BlueBEAR (Linux HPC) FAQ


  If you can't find the answer you're looking for below, or elsewhere on our web pages, please contact the IT Service Desk.

Registering for BlueBEAR Service

Question: How do I register for BlueBEAR (HPC) account


Answer:

Please visit  the BlueBEAR registration page and decide on a registration option on the web page from the following:

  • Registering a Project
  • Registering a username for the general BlueBEAR service
  • Registering a username for specialist BEAR services     

BlueBEAR Technical Support

Question:

Whom do I contact for support?


Answer:

Please log a call through the IT Service Desk, using the "Make a request" option and choosing "Log a Fault with BEAR/CaStLeS".

Password Assistance

Question: How do I change my password, I've forgotten it?


Answer:

Please log a call with the IT Service Desk

Setting up Runtime Environment (Module file)

Question:

How do I use the module to amend my environment


Answer:

A module allows a user to dynamically change their environment to manage various applications and resources on BlueBEAR. More information can be found on the sourceforge website.

Projects and QOS

Question:

What projects and QOS can I use ?


Answer:

Please use the command my_bluebear when logged into BlueBEAR

 

Batch Queue

Question:

How many jobs can I submit ?


Answer:

Please review the following website and go to section: "Resource Limits"

Can I use spaces (or other special characters) in my filenames?

Question:

Can I use spaces (or other special characters) in my filenames ?


Answer:

Some applications on the cluster, including the schedular, do not fully support spaces in filenames. File and directory names should, therefore, consist of letters and digits only. Note that, as with any Linux system, case is significant.

Status of Batch jobs

Question:

How can I see if my job is running?


Answer:

Please use the "squeue" or "showq" commands.

Monitoring Batch Jobs

Question:

Can I be notified when my job finishes?


Answer:

Yes, add

#SBATCH --mail-type ALL

to your job submission script to get a message when each job begins and ends. See the help page for job submission.

Job Status

Question:

How can I tell when my job is likely to start?


Answer:

To get a rough estimate, please use the command "squeue"

Application Packages

Question:

What applications are available?


Answer:

You can find more information about an applications by following the application link page. The link on the application names provides documentation about the software and corresponding example scripts are made available to aid running a batch job

Application Licences

Question:

Why aren't there enough licences?


Answer

In the case of commercial applications, the number of licences purchased for use on BEAR platforms is constrained by the available budget and means we cannot guarantee availability of any particular licence from the shared pool at any specific time.

Linux and Unix Commands in a Shell Error

Question:

Why do I get the following error 'Argument list too long' when I type ' ls', rm, ls, cp or other commands in my directory?


Answer:

This is due to the large quantity of files within the directory you are working in (Working dir.) and the maximum number of bytes a command can have is limited by the operating system, not the shell. The shell expands the ls argument and display an error which report that the command line argument exceeded the command line limit. Each command under Linux and UNIX-like systems accepts a parameter commonly known as command arguments (or args). For example, the command ‘cd /etc’ has one command line arguments, namely, /etc. Some command can accept more than two arguments. The average maximum length of the command line  for most Linux/Unix system argument is limited to “128K” within the Linux kernel. To find the limit for your system, type: getconf ARG_MAXlength. The best way to deal with this problem is a combination of the “find and xargs” commands. The syntax is:

find. -name | xargs ls

You can replace 'ls' with any other commands

Understanding Exit Codes

Question:

What is the Exit_status I see in the email when a job ends?


Answer:

All programs on Linux end with an exit status, also referred to as an exit code.  It is an integer in the range 0-255 that can be used to indicate success or failure of running a program.  In your job email this is the final exit status of your job, which is usually the status returned by the last command run from your job script.

An exit code of 0 is conventionally used to mean that a command ran without error (i.e. successfully completed) and any other number indicates an error occurred.  1 is usually used as a catch-all "unspecified error" code and other codes used to indicate specific error conditions.  You may find a list of exit codes and what they mean in the documentation of your program, especially if using commercial software packages.  For example the Linux Documentation Project has a pretty good table of reserved exit codes at http://www.tldp.org/LDP/abs/html/exitcodes.html and what they are used for in bash, although many are more generally applicable.

X-11 Forwarding From a Windows system using putty

Question:

Why have I started to get the message "X11 connection rejected because of wrong authentication" ?


Answer:

If you get this message when you start an X application, a possible reason is that your $HOME disk quota is full. Check using "bbquota". If you are low on disk space remove unnecessary files from your system:

 

Accessing non-standard BlueBEAR resources

Question:

Why do I get Invalid qos specification?


Answer:

We use "QOS" as a way of controlling access to non-standard resources in BlueBEAR, for example bbgpu (the shared GPU  resources) or research group-owned resources. If you do submit to other QOS then you should note that the change we have made is that a QOS is now attached to a project, rather than a user as it was before. This means that when you submit to certain QOS, using the following in your job submission script:

#SBATCH --qos=[qos name]

You now must explicitly specify to use a project that has access to the QOS, using:

#SBATCH --account=[project name]

 

You can see a list of your QOS and projects using the command:

my_bluebear

When submitting a job, if you see an error message:

sbatch: error: Batch job submission failed: Invalid qos specification

then this means that the project you are using for this job is not allowed to use the specified QOS. In this case you should use the my_bluebear command to check which project you should use to be able to submit to the QOS.

If you would like any help getting your jobs to run then please log a ticket in the IT Service Desk using the "Other BEAR Request" option.



Last modified: 19 March 2019

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