Frequently Asked Questions

Where do I find a QuickStart Guide for CCS systems?

Pegasus Documentation

What operating system does Pegasus have?

CentosOS 6.5 (based on Red Hat Enterprise Linux Server release 6.5)

Where can I find info on Linux/Unix basic commands?

Useful link for Linux basics: Unix Beginner’s commands Useful link: Linux overview

How do I view the usage of my storage and scratch space?

% /share/apps/ccs-tools/mdf/shquota -U

How do I create, edit, or modify a text file?

To create an empty file:

% touch NEWFILENAME

To edit or modify the file, use any standard Linux/Unix text editors, e.g.,

% vi [FILENAME]
% vim [FILENAME]
% nano [FILENAME]

where FILENAME is optional; if none provided, a new blank file is opened.

vi or vim vim wiki, vim cheat sheet nanonano wiki, nano Beginners’ Guide gedit is a simple graphic editor,

% gedit [FILENAME]

gedit wiki ,gedit basics, gedit basics-2

How do I check my environmental variables?

% env
% env | sort

The latter example sorts the env. variables in an alphabetical order.

How do I check which shell I’m using?

Either way will give the answer:

% echo $0
% echo $SHELL

Default shell is bash.

What are Unix/Linux shells?..

How do I submit a job or a parallel job to the cluster?

All the jobs are scheduled by LSF (Load Sharing Facility) and submitted to the queue as the resources become available. You could use your favorite shell script (bash, csh, etc) with extra information needed by LSF, as in the example of a script runMyJob.sh below:

#!/bin/bash
#BSUB -n 32
#BSUB -q general
#BSUB -W 05:00
#BSUB -J myjobname
#BSUB -P myprojectid
#BSUB -o %J.out
#BSUB -e %J.err

cd /scratch/user/jobrundir
 
mpiexec ./job.exe 
wait

#BSUB command description
#BSUB -n number of processors to request
#BSUB -q queue name to submit a job
#BSUB -P the project ID to use when submitting the job
#BSUB -W time limit of the job, in HH:MM, max=168:00
#BSUB -J job name
#BSUB -o standard output file name
#BSUB -e standard error file name
#BSUB -M Memory limit for the whole job, in KBytes
#BSUB -r “span[ptile=16]“ number of processes per node; max = 16
#BSUB -R “usage[mem=28000] memory request for the single node, max=28000 MB
#BSUB -u user@my.address.edu send the notification info about the job, if requested
#BSUB -B send e-mail to the above address when the job starts
#BSUB -N send the job report to the above address when the job finishes

You submit a job to LSF as following:

bsub < ./runMyJob.sh

Checking your job and queue status

bsub – submit a job to a cluster via LSF scheduler. Usage: bsub < ./myjobscript.sh bjobs – see the status of your current running job(s) bkill – kill a running job. Usage: bkill JOBID, where JOBID is the numeric job number. bpeek – Access the output and error files of a job. Usage example: bpeek JOBID. bqueues – shows what the load of different queues bhosts – shows the load of the individual hosts Check the manual pages (“man command“) for the more detailed usage tips!

How do I check if a program or binary file is available, and where it is located?

% which PROGRAM

where PROGRAM is your name of an executable. For example:

% which gcc
% which vim
% which matlab

How do I get help with the installed programs or compilers?

Inquiry the “man” pages for your BINARYNAME:

% man BINARYNAME

How to inspect the current search path for the programs/executables, or libraries?

  • path for the programs/executables, search starting from the first directory:
    % echo $PATH
  • path for the libraries:
    % echo $LD_LIBRARY_PATH
  • path for the “man” pages:
    % echo $MANPATH

How do I check the modules that are available and/or loaded? How add, remove, or use different version of a module?

Use module command for the query. Some of the examples include:

% module list
% module avail
% module load MODULENAME
% module unload MODULENAME
% module display MODULENAME

The arguments for the module command are: list – gives you the list of modules that are loaded upon your login. avail – gives you the list of all available modules that you could add. load MODULENAME – loads the module MODULENAME . unload MODULENAME – unloads the module MODULENAME. display MODULENAME – gives the information about the locations and libraries of the given module For the full list of arguments, use

% man module

How do I change or restore a password?

After establishing a secure connection, point your browser to http://iweb.ccs.miami.edu:8080/account/ In top right menu: click on "Forgot Password". Fill your details with the registered e-mail, and the instructions will be e-mailed to you.

How do I connect to the CCS computers from outside network?

Pegasus and other CCS computers are only available from the University’s secure campus networks (wired or SecureCanes wireless). In order to access Pegasus (pegasus.ccs.miami.edu) while offsite, you will need to open a VPN connection first. CCS does not administer VPN accounts.

Coral Gables Campus https://sphinx.miami.edu
instructions: http://www.miami.edu/it/index.php/services/virtual_private_network_ssl/

Medical Campus https://sg.med.miami.edu
instructions: http://it.med.miami.edu/x687.xml

Rosenstiel School of Marine and Atmospheric Science https://remote.rsmas.miami.edu (rsmas)
instructions: http://www.rsmas.miami.edu/resources/rsmas-computing-facility/software/vpn/

The Coral Gables VPN is only available to faculty, staff and approved vendors. Secure Gateway is available to anyone with a Medical ID. RSMAS VPN requires a RSMAS username and password.

Medical Campus Secure Gateway To use Secure Gateway, you will need the 32-bit jre 1.6 or 1.7. On a Mac, you cannot use Chrome (it does not support 32-bit jre). Go to https://sg.med.miami.edu and login with your CaneID (see below). The network connect client should automatically start. You will be prompted to allow installation of several application, which you must allow.

Third-party VPN Software If you are experiencing difficulty with Secure Gateway or the other VPN sites, another option is to use the Junos Pulse client: http://www.juniper.net/support/downloads/?p=pulse#sw

  • Install and launch Junos Pulse, then “Add Connection” using the + button.
  • Enter the VPN site into “Server URL” and click Connect.
  • When prompted, use your VPN account credentials.

Why am I logged off after some time of inactivity?

The automatic logoff of inactive sessions is intentionally done to improve the performance and reliability of the cluster. You may wish to use an encrypted key to authentication from your machine to Pegasus. The section “7. Use Public/Private Keys for Authentication” on the CentOS wiki provides instructions on how to do this. http://wiki.centos.org/HowTos/Network/SecuringSSH

How do I check the status of my job submitted by bsub?

Use the command

% bjobs

How do I submit a job or launch a program using an interactive queue?

% bsub -q interactive -Is YOURJOB

To launch a graphic interface, make sure to connect to pegasus.ccs.miami.edu. Verify that your local computer allows X11 tunneling (graphics from remote locations). Then submit your request:

% bsub -q interactive -Is -XF YOURJOB

If need to request more than one processor (4, for instance):

% bsub -q interactive -Is -n 4 YOURJOB

How do I increase memory in Java on Pegasus?

First load the java module, then change the value of _JAVA_OPTIONS.

$ module load java
$ echo $_JAVA_OPTIONS
-Xmx512m
$ export _JAVA_OPTIONS="-xmx4g"

How do I get help from CCS if all else fails?..

Please send an email to hpc@ccs.miami.edu, or open a ticket via RT http://rt.ccs.miami.edu/ by logging with the same credentials you use for CCS systems. If you have a problem with software, programs or other errors, please include the following information info:

  • computer system you are using
  • your CCS account id
  • complete path to job script file, program, or job submission
  • complete path to output file (if any)
  • error message(s) received
  • module(s) loaded ($ module list)
  • whether this job ran previously and what has changed since it last worked
  • steps you may have already taken to address your issues

What happens to the user’s data after leaving the University of Miami?

The ownership of the data will be changed to the Principal Investigator (PI) the user reported to. Then the PI has three (3) weeks to remove the data. The user’s home and scratch directories will be deleted after 3 weeks. No data transfer or ownership transfer to other users is done by CCS, or additional access to the date for other users.

HAPPY COMPUTING!

smiley at the computer