Security Hub

2020-07-09T16:50:31Z

Mponce: /* Security Recommendations, Updates and ... */

= Security Recommendations, Updates and ... =

We include here basic security advices, recommendations and the latest updates related to cyber-security topics.

* [https://docs.scinet.utoronto.ca/index.php/SSH SSH]
* [https://docs.scinet.utoronto.ca/index.php/SSH_keys Using SSH keys]
* [https://docs.scinet.utoronto.ca/index.php/SSH#Two-Factor_authentication Multi Factor Authentication (MFA)]
* [https://docs.scinet.utoronto.ca/index.php/Two-Factor_setup Using MFA on Niagara]
* MFA in your own computer

= News and Updates =

* 2020-07-08: New vulnerability found in putty, https://www.tenable.com/cve/CVE-2020-14002
* 2019-05: [https://docs.scinet.utoronto.ca/index.php/SSH_Changes_in_May_2019 SSH Changes on Niagara (May 2019)]

Security

2020-07-09T16:49:05Z

Mponce: Mponce moved page Security to Security Hub

#REDIRECT [[Security Hub]]

Security Hub

2020-07-09T16:49:05Z

Mponce: Mponce moved page Security to Security Hub

= Security Recommendations, Updates and ... =

We include here basic security advices, recommendations and the latest updates related to cyber-security topics.

* [https://docs.scinet.utoronto.ca/index.php/SSH SSH]
* [https://docs.scinet.utoronto.ca/index.php/SSH_keys Using SSH keys]
* [https://docs.scinet.utoronto.ca/index.php/SSH#Two-Factor_authentication Multi Factor Authentication (MFA)]
* Using MFA on Niagara
* MFA in your own computer

= News and Updates =

* 2020-07-08: New vulnerability found in putty, https://www.tenable.com/cve/CVE-2020-14002
* 2019-05: [https://docs.scinet.utoronto.ca/index.php/SSH_Changes_in_May_2019 SSH Changes on Niagara (May 2019)]

Security Hub

2020-07-09T16:42:04Z

Mponce: /* Security Recommendations, Updates and ... */

= Security Recommendations, Updates and ... =

We include here basic security advices, recommendations and the latest updates related to cyber-security topics.

* [https://docs.scinet.utoronto.ca/index.php/SSH SSH]
* [https://docs.scinet.utoronto.ca/index.php/SSH_keys Using SSH keys]
* [https://docs.scinet.utoronto.ca/index.php/SSH#Two-Factor_authentication Multi Factor Authentication (MFA)]
* Using MFA on Niagara
* MFA in your own computer

= News and Updates =

* 2020-07-08: New vulnerability found in putty, https://www.tenable.com/cve/CVE-2020-14002
* 2019-05: [https://docs.scinet.utoronto.ca/index.php/SSH_Changes_in_May_2019 SSH Changes on Niagara (May 2019)]

Security Hub

2020-07-09T16:41:32Z

Mponce:

Security Hub

2020-07-09T16:41:00Z

Mponce: /* News and Updates */

2018-11-15T15:20:35Z

Mponce: /* VisIt */

== 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:

paraview --mesa-swr

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!

== Interactive Visualization ==
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.
For performing an interactive visualization session in this way please follow these steps:
<ol>
<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>

module load visit
visit

module load paraview
paraview --mesa-swr

<li> exit the debug session.
</ol>

== Remote Visualization -- Client-Server Mode ==
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>
<li> accessing data remotely, ie. stored on the cluster
<li> rendering visualizations using the compute nodes as rendering engines
<li> or both
</ul>

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

Choose *one* of the methods bellow:

====Niagara Host Configuration File====
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>
<li> on a Linux/Mac OS place this file in <code>~/.visit/hosts/</code>
<li> on a Windows machine, place the file in <code>My Documents\VisIt 2.13.0\hosts\</code>
</ul>

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

====Manual Niagara Host Configuration====
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:

Host nickname = niagara
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:
<ol>
<li> <code>login</code>: for connecting through the login nodes and accessing data </li>
<li> <code>slurm</code>: for using compute nodes as rendering engines </li>
</ol>
For doing so, click on 'New Profile', set the corresponding profile name, ie. login/slurm.
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"
| [[File:Visit_niagara-02.png|400px|]]
| [[File:Visit_niagara-03.png|400px|]]
|}
<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.

=== ParaView Client-Server Configuration ===
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:
<ol>
<li> Launch an interactive job (debugjob) on Niagara,</li>

debugjob

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

module load paraview
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>

Waiting for client...
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>

ssh YOURusername@niagara.scinet.utoronto.ca -L11111:niaXYZW:11111 -N

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>
name = niagara
server type = Client/Server
host = localhost
port = 11111
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>

====Multiple CPUs====
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>

module load paraview
srun pvserver --mesa

=== Final Considerations ===
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.

== Batch mode and Scripting ==
Both, VisIt and ParaView, allow for batch processing using scripting in different languages.

=== VisIt ===
In order to run or launch the Python interpreter for VisIt, you will need to execute the following command:

<code> visit -cli -no-win -norun engine_par </code>

the 'engine_par' flag is needed in order to run the visualization engine in parallel.

Alternatively, if you want to assign resources from the cluster just from within the script one should add the following line

OpenComputeEngine("localhost", ("-l", "srun", "-np", "40"))

In order to execute scripts you can instead run them in batch mode by executing,

<code> visit -cli -no-win -norun engine_par scriptName.py</code>

recall to add the <code>OpenComputeEnigne(...)</code> line to your script for using parallel processing.

References:
<br>
[https://www.visitusers.org/index.php?title=ParallelPorting#Making_sure_you_actually_have_a_parallel_engine https://www.visitusers.org/index.php?title=ParallelPorting#Making_sure_you_actually_have_a_parallel_engine]
<br>
[https://www.visitusers.org/index.php?title=VisIt-tutorial-Python-scripting https://www.visitusers.org/index.php?title=VisIt-tutorial-Python-scripting]
<br>
[https://www.visitusers.org/index.php?title=Python_examples https://www.visitusers.org/index.php?title=Python_examples]
<br>
[https://www.visitusers.org/index.php?title=VisIt-tutorial-Advanced-scripting https://www.visitusers.org/index.php?title=VisIt-tutorial-Advanced-scripting]

=== ParaView ===
ParaView offers a python interpreter <code>pvbatch</code> to use

pvbatch --mesa-swr-avx2 --force-offscreen-rendering scriptName.py

References:
<br>
[https://www.paraview.org/Wiki/ParaView_and_Batch https://www.paraview.org/Wiki/ParaView_and_Batch]
<br>
[https://www.paraview.org/Wiki/ParaView/Python_Scripting https://www.paraview.org/Wiki/ParaView/Python_Scripting]

== Other Versions ==
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.