CTBP Computing: Frequently Asked Questions

Contents

• How do I get an account on the machines?
• How do I remotely login to these machines?
• How do I transfer files from/to CTBP workstations?
• Does e-mail work on any of these machines?
• How can I start using CTBP mail/webmail services?
• How do I configure my mail client to use CTBP email?
• How do I change my password?
• What software is available?
• What should I do to get a particular piece of software in stalled?
• Where can I run my long-term, CPU-intensive jobs?
• What are SGE scheduling policies for the cluster?
• How much disk space do I have available?
• What about backup?

• How do I get an account on the machines?
  Please see this page. The accounts are distributed by NIS, so an account on one machine will work on all machines.
  
  
• How do I remotely login to these machines?
  The only way to remotely login to the CTBP machines is to use secure shell (ssh). Incoming telnet and FTP connections have been disabled for security reasons. You can freely download SSH clients for SGI's IRIX and other UNIX OSs, MS windows and MacOS. If you're new to ssh check out this introduction.
  
  Please note that ssh logins to CTBP clusters (ctbp1 and ctbp1m) are allowed only from UCSD network. If you are connecting from outside you have to log in to ctbp.ucsd.edu first and then to either ctbp1 or ctbp1m.

  Note: In order to submit your jobs on CTBP computational clusters your account must be set up for password-less ssh login to the nodes. To do this perform the following on ctbp1.ucsd.edu and ctbp1m.ucsd.edu:

  cd $HOME mkdir ~/.ssh chmod 700 ~/.ssh ssh-keygen -t rsa -N "" -f $HOME/.ssh/id_rsa ssh-keygen -t dsa -N "" -f $HOME/.ssh/id_dsa cd .ssh touch authorized_keys cat id_rsa.pub id_dsa.pub >> authorized_keys chmod 640 authorized_keys

  
  
  
• How do I transfer files from/to CTBP workstations?
  • Transferring files from CTBP:
    Either use FTP (if the remote host supports it) or scp (secure copy):
    

    scp your_file remote_username@remote_host:/some/dir
    

  • Transferring files to CTBP:
    login to a CTBP workstation and use scp:
    

    scp remote_username@remote_host:/some/dir/your_remote_file .
    

  
  
• Does e-mail work on any ofthese machines?
  ctbp.ucsd.edu is the CTBP mail server - you can check your mail there either by login to the server (using ssh) or using web interface.
  
  
• How can I start using CTBP mail/webmail services?
  Login to the mailserver (ssh your_login_name@ctbp.ucsd.edu) and execute this command: "rm .forward". From now on all email addressed to your_login_name@ctbp.ucsd.edu will stay on ctbp.ucsd.edu. To read your email either login to the mail server (ctbp.ucsd.edu) or use webmail access and use your login name and password to log in. If you want to have your ctbp email redirected to other mailserver - just edit your .forward file.
  
  
• How do I configure my mail client to use CTBP email?
  If you would like to use IMAP access on ctbp.ucsd.edu, simply set ctbp.ucsd.edu as your incoming IMAP server. We do not have SMTP relaying enabled on that machine so you should use the campus wide smtp.ucsd.edu.
  
  
• How do I change my password?
  Use the 'yppasswd your_login_name' command on any of the workstations. After a brief delay, the password change should propagate to all of the workstations in the lab.
  
  
• What software is available?
  See the available software page for a list of the software that is currently installed and some links to the software home pages.
  
  
• What should I do to get a particular piece of software installed?
  If it's free software, just e-mail ctbp-help @ ctbp.ucsd.edu and let us know what you need and we'll try to get it installed.
  
  
• Where can I run my long-term, CPU-intensive jobs?
  The only platform for non-interactive computational work is the linux cluster (ctbp1.ucsd.edu), please see the CTBP Cluster How-To for more information about this resource.
  
  
• What are SGE scheduling policies for the CTBP cluster?
  Please see SGE How-To for more information.
  
  
• How much disk space do I have available?
  

  Filesystem/home directories layout:

  Host	Filesystem	Quota	Daily backup	Purpose
  ctbp.ucsd.edu (mail/web server)	/home	500MB	yes	for mail/web only
  ctbp1.ucsd.edu (cluster frontend)	/home	2GB	yes	main home directory
  	/gpfs	20GB	no	fast disk for data storage during job runs, accessible from all nodes
  	/scratch on nodes	none	no	very fast local disk space on the nodes

  
  
  You can check your current quota and disk space usage by login to ctbp, ctbp1 or ctbp2 and issuing following command:

  quota -v your_username

  If the default home directory quota is insufficient for your research projects please contact the CTBP administrator and request increase of your quota (please be sure to specify how big increase you're requesting).
  
  
• What about backup?
  The home directories are backed up daily to tapes. However, it is only a good practice for user to do an off-site backups as well.
  
  To do an off-site backup to a remote computer with a tape drive, login either to ctbp1 or ctbp2 and execute the following command:

      tar cvfb  -  20 your_dir | ssh remote_host dd of=/dev/tape obs=20b
      

  To restore files from the tape to your home directory:

      dd if=/dev/tape bs=obs_value |  ssh remote_host tar xvBf -