HPCC FAQs

Frequently Asked Questions (FAQ)

Can’t find the answer? Feel free to e-mail your question to CSDMS@colorado.edu. CSDMS staff will try to respond within a week. Please make sure the question you’re asking is unique and CSDMS-related.

General

1. How can I get an account on Beach?
   Users wishing to get an account on the CSDMS cluster should follow these guidelines to request a one year guest account on our machine. Please note that account requests may take up to one week to process.
2. Where should a new Beach user begin?
   New users should read through the Technical Web pages that list guidelines for using Beach. In particular, new users should become familiar with VPN and ssh by means of the FAQ.
3. Can I receive a letter of support from CSDMS when I apply for outside funding?
   
4. How do I acknowledge CSDMS in my publications?
   You can use our logo in talks. When reporting results that were obtained on the CSDMS cluster, we request that the following language be used as an acknowledgement:
   

"We acknowledge computing time on the CU-CSDMS High-Performance Computing Cluster."

Also, please notify us of any tech reports, conference papers, journal articles, theses, or dissertations which contain results which were obtained on beach. Your assistance will help to ensure that our online bibliography of results is as complete as possible. Citations should be sent to us.

UNIX

1. How do I change my password?
   Use the secure web page, https://identikey.colorado.edu/ to change your password. This changes both your CU VPN password and your password on Beach.
2. How do I change my shell?
   Use the chsh command to change your shell (/bin/bash is a good choice).

Access (SSH)

1. What is SSH?
   Secure Shell (SSH) is a program to log into another computer over a network, to execute commands in a remote machine, and to move files from one machine to another. It provides strong authentication and secure communications over insecure channels. SSH provides secure X connections and secure forwarding of arbitrary TCP connections.
2. How can I upload or download files?
   You must use a utility that uses the SSH protocol. Some option are sftp, scp, or rsync (make sure you specify ssh encryption with -e ssh). These utilities should be provided on most linux/unix platforms (including Max OS X).
3. Where can I find other SSH clients?
   Microsoft Windows users also have several choices for ssh client support, including:
   

• PuTTY
• MindTerm, and
• TTSSH

Batch Processing

1. What is a batch request?
   Batch processing on Beach is managed by the Torque in conjunction with the Maui scheduler. Torque batch requests (jobs) are shell scripts that contain the same set of commands that you enter interactively. These requests may also include options for the batch system that provide requests for resources such as CPU time, memory, and processors. For example submission scripts, see the Help section under the Supercomputing section.
2. How do I submit, check the status, and/or delete a batch job?
   Use qsub to submit, qstat to check the status of your job, and qdel to delete a batch request. For more information, see the online man pages.
3. My job is writing output to TMPDIR, how can I look at it as it's being created?
   First find out what node your job is running on by using the checkjob command and your job's ID

   > checkjob <jobid>
   

   The node (or nodes) on which your job is running is listed under Allocated Nodes. Now that you know what node your job is running on, you can ssh to that node and have a look at your files,

   > ssh <node>
   

   Your files will be under /data2/<jobid>.

Libraries/Software

1. What are environment modules?
   Environment modules are used to manage the environment variable settings associated with software packages in a shell-independent way. They work by setting up a special function or alias in your shell's environment called a module that is used to evaluate commands and set environment variables in a transparent, reversible way. We recommend that you set up modules for you account on beach. Please see our Environment Modules page for a more complete description on how to set up and use modules.