Note: 

Run the following script before submitting your first batch job. You will not need to run it again unless the files it creates are inadvertently deleted or changed:

/ctc/tools/setup_ssh_mpd_linux.sh

This script creates ssh keys and a required MPI file. MPICH2 is the supported MPI implementation on the Linux clusters. Complete details on what the script does are in the Appendix below:

Running Jobs

All jobs must be run on compute nodes, not on the login nodes. Compute machines are only accessible via the Velocity Scheduler (vsched) batch system. The same batch system controls jobs on all CTC Linux and Windows systems. Briefly, to use any of the compute machines, you must first: 

• Create an XML file, describing job parameters like number of minutes and interactive vs. batch
• Write a script in a language like tcsh, giving the commands you wish to run on the primary node (for batch runs)
• Submit the XML file (and the associated batch script) to the scheduler using vsched -s
• You do not need to register your password with vsched to run on the Linux machines. You must do this if you intend to submit jobs to the Windows machines or from a Windows login node.
• All other vsched commands can be issued from both the Windows and Linux environments.
  

Sample Files for a Parallel Batch Job

• Copy and edit the following sample files to make your own files for running a parallel batch job:
• source code, hw.c
• XML file, hw.xml
• tcsh script, hwer
• Note: The .txt extension was added to all three files for viewing purposes only.
• Always verify that the path indicated in the <run> element of the XML file is constructed properly for Linux.

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Appendix

The script /ctc/tools/setup_ssh_mpd_linux.sh performs the steps detailed below.
Note: you do not need to issue any of the commands illustrated here, they are done for you automatically when you run the script.

• Creates an SSH keypair to automate logons .
  • ssh-keygen -b 1024 -t dsa -C <your_userid>

• Adds SSH public key to authorized_keys file (file is visible from all machines.)
  • cat id_dsa.pub >> authorized_keys
  • Note: Use append (>>) when adding keys to the authorized_keys file so any existing keys are not overwritten.
    
    
• Adds a required public key to your authorized_keys file. This is required to allow the scheduler to launch jobs with your userid. In addition to adding the key, it is also necessary to set the proper permissions on both the ssh folder and authorized_keys file for ssh to function.
  • cat /ctc/tools/velocity.pub >> ~<your_userid>/.ssh/authorized_keys
    
    
• Changes permissions on authorized_keys to 600 and on the .ssh directory to 700.  Returns to your home directory:
  • chmod 600 authorized_keys
  • cd ..
  • chmod 700 .ssh
    
    
• Creates the file .mpd.conf in your home folder. It will contain the parameter MPD_SECRETWORD.
  
  
• Sets permissions so only you can read it.
  • chmod 600 .mpd.conf
    

Running the script creates the following files:

$HOME\.ssh\authorized_keys
$HOME\.ssh\id_dsa
$HOME\.ssh\id_dsa.pub
$HOME\.mpd.conf