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Also see our About R and R Studio Server and About Python and JupyterHub server help page.

BRCF account

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management

TACC account no longer required for BRCF account creation

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1) For full remote access (including Samba browsing) the external collaborator need the UT VPN service. This is only available to UT students/staff, but PIs can set up "0-hour appointments" to UT which provide access to the UT VPN and cost nothing (other than the paperwork ). With this path the person could use the BRCF Account Request application to set up their own account, specifying the appropriate PI under Affiliation.

2) For access to SSH and the web applications, the external collaborator would just need a BRCF account. One complication is that access to the BRCF Account Request website is only allowed from within the UT campus network, or using the UT VPN service, which they would not have. A work-around is to have the POD owner or delegate Contact Us and authorize us  create an account for the collaborator (see Available BRCF PODs for POD owners and delegate names). We will do so, and assign a password which we will share with the UT-affiliated requestor in UT's Stache (https://stache.utexas.edu/login). The requestor can then provide that password to the collaborator, which will be needed for web application access. (Also note that password changes can only be made through the network-restricted BRCF Account Request application.

A second complication is that different POD services are restricted in different ways. For example, SSH access outside the UT campus network or without the UT VPN service is only supported using public key encryption. So for SSH access, the collaborator would will need to generate a public/private key pair and email us the public key to install in their home directory. They can then SSH to pod compute servers, without providing a password. See Passwordless Access via SSH for details.

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How to set up password-less access to POD compute servers using public key encryption

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Step by step instructions for setting up UT's VPN software are described here: https://wikisutexas.utexasatlassian.edunet/wiki/pages/viewpage.action?spaceKey=networking&title=Connecting+to+the+UT+VPN+Service. In addition, this remote_computing_software_download_instructions.pdf PDF provides detailed information about how to configure the UT VPN service, set up Duo 2-factor authenticaion, and installing software for remote SSH access in Windows.

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Users have reported problems accessing BRCF resources from a Windows Subsystem for Linux (WSL) Ubuntu 18.04 shell, with the UT VPN service active. The error reported is usually something like "hostname not found", because Internet access is not working at all so the initial hostname-to-IP address DNS lookup fails.

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For GSAF sequencing customers with access to the GSAF_POD, an alternative exists for transferring data. The gsafcbig01.ccbb.utexas.edu compute server has a FUSE mount of the GSAF sequencing data archive: gsafcbig01.ccbb.utexas.edu:/mnt/corral. With appropriate credentials (my_username below), and knowing your GSAF run (SAnnnnn below) and job (JAnnnnn below) numbers, data can be transferred from gsafcbig01 like this, assuming you're logged in to one of the TACC compute clusters:

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The /mnt/corral directory can be accessed directly if you are logged in to gsafcbig01.ccbb.utexas.edu; however, because of the large number of run directories, doing ls /mnt/corral can take a very long time to return results. A faster way to query the FUSE mount contents is to specify the run, e.g. ls /mnt/corral/SAxxxxx.

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If you are a GSAF customer and have a TACC account, you can request access to the GSAF_POD. If you do not yet have a BRCF account, please use the BRCF Account Request application to set one up. If you already have a BRCF account but do not have GSAF POD access, Contact Us to request it.

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alias fqc="/usr/bin/fastqc -java=/usr/lib/jvm/java-11-openjdk-amd64/bin/java"
fqc my.fastq

Running GUI programs

JupyterHub "try restarting it from the hub" message

One issue specific to the JupyterHub web application is getting 503: service unavailable. with the message: try restarting it from the hub after logging in with BRCF credentials. Sometime just clicking on the Restart button will work; if not, try logging in again.

Running GUI programs

What are X-Windows and X11?

X-Windows is the display rendering (windows) system used on Linux/Unix computers. X11 is the protocol used by X-Windows; it specifies how an application window is to be rendered (e.g. a series of lines, boxes, polygons, colors, etc, etc). The application creates a series of such steps according to the X11 protocol specification. The receiver (the X11 client) reads and follows those steps to render an image in its local environment.

The terms X11 and X-Windows are sometimes used interchangeably, but technically X11 is the protocol and X-Windows is a term for applications that use that protocol to render their windows, and the entirety of the components involved.

The important thing about X-windows is that it is a portable system. The application that uses X-windows to render its screens can run on any operating system, not just Linux/Unix. As long as the client (e.g. the Mac Terminal, or an appropriate Windows program) supports X11, the visualizations can be rendered locally. Contrast this with Windows-only or Mac-only applications which use operating system specific API calls. 

The other bottom line is that to run a GUI program installed on a BRCF pod, you'll need an X11-enabled terminal (see below).

How do I invoke a GUI program on a POD compute server?

A terminal enabled for X-Windows (X11) is needed in order to invoke Linux GUI (graphical user interface) program and see the GUI on your laptop or desktop running Windows, Mac OS, or even Linux. This link details what X-Windows software is availablesee the GUI on your laptop or desktop running Windows, Mac OS, or even Linux. This involves installing a 3rd party X-Windows package (Xming on Windows; XQuartz on Mac) then using an X-Windows-capable terminal (PuTTY on Windows, the built-in Terminal on Mac) to SSH to the server where the X-Windows GUI program resides. This link describes the needed configuration: https://uisapp2kb.iu.edu/confluence-prd/pages/viewpage.action?pageId=280461906.d/bdnt (obviously specifying BRCF credentials and servers rather than Indiana University ones).

If you invoke ssh explicitly in your terminalfrom a Mac Terminal, use ssh -Y to connect to the POD compute server (the -Y enables forwarding of the X11 commands to the X-terminal). On Windows, you configure PuTTY to use X11 forwarding automatically when you open a session.

How do I use MATLAB on the POD?

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From your X11-enabled terminal, use ssh -Y to connect to the POD compute server (the -Y enables forwarding of the X11 commands to the X-terminal). Once logged in, type matlab. This will (slowly) open a graphical window to run matlab in.

Here's how to create a script in matlab.

• In the "Command Window" in the middle of the matlab window, type "1+1" and hit return, it should say "2".
• Click the "New Script" button at the upper left (or the "New" Button, then select "Script" if you don't see "New Script").
  
  • This will open an editing window for a script. 
    
• Type "1+1" in the window, then click "Save" from the upper menu. 
  
  • Name it anything with a ".m" extension (such as untitled.m, the default). 
    
• You can then use then "Open" menu, or the "Current Folder" pain, to open that file in the future.
• Once open in the Editor, you can use the "Run" command from the Editor menu to run it.
• Exit matlab (using either the "exit" or "quit" command)
  

To open matlab without the graphical interface, type the not-so-short or intuitive command: matlab -nodisplay -nosplash. This should give an interactive command prompt. To exit, type quit or exit. Other sometimes-useful options for the non-GUI matlab include -nojvm (might speed things up a bit) and -wait (wait until your jobs finish before exiting).

To run the "script" we created above (called untitled.m in your home directory) and exit, you can do something like:

matlab -nodisplay -nosplash -r "run('~/untitled.m');quit"

To add some error checking, you can use:

matlab -nodisplay -nosplash -r "try, run('~/untitled.m'), catch, exit, end, exit"

Another simple example script could be created and executed from the command line as shown below. (It should tell you the answer is "7.3529".)

echo "5^3/(2^4+1)" > ~/untitled2.m
matlab -nodisplay -nosplash -nojvm -r "run('~/untitled2.m');quit"

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