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Also see our About R and R Studio Server help page.

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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.

FTP hangs when attempting to get/put

After successfully connected to an external FTP/SFTP server from a POD compute node, a get or put command may hang. This is beause the FTP protocol from a firewalled server requireds that passive mode be enabled. Passive mode can be enabled using any of the following approaches:

• Enter the passive command after successful FTP login

  • If you see a message like "Passive mode on", you're fine.

    Code Block
    ftp> passive Passive mode on. ftp> ls 227 Entering Passive Mode (130,14,29,35,196,253). 150 Opening BINARY mode data connection for file list

  • If you see something like "Passive mode off", just enter passive again (mode is toggled)
• Pass the -p flag to the ftp program (e.g., ftp -p ftp-private.ncbi.nlm.nih.gov).
• Use the pftp command instead of ftp (e.g., pftp -p ftp-private.ncbi.nlm.nih.gov).
• Edit your configuration file to make passive the default.

Home directory quotas and snapshots

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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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