7 am – 12 am Tuesday July 3rd, storage systems for the pegasus compute cluster, apollo, and visx will undergo hardware maintenance.
During this maintenance period, pegasus batch execution and login nodes will be unavailable – as will the gateway (gw.ccs.miami.edu), apollo, and visx systems.
Due to financial decisions made at the Miller School of Medicine (MSOM), open access on both Pegasus and Bigfoot will no longer be available to MSOM faculty, staff, and students effective October 31, 2017.
Read the full contents for details about how this will affect your CCS account.
CCS Advanced Computing invites you to connect with the Advanced Computing community on Slack: http://umadvancedcomputing.slack.com
The Advanced Computing community Slack channels provide a place for user discussions, information sharing, and informal announcements about CCS resources and developments. All users with an @miami.edu or @umiami.edu email address can create a Slack account in UM Advanced Computing.
Support & FAQ
Links & Forms
- Advanced Computing Policies
- Advanced Computing Documentation
- Account Registration – CCS user accounts are available for all University of Miami faculty, staff, and students.
- Account Management – Manage existing CCS accounts and allocations
- Password Reset – Reset your CCS account password
- Project Request – Collaborative work on the Pegasus supercomputer
- NSF Data Management Plan Template – Template used to create an NSF Data Management Plan.
- Software List – Available software on the Pegasus supercomputer
- Software Request – Request software installations or updates
- Grant Preparation – Equipment, facilities, and other resources at CCS
- CTSI Allocation Request form – Request a CTSI storage allocation
FAQ – Frequently Asked Questions
How do I reset my CCS password?
Via the CCS Portal: https://portal.ccs.miami.edu
Click on “Reset Password”
How do I connect to CCS resources from off-site?
To access CCS resources while offsite, open a VPN connection first.
CCS does not administer VPN accounts.
FAQ Pegasus Software
What software is available?
Software Modules list on the CCS Portal: https://portal.ccs.miami.edu/resources/software/
Software Modules from the command line:
$ module avail
How do I view my currently loaded modules?
$ module list
How do I use software modules?
Software on Pegasus
How do I request global software installation on Pegasus?
Request new global software via the CCS Portal: https://portal.ccs.miami.edu/resources/soft/new
When will my global software request be approved/installed?
When a minimum of 20 users require it. Software requests are reviewed quarterly.
How can I increase Java memory on Pegasus?
Load the java module, then change the value of _JAVA_OPTIONS.
[username@pegasus ~]$ module load java [username@pegasus ~]$ echo $_JAVA_OPTIONS -Xmx512m [username@pegasus ~]$ export _JAVA_OPTIONS="-Xmx4g"
FAQ Pegasus Projects
How do I join a project?
Contact the project owner. Details can be found on the CCS Portal: https://portal.ccs.miami.edu/forms-access/
How do I request a new project?
Any PI or faculty member may request a new project via the CCS Portal: https://portal.ccs.miami.edu/accounts/new/group/
When will my project be created?
When the allocations committee has reviewed and approved it. Check your request status via the CCS Portal under My Pegasus -> My Requests. Scratch requests over 2TB can take a month for the allocations committee to review as availability is limited.
How do projects work?
How can I manage my Projects and Groups?
Manage owned Projects and Groups via the CCS Portal: https://portal.ccs.miami.edu
Click on My Pegasus -> My Projects or My Groups
See Project Management for more information.
FAQ Pegasus Jobs
Pegasus Job Scheduling
May I run resource-intensive jobs on Pegasus login nodes?
No. Resource-intensive jobs must be submitted to LSF.
Is there a limit on how many jobs I can run?
No. Users are limited by number of simultaneous CPUs used. Individual users can run on up to 512 CPUs at a time, projects on up to 1000 CPUs at a time.
Why is my job still pending?
Jobs wait for enough resources to satisfy requirements. When the cluster is under heavy user load, jobs will wait longer. Use
$ bjobs -l jobID to see PENDING REASONS. Check your resource requirements for accuracy and feasibility.
If your job has been pending for more than 24 hours and is not requesting exclusive access or all cores on a node, you may e-mail firstname.lastname@example.org for assistance.
Are other users’ pending jobs slowing my job?
No. The number of pending jobs is irrelevant to job performance in LSF. The scheduler can handle hundres of thousands of jobs.
How do I submit jobs to my Project?
-P flag: LSF
How do I submit an interactive job?
-Is -q interactive flags: LSF Interactive
How do I submit an interactive X11 job?
-Is -q interactive -XF flags: LSF X11
Why was my job killed?
Jobs are killed to protect the cluster and preserve system performance. Common reasons include:
– running on a login node
– using more memory than reserved
– using all the memory on a compute node
– using more CPUs than reserved
– needing more time to complete than reserved
– using more
/tmp space than available on compute nodes
How can I check my shell?
$ echo $SHELL or
$ echo $0
How can I view my environment variables?
$ env or
$ env | sort
How can I check command/software availability and location?
$ which executable, for example
$ which vim
How can I get help with commands/software?
Use the Linux manual pages:
$ man executable, for example
$ man vim
Advanced Computing offers office hours to provide assistance with usage issues on the Pegasus cluster. The team is able to provide onsite assistance with queuing inquiries, software installation, and technical troubleshooting. The team is also able to help answer questions regarding grant proposals and can provide resource information about the Advanced Computing environment.
- Coral Gables Campus: Wednesdays 2:00-4:00 PM | Ungar 330E Dr. Zongjun Hu
- RSMAS Campus: Wednesdays 9:00-11:00 AM | MSC 223 Mr. Warner Baringer
Request help via email to email@example.com. Provide detailed descriptions of the problem, paths to your job file and any outputs, the software modules you have loaded, and your job ID when appropriate.
- computer and operating system you are using
- your CCS account ID
- complete path to your job script file, program, or job submission
- complete path to output files (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