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README.md

Preparing to Work on SDSC HPC Resources: Accounts and Connecting

In this exercise, you must use your SDSC or XSEDE account to log onto the Comet cluster. This exercise verifies that your account is working, that your laptop is properly configured, and that your Comet user environment is correctly setup.

In this document, we will show you how to:

Note: if you have any difficulties completing this task, please contact Institute staff at consult@sdsc.edu.

Obtain your comet account:

To obtain a trial Comet account see the Comet user guids at http://www.sdsc.edu/support/user_guides/comet.html#trial_accounts

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How to Use the Terminal Application:

The terminal applications are used to connect clients (you and your laptop) to remote computers (such as Comet). See https://en.wikipedia.org/wiki/Secure_Shell for more information. The best known example of using a terminal is for logging in/connecting to a remote computer systems by users. This is called a client-server connection. Terminals are interactive: you type in a command to run, and the outputs are displayed on the terminal. Executing any command is done by typing it and pressing Enter.

SSH Connection

SSH provides a secure channel over any network in a client-server architecture. You will be using your laptop to access SDSC’s HPC systems using the secure shell command ssh. It is essential that you be able to run secure shell (or a similar connection tool) with X11 forwarding enabled, which allows you to have data encryption and to launch windows applications (e.g. plotting, or a browser).

*NOTE: The hostname for Comet is comet.sdsc.edu

SSH Connection

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Mac Users

For Mac users, the Terminal application is typically used for connections. This is done from the command line:

ssh -X username@<hostname>

If you are having trouble, try running ssh in verbose mode:

 ssh -v -X username@hostname

To configure your login using passwordless ssh, see this tutorial: https://www.tecmint.com/ssh-passwordless-login-using-ssh-keygen-in-5-easy-steps/

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Windows users

Windows users will need to run an X Server and an ssh-like client. Cygwin provides a comprehensive Linux-like environment and an X server (Cygwin/X). Putty will also work for direct access to Comet, it is only used for file transfers. For download and installation instructions, see:

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Example of a terminal connection:

[localuser@localhost]: ssh -X username@comet.sdsc.edu
Warning: untrusted X11 forwarding setup failed: xauth key data not generated
Last login: Tue Jul 17 12:15:18 2018 from wireless-169-228-90-10.ucsd.edu
Rocks 6.2 (SideWinder)
Profile built 16:44 08-Feb-2016

Kickstarted 17:18 08-Feb-2016

                      WELCOME TO
      __________________  __  _______________
        -----/ ____/ __ \/  |/  / ____/_  __/
          --/ /   / / / / /|_/ / __/   / /
           / /___/ /_/ / /  / / /___  / /
           \____/\____/_/  /_/_____/ /_/

*******************************************************************************

[1] Example Scripts: /share/apps/examples

[2] Filesystems:

     (a) Lustre scratch filesystem : /oasis/scratch/comet/$USER/temp_project
         (Preferred: Scalable large block I/O)

     (b) Compute/GPU node local SSD storage: /scratch/$USER/$SLURM_JOBID
         (Meta-data intensive jobs, high IOPs)

     (c) Lustre projects filesystem: /oasis/projects/nsf

     (d) /home/$USER : Only for source files, libraries, binaries.
         *Do not* use for I/O intensive jobs.

[3] Comet User Guide: http://www.sdsc.edu/support/user_guides/comet.html
******************************************************************************
[username@comet-ln2 ~]$

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Getting Domain Name & Host Information

Each machine you work with will have a <domain_name>, <hostname> or <ip_address>. You can learn about IP addresses and domain names here: https://computer.howstuffworks.com/dns.htm.

  • NOTE: The DN (domain name) for Comet is comet.sdsc.edu

You may need to know the physical IP address of the cluster. To do this, run the nslookup command from the command line of your terminal window

[username@comet:] nslookup comet.sdsc.edu
Server:		192.168.86.1
Address:	192.168.86.1#53

Non-authoritative answer:
Name:	comet.sdsc.edu
Address: 198.202.113.253
Name:	comet.sdsc.edu
Address: 198.202.113.252

The IP address is the line labeled "Address" and for Comet there are two. YOu can log onto Comet using either the DN or the IP addresses.

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Comet User Guide

Please read the Comet user guide and familiarize yourself with the hardware, file systems, batch job submission, compilers and modules. The guide can be found here:

http://www.sdsc.edu/support/user_guides/comet.html