For your convenience, we've compiled a brief list of some of the basic commands/procedures
needed to run jobs at CCR. It's intended to be a reference guide that you can print
out and keep near your workstation. Greater detail on any of the entries are available on
the Getting Started page.

• Accounts on u2
  • Faculty can use an on-line form to apply for accounts for themselves and members of their research group.
• u2 cluster details
• Login to Cluster Front-end
  • You will login to u2.ccr.buffalo.edu. The actual name of the front-end machine is bono.
  • Your login username will be the same as your UBIT username.
  • The password will be sent to you.
  • Your machine must be on the UB network.
  • Use VPN from home or offsite: UB-VPN
• Login from Linux/Unix Machine: ssh u2.ccr.buffalo.edu
• Login from Windows Machine
  • Secure Shell Client: PuTTY or X-win32
• Changing the Password: kpasswd
• Logout of the Front-end Machine: logout
• Basic Unix Commands
  • List files: ls
  • Make a directory: mkdir directory-name
  • Change directory: cd directory-name
  • Change directory back to home directory: cd ..
  • Copy a file: cp old-filename new-filename
  • View a file:
    • cat filename
    • more filename
    • less filename
  • Edit a file:
    • emacs filename
    • vi filename
  • Delete a file: rm filename
• Unix Reference Card
• File Transfer from Linux/Unix Machine: sftp u2.ccr.buffalo.edu
  • put filename
  • get filename
• File Transfer from Windows Machine
  • WinSCP provides a drag and drop interface.
• Home Directory: /san/user/UBIT-username/u2
  • Check quota: quota UBIT-username
• Modules
  • Set paths and variables for application software.
  • Show all available modules: module avail
  • Show what a module does: module show module-name
  • Use a module: module load module-name
• Introduction to Using CCR Tutorial
• Basic Compiling:
  • gcc -o hello-gnu-c hello.c
  • g77 -o hello-gnu-f hello.f
• Compiling and Running with MPI:
  • mpicc -o cpi-gnu cpi.c
  • mpirun -machinefile nodefile -np 4 ./cpi-gnu
  • mpif77 -o fpi-gnu fpi.f
  • mpirun -machinefile nodefile -np 4 ./fpi-gnu
• Running Jobs:
  • Interactive Job: qsub -I -lnodes=1:ppn=2 -lwalltime=01:00:00
    • Requests 1 compute node for 1 hour.
  • Batch Job: qsub your-pbs-script
  • Sample PBS scripts
  • PBS Users Guide Tutorial
• List of Software