol>

For performing parallel rendering using multiple CPUs, <code>pvserver</code> should be run using <code>srun</code>, ie. either submit a job script or request a job using

<source lang="bash"> salloc --ntasks=N*40 --nodes=N --time=1:00:00</source>

   srun pvserver --mesa

Usually both VisIt and ParaView require to use the same version between the local client and the remote host, please try to stick to that to avoid having incompatibility issues, which might result in potential problems during the connections.

Alternatively you can try to use the visualization modules available on the CCEnv stack, for doing so just load the CCEnv module and select your favourite visualization module.

= Upcoming visualization events = <!--T:7-->

Please let us know if you would like to see a visualization workshop at your institution.